2013-08-02
Carlo Torniai
Erik Segerdell
Jie Zheng
Karen Corday
Matthew Brush
Melanie Courtot
Melanie Wilson
Melissa Haendel
Nicole Vasilevsky
Scott Hoffmann
Tenille Johnson
en
An ontology for representing biomedical research resources
editor preferred label
editor preferred term
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred term
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
example
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
GROUP:OBI
OBI_0000277
in branch
has curation status
OBI_0000281
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition
textual definition
definition
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
comment
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
editor note
definition editor
definition editor
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
PERSON:Daniel Schober
definition editor
term editor
alternative term
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
alternative term
definition source
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
has obsolescence reason
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
is denotator type
Alan Ruttenberg
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
relates an class defined in an ontology, to the type of it's denotator
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
imported from
expand expression to
Chris Mungall
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
expand expression to
expand assertion to
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
ObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
expand assertion to
first order logic expression
PERSON:Alan Ruttenberg
first order logic expression
antisymmetric property
Alan Ruttenberg
antisymmetric property
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
An alternative name for a class or property which is unique across the OBO Foundry.
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Person:Alan Ruttenberg
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
has ID range allocated to
Person:Alan Ruttenberg
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
Datatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Person:Alan Ruttenberg
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
term replaced by
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Use on obsolete terms, relating the term to another term that can be used as a substitute
term replaced by
has_role
A relation between a continuant C and a role R. The reciprocal relation of role_of.
GROUP:OBI:<http://obi.sourceforge.net>
PERSON:Chris Mungal
has_role
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
definition needs clean up to indicate directionality
produces
Melissa Haendel
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
produced_by
Melissa Haendel
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
Person:Alan Ruttenberg
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Contributor
An entity responsible for making contributions to the
content of the resource.
Examples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.
Coverage
Coverage will typically include spatial location (a place name
or geographic coordinates), temporal period (a period label,
date, or date range) or jurisdiction (such as a named
administrative entity).
Recommended best practice is to select a value from a
controlled vocabulary (for example, the Thesaurus of Geographic
Names [TGN]) and that, where appropriate, named places or time
periods be used in preference to numeric identifiers such as
sets of coordinates or date ranges.
The extent or scope of the content of the resource.
Creator
An entity primarily responsible for making the content
of the resource.
Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.
Date
A date associated with an event in the life cycle of the
resource.
Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
Description
An account of the content of the resource.
Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.
Format
The physical or digital manifestation of the resource.
Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).
Resource Identifier
An unambiguous reference to the resource within a given context.
Recommended best practice is to identify the resource by means
of a string or number conforming to a formal identification
system.
Example formal identification systems include the Uniform
Resource Identifier (URI) (including the Uniform Resource
Locator (URL)), the Digital Object Identifier (DOI) and the
International Standard Book Number (ISBN).
Language
A language of the intellectual content of the resource.
Recommended best practice is to use RFC 3066 [RFC3066],
which, in conjunction with ISO 639 [ISO639], defines two-
and three-letter primary language tags with optional
subtags. Examples include "en" or "eng" for English,
"akk" for Akkadian, and "en-GB" for English used in the
United Kingdom.
Publisher
An entity responsible for making the resource available
Examples of a Publisher include a person, an organisation,
or a service.
Typically, the name of a Publisher should be used to
indicate the entity.
Relation
Recommended best practice is to reference the resource by means
of a string or number conforming to a formal identification
system.
A reference to a related resource.
Rights Management
Typically, a Rights element will contain a rights
management statement for the resource, or reference
a service providing such information. Rights information
often encompasses Intellectual Property Rights (IPR),
Copyright, and various Property Rights.
If the Rights element is absent, no assumptions can be made
about the status of these and other rights with respect to
the resource.
Information about rights held in and over the resource.
Source
A reference to a resource from which the present resource
is derived.
The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.
Subject and Keywords
The topic of the content of the resource.
Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.
Title
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.
Resource Type
The nature or genre of the content of the resource.
Type includes terms describing general categories, functions,
genres, or aggregation levels for content. Recommended best
practice is to select a value from a controlled vocabulary
(for example, the DCMI Type Vocabulary [DCMITYPE]). To
describe the physical or digital manifestation of the
resource, use the Format element.
Ocre Definition
inheres in
This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant.
This relation belongs in BFO/RO, and will be in BFO 2
agent_in
relationship
derived_into
relationship
derives_from
Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
relationship
has_agent
relationship
has_participant
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
relationship
located_in
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
relationship
location_of
relationship
participates_in
relationship
preceded_by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
relationship
precedes
relationship
transformation_of
When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
relationship
transformed_into
Obsoleted
relationship
has_contact
Name of the primary person responsible for the resource.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The lab manager who maintains an instrument in the lab.
has contact
has_PI
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The PI of a lab.
The principle investigator of a laboratory or research project.
has PI
funds
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Research project that is financially supported by the organization.
The NIH.
is_member_of
A graduate student in the lab.
Identifies the organization or laboratory in which this individual is a member.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
is member of
occurs_in
Hibernation occurs in bears.
Organism in which the biological process occurs.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
occurs in
provides_access_to
An access service that provides access to a flow cytometer.
Instruments, reagents, organisms, or software for which the service provides access.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
change the domain tye to access service
uses
Here there are things to be fixed (for instance a service can use a technique...)
Microsoft powerpoint is commonly used in research laboratories to prepare presentations.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Software or protocol used by the laboratory.
uses
has_expertise
Brian Druker has expertise in cancer research.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Technique in which the person is proficient.
has expertise
has_manufacturer
Organization or person that created the resource.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Santa Cruz Biotechnology is the manufacturer of many antibodies.
has manufacturer
provides_service
A core lab providing cell sorting to individual labs.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Service offered by the organization.
provides services
specifies_the_use_of
A protocol can specify the use of a flow cytometer.
Instruments, techniques, reagents, organisms, or software that are referenced in a protocol.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
specifies the use of
has_affiliation
A researcher has an affiliation with a department.
Institutional, consortia, or other organizational affiliations.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has affiliation
used_by
A laboratory uses Microsoft Word.
Laboratory that uses the protocol or software.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
used by
has_input_type
Imaging processing software that requires .jpg format files for analysis.
PERSON: Carlo Torniai
PERSON: Melissa Haendel
Software data input format.
has input format
has_output_type
Microsoft Excel arranges and saves data in .xlsx format.
PERSON: Carlo Torniai
PERSON: Melissa Haendel
Software data output type.
has output format
achieves_objective
ImageJ software measures characteristics of digital images.
PERSON: Carlo Torniai
PERSON: Melissa Haendel
Transformation objective of the software.
achieves objective
has_author
A journal article has authors.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Person who authored a document.
has author
tobe imported probably from FOAF or anywwre according top vivo
model_of
Disease or condition for which an organism presents some or all defining characteristics.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Transgenic mice are often models for a specific disease.
here we need to have a more clear definition in dependence of the model
model of
has_topic
A research project focuses on a specific topic, such as cancer research.
Organism, biological process, or disease that is the subject matter of the research project or protocol.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has topic
here we need to take care of dofferent domain and is this really the same relation between research project and protocol?
has_biosafety_level
Level of the biocontainment precautions required to isolate dangerous biological agents in an enclosed facility. Levels range from level 1 (lowest) to 4 (highest). In the United States, the Centers for Disease Control and Prevention (CDC) specified these levels.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Working with ebola virus has biosafety level 4.
has biosafety level
service_provided_by
A core laboratory provides a service.
Organization or laboratory performing the service.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
service provided by
performs
A cancer researcher performs apoptosis assays.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Technique carried out by the person or laboratory.
is_performed_by
Confocal microscopy is performed by a confocal core laboratory.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Person or laboratory that performs the service or technique.
is performed by
has_documentation
An antibody has documentation describing attributes of the antibody.
Document that contains relevant resource information.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has documentation
realizes_protocol
A sequencing protocol used for next generation sequencing.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Protocol used to perform the service.
placeholder: need to be modeled for the proper kind of service (production services)
realizes protocol
uses_software
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder needs to be redesign
Sequence analysis software.
Software used to perform the service.
true
uses software
expresses_construct
A cell line that overexpresses a gene.
Construct that has been introduced into the genome of a permanent cell culture.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
expresses construct
related_technique
Flow cytometry is a related technique for a flow cytometer instrument.
Method in which the resource can be used.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
related technique
recognizes_species
An mouse anti-human OX40 antibody recognizes the human OX40 protein.
Organism recognized by the antibody.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
recognizes species
has_immunogenic_material
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Purified OX40 protein.
The material used to generate an immune response to produce an antibody. For example, a tissue, a protein, or a virus.
used_to_study
A study of hibernation in bears.
Biological process studied in the organism.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
used to study
has_sequence_alteration
A point mutation in a gene.
A sequence variation that deviates from a canonical or reference sequence.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has sequence alteration
has_sequence_alteration
has_director
Name of the person who directs the organization.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The director of a core lab.
has director
funded_by
Organization providing financial support.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The lab is funded by the NIH.
funded by
expressed_in_organism
A yeast expression vector is designed to be expressed in yeast cells.
Organism in which the construct is designed to be expressed.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
expressed in organism
shortcut relation for participates_in_ expression process
has_residency_requirement
A research opportunity requires applicants to be US citizens.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
US residency status of applicants that may apply for the student research opportunity.
has residency requirement
related_viral_construct
Construct used to generate active virus.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The construct pWPI-GFP is used to generate GFP viral supernatants.
related viral construct
related_virus
GFP superntants are produced by the pWPI-GFP construct.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Virus produced by viral plasmid.
related virus
related_research_project
A research project studying breast cancer.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Research project during which the biological specimen was collected.
related research project
related_biological_specimen
A breast cancer specimen.
Biological specimen collected as part of the research project.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
related biological specimen
infects_target_organism
A virus that infects human cells.
Organism that the virus infects.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
infects target organism
is_contact_for
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Resources for which the person is a contact.
The PI is the contact for an instrument.
used_to_generate_organism
A construct used to generate a knockdown mouse.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Transgenic organism generated using the construct.
used to generate organism
organism_generated_from_construct
A construct used to generate a knockout mouse.
Construct used to generate a transgenic organism.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
organism generated from construct
has_preparation_technique
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Paraffin embedding of tissue.
Technique used to prepare the biological specimen.
has preparation technique
matching_specimen
Healthy breast tissue is a matching specimen for breast cancer tissue.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Specimen match to a given biological specimen. A matched pair of biological specimens usually includes a control specimen that is either from a non-affected individual or tissue.
matching specimen
is_matching_specimen
Healthy breast tissue is a matching specimen for breast cancer tissue.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Specimen match to a given biological specimen. A matched pair of biological specimens usually includes a control specimen from a non-affected individual or tissue.
is matching specimen
has_derived_specimen
DNA derived from breast cancer tissue.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Specimen derived from another biological specimen, such as a DNA or protein isolate.
has derived specimen
derives_from_specimen
DNA derived from breast cancer tissue.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Specimen that is derived from another biological specimen, such as a DNA or protein isolate.
derives from specimen
related_cell_line
Cell line collected as part of a research project.
HeLa cells used for a research project.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
related cell line
derives_from_material_anatomical_entity
A cell line derived from a kidney.
Anatomical entity from which the resource is derived.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
derives from material anatomical entity
derives_from_organism
A human cell line.
Organism from which the resource is derived.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
derives from organism
has_phase
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Phase 1 clinical trial.
Phase of a clinical trial to evaluate risk and to clinically evaluate the efficacy of drugs or biologicals.
has phase
performs_human_study
Human study performed by the organization.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The Jackson Heart Institute performs human studies on heart disease.
performs human study
human_study_performed_by
Jackson State University performs human studies on heart disease.
Organization that performs the human study.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
human study performed by
derives_from_organism_or_virus
A cell line is derived from a human.
Organism or virus from which the resource is derived.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
derives from organism or virus
antibody_produced_by
An anti-OX40 antibody is produced by a hybridoma.
Hybridoma cell line used to produce the antibody.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
antibody produced by
has_antibody_target
A material that is recognized by an antibody. Most often this is a protein but can also include chemicals, or biological materials such as cells or organisms.
Most often this is a protein but can also include chemicals, or biological materials such as cells or organisms.
PERSON: Matthew Brush
PERSON: Melissa Haendel
ToDo: will be a subproperty of some kind of "recognizes" property.
related_immunotechnique
Antibody related method in which the resource can be used.
Flow cytometry.
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
species_non_reactivity
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
Species in which the antibody has been shown not to cross react.
author_of
A journal article authored by the person.
Document authored by a person.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has_member
has_format
has_phenotype_biological_process
has_software_license
Is a legal instrument (usually by way of contract law) governing the usage or redistribution of software.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Software_license
has_phenotype_anatomical_entity
has_mammalian_phenotype
has_phenotype_quality
has_phenotype_annotation
is_PI_of
A professor in the Department of Biomedical Engineering is the principal investigator (PI) of her research group and laboratory.
Identifies the laboratory or research project for which this individual is the principal investigator.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
is PI of
is_director_of
A professor is the director of a consortium devoted to rare diseases.
Identifies the organization for which this person is the director.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
is director of
objective_achieved_by_operation
Links an objective to a software operation whise execution achieves the objective. Is different from OBI:objective_achieved_by which links an objective to the process that achieves it.
PERSON:Matthew Brush
PERSON:Matthew Brush
a relation between a software objective (data transformation objective) and an operation whose execution in a software tool achieves the objective
software relation expanding to something like:
objective_achieved_by some ('software/algorithm execution' and (specified_by some 'data processing operation'))
has_phenotypic_sex
Describes the phenotypic sex of an organism.
PERSON: Matthew Brush
PERSON: Matthew Brush
has_potency
Describes the types of germ layers into which a stem cell or line is capable of differentiating
PERSON:Matthew Brush
PERSON:Matthew Brush
has_co-developed_line
Describes other cell lines that were co-developed at the same time from the same biological source.
PERSON: Matthew Brush
PERSON: Matthew Brush
derives_from_cell_line
Describes derivation of a cell line from an existing cell line, through some spontaneous or experimetnal modification.
PERSON: Matthew Brush
PERSON: Matthew Brush
has_viability
Describes the viability status of an organism in a study (ie alive or deceased)
PERSON: Matthew Brush
PERSON: Matthew Brush
is_member_of_ethnic_group
Describes an ethnic group of which a human is a part.
PERSON: Matthew Brush
PERSON: Matthew Brush
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
is_realized_by
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
executed_during
has_realization
is_realized_as
is_manufactured_by
Alan Ruttenberg
Liju Fan
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
has_make
has_manufacturer
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
is_manufactured_by
has_function
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
Relation between an independent continuant and a function.
has_function
heart has_function to-pump-blood
realizes
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungal
Relation between a process and a function, where the unfolding of the
process requires the execution of the function. Class level: P realizes F iff:
given any p that instantiates P, there exists some f, t such that f instantiates
F at t and p *realizes* f. Here, *realizes* is the primitive
instance level relation [GOC:cjm]
example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the
function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity'
denotes a function and not a process). We leave open the possibility of defining
in future the sub-relations directly_realizes (as bewteen a function and it's
functioning) and indirectly_realizes.
executes
has_function_part
involves_execution_of
is_realization_of
realizes
is_specified_output_of
PERSON:Bjoern Peters
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
has_role
A relation between a continuant C and a role R. The reciprocal relation of role_of.
GROUP:OBI:<http://obi.sourceforge.net>
PERSON:Chris Mungal
has_role
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
BP, AR, PPPB branch
PPPB branch derived
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
has grain
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has grain
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PERSON: Alan Ruttenberg
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
definition needs clean up to indicate directionality
produces
Melissa Haendel
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
produced_by
Melissa Haendel
bearer_of
inheres in
This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant.
This relation belongs in BFO/RO, and will be in BFO 2
role_of
A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
role_of
implements
is_encoded_in
adjacent_to
Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
relationship
agent_in
relationship
contained_in
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
relationship
contains
relationship
derived_into
relationship
derives_from
Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
relationship
has_agent
relationship
has_improper_part
See reasons for obsoletion of improper_part_of
relationship
has_integral_part
relationship
has_part
relationship
has_participant
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
relationship
has_proper_part
relationship
improper_part_of
OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]
relationship
integral_part_of
relationship
located_in
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
relationship
location_of
relationship
part_of
Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
relationship
participates_in
relationship
preceded_by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
relationship
precedes
relationship
proper_part_of
relationship
relationship
this relation was superfluous, so it has been obsoleted
relationship
transformation_of
When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
relationship
transformed_into
Obsoleted
relationship
DeprecatedProperty
mailing_address
3181 SW Sam Jackson Park Road. Portland, OR 97239
Mailing address for correspondence.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
mailing address
contact_email
Email address of the primary contact.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
email
last name@university.edu
first_name
Individual's forename.
Nicole
PERSON: Melissa Haendel
PERSON: Melissa Haendel
We refer to the Lab contact and not to the person we have contacted in order to have this informatoin
first name
has_inventory_number
An example inventory number can be in the form: 12345
Inventory identifier for the resource.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has inventory number
has_restriction
A restriction on service availability, such as university or consortium affiliation, geographical location, professional certification, or other factors.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Resource is only available to researchers in the department.
has restriction
has_geographic_restriction
Any service limitation tied to geographically-defined areas such as metro areas, counties, states, or regions.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Resource is only available to researchers in Boston area.
has geographic restriction
last_name
Individual’s surname.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Smith
We refer to the Lab contact and not to the person we have contacted in order to have this informatoin
last name
model_number
ABI 9000
Instrument model number, which may be a name, number, or both.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
model number
phone_number
503-555-5555
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The number used to call someone by phone.
phone number
title
Designation used to refer to an individual.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Professor
lab_data_format
Current method or software used to inventory a lab's resources. Examples include Excel, index cards, FileMaker, 3-ring binder, etc.
Excel spreadsheet
PERSON: Melissa Haendel
PERSON: Melissa Haendel
lab data format
lab_delivery_address
Laboratory address where deliveries are made.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Volumn Research Institute, 3rd floor, bay 1
lab delivery address
version
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Software edition, typically a numeral followed by a decimal and another numeral, such as 2.1.
v 1.0
operating_system
Computer operating system used by the software, such as Windows, MacOS, or Linux.
Microsoft Windows
PERSON: Melissa Haendel
PERSON: Melissa Haendel
operating system
has_entrez_gene_id
A unique identifier assigned to each record in the Entrez Gene database.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The entrez gene ID of mouse CD34 is 12490.
has entrez gene id
construct_backbone
Name of the construct backbone. This label is often the first part of a construct name and refers to the part of the construct that is not the insert.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
construct backbone
pENTER
has_accession_number
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The accession number for a gene.
Unique identifier of a biological polymer sequence (DNA, RNA, protein) when it is submitted to a sequence database.
accession number
has_insert_size
A 40bp insert.
Number of base pairs in the insert.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
insert size
has_tag
A FLAG tag on a protein.
Expression tag that allows tracking of the RNA or protein.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
insert tag
has_study_population
African american study population.
Characteristics of the human population being studied. May include number, demographic or geographic information, inclusion or exclusion criteria, or other descriptive information.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
study population
has_CAS_number
CAS number
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The CAS number for NaOH.
Unique numerical identifier for a chemical as defined by the Chemical Abstracts Service (CAS).
has_IUPAC_name
IUPAC name
International Union of Pure and Applied Chemistry (IUPAC) name of the chemical.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The IUPAC name for NaOH.
has_PubChem_CID
PERSON: Melissa Haendel
PERSON: Melissa Haendel
PubChem CID
The PubChem CID for NaOH.
Unique numerical identifier for a chemical as defined by the PubChem database of chemical molecules.
has_purity_grade
99.9% pure ethanol.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Purity Grade
Purity grade of a chemical reagent, often expressed in the product name by means of a quality denomination that follows to the product nomenclature, such as Guaranteed Reagent.
has_url
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
The website for a manufacturer.
Web address of the resource.
has URL
has_selectable_marker
Ampicillin resistance gene.
Gene that confers a trait suitable for selection.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has selectable marker
library_count
100 RNAi oligos in an oligo library.
Number of elements in the library.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
library count
has_uniPROT_ID
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The UniPROT ID for Mad4 protein.
Unique numerical identifier for a chemical as defined by the UniProt database.
has uniPROT ID
has_bacterial_host_strain
Bacterial strain in which the library is hosted.
E.coli is used to host a DNA library.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has bacterial host strain
has_producer_strain
E.coli is used to produce a DNA library.
Organismal or viral strain used to produce the library.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has producer strain
has_producer_cell_type
293T cells are used to produce a lentiviral supernatant.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Type of cell in which the virus may be produced.
has producer cell type
recognizes_protein_uniprot_ID
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The Uniprot ID of the gene product recognized by the antibody.
The antibody recognizes a protein, with a corresponding UniProt ID.
recognizes protein uniprot ID
has_PubMed_ID
PERSON: Melissa Haendel
PERSON: Melissa Haendel
PubMed ID
The PMID for a journal article.
Unique numerical identifier assigned to citation of life sciences and biomedical scientific journal articles in the PubMed database.
has_parental_strain_name
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Parental strain name of modified organisms.
Wild type 293 cells.
has parental strain name
has_gene_symbol
CD4.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
The official symbol for the gene.
has gene symbol
has_affected_gene_entrez_id
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The Entrez Gene ID for the gene that is affected in a transgenic organism.
The entrez gene ID of mouse CD34 is 12490.
has affected gene Entrez ID
has_phenotype
A mouse with a shorter tail.
An observable characteristic or trait of an organism, such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest).
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has phenotype
has_source
A mouse house in a research lab.
Organism’s source environment or clinical setting.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has source
has_infectious_history
A monkey with CMV.
Infectious history of the organism, such as previous viral infections that may affect the usage of the organism for research.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has infectious history
has_eligibility_requirment
A grade point average above 3.5 is an eligibility requirement.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Requirements for research opportunity eligibility. Requirements include: coursework, minimum gradepoint average, state residency, under-represented group status, field of study, or matriculation status.
has eligibility requirement
has_start_date
Beginning time at which the research opportunity is available.
January 1, 2012.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has start date
has_end_date
January 21, 2012.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Time at which the research opportunity is no longer available.
has end date
has_InChI_key
PERSON: Melissa Haendel
PERSON: Melissa Haendel
The InChi key number for NaOH.
Unique numerical identifier for a chemical as defined by the InChI Key database.
has InChI Key
has_diagnosis
A biological specimen collected from a patient with breast cancer.
Free-text description of a diagnosis made on the biological specimen sampled.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
has diagnosis
has_pathological_stage
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Stage IV breast cancer.
Stage that has been assigned to the biological specimen, such as cancer stage, degeneration stage, normal or control.
has pathological stage
has_antibody_registry_ID
AB12345.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
The unique ID number assigned to an antibody in the Neurosicence Information Framework (NIF) antibody registry.
has antibody registry ID
has_clone_ID
Clone identification number assigned to a monoclonal antibody.
N-262.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
has clone ID
has_lot_number
4521
PERSON: Nicole Vasilevsky
The identification number assigned to a particular quantity or lot of material from a single manufacturer.
has lot number
http://www.answers.com/topic/lot-number
has_catalog_number
Catalog number of a commercially manufactured reagent.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
SC-1234
has catalog number
has_conjugate
A molecule conjugated to the antibody, which can be used to detect the presence of the antibody.
FITC.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
has conjugate
target_modification
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Phosphorylation.
Post-translational protein modification.
target_subregion
C-terminus.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
The subregion which is targeted by the antibody, such as the N- or C-terminus or a specific domain.
gene_cross_reactivity
Antibody cross reacts with other gene family members.
Gene(s) for which the antibody has been shown to cross react.
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
has_sequence
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
Possibly import from IAO or SO.
Sequence of an oligo.
The sequence of nucleotide residues or amino acids in a nucleotide or a protein.
has_molecular_weight
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
The molecular weight of the protein target.
age_at_time_of_sampling
PERSON: Matthew Brush
Indicates the age of an organism or human subject at the time a biospecimen was collected.
PERSON: Matthew Brush
originates_from_country
PERSON: Matthew Brush
Indicates the country in which a person was born.
PERSON: Matthew Brush
is_member_of_family
Indicates a family of which a human is a member.
PERSON: Matthew Brush
PERSON: Matthew Brush
relationship to proband
PERSON: Matthew Brush
Describes the relationship between a human subject affected with a disorder and the 'proband' - the related family member who is the first affected subject identified in a study.
http://www.merriam-webster.com/dictionary/proband
MRI Scanner
A measurement device that visualizes detailed internal structure and limited function of the body, using a powerful magnetic field to align the nuclear magnetization of (usually) hydrogen atoms in water in the body.
NMRI scanner
http://en.wikipedia.org/wiki/Magnetic_resonance_imaging
magnetic resonance imaging scanner
nuclear magnetic resonance imaging scanner
PDBML
Taverna workflow format
Format of Taverna workflows.
HTML
html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web.
http://www.w3.org/TR/html401/
laboratory
A cancer research laboratory.
Material entity that performs research, provides services, or processes materials.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
requested in OBI 2894859
true
core laboratory
A flow cytometry core laboratory at a university.
Laboratory that has the mission of providing services. Core Laboratories often charge fees for services or are funded via their affiliated organizations.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Facility_Core
Definition: As defined in http://dictionary.reference.com/browse/facility
requested in OBI 2894859
service laboratory
true
instrument
A flow cytometer.
Material entity that is designed to have a function and play a role in scientific investigation.
PERSON: Melissa Haendel
See OBI listserv discussion for considerations in defining instrument. http://sourceforge.net/tracker/index.php?func=detail&aid=2894801&group_id=177891&atid=886178
http://en.wikipedia.org/wiki/Scientific_instrument
instrument
service offering
A DNA sequencing service performed by a core lab.
An information content entity that describes a service performed by a person or organization with the objective of performing a technique, providing training, providing storage of data or material entities, or providing access to resources for another person or organization
Coordinate with NIF. NIF ID: nlx_res_20090105
PERSON: Melissa Haendel
PERSON: Melissa Haendel
service
reagent
A plasmid can be used as a reagent.
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
Processed material that is used in a chemical reaction or other experimental process to detect, measure, examine, or produce other substances.
http://www.yourdictionary.com/reagent
reagent
technique
A technique is a planned process used to accomplish a specific activity or task.
Flow cytometry is a technique.
PERSON: Melissa Haendel
Protocol is added to eagle-i temporarily until a relationship between the informatio entity "protocol" and these planned processes is created. This class refers to the axtual process not the document
http://en.wikipedia.org/wiki/Technique
antibody reagent
A reagent that is comprised of immunoglobulins produced by B cells in response to an antigen. Antibody reagents can be engineered to have specificity for specific antigens.
An antibody is used to detect proteins in a Western blot assay.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://www.nlm.nih.gov/medlineplus/ency/article/002223.htm
cell line
Atwood et al (2000) OED of Biochemistry and Molecular Biology, Oxford University Press.
HeLa cells are a cancer cell line that were generated from a cervical tumor.
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
Reagent that is a population of cells cultured in vitro that are descended through one or more generations (and possible sub-cultures) from a single primary culture which was originally derived from part of an organism. The cells of such a population share common characteristics.
cell line
service provider role
A role inhering in a person or organization that is realized when the bearer participates in providing a service to meet the need of another person or thing.
A technician in a core laboratory.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
research project
A funded collection of investigations as described in a research proposal.
A project to study the role of a specific protein in cell signaling.
Maybe SameAs "Investigation" but is the subject of funding
PERSON: Melissa Haendel
PERSON: Melissa Haendel
human study
A clinical trial.
OCRe
PERSON: Melissa Haendel
Research project that uses or collects measurements or assessments about humans.
This should be imported from OCRE- but they currently have no generic human study type. Def is modified.
human study
clinical trial
A clinical trial to evaluate the efficacy of a new drug.
An interventional study that contains a set of procedures in medical research and drug development that are conducted to allow safety (or more specifically, information about adverse drug reactions and adverse effects of other treatments) and efficacy data to be collected for health interventions (e.g., drugs, diagnostics, devices, therapy protocols) that is performed over phases.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Clinical_trial
epidemiological study
A human study of diseases in populations of humans or other animals, specifically how, when and where they occur. Epidemiological studies can never prove causation, epidemiological evidence can only show that this risk factor is correlated with a higher incidence of disease in the population exposed to that risk factor. The higher the correlation the more certain the association, but it cannot prove the causation.
A study of the populations and demographic of the avian flu.
PERSON: Karen Corday
epidemiological study
http://pmep.cce.cornell.edu/profiles/extoxnet/TIB/epidemiology.html
genome wide association study
A genome wide association study is an examination of genetic variation across a given genome, designed to identify genetic associations with observable traits.
PERSON: Karen Corday
genome wide association study
http://en.wikipedia.org/wiki/Genome-wide_association_study
biological specimen
Heart tissue obtained from an organism.
Material entity that is a portion or quantity of a biological material for use in testing, examination, or study. A biological specimen can be an individual animal, a population of organisms, or is a part of or derived from an animal, plant, part of a plant, or microorganism. When a taxon is described, it is typically based on a single specimen and is referred to as the holotype.
PERSON: Melissa Haendel
Should have relationship to Organism
biological specimen
biospecimen
http://en.wikipedia.org/wiki/Specimen
software
A general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers.
IAO is a planned specification, in SWO is an Information artifact. In eagle-i, we have a need to collect material instances and is it thus currently classified as a material entity.
Microsoft Word is commonly used word processing software.
PERSON: Melissa Haendel
http://en.wikipedia.org/wiki/Computer_software
software
open source software
ImageJ is open source software from the NIH, used for image quantification and analysis.
PERSON: Nicole Vasilevsky
Software whose source code is published and made available to the public, enabling anyone to modify it.
true
www.en.wikipedia.org/wiki/Open_source
commercial software
Microsoft Office suite is commercial software.
PERSON: Nicole Vasilevsky
Software that is produced for sale or that serves commercial purposes.
true
www.en.wikipedia.org/wiki/Commercial_software
RNA sequence
Data containing the arrangement of nucleotides in a DNA fragment or genome.
PERSON: Nicole Vasilevsky
RNA sequence
The RNA sequence encodes the protein sequence.
http://en.wikipedia.org/wiki/RNA
protein sequence data
A protein sequence data represents the primary structure of a protein and is the order in which amino acid residues, connected by peptide bonds, lie in the chain in proteins.
PERSON: Karen Corday
The protein sequence is encoded by the RNA sequence.
http://en.wikipedia.org/wiki/Peptide_sequence
protein sequence
macromolecular crystallographic information data
Data from the Macromolecular Crystallographic Information File (mmCIF) that is used for describing small molecule structures and associated diffraction experiments.
Macromolectular Crystallographic Information data
PERSON: Karen Corday
http://www.sdsc.edu/pb/papers/methenz97.pdf
electron density map data
Data that are a three-dimensional description of the electron density in a crystal structure, determined from X-ray diffraction experiments. They describe the contents of the unit cells averaged over the whole crystal and not the contents of a single unit cell (a distinction that is important where structural disorder is present).
PERSON: Karen Corday
electron density map
http://reference.iucr.org/dictionary/Electron_density_map
NMR restraint data
Data generated by NMR used as input for structure generation programs.
PERSON: Nicole Vasilevsky
http://www.ccpn.ac.uk/ccpn/data-model/python-api-v2-examples/nmr-restraints
cell assay platform
A flow cytometry set up.
A platform that is an aggregate of the set of instruments and software needed to perform a cell assay procedure.
Erik Segerdell
PERSON: Erik Segerdell
requested in OBI
cell selection device
A device that isolates and detects intended target cells.
An autoMACS cell separator, used to separate cells tagged with magnetic beads.
PERSON: Karen Corday
http://www.rndsystems.com/product_detail_objectname_pluscellectkits.aspx
requested in OBI
electroporator
A nucleofector device.
An instrument that applies an electrical field to a population of cells, which causes a significant increase in the electrical conductivity and permeability of the cell plasma membrane and allows the introduction of some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA.
PERSON: Erik Segerdell
cell porator
http://en.wikipedia.org/wiki/Electroporator
requested in OBI
there is a trade name 'nucleofactor'
environmental control system
A device or system that supports a controlled physical environment.
A fume hood is an environmental control system.
Erik Segerdell
PERSON: Erik Segerdell
requested in OBI
freeze-fracture device
A device that rapidly freezes a fresh tissue or cell suspension for subsequent fracture and downstream analysis.
A device used to break up tumors for subsequent analysis.
PERSON: Karen Corday
freeze-fracture device
http://en.wikipedia.org/wiki/Electron_microscope
requested in OBI
microfluidics platform
A platform that combines several microfluidic functions (e.g. capillary valving, centrifugal pumping, and flow sequencing).
An HPLC apparatus contains a microfluidics platform.
Erik Segerdell
PERSON: Erik Segerdell
proteomics platform
A platform that combines several proteomics functions.
Erik Segerdell
PERSON: Erik Segerdell
workstation
A high-end computer designed for technical or scientific applications.
PERSON: Erik Segerdell
computer workstation
http://en.wikipedia.org/wiki/Workstation
requested in OBI
nucleic acid library
A primer library.
From Richard: RNAi, plasmid, phage, chemical, viral, [also cell libraries]
PERSON: Melissa Haendel
Reagent library that is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning.
http://en.wikipedia.org/wiki/Dna_library
nucleic acid library
protein reagent
An antibody is a protein reagent.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
Reagent that is a sequence of amino acids.
peptide reagent
protein reagent
chemical reagent
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
Reagent that is a material of pure chemical composition, either an element or a compound.
Sodium hydroxide is a common chemical reagent.
http://en.wikipedia.org/wiki/Chemical_substance
DNA electrophoresis
Electrophoresis in which DNA is separated by its resistance to movement and its charge.
PCR products are subjected to DNA electrophoresis to confirm the presence of DNA.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
agarose gel electrophoresis
RNA electrophoresis
Electrophoresis in which RNA is separated it by its resistance to movement and its charge.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
RNA is subjected to electrophoresis in a Northern blot.
protein electrophoresis
Electrophoresis in which protein is separated it by its resistance to movement and its charge.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
The first step in a Western blot.
high performance liquid chromatography
A liquid chromatography technique that can separate a mixture of compounds and is used in biochemistry and analytical chemistry to identify, quantify and purify the individual components of the mixture.
HPLC
PERSON: Nicole Vasilevsky
The proteins present in a sample are identified by HPLC.
high pressure liquid chromatography
http://en.wikipedia.org/wiki/High-performance_liquid_chromatography
cell immortalization
A cell culture technique where primary cell cultures are immortalized, have extended replicative capacity and grow continuously in culture with the replacement of proper growth media.
Cell line generation
PERSON: Nicole Vasilevsky
Transformation of 293 cells.
http://www.bioxys.com/i_Abm/cell_immortalization_products.htm
restriction fragment length polymorphism electrophoresis
A nucleic acid assay that is used to detect RFLPs, which involves fragmenting a sample of DNA by a restriction enzyme. The resulting DNA fragments are then separated by length using agarose gel electrophoresis, and transferred to a membrane via the Southern blot procedure. Hybridization of the membrane to a labeled DNA probe then determines the length of the fragments which are complementary to the probe. A RFLP occurs when the length of a detected fragment varies between individuals.
PERSON: Nicole Vasilevsky
RFLP electrophoresis
RFLP is used in forensic science to identify a perpetrator.
http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
confocal microscopy
A microscopy technique used in optimal imaging that increases optical resolution and contrast of a micrograph by using point illumination and a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. It enables the reconstruction of three-dimensional structures from the obtained images.
CLSM
Colocalization studies of two proteins.
Confocal scanning microscopy
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Confocal_microscopy
microscopy
An imaging assay that uses microscopes to view samples and objects that cannot be seen with the unaided eye (objects that are not within the resolution range of the normal eye).
Cell viability can be visualized by microscopy.
Microscopic examination
PERSON: Nicole Vasilevsky
Sample microscopy
http://en.wikipedia.org/wiki/Microscopy
light box
A device that provides a source of illumination for observation and photography of a wide variety of tests performed in virological, microbiological and clinical laboratories using either white or ultraviolet light.
Coomassie stained gels can more easily be visualized using a light box.
PERSON: Erik Segerdell
United States Patent 4071883
cryoembedding
A histological sample preparation technique involving embedding tissue in a compound that allows them to be frozen rapidly and prepares them for subsequent sectioning.
Cryoembedding heart biospecimens.
Frozen block cryoembedding
PERSON: Nicole Vasilevsky
http://www.tedpella.com/cryo_html/cryo2.htm
immunohistochemistry assay
A tissue/organ assay that is used to detect antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues.
IHC
Immunostaining
PERSON: Nicole Vasilevsky
Used to detect protein expression in a tissue.
http://en.wikipedia.org/wiki/Immunohistochemistry
light microscopy
A microscopy technique that uses visible light and a system of lenses to magnify images of small samples.
LM
Light microscopy is used to examine cell viability.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Optical_microscopy
time lapse light microscopy
Light microscopy where the same object (e.g., a cell) is photographed at regular time intervals over several hours.
PERSON: Nicole Vasilevsky
The migration of a protein through a cell can be captured by time-lapse microscopy.
http://en.wikipedia.org/wiki/Time-lapse_microscopy
time lapse confocal microscopy
Confocal microscopy where the same object (e.g., a cell) is photographed at regular time intervals over a specified period of time.
Migration of a protein in a cell can be captured by time-lapse confocal microscopy.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Time-lapse_microscopy
cryosectioning
A technique used in histological sample preparation where water-rich tissues are hardened by freezing and cut in the frozen state with a freezing microtome or microtome-cryostat.
Biospecimens are removed from an organism and flash frozen, then cryosectioned for subsequent histological analysis.
Cryogenic sectioning
Freeze sectioning
Frozen sectioning
PERSON: Nicole Vasilevsky
cryosectioning
http://www.answers.com/topic/microtome
image analysis
An imaging technique that allows images to be analyzed based on their pixel or voxel composition.
Image analysis of bands on a gel to quantitate the relative difference in protein expression.
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
funding role
A role inhering in a person or organization that is realized when the bearer participates in providing funding to a person or an organization for academic or business purposes.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
The NIH is a funding agency.
educator role
A role inhering in a person or organization that is realized when the bearer participates in providing education to a student or group of students.
A teacher.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
monoclonal antibody reagent
An mouse anti-human Mad4 antibody.
Antibody reagent that recognizes a single epitope.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
polyclonal antibody reagent
A rabbit anti-human SHH antibody.
Antibody reagent that recognizes multiple epitopes.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
fluorescence and luminescence assay detection system
A Licor imager, which can be used to image animals in vivo.
A measurement device that detects fluorescence intensity, fluorescence polarization, time-resolved fluorescence, and luminescence, delivering information in terms of sensitivity, dynamic range, signal-to-noise, and cross-talk.
PERSON: Karen Corday
fluorescence and luminescence assay detection system
http://www.bioresearchonline.com/product.mvc/Analyst-HTS-Assay-Detection-System-0001
laminar flow hood
Device that flows filtered air onto a specially enclosed work surface. This prevents particulate and microbial contamination, while protecting the user from the potential exposure to infectious material being handled.
PERSON: Karen Corday
Tissue culture work is usually done in a laminar flow hood.
http://www.cybersight.org/bins/content_page.asp?cid=1-1581-1642
laminar flow cabinet
laminar flow hood
dispensing well plate
A nanodispenser that is used for the massive parallel delivery of liquid volumes in the range of 50 nL.
DWP
PERSON: Erik Segerdell
Plate replicator.
dispensing well plate
doi:10.1016/j.sna.2004.05.038
robot arm
A mechanical instrument that consists of an upper arm link and a lower arm link that are interconnected by a uniaxial joint. The upper arm link is connected with a structure via a universal joint.
PERSON: Karen Corday
http://www.google.com/patents/about?id=ZqcsAAAAEBAJ
robot arm
compressor
A device that transfers energy to a gaseous fluid for the purpose of raising the pressure of the fluid as is the case when the compressor is the prime mover of the fluid through the process.
Gresh, M.T. (2001). Compressor performance: aerodynamics for the user. Woburn, MA: Butterworth-Heinermann.
PERSON: Karen Corday
compressor
vacuum centrifuge concentrator
A centrifuge that includes a vacuum chamber within which a centrifuge rotord is rotatably mounted for spinning a plurality of vials containing a solution at high speed while subjecting the solution to a vacuum condition for concentration and evaporation.
A speed vac is used to concentrate a sample.
PERSON: Nicole Vasilevsky
http://www.google.com/patents/about?id=J7Q6AAAAEBAJ&dq=4226669
sample concentrator
speed vac
speed vacuum
vacuum centrifuge concentrator
refrigerated centrifuge
A centrifuge that can be operated at low temperatures.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Used to prepare protein lysates.
biological safety cabinet
A fume hood.
An instrument used for containment of biological materials, which functions as a primary barrier to prevent the escape of biological aerosols into the laboratory environment.
PERSON: Karen Corday
biological safety cabinet
biosafety cabinet
http://www.drs.illinois.edu/bss/factsheets/cabinets.aspx
transmission electron microscope
An electron microscope that uses a high voltage electron beam to create an image.
For use in imaging of biological molecules.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Electron_microscope#Transmission_electron_microscope_.28TEM.29
transmission electron microscope
fluorescence microscope
An optical microscope used to study properties of organic or inorganic substances using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption.
Epifluorescence microscope
Fluorescent microscope
PERSON: Karen Corday
Used to visualize biomolecules.
fluorescence microscope
http://en.wikipedia.org/wiki/Fluorescence_microscope
UV crosslinker
A UV crosslinker is used to crosslink RNA to a membrane in Northern blots.
An instrument designed to crosslink molecules, such as DNA or RNA to a surface, such as a membranes.
PERSON: Nicole Vasilevsky
UV crosslinker
http://research.amnh.org/molecular/equipment_folder/Stratalinker%201800.pdf
automatic sputter coater
A sputter coater where the complete sequence of flush, leak, coat and vent is automatically controlled. The solenoid operated leak valve allows the gas pressure to return automatically to pre-set conditions.
For gold deposition of scanning electron microscopy specimens.
PERSON: Karen Corday
automatic sputter coater
http://www.canemco.com/catalog/instruments/Sputter-coaters.htm#Automatic_Sputter_Coater_
industrial robot
A device that is programmable, multifunctional, and mechanical that is designed to move material, parts, tools, or specialized devices through variable programmed motions to perform a variety of tasks.
PERSON: Karen Corday
Robotic arm moving pin array for moving compounds.
http://www.osha.gov/dts/osta/otm/otm_iv/otm_iv_4.html
plate sealer
A mechanical instrument that applies seal material on top of microplates (plates) to seal individual wells.
A plate sealer is used to seal plates for real-time PCR.
PERSON: Karen Corday
http://www.chem.agilent.com/Library/usermanuals/Public/G5402-90001_PlateLocUG_EN.pdf
plate sealer
barcode labeler
An instrument that prints bar code labels and applies them to a product, such as to the side of a microplate.
PERSON: Karen Corday
bar code labeler
http://cp.chem.agilent.com/Library/usermanuals/Public/G5404-90001_LabelerUG_EN.pdf
chip reader
An instrument used to detect and record data provided by a microarray chip.
PERSON: Nicole Vasilevsky
http://www.sciclips.com/sciclips/protein-biomarker-protocol.do?protocol=Ciphergen%20ProteinChip%20SELDI-TOF-MS%20Analysis&type=8166
ultrasonic cell disruptor
A device that uses ultrasound to disrupt cell membranes and release cellular contents.
An ultrasonic cell disruptor is used to break up bacteria during protein purification.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Sonication
ultrasonic cell disruptor
fluidics station
An instrument used for the wash and stain operation of arrays.
PERSON: Nicole Vasilevsky
Wash and stain functions on an automated immunohistochemistry instrument.
http://www.affymetrix.com/browse/products.jsp?productId=131439&navMode=34000&navAction=jump&aId=productsNav#1_1
cell storage device
A CO2 incubator.
Device that has the function of maintaining cell lines, primary cultures or cell isolates in a viable state.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
cell storage device
fermentor
A bioreactor that provides a sterilie environment, ideal for growth of any bacteria, yeast, or fungi.
A bioreactor used to produce monoclonal antibodies from a hybridoma.
PERSON: Nicole Vasilevsky
bioreactor fermentor
http://www.nbsc.com/bioflo510.aspx
fluorescence spectrometer
A spectrophotometer that analyzes fluorescence from a sample. It uses a beam of light, usually ultraviolet light, to excite the electrons in molecules of certain compounds and causes them to emit light of a lower energy, typically, but not necessarily, visible light.
Can be used to quantify DNA.
PERSON: NIcole Vasilevsky
fluorescence detector
fluorescence spectrometer
http://en.wikipedia.org/wiki/Fluorescence_spectroscopy
amino acid analyzer
A high performance liquid chromatography instrument that is used to detect free amino acids automatically by reacting the free amino acids, under basic conditions, with phenylisothiocyanate (PITC) to produce phenylthiocarbamyl (PTC) amino acid derivatives.
An amino acid analyzer can be used to determine the composition of a protein.
PERSON: Karen Corday
amino acid analyzer
http://www.protein.iastate.edu/aaa.html
peptide synthesizer
A device that produces peptides, which are organic compounds in which multiple amino acids are linked via peptide bonds.
A peptide synthesizer is used to generate peptides to be used as antigens in immune models.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Peptide_synthesizer
peptide synthesizer
mass spectrometer sample spotter
A mass spectrometer sample spotter can be used to identify proteins in a sample.
An instrument designed to automatically mix and spot digested proteins and matrix onto any MALDI MS targets.
PERSON: Nicole Vasilevsky
http://www.gelifesciences.com/aptrix/upp01077.nsf/content/Products?OpenDocument&parentid=976027&moduleid=165591&zone=Elpho
mass spectrometer sample spotter
environmental scanning electron microscope
A scanning electron microscope that has a secondary-electron detector capable of operating in the presence of water vapour and pressure-limiting apertures with differential pumping in the path of the electron beam to separate the vacuum region (around the gun and lenses) from the sample chamber, which allows samples to be observed in low-pressure gaseous environments (e.g. 1-50 Torr) and high relative humidity (up to 100%).
Fungal spores in lemon grass leaf can be imaged using an environmental scanning electron microscope.
PERSON: Nicole Vasilevsky
environmental scanning electron microscope
http://en.wikipedia.org/wiki/Scanning_electron_microscope#Environmental_SEM
nanoindenter
An instrument used for indentation hardness tests for nanoindentation, a method for measuring and testing very small volumes of mechanical properties.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Nanoindenter
nanoindenter
nano universal testing machine
A device that is used to measure tensile and bending properties of microscopic materials.
PERSON: Karen Corday
http://mms.postech.ac.kr/
nano universal testing machine
nano-UTM
microscope digital camera
A digital camera for a microscope, which records image data of a sample image obtained by the microscope in a recording medium.
A digital camera hooked up to a microscope, which can be used to capture the images that are visualized by the microscope.
PERSON: Karen Corday
http://www.google.com/patents/about?id=XumGAAAAEBAJ
microscope digital camera
cell separator
A FACS machine can be used to sort cell populations.
An instrument that detects and isolates target cells from a mixed population of cells.
Fisher, D., et al. (Eds.). (1998). Cell separation: a practical approach. Oxford: Oxford University Press. http://books.google.com/books?id=GSWudM-1XGcC
PERSON: Nicole Vasilevsky
cell separator
genomic library
A cDNA library for the mouse genome.
A construct library that carries the entire genome of a source organism.
PERSON: Karen Corday
Placeholder for class to be imported from the Reagent Ontology (ReO).
genomic library
http://en.wikipedia.org/wiki/Genomic_library
RNAi library
A RNAi library for a gene of interest, such as SHH.
Nucleic acid library that is comprised of small interfering RNA molecules.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi library
cDNA construct library
A cDNA library expressing fragments from the mouse genome.
A construct library that is a collection of cDNA plasmids.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
cDNA library
http://en.wikipedia.org/wiki/CDNA_library
miRNA library
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi library that is comrpised of microRNA (21-22 nucelotides). miRNAs are endogenous post-transcriptional regulators that bind to complementary sequences in the three prime untranslated regions (3' UTRs) of mRNA, usually resulting in gene silencing. Each miRNA may repress hundreds of mRNAs. miRNA libraries are NOT in expression vectors but are directly transfected into cells.
miRNA libraries can be used to screen for target drugs.
miRNA library
siRNA library
An siRNA library may be used to knockdown gene expression to study the function of that gene.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi library that is comprised of small (20-25 nucleotides) interfering RNA or silencing RNA that targets mRNA for degradation. siRNAs are synthetic double-stranded RNA. siRNA libraries are NOT in expression vectors. The siRNAs are directly transfected into cells.
siRNA library
shRNA library
An shRNA library may be used to knockdown gene expression to study the function of that gene.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi library that is comprised of small hairpin RNA or short hairpin RNA that target mRNA for degradation. shRNAs are single stranded RNAs containing a tight hairpin turn and are synthesized and inserted into (primarily) Viral Cloning vectors. When expressed in the cell the loop is degraded and what is left is the siRNA (ds RNA) part.
shRNA library
construct
A reagent that is a virus or DNA molecule capable of autonomous replication, used as a vehicle to transfer foreign genetic material into a host cell. A construct may contain an insert of DNA from an external source, and may be used for cloning or for expression purposes.
Cells are transfected with constructs expressing a gene of interest to study the gene function.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
construct
vector
BAC
An artificial chromosome vector that contains portions of the bacterial fertility plasmid (F-plasmid). Used for transforming and cloning in bacteria, usually E. coli.
BAC
Often used to sequence the genome of organisms in genome projects.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
bacterial artificial chromosome
http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome
YAC
An artificial chromosome containing chromosomal features needed for replication and preservation in yeast cells (origin, telomere, and centromere). A YAC is built using an initial circular plasmid, which is typically broken into two linear molecules using restriction enzymes to allow ligation of a sequence or gene of interest and form a single large linear piece of DNA. YACs are useful for the physical mapping of complex genomes and for the cloning of large genes.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
YAC
http://en.wikipedia.org/wiki/Yeast_artificial_chromosome
yeast artificial chromosome
PAC
An artificial chromosome derived from the genome of the P1 bacteriophage. Used for transforming and cloning in bacteria, usually E. coli.
PAC
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
cosmid
A hybrid plasmid that contains cos DNA sequences derived from the Lambda bacteriophage, which allow for DNA packaging in phage capsids for delivery by viral transduction.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
cosmid
http://en.wikipedia.org/wiki/Cosmid
fosmid
A hybrid plasmid that contains sequences from the bacterial F-plasmid to enable packaging in lambda phage for delivery by viral transduction.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
fosmid
http://en.wikipedia.org/wiki/Fosmid
peptide library
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
Reagent library that contains a great number of peptides that have a systematic combination of amino acids. Usually, a peptide library is synthesized on solid phase, mostly on resin, which can be made as flat surface or beads.
http://en.wikipedia.org/wiki/Peptide_library
peptide library
chemical library
A library of kinase inhibitors.
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
Reagent library that is a collection of stored chemicals. Each chemical has associated information stored in some kind of database with information such as the chemical structure, purity, quantity, and physiochemical characteristics of the compound.
chemical library
http://en.wikipedia.org/wiki/Chemical_library
yeast two-hybrid library
A library used to screen interacting proteins.
An expression library that is a collection of yeast two hybrid constructs.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Two-hybrid_screening
yeast two-hybrid library
yeast two-hybrid construct
A construct that can be used to detect protein-protein interactions.
A construct used for yeast two hybrid screening assays, which is engineered to express a protein of interest fused to either the DNA-binding domain (BD) fragment or activation domain (AD) of a transcription factor. Yeast two hybrid constructs are typically plasmids or phagemids.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Two-hybrid_screening
transgenic lambda phage
A lambda phage expressing a gene of interest.
A transgenic virus derived from a lambda phage that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms.
PERSON: Matthew Brush
http://en.wikipedia.org/wiki/Vector_%28molecular_biology%29
lambda phage vector
phage display peptide library
A peptide library that contains phage display, an expression system of peptides, at the surface of phage particles. The construction of a phage display library is accomplished by the incorporation of the nucleotide sequence encoding the peptide to be displayed into a phage genome as a fusion to a gene encoding a phage coat protein. The fusion of the protein with the phage coat protein ensures that the peptide to be displayed is presented at the surface of the mature phage, while the sequence encoding it is contained within the same phage particle, allowing a physical link between the phenotype and genotype of the expressed peptide.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://www.phagedisplay.net/
phage display peptide library
combinatorial peptide library
A peptide library synthesized through combinatorial chemistry techniques.
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
combinatorial peptide library
http://www.genomicglossaries.com/content/libraries_synthesis.asp
overlapping peptide peptide library
A peptide library in which peptide sequences are engineered to exhibit a specified degree of overlap with other peptides in the library. The library generation process is characterized by two parameters, fragment length and offset number, each library is generated by breaking the original protein or peptide into many equal-length overlapping fragment, each has 8 to 20 residues in size.
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://www.genscript.com/overlapping_library.html
overlapping peptide peptide library
alanine scanning peptide library
A peptide library containing peptides in which each non-alanine residue is substituted one at a time with an alanine residue, allowing determination of each residue's contribution to the peptides functionality. Alanine scanning library is able to identify specific amino acid residues responsible for the peptide's function, stability, and conformation.
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
alanine scanning peptide library
http://www.genscript.com/alanine_scanning.html
natural product extracts chemical library
A chemical library that consists of chemicals produced by and extracted from living organisms.
A natural products extracts chemical library can be used to screen for drug targets.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
known bioactives collection chemical library
A chemical library that consists of chemicals known to exert a biological effect in living organisms or cells.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
synthetic chemical library
A chemical library that consists solely of synthetic chemicals.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
IgG
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgA
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgA has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical alpha heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgD
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgD has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical delta heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgE
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgE has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical episilon heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgM
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgM has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical mu heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgG1
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG1 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 1 heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgG2
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2 heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgG2a
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2a has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2a heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgG2b
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2b has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2b heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgG2c
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2c has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2c heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgG3
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG3 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 3 heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
IgG4
PERSON: Nicole Vasilevsky
The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG4 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 4 heavy chains (50-70kD).
http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm
biosafety level
A biosafety level is the level of the biocontainment precautions required to isolate dangerous biological agents in an enclosed facility. The levels of containment range from the lowest biosafety level 1 to the highest at level 4.
PERSON: Karen Corday
Work with ebola virus is a biosafety level 4.
biosafety level
http://en.wikipedia.org/wiki/Biosafety_level
antibody isotype
A subtype of antibodies. In placental mammals there are five antibody isotypes known as IgA, IgD, IgE, IgG and IgM. The "Ig" prefix that stands for immunoglobulin, another name for antibody, and differ in their biological properties, functional locations and ability to deal with different antigens.
IgG is a common antibody isotype for monoclonal antibodies.
PERSON: Nicole Vasilevsky
To be defined differently as subtype of antibody
http://en.wikipedia.org/wiki/Antibody#Isotypes
ultratome
A microtome that can allow for the preparation of extremely thin sections. The linear thermal expansion of the mounting is used to provide very fine control of the thickness allowing for extremely thin cuts, which are especially important for use with transmission electron microscope (TEM).
PERSON: Melissa Haendel
Samples analyzed by transmission electron microscopy are prepared using an ultratome.
http://en.wikipedia.org/wiki/Microtome#Ultramicrotome
ultramicrotome
two-photon confocal microscope
2-photon confocal microscope
A confocal microscope that uses laser-excited autofluorescence and second harmonic signals that can be analyzed to construct a three dimensional, microanatomical, structural image.
PERSON: Karen Corday
Used for imaging of biological samples.
http://web.mit.edu/solab/Documents/Assets/Navarro-2P-A%20nondestructive%20method%20for%20studying%20wound%20healing.pdf
two-photon confocal microscope
DNA quantitation assay
A nucleic acid assay that is used to quantify the amount of DNA.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Quantitating DNA after a plasmid preparation, using a spectrophotometer.
nucleic acid labeling
A labeling technique whereby nucleic acids are labeled with radioisotopes, fluorophores, or other molecular entities for the purposes of tracking nucleic acids in an experimental system.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
mRNA fluorophore labeling for use in microarray analysis.
instrumentation technical support
PERSON: Melissa Haendel
Process whereby technical expertise is given regarding design, repair, upkeep, or by building instruments.
Technical support for computer software.
Technical support to use a flow cytometer.
http://en.wikipedia.org/wiki/Instrumentation
electron microscopy
A microscopy technique that produces an electronically-magnified image of a specimen for detailed observation. The electron microscope (EM) uses a particle beam of electrons to illuminate the specimen and create a magnified image of it. The microscope has a greater resolving power than a light-powered optical microscope, because it uses electrons that have wavelengths about 100,000 times shorter than visible light (photons), and can achieve magnifications of up to 2,000,000x, whereas light microscopes are limited to 2000x magnification.
Cell structure can be examined by electron microscopy.
Diagnostic electron microscopy
EM
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electron_microscope
transmission electron microscopy
An electron microscopy technique whereby a beam of electrons are transmitted through an ultra thin specimen, interacting with the specimen as it passes through. An image is formed from the interaction of the electrons transmitted through the specimen; the image is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Transmission_electron_microscopy
scanning electron microscopy
A type of electron microscopy that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity.
PERSON: Nicole Vasilevsky
SEM
Used to image biomolecules.
http://en.wikipedia.org/wiki/Scanning_electron_microscope
oligonucleotide synthesis
Biomolecule synthesis of relatively short fragments of nucleic acids with defined chemical structure (sequence).
PERSON: Karen Corday
Production of primers.
http://en.wikipedia.org/wiki/Oligonucleotide_synthesis
oligonucleotide synthesis
microcapillary electrophoresis
Electrophoresis designed to separate species based on their size to charge ratio in the interior of a small microcapillary filled with an electrolyte.
PERSON: Karen Corday
The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells on a single platform.
http://en.wikipedia.org/wiki/Capillary_electrophoresis
microcapillary electrophoresis
video
Data containing moving pictures stored in digital and analog formats.
PERSON: Carlo Torniai
http://en.wikipedia.org/wiki/Video
gel image
An image of an agarose gel stained with Ethidium bromide.
Images that are obtained from gels, such as polyacrylamide or agarose gels used to analyze protein or DNA.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
ion trap mass spectrometer
A mass spectrometer that uses three electrodes to trap ions in a small volume. The mass analyzer consists of a ring electrode separating two hemispherical electrodes. A mass spectrum is obtained by changing the electrode voltages to eject the ions from the trap. The ion-trap mass spectrometer has a compact size and the ability to trap and accumulate ions to increase the signal-to-noise ratio of a measurement.
PERSON: Erik Segerdell
http://www.chemistry.adelaide.edu.au/external/soc-rel/content/ion-trap.htm
ion trap mass spectrometer
cell staining
DAPI stain to stain nuclei.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Staining that involves the application of dye to cells.
virus plaque assay
A virus plaque assay is performed to determine viral titers of viral supernatants, that are used to infect cells to study gene function.
An organismal assay that is used to determine viral titers.
PERSON: Melissa Haendel
Plaque assay
http://www.biology-online.org/dictionary/Plaque_assay
virus replication assay
purification
Material processing whereby one material is separated into a pure fraction from one or more other materials.
PERSON: Melissa Haendel
Purification of a protein.
http://www.biology-online.org/dictionary/Purification
virus plaque purification
PERSON: Melissa Haendel
Plaque assay
Production of viral supernatants to study a specific gene.
Purification that is used to purify viral entities.
http://www.biology-online.org/dictionary/Plaque_assay
RNA quantitation assay
An nucleic acid assay that is used to quantify the amount of RNA.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
nested polymerase chain reaction
Amplification of a fragment of DNA.
Nested PCR
PERSON: Melissa Hanedel
Polymerase chain reaction that involves two sets of primers, used in successive runs of polymerase chain reaction whereby the second set of primers is intended to amplify a secondary target within the first run product.
http://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction
viral DNA extraction
Extraction of DNA from an input material that specifically isolates viral DNA.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
inverted microscope
An optical microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up.
Cell lines can be visualized using an inverted microscope.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Inverted_microscope
inverted microscope
experimental posttranslational modification
Chemical modification of a protein after translation in an experimental setting.
Experimental phosphorylation of a protein.
Experimental post-translational modification
Experimental post-translational protein modification
Experimental post-translational protein processing
Experimental protein modification
Experimetnal PTM
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Posttranslational_modification
posttranslational modification
protein identification
A protein assay performed to identify the sequence of proteins in a molecule.
Mass spectrometry is a method for protein identification.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
protein identification
intervention
A planned process used to influence one or more factors in a research study, and the independent variable in an interventional study wherein the influence is measured or evaluated.
An drug intervention for cancer.
PERSON: Melanie Wilson
PERSON: Melissa Haendel
case-only study
A Dictionary of Epidemiology, Fifth Edition, Edited by Miquel Porta. p. 33. ISBN:978-0-19-531449-6 http://prsinfo.clinicaltrials.gov/definitions.html
Observational study whereby there is a single group of individuals with specific characteristics. This is a method that analyzes data from a case series and is used in case-crossover studies, in case-specular designs, and in molecular and genetic epidemiology to assess relationships between environmental exposures and genotypes.
PERSON: Melissa Haendel
case-only study
nucleotide-free workbench
A PCR workstation.
PCR workstation
PERSON: Melissa Haendel
This device provides effective decontamination of solutions, reagents and equipment before carrying out sensitive PCR reactions or other nucleotide-free operations.
http://www.prohealthservicezone.com/Customisation/News/Analysis_Inspection_and_Laboratory/PCR_equipment/Safety_certified_PCR_workstation.asp
water purification system
A portable water purifier.
Device that is used to purify water of contaminants.
PERSON: Melissa Haendel
There are likely numerous subtypes here, but this maybe too granular for our needs.
http://www.millipore.com/lab_water/clw4/tutorial&tabno=5
water purification system
blinded outcome assessor role
A role inhering in a person or organization that is realized when the bearer participates in accessing the outcomes of a blinded study.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
blinded outcome assessor role
blinded caregiver role
A role inhering in a person or organization that is realized when the bearer participates in providing care to a patient without knowledge of the type of treatment or intervention that is used, such as blinding in a clinical trial.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
blinded caregiver role
blinded investigator role
A role inhering in a person or organization that is realized when the bearer performs a study without knowledge of the type of treatment or intervention that is used, such as blinding in a clinical trial.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Randomized_controlled_trial
blinded subject role
A patient is given a treatment, but is unaware if it is the placebo or actual drug.
A role inhering in a person or organization that is realized when the bearer participates in a study, such as a clinical trial but is not aware of the type of treatment or intervention that is used.
PERSON: Nicole Vasilevsky
blinded subject role
http://en.wikipedia.org/wiki/Randomized_controlled_trial
open blinded study
An interventional study in which the person collecting the data and the subject know whether the subjects are in the control or experimental groups.
Open trial
Open-label trial
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/single-blind+study
open blinded study
single blinded study
An interventional study in which the person collecting the data knows whether the subjects are in the control or experimental groups but the subjects do not.
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/single-blind+study
single blinded study
double blinded study
An interventional study in which neither the subjects of the experiment nor the persons administering the experiment know the critical aspects of the experiment; a double-blind procedure is used to guard against both experimenter bias and placebo effects.
PERSON: Nicole Vasilevsky
double blinded study
http://www.thefreedictionary.com/double-blind+study
hemocytometer
A cytometer used for visual counting of cells in a blood sample or other fluid under a microscope.
PERSON: Nicole Vasilevsky
The number of viable cells can be counted on a hemocytometer after trypan blue staining.
http://www.google.com/search?q=hemocytometer&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a#hl=en&client=firefox-a&hs=9NX&rls=org.mozilla:en-US:official&q=hemocytometer&tbs=dfn:1&tbo=u&sa=X&ei=HX1BTqT0BezViAL324WVBQ&ved=0CBYQkQ4&bav=on.2,or.r_gc.r_pw.r_cp.&fp=a5190ac754b40f6f&biw=1505&bih=751
manual cytometer
automatic cytometer
A coulter counter is a commonly used automatic cytometer.
A cytometer that automatically counts and sizes particles and cells by detecting changes in electrical conductance of a small aperture as fluid containing cells are drawn through.
PERSON: Tenille Johnson
automatic cell counter
coulter counter
http://en.wikipedia.org/wiki/Coulter_counter
viability analyzer
controller
A device that interfaces with a peripheral device. This may be a link between two parts of a computer (for example a memory controller that manages access to memory for the computer) or a controller on an external device that manages the operation of (and connection with) that device.
A memory controller that manages access to memory for the computer.
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Controller_%28computing%29
CO2 incubator
A incubator that controls the carbon dioxide (CO2) content of the atmosphere inside.
Carbon dioxide incubator
PERSON: Tenille Johnson
Used to store and house cell lines and cultures.
http://en.wikipedia.org/wiki/Co2_incubator
stereotaxic device
A head is positioned in a stereotaxic device, prior to brain surgery.
Device that immobilizes and positions an organism such that surgery may be performed using an external, three-dimensional frame of reference, usually based on the Cartesian coordinate system.
PERSON: Melissa Haendel
http://www.thefreedictionary.com/stereotaxic
stereotaxic device
stereotaxic lab standard
dual stereotaxic device
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Stereotaxic device which allows positioning of two organisms simultaneously.
dual stereotaxic device
dual stereotaxic lab standard
http://www.kopfinstruments.com/Stereotaxic/902.htm
single stereotaxic device
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Positioning a head in a stereotaxic device prior to brain surgery.
Stereotaxic device which allows positioning of a single organism.
single stereotaxic device
single stereotaxic lab standard
microtome cryostat
Histological sections are cut using a microtome cryostat.
Microtome that cuts frozen tissue within a temperature controlled frozen environment.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
microtome cryostat
anesthesia induction chamber
An inhalation chamber that used to anesthetize organisms that allows for controlled exposure to the anesthesia while eliminating personnel exposure to anesthetic gas.
Mice are placed in an anesthesia induction chamber, for administration of anesthesia.
PERSON: Melissa Haendel
anesthesia induction chamber
http://www.ezanesthesia.com/ez_anesthesia/index.html
infrared spectrophotometer
Infrared spectroscopy is used in quality control, dynamic measurement, and monitoring applications such as the long-term unattended measurement of CO2 concentrations in greenhouses.
PERSON: Melissa Haendel
Spectrophotometer that has a prism or grating for the study and recording of infrared spectra. It usually consists of a radiation source such as a Nernst glower, a monochromator, a detector, an amplifier and a recorder.
http://www.photonics.com/directory/dictionary/Definition.aspx?type=2&DictionaryID=4754
infared spectrophotometer
infrared spectrophotometer
intravenous injection
IV injection
Injection of a substance into the vein of an organism.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Tail vein injection into a mouse.
intravenous injection
deconvolution microscope
Fluorescence microscope that uses a computational method to reduce out-of-focus fluorescence in three-dimensional (3D) microscope image.
McNally et al., Methods. 1999 Nov;19(3):373-85. PMID: 10579932
PERSON: Nicole Vasilevsky
Used to image biological samples.
deconvolution microscope
gavage
Administration of a drug into an animal via gavage.
Agent delivery of substances by means of a small plastic tube passed through the nose or mouth into the stomach, not explicitly 'forcibly'.
Enteral tube feeding
Gastrogavage
PERSON: Karen Corday
Tube feeding
gavage
http://en.wikipedia.org/wiki/Force-feeding
intraperitoneal injection
IP
IP injection
Injection of a substance into the body cavity.
Injection of a substance into the peritoneal cavity.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Intraperitoneal_injection
i.p.
i.p. injection
intraperitoneal injection
subcutaneous injection
Injection of a a bolus into the subcutis, the layer of skin directly below the dermis and epidermis, collectively referred to as the cutis.
Injection of a solution into the scruff of the neck of a rodent.
PERSON: Karen Corday
S.C. injection
SC injection
Sub cu injection
http://en.wikipedia.org/wiki/Subcutaneous_injection
subcutaneous injection
surgery
A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance.
PERSON: Karen Corday
Surgical removal of a mole.
http://en.wikipedia.org/wiki/Surgery
surgery
NMR spectra data
NMR spectra data
NMR spectra is the intensity of the NMR signal as a function of frequency.
Nuclear magnetic resonance spectra data
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance
NMR-based metabolite profiling
A nuclear magnetic resonance assay used for profiling of metabolites (a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism) using nuclear magnetic resonance.
NMR-based metabolite profiling
PERSON: Karen Corday
http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=201425
gas chromatography-mass spectrometry platform
A mass spectrometer that combines the gas-liquid chromatography and mass spectrometry to identify different substances within a test sample.
Can be used for protein identification and characterization.
GC-MS platform
GC/MS platform
PERSON: Karen Corday
gas chromatography-mass spectrometry platform
http://en.wikipedia.org/wiki/Gas_chromatography-mass_spectrometry
electrocardiogram
A physiological assay that is a transthoracic interpretation of the electrical activity of the heart over time captured and externally recorded by skin electrodes. It is a noninvasive recording produced by an electrocardiographic device.
An electrocardiogram is used to measure heart function.
ECG
PERSON: Karen Corday
electrocardiogram
http://en.wikipedia.org/wiki/Electrocardiography
cardiac output measurement
A physiological assay that measures cardiac output, which is the volume of blood being pumped by the heart, in particular by a ventricle in a minute. Methods of measurement range from direct intracardiac catheterisation to non-invasive measurement of the arterial pulse.
An echocardiogram.
PERSON: Karen Corday
cardiac output measurement
http://en.wikipedia.org/wiki/Cardiac_output
echocardiogram
A physiological assay that uses standard ultrasound techniques to take two-dimensional pictures of the cardiovascular system and can produce accurate assessment of the velocity of blood and cardiac tissue at any arbitrary point using pulsed or continuous wave Doppler ultrasound.
Cardiac US scan
Diagnostic ultrasound of heart
Echocardiographic procedure
Echocardiography
PERSON: Karen Corday
US scan of heart
Ultrasonic cardiography
Ultrasonography of heart
Ultrasound of heart
Used to study heart function.
cardiac ECHO
echocardiogram
http://en.wikipedia.org/wiki/Echocardiography
invasive hemodynamic measurement
A physiological assay that measures simultaneously acquired and processed blood flow and blood pressure via the placement of invasive catheters into the vasculature.
PERSON: Karen Corday
Pollack, A. N. (Ed.) (2011). Critical care transport. Sudbury, MA: Jones and Bartlett. ISBN: 978-0- 7637-1223-5. http://books.google.com/books?id=cuWoyV19dq8C
invasive hemodynamic measurement
data acquisition
A technique that samples real world physical conditions and conversion of the resulting samples into digital numeric values that can be manipulated by a computer.
Acquisition of flow cytometry data.
DAQ
PERSON: Karen Corday
data acquisition
http://en.wikipedia.org/wiki/Data_acquisition
tail vein injection
Adoptive transfer of cells via tail vein.
An intravenous injection of a substance into the lateral tail vein of an organism, usually a mouse or rat.
PERSON: Karen Corday
http://www.lab-manual.com/lm_383.htm
tail vein injection
mouse breeding
A laboratory animal care technique performed to produce offspring of laboratory mice by pairing mice as mating pairs. Breeding methods include selective breeding, which is the systematic breeding of animals in order to change certain qualities in them, inbreeding, which is the breeding of genetically related mice, and strain breeding, which concentrates on a certain mouse and its offspring, usually involving moderate inbreeding.
Breeding transgenic mice.
PERSON: Karen Corday
http://www.hiiret.fi/eng/breeding/index.html
mouse breeding
access service
A service offering that describes a service in which the consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service.
Allowing access to a microscope in a core lab.
Coordinate with NIF
PERSON: Matt Brush
PERSON: Matthew Brush
storage service
A computer server.
A service offering that describes a service in which the consumer provides some material or data as input which a service provider stores and returns as output.
PERSON: Matt Brush
PERSON: Matthew Brush
coordinate with NIF. NIF ID:nlx_res_20090419
training service
A service offering that describes a service in which the provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer
Coordinate with NIF. NIF ID: nlx_res_20090444
PERSON: Matt Brush
PERSON: Matthew Brush
Training a researcher to use a microscope.
material processing service
A service offering that describes a service in which the provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer
Biopsy service.
Coordinate with NIF: NIF ID: nlx_res_20090416
PERSON: Nicole Vasilevsky
http://neurolex.org/wiki/Category:Production_service_resource
material analysis service
An analysis service offering that describes a service in which the consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
Coordinate with NIF: NIF ID: nlx_res_20090420
Flow cytometry analysis of T cells.
PERSON: Nicole Vasilevsky
http://neurolex.org/wiki/Category:Analysis_service_resource
material production service
A material processing service offering that describes a service in which the provider makes physical changes to a specified input material that produce a new entity as specified output that is returned the service consumer. The specified output of a material production service can be contained within, derived from, or synthesized from specified input materials, but it represents a material entity that is of a distinct type from any of the specified input materials.
Coordinate with NIF. NIF ID: nlx_res_20090418
PERSON: Matthew Brush
Production of monoclonal antibodies from a hybridoma.
http://neurolex.org/wiki/Category:Material_service_resource
biobank picking station
An instrument comprised of a number of -80 C storage units with liquid carbon dioxide back-up and a centralized automated picking station that reads the 2D barcodes on all tubes and re-arrays any requested samples at 15 C.
PERSON: Bob Garces
Samples can be requested and easily retrieved from a biobank picking station.
Zuo, D., et al. (2006). PlasmID: a centralized repository for plasmid clone information and distribution. Nucleic Acids Research, Database issue D1-D5. DOI:10.1093/nar/gkl898 (http://nar.oxfordjournals.org/cgi/screenpdf/gkl898v1)
barcode reader
An instrument that is used to electronically read printed barcodes
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Barcode_reader
cellular assay
An assay that generates data about the presence, quantity, structure, function, behavior, or activity of cells, or a process that occurs at a cellular level of anatomical granularity (includes subcellular structures and organelles).
Flow cytometry.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
cell analysis
data storage
A data transformation technique that involves the process of recording or retrieving information or data.
Information storage
PERSON: Karen Corday
Storing data on a server.
bulk data storage
data storage
http://en.wikipedia.org/wiki/Data_storage
research data storage
construct insert
A gene, such as p53.
PERSON: Melissa Haendel
Reagent that is part of a construct comprised of DNA from an external source.
construct insert
http://www.answers.com/topic/dna-construct
immunofluorescence microscopy assay
An imaging assay that allows for detection and visualization of the location and relative abundance of any protein in cells or tissues by microscopy using fluorescent tagged antibodies.
Fluorescent immunoassay
IF
IMF
IMF assay
Immunofluorescence assay
Labeling of proteins using fluorescent-tagged antibodies.
PERSON: Nicole Vasilevsky
http://www.bio.davidson.edu/courses/genomics/method/IMF.html
gas chromatography-mass spectrometry metabolite profiling
A mass spectrometry assay used for the screening of apparent or novel metabolic phenotypes in functional genomic studies of plants or microbes.
Can be used for protein identification and characterization.
GC-MS based metabolite profiling
GC/MS metabolite profiling
Kopka, J. (2006). Current challenges and developments in GC-MIS metabolite profiling technology. Journal of Biotechnology, 123, 312-322. PMID: 16434119
PERSON: Karen Corday
protein-ligand interaction assay
A protein interaction detection assay used to study protein-ligand interactions.
An assay to determine if myoglobin binds to its ligand, heme.
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Protein_ligand
ligand binding analysis
protein-ligand interaction assay
single-nucleotide polymorphism analysis
A SNP in the F5 gene causes a hypercoagulability disorder with the variant Factor V Leiden.
A nucleic acid assay used to detect single nucleotide variations in a nucleotide sequence.
PERSON: Nicole Vasilevsky
SNP analysis
http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
microsatellite analysis
A nucleic acid assay used method for detection of chromosomal deletions by loss of heterozygosity studies and for detection of microsatellite instability.
DNA fingerprining
DNA profiling
Forensic genetic analysis
Genetic fingerprinting
Microsatellite instability analysis
PERSON: Karen Corday
STR profiling
Short tandem repeat profiling
Used for genetic analysis.
Wild, P. J. et al. (2004). Laser microdissection for microsatellite analysis in colon and breast cancer. In G. I. Murray and S. Curran (Eds.), Laser capture microdissection: methods and protocols. New York: Springer. doi/10.1385/1-59259-853-6:093
embryonic stem cell culture
Cell culture of embryonic stem cells, which were derived from embryos in vitro.
ES cell culture
Mouse embryonic fibroblast cells.
PERSON: Karen Corday
http://stemcells.nih.gov/info/basics/basics3.asp
embryonic stem cell electroporation
ES cell electroporation
Electroporation in embryonic stem cells to overexpress a protein of interest.
PERSON: Karen Corday
Transfection of a gene into stem cells.
http://en.wikipedia.org/wiki/Electroporation
targeted homologous recombination
Antibody generation in B cells.
Experimental genetic modification that uses homologous recombination to change an endogenous gene. The method can be used to delete a gene, remove exons, add a gene, and introduce point mutations.
Genetic engineering
Genome manipulation
Homologous recombination
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Gene_targeting
embryo transplantation
A material processing technique in which eggs from female animals are mixed with sperm from male animals. After the egg is fertilized and divides into an embryo, the embryo is split into identical embryos, and implanted in separate female surrogates, and allowed to develop normally.
Can be used to generate transgenic mice strains.
Embryo transfer
PERSON: Karen Corday
Paul, N. (2002). Science for you: biology. Cheltenham: Nelson Thomas Ltd. (http://books.google.com/books?id=gTWbFq3gCPUC)
environmental chamber
An anesthesia chamber for rodents.
An environment control instrument used to test the effects of specified environmental conditions on biological samples, industrial products, materials, and electronic devices and components. An environmental chamber can be used as a stand-alone test for environmental effects on test specimens, as preparation of test specimens for further physical tests or chemical tests, or as environmental conditions for conducting testing of specimens.
PERSON: Tenille Johnson
environmental chamber
http://en.wikipedia.org/wiki/Environmental_chamber
charge-coupled device camera
A digital camera that is designed to convert optical brightness into electrical amplitude signals using a plurality of CCDs, and then reproduce the image of a subject using the electric signals without time restriction.
CCD camera
Can be used in medical imaging.
PERSON: Tenille Johnson
charge-coupled device camera
http://www.electronics-manufacturers.com/products/digital-photography/ccd-camera/
charge-coupled device detector
A charged-coupled device camera used for medical imaging.
A photodetector that senses light or other electromagnetic energy using a charge coupled device (CCD), which detects the movement of electrical charge, usually from within the device to an area where the charge can be manipulated.
CCD detector
PERSON: Tenille Johnson
charge-coupled device detector
http://en.wikipedia.org/wiki/Charge-coupled_device
blastocyst injection
Injection into blastocysts (pre-implantation embryos), which are isolated from donor females and microinjected with genetically modified embryonic stem (ES) cells.
PERSON: Karen Corday
Production of transgenic mice.
http://www.imbim.uu.se/resource/Blastocystinjection.html
transfection reagent
A chemical reagent that introduces foreign DNA into a eukaryotic cell.
Lipofectamine is a commonly used transfection reagent.
PERSON: Karen Corday
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://www.iscid.org/encyclopedia/Transfection_Reagents
BAC library
A BAC library containing the mouse genome.
A genomic library that contains discrete collections of host bacteria, each of which carries a DNA insert from a source organism cloned into a BAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of BAC constructs prior to their delivery into the host cells.
BAC library
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Genomic_library
expression library
A construct library that contains expression vectors, which are used to express a specific protein.
An expression library to isolate genes that could confer antibiotic resistance.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
expression library
http://en.wikipedia.org/wiki/Expression_cloning
expression construct
A construct that is designed to be expressed in insect cells.
A construct that is engineered to produce large amounts of stable messenger RNA, and therefore proteins in a specific cell type. The construct often contains regulatory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
expression construct
http://en.wikipedia.org/wiki/Expression_vector
PAC library
A genomic library that contains discrete collections of host bacteria, each of which carries a DNA insert from a source organism cloned into a PAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of PAC constructs prior to their delivery into the host cells.
PAC library
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Genomic_library
fosmid library
A genomic library that contains discrete collections of fosmid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
fosmid library
http://en.wikipedia.org/wiki/Fosmid
YAC library
A genomic library that contains discrete collections of host yeast cells, each of which carries a DNA insert from a source organism cloned into a YAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of YAC constructs prior to their delivery into the host cells.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Genomic_library
cosmid library
A genomic library that contains discrete collections of cosmid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
cosmid library
http://homepages.strath.ac.uk/~dfs99109/BB211/GenomicLibrary.html
lambda phage library
An organism library containing trangenic lambda phage.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
lambda phage library
cold room
Instrument that consists of insulated room and refrigeration components that together maintain the room at a constant temperature below room temperature.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Walk-in refrigerator.
cold room
walk-in refridgerator
chemical fume hood
A chemical fume hood is used when working with highly volatile chemicals.
Instrument that is a local ventilation device that is designed to limit the user's exposure to hazardous or noxious fumes, vapors or dusts. A fume hood is typically a large piece of equipment enclosing five sides of a work area, the bottom of which is most commonly located at a standing work height. Air is drawn in from the front (open) side of the cabinet, and either expelled outside the building or made safe through filtration and fed back into the room.
PERSON: Melissa Haendel
chemical fume hood
fume hood
http://en.wikipedia.org/wiki/Fume_hood
tissue culture incubator
A CO2 incubator designed to house cell cultures.
An incubator that is used in tissue culture rooms for culturing primary cells, cell lines, or tissues.
PERSON: Erik Segerdell
http://www.medterms.com/script/main/art.asp?articlekey=18426
tissue culture incubator
liquid nitrogen dewar
A cryostat that is used for biomedical storage of samples using liquid nitrogen as a refrigerant.
A dewar that is used for long-term storage of cell line stocks.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
liquid nitrogen dewar
liquid nitrogen tank
photometer
A photometer is used to quantitate the concentration of DNA in a sample.
An instrument for measuring light intensity or optical properties of solutions or surfaces. Photometers are used to measure iIlluminance, irradiance, light absorption, scattering of light, reflection of light, fluorescence, phosphorescence, and luminescence.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Photometer
recombinant protein production
Material production of proteins that have been produced by recombinant DNA techniques, which allows the production of large quantities of recombinant protein.
PERSON: Nicole Vasilevsky
Production of recombinant insulin.
http://www.wisegeek.com/what-is-recombinant-protein-production.htm
2D gel spot exciser
2D gel spot exciser
2D spot picker
A spot cutter that is used to excise spots from two-dimensional (2D) electrophoretic gels.
Gel excision of a 2D gel, for subsequent protein analysis.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Two-dimensional_gel_electrophoresis
frequency counter
A coulter counter is used to count the number of cells in a sample.
A device that is used for measuring frequency, which is defined as the number of events of a particular sort occurring in a set period of time.
PERSON: Erik Segerdell
frequency counter
http://en.wikipedia.org/wiki/Frequency_counter
pulmonary function tests
A physiological assay used to measure the ability of the lungs take in and release air and the ability to move gases such as oxygen from the atmosphere into the body's circulation.
Lung function tests
PERSON: Tenille Johnson
PFT
Tests to detect decreased lung capacity.
http://www.nlm.nih.gov/medlineplus/ency/article/003853.htm
pulmonary function tests
spirometry
A pulmonary function test used to measure lung function, specifically the measurement of the amount (volume) and/or speed (flow) of air that can be inhaled and exhaled.
Bronchospirometry
PERSON: Nicole Vasilevsky
Spirogram
http://en.wikipedia.org/wiki/Spirometry
spirometry
gas diffusion tests
A pulmonary function test that measures the amount of oxygen and other gases that cross the lungs' air sacs (alveoli ) per minute. These tests evaluate how well gases are being absorbed into a person's blood from their lungs.
PERSON: Tenille Johnson
gas diffusion tests
http://www.webmd.com/lung/lung-function-tests
body plethysmography
A pulmonary function test that may be used to measure: total lung capacity (TLC), which is the total amount of air your lungs can hold, or residual volume (RV), which is the amount of air that remains in your lungs after you exhale as completely as possible.
Body box plethysmography
PERSON: Tenille Johnson
Total body plethysmography
Whole body plethysmography
body plethysmography
http://www.webmd.com/lung/lung-function-tests
inhalation challenge tests
A pulmonary function test done to measure the response of a person's airways to substances that may be causing asthma or wheezing.
Inhalation bronchial challenge testing
PERSON: Tenille Johnson
Provocation studies
http://www.webmd.com/lung/lung-function-tests
inhalation challenge tests
exercise stress tests
A pulmonary function test done to evaluate the effect of exercise on lung function tests. Spirometry readings are done after exercise and then again at rest.
Exercise stress tests are often performed after a heart attack.
Exercise test
Exercise tolerance test
PERSON: Tenille Johnson
exercise stress tests
http://www.webmd.com/lung/lung-function-tests
multiple-breath washout test
A pulmonary function test performed to check lung function in patients with cystic fibrosis.
PERSON: Tenille Johnson
http://www.webmd.com/lung/lung-function-tests
multiple-breath washout test
spirometer
A spirometer is an apparatus for measuring the volume of air inspired and expired by the lungs. It is a precision differential pressure transducer for the measurements of respiration flow rates. The spirometer records the amount of air and the rate of air that is breathed in and out over a specified period of time.
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Spirometer
spirometer
objective lens
An instrument that contains an optical element that gathers light from the object being observed and focuses the light rays to produce a real image, using either a single lens or combinations of several optical elements. Objective lenses are used in microscopes, telescopes, cameras, slide projectors, CD players and many other optical instruments.
An objective lens of a microscope.
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Objective_lens
object glass
objective
objective glass
objective lens
video camera
A camera used for electronic motion picture acquisition.
Creation of home videos using a video camera.
PERSON: Tenille Johnson
camcorder
http://en.wikipedia.org/wiki/Video_camera
video camera
ELISPOT microplate reader
A plate reader used to count the colored spots that are formed in the course of ELISPOT assays.
An ELISPOT microplate reader can be used to measure protein expression in samples.
ELISPOT microplate reader
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Plate_reader
flow cytometry list mode data
Data containing raw cytometer data files that list the values of the scatter and fluorescence parameters for each event in the order in which the events passed through the cytometer's interrogation point (usually a laser beam). Most cytometers create listmode files in the Flow Cytometry Standard (FCS) format, which is not understood by general purpose scientific software. Converting a listmode file to a plain text ASCII format enables it to be read by such software, or viewed and edited with a word processor.
PERSON: Tenille Johnson
http://www.umass.edu/microbio/mfi/ascii.htm
listmode file
irradiation system
An instrument that contains a shielded cabinet system and is used to irradiate biological specimens.
An x-ray irradiator.
PERSON: Tenille Johnson
http://www.kimtronmedical.com/IC160.html
irradiation system
urine analyzer
A device used for urinalysis testing.
An instrument to detect glucose levels in urine.
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Urine_test_strip#Automated_Urine_Test_Strip_Analyzers
urine analyzer
ultraviolet transilluminator
An instrument that consists of a light box that emits ultraviolet light, used for visualization of agarose and polyacrylamide gels.
DNA gels stained with ethidium bromide are visualized using a UV transilluminator.
PERSON: Nicole Vasilevsky
http://www.topac.com/transilluminators.html
orbital shaker
An instrument that consists of a platform and racks to hold tubes, which continually shakes in an orbital motion, which is used to mix liquids. Depending on the model, the instrument may be located on a counter or on the floor.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Used to shake bacterial cultures, to promote growth.
environmental shaker
atomic force microscope
A scanning force microscope used for determining the surface topography of native biomolecules at subnanometer resolution. It allows biomolecules to be imaged not only under physiological conditions, but also while biological processes are at work.
AFM
PERSON: Karen Corday
Surface topologies with nano-scale roughness (cleaved silicon, e.g.) can be resolved an atomic force microscope.
http://www.mih.unibas.ch/Booklet/Booklet96/Chapter3/Chapter3.html
goniometer
A device that either measures angle or allows an object to be rotated to a precise angular position.
A protractor.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Goniometer
scanning auger electron microprobe
A measurement instrument used to determine the elemental composition of conductive and semiconductive surfaces, in which a highly focused and energetically well-defined electron beam is incident on the sample. Electrons ejected from the sample are analyzed in terms of their kinetic energy and quantity.
Enhanced lateral spatial resolution for elemental analysis.
PERSON: Nicole Vasilevsky
http://www.physics.montana.edu/ical/instrumentation/auger.asp
explosion-proof refrigerator
A cooling appliance used for the safe storage of volatile materials that need to be kept cold, but not freezing.
A refrigerator used to store volatile chemicals.
PERSON: Tenille Johnson
explosion-proof refrigerator
http://www.wisegeek.com/what-is-an-explosion-proof-refrigerator.htm
explosion-proof freezer
A cooling appliance used for the safe storage of volatile materials that need to be kept frozen.
PERSON: Tenille Johnson
Volatile chemicals may be stored in an explosion-proof freezer.
explosion-proof freezer
http://www.wisegeek.com/what-is-an-explosion-proof-refrigerator.htm
microforge
A microforge is used to produce micropipettes, used for microinjection.
Instrument designed for the fabrication and processing of glass micropipettes and other related microtools for use in patch pipette tip polishing, tip size reduction (for holding pipettes), contact stretching (large tip sharpening), tip bending, tip sealing, in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), and pipette production in a variety of pipette configurations.
PERSON: Tenille Johnson
http://www.tritechresearch.com/narishige-needle-overview.html
microforge
microinjector
A device which provides the pressure that is needed to deliver a sample solution from a micropipette into cells.
PERSON: Tenille Johnson
The effects of a drug on an individual cell can be tested by microscope-assisted dosage with a microinjector.
http://en.wikipedia.org/wiki/Microinjectors
microinjector
natural product extraction
Extraction of a biological entity to purify a chemical or biochemical entity or mixture of entities.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Purification of DNA from a blood sample.
natural product extraction
bioactivity assay
A molecular assay that tests the activity of a chemical or biological reagent to affect a biological system.
Overexpression of a plasmid expressing a gene, in a cell culture, to confirm the gene has biological activity in the system.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
bioactivity assay
chemical synthesis
CS
Chem syn
Chemical compounding
Material production technique whereby chemical entities are synthesized from other chemical entities.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
Synthesis of aspirin.
chemical synthesis
nucleic acid preparation station
An instrument used for automated, high-throughput extraction of nucleic acids from samples.
PERSON: Nicole Vasilevsky
http://www.autogen.com/product_autogenprep965.htm
atomic spectrophotometer
A spectrophometer used for the qualitative and quantitative determination of chemical elements employing the absorption of optical radiation (light) by free atoms in the gaseous state.
PERSON: Nicole Vasilevsky
Soil samples from an industrial site can be tested for the presence of mercury using an atomic spectrophotometer.
http://en.wikipedia.org/wiki/Atomic_absorption_spectroscopy
liquid handling
Agent delivery of a selected quantity of reagents, samples or other liquids to a designated container.
An ELISA plate washer.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Liquid_handling_robot
rheometer
An instrument used to measure the way in which a liquid, suspension or slurry flows in response to applied forces. It is used for those fluids which cannot be defined by a single value of viscosity.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Rheometer
tissue embedding
A sample preparation technique where cells or tissue are placed in a supporting medium. The medium can be paraffin wax (paraffin embedding) or plastics (plastic embedding) such as epoxy resins.
A technique performed prior to tissue sectioning and histology.
PERSON: Nicole Vasilevsky
http://www.biology-online.org/dictionary/Tissue_embedding
tissue sectioning
Histological sample preparation of tissue, to cut it into thin sections, usually using a microtome or a cryostat, for further analysis.
PERSON: Nicole Vasilevsky
Preparation of brain slices for subsequent histological analysis.
http://books.google.com/books?id=svzyJdQVsaEC, Burry, R. W. (2010). Immunocytochemistry: a practical guide for biomedical research. New York: Springer.
needle grinder
A device used to sharpen hypodermic needles.
PERSON: Tenille Johnson
http://www.freepatentsonline.com/5495988.html
needle grinder
inertial impact drill
A drill that is designed to operate in conjunction with micropipettes, microelectrodes, and micromanipulators used for microinjection into cells for diverse applications in cytology. The action of the inertial impact drill is like that of a miniature jackhammer.
PERSON: Nicole Vasilevsky
http://www.findthatpatent.com/Inertial_impact_drill_for_cytological_applications,6251658.html
hematology analyzer
A measurement device used to perform complete blood counts, erythrocyte sedimentation rates (ESRs), or coagulation tests.
Blood samples taken from patients are analyzed using a hematology analyzer.
PERSON: Tenille Johnson
haematology analyser
hematology analyzer
http://en.wikipedia.org/wiki/Automated_analyzer#Haematology_analysers
blood gas analyzer
A blood anlayzer used to measure the pH and the partial pressures of oxygen and carbon dioxide in arterial blood, as well as calculate the bicarbonate concentration.
PERSON: Tenille Johnson
blood gas analyzer
http://en.wikipedia.org/wiki/Arterial_blood_gas
infrared microscope
A microscope that uses the infrared region of the electromagnetic radiation spectrum, often used for the study of materials that are uniformly transparent or opaque in the visible spectrum, but have significant absorption or transmission bands in the 700 nanometer-plus wavelength region.
A specimen that is opaque to visible light, such as a blade of grass can be visualized through its thickness by way of its response to infrared light with the use of an infrared microscope.
PERSON: Nicole Vasilevsky
http://www.microscopyu.com/articles/optics/objectivespecial.html
upright microscope
A microscope that has the illumination system below the stage and the lens system above the stage.
An upright microscope is used to view cell lines growing in a flask.
PERSON: Karen Corday
http://science.howstuffworks.com/light-microscope5.htm
PCR/UV workstation
An instrument that uses UV irradiation as a sterilizer to provide a clean workspace to set up PCR reactions. The UV irradiation breaks down DNA sequences so that replication cannot occur in subsequent amplification processes.
PCR reactions are set up in a PCR/UV workstation.
PERSON: Karen Corday
http://www.thistlescientific.co.uk/acatalog/thermal_details/BCUVSC_details.html
electromyography
A physiological assay used to evaluate and record electrical activity produced by skeletal muscles.
Can be used for musculoskeletal evaluations.
EMG
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electromyography
treadmill
Exercise equipment used for running or walking while staying in one place. The machine provides a moving platform with a wide conveyor belt and an electric motor or a flywheel.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Treadmill
pulse pressure injector
An instrument used to produce gas pressure pulses to an injection pipette.
PERSON: Karen Corday
http://www.asiimaging.com/pdfs/MPPI-2_Manual.pdf
slide drying oven
An oven that is used for rapid drying of histology slides, typically consisting of a drying chamber, digital temperature and time controller, and internal fan.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
slide drying oven
tissue drying oven
automatic coverslipper
An automatic coverslipper can be used to prepare slides for microscopic examination.
An material transfer instrument that is used to automatically apply a glass coverslip to a microscope slide.
PERSON: Erik Segerdell
United States Patent 3833449
automatic coverslipper
cover slipper
3T MRI scanner
3 Tesla MRI scanner
3 Tesla magnetic resonance imaging scanner
3T MR system
3T MRI scanner
3T MRI system
3T magnetic resonance imaging scanner
A 3T MRI scanner is used to evaluate brain function.
An MRI scanner with a magnet strength of 3 Tesla.
PERSON: Erik Segerdell
http://www.urmc.rochester.edu/radiology/
digitizing tablet
An instrument that allows one to hand-draw images and graphics, similar to the way one draws images with a pencil and paper.
PERSON: Karen Corday
graphics tablet
http://en.wikipedia.org/wiki/Graphics_tablet
nucleic acid isolation
Material component separation of nucleic acids from biological samples, for research purposes such as cloning or gene expression analysis.
PERSON: Nicole Vasilevsky
Plasmid purification from a bacterial culture.
http://acad.erskine.edu/facultyweb/baker/J05-10_DNA%20Technology/Isolation%20of%20Nucleic%20Acids.doc
auger electron spectroscopy
A materials assay used specifically in the study of surfaces and, more generally, in the area of materials science. Underlying the spectroscopic technique is the Auger effect, as it has come to be called, which is based on the analysis of energetic electrons emitted from an excited atom after a series of internal relaxation events.
High resolution secondary electron analysis.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Auger_electron_spectroscopy
atomic force microscopy
AFM
Force microscopy
Imaging of biomolecules.
Microscopy used to determine the surface topography of native biomolecules at subnanometer resolution. It allows biomolecules to be imaged not only under physiological conditions, but also while biological processes are at work.
PERSON: Nicole Vasilevsky
Scanning force microscopy
http://en.wikipedia.org/wiki/Atomic_force_microscopy
multicapillary electrophoresis system
A 96-well capillary sequencer, used to perform high-throughput analysis of samples.
A capillary electrophoresis instrument containing multiple capillaries, at least one source for the emission of a beam intended to to excite molecules lying in its path and inside the capillaries and means for detecting the fluorescence of the molecules exited by said beam, used for automated analysis of DNA fragments and RNA.
PERSON: Nicole Vasilevsky
http://www.google.com/patents?id=7I93AAAAEBAJ
tissue microarrayer
A manual or automated arrayer that is used to precisely assemble tissue cores, as small as 0.6 mm in diameter, in paraffin blocks for tissue microarray analysis.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Tissue_microarray
tissue microarrayer
tissue specimen profile
Data that describe a clinical tissue specimen, e.g. a tissue profile for new gene and protein targets or a molecular profile for tissue specimens or diseases provided by tissue microarray technology.
PERSON: Erik Segerdell
PMID:11257096
tissue information
tissue specimen profile
X-ray powder diffraction spectrometer
A spectrophotometer that uses monochromatic x-rays to determine the interplanar spacings of the unknown crystalline materials for identification and characterization. Samples are analyzed as powders with grains in random orientations to insure that all crystallographic directions are "sampled" by the beam.
PERSON: Nicole Vasilevsky
http://www.physics.montana.edu/ical/instrumentation/xrd.asp
crystallization
A material processing technique that is the (natural or artificial) process of formation of solid crystals precipitating from a solution, melt or more rarely deposited directly from a gas. Crystallization is also a chemical solid-liquid separation technique, in which mass transfer of a solute from the liquid solution to a pure solid crystalline phase occurs.
PERSON: Karen Corday
Protein structures are determined by crystallization analyses.
http://en.wikipedia.org/wiki/Crystallization
x-ray photoelectron spectroscopy
A spectrophotometry technique that measures the elemental composition, empirical formula, chemical state and electronic state of the elements that exist within a material. XPS spectra are obtained by irradiating a material with a beam of X-rays while simultaneously measuring the kinetic energy and number of electrons that escape from the top 1 to 10 nm of the material being analyzed.
Electron spectroscopy for chemical analysis
PERSON: Karen Corday
X ray photoelectron spectroscopy
XPS
http://en.wikipedia.org/wiki/X-ray_photoelectron_spectroscopy
phosphorimager
An image acquisition device that uses storage phosphor technology in life science imaging applications.
PERSON: Nicole Vasilevsky
Phosphorimaging of a Western blot.
http://imagers.salk.edu/pimager/pimFAQ.html
phosphoimager
multi-imager
A gel imager with light and UV filters.
An image acquisition instrument that captures digital images from single- and multiple-color fluorescence, chemiluminescence, chemifluorescence, and colorimetric samples.
PERSON: Karen Corday
http://ricfacility.byu.edu/fluors.html
scanning electron microscope
An electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity.
PERSON: Karen Corday
SEM
Used to image biomolecules.
http://en.wikipedia.org/wiki/Scanning_electron_microscope
X-ray diffraction sample cooler
A device used for X-ray diffraction and designed for cooling inorganic, small-molecule and macromolecular crystals for X-ray crystallography.
Cryostream
PERSON: Karen Corday
http://journals.iucr.org/d/issues/2000/03/00/me0093/me0093bdy.html
water softener
An instrument used to reduce the dissolved calcium, magnesium, and to some degree manganese and ferrous iron ion concentration in hard water.
PERSON: Karen Corday
Water softener is used in places where the water is hard, to make it more drinkable.
http://www.isws.illinois.edu/chem/psl/Softeners.asp
mechanical stage
A device that can be mounted on the microscope stage and which allows for precise adjustments of the slide.
A mechanical stage on a microscope.
PERSON: Karen Corday
http://www.labessentials.com/microscope-accessories.htm#Mechanical%20Stage
hematocrit centrifuge
A centrifuge used for the determination of volume fraction of erythrocytes in blood.
Blood samples that are taken from patients are subjected to hematocrit centrifugation for subsequent analysis.
PERSON: Karen Corday
http://www.hettichlab.com/appc/content_manager/page.php?ID=160009&dbc=dr0aavhds5jr9hmleoh2k5ske3
protein purification
A protein of interest may be isolated from a bacterial culture overexpressing the protein by protein purification methods.
A purification process intended to isolate a single type of protein from a complex mixture.
PERSON: Karen Corday
Protein separation
http://en.wikipedia.org/wiki/Protein_purification
polisher
An mechanical instrument that enables precise sample thinning and polishing of a wide range of materials.
PERSON: Nicole Vasilevsky
http://www.cns.fas.harvard.edu/facilities/tool_detail.php?MID=20
operant conditioning chamber
An animal cage that is used in the study of both operant conditioning and classical conditioning. The structure forming the shell of a chamber is a box large enough to easily accommodate the organism being used as a subject. It is often sound-proof and light-proof to avoid distracting stimuli. Operant chambers have at least one operandum (or "manipulandum"), and often two or more, that can automatically detect the occurrence of a behavioral response or action.
An operant conditioning chamber is used to study behavior in mice or rat models after treatment with certain drugs to determine their effect on behavior.
PERSON: Tenille Johnson
Skinner box
http://en.wikipedia.org/wiki/Operant_conditioning_chamber
operant conditioning chamber
motorized stage
A mechanical stage using motorized controls.
A microscope stage.
PERSON: Tenille Johnson
PERSON: Tenille Johnson
motorized stage
animal activity data
Animal activity data may be recorded after an experimental procedure.
Data pertaining to the activity of laboratory animals or animals in an experimental setting.
PERSON: Tenille Johnson
PERSON: Tenille Johnson
animal activity data
animal activity monitoring system
A blood pressure monitor.
An animal physiology monitoring system used to monitor the specific behavior of animals in an experimental setting.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
animal activity monitor
animal activity monitoring system
behavioral locomotive activity chamber
arterial blood gas test
A hematology assay that measures the acidity (pH) and the levels of oxygen and carbon dioxide in the blood from an artery. This test is used to check how well the lungs are able to move oxygen into the blood and remove carbon dioxide from the blood.
ABG test
An arterial blood gas (ABG) test is done to check for severe breathing problems and lung diseases, such as asthma, cystic fibrosis, or chronic obstructive pulmonary disease.
PERSON: Tenille Johnson
arterial blood gas test
http://www.webmd.com/lung/arterial-blood-gases
behavioral sensitization
A material procesing technique where psychomotor stimulants are repeatedly administered, leading to the progressive augmentation of behavioral responses. This repeated administration produces gradual and incremental neuroadaptions that render the animals hypersensitive to these agents.
Behavioral sensitization is used for alcoholics to induce reverse tolerance and help treat their addiction.
PERSON: Tenille Johnson
behavioral sensitization
http://nba.uth.tmc.edu/homepage/dafny/neurobehav.html
sound isolation enclosure
An instrument that consists of an enclosed space that is used to reduce or isolate ambient and acoustic noise.
PERSON: Tenille Johnson
http://www.whisperroom.com/
isolation booth
sound isolation enclosure
patch clamp amplifier
A patch clamp amplifier is a voltage amplifier that uses a single electrode clamp, where the voltage measuring and current passing circuits are connected. The electrode is attached to a wire that contacts the current/voltage loop inside the amplifier. Thus the electrode has only an indirect influence on the feedback circuit. The amplifier reads only the voltage at the top of the electrode, and feeds back current to compensate.
A patch clamp amplifier is used to study action potentials in neurons.
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Voltage_clamp#Single-electrode_voltage_clamp
patch clamp amplifier
electrolyte analyzer
An analyzer for measuring the ionic values of electrolytes.
Evaluation of electrolytes in a patient's blood.
PERSON: Tenille Johnson
electrolyte analyzer
http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN%2F4705668
immunoperoxidase labeling
HRP labeling of an antibody.
Labeling of molecules with immunoperoxidase, a type of immunostain used in molecular biology, medical research, and clinical diagnostics. Immunoperoxidase reactions refer to a sub-class of immunohistochemical or immunocytochemical procedures in which the antibodies are visualized via a peroxidase-catalyzed reaction.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Immunoperoxidase
time-of-flight secondary ion mass spectrometer
A mass spectrometer that uses a target modified to achieve biochemical affinity with the analyte compound.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Surface-enhanced_laser_desorption/ionization
nanodispenser
A liquid handling device that is used for the pipetting and dispensing of volumes in the nanoliter range.
PERSON: Erik Segerdell
doi:10.1016/j.sna.2004.05.038
nanodispenser
skin electrode
An instrument that consists of a conductor through which an electric current enters or leaves the skin, whose electrical characteristics are being measured, used, or manipulated.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/electrode
osmometer
An instrument that measures the osmotic strength of a solution, colloid, or compound.
PERSON: Tenille Johnson
http://en.wikipedia.org/wiki/Osmometer
osmometer
cannulation
A material processing technique where a tube is inserted into the body, often for the delivery or removal of fluid or for the gathering of data.
Insertion of cannula
Intubation of a patient to assist with breathing.
PERSON: Nicole Vasilevsky
cannulation
http://en.wikipedia.org/wiki/Cannula
electrophysiology data
Data generated from an electrophysiology assay.
Ion channel recording data from a primate suprachiasmatic nucleus.
PERSON: Tenille Johnson
PERSON: Tenille Johnson
electrophysiology data
technology transfer office
An organization that provides services for commercialization and licensing of technologies at an institution.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Technology Transfer Office
animal shocker
A device that delivers a shock to an animal at programmable intervals.
An animal shocker can be used in classical conditioning models.
PERSON: Karen Corday
Sacchetti, B., Sacco, T., & Strata, P. (2007). Reversible inactivation of amygdala and cerebellum but not perirhinal cortex impairs reactivated fear memories. European Journal of Neuroscience, 25(9), 2875-2884. DOI: 10.1111/j.1460-9568.2007.05508.x
mineralized tissue preparation
Histological sample preparation of biological materials that incorporate minerals into soft matrices to get the stiffness needed for a protective shield or structural support.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Mineralized_tissues
animal physiology monitoring system
A blood pressure monitoring system for mice.
An instrument that is used to monitor mechanical, physical, or biochemical functions in an organism.
PERSON: Erik Segerdell
animal physiology monitor
animal physiology monitoring system
http://en.wikipedia.org/wiki/Physiology
heart perfusion
An organ perfusion technique of perfusing the heart by carrying fluid under pressure into the sectioned aorta and thus into the coronary system.
Langendorff Heart
Langendorff method
PERSON: Tenille Johnson
Perfusion of heart tissue with formaldehyde.
http://www.medilexicon.com/medicaldictionary.php?t=54825
isolated perfused heart assay
Prokaryota
PERSON: Erik Segerdell
Prokaryota
The prokaryotes (pronounced /proʊˈkæri.oʊts/ or /proʊˈkæriəts/) are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles.
http://en.wikipedia.org/wiki/Prokaryote
plate luminometer
A photometer used for measuring very low light levels (as those produced in a luminescent process) in a microplate format.
PERSON: Karen Corday
http://www.merriam-webster.com/medical/luminometer
plate luminometer
organic compound
A chemical substance comprised of two or more elements combined, bonded in a fixed ratio and containing carbon and hydrogen atoms. The following elements can also be found in organic compounds: Nitrogen (N); oxygen (O), Fluor (F), phosphorous (P), sulfur (S), chlorine (Cl), selenium (Se), bromine (Br), iodine (I). Organic compounds do not contain metals.
Benzene.
PERSON: Edgar Miranda
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Chemical_compound
organic compound
bioinorganic compound
A chemical comprised of 2 or more elements combined in a fixed ratio and containing metal, carbon, and hydrogen atoms.
Hemoglobin is a bioinorganic compound.
PERSON: Melissa Haendel
The definition of a compound requires a fixed ratio. Thus table salt, NaCl, is a compound but not a molecule, cecause it is composed of 2 or more elements in a fixed ratio (1:1, satisfying the definition of a compound) but does not have a well-defined number of atoms (so it does not meet the criteria for a molecule). It is instead an array of any number (not fixed) of Na+ and Cl- ions arranged in a 1:1 ratio.
bioinorganic compound
http://en.wikipedia.org/wiki/Chemical_compound
inorganic compound
A chemical consisting of a well-defined number of atoms covalently bonded together, and containing metal atoms. Inorganic compounds do not contain chemical moities consisting of carbon and hydrogen bonded together. Examples of inorganic compounds are: Salts: sodium chloride (NaCl), magnesium sulfate (MgSO4), Oxides: carbon dioxide (CO2), silicon dioxide (SiO2) and Iron (II, III) oxide (Fe3O4), Acids: hydrogen chloride (HCl) and sulfuric acid (H2SO4), Bases: sodium hydroxide (NaOH).
PERSON: Melissa Haendel
Sodium chloride.
The definition of a compound requires a fixed ratio. Thus table salt, NaCl, is a compound but not a molecule, cecause it is composed of 2 or more elements in a fixed ratio (1:1, satisfying the definition of a compound) but does not have a well-defined number of atoms (so it does not meet the criteria for a molecule). It is instead an array of any number (not fixed) of Na+ and Cl- ions arranged in a 1:1 ratio.
http://en.wikipedia.org/wiki/Chemical_compound
inorganic compound
organic small molecule
An organic small molecule is an organic molecule of low molecular weight, which is by definition not a polymer. The term small molecule is usually restricted to a molecule that also binds with high affinity to a biopolymer such as protein, nucleic acid, or polysaccharide and alters the activity or function of the biopolymer. The upper molecular weight limit for a small molecule is approximately 800 Daltons.
PERSON: Melissa Haendel
Phorbol 12-myristate 13-acetate is an organic small molecule that activates protein kinase C.
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Small_molecule
organic small molecule
adeno-associated viruses
AAV vectors have been used for clinical trials for treatment of cystic fibrosis.
adeno-associated viruses
baculoviral plasmid
A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into baculoviral capsids for expression in target cells. Baculoviral expression systems are used for transient and stable protein expression in insect cells (and related invertebrates such as arachnids and crustaceans).
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://cshprotocols.cshlp.org/cgi/content/extract/2006/3/pdb.prot4512
retroviral plasmid
A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into retroviral capsids for expression in target cells. DNA delivered by retroviral systems can be integrated into the host genome in a stable fashion in dividing cells.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Viral_vector
lentiviral plasmid
A lentiviral plasmid expressing a gene of interest.
A viral plasmid that is used to introduce genes into cells, which has the ability to integrate into the genome of non-dividing cells.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Viral_vector
adenoviral plasmid
A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into adenoviral capsids for expression in target cells. DNA delivered by andenoviral systems does not integrate into the genome and is not replicated during cell division. The adenovirus is able to infect post-mitotic cells, making them especially useful for gene transfer into neuronal cells.
An adenoviral plasmid expressing a gene of interest, used to study the function of the gene.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
adenoviral plasmid
http://en.wikipedia.org/wiki/Viral_vector
research opportunity
A planned process carried out by a person or organization with the objective of performing research.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Training grant to perform post-doctoral research.
student research opportunity
educational intervention
An intervention which involves education, training programs, and courses in various fields and disciplines, and for training groups of persons.
MeSH ID: Q000193
PERSON: Melanie Wilson
PERSON: Melanie Wilson
educational intervention
dietary intervention
An intervention that involves dietary and nutritional management. The concept does not include vitamin or mineral supplements, for which "drug intervention" may be used.
MeSH qualifier id: Q000178. Definition excerpted from MeSH.
PERSON: Melanie Wilson
PERSON: Melanie Wilson
To treat some illnesses or conditions, such as diabetes, a dietary intervention may be used.
dietary intervention
drug intervention
A therapeutic intervention involving the administration of drugs, biologicals, chemicals, and antibiotics.
Administration of a chemotherapy to treat cancer.
MeSH ID: Q000188. Definition paraphrased from MeSH.
PERSON: Melanie Wilson
PERSON: Melanie Wilson
drug intervention
radiologic intervention
An intervention that involves the therapeutic use of ionizing and nonionizing radiation. It includes the use of radioisotope therapy.
MesH qualifier ID : Q000532
PERSON: Matthew Brush
Radiation therapy for cancer.
http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi
radiologic intervention
surgical intervention
An intervention involving operative procedures on organs, regions, or tissues in the treatment of diseases, including tissue section by lasers. It excludes transplantation, for which "therapeutic intervention" is used.
MeSH qualifier ID : Q000601
PERSON: Matthew Brush
Surgical removal of a tumor.
http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi
surgical intervention
rehabilitative intervention
An intervention involving surgical procedures for restoration of function of the individual.
MeSH qualifier ID : Q000534
PERSON: Matthew Brush
http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi
rehabilitative intervention
nursing intervention
An intervention involving nursing care and techniques in their management. It includes the nursing role in diagnostic, therapeutic, and preventive procedures.
MeSH qualifier ID : Q000451
PERSON: Matthew Brush
http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi
nursing_intervention
prevention and control intervention
An intervention involving increasing human or animal resistance against disease (e.g., immunization), control of transmission agents, prevention and control of environmental hazards, or prevention and control of social factors leading to disease. It includes preventive measures in individual cases.
MeSH qualifier ID : Q000517
PERSON: Matthew Brush
http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&index=218879&field=qual&HM=&II=&PA=&form=&input=
prevention and control intervention
psychological and behavioral intervention
PERSON: Matthew Brush
PERSON: Melanie Wilson
Psychological or behavior intervention is a combination of program elements, strategies, or modalities designed to influence psychological or behavioral processes or outcomes.
psychological and behavioral intervention
x-ray crystallography assay
A molecular assay used to determine the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and diffracts into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder and various other information.
PERSON: Karen Corday
X ray crystallography assay
Xray Crystallography
http://en.wikipedia.org/wiki/X-ray_crystallography
genome assembly
A data analysis technique taking a large number of short DNA sequences, generated by DNA sequencing, and putting them back together to create a representation of the original chromosomes from which the DNA originated.
PERSON: Karen Corday
http://en.wikipedia.org/wiki/Genome_project
Raman confocal microscope
A confocal microscope that consists of of an optical microscope, an excitation laser, a monochromator, and a sensitive detector (such as a charge-coupled device or photomultiplier tube), has high spatial resolution, and relies on inelastic scattering, or Raman scattering, of monochromatic light.
PERSON: Melanie Wilson
Raman confocal microscope
Raman microscope
Used to image biological samples.
http://en.wikipedia.org/wiki/Raman_spectroscopy
SNP data
Data that describes single nucleotide polymorphisms, or SNPs (pronounced "snips"), which are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered.
PERSON: Matthew Brush
SNP data
http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml
fluorescence recovery after photobleaching
An imaging assay that allows determination of the kinetics of diffusion in living cells (usually) using fluorescence microscopy. The general method is to label a specific cell component with a fluorescent molecule, image that cell, photobleach a small portion of the cell, then image the recovery of fluorescence over time.
Can be used to study cell membrane diffusion.
FRAP
Fluorescence photobleaching recovery
PERSON: Nicole Vasilevsky
http://microscopy.berkeley.edu/courses/tlm/fluor_techniques/FRAP.html
field emission scanning electron microscope
A scanning electron microscope that has electromagnetic coils that form an electron beam that scans the object (scan) and secondary electrons are produced by interaction with the atoms at the surface of the sample.
Can be used to image biomolecules.
FESEM
PERSON: Karen Corday
http://www.vcbio.science.ru.nl/en/fesem/
measurement instrument
A pH meter is used to measure the pH of a sample.
An instrument that has measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
OBI
PERSON: Nicole Vasilevsky
image acquisition instrument
A microscope.
An instrument that has image acquisition function. An image acquisition function is a function to acquire an image of a material.
OBI
PERSON: Nicole Vasilevsky
viral plasmid
A pWPI-Mad4-GFP vector.
A plasmid carrying sequence elements that allow for packaging of genetic cargo into viral capsids, DNA replication, and expression in target cells. Viral plasmids may contain additional genes required for capsid protein production and assembly, or may require helper plasmids which produce these proteins.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
adeno-associated viral plasmid
A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into baculoviral capsids for expression in target cells. Adeno-associated viral expression systems can be used with non-dividing cells, and cargo DNA has the ability to stably integrate into the host cell genome at a specific site (designated AAVS1) in the human chromosome 19.
AAV plasmid
An adeno-associated viral plasmid expressing a gene of interest, used to study the function of the gene.
PERSON: Matt Brush. By David P. Clark, Nanette Jean Pazdernik
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
prokaryotic expression construct
An expression construct that contains promoter elements to drive expression of downstream genes in prokaryotic cells or prokaryote-derived in vitro expression systems.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
center
An organization where a particular activity or service is concentrated.
Center for Environmental and Toxicological Research.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/center
true
information processing instrument
A computer.
An instrument that has information processor function. An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
OBI
PERSON: Nicole Vasilevsky
material separation instrument
A chromatography column.
An instrument that has material separation function. A material separation function is a function that increases the resolution between two or more material entities. The distinction between the entities is usually based on some associated physical quality.
OBI
PERSON: Nicole Vasilevsky
sterilization instrument
An autoclave.
An instrument that has sterilization function. Sterilization function is a function to remove viable organisms from an input material.
OBI
PERSON: Nicole Vasilevsky
mechanical instrument
A drill is a mechanical instrument.
An instrument that has mechanical function. A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
OBI
PERSON: Nicole Vasilevsky
environment control instrument
A laminar flow hood.
An instrument that has environment control function. An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
OBI
PERSON: Nicole Vasilevsky
material transfer instrument
An automatic coverslipper.
An instrument that has transfer function. A transfer function is a function to displace a material from one location to another.
OBI
PERSON: Nicole Vasilevsky
nucleic acid reagent
A primer.
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
Reagent that is a polymer comprised of nucleotides, each of which consists of three components: a nitrogenous heterocyclic base, which is either a purine or a pyrimidine; a pentose sugar; and a phosphate group.
http://en.wikipedia.org/wiki/Nucleic_acid
primer
Nucleic acid reagent that is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis.
Oligos used in PCR.
PERSON: Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29
morpholino
Morpholinos are injected into zebrafish to study a particular gene's function.
Nucleic acid reagent that is a short strand of nucleic acid where the bases are bound to morpholine rings instead of deoxyribose rings and linked through phosphorodiamidate groups instead of phosphates. Morpholinos are used to knockdown gene expression via antisense binding.
PERSON:Melissa Haendel
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Morpholino
spore trap
An instrument designed to capture and quantify a broad spectrum of fungal spores present in the air.
PERSON: Nicole Vasilevsky
http://www.emlab.com/s/sampling/SporetrapSampling.html
calcium imaging assay
Ca imaging
Ca2+ imaging assay
An imaging assay that is designed to show the calcium (Ca2+) levels of a tissue or medium.
Ca imaging assay
Ca2+ imaging
Can be used to assay calcium levels in muscle cells.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Calcium_imaging
apoptotic DNA ladder assay
An apoptosis assay that allows for detection of DNA fragmentation in apoptotic cells. DNA fragments can be visualized by agarose gel electrophoresis.
An apoptotic DNA ladder assay can be used to determine if cells are undergoing apoptosis after treatment with a cytolytic drug.
PERSON: Nicole Vasilevsky
http://www.abcam.com/Apoptotic-DNA-Ladder-Detection-Kit-ab66090.html
cell proliferation assay
A cellular assay that allows for the measurement of the multiplication or reproduction of cells, resulting in the expansion of a cell population.
Cell division assay
OBI
PERSON: Nicole Vasilevsky
Tritiated thymidine incorporation.
multiplex bead assay
A molecular assay that permits the simultaneous measurement of an array of proteins in a single, small volume sample.
Elshal and McCoy (2006) Methods. 38(4): 317–323.
Multiplex assay
PERSON: Nicole Vasilevsky
picogreen assay
An assay used for DNA quantificiation.
An biomolecular label detection assay used for quantification of double-stranded DNA (dsDNA) in molecular biology assays.
PERSON: Nicole Vasilevsky
http://www.topac.com/picogreen.html
cycle sequencing
A DNA sequencing by synthesis technique used to increase the sensitivity of the DNA sequencing process and permits the use of very small amounts of DNA starting material. This is accomplished by using a temperature cycling process similar to that employed in the polymerase chain reaction.
PERSON: Nicole Vasilevsky
Sequencing of a genome.
http://www.answers.com/topic/cycle-sequencing
injection
Agent delivery whereby a substance is introduced into a organism, usually by means of a hypodermic syringe, as a liquid into the veins or muscles of the body.
Injection of a drug.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/injection
intracytoplasmic sperm injection
DISCO
Direct injection of sperm into cytoplasm of the oocyte
ICSI
Injection of a single sperm into a single celled embryo or an egg for the purpose of in vitro fertilization.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Intracytoplasmic_sperm_injection
administration of inhalational agents
Administration of anesthesia to mice.
Agent delivery performed to humanely administer inhalation agents to organism, usually for the purpose of sedation.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
agent delivery
A material processing technique performed to locally deliver an agent to a recipient.
An injection.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
RNA quality analysis
A nucleic acid assay used to determine quality of RNA after purification for the purpose of downstream molecular assays. RNA quality can be checked by electrophoresis in agarose gel, by electrophoresis in polyacrylamide gel, or by in vitro translation.
PERSON: Nicole Vasilevsky
RNA QA
Spectrophotometric analysis of RNA after purification from a sample.
http://www.molecularinfo.com/MTM/C/C3/C3-5/C3-5-5.html
amino acid isolation
Amino acid purification
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Sample preparation for assay that involves the isolation of amino acids from a cell or tissue sample for use in protein chemistry or biological assays.
The collection of adenine from a sample of blood plasma is amino acid isolation.
quantitative southern blot analysis
A Southern blot analysis technique performed to quantitate the bands on a Southern blot to compare the relative expression levels of a particular gene.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
DNA purification
Nucleic acid purification of genomic or plasmid DNA from other impurities, such as bacteria or contaminating materials for the purpose of molecular biology research.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Purification of a plasmid from a bacterial culture.
in vivo reproductive system test
A physiological assay that tests the reproductive system function in the whole, living organism for research purposes.
Clinical monitoring of the menstrual cycle.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
transverse aortic constriction
A surgical procedure performed to stress the heart, which causes a subacute increase in the workload on the heart, which is a commonly used surgical model of cardiac hypertrophy and subsequent failure.
Arany et al (2006) PNAS 103:10086.
Can be used to study stroke.
PERSON: Nicole Vasilevsky
cryoablation
A material processing technique that uses extreme cold (cryo) to remove tissue (ablation).
Cryocautery
Cryodestruction
Cryosurgery
PERSON: Nicole Vasilevsky
Warts are removed by cryoablation.
http://en.wikipedia.org/wiki/Cryoablation
in vivo bioluminescence
An imaging assay that allows detection of bioluminescence from a living organism or organisms.
Detection of GFP in a sample.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
radioimmunoassay
A RAST test (radioallergosorbent test) is an example of radioimmunoassay.
A radioactivity detection technique that uses the binding of a radioactively labeled substances to an antibody in order to analyze minute amounts of proteins in a sample.
PERSON: Nicole Vasilevsky
RIA
http://en.wiktionary.org/wiki/radioimmunoassay
protein quantitation assay
A protein assay used for determination of protein concentrations in solutions that depends upon the change in absorbance of a colored substrate upon binding of protein.
BCA assay
Bradford assay.
PERSON: Nicole Vasilevsky
biuret assay
bradford assay
http://www.animal.ufl.edu/hansen/protocols/minibradford.htm
lowry assay
protein concentration assay
tissue co-culturing
Culturing two cell types together.
OBI branch derived
PERSON: Nicole Vasilevsky
Tissue culture of two or more different types are are combined and allowed to culture as one.
DNA quality analysis
A nucleic acid assay used to determine quality of DNA after purification for molecular biology research. Assays to determine DNA quality include DNA electrophoresis and spectrophotometric determination of the ratio of the A260/A280.
DNA QA
PERSON: Nicole Vasilevsky
Spectrophotometric analysis of DNA after purification from a sample.
www.generationcp.org/capcorner/gcp_training.../practicals_3.doc
identification of differentiated hematopoietic stem cells
A cellular assay used to identify the process by which a hematopoietic stem cell (HSC) becomes a more specialized cell. HSCs are multipotent stem cells that give rise to all the blood cell types including myeloid (monocytes and macrophages, neutrophils, basophils, eosinophils, erythrocytes, megakaryocytes/platelets, dendritic cells), and lymphoid lineages (T cells, B cells, NK cells).
PERSON: Nicole Vasilevsky
Use of flow cytometry to identify differentiation stem cells from undifferentiated cells.
http://en.wikipedia.org/wiki/Hematopoietic_stem_cell
metagenomics analysis
A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research.
PERSON: Nicole Vasilevsky
community genomic analysis
ecogenomic analysis
environmental genomic analysis
http://en.wikipedia.org/wiki/Metagenomics
pathway data analysis
A data analysis technique that allows for analysis of data relating to biological pathways accumulated from genomic, proteomic or other sources.
Analysis of cell signaling data.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
clinical monitoring
A clinical assay that involves oversight and administrative efforts that monitor a participant's health during a clinical trial.
Monitoring a patient in a clinical trial.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Clinical_monitoring
in utero electroporation
Electroporation into the uterus or ovaries of an organism to overexpress a protein of interest.
PERSON: Nicole Vasilevsky
Shimogori and Ogawa (2008) Develop. Growth Differ. 50, 499–506
Transfection of a protein into the uterus.
in utero transfrection
in ovo electroporation
Electroporation into chick embryos to overexpress a protein of interest.
PERSON: Nicole Vasilevsky
Transfection of a plasmid into chick embryos.
http://www.cellscience.com/reviews1/Ovarian_Transplantation_and_Cryopreservation.html
in ovo transfection
ovarian transplantation
PERSON: Nicole Vasilevsky
Transplantation of ovaries into an organism, often performed for women who have lost their fertility due to medical treatment, disease or aging.
http://www.cellscience.com/reviews1/Ovarian_Transplantation_and_Cryopreservation.html
in vitro follicle maturation
Culture and maturation of ovarian follicles in vitro for clinical applications.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/In_vitro_maturation
ovarian radiation
Irridiation of ovaries, usually for the purpose of cancer treatment.
PERSON: Nicole Vasilevsky
http://www.oncologychannel.com/ovariancancer/radiotherapy.shtml
ovarian radiotherapy
mutant strain generation
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Production of transgenic mice.
Specimen creation of mutant strain of cells or an organism for the purpose of studying gene function.
multi-spectral fluorescence
An imaging assay that uses the synergistic combination of imaging and spectroscopy with broad applications in both preclinical and clinical settings.
Imaging of tumor cells in a rodent model that are labels with fluorophores, such as GFP.
PERSON: Nicole Vasilevsky
Zhou and El-Deiry (2009) Journal of Nuclear Medicine 50:1563-1566
virus neutralization
A material processing technique used for detection of virus-specific neutralizing antibodies in a sample.
PERSON: Nicole Vasilevsky
Virus attenuation
Zielinska etl a (2005) Virology Journal 2005, 2:84.
tenocyte differentiation screening
A cellular assay used to screen culture skin-derived tenocyte cells for the proper phenotype for research and clinical applications with tendon tissue.
PERSON: Nicole Vasilevsky
Schulze-Tanzil (2004) 122:219-228
serology assay
A tissue/organ assay that is performed to analyze blood serum and other bodily fluids, to identify antibodies in the serum.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Serology
calorimetry
A molecular assay that is used to measure the heat of chemical reactions or physical changes.
An assay to measure the volume of oxygen consumption and volume of carbon dioxide output in a patient.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Calorimetry
track breeding pairs
A mouse breeding technique to track parental breeders to generate offspring in an animal colony.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Used for development of transgenic mice strains.
reactive oxygen species assay
A molecular assay used to detect the presence of reactive oxygen species on a molecule, to determine if they play a role in physiological or pathophysiological processes.
An assay to detect NOS in a sample.
Dikalov et al (2007) Hypertension 49:717-727.
PERSON: Nicole Vasilevsky
ROS assay
experimental glucuronidation
Chemical modification of a molecule in an experimental setting, to increase the water solubility by adding glucuronic acid.
PERSON: Marc Le Pape
PERSON: Nicole Vasilevsky
tissue fixation
Fixation of biological tissues to preserve them from decay, either through autolysis or putrefaction. Fixation terminates any ongoing biochemical reactions, and may also increase the mechanical strength or stability of the treated tissues. Fixation is usually the first stage in a multistep process to prepare a sample of biological material for microscopy or other analysis
Fixing tissue prior to immunohistochemistry staining.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fixation_%28histology%29
in vivo electrophysiology recording
An electrophysiology assay that measures voltage changes or electric currents in single ion channel proteins to whole organs. In neuroscience, it includes measurements of the electrical activity of neurons, and in particular, action potential activity.
EKG is a common method for electrophysiology recording.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electrophysiology
transcranial magnetic stimulation
A material processing technique used to cause depolarization in the neurons of the brain. TMS uses electromagnetic induction to induce weak electric currents using a rapidly changing magnetic field; this can cause activity in specific or general parts of the brain, allowing the functioning and interconnections of the brain to be studied.
PERSON: Nicole Vasilevsky
TMS
http://en.wikipedia.org/wiki/Transcranial_magnetic_stimulation
mitochondrial oxygen consumption measurement
A cellular assay used to measure oxygen consumption in mitochondria to study mitochondrial respiration, which can be used to diagnosis mitochondrial disorders.
Jonckheere et al (2010) Clinical Chemistry 56:424-431.
PERSON: Nicole Vasilevsky
mitochondrial permeability transition measurement
A cellular assay used to measure membrane potential and permeability transition in the mitochondria during apoptosis. Mitochondrial membrane permeabilization constitutes an early event of the apoptotic process (programmed cell death).
PERSON: Nicole Vasilevsky
Zamzami and Kroemer (2004) Methods in Molecular Biology 282:103-115.
measurement of mitochondrial membrane potential
A cellular assay used to measure mitochondrial membrane potential for the assessment of mitochondrial function.
PERSON: Nicole Vasilevsky
http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-60761-411-1_7
fast live imaging
An imaging assay that involves live imaging of cells, that enables subsecond, multicolor four-dimensional data acquisition, which has the unique capability to probe dynamic processes, linking molecular components and their localization with function.
Carlton et al (2010) 107:16016-16022
Imaging of in vivo biological processes in a cell.
Live cell imaging
PERSON: Nicole Vasilevsky
Time-lapse imaging
Time-lapse microscopy
morphological changes assay
A cellular assay that is performed to analyze changes in the form and structure of organisms and their specific structural features.
Can be used to detect apoptotic cells, which undergo morphological changes.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Morphology_%28biology%29
caspase assay
An apoptosis assay used to measure caspase activity, which are proteases that mediate apoptosis.
Analysis of caspase activity by flow cytometry.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/caspase-2
annexin V assay
An apoptosis assay used to detect apoptosis at a very early stage. This assay takes advantage of the fact that phosphatidylserine (PS; 1–3) is translocated from the inner (cytoplasmic) leaflet of the plasma membrane to the outer (cell surface) leaflet soon after the induction of apoptosis, and that the annexin V protein has a strong, specific affinity for PS (4–6). PS on the outer leaflet is available to bind labeled annexin V, providing the basis for a simple staining assay.
Cells undergoing apoptosis can be detected by Annexin V staining.
PERSON: Nicole Vasilevsky
http://www.clontech.com/products/detail.asp?product_id=10378&tabno=2
in vitro cytotoxicity assay
An assay used to investigate the function of NK cells.
An cellular assay that measures basal cytotoxicity (general cytotoxicity that affects structures or processes intrinsic to all cell types) in response to external insults.
Cytotoxicity assay
PERSON: Nicole Vasilevsky
http://iccvam.niehs.nih.gov/methods/acutetox/acutetox.htm
clinical laboratory results management
A data management technique that specifies how to manage data from clinical laboratory studies, such as chemical, microscopic and bacteriologic tests of blood, tissue and fluids.
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/clinical+laboratory+scientist
blood sampling
Blood drawing for cholesterol screening.
Collection of a blood specimen from an organism, usually performed by a closed method, either a hypodermic syringe or a vacuumized container, usually for the purpose of laboratory examination.
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/blood+sampling
medicine storage
Material storage of medication in a health care setting that allows access to only authorized personel.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
research subject private information management
A clinical trial technique that maintains privacy of patient health records, who are participating as research subjects to protect them from unwarranted invasions of personal privacy.
PERSON: Nicole Vasilevsky
Protection of private patient information in a clinical trial.
http://www.epa.gov/privacy/index.htm; http://en.wikipedia.org/wiki/Human_subject_research
research subject consent
A clinical trial technique used to educate potential subjects to ensure that they can reach a truly informed decision about whether or not to participate in the research. Their consent must be given freely, without coercion and must be based on a clear understanding of what participation involves.
Consent to participate in a clinical trial.
PERSON: Nicole Vasilevsky
http://healthcare.partners.org/phsirb/infcons.htm
informed consent of research subjects
array scanning
A molecular assay used for scanning a surface, consisting of focusing an array of optical beams using optics having an axis, so as to illuminate a region of the surface intercepted by the axis, such that each optical beam illuminates a portion of a respective sub-region within the region.
PERSON: Nicole Vasilevsky
http://www.freshpatents.com/Optical-spot-grid-array-scanning-system-dt20070614ptan20070133077.php
array printing
A material processing technique that involves printing samples onto a solid substrate to allow researchers to efficiently screen thousands of conditions in a very small space for applications in drug screening, molecular biology, and genetic analysis.
Array spotting
PERSON: Nicole Vasilevsky
Screening potential new drug targets.
http://aurorabiomed.com/app_peptide.htm
high throughput sample analysis
An assay that allows for high throughput analysis of samples.
High throughput screening
Next generation sequencing.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
nucleic acid shearing
A material processing technique used to fragment DNA molecules by mechanical force.
DNA shearing
PERSON: Nicole Vasilevsky
Passing DNA through a needle shears the DNA.
http://www.mondofacto.com/facts/dictionary?DNA+shearing
SNP interrogation genotyping
A genotyping technique that interrogates SNPs by hybridizing complementary DNA probes to the SNP site.
DNA sequence variation genotyping
PERSON: Nicole Vasilevsky
SNP analysis
SNP chip analysis
SNP genotyping
SNP sampling
Single nucleotide polymorphism analysis
Single nucleotide polymorphism gentotyping
Single nucleotide polymorphism sampling
http://en.wikipedia.org/wiki/SNP_genotyping
oocyte injection
Brown and Corbin (2002) Methods in Molecular Biology 180:39-70.
Injection of materials into oocytes, the female gametocyte or germ cell involved in reproduction, of an organism for the purpose of generating transgenic offpsring.
PERSON: Nicole Vasilevsky
Transgenic mouse generation.
telemetric blood pressure monitoring procedure
A physiological assay that is used to directly measure blood pressure via an implantable radio telemetry device in an organism, used to study hypertension.
Huetteman and Bogie (2009) Methods Mol Biol. 573:57-73.
PERSON: Nicole Vasilevsky
in vitro fertilization
A culture and propogation technique performed in vitro to the fuse of gametes to produce a new organism.
IVF
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fertilisation
non-web programming
A technique that involves creating a computer program that is non-web based. It involves developing the program logic to solve the particular problem, writing the program logic in a specific programming language (coding the program), assembling or compiling the program to turn it into machine language, and testing and debugging the program.
PERSON: Nicole Vasilevsky
Writing a program in JAVA that can sort numbers.
http://www.pcmag.com/encyclopedia_term/0%2C2542%2Ct%3Dprogramming&i%3D49827%2C00.asp
biological sample processing
A material processing technique that involves the careful handling and storage of precious biological samples with the goal of obtaining a large amount of information from limited samples for cytogenetic, immunological, biochemical or other analyses.
Holland et al (2003) Mutation Research/Reviews in Mutation Research, Volume 543: 217-234
PERSON: Nicole Vasilevsky
Purification of DNA from a sample, for subsequent sequence analysis.
polyclonal antibody production
Antibody production of polyclonal antibodies by immunization of a suitable mammal, such as a mouse, rabbit or goat. An antigen is injected into the mammal. This induces the B-lymphocytes to produce IgG immunoglobulins specific for the antigen. This polyclonal immunoglobulin is purified from the mammal's serum.
PERSON: Nicole Vasilevsky
Polyclonal IgG preparation
Production of a rabbit anti-human OX40 antibody.
http://en.wikipedia.org/wiki/Polyclonal_antibodies
plasmid purification
A purification technique used to extract and purify plasmid DNA. It involves growing bacterial cultures that express the plasmid, harvesting and lysing the bacteria and purifying the plasmid DNA.
PERSON: Nicole Vasilevsky
Purification of a plasmid from a bacterial culture.
http://en.wikipedia.org/wiki/Plasmid_preparation
label free mass spectrometry
A mass spectrometry assay that allows for measurement for endogenous targets in live cell assays, and eliminates the need for tags, dyes, or specialized reagents or engineered cells.
Label free relative quantitative analysis
PERSON: Nicole Vasilevsky
http://www.moleculardevices.com/Products/Instruments/Label-Free-Analysis.html?gclid=CMTUq7Gi3aQCFQsGbAodNhAjKg
multiple reaction monitoring analysis by mass spectrometry
A mass spectrometry based assay, based on multiple reaction monitoring of stable isotope-labeled peptides, that enables highly reproducible quantification of hundreds of nodes (phosphorylation sites) within a signaling network and across multiple conditions simultaneously.
MRM
PERSON: Nicole Vasilevsky
Wolf-Yadlin et al (2007) PNAS 104:5860-5865
post translational modification identification by mass spectrometry
A mass spectrometry assay that identifies post translational modifications to proteins in a sample.
Identification of phosphorylated residues on a protein.
PERSON: Nicole Vasilevsky
http://www.ohsu.edu/xd/research/research-cores/proteomics/request-services/index.cfm
post translational modification localization by mass spectrometry
A mass spectrometry assay used to identify the location and mass shift of the modification on a protein.
Identification of phosphorylated residues on a protein.
PERSON: Nicole Vasilevsky
http://www.ohsu.edu/xd/research/research-cores/proteomics/request-services/index.cfm
protein mass determination by mass spectrometry
A mass spectrometry assay used to determine the molecular weight of a given protein.
Determination of molecular weight of a protein.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Protein mass analysis
partial protein sequencing
A protein sequencing assay used to partially sequence the protein to determine the order of amino acids in protein sequences to identify an unknown protein, typically done by mass spectrometry.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Partial protein sequencing of a purified can be used to confirm the identify of an unknown protein.
human subject recruitment and protection
A clinical trial technique used to recruit human subjects for clinical trials and to protect their privacy.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Recruiting patients for a clinical trial to investigate the usage of a new drug and protecting their privacy.
risk management
A technique used for identification, assessment, and prioritization of risks followed by coordinated and economical application of resources to minimize, monitor, and control the probability and/or impact of unfortunate events or to maximize the realization of opportunities.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Risk_management
autoradiography
A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled. Autoradiography has many applications in the laboratory.
Detection of radiolabeled proteins in a pulse-chase assay.
PERSON: Nicole Vasilevsky
Radioautography
http://www.medterms.com/script/main/art.asp?articlekey=2405
sample irradiation
Irradiation of samples or the condition of samples being exposed to radition. Can be performed for sterilization or for immune suppression.
Irradiation of splenocytes in vitro.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/irradiation
rodent irradiation
Irradiation of mice, prior to bone marrow transplant.
Irradiation of rodents or the condition of rodents being exposed to radiation. Accurate partial or whole body irradiation can be used for many types of investigations, including tumor studies and experiments studying the immune response.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/irradiation, Woo and Nordal (2006) Biomed Imaging Interv J 2:e10.
bone marrow analysis
A tissue/organ assay performed to analyze cells in the bone marrow, such as red blood cells, white blood cells, or platelets for research or diagnostic purposes.
Analysis of the white blood cell count.
PERSON: Nicole Vasilevsky
http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy
fluorescence activated cell sorting (FACS)
A flow cytometry assay that provides a method for sorting a heterogeneous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics of each cell.
FACS
PERSON: Nicole Vasilevsky
Sorting of specific cell populations, such as CD4+ T cells.
http://en.wikipedia.org/wiki/Flow_cytometry
data entry
A data transformation technique that involves transcribing some form of data into another form, usually a computer program.
Entry of data about research resources into eagle-i.
PERSON: Nicole Vasilevsky
http://www.wisegeek.com/what-is-data-entry.htm
patient screening
A clinical assay that is performed as a preliminary procedure, such as a test or examination, to detect the most characteristic sign or signs of a disorder or a condition that may require further investigation.
PERSON: Nicole Vasilevsky
Patients are screened during the recruitment process of a clinical trial, to ensure they meet the criteria.
http://medical-dictionary.thefreedictionary.com/screening
immunogold labeling
Labeling of antibodies with collodial gold particles.
Labeling of of proteins, antigens, and other macromolecules of interest with colloidal gold particles, which are most often attached to secondary antibodies which are in turn attached to primary antibodies designed to bind a specific protein or other cell component.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Immunogold_labelling
antigen capture and purification
A material component separation technique used in the isolation of antigens from complex mixtures.
Desai and Dworecki (2004) Anal Biochem. 328(2):162-5.
Isolation of solubilized proteins from a sample.
PERSON: Nicole Vasilevsky
cell separation
A material component separation technique used to separate populations of two or more cells, such as by magnetic bead sorting.
Cell isolation
Cell purification
Cell segregation
Cell sorting
PERSON: Nicole Vasilevsky
Separation and isolation of CD4 T cells.
http://www.reference.md/files/D002/mD002469.html
drug binding assay
A molecular assay used to assay the binding of a drug to a large molecule in tissues or fluids, e.g. binding to protein in the blood, may affect the metabolism of the drug, especially its rate of excretion.
Assay to determine if a monoclonal antibody drug is reaching it's intended target receptor.
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/drug+binding
lipotoxicity assay
A tissue/organ assay used to assay the fatty acid accumulation in non-adipose tissues.
An assay to analyze pancreatic Î_-Cell function.
PERSON: Nicole Vasilevsky
Schaffer (2003) Curr Opin Lipidol. 14(3):281-287.
riboprobe production
Material production of RNA probes that can be produced by in vitro transcription of cloned DNA inserted in a suitable plasmid downstream of a viral promoter for the purpose of producing sense and antisense riboprobes.
PERSON: Nicole Vasilevsky
Production of riboprobes for in situ hybridization.
http://en.wikipedia.org/wiki/Riboprobe
viral infection
Experimental infection using viruses or viral products to introduce a gene product into in vitro systems or animal models.
Infecting cells with viral supernatants.
PERSON: Nicole Vasilevsky
Transduction
http://en.wikipedia.org/wiki/Lentivirus
nucleic acid amplification
Enzymatic amplification of specific nucleic acids to levels where they can be detected in downstream applications. Examples are PCR, TMA, NASBA, etc.
PERSON: Nicole Vasilevsky
Polymerase chain reaction.
http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-N/nucleic_acid_ampl_assay.html
TUNEL labeling
A labeling method used for detecting the 3'-OH ends of DNA exposed during the internucleosomal cleavage that occurs during apoptosis. Incorporation of biotinylated dUTP allows detection by immunohistochemical procedures. The labeled apoptotic cells may be visualized by light microscopy.
An assay used to detect apoptotic cells.
PERSON: Nicole Vasilevsky
TUNEL staining
http://www.scienceboard.net/resources/protocols.asp?action=article&protocol_id=41&criteria=
terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end labeling
small animal surgery
Induction of stroke in an animal model.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Surgical procedures on small animals for research purposes.
coronary artery ligation
A surgical procedure that involves ligation of the coronary artery in the heart, which is used in in vivo animal models to study myocardial infarction.
Induction of a stroke in an animal model.
Ligation of anomalous coronary artery
PERSON: Nicole Vasilevsky
Ye et al (1997) Molecular and Cellular Biochemistry. 176:227-233.
left anterior descending artery ligation
Coronary artery ligation of the left anterior descending artery, which is performed to induce left ventricular infarction for research purposes.
PERSON: Nicole Vasilevsky
Samsamshariat, Samsamshariat and Movahed (2005) Cardiovasc Revasc Med. 6:121
Used for stroke models.
spinal cord laminectomy
A spinal cord laminectomy can be performed to relieve pain after injury.
A surgical procedure that involves surgical removal of the portion of the vertebral bone called the lamina, which is designed to relieve pressure on the spinal cord (or nerve) from herniated discs, spinal stenosis and other related conditions.
PERSON: Nicole Vasilevsky
http://www.articlesbase.com/diseases-and-conditions-articles/lumbar-laminectomy-a-surgery-on-spinal-cord-1237643.html
spinal decompression
lentivirus production
PERSON: Nicole Vasilevsky
Production of high-titers of lentivirus expressing a gene of interest, to study the function of that gene.
Virus production of high-titer, lentivirus prepartions for use in gene delivery applications.
http://web.mit.edu/jacks-lab/protocols/lentiviralproduction.htm
tissue digestion
A material processing technique that is used to digest human, animal or plant tissue by dissolving the remains by alkaline hydrolysis or other methods for the purpose of disposal of the remains or subsequent analysis of components of the tissue.
PERSON: Nicole Vasilevsky
Tissue from mice is digested prior to genotyping, to isolate the DNA.
http://www.wisegeek.com/what-is-tissue-digestion.htm
site-directed mutagenesis
A material processing technique in which a mutation is created at a defined site in a DNA molecule for research purposes.
Oligonucleotide directed mutagenesis
Oligonucleotide-directed mutagenesis
PERSON: Nicole Vasilevsky
Site specific mutagenesis
Site-directed mutagenesis can be used to alter the function of a protein, such as make the avian flu virus transferrable to other species.
Site-specific mutagenesis
http://en.wikipedia.org/wiki/Site-directed_mutagenesis
bioinformatics analysis
A data transformation technique that involves the analysis of bioinformatics data, which is the application of statistics and computer science to the field of molecular biology.
Analysis of DNA sequence data.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Bioinformatics
research electronic datacapture
A technique designed for the collection of clinical data in electronic format for use mainly in human clinical trials.
Electronic health records.
PERSON: Nicole Vasilevsky
clinical database development
http://en.wikipedia.org/wiki/Electronic_data_capture
web programming
A technique that involves writing the necessary source code to create a Web site. It refers to writing the HTML pages or JavaScript in the pages, and any Web site that provides searches, access to databases or any custom processing for the user requires additional programs that run in the Web server. Web server processing is programmed in Java, VBScript, Perl and other languages.
Creation of a website.
PERSON: Nicole Vasilevsky
Web development
http://www.pcmag.com/encyclopedia_term/0,2542,t=Web+programming&i=54332,00.asp
analog electronics design
An instrument and electronics design technique that involves the design of analog electronics; electronic systems with a continuously variable signal.
Design of an analog instrument, used to measure current.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Analogue_electronics
circuit board layout design
An instrument and electronics design technique that involves the design of printed circuit boards; a component made of one or more layers of insulating materials with electrical conductors, which is used in computers.
PERSON: Nicole Vasilevsky
http://www.smps.us/pcb-design.html
electronic instrument design
An instrument and electronics design technique that involves the design, prototyping, rework, final engineering, and documentation of electronic instruments.
Design of a flow cytometer.
PERSON: Nicole Vasilevsky
http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=3694
gene expression analysis assay
A molecular assay used to analyze the location or quantity of of gene expression.
DNA expression analysis
Gene expression pattern analysis
Gene expression profiling
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
Real-time PCR is performed to detect relative gene expression in a sample.
Transcript expression analysis
Instrumentation fabrication
Fabrication of a robot.
Manufacturing of a flow cytometer.
Manufacturing of an instrument from raw materials.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/fabrication
instrumentation planning
An instrument and electronics design technique that involves planning of instrumentation design and fabrication.
Equipment design and fabrication service provided by a lab.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
optical system design
A instrument and electronics design technique that involves the design, layout and analysis of various optical systems; from single element designs to complex wide angle imaging system designs.
Design of a microscope.
PERSON: Nicole Vasilevsky
http://www.loganopticaldesign.com/
protein interaction detection
A protein assay used to detect protein-molecule interactions, a biological process of proteins binding to cellular molecules, such as DNA, often to carry out their biological function such as gene expression.
Co-immunoprecipitation is used to detect protein-protein interaction.
PERSON: Nicole Vasilevsky
Protein binding assay
http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction
protein-DNA interaction detection
Gel mobility shift assay to detect proteins that bind to specific DNA elements.
PERSON: Nicole Vasilevsky
Protein interaction detection technique used to analyze specific protein-DNA interactions, including DNase I footprinting, gel mobility shift assay, nitrocellulose filter binding assay, genetic analysis or x-ray crystallography for the purpose of studying gene expression or regulation.
Protein-DNA binding assay
http://www.biochem.arizona.edu/classes/bioc568/protein_dna_interactions.htm
skeletal morphogenesis analysis
An organismal assay that is performed to analyze the formation of a skeleton or skeletal elements at various developmental stages in an organism.
Limb development can be studied by analyzing skeletal morphogenesis.
PERSON: Nicole Vasilevsky
http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-065-9:61
printed circuit board design
An instrument and electronics design technique used to design printed circuit boards, which are used to mechanically support and electrically connect electronic components using conductive pathways, tracks or signal traces etched from copper sheets laminated onto a non-conductive substrate. It is also referred to as printed wiring board (PWB) or etched wiring board.
PCB design
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Printed_circuit_board
video over IP
A technique that uses an existing standard video codec to reduce the program material to a bitstream (e.g., an MPEG transport stream), and then to use an Internet Protocol (IP) network to carry that bitstream encapsulated in a stream of IP packets.
PERSON: Nicole Vasilevsky
Professional video over IP
Skype.
http://en.wikipedia.org/wiki/Professional_video_over_IP
streaming media delivery method
A technique that involves streaming multimedia that are constantly received by, and normally presented to, an end-user while being delivered by a streaming provider (including audio or video playback).
PERSON: Nicole Vasilevsky
Streaming radio online.
http://en.wikipedia.org/wiki/Streaming_media
embedded controller design
An instrument and electronics design technique used to design embedded controllers, small microcontroller typically used in laptops for various purposes.
PERSON: Nicole Vasilevsky
http://www.coreboot.org/Embedded_controller
computer interfacing
A technique involving connecting computers and peripherals for usability.
Connecting computers to printers and scanners.
PERSON: Nicole Vasilevsky
http://www.lammertbies.nl/comm/index.html
data transfer
A data transformation technique involving formatting data for transfer into another software program or hardware.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Transferring data via a USB flash drive.
functional autoradiography
A autoradiography technique used to describe the first step of the intracellular signal transduction system by visualizing agonist activated receptors by radiolabeling.
Analysis of G-protein coupled signaling.
PERSON: Nicole Vasilevsky
Sovago et al (2001) Brain Research Reviews 38: 149–164
calculation
A data transformation technique that involves problem solving for numbers or quantities
Calculation of a standard curve.
PERSON: Nicole Vasilevsky
http://wordnetweb.princeton.edu/perl/webwn?s=calculation
concentration calculation
A calculation of the concentration of a chemical substance expressed as the amount of the substance present in a mixture.
Determining the concentration of a protein based on a protein quantification assay.
PERSON: Nicole Vasilevsky
http://www.ilpi.com/msds/ref/concentration.html
pharmacogenomics assay
A nucleic acid assay used to tailor drugs and treatment options to the individual patient by discovering and screening for genetic differences and biomarkers by performing various genetic assays.
Lapp (2009) Basic Biotech. 5:1
PERSON: Nicole Vasilevsky
Pharmacogenetic assay
Pharmacogenetic screening
Pharmacogenetic testing
Pharmacogenomics screening
Pharmacogenomics testing
Testing for breast cancer phenotype, such as BrCa positive, Her2/Neu positive, ER positive or triple negative.
in vitro pathogenesis assay
An organismal assay that conducts systematic, whole-genome screens to identify virulence factors as targets for drug development and exploration of host responses to infections.
PERSON: Nicole Vasilevsky
Screening of viruses to detect potential targets for therapy.
http://ec.asm.org/cgi/content/full/8/8/1218
oestrogen receptor signaling assay
A cellular assay designed to study oestrogen receptor signaling by various gene and protein assays in cells or organisms.
Detection of estrogen levels in tumor cells.
ER signaling assay
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
systems biology analysis
A data analysis technique involving study of biology at the system level; the structure and dynamics of cellular and organismal function.
Kitano (2002) Science 295:1662
PERSON: Nicole Vasilevsky
material component identification
An assay that involves identification of components and materials in a mixture.
Mass spectrometry.
PERSON: Nicole Vasilevsky
http://jp.fujitsu.com/group/fql/en/services/rohs/material/
tissue co-culture with ELISA
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Tissue co-culturing combined with ELISA to assay protein expression.
in situ hybridization
A nucleic acid assay that uses a labeled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough (e.g. plant seeds, Drosophila embryos), in the entire tissue (whole mount ISH).
ISH
PERSON: Nicole Vasilevsky
The pattern of gene expression in a developing organism can be analyzed by ISH.
http://en.wikipedia.org/wiki/In_situ_hybridization
in situ analysis
northern blot analysis
A nucleic acid assay used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample by separating samples by electrophoresis and detection with a hybridization probe complementary to part or the entire target sequence.
Gene expression in a sample can be analyzed by Northern blot.
Northern blot assay
Northern blotting
PERSON: Nicole Vasilevsky
RNA blot
RNA blot analysis
RNA blotting
http://en.wikipedia.org/wiki/Northern_blot
RNA probe
A RNA oligonucleotide that is an RNA segment used to probe for a complementary nucleotide sequence either in the mRNA pool or in the DNA of a cell.
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
Riboprobe
http://www.mondofacto.com/facts/dictionary?riboprobe
US resident role
A role that inheres in a person who maintains residency in the United states.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
US citizen role
A US resident role that inheres in an individual that is a legally recognized as a member of a state, with associated rights and obligations.
PERSON: Nicole Vasilevsky
http://en.wiktionary.org/wiki/citizen
non-US citizen
A US resident role that inheres in an individual who is not a legally recognized subject or national of the United States.
PERSON: Nicole Vasilevsky
https://www.google.com/search?q=residency+status&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a#hl=en&client=firefox-a&hs=Bcx&rls=org.mozilla:en-US:official&q=citizen&tbs=dfn:1&tbo=u&sa=X&ei=micXT_DwMIjUiAK15tDUDw&ved=0CCgQkQ4&bav=on.2,or.r_gc.r_pw.,cf.osb&fp=7b67128a22f602af&biw=1609&bih=794
permanent resident role
An role that inheres in an individual who is not a citizen but who legally resides in another nation on a permanent or extended basis.
PERSON: Nicole Vasilevsky
http://connection.ebscohost.com/us/immigration-restrictions/overview-legal-and-illegal-immigration
non-permanent resident role
A non-US citizen role that inheres in an individual who is residing in a country, but is neither a citizen nor a permanent resident.
PERSON: Nicole Vasilevsky
http://www.irs.gov/taxtopics/tc851.html
student role
A college student.
A role inhering in a person that is realized when the bearer participates a course of study, as in a school, college, university, etc.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/student
undergraduate student role
A college student.
A student role inhering in a person that is realized when the bearer participates in a course of study at a college, university, etc. in pursuit of an associate or bachelor degree.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/student
graduate student role
A PhD student at a university.
A student role inhering in a person that is realized when the bearer participates a course of study at a university or institution in pursuit of an graduate or professional degree.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/student
high school student role
A freshman in high school.
A student role inhering in a person that is realized when the bearer participates in a course of study at a secondary learning institution.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/student
employee role
A role inhering in a person that is realized when the bearer participates in an occupation by which a person earns a living or spends their time.
An employee at a university.
PERSON: Nicole Vasilevsky
http://dictionary.reference.com/browse/employment
faculty role
A professor at a university.
An employee role inhering in a person that is realized when the bearer participates in the teaching and/or administrative force of a university, college, or school.
PERSON: Nicole Vasilevsky
http://dictionary.reference.com/browse/faculty
staff role
A research technician in a lab.
An employee role inhering in a person that is realized when the bearer is employed by an employer.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
post-baccalaureate trainee
A student role inhering in a person that is realized when the bearer participates in a post-baccalaureate training program in pursuit of an additional bachelor degree or new or additional training in a particular field.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
yeast two hybrid screening
A protein interaction detection assay used to discover protein-protein interactions and protein-DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively.
PERSON: Nicole Vasilevsky
Screening proteins that interact with the activation domain of p53.
Yeast two hybrid interaction screening
http://en.wikipedia.org/wiki/Two-hybrid_screening
restriction enzyme digestion
Digestion of DNA at BamHI sites.
Enzymatic cleavage of DNA at specific sequences resulting in restriction fragments with restriction enzymes, which are enzymes isolated from bacteria that recognize specific restriction sequences in DNA. Restriction enzymes play a very important role in the construction of recombinant DNA molecules, as is done in gene cloning experiments.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Restriction_enzyme
transfection
Agent delivery of nucleic acids into cells. Transfection typically involves opening transient pores or holes in the cell membrane, to allow the uptake of material. Transfection can be carried out using calcium phosphate, by electroporation, or by mixing a cationic lipid with the material to produce liposomes, which fuse with the cell membrane and deposit their cargo inside.
PERSON: Nicole Vasilevsky
Transfection of a cell line with a plasmid expressing a gene of interest.
http://en.wikipedia.org/wiki/Transfection
anesthesia machine
An environment control instrument that is used to support the administration of anaesthesia. It contains a breathing system for delivering a gas mixture, including an anesthetic gas, to a patient for inhalation.
An isofluorane machine.
PERSON: Nicole Vasilevsky
http://www.freepatentsonline.com/5568910.html
cage washer
An instrument that is used to clean the cages used to house organisms.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
squeeze chute
An instrument that is used to restrain large animals.
PERSON: Nicole Vasilevsky
Used to restrain animals for tail injections.
chute stock
http://medical-dictionary.thefreedictionary.com/squeeze+chute
anaesthetic vaporiser
A device that delivers a given concentration of a volatile anaesthetic agent, which is which is generally attached to an anaesthetic machine, commonly used for animal experimentation.
PERSON: Nicole Vasilevsky
Used for delivering anesthesia to rodents prior to injection.
enflurane vaporizer
http://en.wikipedia.org/wiki/Anaesthetic_vaporiser
isoflurane vaporizer
animal ventilator
An anesthesia machine with a nose cone.
An instrument designed to control air that is breathed through it or to either intermittently or continuously assist or control pulmonary ventilation.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/ventilator-203
respirator
insect rearing chamber
An instrument designed to provide a temperature controlled chamber for insect rearing.
PERSON: Nicole Vasilevsky
Used to breed insects for experimental purposes.
http://www.biocold.com/fp_insect_chambers.php
small-animal surgery workstation
A workstation used for animal stroke models.
An instrument designed to provide a ventilated small animal surgery table that functions to control, capture and exhaust waste anesthesia gases down and away from the face of personnel when connected to negative air source.
PERSON: Nicole Vasilevsky
http://www.tbjinc.com/Products/Docs/32-26%20DD-ST-M.pdf
live trap
An instrument that is used to catch live animals.
PERSON: Nicole Vasilevsky
Trap wild animals for study.
http://www.shermantraps.com/
animal cage rack
An instrument designed to hold animal cages, while allowing for proper ventillation and access to water. Typically the cage racks have wheels on the bottom for ease of movement.
Mouse cages are stored on an animal cage rack.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
tattoo machine
An instrument designed to permanently tattoo identifying features such as numbers onto an organism.
Laboratory animals can be labeled with a tattoo machine, for identification purposes.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
MASCIS impactor
A device designed to deliver graded reproducible spinal cord contusions to an organism.
NYU Impactor
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Used to study spinal cord injuries.
flow injection system
An autosampler used for automated handling of sample and reagent solutions with a strict control of reaction conditions.
Flow injection into an HPLC apparatus.
PERSON: Nicole Vasilevsky
http://www.flowinjection.com/method2.html
microbalance
A microbalance is an instrument capable of making precise measurements of weight of objects of relatively small mass: of the order of a million parts of a gram.
An instrument used to weigh small quantities of a substance.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Microbalance
cytospin centrifuge
A centrifuge that is used to spin a cell suspension onto a slide for viewing under a microscope.
PERSON: Nicole Vasilevsky
Used in cytology analysis.
http://ricfacility.byu.edu/cytospin.html
tabletop centrifuge
A centrifuge that sits on top of a tabletop or benchtop and have adaptors for tubes ranging from 0.2-100mls.
PERSON: Nicole Vasilevsky
Used to spin samples.
benchtop centrifuge
www.fishersci.com/wps/downloads/segment/.../pdf/Sorvall_TT.pdf
mechanical cell lysis device
A chromatography pump system used to mechanically lyse cells for rapid intracellular protein extraction.
A fast-prep bead beater.
PERSON: Nicole Vasilevsky
Yun et al (2010) Lab Chip 10:1442-1446.
electrophysiology data acquisition system
ADInstruments PowerLab/8SP.
An instrument used to capture and record analog inputs, digital inputs, temperature, humidity, pulse and logic signals, for electrophysiology.
PERSON: Nicole Vasilevsky
multichannel acquisition system
www.microdaq.com/data-logger/data-acquisition.php
electrophoretic transfer cell
A transfer apparatus used in a Western blot.
An electrophoresis system designed for the electrophoretic transfer of macromolecules such as DNA, RNA or proteins from agarose or polyacrylamide gels to a membrane.
PERSON: Nicole Vasilevsky
Towbin H, Staehelin T, Gordon J. (1979) Proc Natl Acad Sci U S A. 76(9):4350-4.
transfer apparatus
cold vapor atomic fluorescence spectrophotometry detector
A fluorometer that is used for the analytical technique known as atomic fluorescence spectroscopy (AFS).
CVAFS detector
PERSON: Nicole Vasilevsky
Used to analyze fluorescence from a sample.
http://en.wikipedia.org/wiki/Cold_vapour_atomic_fluorescence_spectroscopy
serum analyzer
A hematology analyzer used to analyze blood serum.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
blood serum analyzer
in vivo bioluminescence imaging system
An image acquisition instrument that is designed for non-invasive in vivo use, to detect bioluminescence, which is based on the expression of luciferase, the light-emitting enzyme of the firefly Photinus pyralis. After the administration of the substrate luciferin, an ATP- and O2-dependent photochemical reaction occurs, resulting in the release of photons by living cells containing luciferase. This photon emission can be detected by a cooled charge-coupled device (CCD) camera, minutes after the administration of the substrate.
Contag et al (1997) Photochem Photobiol 66: 523–531
GFP expressing cells can be visualized by in vivo bioluminescence imaging.
PERSON: Nicole Vasilevsky
in vivo fluorescence imaging system
An image acquisition instrument used to detect fluorescence emission from fluorophores in whole-body living organism.
PERSON: Nicole Vasilevsky
Rao, Dragulescu-Andrasi, Yao. (2007) Curr Opin Biotechnol. 18(1):17-25.
Used to detect GFP in a GFP transgenic mouse.
imager
A workstation set up with a microscope, digital camera and computer.
An instrument that is used for high performance digital imaging and quantitative analysis of labels, such as chemiluminescent, fluorescent, chromogenic, and radioisotopic labels.
PERSON: Nicole Vasilevsky
http://www.raytest.de/bio_imaging/products/image_station_2000_r/image_station_2000_r.html
ultracentrifuge
A centrifuge optimized for spinning a rotor at very high speeds, capable of generating acceleration as high as 1,000,000 g (9,800 km/s²).
PERSON: Nicole Vasilevsky
Used in subcellular fractionation.
http://en.wikipedia.org/wiki/Ultracentrifuge
ultracentrifuge rotor
A device consisting of the rotating part of an ultracentrifuge, which is a high-velocity centrifuge. The ultracentrifuge rotor can hold tubes that are spun around a central axis to separate contained materials of different specific gravities, or to separate colloidal particles or submicroscopic particles.
PERSON: Nicole Vasilevsky
Part of an ultracentrifuge.
http://www.answers.com/topic/ultracentrifuge, http://www.answers.com/topic/centrifuge
video dimension analyzer
An instrument that is a self-contained video processor designed to provide an analog output proportional to the distance between two features perpendicular to the raster lines, in a televised scene. This hardware edge detector tracks blood vessel diameter, and left and right wall thicknesses using an analog video signal. The principle of the instrument is based on sensing optical density changes of the vessel image at a chosen scan line seen on the TV monitor.
PERSON: Nicole Vasilevsky
http://vistaelectronicsco.com/viddimanalyzer.shtml, http://www.livingsys.com/video/vda-10.html
typhoon fluorescence scanner
An instrument which has a multimode scanner with capabilities for storage phosphor, fluorescence, and chemiluminescence detection of gels. The instrument combines laser excitation sources with efficient optics for sensitive fluorescent imaging. Emissions are recorded in an image file for quantitative analysis.
PERSON: Nicole Vasilevsky
http://imagers.salk.edu/typhoon/typhoon-faq.html
temperature controller
A heater or air conditioner.
An instrument used to maintain the temperature of an enclosed space.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/temperature-control
skin temperature sensor
An instrument which allows one to monitor an organism's skin surface temperature during a procedure.
PERSON: Nicole Vasilevsky
http://www.smiths-medical.com/catalog/temperature-probes/disposables/skin/skin-temperature-probes.html
lab rotator
An instrument used for rotation of flasks, test tube racks, beakers, vials, Petri dishes, microwell plates, culture plates, plastic/glass trays, and slides in microbiological, immunological and general clinical applications.
Co-IP reactions are allowed to incubate in a lab rotator, at 4C.
PERSON: Nicole Vasilevsky
http://www.thermoscientific.com/wps/portal/ts/products/detail?navigationId=L10529&categoryId=81886&productId=11954377
roller drum
An instrument used for growing mini preps, as well as tissue and bacterial cultures by the roller tube method.
PERSON: Nicole Vasilevsky
http://www.nbsc.com/rollerdrums.aspx
total internal reflection fluorescence instrument
An instrument used to observe single molecule fluorescence at surfaces and interfaces. The technique is commonly employed to investigate the interaction of molecules with surfaces.
PERSON: Nicole Vasilevsky
TIRF instrument
http://www.olympusmicro.com/primer/techniques/fluorescence/tirf/tirfhome.html
blunt needle end delivery probe
An instrument that can be used for surface measurements, inserted into tissue or used for single vessel measurements.
PERSON: Nicole Vasilevsky
http://www.moor.co.uk/products/monitoring/DRT4/probes
crash cart
A defibrillator is part of a crash cart.
An instrument which has a set of trays/drawers/shelves on wheels used in hospital emergency rooms for transportation and dispensing of emergency medication/equipment at site of medical/surgical emergency for life support protocols.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Crash_cart
defibrillator
An instrument which delivers a therapeutic dose of electrical energy to the heart. This depolarizes a critical mass of the heart muscle, terminates the arrhythmia, and allows normal sinus rhythm to be reestablished by the body's natural pacemaker, in the sinoatrial node of the heart. Defibrillators can be external, transvenous, or implanted, depending on the type of device used or needed.
PERSON: Nicole Vasilevsky
Used on a coding patient.
http://en.wikipedia.org/wiki/Defibrillation
hyfrecator
An instrument that is a low-powered medical apparatus used in electrosurgery on conscious patients, usually in an office setting. It works by emitting low-power high-frequency A.C. electrical pulses, via an electrode mounted on a handpiece, directly to the affected area of the body. The amount of output power needed is adjustable, and the device is equipped with different tips, electrodes and forceps, depending on the electrosurgical requirement.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Hyfrecator
oocyte clamp
An instrument that is designed for two-electrode, whole-cell voltage clamping of Xenopus oocytes.
Commonly used as host cells for the study of ion channels.
PERSON: Nicole Vasilevsky
http://www.warneronline.com/product_info.cfm?id=168&CFID=5491126&CFTOKEN=40558311
molecular assay
An assay that generates data about the presence, abundance, structure, function, or activity of biological molecules, or a process that occurs at a molecular level of granularity.
PCR.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
multiparameter monitor
A monitoring device that monitors vital signs, such as temperature, blood pressure, and ECG.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
ECG monitor
A monitoring device which non-invasively records the transthoracic interpretation of the electrical activity of the heart over time captured and externally recorded by skin electrodes.
PERSON: Nicole Vasilevsky
Used to measure heart function.
http://en.wikipedia.org/wiki/Electrocardiography
cauters
An instrument that is a hot iron for searing or cauterizing.
Blood vessels are cauterized during surgery to prevent excessive bleeding.
PERSON: Nicole Vasilevsky
http://www.lexic.us/definition-of/cauter
blood pressure transducer
A blood pressure cuff.
An instrument that provides consistent and accurate readings during invasive blood pressure monitoring.
PERSON: Nicole Vasilevsky
http://www.utahmed.com/deltran.htm
blood pressure monitor
A blood pressure cuff.
A monitoring device used to measure blood pressure, comprising an inflatable cuff to restrict blood flow, and a mercury or mechanical manometer to measure the pressure.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Blood_pressure_monitor
telemetry system
An instrument that allows remote measurement and reporting of information.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Telemetry
thermomixer
A heating instrument that can be programmed to shakes tubes, which usually contain solutions, at a specified speed and for a specified time, in order to mix the contents.
A thermomixer can be used to mix and incubate bacterial cultures.
PERSON: Nicole Vasilevsky
http://vwrlabshop.com/eppendorf-thermomixer-and-thermomixer-r-mixers-brinkmann/p/0020628/
gas mixer
An instrument that is used to create custom respiratory gas mixtures.
PERSON: Nicole Vasilevsky
http://www.cwe-inc.com/images/GSM-3.pdf
potentiostat
An instrument used to control a three electrode cell and run electroanalytical experiments.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Potentiostat
chip programmer
An instrument that configures programmable non-volatile circuits.
PERSON: Nicole Vasilevsky
Programming of circuits, such as EPROMs, EEPROMs, Flashs, PALs, FPGAs or programmable logic circuits.
http://en.wikipedia.org/wiki/Programmer_%28hardware%29
hand brake
A device for slowing or stopping motion, as of a vehicle, especially by contact friction which is adminstered by hand.
An emergency brake in a car.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/brake
surface grinder
An instrument used to produce a smooth finish on flat surfaces. It is a widely used abrasive machining process in which a spinning wheel covered in rough particles (grinding wheel) cuts chips of metallic or non metallic substance from a workpiece, making a face of it flat or smooth.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Surface_grinding
lathe
An instrument type which spins the workpiece to perform various operations such as cutting, sanding, knurling, drilling, or deformation with tools that are applied to the workpiece to create an object which has symmetry about an axis of rotation.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Lathe
milling machine
An instrument which is a machine tool used to machine solid materials.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Milling_machine
soxhlet extractor
An instrument designed for the extraction of a lipid from a solid material.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Soxhlet_extractor
UV-ozone surface cleaner
An instrument designed to remove molecular levels of contamination to achieve the cleanest possible probes and surfaces.
PERSON: Nicole Vasilevsky
http://www.bioforcenano.com/index.php?id=290
spin coater
An instrument used to apply uniform thin films to flat substrates by centrifugal force.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Spin_coating
spinner
mask aligner
An instrument used in the production of semiconductor integrated circuits.
PERSON: Nicole Vasilevsky
http://www.abmfg.com/
accelerated solvent extraction system
An instrument which is fully automated and uses common solvents to rapidly extract solid and semisolid samples.
Extraction of solvents for histological sample preparation.
PERSON: Nicole Vasilevsky
http://chromatographyonline.findanalytichem.com/lcgc/App+Notes+Enviro/Accelerated-Solvent-Extraction-Sample-Preparation-/ArticleStandard/Article/detail/479946
gravity convection oven
An oven that gently moves air vertically through the oven chamber to heat samples.
PERSON: Nicole Vasilevsky
http://www.amazon.com/LINDBERG-BLUE-GRAVITY-CONVECTION-MICROPROCESSOR/dp/B003NVENII
lipid bilayer workstation
An instrument that allows for pico- or nano-scale charge current measurements across an artifical lipid membrane through reconstituted, ion-conducting single channels. Currents are measured via silver electrodes, digitized and amplified.
PERSON: Nicole Vasilevsky
http://www.instmeth.uni-freiburg.de/methods/iocbc/oe/m-plb-workstation.html
beveler machine
An instrument consisting of two rules or arms, jointed together at one end, and opening to any angle, for adjusting the surfaces of work to the same or a given inclination.
Beveled edges are a common aesthetic nicety added to window panes and mirrors.
PERSON: Nicole Vasilevsky
bevel square
http://www.websters-online-dictionary.org/definitions/bevel?cx=partner-pub-0939450753529744%3Av0qd01-tdlq&cof=FORID%3A9&ie=UTF-8&q=bevel&sa=Search#922
electromyography device
A instrument used for evaluating and recording the electrical activity produced by skeletal muscles.
PERSON: Nicole Vasilevsky
Used to measure muscle function.
http://en.wikipedia.org/wiki/Electromyography
polygraph
A lie detector.
An instrument for the simultaneous electrical or mechanical recording of several involuntary physiological activities, including blood pressure, skin resistivity, pulse rate, respiration, etc.
PERSON: Melissa Haendel
http://en.wikipedia.org/wiki/Polygraph
oxygraph system
A measurement instrument used to measure oxygen evolution or consumption from liquid-phase samples in cellular respiration and photosynthesis research applications.
PERSON: Nicole Vasilevsky
http://www.hansatech-instruments.com/oxyg1.htm
oxygen electrode
micro-iontophoresis device
An instrument used to drive positive or negative ions into a tissue, in which two electrodes are placed in contact with tissue, one of the electrodes being a pad of absorbent material soaked with a solution of the material to be administered, and a voltage is applied between the electrodes.
PERSON: Nicole Vasilevsky
http://encyclopedia2.thefreedictionary.com/iontophoresis
stimulus isolator
An instrument that provides isolated electrical stimulation to tissues in either constant currents or constant voltages.
PERSON: Nicole Vasilevsky
http://www.harvardapparatus.com/webapp/wcs/stores/servlet/haicat3_10001_11051_37793_-1_HAI_Categories__37757_37791
stimulator
An instrument used for nerve and muscle stimulation procedures.
Can be used to study nerve or muscle function.
PERSON: Nicole Vasilevsky
http://www.grasstechnologies.com/products/stimulators/stims88x.html
rapid multi-assay analyzer
An instrument used to measure key analytes in clinical research studies, such as glucose, triglycerides, pyruvate, etc. It measures the rate of oxygen consumption, which is directly proportional to the substrate concentration.
PERSON: Nicole Vasilevsky
http://www.analox.com/downloads/gm7uk.pdf
microcapillaries
An device consisting of a capillary tube with a very small diameter that is used for various applications including microscopy and HPLC.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/capillary
CNC Lathe
A lathe that is designed to use modern carbide tooling and fully use modern processes. The part may be designed and the toolpaths programmed by the CAD/CAM process, and the resulting file uploaded to the machine, and once set and trialled the machine will continue to turn out parts under the occasional supervision of an operator.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Lathe_%28metal%29
laser doppler flowmeter
An image acquisition instrument used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy
fast protein liquid chromatography instrument
A liquid chromatograhy column that is used to separate or purify proteins from complex mixtures. FPLC is a type of liquid chromatography where the solvent velocity is controlled by pumps to control the constant flow rate of solvents. The solvents are accessed through tubing from an outside reservoir.
Can be used for protein identification and characterization.
FPLC
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fast_protein_liquid_chromatography
microelectrode
A measurement device that consists of a very small electrode, often used to study electrical characteristics of living cells and tissues.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/microelectrode
stadiometer
A measurement device that measures the length of curves, dashes, etc., by running a toothed wheel along them.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/stadiometer
laser doppler blood flow monitor
A measurement device used for non-invasive, continuous measurement of microcirculation. The technique is based on the values of the Doppler Effect of low-power laser light scattered randomly by static structures and moving tissue particulates.
PERSON: Nicole Vasilevsky
http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi
nitric oxide monitor
A measurement instrument that measures nitrogen oxide by employing polarography, which measures concentration of nitrogen oxide in blood and any other portion of a living organism.
PERSON: Nicole Vasilevsky
http://www.intermedical.co.jp/homepage/products/im/imn-111-e.html
respirometry system
A flow meter.
A measurement instrument that is used to obtain estimates of the rates of metabolism of vertebrates, invertebrates, plants, tissues, cells, or microorganisms via an indirect measure of heat production (calorimetry).
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Respirometry
carbon dioxide analyzer
A measurement instrument that is used to detect carbon dioxide concentration in a given environment.
PERSON: Nicole Vasilevsky
Used to measure CO2 levels in an incubator.
http://www.thomasnet.com/products/analyzers-carbon-dioxide-1645506-1.html
oxygen monitor
A measurement device, usually attached to the earlobe or fingertip, that measures the oxygen saturation of arterial blood.
PERSON: Nicole Vasilevsky
Patients admitted to a hospital are routinely monitored for oxygen levels.
blood oxygen monitor
http://en.wikipedia.org/wiki/Pulse_oximeter
pulse oximeter
blood analyzer
A hematology analyzer.
A measurement device that tests a blood sample for certain predetermined constituents.
PERSON: Nicole Vasilevsky
http://www.nasa.gov/mission_pages/station/science/experiments/PCBA.html
fixed stage microscope
A microscope which contains a small platform on a microscope where the specimen is mounted for examination. Commonly used for electrophysiological research, such as patch clamp experiments on nerve cells, examinations of brain sections, and for measuring electrical signals on cells.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/microscope+stage, http://www.dddmag.com/Product-Axio-Examiner-Fixed-Stage-Microscope-908.aspx
surgical microscope
A microscope used to visualize fine structures within the area of a surgical procedure.
PERSON: Nicole Vasilevsky
http://www.zeiss.com/C125716F004E0776/0/3168C434988E2189C1257177006C0635/$File/Innovation_14_18.pdf
sample preparation system
A microplate dispenser workstation that can be used to distribute quantitative liquid samples with an extraordinary level of precision and reproducibility.
PERSON: Richard Pearse
PERSON: Scott Hoffmann
microwave sample preparation system
An instrument used for for sample preparation applications such as digestion, extraction, evaporation or drying of sample materials.
Digestion of tissues prior to DNA extraction.
PERSON: Nicole Vasilevsky
http://www.beverageonline.com/product.mvc/Multiwave-3000-Microwave-Sample-Preparation-P-0001?VNETCOOKIE=NO
microwave tissue processor
A microwave sample preparation system used for processing tissues for immunohistochemistry and microscopic examination.
PERSON: Nicole Vasilevsky
Panja, Sriram, Saraswathi, Sivapathasundharam (2007) JOMFP 11: 15-17
CNC milling machine
A milling machine tool used to machine solid materials. CNC milling machine has features such as an automatic tool changer (ATC) that includes a tool magazine (carousel), and sometimes an automatic pallet changer (APC).
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Milling_machine
machining center
mill
miller
preclinical MRI scanner
An MRI scanner which is compact and can sit on a desktop and is used for preclinical magnetic resonance imaging (MRI) within molecular imaging laboratories for routine preclinical and molecular imaging in biomedical and pharmaceutical applications.
Can be used for preclinical testing of new drugs, to study effect on the brain.
PERSON: Nicole Vasilevsky
http://www.dotmed.com/news/story/14254/
PET animal imager
A small animal image acquisition device that uses positron emission tomography (PET) for non-invasive, in vivo imaging of small animals for the purposes of research or pre-clinical applications.
Can be used to assess cell, tissue, and organ function in vivo in animals after experimental treatment.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Positron_emission_tomography
SPECT animal imager
A SPECT scanner that is used for non-invasive, in vivo imaging of small animals for the purposes of research or pre-clinical applications.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
2D gel electrophoresis apparatus
A protein separation apparatus employed for two-dimensional protein separation.
An instrument that can be used in proteomics, to run a 2D gel.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Two-dimensional gel electrophoresis apparatus
end over end rotator
A lab rotator that provides provide 360° vertical rotation, used to mix samples.
Can be used to mix samples during a co-IP reaction.
PERSON: Nicole Vasilevsky
http://www.selectscience.net/products/end-over-end-rotator/?prodID=11939
electromyography stimulator
An instrument used to stimulate the electrical activity of muscles.
PERSON: Nicole Vasilevsky
http://www.emedicinehealth.com/electromyography_emg/article_em.htm
planetary mixer
An instrument designed to mix, disperse and degas materials in seconds to minutes, in a sealed or lid-less container such as a jar, beaker, syringe tube or cartridge.
PERSON: Nicole Vasilevsky
http://www.intertronics.co.uk/products/thiare25001.htm
profilometer
An instrument used to measure a surface's profile, in order to quantify its roughness.
PERSON: Nicole Vasilevsky
Surface profiler
http://en.wikipedia.org/wiki/Profilometer
vacuum coating system
PERSON: Nicole Vasilevsky
This device uses vacuum drying or sputtering to deposit materials on a sample's surface to increase contrast for electron microscopy.
http://www.leica-microsystems.com/products/em-sample-preparation/biological-specimens/low-temperature-techniques/freeze-etchingfracture/details/product/leica-em-med020/
shadow caster
finger stimulator
A stimulator designed for finger stimulation, that can be used in classical conditioning animal models.
An aversive electric stimulator, designed for finger stimulation, using in classical conditioning animal models.
PERSON: Nicole Vasilevsky
UV/vis spectrophotometer
A spectrophotometer which measures emissions in the ultraviolet-visible spectral region.
DNA can be quantified on a UV spectrophotometer.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Ultraviolet%E2%80%93visible_spectroscopy
ultraviolet-visible spectrophotometer
temperature monitor
A measurement device that is capable of continuous monitoring of multiple temperatures
A thermometer.
PERSON: Nicole Vasilevsky
http://www.vitalmedikal.com/Deroyal_Temp_Monitoring.pdf
inhalation chamber
An environmental chamber used to administer aerosolized agents or particles.
Can be used to administer anesthesia.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
hypoxic chamber
An environmental chamber used to adminster microaerophilic (hypoxic) conditions for research purposes.
PERSON: Nicole Vasilevsky
http://www.ruskinn.com/prod_concept1000invivo2.php
heat therapy pump
An instrument that supplies water of a controlled temperature through hoses to a pad that it applied to the patient for localized warming for pain treatment.
PERSON: Nicole Vasilevsky
http://www.alldaymedical.com/heat-cold-therapy/heating-cooling-systems/gaymar-t-pump-localized-heat-therapy-system.html
image plate detector
An image acquisition device used to detect single crystal diffraction measurements of large and small molecules.
PERSON: Nicole Vasilevsky
http://www.rayonix.com/products/mar345.htm
fourier transport infrared spectrometer
An infrared spectrophotometer that collects spectra based on measurements of the coherence of a radiative source, using time-domain or space-domain measurements of the electromagnetic radiation or other types of radiation.
FT-IR spectrometer
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fourier_transform_spectroscopy
virtual reality instrument
An instrument that uses computer-simulated environments to simulate reality or imaginary places.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Virtual_reality
video splitter
An instrument used to take high definition video from a single HDMI media source and direct it to 2 separate HD TVs or displays.
PERSON: Nicole Vasilevsky
http://www.iogear.com/video-splitter.htm
low temperature freezing
A -80C lab freezer.
A material processing technique involving freezing a specimen or sample to sub zero temperatures, commonly to -80C or on liquid nitrogen.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
in vitro transcription
Biomolecule synthesis of RNA in vitro used for applications such as can be used in blot hybridizations and nuclease protection assays.
PERSON: Nicole Vasilevsky
http://www.ambion.com/techlib/basics/transcription/index.html
in vitro translation
Biomolecule synthesis of proteins in vitro, in cell-free extracts, which can be used for applications such as rapid identification of gene products (e.g., proteomics), localization of mutations through synthesis of truncated gene products, protein folding studies, and incorporation of modified or unnatural amino acids for functional studies.
Can be used for protein-protein interaction analysis, like a GST-pull down assay.
PERSON: Nicole Vasilevsky
http://www.ambion.com/techlib/basics/translation/index.html
electrophoretic gel mobility shift
A molecular assay used to study protein-DNA or protein-RNA interactions. This procedure can determine if a protein or mixture of proteins is capable of binding to a given DNA or RNA sequence, and can sometimes indicate if more than one protein molecule is involved in the binding complex.
EMSA
PERSON: Nicole Vasilevsky
Protein-DNA interactions can be determined using an EMSA.
gel shift assay
http://en.wikipedia.org/wiki/Electrophoretic_mobility_shift_assay
electro-elution
Elution of nucleic acids or a protein sample from a gel by electrophoresis.
Nucleic acids can be extracted from an agarose gel by electro-elution.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electroelution
material surface analysis
A materials assay used to analyze the surface of materials by methods such as x-ray photoelectron spectroscopy (XPS, also known as ESCA, electron spectroscopy for chemical analysis), auger electron spectroscopy (AES), and secondary ion mass spectrometry (SIMS).
An photoelectron spectrometer can be used for material surface analysis.
PERSON: Nicole Vasilevsky
http://www.materialinterface.com/
drug combination effect modeling
A data analysis technique used for identifying and quantitating departures from additivity (i.e., synergism and antagonism) when drugs having like effects are given in combination.
Can be used to test if specific drugs are more effective when used in combination, rather than separately.
PERSON: Nicole Vasilevsky
Plummer and Short (1990) J Pharmacol Methods. 23(4):297-309.
microelectrode positioning system
A device used to position microelectrodes for electrophysiology recording.
PERSON: Nicole Vasilevsky
http://npielectronic.com/
plasma etcher
An instrument used to fabricate integrated circuits.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Plasma_etching
post-graduate student trainee role
A post-doctoral fellow.
A student role inhering in a person that is realized when the bearer participates in a post-graduate training program in pursuit of new or additional training in a particular field, such as a post-doctoral fellowship.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
dsRNA library
PERSON: Melissa Haendel
PMID: 16607398; Echeverri CJ, Perrimon N. Nat Rev Genet. 2006 May;7(5):373-84.
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi library that is comprised of double-stranded RNA molecules, where the dsRNA molecules may or may not be in constructs.
dsRNA libraries are transfected into cells to knockdown gene expression, but a concern with using libraries is off target effects.
protein mixture
A polyclonal antibody.
A protein reagent that contains more than one species of protein mixed together in a single container.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
purified protein reagent
A protein reagent that contains a single species of protein.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
Purified insulin protein.
phenotype characterization
An organismal assay that involves characterization of a phenotype; any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest). Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two.
Characterization of the phenotype is often done in transgenic or knockout mice.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Phenotype
demineralized tissue preparation
Histological sample preparation that removes dissolved salts from tissue.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/demineralize
transcriptional activation assay
A molecular assay used to determine if interacting proteins can transcriptionally activate a target gene. One target protein is fused to an activation domain and another target protein is fused to a DNA binding domain and if the two proteins interact, the gene target will be activated and detected by a reporter.
A technique used to determine if a protein functions as a transcription factor.
He and Li (2008) Methods in Molecular Biology 439:327-337
PERSON: Nicole Vasilevsky
chromatin immunoprecipitation
An immunoprecipitation technique used to determine whether a given protein binds to or is localized to a specific DNA sequence in vivo.
CHIP assay
ChIP
Chromatin IP
PERSON: Nicole Vasilevsky
Used to determine if a transcription factor binds a promoter.
http://www.bio.brandeis.edu/haberlab/jehsite/chIP.html
embryo culture
Culture and propogation of embryos performed immediately following egg retrieval prior to in vitro fertilization (IVF). The eggs and sperm are combined to produce a fertilized egg (known as an zygote). Once a zygote has been formed, the culture process will continue in order to encourage the growth of the zygote into an embryo. Lasting from 2 to 5 days, the embryo culture process is vital to the success of any IVF procedure.
PERSON: Nicole Vasilevsky
http://www.sharedjourney.com/define/culture.html
DNA footprinting
A nucleic acid assay that involves treating live cells with a chemical agent that causes DNA damage. If a protein is bound to the DNA, it can protect the strands it covers from this damage, and its binding site can be deduced.
PERSON: Nicole Vasilevsky
Protein-DNA binding sites can be determined by DNA footprinting.
http://mbg.cornell.edu/cals/mbg/research/lis-lab/researchdetails.cfm#CP_JUMP_49328
nuclease protection assay
A nucleic acid assay used to identify individual RNA molecules in a heterogeneous RNA sample extracted from cells. Extracted RNA is mixed with antisense RNA or DNA probes that are complementary to the sequence(s) of interest and the complementary strands are hybridized to form double-stranded RNA (or a DNA-RNA hybrid). The mixture is then exposed to ribonucleases that specifically cleave only single-stranded RNA but have no activity against double-stranded RNA. When the reaction runs to completion, susceptible RNA regions are degraded to very short oligomers or to individual nucleotides; the surviving RNA fragments are those that were complementary to the added antisense strand and thus contained the sequence of interest.
A reaction that is used for simultaneous detection of several RNA species in a sample.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Nuclease_protection_assay
run-on transcription assay
A molecular assay that is conducted to identify the genes that are being transcribed in a cell nucleus at a certain time.
Can be used to detect gene expression after experimental treatment.
Nuclear run on assay
Nuclear run-on assay
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Nuclear_run-on
histone analysis
A protein assay used to analyze which proteins associate with core histones.
PERSON: Nicole Vasilevsky
Post-translational modifications of histone tails are important for epigenetic regulation of gene expression.
Source: Keener et al (1997) Proc Natl Acad Sci 94(25): 13458-13462.
vacuum evaporator
A speed vac sample concentrator.
An instrument used to cause the pressure in a liquid-filled container to be reduced below the vapor pressure of the liquid, causing the liquid to evaporate at a lower temperature than normal.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Vacuum_evaporation
fluorescence compound microscope
A fluorescence microscope in which magnification is achieved in two stages. It utilizes an objective lens, usually several of different power on a turret and an eyepiece that is used to further magnify the image formed by the objective lens.
PERSON: Nicole Vasilevsky
Used to visualize biomolecules.
http://www.microscopehelp.com/thecompoundmicroscope.html
langendorff heart system
An instrument that includes the components for all of the main measurements required from a Langendorff experiment with hearts from small animals such as rats and mice.
PERSON: Nicole Vasilevsky
http://www.adinstruments.com/solutions/research/Langendorff-Heart/
MRI display system
An instrument that uses a projection system for presenting visual stimulation in an MRI machine.
Glucose uptake can be displayed in an MRI display system.
PERSON: Nicole Vasilevsky
http://www.neurospec.com/?p=prodresearch_acqdiag_avotec
energy filtering transmission electron microscope
A transmission electron microscope that produces an image of an object by electron scattering. The contrast is optimized by filtering out the contrast-reducing electrons from the spectrum of transmitted electrons, or by only allowing electrons containing specific information to be used for imaging.
Can be used to image biomolecules.
EFTEM
PERSON: Nicole Vasilevsky
http://www.smt.zeiss.com/c1256e4600305472/Contents-Frame/9c02420a02765bc1c1256e5800335569
critical point dryer
An instrument designed to dry biological specimens precisely and without damage typical of drying by heat alone. The instrument makes use of the equality of liquid and vapor density above the thermodynamic critical point to remove pockets of liquid without expansion (and resulting damage to the sample).
Lyophilization of blood samples.
PERSON: Nicole Vasilevsky
Supercritical processor
http://en.wikipedia.org/wiki/Supercritical_drying
langmuir-blodgett trough
An instrument that is used to compress monolayers of molecules on the surface of a given subphase (usually water) and measures surface phenomena due to this compression. It can also be used to deposit single or multiple monolayers on a solid substrate.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Langmuir-Blodgett_trough
photon counting module
An instrument used to detect photons used for applications such as Single Molecule Spectroscopy.
PERSON: Nicole Vasilevsky
http://picoquant.com/getfs.htm?products/instrumentation.htm
microplate autosampler
An instrument that automatically injects samples into high performance liquid chromatography (HPLC) system.
PERSON: Nicole Vasilevsky
http://www.meadowshplc.com/hplc_instruments_waters_hplc_717.htm
drop shape analysis
A materials assay used to measure contact angles and thereby determine surface energy.
PERSON: Nicole Vasilevsky
www.firsttenangstroms.com/pdfdocs/CAPaper.pdf
flame atomic absorption spectrometer
A spectrophotometer used to detect metals and metalloids in environmental samples.
Detection of mercury levels in a sample.
PERSON: Nicole Vasilevsky
http://www.cee.vt.edu/ewr/environmental/teach/smprimer/aa/aa.html
clinical centrifuge
A centrifuge that has been approved for clinical use.
A centrifuge used to prepare patient samples.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
amplifier
An amplifier connected to a CD player.
An instrument that changes, usually increases, the amplitude of a signal. The relationship of the input to the output of an amplifier, usually expressed as a function of the input frequency, is called the transfer function of the amplifier, and the magnitude of the transfer function is termed the gain.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Amplifier
microelectrode amplifier
Amplifier that measures very small currents or voltage (often in a cell or patch of membrane) and passes that measurement on for recording and analysis. Microelectrode amplifiers may also control current and voltage in current-clamp and voltage-clamp mode.
Can be used in electrophysiology studies.
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
liquid handling system
An automatic pipetting device.
An instrument that is designed to accurately deliver set volumes of liquid to samples.
PERSON: Nicole Vasilevsky
http://www.labcyte.com/Echo_Liquid_Handling_Systems/Default.81.html
data acquisition system
A flow cytometer.
An instrument that converts analog waveforms into digital values for processing.
PERSON: Nicole Vasilevsky
data acquisition device
http://en.wikipedia.org/wiki/Data_acquisition
slide scanner
An instrument that allows film negatives and slides to be converted into digital files.
PERSON: Nicole Vasilevsky
http://www.35mmslidescanner.org/
96-channel pipetting device
An instrument that can automatically pipette predetermined volumes of liquid into 96 wells at a time.
Automated pipetting into a 96-well plate.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
variable mode imager
An instrument which is a high performance gel and blot imager that unites storage phosphor autoradiography technology with four-color fluorescent labeling techniques. It can be used to scan and store phosphor screens, fluorescent DNA and protein gels, chemifluorescent DNA/RNA and protein blots, and chemiluminescent Western blots.
PERSON: Nicole Vasilevsky
http://www.uri.edu/inbre/corelab/equipment/typhoon.shtml
colony picker
An instrument used for contamination-free automatic colony transfer.
PERSON: Nicole Vasilevsky
Used to screen colonies to determine if they express a plasmid of interest.
http://nition.com/en/products/pm-1.htm
focusing optics
Allows focusing on an object with a microscope.
An instrument that allows precise focusing on an object.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
osmium coater
An instrument that is used to coat samples with osmium for scanning electron microscopy.
PERSON: Nicole Vasilevsky
www.2spi.com/catalog/osmium-plasma-coater-opc-60.shtml
animal MRI system
A small-animal image acquisition device used to acquire MRI images.
Acquisition of neuroanatomical images of an animal model.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
lab on a chip
A device that integrates one or several laboratory functions on a single chip. LOCs deal with the handling of extremely small fluid volumes down to less than picoliters.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Lab-on-a-chip
dissecting surgical microscope
A microscope that allows for maneuverability around the patient during surgery.
PERSON: Nicole Vasilevsky
Used for microinjection into blastocysts.
http://www.peternordland.com/microscope/
wet chemical bench
An instrument that is a specialized bench used for nano-scale manufacturing such as for use in etching and cleaning samples.
PERSON: Nicole Vasilevsky
http://www.nist.gov/cnst/nanofab/nanofab_bench6.cfm
response pad
An instrument that measures a participant's reaction time in hardware and provide additional timing facilities for the stimulus presentation program.
Cedrus RB-830 color response pad.
PERSON: Nicole Vasilevsky
http://www.cedrus.com/responsepads/rb_series.htm
automated light microscopy scan
An image acquisition instrument that is a microscope-based imaging platform designed for fully automated image acquisition and data analysis of biological samples.
Imaging of a biological sample.
PERSON: Nicole Vasilevsky
http://www.microscopy.olympus.eu/microscopes/Life_Science_Microscopes_scan_R.htm
saw
An instrument that uses a hard blade or wire with an abrasive edge to cut through softer materials. The cutting edge of a saw is either a serrated blade or an abrasive. A saw may be worked by hand, or powered by steam, water, electricity or other power.
Can be used to cut up wood.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Saw
wet saw
A saw equipped with a diamond-edged carbide blade which has continually recirculating "fountain" of water to keep the blade and materials cool and to reduce the dust and flying particles and is used to cut hard materials such as tile.
PERSON: Nicole Vasilevsky
http://homerenovations.about.com/od/toolsbuildingmaterials/f/wettilesaw.htm
precision trim saw
A saw that precisely cuts and is used for high-quality commercial applications or general trim work that demands precise cuts.
PERSON: Nicole Vasilevsky
http://justsawblades.com/systimatic/precision_trim.htm
mineralized tissue thin sectioning system
An instrument that creates precise, thin sections, down to 35μm, of a wide variety of geological specimens such as rocks and minerals, ceramics, refractories, concrete, etc.
PERSON: Nicole Vasilevsky
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=6&ved=0CEQQFjAF&url=http%3A%2F%2Fwww.instrument.com.cn%2Fdownload.asp%3Furl%3D%252FShow%252FLiterature%252FC59226.pdf&ei=Cl3FTtjdFYGmiQL9wKnFBQ&usg=AFQjCNEt5OiDCb2XerYyOKOfWqmex4bP1w&sig2=U1lPRRXmhp-V9V_3aX0Fzw
transcranial magnetic stimulator
A stimulator used to noninvasively cause depolarization in the neurons of the brain. TMS uses electromagnetic induction to induce weak electric currents using a rapidly changing magnetic field; this can cause activity in specific or general parts of the brain with minimal discomfort, allowing the functioning and interconnections of the brain to be studied.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Transcranial_magnetic_stimulation
impactor device
An instrument designed to deliver graded reproducible spinal cord contusions.
PERSON: Nicole Vasilevsky
Used for a rodent spinal cord injury model.
http://keck.rutgers.edu/MASCIS/mascis.html
location tracking device
A location tracking device on the iPhone.
An instrument used to determine or monitor the location of a person or an object or the status of an object.
PERSON: Nicole Vasilevsky
www.austlii.edu.au/au/legis/cth/consol_act/sda2004210/s6.html
door sensors
A sensor to measure opening and closing of a door.
An instrument that is affixed to a door that will sense when the door is opened.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
motion sensors
An instrument that senses motion by measuring change in speed or vector of an object or objects in the field of view.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Motion_sensor
home computer tracking device
A location tracking device used for home computers.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
medication tracking device
A location tracking device used for medication.
Eagle-curator (Nicole Vasilevsky)
PERSON: Nicole Vasilevsky
automated mercury analysis system
An instrument that uses automated technology to determine trace mercury levels in samples.
Detection of mercury in a marine sample.
PERSON: Nicole Vasilevsky
http://www.mercury-instrumentsusa.com/AULA254.htm
electrophysiology station
An instrument used to study the electrical properties of biological cells and tissues. It involves measurements of voltage change or electric current on a wide variety of scales from single ion channel proteins to whole organs like the heart. In neuroscience, it includes measurements of the electrical activity of neurons, and particularly action potential activity.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electrophysiology
high-speed motion picture camera
A video camera that takes repeated pictures at high speed.
PERSON: Nicole Vasilevsky
http://www.charlesedisonfund.org/tomedisonbio/ch12.html
protein spot cutter
A 2D spot cutter, used for mass spectrometry.
An instrument that accurately locates and excises protein bands or spots from 1-D and 2-D gels or blots for downstream processing and analysis.
PERSON: Nicole Vasilevsky
http://www.bio-rad.com/prd/en/US/adirect/biorad;jsessionid=PYxzMKnGvPxfn8mLQQ8z9J2Cbdv246ZJJQMLkFyVV2YZw93nQsSn!607464423?cmd=BRCatgProductDetail&vertical=LSR&javascriptDisabled=true&entryPoint=adirect&lang=en&ts=1&country=US&catID=d3f27dd1-a47f-4fb7-9ffd-a3bdf436ea02&messageType=BRCatgProductDetail
inductively coupled plasma mass spectrometer
A mass spectrometer that is highly sensitive and capable of the determination of a range of metals and several non-metals at concentrations below one part in 1012 (part per trillion). It is based on coupling together an inductively coupled plasma as a method of producing ions (ionization) with a mass spectrometer as a method of separating and detecting the ions.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Inductively_coupled_plasma_mass_spectrometry
inverted stereo microscope
A stereo microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up.
An optical stereo microscope.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Inverted_microscope
freezer
An instrument that consists of a thermally insulated compartment, cabinet, or room in which a subfreezing temperature is maintained for the rapid freezing and storing of perishable items.
PERSON: Nicole Vasilevsky
Storage of perishable items in a freezer.
http://www.answers.com/topic/freezer
obsoleting because its a common resource
ultra low temperature freezer
A freezer in the minus 45 to minus 85 celcius temperature range.
PERSON: Marc LePape
PERSON: Nicole Vasilevsky
Used to for long-term storage biological samples.
film scanner
An instrument that allows film to be converted into digital files.
PERSON: Nicole Vasilevsky
Scanning a photograph.
http://www.35mmslidescanner.org/
flatbed scanner
A device that optically scans images, printed text, handwriting, or an object, and converts it to a digital image.
PERSON: Nicole Vasilevsky
Used to scan photographs.
http://en.wikipedia.org/wiki/Flatbed_scanner
scanning camera
An instrument designed for applications in the life sciences, in particular, it has been engineered to create high-quality images of 2-D Fluorescence Difference Gel Electrophoresis (DIGE) gels.
PERSON: Nicole Vasilevsky
http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/2d_electrophoresis~scanners~ettan_dige_imager?OpenDocument&parentid=63005642&moduleid=166483
genotype analysis platform
A device used for determinations of nucleotide acid sequences of single-nucleotide polymorphisms.
PERSON: Nicole Vasilevsky
Rom, W.N. (ed.). Environmental and occupational medicine. (4th ed.) Philadelphia: Lippincott, Williams, & Wilkins.
Such as a PCR machine.
non viral organism
A unicellular or multicellular individual living system that is capable of replicating or reproducing and growth and maintenance in the right environment. Examples: animal, plant, bacteria, fungus.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
phone sensor
An instrument used to track phone calls.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
binocular display system
An instrument used in MRI research, to convey light to the subject's eyes. The subjects view the display apparatus through lenses that serve as a set of binoculars. The purpose is to increase the visual angle subtended by the stimulus at the eye of the subject.
Functional MRI, By Chrit T. W. Moonen, Peter A. Bandettini
PERSON: Nicole Vasilevsky
human biological specimen
A tumor derived from a human.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Primate biological specimen that was derived from a human.
human biospecimen
mouse biological specimen
Biological specimen that was derived from a mouse.
Heart tissue derived from a mouse.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
mouse biospecimen
primate biological specimen
Biological specimen that was derived from a primate.
Heart tissue procured from a monkey.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
primate biospecimen
non-binocular display system
An instrument used in MRI research, to convey light to the subject's eyes using a non-binocular display system such as having the subjects view the display apparatus (LCD or CRT) through fiber optic cable or through a rear-projection screen.
Functional MRI, By Chrit T. W. Moonen, Peter A. Bandettini
PERSON: Nicole Vasilevsky
chiller
An instrument that recirculates chilled fluids that is used for applications requiring heat removal across a wide temperature range.
PERSON: Nicole Vasilevsky
http://www.thermo.com/eThermo/CMA/PDFs/Various/File_51918.pdf
independent cooling and heating system
An instrument used for cooling and heating of lab samples, specifically for test tubes.
PERSON: Edgar Miranda
PERSON: Nicole Vasilevsky
X-ray film processor
An instrument used to develop images that have been exposed to x-ray film.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Used to develop a Western blot exposed to x-ray film.
digital recording transcribing kit
An instrument used to digitally record speech for transcription.
PERSON: Nicole Vasilevsky
Transcription of a patients medical records.
http://www.beachaudio.com/Philips/Lfh9397-00b-p-302833.html?utm_source=froogle&utm_medium=cpc&utm_campaign=lfh9397-00b&utm_content=atr
digital recorder
A voice recorder.
An instrument used to digitally record speech.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
skinfold calipers
A measurement instrument used to assess body fat.
PERSON: Nicole Vasilevsky
http://www.sport-fitness-advisor.com/bodyfatcalipers.html
automated blood pressure cuff
An instrument that is used to measure blood pressure, where the cuff automatically inflates.
PERSON: Nicole Vasilevsky
http://www.consumersearch.com/blood-pressure-monitors/review
fluorescence camera
An microscope digital camera designed for low-light life science imaging applications.
Images of GFP expressing cells can be captured with a fluorescence camera.
PERSON: Nicole Vasilevsky
http://www.directindustry.com/prod/photometrics/high-resolution-fluorescence-camera-for-microscopy-35150-220299.html
fluidics platform
A fluidics platform on a flow cytometer.
An instrument that uses fluid or compressible medium to perform analog or digital operations similar to those performed with electronics.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fluidics
gas analysis system
A measurement device that provides accurate and reliable data for vacuum process monitoring, process diagnostics, and leak detection in semiconductor manufacturing.
PERSON: Nicole Vasilevsky
http://www.inficongasanalyzers.com/en/transpector2gasanalysis.html
body composition analyzer
A measurement instrument that measures weight into muscle mass, water, and body fat.
PERSON: NIcole Vasilevsky
Sliding calipers are used to measure body fat.
http://www.tanita.com/en/body-composition-analyzer/
blood lipid analyzer
A blood anlayzer that is used to measure cholesterol and triglyceride levels in the blood.
Allows field measurement of blood lipids (total Cholesteral, HDL, LDL, Triglycerides) & glucose.
PERSON: Nicole Vasilevsky
http://www.emedicinehealth.com/cholesterol_tests/article_em.htm
heart rate recorder
A measurement device used to acquire and store the average heart rate of a subject during normal daily activities.
Baharestani et al (1979) Medical and Biological Engineering and Computing 17: 719-723
PERSON: Nicole Vasilevsky
teaching microscope
A microscope with multiple binocular heads simultaneously displaying the same microscopic image.
Histology sections can be simultaneously viewed with a teaching microscope.
PERSON: Nicole Vasilevsky
http://www.teachingmicroscopes.com/
microsurgical instrument
An instrument used to perform microsurgery.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
To be logically defined based on its participation in a microsurgical process.
dart gun
A tranquilizing gun.
An instrument that fires a dart.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Dart_gun
coherence tomography scanner
An optical microscope used to obtain sub-surface images of translucent or opaque materials at a resolution equivalent to a low-power microscope.
PERSON: Nicole Vasilevsky
Used to image biological samples.
http://en.wikipedia.org/wiki/Optical_coherence_tomography#Laypersons_explanation
polarized light camera
An image acquisition instrument used to make clear demarcation between regions on an image.
PERSON: Nicole Vasilevsky
http://www.bme.ogi.edu/biomedicaloptics/biophotonics/projects.html#polcam
V-blender
An instrument that is a type of tumble mixer commonly used in industrial processes to mix pharmaceutical materials.
PERSON: Nicole Vasilevsky
http://www.pharmainfo.net/%5Bvocab-raw%5D/v-blender-2-d-simulation
dissolution tester
An instrument used to measure the stability of the investigational product during drug formulation tool in the process of drug discovery.
PERSON: NIcole Vasilevsky
http://en.wikipedia.org/wiki/Dissolution_testing
flow through cell apparatus
A disolution testing instrument used to provide a controlled hydrodynamic environment and renewable solvent stream to the sample.
PERSON: Nicole Vasilevsky
www.dissolutiontech.com/DTresour/.../DT200505_A05.pdf
sieve shaker
An instrument used to assess the particle size distribution (also called gradation) of a granular material.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Sieve_analysis
disintegrator
An instrument used to break-up tablets to get them into solution for use in drug formulation.
Dilution of a tablet in water.
PERSON: Nicole Vasilevsky
http://www.pharmainfo.net/tablet-evaluation-tests/disintegration
flow meter
An instrument used to measure linear, nonlinear, mass or volumetric flow rate of a liquid or a gas.
PERSON: Nicole Vasilevsky
http://www.omega.com/prodinfo/flowmeters.html
spray dryer
An instrument used to produce a dry powder from a liquid or slurry by rapidly drying with a hot gas.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Spray_drying
rotary evaporator
An instrument used in chemical laboratories for the efficient and gentle removal of solvents from samples by evaporation.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Rotary_evaporator
ultrasonic cleaner
An instrument that uses ultrasound (usually from 20–400 kHz) and an appropriate cleaning solution to clean delicate items.
An instrument used for precision cleaning of instruments.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Ultrasonic_cleaning
stoke granulator
An instrument that is designed for the reduction of both wet and dry materials into a granular product to a specific size distribution.
PERSON: Nicole Vasilevsky
http://www.ccstabletpress.com/model-43-6.html
turbula mixer
An instrument used for exacting powder blending and mixing applications.
PERSON: Nicole Vasilevsky
http://www.glenmills.com/index-turbula.shtml
high shear granulator
An instrument consisting of an inline or batch high shear mixer and a fluid bed dryer. In a granulation process, only the solid component of the mixture is required. Fluid is used only as an aid to processing. The high shear mixer processes the solid material down to the desired particle size, and the mixture is then pumped to the drying bed where the fluid is removed, leaving behind the granular product.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/High_shear_mixer#High_shear_granulators
automated microbiology analysis system
An instrument used to automate reading and interpretation of antibiotic susceptibility tests for bacteria and yeast.
Detection of MRSA in a bacterial culture.
PERSON: Nicole Vasilevsky
http://www.vajrabiometrix.com/biomic.html
diluter
An instrument that makes a solution less concentrated by adding a liquid such as water.
Dilution of a solution.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/Diluter
X-ray confocal optics system
A confocal microscope that is used as a novel three-dimensional X-ray imaging method. The system consists of an X-ray illuminating `sheet-beam' whose beam shape is micrified only in one dimension, and an X-ray full-field microscope whose optical axis is normal to the illuminating sheet beam. An arbitral cross-sectional region of the object is irradiated by the sheet-beam, and secondary X-ray emission such as fluorescent X-rays from this region is imaged simultaneously using the full-field microscope. This system enables a virtual sliced image of a specimen to be obtained as a two-dimensional magnified image, and three-dimensional observation is available only by a linear translation of the object along the optical axis of the full-field microscope.
PERSON: Nicole Vasilevsky
http://scripts.iucr.org/cgi-bin/paper?ia5036
sheet metal shears
An instrument that is designed to cut sheet metal.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
sheet metal scissors
comparitor
An instrument that is an op-amp circuit that compares two inputs and provides a DC output indicating the polarity relationship between the inputs.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/comparitor
laser doppler calibration device
An instrument used for calibrating laser Doppler velocimeters having one or more intersecting beam pairs.
PERSON: Nicole Vasilevsky
http://www.freepatentsonline.com/4600301.html
microplate spectrophotometer
A spectrophotometer that merges microplate formats with a spectrophotometer. It can be used to quantitate nucleic acids in the low UV range, or automatically run spectral scans for peak absorbance measurements without using filters, and perform conventional enzyme immunoassays at virtually any wavelength.
ELISAs are often analyzed on a microplate spectrophotometer.
PERSON: Nicole Vasilevsky
http://www.biotek.com/microplate-spectrophotometers.htm
bipolar electrosurgical generator
An instrument used for biopolar electrosurgery, where both the active electrode and return electrode functions are performed at the site of surgery. In biopolar electrosurgery, the current flows from the generator to the instrument, typically forceps. One tine of the forceps acts as the active electrode and directs the current through the patient tissue to the other tine, which acts as the return electrode and enables the flow to return to the generator to complete the circuit.
Can be used too cut, coagulate, desiccate, or fulgurate biological tissue.
PERSON: Nicole Vasilevsky
http://www.corexcel.com/rw/html/body_electrosurgery_page1.htm
motorized microscope stage
An instrument that contains a small motorized platform on a microscope where the specimen is mounted for examination.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/microscope+stage, http://www.dddmag.com/Product-Axio-Examiner-Fixed-Stage-Microscope-908.aspx
coimmunoprecipitation
An assay used to detect protein-protein interactions.
Immunoprecipitation of intact protein complexes (ie: antigen) along with any proteins or ligands that are bound to it.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Immunoprecipitation
transcriptional repression assay
A molecular assay used to determine if transcription factors act as transcriptional repressors.
Assay to determine if Mad4 is a transcriptional repressor.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
histone deacetylase assay
A protein assay designed to measure histone deacetylase complex (HDAC) activity in cell or nuclear extracts, immunoprecipitates or purified enzymes.
Determination of histone deacetylase activity in tumor cells.
PERSON: Nicole Vasilevsky
http://www.biocompare.com/ProductDetails/2043333/HDAC-Activity-Assay-Kit.html?
aquatic housing system
A fish tank.
An instrument used to house aquatic organisms.
PERSON: Nicole Vasilevsky
aquatic habitat
http://www.aquatichabitats.com/
divide and conquer
A data analysis technique used to analyze underdetermined biochemical models in bioinformatics.
Analysis of blood flow modeling.
PERSON: Nicole Vasilevsky
http://bioinformatics.oxfordjournals.org/content/25/4/519.abstract
polar scan system
An instrument that consists of an multi-directional incident ultrasonic scanner used for for the nondestructive evaluation of composites and other materials.
PERSON: Nicole Vasilevsky
http://www.biomedsearch.com/nih/Ultrasonic-polar-c-scan-system/18531816.html
computer server
A RAID server.
A computer, or series of computers, that link other computers or electronic devices together.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Server_%28computing%29
hearing assistance system
A hearing aid.
An instrument that is used for hearing assistance; it includes a transmitter with a microphone and receivers with headphones.
PERSON: Nicole Vasilevsky
http://www.williamssound.com/productdetail.aspx?product_id=312
specimen preparation for storage
A material processing technique that involves preparing specimens for storage at a specific temperature, for either short-term or long-term storage, which may include aliquoting, and labeling the samples.
Aliquoting an antibody and freezing it at -80C.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
multichannel acquisition system
An instrument used to capture and record analog inputs, digital inputs, temperature, humidity, pulse and logic signals, for electrophysiology.
PERSON: Nicole Vasilevsky
www.microdaq.com/data-logger/data-acquisition.php
organic macromolecule
A carbohydrate.
An organic compound with a large relative molecular mass, commonly created by some form of polymerization.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Macromolecule
tissue harvesting
Collection of a tissue from an organism to be used for experimental purposes.
Collection of lymph nodes from a mouse.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Organ_harvesting
parasite culture
Culture and propogation of parasites under controlled conditions in vitro.
Culture of tapeworms.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Cell_culture
animal tattooing
A laboratory animal care technique that involves tattooing animals with identifying features such as numbers to permanently identify animals in an animal colony.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Technique used to label animals in an animal colony.
estrus synchronization
A laboratory animal care technique that involves synchronization of estrus (heat) by manipulating the estrous cycle of female animals so they can be bred at approximately the same time.
PERSON: Nicole Vasilevsky
Used for animal breeding.
http://beef.unl.edu/learning/estrussynch.shtml
transgenic organism
A non-viral organism whose genetic material has been altered using genetic engineering techniques.
A transgenic organism expressing GFP.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Genetically_modified_organism
fiber optics transilumination
A material processing technique that involves the the transmission of light through through fibers made of transparent materials such as glasses and plastics.
FOTI
PERSON: Nicole Vasilevsky
http://www.its.bldrdoc.gov/fs-1037/dir-015/_2213.htm
subdermal chip implantation
Bio-chip implant
Implantation of an integrated circuit device or RFID transponder encased in silicate glass under the skin of an organism. The chip typically contains a unique ID number that can be linked to information contained in an external database, used for identification purposes.
Microchipping pets.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Microchip_implant_%28human%29
growth and developmental manipulation
A material processing technique involving the manipulation of an organism at the developmental stage, for the purpose of understanding organismal development.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Use of transgenic mice to conditionally knockout a gene responsible for development.
in vitro cell stimulation
Agent delivery of a molecule or protein that mimics the endogenous stimulant that is used to stimulate or activate cells in culture.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Pulsing dendrtic cells with peptides in vitro.
computer privacy management
A technique used to protect computer based personal or proprietary information and data from unauthorized viewers.
PERSON: Nicole Vasilevsky
Password protection on a document.
http://www.wisegeek.com/what-is-privacy-management.htm
bronchoalveolar lavage
Bronchial lavage
Can be used to test for a lung infection.
Lavage using a bronchoscope, which is passed through the mouth or nose into the lungs and fluid is squirted into a small part of the lung and then recollected for examination.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Bronchoalveolar_lavage
cerebro-spinal tap
A spinal tap may be performed to determine if a patient has a neurological disorder.
A technique used to collect cerebrospinal fluid (CSF) from an organism, which involves inserting a needle between the third and fourth lumbar vertebrae in the back and extracting a sample of fluid.
CSF collection
Cerebrospinal fluid collection
PERSON: Nicole Vasilevsky
Spinal tap
http://www.weissandnewberrymds.com/services.htm
calcium detector
An instrument used to detect calcium levels in a biological sample.
Can be used to record myocyte calcium and contractility.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
animal physiology monitoring
A physiological assay that is performed to monitor animal physiology in response to experimental conditions.
Blood pressure monitoring in an animal.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Locomotor_activity
real-time PCR
A PCR technique that allows for detection and quantification of PCR products on a real-time basis.
PERSON: Nicole Vasilevsky
Quantitative PCR
Quantitative real time RT-PCR
Quantitative real-time PCR can be used to detect differences in gene expression between samples.
RT-PCR
Real time PCR
http://www.ambion.com/techlib/basics/rtpcr/index.html#1
qPCR
gene delivery
Agent delivery of foreign DNA into host organisms or cells.
PERSON: Nicole Vasilevsky
Transfection of a plasmid into a cell.
http://en.wikipedia.org/wiki/Gene_delivery
nucleofector device
An electroporator that consists of a single cuvette based system that allows efficient transfection of hard-to-transfect cell lines and primary cells with different substrates, e.g. DNA vectors or siRNA oligonucleotides, in low throughput format.
Can be used to transfect T cells with plasmids or oligos.
PERSON: Nicole Vasilevsky
http://www.lonzabio.com/cell-biology/transfection/nucleofectiontrade-products/nucleofector/
urodynamics
A physiological assay that uses a small catheter inserted in the bladder to fill the bladder with water to study the function of the bladder and urethra during filling and urinating, to assess the pelvic floor muscle functions.
PERSON: Nicole Vasilevsky
www.urogyncenter.com/ug-glossary.htm
ultra performance liquid chromatography instrument
A Waters nanoACQUITY UPLC.
A high performance liquid chromatography instrument that can operate at higher pressures, up to 100 MPa (15,000 lbf/in²), or about 1000 atmospheres.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/High-performance_liquid_chromatography
Nucleic acid microarray assay
A nucleic acid assay used to measure changes in gene expression levels, to detect single nucleotide polymorphisms (SNPs), or to genotype or resequence mutant genomes. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles (10−12 moles) of a specific DNA sequence, known as probes (or reporters). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample (called target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. Since an array can contain tens of thousands of probes, a microarray experiment can accomplish many genetic tests in parallel.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/DNA_microarray
microdialysis
A dialysis technique that requires the insertion of a small microdialysis catheter (also referred to as microdialysis probe) into the tissue of interest. The microdialysis probe is designed to mimic a blood capillary and consists of a shaft with a semipermeable hollow fiber membrane at its tip, which is connected to inlet and outlet tubing.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Microdialysis
photo enlarger
An instrument that consists of a specialized transparency projector used to produce photographic prints from film or glass negatives using the gelatin-silver process, or transparencies. All enlargers consist of a light source, normally an incandescent light bulb, a holder for the negative or transparency, and a specialised lens for projection. The light passes through a film holder, which holds a photographic negative or transparency, having been previously exposed in a camera and developed.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Enlarger
print processor
An instrument that tells the spooler to alter a job according to the document data type. It works together with the printer driver to move the spooled print jobs from the hard disk drive to the printer. Localspl.dll is the print processor for all Windows-compatible printing; Sfmpsprt.dll is used to print to Apple devices.
PERSON: Nicole Vasilevsky
http://technet.microsoft.com/en-us/library/cc976744.aspx
capillary electrophoresis laser-induced fluorescence assay for amino acid analysis
A protein assay used to identify and quantitate amino acids at amol (10(-18)) concentration.
CE-LIF
Can be used for protein identification.
PERSON: Nicole Vasilevsky
Ummadi M and Weimer BC. (2002) J Chromatogr A. 2002 Jul 26;964(1-2):243-53.
anemometer
A measurement instrument used for for measuring wind speed, commonly used at weather stations.
Measurements of wind speed at a weather station can be gathered using an anemometer.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Anemometer
optical bench
An instrument that consists of a table or bench that is used for optics experiments and engineering.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Optical_table
laser diode driver
A diode laser that is a constant current source, linear, noiseless, and accurate, that delivers exactly the current to the laser diode that it needs to operate for a particular application.
PERSON: Nicole Vasilevsky
http://www.teamwavelength.com/info/laserdiodedrivers.php
electronic test equipment
An instrument that is used to create signals and capture responses from electronic Devices Under Test (DUTs). In this way, the proper operation of the DUT can be proven or faults in the device can be traced and repaired.
Bench top
PERSON: Nicole Vasilevsky
Testgear
http://en.wikipedia.org/wiki/Electronic_test_equipment
embryo microinjection station
An instrument used for transgenic animal production.
Instruments used for microinjection into embryos, consisting of an inverted, epifluorescent microscope, pair of micromanipulators, CCD camera with monitor, Bionomic temperature controller for stage, Sutter pressure injector, and anti-vibration table.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
spectrum analyzer
An instrument used to examine the spectral composition of some electrical, acoustic, or optical waveform. It may also measure the power spectrum.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Spectrum_analyzer
pulse generator
An instrument that is either an internal circuit or a piece of electronic test equipment used to generate pulses.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Pulse_generator
medical device
A blood pressure monitor is a medical device.
An instrument used in the diagnosis of disease or other conditions or for use in the care, treatment, or prevention of disease that does not achieve any of its primary intended purposes by chemical action or by being metabolized.
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/medical+device
electron paramagnetic resonance spectroscopy
A molecular assay used to study chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.
EPR
EPR spectroscopy
ESR
Electron spin resonance measurement
Electron spin resonance spectroscopy
PERSON: Nicole Vasilevsky
Used for the detection and identification of free radicals in a sample.
http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance
retrovirus production
Can be used to infect cells with retroviruses expressing a gene of interest.
PERSON: Nicole Vasilevsky
Virus production of high-titer, retrovirus prepartions for use in gene delivery applications.
http://books.google.com/books?id=oqs7CyFj0FUC&pg=PA475&lpg=PA475&dq=define+retrovirus+production&source=bl&ots=e8Yu8tLGSt&sig=c5V7OK32FUrpBricfX59CrKGquw&hl=en&ei=cBE2TaDXG5OssAPA1-yEBg&sa=X&oi=book_result&ct=result&resnum=9&ved=0CF0Q6AEwCA#v=onepage&q&f=false
urodynamic testing system
A measurement instrument that is used to asses how the bladder and urethra function of storing and releasing urine.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Urodynamics
gene chip scanner
An array scanner that scans next-generation higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays.
PERSON: Nicole Vasilevsky
http://www.affymetrix.com/estore/browse/products.jsp;jsessionid=314AF279151A26564770FA336CB6F033?categoryIdClicked=&productId=131503#1_1
endoscopic workstation
A workstation set up to perform endoscopic evaluation of patients.
An instrument used to investigate the digestive tract to diagnose a digestive disease. The endoscopic workstation comprises of endoscopic instruments and a computer, allowing for acquisition of electronic images during the endoscopy and images can be used as support of the information about the results of the procedure.
Delvaux et al. J Clin Gastroenterol. 1999 Sep;29(2):118-26.
PERSON: Nicole Vasilevsky
in situ hybridization workstation
A setup for high throughput in situ hybridization, to analyze gene expression in samples.
An instrument that automates the principal slide staining activities for slide processing used in immunohistochemistry (IHC), in situ hybridization (ISH), fluorescent in situ hybridization (FISH), and microarray slide processing applications.
PERSON: Nicole Vasilevsky
http://www.ventanadiscovery.com/
HPLC autosampler
An instrument that is an automatic sampler designed to operate with a HPLC system, which can inject samples into the HPLC system.
PERSON: Nicole Vasilevsky
http://www.labhut.com/products/autosamplers/autosampler_ht300l.php
portable X-ray machine
An x-ray source that is portable and can be brought to the patient or object.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/X-ray_generator
chemistry analyzer
A sample selective analyzer used to analyze biological samples such as serum.
An instrument used for separation, identification, and quantification of the chemical components of natural and artificial materials.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Analytical_chemistry
cryostage
A crytostage is used to mount biospecimens, prior to sectioning with a cryostat.
An instrument which maintains subzero temperature for heat labile samples undergoing microscopic analysis.
PERSON: Nicole Vasilevsky
http://www.linkam.co.uk/index.php?page=shop.product_details&flypage=flypage-noprice.tpl&product_id=27&category_id=13&option=com_virtuemart&Itemid=70
macroscope
An improvised microscope made of photographic lenses that provides much larger numerical aperture (NA) for low magnification (for example, one or less) than a standard microscope objective.
Can be used to image biological samples.
PERSON: Nicole Vasilevsky
www.nature.com/nrn/journal/v5/n11/glossary/nrn1536_glossary.html
voice recording equipment
A tape recorder.
An instrument used for audio recording of speech.
PERSON: Nicole Vasilevsky
http://www.phon.ucl.ac.uk/resource/audio/recording.html
UV detector
A part of a liquid chromatography instrument that detects absorption of UV light by samples. The output is recorded as a series of peaks - each one representing a compound in the mixture passing through the detector and absorbing UV light.
PERSON: Nicole Vasilevsky
Used to detect ethidium bromide bound to DNA.
http://www.chemguide.co.uk/analysis/chromatography/hplc.html
data analysis workstation
A flow cytometry analysis workstation, set up with software to analyze flow cytometry data.
An instrument which consists of computers used for data analysis.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
gene trapping
Experimental genetic modification used to introduce insertional mutations across the mammalian genome using a gene trap vector.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Gene_trapping
intubation
Agent delivery of a tube into an external or internal orifice of the body for the purpose of adding or removing fluids or air.
Entubation
Intubation of a patient whose airway is blocked.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Intubation
ovarectomy
An ovaectomy may be performed for a patient with ovarian cancer.
PERSON: Nicole Vasilevsky
Surgical removal of one or both ovaries.
http://cancer-symptoms.org/cancer-treatments/ovariectomy.htm
surface tension and contact angle measurement system
A measurement instrument used to determine surface properties of solids and liquids.
PERSON: Nicole Vasilevsky
microlab.berkeley.edu/labmanual/chap8/kruss.pdf
protein expression data
Mass spectrometry data.
PERSON: Nicole Vasilevsky
Protein expression data displays identification of unknown proteins, protein modifications, distinguishes protein isoforms and subsets and quantification of samples.
http://www.selectscience.net/products/proteinpilot-software/?prodID=83453
image acquisition and analysis
An image analysis technique where images are acquired through a medical or scientific instrumentation and analyzed.
Image acquisition and analysis of an MRI.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
image visualization and analysis
An image analysis technique where images acquired through clinical or scientific instrumentation are visualized and analyzed.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Visualization of bands on a gel and quantification using ImageJ software.
behavioral assay
A morris water maze is a behavioral assay.
An organismal assay used to study the relationship of behavior to the environment or an experimental condition.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Applied_behavior_analysis
nuclear magnetic resonance data
Data depicting NMR spectra from a sample.
NMR data
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/NMR_spectra_database
monitoring device
A blood pressure monitor.
A visualization produced by a device that takes signals and displays them on a television screen or a computer monitor.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/monitoring+device
super 16 analyzer projector
An instrument that utilizes 16mm film and is used for data analysis, optical blowup or digital scanning.
PERSON: Nicole Vasilevsky
http://cgi.ebay.com/ws/eBayISAPI.dll?ViewItem&item=260683422104
super 8 analyzer projector
An instrument that utilizes 8mm film and is used for data analysis, optical blowup or digital scanning.
PERSON: Nicole Vasilevsky
http://cgi.ebay.com/ws/eBayISAPI.dll?ViewItem&item=260683422104
X-ray photoelectron spectrometer
A spectrophotometer that measures the elemental composition, empirical formula, chemical state and electronic state of the elements that exist within a material.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/X-ray_photoelectron_spectroscopy
electrocardiogram data
ECG data
PERSON: Nicole Vasilevsky
Software that records heart rate, inter-beat-interval (IBI), and physical activity and digitizes the ECG signal and determines the IBI from the R-to-R interval. From the IBI recordings, the heart rate and heart rate variability parameters are calculated. Caloric expenditure can be obtained through the use of a software algorithm that combines concurrent heart rate and activity data.
http://www.camntech.com/cnt_actiheart.htm
dietary analysis
A behavioral assay used for collection and analyses of 24-hour dietary recalls and the analysis of food records, menus, and recipes. Calculation of nutrients occur immediately providing data per ingredient, food, meal, and day in report and analysis file formats.
Analysis of nutritional content of food.
PERSON: Nicole Vasilevsky
http://www.ncc.umn.edu/products/ndsr.html
artificial chromosome
A construct that is generated by inserting exogenous DNA into a plasmid containing features of a eukaryotic chromosome or prokaryotic episome that support replication and preservation in a host cell. Artificial chromosomes are used to clone large DNA fragments between 100,000 bases and 3,000,000 bases in size.
An artificial mouse chromosome.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
phagemid
A hybrid plasmid that carries elements from the filamentous bacteriophage M13, including the M13 origin. A phagemid can be replicated form its plasmid origin as a circular double-stranded plasmid, or replicated from its M13 origin and packaged as single stranded DNA in viral particles in the presence of a helper phage.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Phagemid
RNA interference plasmid
A plasmid expressing transcripts that are processed into small RNA molecules, which target genes for post-transcriptional silencing through the RNAi pathway.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi plasmid
shRNA plasmid
An RNA interference plasmid that expresses a short sequence of RNA that forms a short hairpin duplex. This gene product is processed by endogenous RNAi pathway machinery into a small interfering RNA (siRNA) molecule used to silence target gene expression.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
Short hairpin RNA plasmid
Small hairpin RNA plasmid
http://www.medterms.com/script/main/art.asp?articlekey=25734
dsRNA plasmid
An RNA interference plasmid engineered to express complementary strands of RNA that form double-stranded duplexes, which are processed through the RNAi pathway into short interfering RNA (siRNA) molecules used to silence target gene expression.
Double stranded RNA plasmid
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
Used to knockdown gene function.
miRNA plasmid
An RNA interference plasmid that expresses a short sequence of RNA that includes elements required for processing by endogenous microRNA processing machinery into active microRNA molecules.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
The gene specific targeting sequences in these small RNAs may or may not represent a naturally occurring miRNA, but they will contain flanking RNA regions that allow processing by endogenous miRNA pathway.
micro RNA plasmid
miRNA cDNA plasmid
A cDNA plasmid that carries a small cDNA insert from a pool of size-selected cDNAs, representing putative endogenous miRNAs.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
micro RNA cDNA plasmid
gene trap plasmid
A plasmid containing a reporter gene that is only expressed upon integration in a functional gene.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
TREX-Hygro gene trap plasmid.
http://www.nature.com/nbt/journal/v19/n6/full/nbt0601_579.html
nucleic acid oligonucleotide library
A nucleic acid library that is a collection of nucleic acid molecules, stored in pools containing a single species of nucleic acid.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
nucleic acid molecule library
nucleic acid oligo library
construct library
A cDNA construct library.
A nucleic acid library that contains a collection of distinct populations of microorganisms, each of which expresses a DNA construct carrying a piece of DNA from a source organism or cell line. In certain cases, this term can also refer to the collection of DNA constructs themselves.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
primer library
A nucleic acid molecule library that contains primer sets used for amplification of target nucleic acid sequences.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://www.realtimeprimers.com/hustceprli.html
RNA interference oligonucleotide library
A nucleic acid molecule library containing RNA oligonucleotides used to silence gene expression in cells through the RNAi pathway.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi oligo library
dsRNA oligonucleotide library
An RNAi oligonucleotide library that contains dsRNA oligonucleotides used to silence gene expression
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
Used to knockdown gene function.
double stranded oligonucleotide library
dsRNA oligo library
miRNA oligonucleotide library
An RNAi oligonucleotide library that contains miRNA oligonucleotides used to silence gene expression.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
miRNA oligo library
micro RNA oliognucleotide library
siRNA oligonucleotide library
An RNAi oligonucleotide library that contains siRNA oligonucleotides used to silence gene expression.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
siRNA oligo library
small interfering RNA oligonucleotide library
miRNA cDNA library
A cDNA construct library that carries small cDNA inserts from a pool of size-selected cDNAs, representing putative endogenous miRNAs.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
micro RNA cDNA library
miRNA construct library
An RNA interference construct library that is a collection of miRNA plasmids.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
micro RNA construct library
RNA interference construct library
A construct library that is a collection of constructs expressing transcripts, which are processed into small RNA molecules that target genes for post-transcriptional silencing through the RNAi pathway.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi construct library
shRNA construct library
An RNA interference construct library that is a collection of shRNA constructs.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://www.medterms.com/script/main/art.asp?articlekey=25734
short hairpin RNA construct library
small hairpin RNA construct library
dsRNA construct library
An RNA interference construct library that is a collection of dsRNA constructs used to generate dsRNA, which serve as substrates for the RNAi pathway to generate siRNA molecules
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
Used to knockdown gene function.
double stranded RNA construct library
http://cshprotocols.cshlp.org/cgi/content/extract/2006/3/pdb.prot4512
HAC
An artificial chromosome containing chromosomal features needed for replication and preservation in human cells, and used to propagate large sequences of DNA.
Human artificial chromosome
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
phagemid library
A genomic library that contains discrete collections of phagemid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Phagemid
miRNA inhibitor siRNA library
An siRNA oligonucleotide library that contains miRNA inhibitors, which are chemically synthesized siRNAs, which specifically inhibit endogenous miRNA function after transfection into cells.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://www.qiagen.com/products/miscriptmirnainhibitors.aspx#Tabs=t0
micro RNA inhibitor siRNA library
high pressure freezer
An instrument used for vitrifying samples up to 200µm in thickness without the artefacts of chemical fixation for light microscopy or electron microscopy applications.
PERSON: Nicole Vasilevsky
http://www.leica-microsystems.com/products/electron-microscope-sample-preparation/industrial-materials/cryo-preparation/details/product/leica-em-pact2/
simulator
An accupulser.
An instrument that creates an environment that is as close as possible to reality.
PERSON: Nicole Vasilevsky
http://www.spaceday.org/index.php/Glossary-of-Aeronautics-Terms.html
teleconference equipment
Instruments used to support teleconferencing by providing one or more of the following: audio, video, and/or data services by one or more means, such as telephone, computer, telegraph, teletype, radio, and television.
PERSON: Nicole Vasilevsky
Phone conferencing.
http://en.wikipedia.org/wiki/Teleconference
screen display
A computer monitor.
An instrument where an image is superimposed on a screen picture, commonly used by modern television sets, VCRs, and DVD players to display information such as volume, channel, and time.
PERSON: Nicole Vasilevsky
Plasma display
http://en.wikipedia.org/wiki/On-screen_display
head-mounted display
An instrument that functions as a display device, worn on the head or as part of a helmet, that has a small display optic in front of one (monocular HMD) or each eye (binocular HMD).
Can be used to assist with visualization during surgery.
HMD
Helmet mounted display
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Head-mounted_display
projector system
An instrument used for projecting an image onto a screen or other surface.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/projector
fluorescent in situ hybridization
An in situ hybridization technique that is used to detect and localize the presence or absence of specific DNA sequences on chromosomes. FISH uses fluorescent probes that bind to only those parts of the chromosome with which they show a high degree of sequence similarity. Fluorescence microscopy can be used to find out where the fluorescent probe is bound to the chromosomes.
Can be used to fluorescently label proteins and study localization within a tissue.
FISH
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization
gamma camera
An instrument used to image gamma radiation emitting radioisotopes, a technique known as scintigraphy.
Anger camera
Imaging of radiolabeled biomolecules.
PERSON: Nicole Vasilevsky
Scintillation camera
https://secure.wikimedia.org/wikipedia/en/wiki/Gamma_camera
colposcope
A colposcope is used during a colonoscopy.
Instrument that is used to visually distinguish normal from abnormal appearing tissue and take directed biopsies for further pathological examination.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Colposcopy
sympathetic nerve simulator
An instrument used to exert pulsed electrical signals to the sympathetic nerves in the legs or spine.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Spinal_cord_stimulator
in vitro electrophysiology recording
An electrophysiology assay used to record electrical properties of biological cells and tissues in vitro.
Electrophysiology recording of a brain slice.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electrophysiology
peristaltic pump
An instrument used for multichannel pumping with accurate flow control and broad flow range.
PERSON: Nicole Vasilevsky
http://www.thermoscientific.com/wps/portal/ts/products/detail?navigationId=L10523&categoryId=81880&productId=12710612
ex vivo genetic manipulation of cells
Experimental genetic modification of cells ex vivo to alter gene expression followed by reintroduction into a host organism.
PERSON: Nicole Vasilevsky
Pulsing T cells with tumor antigen, prior to adoptive transfer back into the patient, for tumor immunotherapy.
http://www.dfhcc.harvard.edu/core-facilities/cell-manipulation/services-and-policies/
remote manipulator arm
A instrument used for transmitting hand and finger movements to a remote robotic device, allowing the manipulation of objects that are too heavy, dangerous, small, or otherwise difficult to handle directly.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/Remote+manipulator
electronic health record data
A patient record from a doctor visit.
Data that contains patient health information generated by one or more encounters in any care delivery setting. Included in this information are patient demographics, progress notes, problems, medications, vital signs, past medical history, immunizations, laboratory data and radiology reports.
EHR
PERSON: Nicole Vasilevsky
http://www.himss.org/ASP/topics_ehr.asp
sputter coater
An instrument that is used to coat specimens with a thin metal film that acts as a conduction path for the electrons that strike it during electron microscopy.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Sputter_coating
nucleofection
Electroporation using an Amaxa nucelofector device.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
carbon evaporator
An instrument designed to coat specimens with precise, thin films of carbon. These carbon films can offer a flat, orderly, insulating surface on which to place a specimen for electron microscopy.
PERSON: Nicole Vasilevsky
http://www.snaggledworks.com/em_for_dummies/carbon_evaporation.html and http://en.wikipedia.org/wiki/Scanning_electron_microscope#Biological_samples
microdissection
A material processing technique performed to dissect tissues under magnification.
Dissection of brain tissue to isolate the hippocampus.
PERSON: Nicole Vasilevsky
http://medical-dictionary.thefreedictionary.com/microdissection
apoptosis assay
A cellular assay used to determine when cells are undergoing apoptosis: the process of programmed cell death (PCD) that occurs in multicellular organisms.
Annexin V is an apoptosis assay.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Apoptosis
next generation sequencing
A DNA sequencing technique that became commercially available in 2004 and is used by specific commercial platforms that embody a complex interplay of enzymology, chemistry, high-resolution optics, hardware, and software engineering. These instruments allow highly streamlined sample preparation steps prior to DNA sequencing, which provides a significant time savings and a minimal requirement for associated equipment in comparison to the highly automated, multistep pipelines necessary for clone-based high-throughput sequencing. Each technology amplifies single strands of a fragment library and perform sequencing reactions on the amplified strands. The fragment libraries are obtained by annealing platform-specific linkers to blunt-ended fragments generated directly from a genome or DNA source of interest. Because the presence of adapter sequences means that the molecules then can be selectively amplified by PCR, and no bacterial cloning step is required to amplify the genomic fragment in a bacterial intermediate as is done in traditional sequencing approaches.
Genome sequencing
High throughput DNA sequencing
High throughput nucleotide sequencing
Mardis (2008) Annu. Rev. Genomics Hum. Genet. 9:387-402
NGS
Next gen
Next gen sequencing
Next generation sequencing of target genes
Nucleotide sequencing, high-throughput
PERSON: Nicole Vasilevsky
Second generation sequencing
Sequencing, high-throughput nucleotide
motion analysis data
Data about time-dependent, quantitative data on captured movements.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Motion_analysis
schematic design
Computer aided design of a structural or procedural diagram, especially of an electrical or mechanical system.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/schematic
physiological data
Data from an electrocardiogram.
Data related to physiological recording or monitoring.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/physiological
labelled DNA fragment data
Data input captured by the labeled DNA sequence.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
transgenic virus
A virus expressing a gene of interest.
A virus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms.
PERSON: Matthew Brush
PERSON: Matthew Brush
transgenic baculovirus
A baculovirus expressing a gene of interest.
A transgenic virus derived from a baculovirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms.
Baculovirus supernatant
Baculovirus vector
PERSON: Matthew Brush
PERSON: Matthew Brush
transgenic retrovirus
A transgenic virus derived from a lentivirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms.
PERSON: Matthew Brush
PERSON: Matthew Brush
Retrovirus expressing a gene of interest.
Retrovirus supernatant
Retrovirus vector
transgenic adenovirus
A transgenic virus derived from an adenovirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms.
Adenovirus supernatant
Adenovirus vector
An adenovirus overexpressing a gene of interest.
PERSON: Matthew Brush
PERSON: Matthew Brush
transgenic lentivirus
A transgenic virus derived from a lentivirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms.
Lentivirus expressing a gene of interest.
Lentivirus supernatant
Lentivirus vector
PERSON: Matthew Brush
PERSON: Matthew Brush
transgenic adeno-associated virus
A transgenic virus derived from an andeno-associated virus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms.
Adeno-associated virus supernatant
Adeno-associated virus vector
An adeno-associated virus overexpressing a gene of interest.
PERSON: Matthew Brush
PERSON: Matthew Brush
reagent library
A reagent that consists of a collection of individual reagents of a given type.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
cDNA plasmid
A plasmid expressing cDNA of a gene of interest.
A plasmid with an insert derived from a cDNA molecule.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
gene knockdown function
A perturb function that results in decreased expression levels of a target gene. This can be achieved through targeting a gene directly through gene knockout or modification of the its DNA sequence, or targeting of the mRNA product of a gene using technologies such as RNAi.
Gene repression function
Gene silencing function
Knockdown the function of a gene, to study the function of that gene.
PERSON: Matthew Brush
PERSON: Matthew Brush
RNA interference function
A gene knockdown function that targets genes for post-transcriptional silencing through the RNA interference pathway.
PERSON: Matthew Brush
PERSON: Matthew Brush
RNAi function
gene knockdown library
A nucleic acid library that consists of a collection of gene knockdown reagents, which are capable of reducing the expression of target genes in a biological system.
A siRNA library.
Gene repression library
Gene silencing library
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNA interference library
A gene knockdown library that consists of a collection of RNAi oligonucleotides or RNAi plasmids.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi library
gene knockdown reagent
A reagent that is capable of reducing the expression of a target gene in a biological system.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
siRNA oligos.
DNA reagent
A primer.
A reagent that is a polymer comprised of DNA nucleotides.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNA reagent
A reagent that is a polymer comprised of RNA nucleotides.
A riboprobe.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
DNA oligonucleotide
A DNA reagent consisting of a short, linear DNA polymer, typically with 100 or fewer bases.
A primer.
DNA oligo
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://en.wikipedia.org/wiki/Oligonucleotide, http://www.operon.com/products/custom_oligos/glossary.aspx
DNA probe
A DNA oligonucleotide that is a single-stranded DNA molecule used to detect the presence of a complementary sequence among a mixture of other nucleic acid molecules.
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
Used for Southern blot anlaysis.
http://www.everythingbio.com/glos/definition.php?word=DNA+probe
RNA oligonucleotide
An RNA reagent consisting of a short, linear RNA polymer, typically with 100 or fewer bases.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNA oligo
RNA interference oligonucleotide
An RNA interference reagent used to silence expression of a target gene in cells, through the RNA interference pathway.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi oligonucleotide
dsRNA oligonucletide
An RNA interference oligonucleotide comprised of complementary strands of RNA that form double-stranded duplexes, and can be processed through the RNAi pathway into short interfering RNA (siRNA) molecules used to silence target gene expression.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
Used to knockdown gene function.
dsRNA oligo
miRNA oligonucleotide
An RNA interference oligonucleotide that includes gene-specific targeting sequences intended to silence expression of a target gene through the RNAi pathway, and also contains flanking miRNA sequence elements that allow for processing by cellular microRNA processing machinery into active miRNA molecules.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
miRNA oligo
siRNA oligonucleotide
An RNA interference oligonucleotide capable of silencing expression of a target gene through the RNAi pathway. siRNAs are synthesized as single-stranded molecules, typically 19-25 nucleotides in length, and paired with complementary sequences to form duplexes that serve as substrates for cellular RNAi processing machinery.
MHB, http://www.sigmaaldrich.com/life-science/custom-oligos/sirna-oligos.html
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
siRNA oligo
RNA interference reagent
A gene knockdown reagent that is capable of reducing the expression of a target gene in a biological system through the RNA interference pathway.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
RNAi reagent
massively parallel signature sequencing
A DNA sequencing by ligation technique that involves a bead-based method that uses a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides; this method made it susceptible to sequence-specific bias or loss of specific sequences.
Can be used to identify genome sequences.
Lynx Therapeutics' Massively Parallel Signature Sequencing
MPSS
Massively Parallel Sequencing
Massively-Parallel Sequencing
PERSON: Nicole Vasilevsky
Sequencing, Massively-Parallel
Sequencings, Massively-Parallel
http://en.wikipedia.org/wiki/DNA_sequencing#High-throughput_sequencing
organism library
A reagent library consisting of a collection of organisms.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
miRNA inhibitor siRNA oligonucleotide
A siRNA oligonucleotide that specifically inhibits endogenous miRNA function in cells.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
miRNA inhibitor siRNA oligo
nucleic acid fragment analysis
A nucleic acid assay used to determine the size of your DNA or RNA fragments by using a fluorescence-based detection system.
Fragment analysis
PERSON: Nicole Vasilevsky
http://www.brc.cornell.edu/brcinfo/?p=fraganalysis
amplified fragment length polymorphism PCR
A PCR based technique used to detect polymorphisms in DNA. It uses restriction enzymes to digest genomic DNA, followed by ligation of adaptors to the sticky ends of the restriction fragments. A subset of the restriction fragments are then selected to be amplified and the amplified fragments are visualized on denaturing polyacrylamide gels either through autoradiography or fluorescence methodologies.
AFLP
AFLP-PCR
PERSON: Nicole Vasilevsky
Used to detect various polymorphisms in different genomic regions simultaneously.
http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism
terminal restriction fragment length polymorphism
An RFLP technique for profiling of microbial communities based on the position of a restriction site closest to a labeled end of an amplified gene. The method is based on digesting a mixture of PCR amplified variants of a single gene using one or more restriction enzymes and detecting the size of each of the individual resulting terminal fragments using a DNA sequencer.
DNA fragment analysis.
PERSON: Nicole Vasilevsky
T-RFLP
TRFLP
http://en.wikipedia.org/wiki/Terminal_restriction_fragment_length_polymorphism
data management
A data transformation technique that comprises all the disciplines related to managing data as a valuable resource.
Biocuration for a databse.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Data_management
quality control
A technique used to ensure a certain level of quality in a product or service.
PERSON: Nicole Vasilevsky
QC
Quality control over drug manufacturing.
http://www.wisegeek.com/what-is-quality-control.htm
autopsy
An organismal assay used to examine the organs of a dead body to determine the cause of death or to study the pathologic changes present.
Analysis of tumor size and composition in a deceased mouse exposed to a mutagenic substance.
Necropsy
PERSON: Nicole Vasilevsky
http://www.medilexicon.com/medicaldictionary.php?t=8793
database maintenance
A data transformation technique that is used to keep a database running smoothly.
Maintaining the eagle-i repositories.
PERSON: Nicole Vasilevsky
http://www.wisegeek.com/what-is-database-maintenance.htm
database development
A data transformation technique used to describe the process of database design and implementation.
Development of the eagle-i data repositories.
PERSON: Nicole Vasilevsky
www.cs.uiowa.edu/~jni/courses/DatabaseManagementSystem/presentation/keyTermsChap06.doc
sterilization
A material processing technique that eliminates (removes) or kills all forms of life, including transmissible agents (such as fungi, bacteria, viruses, spore forms, etc.) present on a surface, contained in a fluid, in medication, or in a compound such as biological culture media.
PERSON: Nicole Vasilevsky
Sterilization of surgical instruments.
http://www.ph.ucla.edu/epi/bioter/anthapha_def_a.html
microorganism culture and propagation
Culture and propogation of microorganisms, which are microscopic, unicellular, and cell-cluster organisms.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Microbiology
anaerobic culture
Anaerobic bacteria culture
Anaerobic bacterial cultures are performed to identify bacteria that grow only in the absence of oxygen and which may cause human infection.
Microorganism culture and propogation in a non-oxygenated environment.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Anaerobic_organism
aerobic culture
Culture, routine
Bacterial culture expressing a plasmid of interest, used for cloning.
Microorganism culture and propogation in an oxygenated environment.
PERSON: Nicole Vasilevsky
Routine culture
Wound culture
http://en.wikipedia.org/wiki/Aerobic_organism
dermatophyte culture
Microorganism culture and propogation of dermatophytes, fungi that commonly causes skin disease in animals and humans.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Dermatophyte
CO2 enriched culture
Bacterial culture used for subcloning.
Carbon dioxide enriched culture
Microorganism culture and propogation where carbon dioxide is added in the culture mediums to enhance the culture conditions.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
animal transporting
A laboratory animal care technique used to safely transport animals from one location to another.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Preparing mice for air travel.
tissue procurement
A material processing technique performed to procure tissue from surgical resection specimens for research purposes.
Harvesting lymph nodes from a mouse.
PERSON: Nicole Vasilevsky
Tissue harvesting
http://www.pathology.med.umich.edu/giordano_lab/tps.htm
multiplexed cytokine assay
A molecular assay used for cytokine detection in a sample, where the multiplex capture antibody is attached to a bead.
Can be used to detect IL-2 levels in a sample.
Multi-plex cytokine assay
Multiplex cytokine assay
PERSON: Nicole Vasilevsky
http://www.dartmouth.edu/~dartlab/index.php?page=multiplexed-cytokines
congenic backcrossing
A mouse breeding technique used to generate congenic strains; strains generated by repeated backcrossing (at least 10 generations) that differ from one another only with respect to a small chromosomal segment. Many congenic mouse strains differ only in a segment containing the major histocompatibility complex.
Breeding a MHC congenic mouse.
PERSON: Nicole Vasilevsky
http://mouse.ornl.gov/mmdb/Search-pulldownglossary.html
magnetic resonance imaging
A physiological assay that uses nuclear magnetic resonance of protons to produce proton density images.
MRI
PERSON: Nicole Vasilevsky
Used to study brain function and activity.
http://wordnetweb.princeton.edu/perl/webwn?s=mri
magnetic resonance spectroscopy
A physiological assay that complements magnetic resonance imaging (MRI) as a non-invasive means for the characterization of tissue. While MRI uses the signal from hydrogen protons to form anatomic images, proton MRS uses this information to determine the concentration of brain metabolites such as N-acetyl aspartate (NAA), choline (Cho), creatine (Cr) and lactate in the tissue examined.
MRS
PERSON: Nicole Vasilevsky
Used to study brain function and activity.
http://www.ncbi.nlm.nih.gov/pubmed/16148633
transgenic organism model generation
A material processsing technique used to produce an organism in which there has been a deliberate modification of the genome in contrast to spontaneous mutation. Foreign DNA is introduced into the animal, using recombinant DNA technology, and then must be transmitted through the germ line so that every cell, including germ cells, of the animal contain the same modified genetic material.
Generation of a transgenic animal that is homozygous for the Mad4 gene.
Mutant animal model generation
PERSON: Nicole Vasilevsky
http://people.ucalgary.ca/~browder/transgenic.html
spectrophotometry
A molecular assay that is the quantitative measurement of the reflection or transmission properties of a material as a function of wavelength.
PERSON: Nicole Vasilevsky
Spectroscopy
http://en.wikipedia.org/wiki/Spectrophotometry
immunocytochemistry
A cellular assay that uses antibodies that target specific peptides or protein antigens in the cell via specific epitopes. These bound antibodies can then be detected using several different methods.
ICC
PERSON: Nicole Vasilevsky
Using antibodies to identify proteins in a cell.
http://en.wikipedia.org/wiki/Immunocytochemistry
cell phenotyping
A cellular assay used to identify the characteristics of an organism collectively, including anatomical and psychological traits, that result from both its heredity and its environment.
Cellular phenotyping
PERSON: Nicole Vasilevsky
Use of flow cytometry to identify a population of cells.
http://www.yourdictionary.com/phenotype
laser capture microdissection
A technique used for isolating specific cells of interest from microscopic regions of tissue/cells/organisms.
LAM
LCM
LMD
Laser MicroDissection
Laser capture microscopy
Laser-assisted microdissection
Microdissection
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Laser_capture_microdissection
animal handling
A laboratory animal care technique used to humanely handle animals in a way that causes the least amount of stress to the animal for experimentation purposes.
How to handle animals when performing i.p. injections.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
licensing
A technique that authorizes a use (such as copying software or using a (patented) invention) to a licensee, sparing the licensee from a claim of infringement brought by the licensor.
Licensing of a new technology.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/License
peptide library construction
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Reagent library preparation of peptides used for research purposes.
blood pressure analysis
A physiological assay used to measure blood pressure in an organism.
Blood pressure assessment
Blood pressure measurement
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
animal modeling of ischemic stroke
Experimental disease induction performed to induce cerebral ischemia in an animal model, to study of basic processes or potential therapeutic interventions in this disease, and the extension of the pathophysiological knowledge on and/or the improvement of medical treatment of human ischemic stroke.
Hind limb ischemia model.
Ischemia induction
Ischemia model
Ischemia modeling
Ischemic induction
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Animal_models_of_ischemic_stroke
photography
An imaging technique that involves the process, activity and art of creating still or moving pictures by recording radiation on a sensitive medium, such as a photographic film, or an electronic sensor.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Photography
computational modeling technique
3D modeling of blood flow.
A technique that uses mathematical models in computational science that requires extensive computational resources to study the behavior of a complex system by computer simulation.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Computational_model
3D computational fluid-dynamics modeling
A technique that models the complexities of a fluid-flow, given system geometry and a set of known or approximated boundary conditions.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
The application of a computer model to blood flow.
blood transport computational modeling
A 3D computational fluid-dynamics modeling technique that simulates exclusively blood flow.
Analysis of blood flow in a developing chick.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
transport service
A service offering that describes a service in which the provider facilitates the transport of some material entity to a specified destination for the service consumer.
PERSON: Matt Brush
PERSON: Matthew Brush
Transport of a patient within a hospital.
support service
A service offering that describes a service in which the provider assists the consumer in activities directly or indirectly associated with the production and analysis or experimental research data.
PERSON: Matt Brush
PERSON: Matthew Brush
Technical support.
material storage service
A storage service offering that describes a service in which the consumer provides some material as input which a service provider stores and returns as output
Cryopreservation service.
PERSON: Matt Brush
PERSON: Matthew Brush
data storage service
A storage service offering that describes a service in which the consumer provides data as input, which a service provider stores and returns as output in its original form.
PERSON: Matt Brush
PERSON: Matthew Brush
Storing data on a server.
maintenance service
A service offering that describes a service in which the provider actively maintains a material or data resource (e.g. a model organism colony or database) for the service consumer. This may involved making physical alterations to the material or data with the goal of maintaining its integrity or features.
PERSON: Matt Brush
PERSON: Matthew Brush
material maintenance service
A maintenance service offering that describes a service in which the provider actively maintains a material resource (e.g. a model organism colony) for the service consumer. A material maintenance service may or may not include storage of the material input.
Maintaining an animal coloy.
PERSON: Matt Brush
PERSON: Matthew Brush
data maintenance service
A maintenance service offering that describes a service in which the provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance.
Maintaining a database.
PERSON: Matt Brush
PERSON: Matthew Brush
analysis service
A service offering that describes a service in which the consumer provides some input material or data and a service provider returns data about the input material or data.
Flow cytometry analysis service.
PERSON: Matt Brush
PERSON: Matthew Brush
data analysis service
An analysis service offering that describes a service in which the consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output
PERSON: Matt Brush
PERSON: Matthew Brush
Sequence data analysis.
data processing service
data transformation service
material modification service
A material processing service offering that describes a service in which the provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
Histology service.
PERSON: Matt Brush
PERSON: Matthew Brush
transgenic mouse model generation
A GFP expressing mouse.
A transgenic animal model generation of a transgenic mouse or mice.
Mutant mouse generation
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Transgenic mouse generation
affymetrix array
A nucleic acid microarray assay that uses the GeneChip® System as the platform for analyzing complex genetic information.
Affy
Affy array
Affymetric SNP array
Affymetric microarray
Affymetrix SNP array
Affymetrix microarray
PERSON: Nicole Vasilevsky
Used to compare differential gene expression between samples.
http://www.affymetrix.com/estore/browse/brand/brandOverview.jsp;jsessionid=44DD3FD76424BB1861E4818FE5C48E4F?category=35677&categoryIdClicked=35677&rootCategoryId=35677&navMode=35677&aId=brandsNav
chicken embryo preparation
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
Sample preparation of chicken embryos for experimental research.
4-D image reconstruction algorithm
A data transformation technique used to coordinate and arrange sets of spatial images with their time stamps to produce a 4D image.
Mathematical modeling of a heart.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
digital imaging
An imaging technique used to create digital images, typically from a physical scene.
Digital image acquisition
MRI imaging.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Digital_imaging
doppler OCT
Doppler optical coherence tomography
Optical coherence tomography that uses time domain optical coherence tomography and Doppler shifts from a moving objective to acquire and process images.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Optical_coherence_tomography
fluid velocity measurements
A materials assay for quantifying the velocity of bulk fluid flows.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Flow_measurement
synchronization of 4D non-gated images by OCT
An imaging OCT technique that arranges images collected without external triggering from time domain optical coherence tomography sequentially in time.
PERSON: Nicole Vasilevsky
Synchronization of 4D non-gated images by optical coherence tomography
http://en.wikipedia.org/wiki/Optical_coherence_tomography
spectral doppler optical coherence tomography
A doppler OCT technique that provides complementary temporal flow information to the spatially distributed flow information of Doppler imaging.
PERSON: Nicole Vasilevsky
SDI
SDOCT
Spectral doppler imaging
http://adsabs.harvard.edu/abs/2010SPIE.7554E..47Y
doppler velocity measurements
A fluid velocity measurement technique for non-invasive, real-time measurement of the complete velocity profile of a liquids containing particles in suspension.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Doppler_effect#Velocity_profile_measurement
neuroantomical mapping
A physiological assay predicated on the mapping of (biological) quantities or properties onto spatial representations of the (human or non-human) brain resulting in maps.
Brain mapping
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Brain_mapping
radioactive in situ hybridization
An in situ hybridization technique that uses radioactive probes to detect the gene of interest.
ISH using zebra finch zRalDH digoxigenin-labeled riboprobes.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Radioactive ISH
Radioactive in situ analysis
Radioactive in-situ hybridization
retrograde labeling
A cellular assay used to trace neural connections from their point of termination (the synapse) to their source (the cell body).
PERSON: Nicole Vasilevsky
Use of viral strains as markers of a cell’s connectivity to the injection site.
http://en.wikipedia.org/wiki/Retrograde_tracing
iontophoresis
Agent delivery of a substance into the skin or tissue via an electrical charge.
PERSON: Nicole Vasilevsky
http://minneapolis.injuryboard.com/miscellaneous/iontophoresis-injection-without-the-needle.aspx?googleid=287626
mutant organism
A transgenic mouse.
Organism that has a sequence alteration, generally one that causes a change in phenotype or gene disfunction.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
tissue/organ assay
An assay that generates data about anatomical entities or processes at a tissue or organ scale of granularity.
Immunohistochemistry is a tissue assay.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
culture and propagation
A material processing technique used to create and maintain conditions suitable for growth of a living entity such as tissue cells, or bacteria.
Culture of cell lines.
In vitro culture and propagation
PERSON: Nicole Vasilevsky
http://oxforddictionaries.com/definition/culture?region=us
protein assay
A molecular assay that generates data about the presence, abundance, structure, function, or activity of proteins.
Mass spectrometry.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
organismal assay
An assay that generates data about the physical characteristics, physological functions, or behavior of organisms or viruses.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Phenotype characterization of a transgenic mouse.
nucleic acid assay
A molecular assay that generates data about the presence, abundance, structure, function, or activity of nucleic acids.
PCR.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
protein sequencing
A protein assay that involves the determination of the arrangement of the amino acid sequence of a protein.
PERSON: Nicole Vasilevsky
Sequencing of a novel protein.
http://www.answers.com/topic/protein-sequencing
clinical assay
An organismal assay designed to capture information about clinical samples or specimens.
Clinical diagnosis of a disease.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
electrophysiology assay
A cellular assay used to study electrical properties of biological cells and tissues, which involves measurements of voltage change or electric current.
PERSON: Nicole Vasilevsky
Used to test brain activity.
http://en.wikipedia.org/wiki/Electrophysiology
monoclonal antibody production
Antibody production in which of large quantities of identical antibody molecules (targeted against a particular antigen) are produced.
PERSON: Nicole Vasilevsky
Production of an mouse anti-human OX40 antibody.
http://www.accessexcellence.org/RC/VL/GG/monoclonal.php
organ perfusion
A material processing technique that forces blood or other fluid to flow from the artery through the vascular bed of a tissue or organ or to flow through the lumen of a hollow structure, for example an isolated renal tubule.
PERSON: Nicole Vasilevsky
http://www.medilexicon.com/medicaldictionary.php?t=66872
physiological assay
An organismal assay designed to capture information pertaining to the the organic processes and phenomena of an organism or any of its parts or of a particular bodily process.
Electrocardiogram.
PERSON: Nicole Vasilevsky
http://www.merriam-webster.com/dictionary/physiology
construct engineering
A material processing technique used to engineer a construct.
Construct construction
Generating a plasmid that overexpresses a gene of interest tagged to GFP.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Vector construction
Vector engineering
instrument and electronics design
A technique involving a strategic approach to creating an instrument or electronic device.
Design of a flow cytometer.
Device design
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
materials assay
An assay that generates data about the physical features of materials not of biological origin.
Metallurgy.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
experimental genetic modification
A material processing technique that involves the direct human manipulation of an organism's genome using modern DNA technology in an experimental setting.
Experimental genetic engineering
Gene therapy.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Genetic_engineering
chemical modification
A material processing technique in which substrate material is modified by the addition of a chemical agent that modifies the chemical structure of the substrate.
Fixing tissue with formaldehyde.
Molecular modification
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
biomolecule synthesis
Carbohydrate synthesis.
Chemical synthesis of a biomolecule; any molecule that is produced by a living organism, including large polymeric molecules such as proteins, polysaccharides, lipids, and nucleic acids as well as small molecules such as primary metabolites, secondary metabolites, and natural products.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Biomolecule
fixation
Fixation of tissue, prior to immunohistochemistry.
Histological sample preparation that uses agents which permeate tissues and cells and combine covalently with their major biochemical constituents (lipids, proteins and carbohydrates) and fix them into place.
PERSON: Nicole Vasilevsky
http://www.udel.edu/biology/Wags/b617/temprep/temprep1.htm
infarction model
Experimental disease induction used to model infarction, the formation of an infarct, an area of tissue death (necrosis) due to a local lack of oxygen caused by obstruction of the tissue's blood supply.
PERSON: Nicole Vasilevsky
Used for stroke models.
http://en.wikipedia.org/wiki/Infarction
reagent library preparation
Material production of a library or reagents, for use in a chemical reaction or other experimental processes, to detect, measure, examine, or produce other substances.
PERSON: Nicole Vasilevsky
Preparation of a cDNA library.
http://www.yourdictionary.com/reagent
implantation
Agent delivery of a thing implanted in something else, such as a piece of tissue, prosthetic device, or other object implanted in the body.
Implantation of a piece of tissue into a blastocyst.
PERSON: Nicole Vasilevsky
http://oxforddictionaries.com/definition/implant
tissue culture
Culture and propogation of tissues and/or cells separate from the organism.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Tissue_culture
experimental infection
Agent delivery of a host organization by a foreign species in an experimental setting.
Infection of a cell line with viral supernatants.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Infection_%28disambiguation%29
BAC construction
A construct engineering technique used to engineer a bacterial artificial chromsome (BAC).
BAC engineering
Bacterial artificial chromosome construction
Bacterial artificial chromosome engineering
Construction of a BAC expressing a gene of interest.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
plasmid construction
A construct engineering technique used to assemble or modify a DNA plasmid to contain desired sequence elements, such as promoters, genes of interest, antibiotic resistance genes, multiple cloning sites, origins of replication, or other specified sequences.
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
Plasmid engineering
Subcloning of a plasmid expressing a gene of interest fused to GFP.
data analysis
A data transformation technique used to analyze and interpret data to gain a better understanding of it.
Data analysis of flow cytometry data.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Analysis
clinical trial technique
A technique performed to prepare or implement a clinical trial.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Screening patients for a clinical trial.
material storage
A technique that provides storage of a material.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Storage of cell lines in liquid nitrogen.
imaging technique
A technique used to create a representation or reproduction of an object's outward form; especially a visual representation (i.e., the formation of an image).
MRI.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Imaging
material production
A material processing technique in which physical changes are made to a specified input material that produce a new entity as specified output. The specified output of a material production technique can be contained within, derived from, or synthesized from specified input materials, but it represents a material entity that is of a distinct type from any of the specified input materials.
Monoclonal antibody production.
PERSON: Nicole Vasilevsky
http://neurolex.org/wiki/Category:Material_service_resource
antibody production
Material production of monoclonal or polyclonal antibodies for experimental purposes.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Production of an mouse anti-mouse OX40 monoclonal antibody.
virus production
Material production of viral supernatants using vectors expressing a gene of interest. Virus is produced by transfecting cells and collecting supernatant and the supernatant is then used to directly infect cells for the purpose of studying the function of a particular gene or set of genes.
PERSON: Nicole Vasilevsky
Production of viral supernatants expressing GFP.
http://web.mit.edu/jacks-lab/protocols/lentiviralproduction.htm
observational method
A method in which the investigators do not seek to intervene, and just simply observe the course of events.
Person: Melanie Wilson
Person: Melanie Wilson
testing method
An observational method that produces a test result based on a quantitative, categorical or qualitative test.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Test_method
measurement method
An observational method where quantitative measurements are made based on the observations.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
survey method
An observational method of gathering data by asking questions or providing a formal questionnaire to individuals who are thought to have desired information.
PERSON: Nicole Vasilevsky
http://www.managementstudyguide.com/survey_method.htm
interview method
An observational method of gathering data by interviewing individuals.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
visual observation method
An observational method where observations are made visually.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
audio observation method
An observational method using an auditory source.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
fabrication
A material production technique used to make a product from raw materials.
Fabrication of a instrument.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/fabrication
ultrasonography
An imaging technique used for visualizing subcutaneous body structures including tendons, muscles, joints, vessels and internal organs for possible pathology or lesions. Obstetric sonography is commonly used during pregnancy for fetal imaging.
Medical sonography
PERSON: Nicole Vasilevsky
Ultrasound
http://en.wikipedia.org/wiki/Sonography
cell enrichment
A cell separation technique used to enrich mixed populations of cells out into two or more populations that usually occupying different parts of the same aggregate or separate into different aggregates.
PERSON: Nicole Vasilevsky
Use of FACS to sort for a specific population of cells.
http://www.mondofacto.com/facts/dictionary?cell+sorting
rehabilitation
A technique that is performed to restore some or all of the patient's physical, sensory, and mental capabilities that were lost due to injury, illness, or disease.
PERSON: Nicole Vasilevsky
Rehabilitation for alcohol abuse.
http://medical-dictionary.thefreedictionary.com/rehabilitation
gas chromatography-mass spectrometry
A mass spectrometry technique that combines the features of gas-liquid chromatography and mass spectrometry to identify different substances within a test sample.
Can be used to identify proteins.
GC-MS
GC/MS
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Gas_chromatography-mass_spectrometry
liquid chromatography-mass spectrometry
A mass spectrometry technique that combines the physical separation capabilities of liquid chromatography (or HPLC) with the mass analysis capabilities of mass spectrometry. Generally its application is oriented towards the specific detection and potential identification of chemicals in the presence of other chemicals (in a complex mixture).
HPLC-MS
LC-MS
LC/MS
PERSON: Nicole Vasilevsky
Used to identify protein sequences.
http://en.wikipedia.org/wiki/Liquid_chromatography-mass_spectrometry
neuropsychological testing
A physiological assay that utilizes systematic administration of defined procedures to measure specific psychological functions known to be linked to particular brain structures or pathways in humans.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Neuropsychological_test
electrospray ionization
A mass spectrometry technique used to produce ions. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized.
Can be used for protein identification.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electrospray_ionization
capillary electrophoresis
An electrophoresis technique used to separate ionic species by their charge and frictional forces and hydrodynamic radius.
CE
CZE
Can be used to identify chiral molecules.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Capillary_zone_electrophoresis
two dimensional polyacrylamide gel electrophoresis
2D gel electrophoresis
2D polyacrylamide gel electrophoresis
A 2D gel used for proteomics analysis.
A polyacrylamide gel electrophoresis technique used to separate molecules based on two properties, the isoelectric point and their molecular weight. In the first dimension, molecules are resolved in according to their isoelectric points (pIs) using immobilized pH gradient electrophoresis (IPGE), isoelectric focusing (IEF), or non-equilibrium pH gradient electrophoresis (NEPHGE). In the second dimension, proteins are separated according to their approximate molecular weight using sodium dodecyl sulfate poly-acrylamide-electrophoresis (SDS-PAGE).
PERSON: Nicole Vasilevsky
http://www-lmmb.ncifcrf.gov/phosphoDB/2d-description.html
biopsy
Biopsy of a potentially cancerous mole.
PERSON: Nicole Vasilevsky
Specimen creation of a sample of tissue from a living body for diagnostic purposes.
http://www.thefreedictionary.com/biopsy
fat biopsy
A biopsy that involves the removal of a small part of the abdominal wall fat pad.
PERSON: Nicole Vasilevsky
The makeup of fat in the abdominal wall can be investigated by fat biopsy.
http://www.pennmedicine.org/encyclopedia/em_PrintArticle.aspx?gcid=003841&ptid=1
skinpunch biopsy
A biopsy that involves the removal of a cylinder of skin using a punch tool.
PERSON: Nicole Vasilevsky
Punch biopsy
Skin biopsy
Used to biopsy a potentially cancerous mole.
http://healthlibrary.epnet.com/GetContent.aspx?token=b93d114e-5009-4f6a-9917-6c594254fcc7&chunkiid=14861
electroencephalography
A physiological assay that uses an electronic monitoring device to measure and record electrical activity in the brain.
EEG
PERSON: Nicole Vasilevsky
Used to measure brain activity.
http://medical-dictionary.thefreedictionary.com/electroencephalography
tail biopsy
A biopsy used to obtain tail issue from animal for DNA analysis.
PERSON: Nicole Vasilevsky
Used for genotyping.
http://labanimals.case.edu/templates_tail_biopsy.html
flow-mediated dilation
A physiological assay used to evaluate endothelial dysfunction non-invasively and used for early detection of atherosclerosis and determining the efficacy of treatment.
FMD
PERSON: Nicole Vasilevsky
http://www.aloka-europe.com/entity7.aspx
cryopreservation
A material processing technique where a living organism is frozen at ultra- low-temperature such that it can be revived and restored to the same living state as before it was stored.
Cryopreservation of cell lines.
PERSON: Nicole Vasilevsky
http://www-cyanosite.bio.purdue.edu/protocols/cryo.html
formalin fixation
A fixation technique that uses formalin, an aqueous solution containing formaldehyde to fix tissue or cells.
Can be used to fix tissue prior to immunohistochemistry.
Formaldehyde fixation
PERSON: Nicole Vasilevsky
http://dictionary.reference.com/browse/formalin
microneurography
A physiological assay that involves the insertion of metal microelectrodes into nerve fascicles that is used to study autonomic nervous system function.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Microneurography
habituation
A laboratory animal care technique in which organisms are habituated to an environment; where there is a decrease in response to a stimulus after repeated presentations.
PERSON: Nicole Vasilevsky
http://psychology.about.com/od/hindex/g/def_habituation.htm
brain slice preparation
PERSON: Nicole Vasilevsky
Preparation of diseased tissue, to analyze function.
Tissue sectioning of brain used for electrophysiology that allows the study of a synapse or neural circuit in isolation from the rest of the brain, in controlled physiological conditions.
http://en.wikipedia.org/wiki/Slice_preparation
electrooculography
A physiological assay used to measure the resting potential of the retina.
PERSON: Nicole Vasilevsky
Performed to test for retinal diseases.
http://en.wikipedia.org/wiki/Electrooculography
humanized mice generation
A mouse with a humanized immune system.
Generation of a transgenic mouse that carries partial or complete human physiological systems.
Macchiarini et al (2005) J Exp Med 2005 202:1307-1311.
PERSON: Nicole Vasilevsky
colony picking
A material component separation technique used to pick colonies from agar plates and transfer them into culture media.
PERSON: Nicole Vasilevsky
Picking colonies to screen for bacteria that express the plasmid of interest.
http://www.jgi.doe.gov/education/how/how_5.html
liquid chromatography–tandem mass spectrometry
A liquid chromatography-mass spectrometry technique in which high-performance liquid chromatography is linked directly to a tandem mass spectrometer through electrospray ionization.
LC-MS-MS
LC/MS/MS
PERSON: Nicole Vasilevsky
Used to identify protein sequences.
http://en.wikipedia.org/wiki/Liquid_chromatography%E2%80%93mass_spectrometry
planar imaging
An imaging technique used for acquisition of a planar image. With planar imaging, the detector array is stationary over the patient, and acquires data only from this one angle. The image created with this type of acquisition is similar to an X-ray radiograph.
PERSON: Nicole Vasilevsky
http://www.physics.ubc.ca/~mirg/home/tutorial/acquisition.html
single photon emission computed tomography
An imaging technique, in which a gamma camera rotates around the patient and takes pictures from many angles, and a tomographic (cross-sectional) image is generated.
PERSON: Nicole Vasilevsky
SPECT
http://www.medterms.com/script/main/art.asp?articlekey=18450
cell viability assay
A cellular assay used to determine cell viability in an experimental setting; the capability of developing, growing, and otherwise sustaining life.
Cell viability
Cell viability analysis
Live/dead assay
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Use of trypan blue exclusion to determine cell viability.
inductively coupled plasma mass spectrometry
A mass spectrometry technique that is highly sensitive and capable of the determination of a range of metals and several non-metals at concentrations below one part in 1012 (part per trillion). It is based on coupling together an inductively coupled plasma as a method of producing ions (ionization) with a mass spectrometer as a method of separating and detecting the ions.
ICP-MS
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Inductively_coupled_plasma_mass_spectrometry
1D electrophoresis
An electrophoresis technique for separating proteins based on their ability to move within an electrical current, which is a function of the length of their polypeptide chains or of their molecular weight in a 1-dimensional gel.
PERSON: Nicole Vasilevsky
Separation of proteins in an acrylamide gel.
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Protein-Gel-Electrophoresis/1D-Electrophoresis.html
fluorescent microscopy
A light microscopy technique that is used for imaging of fluorescent compounds using fluorescent filters.
Can be used to examine GFP expressing cells.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
fluorescence loss in photobleaching
A fluorescent microscopy technique which can be used to examine the movement or diffusion of molecules inside cells or membranes. Typically a cell membrane is labelled with a fluorescent dye, and a specific area of the labeled membrane is bleached using the beam from a confocal laser scanning microscope. The fluorescence intensity from that region of the membrane is measured over time. Motion of fluorescent molecules into and along the membrane slowly restores the fluorescence in the bleached region, while depleting the fluorescence in other regions (by exchange of bleached for unbleached fluorophores).
Can be used to study ligands binding to receptors at the cell surface.
FLIP
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fluorescence_loss_in_photobleaching
multiplex ligation-dependent probe amplification
A polymerase chain reaction technique that that permits multiple targets to be amplified with only a single primer pair.
MLPA
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Multiplex_ligation-dependent_probe_amplification
cell cycle analysis assay
A cellular assay performed to determine the stage of the cell cycle for a population of cells; whether the cell is in G0/G1, S, or G2/M.
Analysis of cell cycle of proliferating cells.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
stereology
An imaging assay that is used for the three-dimensional interpretation of planar sections of materials or tissues.
PERSON: Nicole Vasilevsky
http://www.mbfbioscience.com/solutions/stereology
photolithography
A material processing technique used in microfabrication to selectively remove parts of a thin film or the bulk of a substrate.
Optical lithography
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Photolithography
immunoassay
An assay that enables the presence or the concentration of a substance in a material to be measured by exploiting the specific binding between an analyte and the corresponding detection antibody.
Immunohistochemistry.
Nature Biotechnology 28,434–435 (2010)
PERSON: Nicole Vasilevsky
liquid scintillation counting
A material processing technique used for measuring radiation from beta-emitting nuclides.
Can be used for a tritiated thymidine proliferation assay.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Liquid_scintillation_counting
isotope analysis
A molecular assay used to identify isotopic signature, the distribution of certain stable isotopes and chemical elements within chemical compounds.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Isotope_analysis
virus preparation
A sample preparation technique used to prepare virus supernatants for molecular assays.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Preparation of supernatants that can be used to infect cell lines.
high-throughput virus preparation
A virus preparation technique that uses expedited, often automated technologies to prepare large quantities of viral stocks.
PERSON: Nicole Vasilevsky
http://www.abta.org/index.cfm?contentid=131
knockout mouse generation
A transgenic mouse generation technique that allows particular genes on the DNA strand to be altered, usually removed, but they may also be inactivated or inserted, which allows researchers to determine the exact function of a particular gene.
Generation of a mouse that is homozygous for the Mad4 gene.
PERSON: Nicole Vasilevsky
http://www.animalresearch.info/en/science/animalsused/mouseGM#whattrans
fluorescence resonance energy transfer
An imaging assay used to measure the proximity of two fluorophores.Resonance energy transfer occurs only over very short distances, typically within 10nm, and involves the direct transfer of excited state energy from the donor fluorophore to an acceptor fluorophore as an alternative to fluorescence emissive decay from the donor.
Can be used to study protein interactions.
EET
Electronic energy transfer
FRET
Förster resonance energy transfer
PERSON: Nicole Vasilevsky
RET
Resonance energy transfer
http://www.andor.com/learning/applications/Fluorescence_Resonance/
induced asphyxia
A surgical technique used to induce asphyxia; a condition of severely deficient supply of oxygen to the body that arises from being unable to breathe normally.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Asphyxia
induced hemorrhagic shock
A surgical technique used to induce tissue perfusion, resulting in the inadequate delivery of oxygen and nutrients that are necessary for cellular function.
PERSON: Nicole Vasilevsky
http://emedicine.medscape.com/article/432650-overview
laparotomy
A surgical technique involving a large incision through the abdominal wall to gain access into the abdominal cavity.
Coeliotomy
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Laparotomy
abdominal implantation
A surgical technique involving implantation of material into the abdomen.
Implantation of a drug into the abdominal cavity.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
microplate dispenser
A liquid handler that can provide bulk dispensing of liquids into multi-well plates.
PERSON: Nicole Vasilevsky
http://www.biotek.com/products/liquid_handling/multiflo_microplate_dispenser.html
sliding caliper
A measurement instrument used to measure the distance between two opposing sides of an object.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Caliper
anthropometer
A measurement instrument that consists of a calibrated, vertical rod to which are attached two horizontal arms, one fixed and one movable, for measuring the human trunk and limbs.
PERSON: Nicole Vasilevsky
Used for posture evaluation.
http://dictionary.reference.com/browse/anthropometer
torque sensor
A mechanical instrument that converts a torsional mechanical input into an electrical output signal.
PERSON: Nicole Vasilevsky
http://www.futek.com/product.aspx?t=torque
robot
A mechanical instrument that can perform tasks with guidance by computer and electronic programming.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Robot
rehabilitation robot
A robot used for assessing and treating motor impairments in both the upper and lower extremities as a part of rehabilitation.
PERSON: Nicole Vasilevsky
Rehabilitation for Parkinson's patients.
http://cabrr.cua.edu/research/RehabilitationRobotics.cfm
wavelength scanned cavity ring-down spectrometer
A isotype ratio mass spectrometer that enables measurement of absolute optical extinction by samples that scatter and absorb light over a broad range of wavelengths.
PERSON: Nicole Vasilevsky
WS-CRDS
http://en.wikipedia.org/wiki/Cavity_ring-down_spectroscopy
continuous flow isotope ratio mass spectrometer
An isotype ratio mass spectrometer in which the relative abundance of isotopes in a continuously flowed gas sample is determined.
CF-IRMS
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Isotope-ratio_mass_spectrometry
animal activity monitoring
A behavioral assay that can be done manually or using an electronic monitoring device to measure and record behavioral activity by a study animal.
A behavioral locomotive activity chamber for animals.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
stable isotope analysis
An isotope analysis assay used to identify stable isotopes within chemical compounds.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
wind tunnel
An instrument used to study the effects of air moving past solid objects, often used in aerodynamic research.
Can be used to study flight patterns in geese.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Wind_tunnel
hydrogen peroxide meter
An instrument designed to continuously monitor processes that utilize hydrogen peroxide for bleaching or disinfection purposes.
PERSON: Nicole Vasilevsky
http://www.analyticaltechnology.com/cms/Default.aspx?tabid=105
cascade impactor
An instrument used to determine concentration and particle size distribution using the principle of inertial separation to size segregate particle samples from a particle laden gas stream.
PERSON: Nicole Vasilevsky
http://www.thermoscientific.com/ecomm/servlet/productsdetail?productId=11961543&groupType=PRODUCT&searchType=0&storeId=11152 , http://en.wikipedia.org/wiki/Particle_size_distribution
2D microfluidic liquid chromatography system
A liquid chromatography instrument used for separation in two dimensions by way of microfluidic control of the particles in a sample.
PERSON: Nicole Vasilevsky
The proteins of a cytosolic extract can be sorted according to their size using a 2-D microfluidic liquid chromatography system.
http://www.hsph.harvard.edu/research/proteomics/mass-spectrometry-services/mass-spectrometry-services-equipment/index.html
X-ray fluorescence detector
An instrument designed to capture characteristic "secondary" (or fluorescent) x-rays from a material that has been excited by bombarding with high-energy x-rays or gamma rays.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/X-ray_fluorescence
nebulizer
A medical device used to administer medication in the form of a mist inhaled into the lungs.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Nebulizer
CHN analyzer
An instrument which can determine the elemental composition of a sample. The name derives from the three primary elements measured by the device: carbon (C), hydrogen (H) and nitrogen (N). Sulfur (S) and oxygen (O) can also be measured.
Can be used to identify organic compounds.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/CHN_analyzer
reflectometer
An instrument for measuring the reflectance of a surface.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/reflectometer
electrosprayer
An instrument that is used to generate a very fine liquid aerosol through electrostatic charging, rather than gas (pneumatic) methods.
ESI source
PERSON: Nicole Vasilevsky
http://www.newobjective.com/electrospray/index.html
plunge freezing instrument
An instrument used to prepare frozen, hydrated specimens for cryo-electron microscopy. The technique fixes biological samples by ultra-rapid cooling to liquid nitrogen temperatures and below.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Cryo-electron_microscopy and http://en.wikipedia.org/wiki/Cryofixation
suction machine
A medical device used to drain fluids from the body (unwanted fluids, such as mucus and serum).
Can be used to suction fluids during surgery.
PERSON: Nicole Vasilevsky
http://www.ehow.com/list_5966694_suction-machine-uses.html
tendon vibrator
An instrument used to mechanically stimulate tendons with user-defined frequency, duration, and intensity.
Muscle vibrator for rehabilitation.
PERSON: Nicole Vasilevsky
http://mahilab.rice.edu/sites/mahilab.rice.edu/files/publications/111-Celik2009WHC.pdf
cancer cell line
A HeLa cell.
A cell line that is derived from a transformed cell that was part of a malignant tumor.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
Tumor cell line
embryonic cell line
A cell line derived from an embryo.
Embryo cell line
Mouse embryonic fibroblast cell line.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
fibroblast derived cell line
A cell line derived from a fibroblast; a connective tissue cell that makes and secretes collagen proteins.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://ghr.nlm.nih.gov/glossary=fibroblast
primary cell culture
A culture of primary lymphocytes.
Any cell line that has yet to be passaged and/or a cell that has not been immortalized.
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
Primary cells
stem cell derived cell line
A cell line that is derived from a stem cell.
Mouse embryonic fibroblasts
PERSON: Matthew Brush
PERSON: Matthew Brush
Placeholder for class to be imported from the Reagent Ontology (ReO).
Stem cell line
feasibility study
Dictionary of Epidemiology, 5th edition.
A preliminary study to determine the practicability of a proposed health program or procedure or of a larger study and to appraise the factors that may influence its practicability. A feasibility study aims to discover those things which may affect successful study conduct on a larger scale.
PERSON: Melanie Wilson
c-mount
An instrument that is used to position a digital camera in space.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/C_mount
forced convection oven
An oven that heats samples by moving of gas or liquid by using external surface forces such as a fan or pump.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Convection_oven
laryngograph
PERSON: Nicole Vasilevsky
Voice recording equipment used for recording the larynx movements in speech.
http://www.thefreedictionary.com/Laryngograph
dialysis system
A medical device used to provide an artificial replacement for lost kidney function through diffusion (waste removal) and ultrafiltration (fluid removal).
A patient suffering from kidney failure can utilize a dialysis system in place of normal kidney function.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Dialysis
fluid pressure measurement system
An instrument that quantifies fluid movement in a system.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Flow_measurement
multi-electrode array system
An instrument that contains multiple plates or shanks through which neural signals are obtained or delivered, essentially serving as neural interfaces that connect neurons to electronic circuitry.
MEA
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Multielectrode_array
sit up force table
A measurement instrument used to measure vertical and horizontal reaction forces as a person does a sit up.
A table that records the vertical and horizontal reaction forces.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
GPS navigation system
An iPhone has a built-in GPS.
An instrument that receives Global Positioning System (GPS) signals for the purpose of determining the device's current location on Earth.
GPS
Navigation system
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/GPS_navigation_device
autonomous underwater vehicle
A robot which travels underwater without requiring input from an operator.
A seaglider.
AUV
PERSON: Nicole Vasilevsky
Seaglider
http://en.wikipedia.org/wiki/AUV
reagent titrator
A measurement instrument used for performing a titration; the process, operation, or method of determining the concentration of a substance in solution by adding to it a standard reagent of known concentration in carefully measured amounts until a reaction of definite and known proportion is completed, as shown by a color change or by electrical measurement, and then calculating the unknown concentration.
PERSON: Nicole Vasilevsky
Titrator
http://www.thefreedictionary.com/titration
fibrometer
An instrument that measures clot formation (as in tests for blood clotting in vitro) by mechanical detection of the clot by a moving probe.
PERSON: Nicole Vasilevsky
http://www.drugs.com/dict/fibrometer.html
signal generator
An electronic test device that generates repeating or non-repeating electronic signals (in either the analog or digital domains).
Arbitrary waveform generator
Digital pattern generator
Frequency generator
Function generator
PERSON: Nicole Vasilevsky
Pitch generator
http://en.wikipedia.org/wiki/Signal_generator
comet assay analysis system
An instrument used to analyze comet assays which utilize gel electropheris on single cells exposed to a challenge, to provide quantitative information on DNA damage (DNA breakage).
Can be used to analyze cells after treatment with DNA damaging agents.
PERSON: Nicole Vasilevsky
PMID:7686265
SCGE assay analysis system
Single cell gel electrophoresis assay analysis system
decontamination chamber
An instrument designed to eliminate unwanted, poisonous or otherwise harmful substances, such as contaminants, noxious chemicals or radioactive material.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/decontamination
western processing system
An instrument designed to automate the immunodetection portion of western blot analysis workflow. The system performs blocking, antibody incubations and washing steps required for the detection in a consistent and reproducible way.
Automated western processing system
PERSON: Nicole Vasilevsky
Used to automate the Western blot process, to examine protein expression in cells.
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/PEIA-Misc/benchpro-4100-western-processing-system.html?CID=fl-benchpro
algometer
Algesichronometer
Algesiometer
Algonometer
An instrument used to measure pain threshold and pain tolerance.
Analgesia meter
Dolorimeter
PERSON: Nicole Vasilevsky
Pressure-algometer
Prick-algesimeter
Used in pain research and testing for pain medication.
http://en.wikipedia.org/wiki/Dolorimeter
micropressure measuring device
A measurement instrument used to determine fluid pressures in microscopic structures.
PERSON: Nicole Vasilevsky
http://vistaelectronicsco.com/servnull.shtml
eye tracking device
A measurement instrument used for measuring eye positions and eye movement.
Can be used to diagnose eye disorders.
Eye tracker
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Eye_tracking
visual stimulation equipment
An MRI visual stimulation system.
An instrument used for presenting visual stimuli for optical measurements and assessment.
PERSON: Nicole Vasilevsky
http://www.nordicneurolab.com/Products_and_Solutions/fMRI_Hardware/VisualSystem.aspx
auditory stimulation equipment
An instrument used for presenting auditory stimuli for auditory measurements and assessment.
Electrostatic ear-plug-style headphones.
PERSON: Nicole Vasilevsky
http://www.nordicneurolab.com/Products_and_Solutions/fMRI_Hardware/VisualSystem.aspx
fluid flow velocity measurement device
A fluid pressure measurement device designed to monitor flow velocity at one or more locations.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Flow_measurement
dynamometer
A measurement instrument used for measuring force, moment of force (torque), or power.
Can be used for musculoskeletal evaluations.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Dynamometer
nutritional educational device
A device used to teach topics relating to food and nourishment.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/nutrition
ussing chambers
A measurement instrument used to measure the short-circuit current as an indicator of net ion transport taking place across an epithelium.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Ussing_chamber
pressure isolator
An instrument that operates at a pressure higher than the atmospheric. This technology is used for the protection of any products inside the isolator from outside contaminants.
PERSON: Nicole Vasilevsky
http://www.mecalab.com/mecalab-glossary-isolator-posittive-pressure.htm
watercraft
A submarine.
An instrument that is a vessel or craft designed to move across or through water.
An instrument that is a vessel or craft designed to move across or through water.
PERSON: Nicole Vasilevsky
Ship
elemental analyzer
A measurement instrument used to analyze material for its elemental and sometimes isotopic composition.
Determination of the nitrogen content in a sample.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Elemental_analysis
submarine
An instrument that is designed to move across or through water and is capable of independent operation below the surface of the water.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Submarine
earphones
An instrument that consists of a pair of small loudspeakers, or less commonly a single speaker, held close to a user's ears and connected to a signal source such as an audio amplifier, radio, CD player or portable media player.
Earbuds
Headphones
Headsets
PERSON: Nicole Vasilevsky
Stereophones
Used to listen to music.
http://en.wikipedia.org/wiki/Headphones
curette
An instrument designed for scraping biological tissue or debris in a biopsy, excision, or cleaning procedure.
PERSON: Nicole Vasilevsky
Used in dentistry to clean teeth.
http://en.wikipedia.org/wiki/Curette
dental instrument
A dental drill.
An instrument used to diagnose, prevent, or treat diseases of the teeth, gums, and related structures of the mouth.
PERSON: Nicole Vasilevsky
http://www.thefreedictionary.com/dentistry
mouth mirror
A dental instrument that allows indirect vision by the dentist, reflecting light onto desired surfaces, and retraction of soft tissues.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Mouth_mirror
fluid measurement device
An instrument used to characterize a static or dynamic fluid.
Gingival crevicular fluid measurement device used for dentistry.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
periodontal probe
A dental instrument commonly used to measure pocket depths around a tooth in order to establish the state of health of the periodontium.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Periodontal_probe
mobile dental cart
An instrument used to safely and hygienically store and transport other dental instruments.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
filtration system
An instrument used to separate solids from fluids (liquids or gases) by interposing a medium through which only the fluid can pass.
Filtration of tissue culture media.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Filtration
hybridoma cell line
A cell line that derives from a hybrid cell resulting from the fusion of a lymphocyte and a tumor cell; used to culture a specific monoclonal antibody.
Hybridomas are often used to produce monoclonal antibodies.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://wordnetweb.princeton.edu/perl/webwn?s=hybridoma
plasma cleaner
An instrument used to automatically and quickly removes organic contamination (hydrocarbon) from electron microscopy (EM) specimens and specimen holders.
PERSON: Nicole Vasilevsky
http://www.fischione.com/products/model_1020.asp
ultrasonic cutter
An instrument that allows its blade to vibrate ultrasonically, enabling the blade to cut a wide range of materials.
PERSON: Nicole Vasilevsky
http://www.sonotec.com/ecutter.htm
fluid jet polisher
An instrument that uses a fine stream of slurry to accurately remove nanometers of material.
PERSON: Nicole Vasilevsky
http://www.lightmachinery.com/Fluid-Jet-Polishing.html
scanning transmission electron microscope
A transmission electron microscope where the electrons pass through a sufficiently thin specimen by focusing the electron beam into a narrow spot which is scanned over the sample in a raster.
For use in imaging of biological molecules.
PERSON: Nicole Vasilevsky
STEM
https://secure.wikimedia.org/wikipedia/en/wiki/Scanning_transmission_electron_microscopy
dimpler
A sample of silicon to be imaged by transmission electron microscopy can be pared to an appropriate thickness using a dimpler.
An instrument used for transmission electron microscopy sample preparation, which is a precision electro-mechanical metallographic lapping instrument.
PERSON: Nicole Vasilevsky
http://www.emsdiasum.com/microscopy/products/materials/dimpler.aspx
dry pumping station
An instrument that is used for pumping and housing transmission electron microscope holders to ensure the cryo holder is properly pumped out before use and is maintained in a clean and dry environment.
PERSON: Nicole Vasilevsky
http://www.cns.fas.harvard.edu/facilities/tool_detail.php?MID=264
diamond knife
An instrument that consists of a very sharp knife with a blade made from diamond, which is used for scientific applications where an extremely sharp and long-lasting edge is essential.
PERSON: Nicole Vasilevsky
Used to cut biospecimens into extremely thin slices or sections.
http://en.wikipedia.org/wiki/Diamond_knife
diagnostic device
A blood pressure cuff.
A medical device used to diagnose medical conditions.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
semiconductor stripper
An instrument used for plasma cleaning and stripping, for precise surface treatment and surface modification.
PERSON: Nicole Vasilevsky
Semiconductor cleaner
http://www.plasmaclean.com/
rapid thermal processor
An instrument used in the semiconductor manufacturing process which heats silicon wafers to high temperatures (up to 1,200 °C or greater) on a timescale of several seconds or less, which is used for a wide variety of applications in semiconductor manufacturing including dopant activation, thermal oxidation, metal reflow and chemical vapor deposition.
PERSON: Nicole Vasilevsky
RTP
https://secure.wikimedia.org/wikipedia/en/wiki/Rapid_thermal_processing
electron beam lithography system
An instrument which emits a beam of electrons in a patterned fashion across a surface covered with a resist film. The electrons expose the resist and allow for selective removal of either exposed or non-exposed regions of the resist.
E-beam lithography system
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electron_beam_lithography
reactive ion etcher
An instrument used for reactive-ion etching, an etching technology used in microfabrication.
PERSON: Nicole Vasilevsky
RIE
http://en.wikipedia.org/wiki/Electron_beam_lithography
electron beam physical vapor deposition system
An instrument that uses physical vapor deposition to generate thin films on substrates. In electron beam physical vapor deposition a target anode is bombarded with an electron beam given off by a charged tungsten filament under high vacuum. The electron beam causes atoms from the target to transform into the gaseous phase. These atoms then precipitate into solid form, coating everything in the vacuum chamber (within line of sight) with a thin layer of the anode material.
EBPVD
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electron_beam_physical_vapor_deposition
thermal evaporator
An instrument used for thin film deposition where metal wire is fed onto heated ceramic evaporators known as "boats" due to their shape. A pool of melted metal forms in the boat cavity and evaporates into a cloud above the source.
PERSON: Nicole Vasilevsky
Thermal deposition system
https://secure.wikimedia.org/wikipedia/en/wiki/Evaporation_%28deposition%29
chemical vapor deposition furnace
A chemical vapor deposition system used for annealing, the process of heating a material above its recrystallization temperature, maintaining a suitable temperature, and then cooling.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Annealing_%28metallurgy%29
ellipsometer
An instrument used for optical investigation of the dielectric properties (complex refractive index or dielectric function) of thin films.
Can be used for measurements on unstable liquid surfaces.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Ellipsometer
chemical vapor deposition system
An instrument used to produce high-purity, high-performance solid materials, often used in the semiconductor industry to produce thin films.
CVD system
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Chemical_vapor_deposition
maskless lithography system
An instrument that uses radiation that is focused to a narrow beam and is then used to directly write the image into photoresist, one or more pixels at a time.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Maskless_lithography
atomic layer deposition system
ALD system
An instrument that uses a thin film deposition technique that is based on the sequential use of a gas phase chemical process. The majority of ALD reactions use two chemicals, typically called precursors. These precursors react with a surface one-at-a-time in a sequential manner. By exposing the precursors to the growth surface repeatedly, a thin film is deposited.
PERSON: Nicole Vasilevsky
The construction of a mono-layer of aluminum oxide on a biological structure can be achieved by atomic layer deposition system.
https://secure.wikimedia.org/wikipedia/en/wiki/Atomic_layer_deposition
thermal oxidation furnace
An instrument that is used for the formation of silicon dioxide on a silicon surface for semiconductor manufacturing.
PERSON: Nicole Vasilevsky
http://www.siliconfareast.com/oxidation.htm
flip chip bonder
An instrument used for interconnecting semiconductor devices, such as IC chips and microelectromechanical systems (MEMS), to external circuitry with solder bumps that have been deposited onto the chip pads.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Flip_chip
wire bonder
An instrument that is used to make interconnections between an integrated circuit (IC) and a printed circuit board (PCB) during semiconductor device fabrication.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Wire_bonding
ion chromatograph
A chromatography device that allows the separation of ions and polar molecules based on their charge.
PERSON: Nicole Vasilevsky
Separation of proteins based on their charge.
http://en.wikipedia.org/wiki/Ion_chromatography
isotope ratio mass spectrometer
A mass spectrometer used to measure the relative abundance of isotopes in a given sample.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Isotope-ratio_mass_spectrometry
cryogenic mill
A milling machine designed for grinding and pulverizing tough and/or temperature sensitive samples immersed in liquid nitrogen.
PERSON: Nicole Vasilevsky
http://www.spexsampleprep.com/equipment-and-accessories/equipment_product.aspx?typeid=2
vacuum extraction line
An instrument used for vacuum extraction of materials for purification and analysis.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Used in plasmid purification kits.
thin film stress measurement system
An instrument used to measure thin film stresses in wafers via comparison of 2D and 3D topography maps before and after thin film deposition.
PERSON: Nicole Vasilevsky
http://www.frontiersemi.com/applications1.htm
fusion splicer
An instrument used to join two optical fibers end-to-end using heat.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Fusion_splicing
mechanical probe station
An instrument used to physically acquire signals from the internal nodes of a semiconductor device, often used in the failure analysis of semiconductor devices.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Mechanical_probe_station
cryogenic probe station
An instrument used for non-destructive testing of devices on full and partial wafers at low temperatures.
Cryogenic mechanical probe station
PERSON: Nicole Vasilevsky
http://www.lakeshore.com/sys/probestations/cpxpo.html
Hall effect measurement system
An instrument used to measure the Hall effect, the production of a voltage difference (the Hall voltage) across an electrical conductor, transverse to an electric current in the conductor and a magnetic field perpendicular to the current.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Hall_effect
scriber
An instrument that employs a "break wheel" that rolls over the length of a scribe line. The break wheel is shaped such that it places the wafer in three-point bending over an angled mandrel thereby applying tensile strain lateral to the scribe line. It is both the geometry of the wheel and the shape of the mandrel that control the strain placed on the scribe.
Cleaver
PERSON: Nicole Vasilevsky
http://www.loomisinc.com/products/lsd100_overview.html
spin rinse dryer
An instrument for cleaning silicon wafers. It spins the wafers and uses deionized water and nitrogen to clean and dry the wafers.
PERSON: Nicole Vasilevsky
SRD
http://grover.mirc.gatech.edu/equipment/textInstructions.php?id=56
dynamic light scattering instrument photon correlation spectrometer
A spectrophotometer based on the Photon Correlation Spectroscopy (PCS) technique and designed for measurements of sub-micron particle sizes, diffusion coefficients, viscosities, and molecular weights of polymers in basic and applied studies.
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Dynamic_light_scattering
laser cutter
An instrument that uses a laser to cut materials.
Laser engraver
Laser plotter
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Laser_cutting
total organic carbon analyzer
A chemistry analyzer used to measure the total organic carbon (TOC), the amount of carbon bound in an organic compound. It is often used as a non-specific indicator of water quality or cleanliness of pharmaceutical manufacturing equipment.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Total_organic_carbon
radial arm maze
A maze used to measure spatial learning and memory in rats.
PERSON: Nicole Vasilevsky
Used to study memory function in rat models after treatment with a experimental drug.
http://en.wikipedia.org/wiki/Radial_arm_maze
chemiluminescence analyzer
A Western blot can be detected by chemilluminescence.
An instrument used to detect chemiluminescence, the emission of light with limited emission of heat (luminescence), as the result of a chemical reaction.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Chemiluminescence
morris water maze
A maze used to study place-learning and memory in rodents, which consists of a round tank (pool) of water and an escape platform.
PERSON: Nicole Vasilevsky
Used to study memory function in rodents, in experimental conditions.
http://www.watermaze.org/
endotoxin detector
An instrument used to detect endotoxin and microbiological products by using an LAL test cartridge along with a handheld spectrophotometer to provide point-of-use results.
Can be used to test endotoxin contamination in an antibody stock.
PERSON: Nicole Vasilevsky
http://info.criver.com/endotoxin_and_rapid_microbiological_products/rapid_microbiological_methods/pts.html
exercise equipment
A mechanical instrument used for physical exercise.
A treadmill.
Exercise machine
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Exercise_machine
ergometer
Exercise equipment used for measuring the work a person exerts while exercising. It is often used in training, cardiac stress tests or other medical tests.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Exercise_machine
laser scanning cytometer
A cytometer that uses laser-based opto-electronics and automated analysis capabilities to simultaneously and rapidly measure biochemical constituents and evaluate cell morphologies.
PERSON: Nicole Vasilevsky
http://www.compucyte.com/laserscanning.htm
physical therapy pool
An instrument that holds a large body of water, which is used in physical medicine and rehabilitation.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Instruments_used_in_physical_medicine_%26_rehabilitation
electrometer
A measurement instrument used to measure electric charge or electrical potential difference.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electrometer
in vivo imaging system
An MRI is an in vivo imaging system.
An image acquisition instrument that is used to image processes taking place in a live organism.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
gas sterilizer
A sterilization instrument that functions by exposing the articles to be sterilized to high concentrations (typically 5 - 10% v/v) of very reactive gases (alkylating agents such as ethylene oxide, and oxidizing agents such as hydrogen peroxide and ozone).
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Sterilization_%28microbiology%29
cyclotron
An instrument used to accelerate charged particles using a high-frequency, alternating voltage (potential difference).
PERSON: Nicole Vasilevsky
https://secure.wikimedia.org/wikipedia/en/wiki/Cyclotron
dual MRI-PET scanner
An MRI scanner that is combined with a positron emission topography (PET) scanner, which displays both anatomic and metabolic information.
Can be used to evaluate brain activity and function.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
mass flow controller
An instrument used to control separate mass flow control valves or mass flow meters simultaneously.
PERSON: Nicole Vasilevsky
http://www.sablesys.com/products-prod_mfc-4.html?sub=details
precision measurement tool
A measurement instrument used for precise measurements.
A precision trim saw.
PERSON: Nicole Vasilevsky
http://www.starrett.com/metrology/metrology-products/precision-measuring-tools
fluid flow measurement
A material assay used for the quantification of bulk fluid movement.
Measurement of blood flow.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Flow_measurement
atomic absorption spectroscopy
A molecular assay used for the qualitative and quantitative determination of chemical elements employing the absorption of optical radiation (light) by free atoms in the gaseous state.
PERSON: Nicole Vasilevsky
Quantitation of chemical elements in a sample.
http://en.wikipedia.org/wiki/Atomic_absorption_spectroscopy
cardiac puncture
A specimen collection technique used to obtain a single, large, high-quality sample of blood from a euthanized organism or an organism under terminal anaesthesia if coagulation parameters, a separate arterial or venous sample or cardiac histology are not required.
PERSON: Nicole Vasilevsky
http://www.nc3rs.org.uk/bloodsamplingmicrosite/page.asp?id=343
fluid flow pressure measurement
A fluid flow measurement technique in which the pressure at one or many points in a fluid flow is collected.
Measurement of blood pressure.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
fluid flow velocity measurement
A flow measurement technique in which fluid velocity at one or many points in a flow is collected.
Measurement of blood flow velocity.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
recirculating immuno-magnetic separation
A material component separation technique used for the detection of materials, such as pathogens in samples, by recirculating samples over antibody-coated paramagnetic beads.
PERSON: Nicole Vasilevsky
RIMS
http://en.wikipedia.org/wiki/Pathatrix
gas chromatography
A chromatography technique used for separating and analyzing compounds that can be vaporized without decomposition.
Can be used to identify proteins.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Gas_chromatography
elemental analysis
A molecular assay used to analyze material for its elemental and sometimes isotopic composition.
Can be used to identify biomolecules.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Elemental_analysis
liquid chromatography
A chromatography technique in which the mobile phase is a liquid and is carried out either in a column or a plane for the purpose of separating mixtures.
PERSON: Nicole Vasilevsky
Used to identify protein sequences.
http://en.wikipedia.org/wiki/Chromatography#Liquid_chromatography
ion chromatography
A chromatography technique that allows the separation of ions and polar molecules based on their charge.
Ion-exchange chromatography
PERSON: Nicole Vasilevsky
Separation of proteins based on their charge.
http://en.wikipedia.org/wiki/Ion_chromatography
freeze drying
A material processing technique that uses a dehydration process, typically used to preserve a perishable material or make the material more convenient for transport.
Freeze drying of tissues for future use.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Freeze-drying
microinjection
Injection of substances into a single living cell at a microscopic or borderline macroscopic level using a glass micropipette.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Microinjection
fast protein liquid chromatography
A liquid chromatography technique where the solvent velocity, controlled by pumps, is used to produce a constant flow rate of solvents. The solvents are accessed through tubing from an outside reservoir.
Can be used for protein identification and characterization.
FPLC
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fast_protein_liquid_chromatography
subcellular fractionation
A material component separation technique used to separate homogeneous sets, usually organelles, from a heterogeneous population of cells.
PERSON: Nicole Vasilevsky
Subcelullar fractionation of nuclei and cytoplasm from cells.
http://en.wikipedia.org/wiki/Cell_fractionation
protein fingerprinting
A molecular assay used for identifying or differentiating proteins in a sample.
Identifying protein expression in an experimental sample compared to a control.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Protein_fingerprinting
computer aided design
A data transformation technique that uses computer technology for the process of design and design-documentation.
CADD
Can be used in architectural design.
Computer-aided design and drafting
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Computer-aided_design
karyotyping
A molecular assay used to determine the number and appearance of chromosomes in the nucleus of a eukaryotic cell.
Chromosomal analysis
Karyotyping of patient to determine if they carry a genetic disease.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Karyotype
community-based participatory research
A technique that identifies a unique skill set facilitating successful engagement of communities, which for any number of reasons might be less inclined to participate in more traditional research partnerships.
PERSON: Nicole Vasilevsky
PERSON: Quinton King
radiolabeling
A labeling technique used for tracking the passage of a sample of substance through a system. The substance is 'labeled' by including unusual isotopes in its chemical composition. If these unusual isotopes are later detected in a certain part of the system, they must have come from the labeled substance.
Isotopic labeling
PERSON: Nicole Vasilevsky
Radiolabeling of lipoproteins.
http://en.wikipedia.org/wiki/Isotopic_labeling
laser doppler flowmetry
An assay used for the real-time measurement of microvascular red blood cell (or erythrocyte) perfusion in tissue.
PERSON: Nicole Vasilevsky
http://www.discovtech.com/PAGE5.htm
cell adhesion assay
An assay used to screen and quantify the adhesive properties of cell-cell interactions or of cells to an immobilized substrate in vitro.
Analysis of cell adhesion of epithelial cells.
PERSON: Nicole Vasilevsky
http://www.millipore.com/catalogue/item/ecm645
sample loader
A sample loader on a light cycler PCR machine.
An instrument that holds samples for automatic loading onto an instrument, such as a flow cytometer or PCR machine.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Sample carousel
helper plasmid
A packaging plasmid that is co-transfected with a viral plasmid.
A plasmid that allows for the beginning of replication and transfer of other plasmids from a donor to a recipient. Without a helper plasmid, transposons will not be expressed in the recipient.
PERSON: Nicole Vasilevsky
Placeholder for class to be imported from the Reagent Ontology (ReO).
http://wiki.answers.com/Q/What_is_a_helper_plasmid
immunotechnique
A technique that uses an antibody reagent.
Antibody technique
PERSON: Matthew Brush
PERSON: Nicole Vasilevsky
flow cytometry immunoassay
A flow cytometry assay in which individual particles, such as cells or molecules are labeled with an antibody.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
snap freeze
Flash freeze
Low temperature, rapid freezing of tissue that is usually achieved by submersion in liquid nitrogen.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
material antibody target
A material entity that has as part some molecular antigen that is recognized by an antibody.
PERSON: Matthew Brush
PERSON: Matthew Brush
to be imported from ReO.
biological target
A material entity of biological origin (ie produced by or deriving from an organism) that has as part some molecular antigen that is recognized by an antibody.
Note that these subclasses will be replaced with equivalent classes that are CARO types with antibody target or immunogen roles.
PERSON: Matthew Brush
PERSON: Matthew Brush
chemical target
A non-biological chemical entity (a compound, molecule or aggregate) that has as part some molecular antigen that is recognized by an antibody.
PERSON: Matthew Brush
PERSON: Matthew Brush
whole organism or virus target
An organism or virus that has as part some molecular antigen that is recognized by an antibody.
PERSON: Matthew Brush
PERSON: Matthew Brush
gross anatomical target
A gross anatomical entity (anatomical entities at scale above cell but below organism) that has as part some molecular antigen that is recognized by an antibody.
PERSON: Matthew Brush
PERSON: Matthew Brush
cell target
A cell that has as part some molecular antigen that is recognized by an antibody.
PERSON: Matthew Brush
PERSON: Matthew Brush
biomolecule target
A molecular entity of biological origin that is recognized by an antibody.
PERSON: Matthew Brush
PERSON: Matthew Brush
nucleic acid target
A polynucleotide or nucleic acid this is recognized by an antibody.
BrdU incorporating nucleic acids.
PERSON: Matthew Brush
PERSON: Matthew Brush
carbohydrate target
A carbohydrate molecule or complex that is recognized by an antibody.
Glycans that are linked to protein.
PERSON: Matthew Brush
PERSON: Matthew Brush
lipid target
A lipid that is recognized by an antibody.
Membrane phospholipids.
PERSON: Matthew Brush
PERSON: Matthew Brush
protein target
A peptide, protein, or protein complex that is recognized by an antibody.
A phospho-Akt protein or GAPDH protein.
PERSON: Matthew Brush
PERSON: Matthew Brush
immunogenic material
A material entity that has as part some molecular immunogen that stimulates an adaptive immune response upon interacting with a surface immunoglobulin receptor on a naive B cell, leading to proliferation and differentiation of naïve B cells into memory B cells and antibody secreting plasma cells.
PERSON: Matthew Brush
PERSON: Matthew Brush
cellular component target
A celllular component that has part some molecular antigen that is recognized by an antibody.
PERSON: Matthew Brush
PERSON: Matthew Brush
biologic intervention
A monoclonal antibody intervention used to treat rheumatoid arthritis.
An intervention involving use of medicinal product(s) created by biologic processes, rather than being chemically synthesized. For example, a vaccine, blood or blood component, allergenic, somatic cell, gene therapy, tissue, recombinant therapeutic protein, or living cells.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Biologic
data
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
Data items include counts of things, analyte concentrations, and statistical summaries.
Most of the data subclasses canbe defined as output of a specific assay.
PERSON: Melissa Haendel
PERSON: Melissa Haendel
nucleic acid purification
A purification technique that involves separation of nucleic acids from other impurities, such as bacteria or other contaminating materials for the purpose of molecular biology research.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
Purification of nucleic acids from blood.
gel imaging
An imaging assay to produce an image of a laboratory gel.
Imaging of a polyacrylamide gel stained stained with coomassie.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
x-ray film processing
A material processing technique used to develop images that have been exposed to x-ray film.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
nanoparticle imaging
An imaging assay that makes use of the unique properties of nanoparticles to elucidate specific targets in an image.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
grid computing
A data processing technique that makes use of federated computer resources from multiple administrative domains to reach a common goal. The grid can be thought of as a distributed system with non-interactive workloads that involve a large number of files. What distinguishes grid computing from conventional high performance computing systems such as cluster computing is that grids tend to be more loosely coupled, heterogeneous, and geographically dispersed.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Grid_computing
electrical capacitance tomography
An imaging technique used to produce an image of the dielectric permittivity distribution in the interior of an object from external capacitance measurements.
ECT
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Electrical_capacitance_tomography
electrical impedance tomography
An imaging technique in which an image of the conductivity or permittivity of a specimen is inferred from surface electrical measurements.
EIT
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Electrical_impedance_tomography
bioreactor fermentation
A chemical synthesis technique that uses a device designed to support biologicall active organisms, which convert nutrients to alcohols and acids via an energy-yielding anaerobic metabolic process.
Fermentation
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Bioreactor
recirculating immuno-magnetic separation instrument
An instrument used for the detection of materials, such as proteins, in samples by recirculating samples over antibody-coated paramagnetic beads.
PERSON: Nicole Vasilevsky
RIMS instrument
http://en.wikipedia.org/wiki/Pathatrix
single-cell gene expression analysis
A gene expression analysis technique able to resolve gene expression at the resolution of an individual cell.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
focused ion beam imaging
An imaging technique that utilizes a relatively low-current focused ion beam to produce a topographical image of a sample by analyzing the trajectory of secondary electrons and secondary ions that are produced by the primary ion beam's interaction with the sample surface.
FIB imaging
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Focused_ion_beam#FIB_imaging
grinder and polisher
A polisher that performs both grinding and polishing functions on samples.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
Polisher and grinder
thermogravimetric analyzer
An instrument used to determine the percent mass ratio of a solute by heating it to the point that one of the components decomposes into a gas while carefully monitoring the mass of the sample.
PERSON: Scott Hoffmann
https://en.wikipedia.org/wiki/Thermogravimetric_analysis
morphometry
A technique that deals with quantitative analysis of form, a concept that encompasses size and shape. Morphometric analyses are commonly performed on organisms, and are useful in analyzing their fossil record, the impact of mutations on shape, developmental changes in form, covariances between ecological factors and shape, as well for estimating quantitative-genetic parameters of shape.
PERSON: Scott Hoffmann
https://en.wikipedia.org/wiki/Morphometry
morphology analysis
vector network analyzer
Electronic test equipment used to measure the network parameters of electrical networks. Network analyzers commonly measure s-parameters, y-parameters, z-parameters, and h-parameters. Network analyzers are often used to characterize two-port networks such as amplifiers and filters, but they can be used on networks with an arbitrary number of ports.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Network_analyzer_%28electrical%29
hot embosser
An instrument used to stamp a pattern into a polymer softened by raising the temperature of the polymer just above its glass transition temperature. The stamp is used to define a pattern in the polymer that can be used for the micromachining of silicon.
PERSON: Scott Hoffmann
http://www.mems-exchange.org/catalog/hot_embossing/
interferometer
An instrument that uses the superimposition of electromagnetic waves to extract information about the waves.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Interferometry
mechanical testing system
An instrument that is used for static testing in a tensile or compression mode within a single frame. They are also referred to as pull testers. Additional test types include tensile, compression, shear, flexure, peel, tear, cyclic, and bend tests.
Electromechanical testing machine
MTS
PERSON: Scott Hoffmann
Pull tester
Tensile tester
Tensile testing machine
Universal testing machine
http://www.instron.us/wa/product/Universal-Electromechanical-Systems.aspx
porosimiter
An instrument that is used to determine various quantifiable aspects of a material's porous nature, such as pore diameter, total pore volume, surface area, and bulk and absolute densities.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Porosimetry
UV light source
A light source that emits electromagnetic radiation with a wavelength shorter than that of visible light, but longer than X-rays, in the range 10 nm to 400 nm, and of energies from 3 eV to 124 eV.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/UV
air monitoring instrument
Air quality monitoring instrument
Air sampling instrument
An instrument used to detect various gases, chemicals, and particulates in ambient air or air emissions.
PERSON: Scott Hoffmann
http://www.pine-environmental.com/air-monitoring.htm#content
DNA shearing instrument
An instrument used to fragment DNA molecules by mechanical force.
PERSON: Nicole Vasilevsky
http://www.mondofacto.com/facts/dictionary?DNA+shearing
nucleic acid shearing instrument
four-terminal resistance sensor
4-point probe
4-wire sensor
4T sensors
An electrical impedance measuring instrument that uses separate pairs of current-carrying and voltage-sensing electrodes to make accurate measurements that can be used to compute a material's electrical resistance.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Four-terminal_sensing
monochromator
An optical device that transmits a mechanically selectable narrow band of wavelengths of light or other radiation chosen from a wider range of wavelengths available at the input.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Monochromator
engraving system
An instrument used for incising a design on to a hard, usually flat surface, by cutting grooves into it.
PERSON: Scott Hoffmann
engraver
http://en.wikipedia.org/wiki/Engraving
targeted mutation analysis
A nucleic acid assay for testing for either a nucleotide repeat expansion (e.g., the trinucleotide repeat expansion associated with Huntington disease) or one or more specific mutations (e.g., Glu6Val for sickle cell anemia, a panel of mutations for cystic fibrosis). Deletion/duplication analysis and family-specific mutation analysis are excluded from this definition.
Allele-specific oligonucleotide testing
Analysis of the entire coding region: Mutation scanning
Analysis of the entire coding region: Sequence analysis
PERSON: Nicole Vasilevsky
Southern blot
Trinucleotide repeat testing
http://www.ncbi.nlm.nih.gov/books/NBK5191/?rendertype=def-item&id=targeted-mutation-analysis
field emission gun
FEG
PERSON: Scott Hoffmann
An instrument in which a sharply-pointed electron emitter is held at several kilovolts negative potential relative to a nearby electrode, so that there is sufficient potential gradient at the emitter surface to cause field electron emission.
http://en.wikipedia.org/wiki/Field_emission_gun
denaturing high performance liquid chromatography
An HPLC technique that uses reversed-phase HPLC to interrogate SNPs.
Denaturing HPLC
PERSON: Nicole Vasilevsky
https://en.wikipedia.org/wiki/Dhplc#Denaturing_high_performance_liquid_chromatography
automated flow cell cluster generation station
Instrument that is a specialized robot that combines multiple functions of library development for next generation sequencing including, immobilization of the sample to templates, "bridge"-amplification, linearization, blocking and primer hybridization.
PERSON: Nicole Vasilevsky
PERSON: R Steen (Harvard lab user)
oven
An instrument used for heating materials at high temperatures.
An oven is used for baking bread.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Oven
hydraulic press
A machine press that uses a hydraulic cylinder to generate a compressive force.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Hydraulic_press
high temperature furnace
An instrument used for heating materials at high temperatures.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
dual energy x-ray absorptiometry
A technique used to measure bone mineral density (BMD). Two X-ray beams with differing energy levels are aimed at the patient's bones. When soft tissue absorption is subtracted out, the BMD can be determined from the absorption of each beam by bone.
DEXA
DXA
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Dual-energy_X-ray_absorptiometry
mycoplasma testing
An assay performed to detect mycoplasma contamination in a sample.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
nitrogen evaporator
An instrument that is used to heat samples frozen with chilled nitrogen in a controlled manner.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
isothermal titration calorimeter
An instrument used to determine the thermodynamic parameters of interactions in solution. It is most often used to study the binding of small molecules (such as medicinal compounds) to larger macromolecules (proteins, DNA etc.).
PERSON: Nicole Vasilevsky
https://en.wikipedia.org/wiki/Isothermal_titration_calorimetry
fluorescence anisotropy analyzer
An instrument used for measuring molecular rotation or tumbling by observing the loss of polarization of light emitted by a fluorophore or the decorrelation of polarization between the exciting and emitted (fluorescent) photon.
PERSON: Nicole Vasilevsky
https://en.wikipedia.org/wiki/Fluorescence_anisotropy
drop shape analyzer
An instrument used to measure contact angles and thereby determine surface energy.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
www.firsttenangstroms.com/pdfdocs/CAPaper.pdf
field flow fractionator
An instrument in which a field is applied to a fluid suspension or solution pumped through a long and narrow channel, perpendicular to the direction of flow, in order to cause separation of the particles present in the fluid, dependent on their differing "mobilities" under the force exerted by the field.
PERSON: Nicole Vasilevsky
https://en.wikipedia.org/wiki/Field_flow_fractionation
sedimentation field flow fractionator
A field flow fractionator that uses gravity as the field in which differences in mobility are exploited to separate a mixture.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Field_flow_fractionation
hydrodynamic field flow fractionator
A field flow fractionator in which an electric field controls the velocity by controlling the lateral position of either a charged (having electrophoretic mobility) or polarized (being levitated in a non-uniform field) species in a capillary channel with a hydrodynamically parabolic flow-velocity profile. In this way, the velocity of the pumped fluid is highest midway between the walls of the channel and it monotonically decays to a minimum of zero at the wall surface.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Field_flow_fractionation
static light scattering analyzer
An instrument which measures the intensity of the scattered light to obtain the average molecular weight Mw of a macromolecule like a polymer or a protein.
PERSON: Nicole Vasilevsky
https://en.wikipedia.org/wiki/Static_light_scattering
polarimeter
A measurement instrument to measure optical rotation of "optically active matter" such as saccharin, ascorbic acid and sodium glutamate.
PERSON: Nicole Vasilevsky
http://www.atago.net/english/products_polari.php#03
protein microarray assay
A protein assay used to measure changes in protein expression levels, identify protein–protein interactions, to identify the substrates of protein kinases, to identify transcription factor protein-activation, or to identify the targets of biologically active small molecules. The array is a piece of glass on which different molecules of protein or specific DNA binding sequences (as capture probes for the proteins) have been affixed at separate locations in an ordered manner thus forming a microscopic array.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Protein_microarray
muscle lever system
An measurement instrument used for measuring the dynamic physical properties of muscles and connective tissues.
PERSON: Scott Hoffmann
http://www.aurorascientific.com/product/series-300/
bi-phase stimulator
A stimulator which can provide positive, negative or alternating (bi-phase) pulses.
PERSON: Scott Hoffmann
http://www.aurorascientific.com/product/mp-model-701/
muscle test system
A measurement instrument for evaluating the mechanical characteristics of intact muscle, either isolated in situ, ex vivo, or isolated in vitro.
PERSON: Scott Hoffmann
http://www.aurorascientific.com/product/mp-model-1300/
force transducer
An signal conversion instrument used to convert measured forces into electrical output signals.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
histone modification analysis
A protein assay to detect modification to histones such as lysine acetylation, lysine and arginine methylation, serine and threonine phosphorylation, and lysine ubiquitination and sumoylation.
PERSON: Nicole Vasilevsky
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/epigenetics-noncoding-rna-research/Epigenetics-Learning-Center/Chromatin/Histone-Modification.html
hematoxylin and eosin stain
A histology technique that involves the staining of cells with a blue nuclear stain, hemalum followed by counterstaining with eosin, which stains eosinophilic structures in various shades of red, pink and orange.
H&E stain
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/H%26E_stain
antibody modification
Material processing of antibody to modify the antibody in a specific way, such as labeling, conjugating or fragmenting the antibody.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
exome sequencing
A DNA sequencing assay in which the coding regions of the genome are selectively sequenced.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Exome_sequencing
targeted exome capture
dual polarization interferometry
DPI
PERSON: Scott Hoffmann
Protein-protein interaction detection that uses a waveguide coated with adsorbed proteins and the evanescent wave of a laser beam confined to the waveguide to determine interaction properties of the adsorbed molecular scale layers.
http://en.wikipedia.org/wiki/Dual_polarization_interferometry
microscale thermophoresis
MST
PERSON: Scott Hoffmann
Protein-protein interaction detection that uses directed movement of particles in a microscopic temperature gradient to analyze biomolecules.
http://en.wikipedia.org/wiki/Microscale_thermophoresis
robotics
Material production that deals with design, construction, operation, structural disposition, manufacture and application of robots and computer systems for their control, sensory feedback, and information processing.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Robotics
peptide synthesis
A biomolecule synthesis technique in which amino acids are linked by amide bonds to form peptides.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Peptide_synthesis
antibody conjugation
A biomolecule synthesis technique in which an antibody is linked to another molecule.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
peptide conjugation
A biomolecule synthesis technique which joins a peptide to another peptide.
PERSON: Scott Hoffmann
http://www.pbcpeptide.com/Conjugation.htm
protein conjugation
A biomolecule synthesis technique which joins two or more proteins.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Conjugated_protein
differential scanning calorimetry
A calorimetry technique in which the difference in the amount of heat required to increase the temperature of a sample and reference is measured as a function of temperature. Both the sample and reference are maintained at nearly the same temperature throughout the experiment.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Differential_scanning_calorimetry
isothermal titration calorimetry
A calorimetry technique which is used to determine the thermodynamic parameters of interactions in solution at constant temperature.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Isothermal_titration_calorimetry
pressure perturbation calorimetry
A calorimetry technique which measures differential heat change in a solution when the pressure above the solution is changed. The differential heat change is used to calculate volumetric properties of the solution.
PERSON: Scott Hoffmann
http://www.microcal.com/products/software-accessories/pressure-perturbation-calorimetry.asp
analytical ultracentrifugation
A centrifuge technique where the concentration distribution of the sample is determined at known times using absorbance measurements.
AUC
PERSON: Scott Hoffmann
http://www.bioc.rice.edu/bios576/AU/AU_Page.html#au
size-exclusion chromatography
A chromatography technique in which molecules in solution are separated by their size, and in some cases molecular weight.
PERSON: Scott Hoffmann
SEC
http://en.wikipedia.org/wiki/Size-exclusion_chromatography
size exclusion chromatography
protein crystallization
A crystallization technique in which individual protein molecules align themselves in a repeating series of unit cells by adopting a consistent orientation. The crystalline lattice that forms is held together by noncovalent interactions.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Protein_crystallization
image correlation spectroscopy
A confocal microscopy technique in which a fluorescence correlation spectroscopy experiment is repeated in multiple spatial points in parallel, using a laser scanning confocal microscope.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Fluorescence_correlation_spectroscopy#Image_correlation_spectroscopy_.28ICS.29
transmitted light microscopy
A light microscopy technique in which light is transmitted from a source on the opposite side of the specimen from the objective.
PERSON: Scott Hoffmann
http://www.gonda.ucla.edu/bri_core/trlight.htm
surface-enhanced laser desorption/ionization mass spectrometry
A mass spectrometry technique in which a protein mixture is spotted on a surface modified with a chemical functionality. Selective binding to this surface acts as a separation step and the subset of proteins that bind to the surface are analyzed.
PERSON: Scott Hoffmann
SELDI
http://en.wikipedia.org/wiki/Surface-enhanced_laser_desorption/ionization
chemical ionization mass spectrometry
A mass spectrometry technique in which trace neutral gases are converted to unique ions by reaction with a suitable precursor ion. The ions can then be detected without interference from background atmospheric species since there is virtually no ion background in the atmosphere.
CIMS
PERSON: Scott Hoffmann
http://cloud1.arc.nasa.gov/solve/payload/dc8/cims8.html
high resolution mass spectrometry
A mass spectrometry technique which generates data with improved resolution by better separation of peaks.
HR-MS
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Resolution_%28mass_spectrometry%29
matrix-assisted laser desorption ionization time-of-flight mass spectrometry
A mass spectrometry technique which uses soft ionization to allow analysis of biomolecules and large organic molecules, which tend to be fragile and fragment when ionized by more conventional ionization methods.
MALDI TOF
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization
electrospray ionization mass spectrometry
A mass spectrometry technique which uses soft ionization to determine the molecular weights of proteins, peptides, and other biological macromolecules by turning the macromolecule being ionized into small droplets.
ESI-MS
PERSON: Scott Hoffmann
http://chemwiki.ucdavis.edu/Analytical_Chemistry/Instrumental_Analysis/Mass_Spectrometry/Electrospray_Ionization_Mass_Spectrometry
off-gel isoelectric focusing
A material component separation techique which fractionates proteins and peptides in solution according to their isoelectric point (pI).
IEF
OGE
PERSON: Scott Hoffmann
http://www.chibi.ubc.ca/pcf/instruments/offgel
free flow electrophoresis
A material component separation technique used to fractionate preparatively charged particles ranging in size from molecular to cellular dimensions according to their electrophoretic mobilities (EPMs) or isoelectric points (pIs) without a stationary phase.
FFE
Off-gel electrophoresis
PERSON: Scott Hoffmann
http://www.aesociety.org/areas/ffe1.php
electroblot
A material component separation technique used to transfer proteins or nucleic acids onto a PVDF or nitrocellulose membrane after gel electrophoresis.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Electroblotting
solid phase isoelectric focusing
A material component separation technique that combines solid-phase microextraction (SPME) and capillary electrophoresis (CE) to extract specific components from a sample.
PERSON: Scott Hoffmann
http://chromsci.oxfordjournals.org/content/44/6/366.abstract
chiral separation
A material component separation technique that is used for the separation of racemic compounds into their enantiomers.
PERSON: Scott Hoffmann
chiral resolution
http://en.wikipedia.org/wiki/Chiral_resolution
optical resolution
competent cell production
A material processing technique that is used to generate and sustain cells with the ability to take up extracellular ("naked") DNA from their environments, usually by heat shock or electroporation.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Natural_competence
scanning probe microscopy
A microscopy technique in which a representation of a surface characteristic is generated by sweeping an extremely sharp probe (3-50 nm radius of curvature) across the sample's surface.
PERSON: Scott Hoffmann
SPM
http://www.mobot.org/jwcross/spm/
phase contrast microscopy
A microscopy technique that converts phase shifts in light passing through a transparent specimen to brightness changes in the image.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Phase_contrast_microscopy
differential interference contrast microscopy
A microscopy technique used to enhance the contrast in unstained, transparent samples by using the principle of interferometry to gain information about optical path lengths through the sample.
DIC microscopy
NIC microscopy
Nomarski interference contrast microscopy
Nomarski microscopy
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Differential_interference_contrast_microscopy
intravital microscopy
A microscopy technique used to observe biological systems in vivo at high resolution through an attached window preparation.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Intravital_microscopy
structured illumination microscopy
A microscopy technique which illuminates cells with stripes of light called an interference pattern and has a resolution of about 100 nanometers.
PERSON: John Sedat
PERSON: Scott Hoffmann
multiphoton microscopy
A microscopy technique that images samples by illuminating them with pulsed, long-wavelength light to excite fluorophores within the specimen being observed.
MFM
Multiphoton fluorescence microscopy
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Multiphoton_fluorescence_microscope
ion beam microscopy
A microscopy technique that uses secondary electrons and secondary ions from a low-energy focused ion beam to generate an image of the sample.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Focused_ion_beam#FIB_imaging
ion torrent next generation sequencing
A next generation sequencing that monitors the incorporation of a nucleotide into a strand of DNA by sensing pH change from the release of a hydrogen ion corresponding to a bonding event.
Ion torrent NGS
NGS
PERSON: Scott Hoffmann
http://uagc.arl.arizona.edu/index.php/next-gen-sequencing-services/ion-torrent.html
peptide nucleic acid synthesis
PERSON: Nicole Vasilevsky
PNA synthesis
Synthesis of a peptide nucleic acid polymer, in which the phosphate ribose ring of DNA is replaced with the polyamide backbone, that functions as a DNA analog.
http://www.panagene.com/eng/menu2/menu2_1.php
methylation analysis
A nucleic acid assay which analyzes DNA for the presence of a methyl group(s) on the 5-carbon of cytosine in a CpG dinucleotide.
PERSON: Scott Hoffmann
http://www.protocol-online.org/prot/Molecular_Biology/DNA/Methylation_analysis/index.html
heteroduplex mutation detection
A nucleic acid assay that is used to detect double-stranded (duplex) molecules of nucleic acid originatinating from the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Heteroduplex
native polyacrylamide gel electrophoresis
An electrophoresis technique in which complexes remain—for the most part—associated and folded as they would be in the cell.
Native PAGE
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Native_gel_electrophoresis#Native
linear-after-the-exponential PCR
A polymerase chain reaction technique that uses multiple special primers per target to generate single stranded amplicons after a short period of exponential amplification. This enables the detection of low numbers of target organisms, performance of endpoint analysis, significantly increased levels of multiplexing in an assay, and the ability to identify and differentiate bacteria at the strain level.
LATE PCR
PERSON: Scott Hoffmann
http://www.smithsdetection.com/technology_LATE_PCR.php
multidimensional protein identification technology
A protein assay used to identify proteins from complex mixtures. The technique consists of a 2-dimensional chromatography separation, prior to electrospray mass spectrometry. By exploiting a peptide's unique physical properties of charge and hydrophobicity, complex mixtures can be separated prior to sequencing by tandem MS. The first dimension is normally a strong cation exchange (SCX) column, as these have high loading capacities. The second dimension is reverse phase chromatography (RP), which complements the SCX as it is efficient at removing salts and has the added advantage of being compatible with electrospray mass spectrometry.
MudPIT
PERSON: Scott Hoffmann
http://www.proteome.soton.ac.uk/mudpit.htm
albumin depletion
Material component separation of albumin from a biological sample.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
mass spectrometry protein sequencing
A protein sequencing assay in which peptides are ionized, fragmented run through a mass spectrometer such that the mass-to-charge ratios of the fragments can be measured and analyzed to determine the protein's sequence.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Protein_sequencing#Mass_spectrometry
fluorescence correlation spectroscopy
A spectrophotometry technique used to measure the correlation of fluctuation of the fluorescence intensity to determine the parameters of the physics under the fluctuations with the end result of characterizing a molecule.
FCS
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Fluorescence_correlation_spectroscopy
circular dichroism spectroscopy
A spectrophotometry technique that uses the differential absorption of left and right circularly polarized light for structural studies of small organic molecules, proteins and DNA
CD spectroscopy
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Circular_dichroism
atom probe tomography
APT
An imaging technique in which the atoms from a sharp-tipped sample are progressively removed from the tip and collected on a planar detector. Data from the detector is used to reconstruct a 3D image of the material on the atomic scale.
PERSON: Scott Hoffmann
http://www.imago.com/instruments-for-research/atom-probe.aspx
aptamer screening
A high throughput sample analysis technique in which oligonucleic or peptide aptamers are screened for specific binding capacity for a target.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Aptamer
high content screening
An image analysis technique combining automated fluorescence microscopy with multi-parameter quantitative image analysis for the large scale study of cells (cellomics).
HCA
HCS
High content analysis
Imaging cytometry
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/High-content_screening
DNA library screen
A nucleic acid assay where particular DNA sequences can be detected in a DNA library using nucleic acid probes.
PERSON: Nicole Vasilevsky
http://www.link.vet.ed.ac.uk/clive/cal/dna_1/4_lib_screen.htm
homozygosity mapping
A nucleic acid assay used to map the genome of an organism, that is used to detect genes that confer to a specific phenotype only when both copies in an individual are mutated (i.e. the genes are homozygous, or the same).
PERSON: Nicole Vasilevsky
http://biotech.about.com/b/2009/01/26/homozygosity-mapping-for-outbred-individuals.htm
RNA sequencing
A nucleic acid assay that uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact using a sequencer instrument.
OBI
PERSON: Nicole Vasilevsky
RNA-Seq
Transcriptome sequencing
antibody-dependent cell-mediated cytotoxicity assay
ADCC assay
An in vitro cytotoxicity assay that measures cytotoxicity of specific molecules or cells to antibody-bound targets.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
shotgun proteomics
A protein assay used for identifying proteins in complex mixtures by a combination of high performance liquid chromatography and mass spectrometry.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Shotgun_proteomics
multiple reaction monitoring
A mass spectrometry assay that is highly sensitive and selective, for the targeted quantitation of protein/peptide abundances in complex biological samples.
MRM
PERSON: Nicole Vasilevsky
SRM
Selective reaction monitoring
http://www.mrmproteomics.com/multiple-reaction-monitoring-mrm.html
antibody epitope mapping
A protein assay used to identify the binding sites, or ‘epitopes’, that are recognized by antibodies.
PERSON: Nicole Vasilevsky
http://www.nature.com.liboff.ohsu.edu/nmeth/journal/v5/n12/full/nmeth.1272.html
peptide mapping
A molecular assay used to map peptide sequences. Produced by using either proteolytic enzymes such as trypsin or chemicals such as cyanogen bromide to cut proteins at a relatively small number of particular sites, the peptide fragments are then separated by chromatographic or electrophoretic procedures.
PERSON: Nicole Vasilevsky
Peptide fingerprinting
http://medical-dictionary.thefreedictionary.com/Peptide+mapping
antibody isotype analysis
A protein assay that is used to determine the genetic variations or differences in the constant regions of the antibody heavy and light chains, such as IgG, etc..
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Isotype_%28immunology%29
isobaric tags for relative and absolute quantitation
A protein assay used to quantify proteins from different sources using isotope-coded covalent tags. iTRAQ is used in proteomics to study quantitative changes in the proteome.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Isobaric_tag_for_relative_and_absolute_quantitation
iTRAQ
amino acid analysis
A protein assay that provides detailed information regarding the relative amino acid composition and free amino acids in a protein.
PERSON: Nicole Vasilevsky
http://www.sigmaaldrich.com/analytical-chromatography/analytical-reagents/amino-acid-analysis.html
lipoprotein isolation
A protein assay which makes use of characteristic densities of various types of lipoproteins to rapidly isolate them by density gradient centrifugation.
PERSON: Scott Hoffmann
http://www.sfu.ca/bisc/bisc-429/lipoprotein.html
peptide mass fingerprinting
A mass spectrometry assay in which an unknown protein of interest is cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer. These masses are then compared to values in a database containing known protein sequences.
PERSON: Scott Hoffmann
PMF
Peptide mass mapping
http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting
small molecule identification
A molecular used to identify targets of small molecules for potential use in drug discovery or similar applications.
PERSON: Nicole Vasilevsky
http://www.broadinstitute.org/scientific-community/science/programs/chemical-biology/project-target-pathway-id/small-molecule-targ
mass spectrometry data analysis
Data analysis of mass spectrometry data to identify proteins in a sample.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
antibody purification
A protein purification technique which involves selective enrichment or specific isolation of antibodies from serum (polyclonal antibodies), ascites fluid or cell culture supernatant of a hybridoma cell line (monoclonal antibodies).
PERSON: Scott Hoffmann
http://www.piercenet.com/browse.cfm?fldID=4E032172-5056-8A76-4EAE-8D395D2DCDA3#intro
bacterial based recombinant protein production
A recombinant protein production technique where bacteria are used as a host for recombinant plasmids expressing a protein of interest and are grown in culture and can be induced to produce the target protein.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
insect cell based recombinant protein production
A recombinant protein production technique where insects cells are used as a host for recombinant plasmids expressing a protein of interest and are grown in culture and can be induced to produce the target protein.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
mammalian cell based recombinant protein production
A recombinant protein production technique where mammalian cells are used as a host for recombinant plasmids expressing a protein of interest and are grown in culture and can be induced to produce the target protein.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
inductively coupled plasma atomic emission spectroscopy
A spectrophotometry technique that exploits the fact that excited electrons emit energy at a given wavelength as they return to ground state.
ICP-AES
PERSON: Scott Hoffmann
http://www-odp.tamu.edu/publications/tnotes/tn29/technot2.htm
fluorescence anisotropy
A spectrophotometry technique that makes use of the phenomena whereby light emitted by a fluorophore has unequal intensities along different axes of polarization to analyze the physical properties of a sample molecule.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Fluorescence_anisotropy#Applications
Raman spectroscopy
A spectroscopy technique that uses inelastic scattering, or Raman scattering, of monochromatic light used to study vibrational, rotational, and other low-frequency modes in a system.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Raman_spectroscopy
immunophenotyping
A protein assay used to determine cellular protein expression using antibody-based assays such as flow cytometry or immunocytochemistry.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
microbial testing
An assay used to detect the presence of microorganisms in a sample.
PERSON: Scott Hoffmann
http://www.wisegeek.com/what-is-a-microbial-test.htm
polyacrylamide gel electrophoresis
An electrophoresis technique that is used to separate molecules on a polyacrylamide gel based their size.
PAGE
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/SDS-PAGE
differential gel electrophoresis
An electrophoresis technique used to monitor the differences in proteomic profile between cells in different functional states. This is done in three steps. First, samples are tagged with unique flourescent dyes. Second, they are run together on the same 2D-PAGE gel. Finally, after the run completes, the different fluorescent images of the same gel are superimposed over each other. DIGE allows the study of proteins that are expressed differentially, as well as those that are common between samples. This technology allows for simultaneous separation and comparison of up to three samples on one gel.
DIGE
Differential in gel electrophoresis
PERSON: Nicole Vasilevsky
http://en.wikibooks.org/wiki/Proteomics/Protein_Separations-_Electrophoresis/Differential_in_Gel_Electrophoresis%28DIGE%29
protein extraction
An extraction where the desired output material is protein.
OBI
PERSON: Nicole Vasilevsky
antisense oligonucleotide synthesis
Oligonucleotide synthesis of single strands of DNA or RNA that are complementary to a chosen sequence that are used to prevent protein translation of messenger RNA target strands by binding to them.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Oligonucleotide
siRNA synthesis
A biomolecule synthesis technique used to generate small-interfering RNA molecules, which can be used to knockdown gene expression of target sequences.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
patch clamp technique
An electrophysiology assay used to study single or multiple ion channels in cells by using a glass micropipette as an electrode, that has an open tip diameter of about one micrometre, a size enclosing a membrane surface area or "patch" that often contains just one or a few ion channel molecules.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Patch_clamp
compound library screening
High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.
PERSON: Nicole Vasilevsky
http://www.rdchemicals.com/compound-libraries/
peptide screening
High throughput sample analysis of collections of peptides for bioactivity.
PERSON: Nicole Vasilevsky
http://www.cellecta.com/technology/bioactive-peptide-screening/
RNAi screening
High throughput sample analysis of RNAi molecules for potential application in gene knockdown or gene silencing of target genes.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
shRNA screening
siRNA screening
phosphor imaging
An imaging assay used to measure radioisotope emission, chemiluminescence and fluorescence from a sample.
PERSON: Nicole Vasilevsky
Phosphorimaging
http://www.etsu.edu/com/mbcf/Services/Phosphorimaging.aspx
stable isotope mass spectrometry
Mass spectrometry where the relative abundance of isotopes in a continuously flowed gas sample is determined.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Isotope-ratio_mass_spectrometry
gel staining
A staining technique used to make the molecules in a gel visible via a protein-specific, dye-binding or color-producing chemical reaction.
PERSON: Nicole Vasilevsky
http://www.piercenet.com/browse.cfm?fldID=B06FFE8F-5056-8A76-4E15-AF49E5F5A91F
long non-coding RNA microarray profiling
A nucleic acid microarray assay of long non-coding RNAs, which are evolutionarily conserved, longer than 200 nt, non-coding RNA molecules found in eukaryotes.
LncRNA profiling
PERSON: Nicole Vasilevsky
http://www.arraystar.com/Microarray/service_main.asp?id=198
sodium dodecyl sulfate polyacrylamide gel electrophoresis
PERSON: Nicole Vasilevsky
Polyacrylamide gel electrophoresis using sodium dodecyl sulfate. the binding of SDS (a detergent) to the polypeptide chain of proteins imparts aneven distribution of charge per unit mass, thereby resulting in a fractionation by approximate size during electrophoresis.
SDS PAGE
SDS-PAGE
http://www.davidson.edu/academic/biology/courses/molbio/sdspage/sdspage.html
complement-dependent cytotoxicity assay
An in vitro cytotoxicity assay that is mediated by the complement system.
CDC assay
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Cytotoxicity
N-terminal deblocking
A chemical modification of proteins to deblock N-terminal residues prior to protein sequencing.
PERSON: Nicole Vasilevsky
Wellner et al (1989) PNAS 87: 1947.
real time qPCR microRNA quantitation
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Real-time PCR of microRNA abundance in a sample.
diagnostic intervention
An intervention that evaluates methods of detecting disease.
PERSON: Nicole Vasilevsky
http://training.cancer.gov/clinicaltrialsbasics/s01/glossary.php
frozen block embedding
Frozen tissue embedding
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Tissue embedding in specialized medium that allows rapid freezing of the tissue when exposed to freezing temperatures, for subsequent sectioning or preservation.
glucose analyzer
A measurement instrument that precisely measures glucose levels from a sample, such as from whole blood, plasma or serum.
Blood glucose analyzer
Blood sugar analyzer
PERSON: Nicole Vasilevsky
http://www.gmi-inc.com/Products/Glucose%20Anaylzers%20Headline.html
automated dewaxing and epitope recovery device
A mechanical device that is designed to perform dewaxing and epitope recovery on slides prior to immunostaining.
PERSON: Nicole Vasilevsky
http://www.labvision.com/lv.cfm?first=Reagent&second=Lab%20Vision%20PT%20Module%20%28Automated%20Dewaxing%20and%20Epitope%20recovery%20Device%20for%20Lab%20Vision%20autostainers%29
cryogenic freezer
A freezer that is used to store samples at cryogenic temperatures.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
array-based expression analysis
Gene expression analysis of samples hybridized to a microarray probe.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
raman spectrometer
A spectrophotometer used to study vibrational, rotational, and other low-frequency modes in a system.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Raman_spectroscopy
MALDI-TOF mass spectrometer
A mass spectrometer that uses soft ionization to allow analysis of biomolecules and large organic molecules, which tend to be fragile and fragment when ionized by more conventional ionization methods.
MALDI-TOF MS
Matrix-assisted laser desorption ionization time-of-flight mass spectrometer
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization
bioavailability analysis
An analyte assay that is performed to determine the fraction of an administered dose of unchanged drug that reaches the systemic circulation for pharmacokinetic drugs.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Bioavailability
biospecimen to be prepared role
A role inhering in a biological specimen that is realized when the bearer participates in a specimen preparation process.
biospecimen preparation
A technique used to prepare a biospecimen for use or storage.
Formalin fixation of a zebrafish embryo for immunostaining assays.
PERSON:Melissa Haendel
PERSON:Melissa Haendel
heat fixation
Fixation using heat to heat-kill and adhere tissue or cells to a surface, such as a slide.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fixation_%28histology%29
chemical fixation
Fixation using chemical fixative to stabilize the proteins, nucleic acids and mucosubstances of the tissue or cells by making them insoluble.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fixation_%28histology%29
alcohol fixation
Chemical fixation using alcohols, that act by reducing the solubility of protein molecules and (often) by disrupting the hydrophobic interactions that give many proteins their tertiary structure.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fixation_%28histology%29
methanol fixation
Alcohol fixation using a solution primarily containing methanol.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
ethanol fixation
Alcohol fixation using a solution primarily containing ethanol.
PERSON: Nicole Vasilevskly
PERSON: Nicole Vasilevsky
oxidizing agent fixation
Chemical fixation using an oxidizing agent to fix cells or tissue, which can react with various side chains of proteins and other biomolecules, allowing formation of crosslinks that stabilize tissue structure.
Oxidising agent fixation
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Fixation_%28histology%29
database
A database is an organized collection of data, today typically in digital form.
Just a place horder. It will probably be replaced by NIF term: http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Resource.owl#nlx_res_20090405
PERSON: Carlo Torniai
http://en.wikipedia.org/wiki/Database
synchrotron
An instrument that is a cyclic particle accelerator in which the guiding magnetic field (bending the particles into a closed path) is time-dependent and is used to synchronize the particle beam to increase its kinetic energy.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Synchrotron
antibody optimization
A technique used to determine the optimal conditions for use of an antibody reagent in a particular assay.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
transmission electron microscopy with EDAX
PERSON: Nicole Vasilevsky
Transmission electron microscopy that has the ability to analyze the elemental or chemical characterization of a sample.
Transmission electron microscopy with energy dispersive spectroscopy
http://en.wikipedia.org/wiki/Energy-dispersive_X-ray_spectroscopy
scanning electron microscopy with EDAX
PERSON: Nicole Vasilevsky
Scanning electron microscopy that has the ability to analyze the elemental or chemical characterization of a sample.
Scanning electron microscopy with energy dispersive spectroscopy
http://en.wikipedia.org/wiki/Energy-dispersive_X-ray_spectroscopy
bibliographic management
Citation management
Data storage and organization of bibliographic citations (references).
PERSON: Nicole Vasilevsky
Reference management
http://en.wikipedia.org/wiki/Reference_management_software
CLAMS system
An animal physiology monitoring system that allows for simultaneous measurement of numerous parameters including oxygen consumption (VO2), carbon dioxide (CO2) production, respiratory exchange ratio (RER), food and drinking behavior, activity level, and caloric heat production.
PERSON: Nicole Vasilevsky
http://www.joslindiabetescenter.com/diabetes-research/animal-physiology.html
miRNA quality analysis
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
RNA quality analysis of micro RNA (miRNA).
small molecule screening
High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.
PERSON: Nicole Vasilevsky
http://www.lerner.ccf.org/services/smsc/
synchrotron radiation
PERSON: Nicole Vasilevsky
Sample irradiation using synchrotron radiation, the electromagnetic radiation emitted when charged particles are accelerated radially.
http://en.wikipedia.org/wiki/Synchrotron_radiation
miRNA expression analysis
A gene expression analysis assay of micro RNA (miRNA) in a sample.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
AlphaScreen
A molecular assay that measures the interaction of two molecules bioconjugated to donor and acceptor beads.
ALPHA
Alpha Screen
Amplified luminescence proximity homogeneous assay
PERSON: Nicole Vasilevsky
http://www.bmglabtech.com/technology/alphascreen.cfm
photomacrography
PERSON: Nicole Vasilevsky
Photography where the image is magnified 1X or higher.
http://www.microscopy-uk.org.uk/mag/indexmag.html?http://www.microscopy-uk.org.uk/mag/artmar05/chmacro.html
semen analysis
A tissue/organ assay that is performed to analyze the motility, morphology, viability, and number of semen in a given sample.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
trace metal analysis
A materials assay to analyze the presence or concentration of trace metal(s) in a sample.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
cell storage
Cell banking
Material storage of cells in freezing media, at sub-zero temperatures, that is intended to sustain viability for later use.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
prototype development
Material production of an early sample or model built to test a concept or process or to act as a thing to be replicated or learned from.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Prototype
nanofabrication
Fabrication of devices with dimensions measured in nanometers.
PERSON: Nicole Vasilevsky
http://whatis.techtarget.com/definition/nanofabrication
coverslipping machine
A robot that processes histology sides by positioning them and mounting coverslips on top of the slide.
PERSON: Nicole Vasilevsky
http://www.al-tar.com/online-laboratory-store/hackermeisei-coverslipping-machine-rcm-3655
air monitoring
An assay for detection of various gases, chemicals, and particulates in ambient air or air emissions.
PERSON: Scott Hoffmann
http://www.pine-environmental.com/air-monitoring.htm#content
immunochemiluminescence
An immunoassay used to detect an antigen-antibody interaction, based on a brief emission of light by a luminophor component (signal) in response to chemical energy.
Hachem H et al (1991) A sensitive immunochemiluminescence assay for human serum amyloid A protein. Clin Biochem. 1991 Apr;24(2):143-7.
PERSON: Nicole Vasilevsky
metabolic phenotyping
An assay used to measure the set of metabolites in biofluids, which can reflect an individual’s health status.
PERSON: Nicole Vasilevsky
http://fgp.ucdavis.edu/prog/mp
tissue microarray assay
An assay that uses paraffin blocks in which separate tissue cores are assembled in array fashion to allow multiplex histological analysis.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Tissue_microarray
antimicrobial susceptibility testing
An assay used to detect possible drug resistance in common pathogens and to assure susceptibility to drugs of choice for particular infections.
PERSON: Nicole Vasilevsky
Reller et al (2009) Antimicrobial Susceptibility Testing: A Review of General Principles and Contemporary Practices. Clin Infect Dis. 49 (11): 1749-1755.
organism strain rederivation
A material processing technique in which a particular strain of an organism is rederived from an embro by implantation into pathogen-free pseudopregnant recipients.
PERSON: Nicole Vasilevsky
http://www.biotech.wisc.edu/facilities/transgenicanimal/services/StrainRederivation2
quarantine housing maintenance
Laboratory animal care in which animals are housed in a pathogen-free environment.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
next generation sequencer
A DNA sequencer that is used by specific commercial platforms that embody a complex interplay of enzymology, chemistry, high-resolution optics, hardware, and software engineering. These instruments allow highly streamlined sample preparation steps prior to DNA sequencing, which provides a significant time savings and a minimal requirement for associated equipment in comparison to the highly automated, multistep pipelines necessary for clone-based high-throughput sequencing. Each technology amplifies single strands of a fragment library and perform sequencing reactions on the amplified strands. The fragment libraries are obtained by annealing platform-specific linkers to blunt-ended fragments generated directly from a genome or DNA source of interest. Because the presence of adapter sequences means that the molecules then can be selectively amplified by PCR, and no bacterial cloning step is required to amplify the genomic fragment in a bacterial intermediate as is done in traditional sequencing approaches.
Mardis (2008) Annu. Rev. Genomics Hum. Genet. 9:387-402
PERSON: Nicole Vasilevsky
blood plasma isolation
Material component separation of plasma from a blood sample.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
blood serum isolation
Material component separation of serum from a blood sample.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
solid phase synthesis
Fluorenylmethyloxycarbonyl solid phase synthesis
PERSON: Nicole Vasilevsky
Synthesis in which molecules are bound on a bead and synthesized step-by-step in a reactant solution.
http://en.wikipedia.org/wiki/Solid-phase_synthesis
pulsed-field gel electrophoresis
Electrophoresis of molecules using an electric field that periodically changes direction to a gel matrix.
PERSON: Nicole Vasilevsky
Pulsed field gel electrophoresis
http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis
raman-atomic force microscope
An atomic force microscope that has inegrated raman spectroscopy, for examination of chemical and structural properties of materials at sub-micrometer scales.
PERSON: Nicole Vasilevsky
Raman-AFM system
http://www.renishaw.com/en/raman-afm-system--6638
total internal reflection fluorescence atomic force microscope
PERSON: Nicole Vasilevsky
TIRF AFM
Total Internal Reflection Fluorescence AFM
Total internal reflection fluorescence instrument combined with atomic force microscope used to detect and confirm the result of cellular level manipulations made with the AFM part through the detection system of the highly sensitive fluorescence microscope part.
http://www.ncbi.nlm.nih.gov/pubmed/12211478
interfacial force microscope
A microscope capable of measuring normal and lateral forces between a probe and sample.
IFM
PERSON: Nicole Vasilevsky
www.nanotech.upenn.edu/facilities_images/IFM.pdf
maze
An instrument that is a tour puzzle in the form of a complex branching passage through which the solver must find a route. Often used in animal models to test behavior.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Maze
elevated plus maze
A maze used for rodent models of anxiety, which is used as a screening test for putative anxiolytic or anxiogenic compounds and as a general research tool in neurobiological anxiety research.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Elevated_plus_maze
zero maze
An elevated plus maze that lacks a center square, used to measure animal behavior in the time spent in open and closed spaces.
PERSON: Nicole Vasilevsky
http://www.noldus.com/animal-behavior-research/solutions/research-small-lab-animals/zero-maze-set
light/dark chamber
An animal activity monitoring system that transistions between light and dark, using a light/dark transition test, which is widely used to measure anxiety-like behavior in mice.
PERSON: Nicole Vasilevsky
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504462/
passive/active avoidance chambers
An animal activity monitoring system is an automated system employed in the testing of avoidance behavior. Each subject is housed within a cage that has been divided by a centrally located wall. The wall has an opening that allows the subject to pass between the compartments. The lid of each compartment contains an acoustic source. The light is on the center divider. The subject walks on a shocker grid assembly that spans the entire floor area of both compartments. A series of photocells detects the subject position within the cage.
PERSON: Nicole Vasilevsky
http://www.colinst.com/brief.php?id=12
hole poke arenas
An animal activity monitoring system that consists of a hole poke board with holes lying over horzontal X and Y axis sensors.Data collected includes frequency and duration of each "nose poke" as well as positional and ambulatory data (distance traveled, zone entries, ambulatory vs. total movement, etc.).
PERSON: Nicole Vasilevsky
http://www.colinst.com/brief.php?id=90
metabolic chamber
An environmental chamber that is used to measure oxygen consumption in an organism.
PERSON: Nicole Vasilevsky
http://csm.jmu.edu/biology/danie2jc/metabolism_lab.htm
metabolic cart
A measurement instrument used to measure the body’s metabolism through the amount of heat produced when the body is at rest.
PERSON: Nicole Vasilevsky
http://www.wisegeek.com/what-is-a-metabolic-cart.htm
EBV transformation
A cell culture technique in which lymphocytes are treated with EBV and become capable of indefinite growth as a consequence of viral protein expression.
Epstein–Barr virus transformation
Lymphoblast transformation
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Epstein%E2%80%93Barr_virus
bone marrow aspiration
A biopsy where a small amount of bone and a small amount of fluid and cells from inside the bone (bone marrow) are removed.
PERSON: Nicole Vasilevsky
http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy
immunomagnetic selection
An antibody related technique that uses paramagnetic beads coated with antibodies to bind to antigens present on the surface of cells thus capturing the cells and facilitating the concentration of these bead-attached cells. The concentration process is created by a magnet placed on the side of the test tube bringing the beads to it.
Immunomagnetic cell separation
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Immunomagnetic_separation
actigraphy
A physiological assay used to monitor human rest/activity cycles.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Actigraphy
polysomnography
A physiological assay used in the study of sleep and as a diagnostic tool in sleep medicine.
PERSON: Nicole Vasilevsky
Sleep study
http://en.wikipedia.org/wiki/Polysomnography
anthropometric analysis
A physiological assay of the human body that uses such tools as body mass index, basal metabolic rate, bioelectrical impedance, and dual energy x-ray absorptiometry, along with measurements of skinfold thickness and arm muscle circumference, to assess the structure, form, and composition of the body for purposes of comparison.
PERSON: Nicole Vasilevsky
http://www.answers.com/topic/anthropometric-analysis
hemocytometry
An assay used to count cells.
PERSON: Nicole Vasilevsky
http://dictionary.reference.com/browse/hemocytometry
psychoeducational test administration
A technique that utilizes standardized tests and questionnaires in an effort to identify a student’s strengths and weaknesses across many areas of functioning and attributes.
PERSON: Nicole Vasilevsky
http://www.vdps.net/special/test.html
natural product drug discovery
An assay that is performed to find new bioactive chemical entities from natural sources, to be used a therapeutic drug targets.
PERSON: Nicole Vasilevsky
Screening herbs for use as potential drug targets.
http://en.wikipedia.org/wiki/Drug_discovery#Plant-derived
nanoparticle size analyzer
A measurement device used to calculate the mass of nano-scale particles.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
energy-dispersive X-ray spectroscopy
A spectroscopy technique used for the elemental analysis or chemical characterization of a sample. It relies on the investigation of an interaction of some source of X-ray excitation and a sample. Its characterization capabilities are due in large part to the fundamental principle that each element has a unique atomic structure allowing unique set of peaks on its X-ray spectrum.
EDS
EDX
PERSON: Nicole Vasilevsky
Qualitative elemental analysis of nanomaterials.
http://en.wikipedia.org/wiki/Energy-dispersive_X-ray_spectroscopy
electron energy loss spectroscopy
A spectroscopy technique that measures the change in kinetic energy of electrons after they have interacted with a specimen. When carried out in a modern transmission electron microscope, EELS is capable of giving structural and chemical information about a solid, with a spatial resolution down to the atomic level in favourable cases.
EELS
PERSON: Nicole Vasilevsky
R.F. Egerton (2009). Reports on Progress in Physics. 72 016502 doi:10.1088/0034-4885/72/1/016502 (http://iopscience.iop.org/0034-4885/72/1/016502/)
cryo-electron microscopy
A form of transmission electron microscopy where the sample is studied at cryogenic temperatures (generally liquid nitrogen temperatures).
Cryo-EM
Cryoelectron microscopy
Electron cryomicroscopy
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Cryo-electron_microscopy
cryoultramicrotomy
A cryosectioning technique that creates thin sections of constant thickness with very soft materials that cannot be cut at ambient temperature. After cooling down of the specimen, a section is sliced up using a diamond knife which has been previously cooled down. The material is brought close to transition temperature Tg (if known) to obtain a harder consistency.
Cryo-ultramicrotomy
PERSON: Nicole Vasilevsky
http://cime.epfl.ch/page-26804-en.html
cryostat sectioning
Cryosectioning using a cryostat to maintain the freezing temperature.
PERSON: Nicole Vasilevsky
cryotome sectioning
Cryosectioning using a cryotome to maintain the freezing temperature.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
network attached storage
A file-level computer data storage connected to a computer network providing data access to heterogeneous clients. NAS not only operates as a file server, but is specialized for this task either by its hardware, software, or configuration of those elements. NAS is often manufactured as a computer appliance – a specialized computer built from the ground up for storing and serving files – rather than simply a general purpose computer being used for the role.
NAS
Network-attached storage
PERSON: Nicole Vasilevsky
To describe a data and file storage resource.
http://en.wikipedia.org/wiki/Network-attached_storage
digital polymerase chain reaction system
A PCR machine that can be used to directly quantify and clonally amplify nucleic acids including DNA, cDNA or RNA.
Digital PCR
DigitalPCR
PERSON: Nicole Vasilevsky
dPCR
dePCR
http://en.wikipedia.org/wiki/Digital_PCR
aerosol biosampler
A measurement instrument that collects and measure the amount of bioaerosols in a sample (airborne particles of biological origin (e.g., bacteria, fungi, pollen, viruses) and their by-products such as endotoxins or mycotoxins and other fragments.)
PERSON: Nicole Vasilevsky
Sampling of biologicals from various air-borne sources.
http://www.skcinc.com/prod/225-9594.asp
functional MRI scanner
A MRI Scanner that uses the change in magnetization between oxygen-rich and oxygen-poor blood as its basic measure to measures brain activity.
Functional magnetic resonance imager
Functional magnetic resonance imaging scanner
PERSON: Nicole Vasilevsky
fMRI
http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging
abbe refractometer
A measurement instrumentat that is a bench-top device for the high-precision measurement of an index of refraction.
Measuring the index of refraction of aqueous solutions between n=1.3 and n=1.7
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Abbe_refractometer
solid ink printer
A printer that uses 1 cubic inch rectangular solid-state ink blocks, which are loaded into the top of the printer. The ink blocks are melted and the ink is transferred onto a rotating, oil coated print drum using a piezo inkjet head. The paper then passes over the print drum, at which time the image is transferred, or transfixed, to the page. This system is similar to water-based inkjets, provided that the ink has low viscosity at the jetting temperature (140°C).
PERSON: Nicole Vasilevsky
Phaser printer
Solid ink printer is used to fabricate paper-based microfluidic devices. Ink droplet is about 50 to 60 um in diameter. Ink is compatible with aqueous solution with various pH.
Wax printer
https://en.wikipedia.org/wiki/Thermal_transfer_printing
atom probe
A microscope used in material science in which the magnification effect comes from the magnification provided by a highly curved electric field. The method is destructive in nature removing ions from a sample surface in order to image and identify them, generating magnifications sufficient to observe individual atoms as they are removed from the sample surface. Through coupling of this magnification method with time of flight mass spectrometry, ions evaporated by application of electric pulses can have their mass-to-charge ratio computed.
PERSON: Nicole Vasilevsky
The LEAP 4000X HRTM is a high performance 3D am probe microscope which provides nano-scale surface, bulk and interfacial materials analysis of simple and complex structures with atom by atom identification and accurate spatial positioning.
http://en.wikipedia.org/wiki/Atom_probe
pulse oximetry
A physiological assay used to monitor the saturation of a patient's hemoglobin.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Pulse_oximetry
impedence analyzer
Electronic test equipment used to measure the opposition of a circuit to the passage of a current when a voltage is applied.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electrical_impedance
electron tomography
An electron microscopy method for three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images (i.e. from a tilt series) recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
PERSON: Nicole Vasilevsky
http://www.ncbi.nlm.nih.gov/pubmed/12160704
cryogenic electron microscopy
A form of transmission electron microscopy where the sample is studied at cryogenic temperatures (generally liquid nitrogen temperatures).
Cryo-EM
Cryo-electron microscopy
Electron cryomicroscopy
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Cryo-electron_microscopy
image processing technique
Any form of signal processing for which the input is an image, such as a photograph or video frame; the output of image processing may be either an image or a set of characteristics or parameters related to the image.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Image_processing
deconvolution microscopy
Image processing to improve the contrast and resolution of digital images captured in the microscope, most commonly to address deblurring and image restoration.
PERSON: Nicole Vasilevsky
http://www.olympusmicro.com/primer/digitalimaging/deconvolution/deconvolutionhome.html
single particle analysis
An image processing technique used to analyze images from transmission electron microscopy. These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained particles are very noisy, and so hard to interpret. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Single_particle_analysis
hot plate
A heating instrument that is a self-contained tabletop small appliance that features one, two or more gas burners or electric heating elements.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Hot_plate
machine press
A press brake is a special type of machine press that bends sheet metal into shape.
An instrument that changes the shape of a workpiece.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Machine_press
punch press
A machine press used to cut holes in material.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Punch_press
polymer mixer
A mechanical instrument used for the rapid mixing and grinding of polymer materials that would otherwise require large amounts of time and/or effort to mix and/or grind.
PERSON: Nicole Vasilevsky
http://www.speedmixer.com/dac150.1fvzk.php
automated colony counter
An automated instrument that quickly and accurately counts colonies in a petri dish or tissue culture dish.
PERSON: Nicole Vasilevsky
http://www.uvp.com/colony.html
electrochemiluminescence detection
An assay that detects luminescence produced during electrochemical reactions in solutions.
ECL
Electrogenerated chemiluminescence detection
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Electrochemiluminescence
tablet press
A machine press that compresses powder into tablets of uniform size and weight.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Tablet_press
zeta potential analyzer
An instrument used for characterizing zeta potential as a property of interfacial layer in liquid particulates (dispersions, emulsions) and porous bodies.
PERSON: Nicole Vasilevsky
http://www.dispersion.com/zeta-potential-analyzer.html
particle size analyzer
A measurement instrument that analyzes the particle size distributions in a sample or during a process.
PERSON: Nicole Vasilevsky
http://www.malvern.com/labeng/products/iwtm/particle_size_analysis.htm
variable pressure analytical field emission scanning electron microscope
A field emission scanning electron microscope that allows for a variable pressure mode.
Analytical variable pressure FE-SEM
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
ultra high performance liquid chromatography with mass spectrometer
An UPLC coupled to a mass spectrometer.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
UPLC-MS
UPLC/MS
laser diffraction particle size analyzer
A particle size analyzer that uses laser diffraction technology.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
surface area analyzer
An instrument that measures of how much exposed area an object has.
PERSON: Nicole Vasilevsky
http://www.azom.com/materials-equipment.aspx?cat=18
fluid bed processor
An instrument used to heat, cool, dry, or moisturize your bulk solid material.
PERSON: Nicole Vasilevsky
http://www.carmanindustries.com/Pages/fluidbed.html
differential scanning calorimeter
A calorimeter in which the difference in the amount of heat required to increase the temperature of a sample and reference is measured as a function of temperature.
DSC
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Differential_scanning_calorimetry
measurement scale
level of measurement
https://en.wikipedia.org/wiki/Level_of_measurement
an information content entity used to classify data based on how data are collected, according to theory of scale types developed by the psychologist Stanley Smith Stevens
PERSON: Matthew Brush
cryogenic transmission electron microscope
A transmission electron microscope where the sample is studied at cryogenic temperatures (generally liquid nitrogen temperatures).
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Cryo-electron_microscopy
printer
An instrument used in computing, which produces a text or graphics of documents stored in electronic form, usually on physical print media such as paper or transparencies.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Printer_(computing)
pulsed laser deposition
A material processing technique where a high power pulsed laser beam is focused inside a vacuum chamber to strike a target of the material that is to be deposited. This material is vaporized from the target (in a plasma plume) which deposits it as a thin film on a substrate (such as a silicon wafer facing the target). This process can occur in ultra high vacuum or in the presence of a background gas, such as oxygen which is commonly used when depositing oxides to fully oxygenate the deposited films.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Pulsed_laser_deposition
pulsed laser deposition system
An instrument used for thin film and nanocyrstal growth where the target material is ablated with a laser and a plume deposists material on a substrate.
PERSON: Nicole Vasilevsky
http://www.vanderbilt.edu/vinse/facility_details.php?FacilityID=3
indirect calorimetry
A calorimetry method that calculates heat that living organisms produce from their production of carbon dioxide and nitrogen waste (frequently ammonia in aquatic organisms, or urea in terrestrial ones), or from their consumption of oxygen.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Calorimetry
physiological assessment
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Physiological assays used to measure various outcomes to determine clinical picture of the health status of an individual.
fluorescence molecular tomography platform
An imaging modality that enables 3D quantitative determination of fluorochrome distribution in tissues of live small animals at any depth.
FMT
PERSON: Nicole Vasilevsky
http://www.ncbi.nlm.nih.gov/pubmed/17985393
optical tomography
An imaging technique that creates a digital volumetric model of an object by reconstructing images made from light transmitted and scattered through an object.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Optical_tomography
gamma radiation measurement
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Radioactivity detection and measurement of the amount of gamma radiation in a sample.
primer design
A data processing technique to design primers for specific nucleotide sequences to be used in applications such as PCR.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
microarray comparative genomic hybridization
A molecular assay that detects genomic imbalance, i.e. gains and losses of genetic material, which can be used for the diagnosis of developmental delay, mental retardation, autism and birth defects.
Array CGH
PERSON: Nicole Vasilevsky
aCGH
http://www.ohsu.edu/xd/health/services/lab-services/labtests/results.cfm?input1=Microarray+Comparative+Genomic+Hybridization&labtestid=DA697BEA-F784-F999-323B53E182A5134D&keywords=&ohsuservicecode=&eapcode=&cptcode=&labsectionid=
VO2 max measurement
A physiological assay to determine the maximum capacity of an individual's body to transport and use oxygen during incremental exercise, which reflects the physical fitness of the individual.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/VO2_max
MR relaxometry imaging
MRI that acquires the relaxation rate dispersion curves from magnetic resonance images.
PERSON: Nicole Vasilevsky
http://www.ncbi.nlm.nih.gov/pubmed/1509044
biological process phenotype annotation
Conclusion textual entity about a biological process phenotype.
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
anatomical phenotype annotation
Conclusion textual entity about an anatomical phenotype.
PERSON: Melissa Haendel
PERSON: Nicole Vasilevsky
phenotypic annotation
A conclusion textual entity that is an observable characteristic or trait of an organism, such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest).
PERSON: Melissa Haendel
PERSON: Melissa Haendel
shielded nuclear radiation containment chamber
An instrument used to protect individuals from radioactive isotopes by providing a safe containment box in which they can control and manipulate the equipment required.
Hot cell
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Hot_cell
positron emission tomography
An imaging technique that produces a three-dimensional image or picture of functional processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. Three-dimensional images of tracer concentration within the body are then constructed by computer analysis.
PERSON: Nicole Vasilevsky
PET
http://en.wikipedia.org/wiki/Positron_emission_tomography
drill press
A drill that is a fixed style of drill that may be mounted on a stand or bolted to the floor or workbench.
Bench drill
PERSON: Nicole Vasilevsky
Pedestal drill
Pillar drill
http://en.wikipedia.org/wiki/Drill#Drill_press
radio-HPLC
An HPLC that can monitor radio-labelled compounds separated by chromatographic techniques.
PERSON: Nicole Vasilevsky
Radio-High Performance Liquid Chromatography
https://www.berthold.com/en/bio/radio-hplc-detectors
drill
A mechanical instrument fitted with a cutting tool attachment or driving tool attachment, usually a drill bit or driver bit, used for drilling holes in various materials or fastening various materials together with the use of fasteners.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Drill
radio-TLC imaging scanner
An instrument used for detection of radiolabeled compounds in thin layer chromatography (TLC) plates.
PERSON: Nicole Vasilevsky
Radio-thin layer chromatography imaging scanner
http://www.bioscan.com/index.php?page=ar-2000-radio-tlc-imaging-scanner
microwave accelerator
An instrument capable of rapidly depositing high energy in a small volume.
PERSON: Nicole Vasilevsky
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553010/
mammalian phenotype annotation
Conclusion textual entity about a mammalian phenotype.
PERSON: Melissa Haendel
PERSON: Scott Hoffmann
algorithmic software suite
Algorithmic software pipeline
Algorithmic software platform
Algorithmic software toolkit
Software that implements two or more algorithmic software components
algorithmic software component
Software that implements an individual algorithm.
imaging OCT
Optical Coherence Tomography (OCT) that uses coherent interferometry to construct a cross-sectional view of the objective, often with micrometer accuracy.
PERSON: Scott Hoffmann
http://www.opsweb.org/?page=octimaging
imaging optical coherence tomography
OCT
An imaging assay used to acquire and process micrometer-resolution, three-dimensional images from within optical scattering media.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Optical_coherence_tomography
optical coherence tomography
registry
An organization dedicated to the collection, storage and dissemination of a set of scientific or clinical data.
PERSON: Nicole Vasilevsky
PERSON: Scott Hoffmann
biorepository
An organization that governs the storage of biospecimens that includes tissue samples, fluids, and molecular derivatives such as DNA, RNA, and proteins. The biorepository has stringent guidelines regarding the standardized collection, handling, storage, and documentation of biological specimens.
Biobank
PERSON: Nicole Vasilevsky
Specimen bank
http://bioportal.bioontology.org/ontologies/45400/?p=terms&conceptid=Biorepository
ActionScript
Ada
AppleScript
Assembly
C
C Sharp
C++
COBOL
ColdFusion
D
Delphi
Dylan
Eiffel
Forth
Fortran
Groovy
Haskell
JavaScript
LabVIEW
Lisp
Lua
Maple
Mathematica
Pascal
Perl
PHP
Prolog
Python
REXX
Ruby
SAS
Scala
Scheme
Shell
Smalltalk
SQL
Turing
Verilog
VHDL
Visual Basic
.csv
Comma-separated values
.mgf
MASCOT generic format
.sql
SQL format
.mysql
MySQL format
.fastq
.fq
FASTQ
.maf
MAF
Multiple Alignment Format
.gz
GZipped format
.zip
Zipped format
.bw
BigWig format
.wig
Wiggle format
.sam
Sequence Alignment/Map format
Fourier transform mass spectrometer
A mass spectrometer that is used to determine the mass-to-charge ratio of ions based on the cyclotron frequency of the ions in a fixed magnetic field. After ion excitation, the signal is detected as an image current on a pair of plates consisting of a superposition of sine waves. The useful signal is extracted from this data by performing a Fourier transform to give a mass spectrum.
FTICR-MS
Fourier transform ion cyclotron resonance mass spectrometer
PERSON: Scott Hoffmann
https://en.wikipedia.org/wiki/Fourier_transform_ion_cyclotron_resonance
hydrogenation reactor
An instrument that performs continuous hydrogenation reactions in a flow system
PERSON: Nicole Vasilevsky
http://www.thalesnano.com/products/h-cube
scanning tunneling microscopy
Microscopy that produces a view of the surface of a sample at the atomic level by detecting variations in the current between a conducting tip and the reactive elements within the sample.
NCI Thesaurus
PERSON: Nicole Vasilevsky
cell counting
A cellular assay that uses various methods to quantify cells in a culture.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
CT scan
An imaging method that employs tomography. Tomography is the process of generating a two-dimensional image of a slice or section through a 3-dimensional object (a tomogram).
CAT scan
Computed tomography scan
Computer axial tomography scan
PERSON: Nicole Vasilevsky
http://www.medicalnewstoday.com/articles/153201.php
atomic mass spectrometry
A mass spectrometry assay that uses an ion source, a mass analyzer, and a detector. Atoms' identities are determined by their mass-to-charge ratio (via the mass analyzer) and their concentrations are determined by the number of ions detected.
PERSON: Nicole Vasilevsky
http://en.wikipedia.org/wiki/Atomic_spectroscopy
bioluminescent assay
A molecular assay that uses bioluminescence to detect the presence or concentration of molecules in a sample.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
bead-based multiplex
An instrument that utilizes beads that are coated with a reagent specific to a particular bioassay, allowing the capture and detection of specific analytes from a sample.
PERSON: Nicole Vasilevsky
http://www.luminexcorp.com/TechnologiesScience/xMAPTechnology/index.htm
fast phototaxis assay
A physiological assay used to measure the locomotive response of an organism to light stimulus.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Phototaxis
binary
categorical
nominal
ordinal
interval
ratio
continuous
survival
time to failure
sequential
data collection method
a planned process in which data is collection through observations or measurements of subjects/specimens under investigation
PERSON:Matthew Brush
PERSON:Matthew Brush
independent data collection method
paired data collection method
clustered data collection method
longitudinal data collection method
repeated measurement method
fertility measurement assay
A behavioral assay used to measure an organism's capability to produce offspring.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Fertility
courtship assay
A behavioral assay used to measure organismal behaviors that result in mating and copulation.
PERSON: Scott Hoffmann
http://www.britannica.com/EBchecked/topic/140848/courtship
split Gal4 assay
A gene expression analysis assay to examine co-expression of genes in given cells/tissues. In this assay, the GAL4 coding sequence is split and each half is driven by distinct endogenous promoters/enhancers. From these constructs organism lines are derived. In a simple line, GAL4 activity is not reconstituted and thus a target reporter gene driven by the GAL4 promoter remains inactive. Crossing lines carrying complementary halves of GAL4 can reveal cells/tissues where both endogenous promoters/enhancers are active, which results in expression and reconstitution of the complete GAL4 protein and activation of a GAL4-driven reporter gene.
PERSON: Matthew Brush
UAS
Upstream Activation Sequence
http://en.wikipedia.org/wiki/GAL4/UAS_system
digital sleep recorder
An instrument for non-invasive measurement of physiological signals in both humans and animals specifically during sleep.
PERSON: Faith Coldren
PERSON: Scott Hoffmann
Nexus format
super-resolution microscopy
A light microscopy technique used to capture images with a higher resolution than the diffraction limit
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Super_resolution_microscopy
melt curve analysis
A technique used for the assessment of the dissociation-characteristics of double-stranded DNA during heating.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Melting_curve_analysis
super-resolution microscope
A microscope that uses light to capture images with a higher resolution than the diffraction limit
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Super_resolution_microscopy
incubator microscope
A microscope fitted with an environmental control chamber used to image live samples.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
total internal reflection fluorescence
An assay used to observe single molecule fluorescence at surfaces and interfaces which is commonly employed to investigate the interaction of molecules with surfaces.
PERSON: Scott Hoffmann
TIRF
http://www.olympusmicro.com/primer/techniques/fluorescence/tirf/tirfhome.html
data backup
A technique for copying and archiving computer data so it may be used to restore the original after a data loss event.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Backup
disk data backup
A data backup technique in which archived data is stored to a second hard disk.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Backup
tape data backup
A data backup technique in which archived data is stored to magnetic tape.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Backup
off-site data backup
A data backup technique in which the archived data is stored at a facility different than the source data.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
remote data backup
secure data storage
A data storage technique in which information is encoded in such a way that eavesdroppers or hackers cannot read it, but that authorized parties can.
PERSON: Scott Hoffmann
encrypted data storage
http://en.wikipedia.org/wiki/Encryption
redundant data storage
A data storage technique in which data generated by a user is archived on more than one storage medium (often multiple harddrives in the same machine).
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
RAID data storage
redundant array of independent disks
reliable data storage
remote data storage
A data storage technique in which information is maintained at a facility different than that of the user.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
cloud data storage
collaborative data storage
data hosting
A data transformation techique which allows organizations and individuals to serve information to users via the internet.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Internet_hosting
website hosting
A data hosting technique where a server makes a user-designed website available to other computers via the internet.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Website_hosting
server hosting
A data hosting technique where a single computer is configured to serve other computers that request processes of it via the internet.
Linux server hosting
PERSON: Scott Hoffmann
Solaris server hosting
Windows server hosting
http://en.wikipedia.org/wiki/Server_%28computing%29
physical server hosting
virtual server hosting
database hosting
A data hosting technique in which data arranged as a database (SQL for example) is made available to access via the internet.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
computer cluster hosting
A data hosting technique in which multiple computers are linked together such that they act like a single entity.
PERSON: Scott Hoffmann
http://www.wisegeek.org/what-is-cluster-computing.htm
application hosting
A data hosting technique that offers users access to applications via an internet connection.
PERSON: Scott Hoffmann
PERSON: Scott Hoffmann
induced pluripotent stem cell line
A cell line comprised of pluripotent stem cells experimentally derived from a non-pluripotent cells, typically an adult somatic cell, by inducing a forced expression of specific genes.
PERSON: Matthew Brush
iPS cell line
http://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell
establishing induced pluripotent cell line
A material production technique in which non-pluripotent cells are induced in culture to revert to pluripotency by initiating expression of specific genes, and propagated in culture to establish a cell line.
PERSON: Matthew Brush
establishing iPS cell line
http://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell
iPS cells are typically derived by transfection of certain stem cell-associated genes into non-pluripotent cells, such as adult fibroblasts. Transfection is typically achieved through viral vectors, such as retroviruses. Transfected genes include the master transcriptional regulators Oct-3/4 (Pou5f1) and Sox2, although it is suggested that other genes enhance the efficiency of induction. After 3–4 weeks, small numbers of transfected cells begin to become morphologically and biochemically similar to pluripotent stem cells, and are typically isolated through morphological selection, doubling time, or through a reporter gene and antibiotic selection. Notably, a DNA transfection-based this technique is becoming less popular since it is known to be prone to inducing cancer formation. A strictly protein mediated approach has also been demonstrated to work.
human subject
A homo sapiens that bears an experimental subject role which is realized through his/her participation in a scientific technique as the subject of interest (ie as the subject about which data is generated in an assay or study, or the entity that is transformed or modified in a material processing technique).
A patient in a clinical trial. A person from whom a biological sample is extracted.
PERSON: Matthew Brush
PERSON: Matthew Brush
experimental subject role
A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken)
PERSON: Matthew Brush
PERSON: Matthew Brush
ethnic group
PERSON: Matthew Brush
A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease.
NCI Thesaurus C16564 ‘Ethnic Group’
African American
Caucasian
Caucasian of European descent
Caucasian of Middle Eastern descent
Ashkenazi Jew
Sephardic Jew
Hispanic
Asian
Pacific Islander
African
Native American
sinker EDM
An instrument that consists of an electrode and workpiece submerged in an insulating liquid such as, more typically, oil or, less frequently, other dielectric fluids. The electrode and workpiece are connected to a suitable power supply. The power supply generates an electrical potential between the two parts. As the electrode approaches the workpiece, dielectric breakdown occurs in the fluid, forming a plasma channel, and a small spark jumps.
PERSON: Scott Hoffmann
cavity-type EDM
http://en.wikipedia.org/wiki/Electrical_discharge_machining
volume EDM
water jet cutter
An instrument capable of cutting a wide variety of materials using a very high-pressure jet of water, or a mixture of water and an abrasive substance.
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/Water_jet_cutting
waterjet
3D printer
A printer that creates a plastic or metal part one layer at a time (the additive fabrication method). Used mostly for quickly creating prototypes and molds, 3D printers are also used to build final parts. Available for myriad industrial uses as well as for the hobbyist, a variety of different technologies are used to form the layers.
PERSON: Scott Hoffmann
http://encyclopedia2.thefreedictionary.com/3D+printer
materials printer
electric discharge machining
A material processing technique whereby a desired shape is obtained using electrical discharges (sparks). Material is removed from the workpiece by a series of rapidly recurring current discharges between two electrodes, separated by a dielectric liquid and subject to an electric voltage. One of the electrodes is called the tool-electrode, or simply the ‘tool’ or ‘electrode’, while the other is called the workpiece-electrode, or ‘workpiece’.
PERSON: Scott Hoffmann
die sinking
http://en.wikipedia.org/wiki/Electrical_discharge_machining
spark eroding
spark machining
wire erosion
additive manufacturing
3D printing
A material processing technique used for making a three-dimensional solid object of virtually any shape from a digital model. 3D printing is achieved using an additive process, where successive layers of material are laid down in different shapes. 3D printing is considered distinct from traditional machining techniques, which mostly rely on the removal of material by methods such as cutting or drilling (subtractive processes).
PERSON: Scott Hoffmann
http://en.wikipedia.org/wiki/3D_printing
data transformation objective
Is opposed to / disjoint from "data analysis objective". In transformations, there is input of some input of collected data that is processed/operated on - but is not analyzed to generate new information (ie no statistical operations performed)
data processing objective
objectives to process data in a way that no analysis is performed and no new information is generated
process-based data transformation objective
objective of using a particular type of process/operation to process and transform data. This hierarchy classifies software objectives based on the type of operation that is specified to be performed
data assembly objective
data parsing objective
placeholder for SWO:parse objective
data pre-processing objective
data refinement and optimization objective
data cleaning objective
audio data cleaning objective
data retrieval objective
objective to obtain existing data from some data set, database, or corpus
data ingest objective
objective to retrieve an unfiltered/unaltered view of a data set
data search and retrieval objective
examples include search engines and serch UIs for biomedical repositories
objective to retrieve some filtered slice of data from a corpus/set based on user/agent specified search parameters
document search and retrieval objective
e.g. pubmed
metadata search and retrieval objective
resource metadata search and retrieval objective
sequence search and retrieval objective
data scaling objective
objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
placeholder for OBI:scaling objective
data transfer objective
objective to facilitate delivery of data between two parties
file processing objective
input is a single file or set of files
file compression objective
image file compression objective
image compression objective
placeholder for SWO:image compression objective
file rendering objective
objective whereby data is input is a file and processed to be presented in different ways/views, but no new data generated, and generally no interface for users to directly manipulate the presentaiton (other than altering inputs, parameters, or variables used for configuring the display)
placeholder for SWO:file rendering objective
format conversion objective
image format conversion objective
sequence format conversion objective
image processing objective
image processing alters an image but does not perform an analysis to generate new information (as is achieved in image analysis)
image transformation objective
objective whereby data from an image are digitized and various mathematical operations are applied to the data, generally with a digital computer, in order to create an enhanced image.
sequence comparison objective
objective to compare sequence-based features of tow or more macromolecules
sequence alignment objective
objective to display graphically how the sequences of two or more macromolecules align along a linear axis
genetic polymorphism analysis objective
microarray data analysis objective
statistical analysis and modeling objective
Would apply to software made for the end purpose of general statistical analysis of any type of data- not just software that applies statistical methods toward some particular type of analysis (which is much of the data analysis software).
statistical analysis objective
statistical modeling objective
data analysis objective
analysis generates "new" information about some biomedical entity, as opposed to data transformation objectives which aim to process data in a way that no analysis is performed and no new information is generated.
analysis objective
objective to perform and/or support data analysis, whereby data is input and processed to achieve a better understanding of it. This will involve generation "new" information through algorithmic processing and/or statistical calculations.
classification objective
molecular modeling objective
molecular structure modeling objective
objective to genrate in silico data-based molecular structures and testing of their physical/chemcial/electronic properties (and that of their interactions with ligands or cofactors)
source-based data transformation objective
objective to process and transform data that is output from a specific type of technique, technology, or instrument.
mass spectrometry data transformation objective
microarray data transformation objective
subject-based data transformation objective
biomedical data type-specific transformation objectives
data type-specific transformation objectives
objective to process and transform data about biological and/or medical phenomenon at a certain level of granularity. This hierarchy classifies software objectives based on the type/granularity of biomedical entity which the data they transform are about.
topic-based data transformation objectives
gene expression data transformation objective
gene expression data correction objective
gene expression data normalization objective
gene expression data pre-processing objective
gene expression data rendering and visualization objective
molecular structure data transformation objective
molecular structure rendering and visualization objective
network and pathway data transformation objective
molecular interaction network rendering and visualization objective
protein interaction network rendering and visualization objective
sequence data transformation objective
molecular sequence data transformation objective
sequence assembly objective
contig assembly
scaffold gap completion
sequence scaffolding
sequence profile processing objective
objective to process a sequence profile (ie a collection of related/aligned sequences)
sequence rendering and visualization objective
communication platform objective
e.g. WebEx, Adobe connect, Google docs and other platfoms that allow real-time collaborative editting, chat platforms
live communication platform objective
real-time communication platform objective
audio/video conferencing objective
e.g. skype, Webex, adobe connect, join.me
content development objective
objective of software to support user generated content creation, editing, annotation data (e,g, documents, databases, audio/video, etc), that does hae a primary reliance on data analyses or transformations.
user-generated content devleopment objective,
sequence annotation objective
document creation and editing
collaborative document creation and editing objective
concept model creation and editing objective
data graph creation objective
image creation and editing objective
multimedia document creation and editing objective
ontology creation and editing objective
ontology engineering objective
placeholder for SWO:ontology engineering
presentation creation and editing objective
spreadsheet creation and editing objective
placeholder for SWO:spreadsheet editing
video creation and editing objective
word processing objective
placeholder for SWO:word processing
documentation generation objective
objective of software to support creating, managing, organizing documentation of projects such as software development
information management objective
information management platform objective
software development objective
placeholder for SWO:software devleopment
social networking objective
objective to support entry and querying and presentation and management of personal and/or professional information to be shared in a social network of peers
citation management objective
e.g. Endnote
placeholder for SWO:citation management
laboratory information management objective
placeholder for SWO:laboratory information management
process-based data analysis objective
objective of using a particular type of process/operation to process and analyze data. This hierarchy classifies software objectives based on the type of operation that is specified to be performed
operation-based data analysis objectives
averaging objective
placeholder for OBI:averaging objective
comparison objective
data collection and processing objective
data acquisition objective
objective to support measurement of real-world conditions and convert these to a quantifiable numerical representation that can be processed as data by a computer
auditory signal collection and processing objective
auditory signal acquisition objective
auditory signal processing objective
collection and analysis of an auditory signal (conversion of signal to quantifiable numerical data)
speech processing objective
autoradiography data collection and processing objective
autoradiography data acquisition objective
collection and analysis (conversion of signal to quantifiable numerical data) of singal from emission of radiation
spectral data collection and processing objective
collection and analysis (conversion of signal to quantifiable numerical data) of light emission/transmission
data integration objective
data element mapping objective
data validation objective
internal data validation objective
objective to ensure data meets internal quality, format, specification standards
placeholder for OBI:data validation objective
primary data validation objective
dataset evaluation objective
data set evaluation objective
secondary data evaluation objective
dataset comparison objective
data set comparison objective
placeholder for SWO:dataset comparison objective
inter-rater reliability analysis objective
objective of determining the concordance or agreement between human judges.
placeholder for OBI:inter-rater reliability objective
image analysis objective
image processing and analysis objective
the objective to extract of meaningful information from images; mainly from digital images by means of digital image processing techniques. this information is often quantified or subjected to statistical calculations to generate new information about the subject. (http://en.wikipedia.org/wiki/Image_analysis)
feature extraction objective
image feature extraction objective
objective to generate quantified values from a scanned image.
placeholder for SWO:feature extraction objective
microarray image analysis objective
microarray signal intensity analysis objective
modeling and simulation objective
Models are mathematical representations of biological/biomedical phenomena that allow predictions of behavior of real world entities. Typically based on experimental data. "A mathematical model is a description of a system using mathematical concepts and language. A model may help to explain a system and to study the effects of different components, and to make predictions about behaviour. Mathematical models can take many forms, including but not limited to dynamical systems, statistical models, differential equations, or game theoretic models. These and other types of models can overlap, with a given model involving a variety of abstract structures. In general, mathematical models may include logical models, as far as logic is taken as a part of mathematics." (Wikipedia:)
mathematical modeling objective
modeling objective
network analysis objective
pathway analysis objective
the idea is a class to annotate software meant to support analysis/modeling of any kind of network/graph, including but not limited to biomedical data networks such as gene interaction or cell signaling networks.
text processing and analysis objective
PERSON:Kyle Ambert
an objective understanding textual data through the application of algorithmic approaches
text analysis objective
text analytics objective
text processing objective
descriptive statistical text analysis objective
PERSON:Kyle Ambert
an objective to understand general/descriptive statistical attributes of text (e.g. word count, length, etc)
statistical learning text analysis objective
natural language processing objective
PERSON:Kyle Ambert
an objective to understand texual data by leveraging the human-imposed patterns and structures that exist in language
distinct from text mining which ignores this these human-imposed features and takes a primarily machine-learning approach
part-of-speech tagging objective
POS tagging objective
an objective to identify and tag terms with information concerning their part-of-speech (e.g. noun, verb, adjective, etc)
grammatical tagging objective
http://en.wikipedia.org/wiki/Part-of-speech_tagging
word category disambiguation objective
statistical part-of-speech tagging objective
an objective to apply statistical approaches to identify and tag terms with information concerning their part-of-speech (e.g. noun, verb, adjective, etc)
statistical POS objective
sentiment analysis objective
an objective to identify and extract subjective information in source materials (e.g. the attitude of the speaker, or the overall contextual polarity of a document)
http://en.wikipedia.org/wiki/Sentiment_analysis
text-to-speech articulation analysis objective
an objective to facilitate conversion of written text to accurate and natural spoken language
text to speech word pattern analysis
text mining objective
PERSON:Kyle Ambert
an objective to understand content of text using approaches primarily based on computational/mathematical machine learning techniques (and not based on the inherent structure of human language)
supervised text mining objective
PERSON:Kyle Ambert
an objective to understand the content of text by using machine learning algorithms to train models based on gold standard labeled text
machine learning text processing objective
active learning text mining objective
active machine learning text mining objective
an objective to understand the content of text by using machine learning algorithms that are able to interactively query the user (or some other information source) to obtain the desired outputs at new data points.
http://en.wikipedia.org/wiki/Active_learning_%28machine_learning%29
document classification objective
document classification objective
objective to algorithmically assign a document to one or more classes or categories
text classification objective
text recommendation objective
document clustering objective
text clustering objective
information extraction objective
PERSON:Kyle Ambert
knowledge extraction objective
the objective to identify specficic informtion within text
named-entity recognition objective
NER objective
PERSON:Kyle Ambert
an objective to identify and classify atomic elements in text into predefined categories such as the names of persons, organizations, locations, expressions of times, quantities, monetary values, percentages, etc.
entity extraction objective
entity identification objective
http://en.wikipedia.org/wiki/Named_entity_recognition
unsupervised text mining objective
PERSON:Kyle Ambert
an objective to use machine learning algorithms to group textual entities in the absence of gold standard labeled text
latent discriminant analysis objective
LDA objective
source-based data analysis objective
objective to process and analyze data that is output from a specific type of technique, technology, or instrument.
ChIP-Chip data analysis objective
FACS data analysis objective
mass spectrometry data analysis objective
subject-based data analysis objective
biomedical data type-specific analysis objectives
data type-specific analysis objectives
objective to process and analyze data in order to generate new information about biological and/or medical phenomenon at a certain level of granularity. This hierarchy classifies software objectives based on the type/granularity of biomedical entity which the data they produce are about.
topic-based data analysis objectives
anatomical data analysis objective
anatomical analysis objective
objective to analyze data to investigate phenomenon at the level/granularity of gross anatomical structures (ie from anatomical systems and organs/tissues down to multi-cellular structures, inclusive)
organism feature analysis objective
anatomical image analysis objective
anatomical feature detection objective
anatomical disorder detection/diagnosis objective
anatomical anomoly diagnosis objective
anatomical disorder detection objective
anatomical disorder diagnosis assistance objective
behavioral data analysis objective
behavior analysis objective
objective to analyze data to investigate phenomenon concerning mental processes and/or resulting behavioral activity of an organism or group of organisms
psychological analysis objective
activity analysis objective
decision analysis objective
biomechanics data analysis objective
biomechanical data analysis objective
biomechanics analysis objective
objective to analyze data concerning biomechanical/physical forces
mechanical modeling and simulation objective
contact modeling objective
multibody dynamics analysis objective
cellular data analysis objective
cell analysis objective
cellular analysis objective
objective to analyze data about phenomenon at the level/granularity of cells (cellular processes, morphology, and interactions, protein expression, etc) or collections of cells.
cell modeling objective
cell dynamics modeling objective
modeling cellular level processes/behaviors based on input of biological data/parameters
cellular image analysis objective
cellular feature detection objective
cell feature analysis objective
cell image analysis objective
objective to analyze data about the physical features of cells or a populations of cells
cellular process network analysis objective
cellular process pathway analysis objective
disease analysis objective
disorder analysis objective
objective to perform data analysis which generates new information about physiological malfunctioning and anatomical disorders characteristic of disease
disease detection/diagnosis objective
physiological disorder detection and diagnosis assistance objective
disease outcome analysis objective
objective to understand factors that effect disease outcomes
anatomical disorder detection objective
anatomical disorder diagnosis objective
psychological disorder diagnosis objective
behavioral disorder detection objective
psychological disorder diagnosis assistance objective
disease pathway analysis objective
disease pathway analysis objective
disease process modeling objective
disease modeling objective
molecular data analysis objective
molecular analysis objective
objective of analyzing data to generate information about molecules/molecular complexes or the processes in which they are involved (molecular structures, sequences, interactions, networks, actrivities, etc)
OMICs data analysis objective
Here, the objective is "about" an ____ome-wide collection of moelcular entities of a particular type (eg a full genome of sequecnes instead of a single sequence).
large-scale molecular data analysis objective
objective to analyze large scale data sets representing a broad profile of some molecular-level feature of a subject or specimen (e.g. some totality of its genes, proteins, metabolic products, transcripts, etc). Covers range of objectives related to the analysis of OMICs data (transcriptomics, genomics, proteomics, metabolomics, etc)
chemical reaction data analysis objective
reaction data analysis objective
enzyme kinetics analysis objective
gene expression profile clustering objective
independent gene expression analysis objective
analysis of expression in a single sample (as opposed to differential expression analysis)
genetic mapping and linkage analysis objective
examples include objectives to estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. (EDAM)
objective to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyze genetic linkage and synteny (EDAM)
genetic map construction objective
DNA transduciton map construction objective
QTL map construction objective
cytogenetic map construction objective
haplotype map construction objective
macromolecular sequence design objective
an objective is to design a new molecular structure or macromolecular sequence that meets specified criteria
molecular sequence design objective
sequence molecule design objective
nucleic acid design objective
oligonucleotide design objective
objective to analyze sequences for suitability as primers, probes for a particular application
primer/probe design objective
peptide design objective
objective to specify a amino acid sequence to meet certain needs (e.g, be a good immunogen for antibody production)
sequence classification objective
molecular sequence classification objective
objective to classify an entire sequence macromolecule or gene as belonging to a particular class (e.g. based on localization, function, evolutionary conservation, etc)
nucleic acid sequence classification objective
RNA family classification objective
gene family classification objective
protein sequence classification objective
cellular localization classification objective
protein family classification objective
transmembrane protein classification objective
membrane topology classification objective
sequence feature analysis objective
objective to identify, discover, and/or analyze sequence-based functional regions of sequence macromolecules
sequence function analysis
sequence feature discovery objective
objective to identify new/novel domains or motifs linked to protein or nucleic acid functions (typically through statistical analysis of sequences known to exhibit some common activity)
sequence feature definition objective
gene family discovery objective
nucleic acid motif discovery objective
nucleic acid motif definition objective
protein domain discovery objective
protein domain definition objective
protein motif definition objective
protein motif discovery objective
sequence feature identification objective
objective to identify presence of known sequence domains/motifs in a macromolecule
seqeunce feature inference objective
sequence feature detection objective
sequence feature prediction objective
nucleic acid sequence feature identification objective
lots more specific subtypes in EDAM:Operation>Nucleic acid feature prediction hierarchy
nucleic acid sequence feature inference objective
nucleic acid sequence feature prediction objective
DNA binding site prediction objective
transcription factor binding site prediction objective
transcription factor binding site inference objective
DNA modification site prediction objective
gene prediction objective
promoter prediction objective
transcript splicing prediction objective
protein sequence feature identification objective
protein sequence feature detection objective
protein sequence feature prediction objective
protein cleavage site prediction objective
protein domain prediction objective
protein domain identification objective
protein domain recognition objective
protein motif prediction objective
protein modification site prediction objective
protein modification site recognition objective
sequence generation objective
objective to generate novel sequence or sequence profiles based on analysis or transformation of input biological sequence data
sequence transformation objective
nucleic acid restriction digest profile generation
nucleic acid reverse and complement generation
nucleic acid transcription or translation objective
molecular physical property analysis objective
molecule physical property calculation
objective to calculate or predict physical or chemical properties of molecules, including any non-positional properties of a macromolecular sequence
nucleic acid physical property analysis objective
nucleic acid curvature calculation
nucleic acid thermodynamic property calculation
nucleic acid entropy analysis objective
nucleic acid melting temperature calculation
protein physical property analysis objective
many more examples under EDAM/SWO:Core Data>Molecular Property>Protein Property
peptide immunogenicity analysis objective
protein felxibility analysis objective
protein hydropathy profile analysis objective
protein isoelectric point calculation objective
sequence composition analysis objective
objective to analyze the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats (EDAM)
sequence ambiguity analysis, sequence complexity analysis, repeat sequence organization analysis, nucleic acid density analysis
sequence composition calculation objective
genetic sequence variation analysis
This objective concerns a collection of sequences - specifically the sequence variation within the collection. This is different than a "sequence comparison objective" which is about a particular sequence and its conservation relative to other sequences. Different than phylogenetics because goal does not extend to predicting an evolutionary relationship. It is concerned with sequences, not organisms/populations/species, and stops with measuring variation of these sequences in some way.
comparative genomics analysis objective
macromolecular sequence variation analysis
objective to quantify or analyze variations at specific loci in the genomes of organisms (mutation and polymorphism) across or within a species, population, or individual (e.g healthy vs diseased tissue).
genetic structural variation analysis objective
objective to analyze variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. (EDAM)
genetic variant discovery objective
gene variant discovery objective
SNP discovery objective
single nucleotide polymorphism discovery objective
SNP analysis objective
single nucleotide polymorphism analysis objective
multiple sequence alignment objective
hybrid sequence alignment objective
objective to produce a sequence alignments between sequences of different types, for example genomic DNA to EST, cDNA or mRNA. (EDAM)
pairwise sequence alignment objective
molecular interaction analysis objective
direct molecular interaction analysis objective
key is that this refers to the analysis of a single moelcular interaction data, not large-scale analysis of interaction data (ie OMICs). distinguished from the more generic type of "interaction" analysis which may not require a direct physical interaciton, e.g. genetic interactions between genes
molecular binding analysis objective
objective to analyze thef physiochemical properties of a direct physical interaction of two or more molecules with each other
molecular interaction modeling objective
objective to model the direct interaction between two or more molecules
protein interaction analysis objective
distinct from protein interaction network analysis which is concerned with a larger network comprised of manifold protein interactions
objective to analyze or predict the physiochemical properties of the interaction between a protein with some other molecule(s)
protein-protein, protein-ligand, protein-drug, protein-nucleic acid interaction analysis objectives
protein interaction modeling
single molecule dynamics analysis objective
intramolecular interaction analysis objective
protein residue interaction analysis objective
molecular network analysis objective
molecular pathway analysis objective
placeholder for SWO:Simulation and analysis of biochemical networks
genetic network analysis objective
genetic pathway analysis objective
gene expression profile pathway mapping objective
objective to map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway (EDAM)
gene regulatory network analysis objective
objective to analyze dynaimcs of gene regulatory networks to make hypothesis or draw conclusions . . .
gene regulatory network construction objective
gene regulatory network discovery objective
gene regulatory network prediction objective
objective to define novel networks of genetic interactions at the level of gene regulation
metabolic network analysis objective
molecular interaction network analysis objective
protein-protein interaction network analysis objective
protein interaction network analysis objective
molecular signaling network modeling objective
objective to use biological data to model/predict molecular pathway behavior
signaling pathway modeling objective
signal transduction network analysis objective
cell signaling network analysis objective
cell signaling pathway analysis objective
molecular signaling network analysis objective
objective to analyzie data about direct molecular cell signaling networks or pathways, including predictions/modeling of how changes at certain nodes will affect the global network, and discovery/construction of new pathways or pathway connections (pathway discovery/construction)
signal transduction pathway analysis objective
signal transduction network construction objective
cell signaling network construction objective
cell signaling pathway construction objective
objective to define novel networks of molecular or geneitc signaling in or between cells, or discover new interactions/connections in a knownn network/pathway
signal transduction pathway construction objective
signaling network construction objective
signaling network discovery objective
molecular structure analysis objective
objective to analyze the structure of a molecular eneity (a chemical small molecule or a macromolecule)
chemical structure analysis
non-macromolecular chemical structure analysis
objective to analyse the structure of a chemical (ie a non-macromolecule)
small molecule structure analysis
chemical structure classification objective
chemical structure comparison objective
chemical structure modeling objective
macromolecular structure analysis objective
macromolecular structure classification objective
macromolecular structure comparison objective
macromolecular structure alignment objective
macromolecular structure comparison objective
objective to predict secondary or tertiary structure alignment between two or more macromolecules
protein structure alignment objective
secondary structural alignment objective
structural 3D profiling objective
structural clustering objective
tertiary structure alignment objective
macromolecular structure generation objective
3d structure generation
macromolecular structure modeling
objective to analyze physical data about an actual macromolecule structure and generate a three-dimensional model of its structure, e.g. taking crystallography/NMR data and using it to generate a 3D structure (not a "prediction" based on other inputs such as sequence data).
three dimensional structure generation
macromolecular structure prediction objective
objective to infer a predicted structure for a macromolecule based on secondary data/information such as seqeunce or homology (ie not based on physical data colelcted about the actual macromolecule in question, as is done in techniques such as x-ray chrystalography)
nucleic acid structure prediction objective
sequence-based nucleic acid structure prediction objective
sequence-based nucleic acid secondary structure prediction objective
sequence-based nucleic acid tertiary structure prediction objective
protein structure prediction objective
sequence-based protein structure prediction objective
homology modeling objective
sequence-based protein secondary structure prediction objective
sequence-based protein tertiary structure prediction objective
molecular structure classification objective
structural classification objective
molecular structure comparison objective
physiological data analysis objective
objective to analyze data to investigate biological processes at the level of single organism anatomy, including abnormal functioning of physiology in disease
physiological analysis objective
physiology analysis objective
physiological process data collection and processing objective
physiological process monitoring objective
physiological process modeling objective
objective to model a physiological process or dynamics of a physiological system or entity
physiological system modeling objective
cardiovascular system modeling objective
population data analysis objective
objective to analyze data to investigate phenomenon at the level of populations or species of organisms . . . including analysis of their genetic make-up
population analysis objective
population and evolutionary analysis objective
familial genetics analysis objective
objective to explore genetic relaationships in families of individuals (e.g. family tree construciton, relatedness, inheritance patterns, etc)
population dynamics analysis objective
objective to analyze interactions among, growth or changes in,or evolution of a population of organisms
population modeling objective
population dynamics modeling objective
population genetics analysis objective
objective to analyze the genetics of a population of organisms, e.g. the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow (EDAM)
the objective here is not to necessarily make any inferences about evolutionary relatedness . . . ie could include assessment of genetic variation for its own sake
phylogenetic analysis objective
evolutionary analysis objective
evolutionary relationship analysis objective
objective to analyze evolutionary relatedness across a population of organisms
evolutionary modeling objective
objective to model or simulate evolutionary processes
morphology-based phylogenetic analysis objective
phenotype-based phylogenetic analysis objective
phenotypic evolutionary analysis objective
morphology-based phylogenetic tree analysis objective
morphology-based phylogenetic tree creation objective
sequence-based phylogenetic analysis objective
phylogenomic analysis objective
gene cluster conservation analysis objective
sequence-based phylogenetic tree analysis objective
phylogenomic tree analysis objective
sequence-based phylogenetic tree construction objective
phylogenomic tree construction objective
phylogenomic tree creation objective
phylogenomic tree reconstruction objective
sequence-based population divergence analysis objective
ChIP-Chip data
mass spectrometry data
data processing operation
Placeholder for EDAM operation class.
operation
data analysis operation
Placeholder for EDAM operation class.
alignment analysis operation
Placeholder for EDAM operation class.
classification analysis operation
Placeholder for EDAM operation class.
clustering analysis operation
Placeholder for EDAM operation class.
comparison analysis operation
Placeholder for EDAM operation class.
feature comparison analysis operation
Placeholder for EDAM operation class.
feature alignment analysis operation
Placeholder for EDAM operation class.
data aquisition operation
Placeholder for EDAM operation class.
data evaluation operation
Placeholder for EDAM operation class.
data validation operation
Placeholder for EDAM operation class.
feature detection analysis operation
Placeholder for EDAM operation class.
identification of some part of a specimen (e.g. an anatomical, molecular, cellular specimen) that represents a feature of interest
feature prediction analysis operation
Placeholder for EDAM operation class.
feature discovery analysis operation
Placeholder for EDAM operation class.
network analysis operation
Placeholder for EDAM operation class.
pathway analysis operation
graph-based analysis operation
Placeholder for EDAM operation class.
image analysis operation
Placeholder for EDAM operation class.
modeling and simulation operation
Placeholder for EDAM operation class.
mathematical modeling and simulation
molecular design analysis operation
Placeholder for EDAM operation class.
image processing operation
Placeholder for EDAM operation class.
data assembly operation
Placeholder for EDAM operation class.
data transfer operation
Placeholder for EDAM operation class.
data cleaning operation
Placeholder for EDAM operation class.
data correction operation
Placeholder for EDAM operation class.
data normalilzation operation
Placeholder for EDAM operation class.
data pre-processing operation
Placeholder for EDAM operation class.
data rendering and visualization operation
Placeholder for EDAM operation class.
data retrieval operation
Placeholder for EDAM operation class.
data transformation operation
Placeholder for EDAM operation class.
algorithm execution
center calculation objective
placeholder for OBI:center calculation objective
clustering analysis objective
error analysis objective
group comparison objective
permutation test objective
power-sample size analysis objective
regression analysis objective
statistical classification analysis objective
statistical distribution fitting objective
probability distribution fitting objective
statistical parameter determination objective
objective to determine aspects of study design needed to achieve a desired statistical power or rigour
statistical parameter calculation objective
drug design objective
quantitative PCR data analysis objective
DNA fragment analysis objective
A sequence analysis objective that analyzes the sequence of DNA fragments.
PERSON: Nicole Vasilevsky
PERSON: Nicole Vasilevsky
Fourier transform
Burrows-Wheeler technique
BOWTIE
Burrows-Wheeler indexing
Burrows-Wheeler transformation
Jonckheere–Terpstra test
JT test
Jonckheere trend test
Kendall's tau coefficient
Kendall rank correlation coefficient
Harding algorithm
Derivative Log ratio spread
Z-scoring for aberrant regions
ADM-1
GWT
academic software license
non-commercial proprietary software license
Monte Carlo method
least squares fitting
spline-curve spatial analysis
spline-curve dynamics analysis
de Bruijn graph-based method
text-to-speech synthesis
human study data analysis objective
PERSON:Matthew Brush
PERSON:Matthew Brush
objective to analyze data about a population of human subjects in a human study
anatomical data
behavioral data
biomechanical data
cell data
disease data
molecular data
data that is about molecules or phenomena occurring at a molecular level (e.g. processes such as molecular interactions, chemical reactions, gene expression etc).
protein secondary structure data
population data
anatomical image data
cell image data
genetic mapping data
reaction data
chemical reaction data
gene expression data
sequence data
sequence similarity calculation objective
objective to calculate level of sequence conservation/similarity between macromolecules
molecular structure data
protein structure data
flow cytometry data
audio format
sequence variation data
sequence alignment data
molecular network data
RIFF
Resource Interchange File Format
nucleic acid secondary structure data
protein tertiary structure data
organism data
data about organisms and phenomenon at the level/granularity of organisms, their superficial features, and their behavior
organismal data analysis objective
objective to analyze data to investigate phenomenon at the level/granularity of organisms, their superficial features, and their behavior
medical data
health data
population genetics data
phylogenetic data
morphological data
Markov Cluster algorithm
SVM-Light algorithm
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
biological process
physiological process
measurement unit label
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Examples of measurement unit labels are liters, inches, weight per volume.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
OBI_0000217
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
objective specification
purpose of a study; support of hypothesis, discovery of new information
action specification
Alan Ruttenberg
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
label
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
OBI_0000159
a report that is published in a journal
group:OBI
journal article
person:Alan Ruttenberg
person:Chris Stoeckert
programming language
A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
OBI_0000058
group:OBI
person:Alan Ruttenberg
person:Chris Stoeckert
data item
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
Data items include counts of things, analyte concentrations, and statistical summaries.
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data
data item
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
OBI_0000142
PERSON: Chris Stoeckert
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
information content entity
directive information entity
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
algorithm
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
OBI_0000270
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
PERSON:Bill Bug
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
curation status specification
data format specification
OBI branch derived
OBI_0000187
PERSON: Alan Ruttenberg
PlanAndPlannedProcess Branch
data format specification
data about an ontology part
Person:Alan Ruttenberg
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
Alan Ruttenberg
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI Plan and Planned Process branch
OBI_0000344
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
plan specification
conclusion textual entity
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
Person:Alan Ruttenberg
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
obsolescence reason specification
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
obsolescence reason specification
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
PERSON: Lawrence Hunter
document
denotator type
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
mammalian phenotype
the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan
Dipodomys
kangaroo rats
Pterocarpus
Cricetinae
hamsters
Cricetulus
Cricetulus griseus
Chinese hamster
Chinese hamsters
Cricetulus aureus
Cricetulus barabensis griseus
Cricetus griseus
Cricetulus migratorius
Armenian hamster
gray dwarf hamster
grey hamster
Mesocricetus auratus
Golden hamsters
Microcricetus aureus
Syrian golden hamster
Syrian golden hamsters
Syrian hamster
Syrian hamsters
golden hamster
Gerbillinae
gerbils
Ophiopogon japonicus
Asparagus cochinchinensis
Asparagus cochinchinensis (Lour.) Merr.
Mus <mouse, genus>
Mus
mice
Mus musculus
Mus muscaris
house mouse
mice C57BL/6xCBA/CaJ hybrid
mouse
Rattus
rat
rats
Rattus norvegicus
Gunn rats
Norway rat
Rattus norvegicus8
Rattus norwegicus
Rattus rattiscus
Rattus sp. strain Wistar
brown rat
rat
rats
Rattus rattus
Rattus rattoides
black rat
house rat
roof rat
Cavia porcellus
Cavia aperea porcellus
Cavia cobaya
Cavia cobya
domestic guinea pig
guinea pig
Prunus mume
Armeniaca mume
Japanese apricot
Prunus armeniaca var bungo
Prunus mume Siebold & Zucc.
ume
Benincasa hispida
Cucurbita hispida
Curcurbita hispida
ash gourd
wax gourd
winter melon
Viruses
Vira
Viridae
viruses
Poxviridae
Vaccinia virus
vaccinia virus VV
Variola virus
small pox virus
smallpox
smallpox virus
variola virus VAR
Ulmus rubra
slippery elm
Eutrochium purpureum
Eupatoriadelphus purpureus
Eupatoriadelphus purpureus (L.) R.M.King & H.Rob.
Eupatorium purpureum L.
Eutrochium purpureum (L.) E.E.Lamont
joe-pye-weed
Eupatorium perfoliatum
Eupatorium perfoliatum L.
common boneset
Herpesviridae
Human herpesvirus 2
Herpes simplex virus (type 2)
Herpes simplex virus 2
Herpes simplex virus type 2
herpes simplex virus type 2 HSV-2
Vitis rotundifolia
Muscadinia rotundifolia
fox grape
muscadine
Suid herpesvirus 1
Alphaherpesvirus pseudorabies virus PRV
Aujeszky's disease virus
Pseudorabies Virus PRV
Pseudorabies virus
Suid herpesvirus type 1
Hepadnaviridae
hepatitis B-type viruses
Hepatitis B virus
Human hepatitis B virus
hepatitis B virus (HBV)
hepatitis B virus HBV
hepatitis B virus, HBV
human hepatitis B virus HBV
Baculoviridae
Adenoviridae
Elettaria cardamomum
Eletaria cardamomum
Elettaria cardamom
cardamom
cardamon
Echinometra lucunter
Echinometra lacunter
rock boring urchin
Lonicera japonica
Japanese honeysuckle
Polyomavirus
Polyomaviruses
Simian virus 40
Polyomavirus maccacae
Polyomavirus maccacae 1
Rhesus macaque polyomavirus
rhesus polyomavirus
Cauliflower mosaic virus
cauliflower mosaic virus CaMV
Chaenomeles speciosa
Chaenomeles lagenaria
boke
mu gua
Smilax officinalis
Smilax vanilliodora
Fritillaria cirrhosa
Fritillaria thunbergii
Reoviridae
Flaviviridae
Flavivirus (arbovirus group B)
Flavivirus
arboviruses group B
Coronaviridae
Paramyxoviridae
Cyanobacteria
Cyanophyceae
Cyanophycota
Cyanophyta
Oxygenic photosynthetic bacteria
Oxyphotobacteria
blue-green algae
blue-green bacteria
cyanobacteria
cyanophytes
Measles virus
Cell-associated subacute sclerosing panencephalitis
Subacute sclerosing panencephalitis virus
measles virus MV
rougeole virus
rubeola virus
subacute sclerose panencephalitis virus
subacute sclerosing panencephalitis virus, SSPEV
Rhabdoviridae
Chamaelirium luteum
Lycium barbarum
Duke of Argyll's teatree
Lycium barbarum L.
goji berry
matrimony vine
ning xia gou qi
wolfberry
Lycium chinense
Chinese boxthorn
Chinese wolfberry
gou qi
kuko
Rabies virus
Orthomyxoviridae
Influenza A virus
Influenza virus type A
influenza A virus INF A
Gardenia jasminoides
Gardenia angusta
Gardenia augusta
Gardenla jasminoides
Spirulina <Cyanobacteria>
Spirulina
Euterpe oleracea
Sargassum pallidum
Retroviridae
Lentivirus
Lentivirinae
Hyperotreti
Agnatha
fish
fishes
Apium graveolens Dulce Group
Apium graveolens var. dulce
celery
stalk celery
Murine leukemia virus
Murine leukemia viruses
murine leukemia virus MLV
murine leukemia virus MuLV
Arthrospira platensis
Spirulina platensis
Avian myeloblastosis virus
avian myeloblastosis virus AMV
Tussilago farfara
Tussilago farfara L.
coltsfoot
mat'-i-machekha
Rous sarcoma virus
Rous sarcoma virus RSV
Carpesium abrotanoides
Inula britannica
Inula britanica
Inula britannica L.
Inula brittanica
xuan fu hua
Cinnamomum aromaticum
Chinese cinnamon
Cinnamomum cassia
cassia-bark
Cinnamomum burmannii
Batavia cinnamon
Cinnamomum burmannii (Nees & T.Nees) Blume
Ulocladium
Picornaviridae
Picormavirus
Picornavirus
Hepatitis A virus
Proteobacteria
proteobacteria
purple bacteria
purple bacteria and relatives
purple non-sulfur bacteria
purple photosynthetic bacteria
purple photosynthetic bacteria and relatives
Tobacco mosaic virus
tobacco mosaic virus TMV
tobacco mosaic virus, TMV
unclassified phages
unclassified bacteriophages
Acorus tatarinowii
Acorus tatarinowii Schott
Firmicutes
Bacillus/Clostridium group
Clostridium group firmicutes
Firmacutes
Gram positive bacteria
Gram-positive bacteria
Low G+C firmicutes
clostridial firmicutes
firmicutes
low G+C Gram-positive bacteria
low GC Gram+
Illicium verum
Chinese star-anise
Illicium verum Hook.f.
Azadirachta indica
Indian-lilac
Melia azadirachta
margosa
neem
neem tree
Alpinia oxyphylla
Alpinia oxyphylla Miq.
sharp-leaf galangal
yi zhi
Chionanthus virginicus
Dengue virus
Forsythia suspensa
Jasminum officinale
Jasminum officinale L.
common jasmine
jessamine
su fang hua
Fraxinus chinensis subsp. rhynchophylla
Fraxinus chinensis var. rhynchophylla
Fraxinus rhynchophylla
Fraxinus rynchophylla
Withania somnifera
ashwagandha
Human immunodeficiency virus
AIDS virus
Staphylococcus
Aurococcus
Matricaria chamomilla var. recutita
German chamomile
Matricaria recutita
Tanacetum parthenium
Chrysanthemum parthenium
Pyrethrum parthenium
feverfew
Staphylococcus aureus
Micrococcus aureus
Micrococcus pyogenes
Staphilococcus aureus
Staphlococcus pyogenes citreus
Staphylococcus pyogenes aureus
Staphylococus aureus
Streptococcus aureus
Tanacetum vulgare
Tanacetum boreale
Tanacetum boreale Fisch. ex DC.
Tanacetum vulgare L.
Tanacetum vulgare var. boreale
Tanacetum vulgare var. boreale (Fisch. ex DC.) Trautv. & C.A.Mey
tansy
Dimocarpus longan
longan
Staphylococcus epidermidis
Albococcus epidermidis
Micrococcus epidermidis
Staphylococcus epidermidis albus
Uncaria tomentosa
Deinococcus-Thermus
'Deinococcus-Thermus'
Thermus/Deinococcus group
Deinococcus radiodurans
Deinococcus radiidurans
Micrococcus radiodurans
Streptococcaceae
Piper auritum
Piper methysticum
Piper methysticum G.Forst.
kava
Streptococcus sanguinis
Streptococcus sanguis
Juniperus
Juniperus L.
junipers
Streptococcus pneumoniae
Diplococcus pneumoniae
Micrococcus pneumoniae
Streptococcus pyogenes
Micrococcus scarlatinae
Streptococcus erysipelatos
Streptococcus hemolyticus
Streptococcus pyrogenes
Streptococcus scarlatinae
Piper
Piper nigrum
Piper lampong
Piper nigrum L.
Stellaria
Stellaria L.
Stellaria media
Achillea millefolium
Streptococcus equi
Borago officinalis
Borago officinalis L.
Burkholderia mallei
Acinetobacter mallei
Actinobacillus mallei
Bacillus mallei
Loefferella mallei
Malleomyces mallei
Pfeifferella mallei
Pseudomonas mallei
Calluna vulgaris
heather flower
Carcharodon carcharias
great white shark
white shark
Chrysanthemum
Chrysanthemum L.
Dendranthema
Dendranthema (DC.) Des Moul.
Dendrathema
Dendrathemum
Cichorium intybus
Cichorium intybus var. foliosum
Cichorium intybus var. sativum
Cychorium intybus
chicory
radicchio
succory
witloof
Cinnamomum
Eupatorium
Eupatorium L.
Schizonepeta tenuifolia
Schizonepeta tenuifolia (Bentham) Briq.
Hydrastis canadensis
Hydrastis canadensis L.
goldenseal
Juncus effusus
common rush
Curcuma longa
Curcuma domestica
Curcuma domestica Valeton
Curcuma longa L.
turmeric
Curcuma phaeocaulis
Curcuma phaeocaulis Valeton
Curcuma wenyujin
Curcuma wenchowensis
Curcuma wenchowensis Y.H.Chen & C.Ling
Curcuma wenyujin Y.H.Chen & C.Ling
Paeonia
peonies
Pulmonaria officinalis
lungwort
Rheum palmatum
Rheum palmatum L.
Pelodiscus sinensis
Chinese soft-shelled turtle
Chinese softshell turtle
Torionyx sinensis
Trionyx sinensis
Sanguisorba officinalis
Vaccinium
Viola <angiosperm>
Viola
Viola L.,1753
Polygonum aviculare
Adiantum
Lygodium japonicum
Lygodium japanicum
Lygodium japonicum (Thunb.) Sw.
Bacillus <bacterium>
Bacillus
Bacillus rRNA group 1
Cocos nucifera
Cocos nucifera L.
coconut palm
Bacillus anthracis
Bacillus cereus var. anthracis
Bacteridium anthracis
anthrax
anthrax bacterium
Bacillus cereus
Bacillus endorhythmos
Bacillus medusa
Bacillus sp. JKR66
Prunus cerasus
Cerasus vulgaris
Prunus cerasus L.
pie cherry
sour cherry
Crataegus monogyna
Craetegus monogina
Crataegus monogyna Jacq.
Lawsonia inermis
Jamaica mignonette
Lawsonia indica
alcana
henna
Asclepias tuberosa
Asclepias tuberosa L.
Bacillus subtilis
Bacillus globigii
Bacillus natto
Bacillus subtilis8
Bacillus uniflagellatus
Vibrio subtilis
Bacillus thuringiensis
Bacillus cereus var. thuringiensis
Bacillus thuringiensi
Usnea longissima
Althaea officinalis
Althaea officinalis L.
marshmallow
white mallow
Malva sylvestris
Chrysanthemum indicum
Chrysanthemum indicum L.
Dendranthema indicum
Litchi chinensis
Litchi chinensis Sonn.
litchi
lychee
Papillomaviridae
Papillomavirus
Polyomaviridae
Dichroa febrifuga
Sinomenium acutum
Lepidium apetalum
Terminalia chebula
Terminalia chebula Retz.
black myrobalan
harra
Akebia trifoliata
Vincetoxicum atratum
Cynanchum atratum
Cynanchum atratum Bunge
Vincetoxicum atratum (Bunge) C.Morren & Decne.
Gaultheria procumbens
checkerberry
teaberry
wintergreen
Polyporus umbellatus
Betta
Passiflora incarnata
Passiflora incarnata L.
Isatis tinctoria
Isatis indigotica
woad
Beta vulgaris
Beta altissima
Beta vulgaris L.
beet
Polygonatum
King Solomon's seals
Solomon's seals
Emericella nidulans
A. nidulans
Aspergillus nidulans
Aspergillus nidulellus
Aspergilus nidulans
Listeria monocytogenes
Bacterium monocytogenes
Bacterium monocytogenes hominis
Corynebacterium infantisepticum
Corynebacterium parvulum
Erysipelothrix monocytogenes
Listerella hepatolytica
Lysteria monocytogenes
Angelica sinensis
Angelica sinensis (Oliv.) Diels
Chinese angelica
dong gui
dong quai
Hyriopsis cumingii
Hypriopsis cumingii
Actinomyces naeslundii
Actinomyces israelii
Actinobacterium israeli
Brevistreptothrix israeli
Cohnistreptothrix israeli
Corynebacterium israeli
Discomyces israeli
Nocardia israeli
Oospora israeli
Proactinomyces israeli
Streptothrix israeli
Juglans
Juglans L.
walnut
Juglans nigra
Juglans nigra L.
black walnut
Stachyurus himalaicus
Stachyurus himalaicus Hook.f. & Thomson
Houttuynia cordata
Houttuynia cordata Thunb.
chameleon-plant
dokudami
Cornus officinalis
Cornus officinalis Siebold & Zucc.
Japanese cornel
Achyranthes
Achyranthes L.
Laminaria setchellii
Pausinystalia johimbe
Citrus medica
Buddha's hand
citron
Centaurium erythraea
Terminalia arjuna
Terminalia arjuna (Roxb. ex DC.) Wight & Arn.
Broussonetia papyrifera
Broussonetia papyrifera L'Her. ex Vent.
aka
gou shu
paper-mulberry
Boswellia sacra
frankincense
Monstera deliciosa
Monstera delociosa
Monstera diliciosa
Swiss-cheese-plant
cut-leaf-philodendron
harpon
Pueraria montana var. thomsonii
Pueraria lobata var. thomsonii
Pueraria montana var. chinensis
Pueraria thomsonii
fen ke
mealy kudzu
Rumex crispus
Andrographis paniculata
Andrographis paniculata (Burm.f.) Nees
Hylocereus undatus
dragon fruit
Mycobacterium smegmatis
Bacillus smegmatis
Bacterium smegmatis
Mycobacterium paratuberculosis smegmatis
Mycobacterium tuberculosis
Bacillus tuberculosis
Bacterium tuberculosis
Mycobacterium tuberculosis typus humanus
Mycobacterium tuberculosis var. hominis
Mycobacterium marinum
Mycobacterium balnei
Mycobacterium platypoecilus
Dipsacus asperoides
Dipsacus asperoides C.Y.Cheng & T.M.Ai
Vaccinium myrtillus
bilberry
whortleberry
Hibiscus sabdariffa
red-sorrel
roselle
sereni
Patrinia villosa
Patrinia villosa (Thunb.) Juss.
Plantago ovata
Plantago ovata Forssk.
blond psyllium
ispaghul
Sigesbeckia orientalis
Siegesbeckia orientalis
Siegesbeckia orientalis L.
common St. Paul's wort
Ilex paraguariensis
Brazilian-tea
Ilex paraguariensis A.St.-Hil.
Ilex paraguensis
mate
yerba-mate
Ilex pubescens
Selaginella doederleinii
Caulimoviridae
Adenophora triphylla
Adenophora tetraphylla
Adenophora tetraphylla (Thunb.) Fisch.
Adenophora triphylla (Thunb.) A.DC.
nan sha shen
Pyrrosia lingua
Pyrrosia lingua Farwell
Amomum
Amomum Roxb.
Scaphium lychnophorum
Firmiana lychnophora
Sterculia lychnophora
Periploca sepium
Periploca sepium Bunge
Caesalpinia bonduc
Caesalpinia bundoc
yellow nicker
Campylobacter
Ampylobacter
Plantago asiatica
Asian plantain
Plantago asiatica L.
Indigofera tinctoria
Pinellia ternata
Pinellia tuberifera
Alpinia officinarum
Alpinia officinarum Hance
Chinese-ginger
lesser galangal
Amomum villosum
Amomum villosum Lour.
sha ren
Bacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
eubacteria
not Bacteria Haeckel 1894
prokaryote
prokaryotes
Fumaria officinalis
common fumitory
earth-smoke
wax-dolls
Actinobacteria <phylum>
'Actinobacteria'
Actinobacteria
actinobacteria
not Actinobacteria Cavalier-Smith 2002
Campylobacter rectus
Campylobacter rectus (Tanner et al. 1981) Vandamme et al. 1991
Wolinella recta
Wolinella recta Tanner et al. 1981
Rhodiola kirilowii
Sedum kirilowii
Berberis aquifolium
Mahonia aquifolium
hollyleaf barberry
Ceratonia siliqua
Ceratonia siliqua L.
St. John's-bread
carob
Sparganium stoloniferum
Sparganium erectum subsp. stoloniferum
Astragalus
Vitex trifolia
Indian privet
Vitex trifoliata
hand-of-Mary
man jing
san ye man jing
Thyonella gemmata
Hymenaea courbaril
Hymenaea coubaril
Maranta arundinacea
Brucea javanica
Rhus javanica
Tribulus terrestris
Tribulus terrester
Mycoplasma pneumoniae
Filterable agent of primary atypical pneumonia
Schizoplasma pneumoniae
Potentilla chinensis
Potentilla chinensis Ser.
Rubus fruticosus
shrubby blackberry
Lysimachia christinae
Lysimachia christiniae
guo lu huang
Gentiana
gentian
Archaea
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
Lithospermum
Lithospermum L.
Mentha
mints
Salvia
Salvia L.
sages
Syzygium aromaticum
Eugenia aromatica
clove
Verbena
Verbena L.
vervains
Tegillarca granosa
Anadara (Tegillarca) granosa
Anadara granosa
Arca granosa
Salvia miltiorrhiza
Chinese salvia
Salvia mihiorrhiza
Salvia miltiorhiza
dan shen
redroot sage
Punica granatum
Typhonium giganteum
Typhonium giganteum Engl.
Berberis
barberry
Taxillus chinensis
Taxillus chinensis (DC.) Danser
Arisaema erubescens
Agrimonia
Crataegus
Crataegus L.
hawthorn
Prunus serotina
black cherry
Rubus
Rubus L.
bramble
Scutellaria lateriflora
Scutellaria lateriflora L.
blue skullcap
Viburnum prunifolium
Viburnum prunifolium L.
Ailanthus altissima
China-sumac
stinking sumac
tree-of-heaven
Aconitum kusnezoffii
Epimedium grandiflorum
Epimedium grandiflorum C.Morren
barrenwort
yin yang huo
Lycium
Amomum tsao-ko
Amomum tsaoko
cao guo
tsao ko
Oldenlandia diffusa
Hedyotis diffusa
Hedyotis diffusa Willd.
Oldenlandia diffusa (Willd.) Roxb.
Rubia
Berberis vulgaris
European barberry
common barberry
Artemisia argyi
Eriocaulon
Eriocaulon L.
Mauremys reevesii
Chinemys reevesii
Geoclemys reevesii
Geoclemys reevessi
Mauremys reevesi
Reeves's turtle
Citrullus lanatus subsp. vulgaris
Citrullus lanatus subsp. vulgaris (Schrad.) Fursa
Citrullus lanatus var. lanatus
Citrullus vulgaris
Citrullus vulgaris Schrad. ex Eckl. & Zeyh.
watermelon
Polygonatum sibiricum
huang jing
Coptis chinensis
Helichrysum italicum
Alisma orientale
Alisma orientale (Samuel) Juz.
Alisma plantago-aquatica subsp. orientale
Alisma plantago-aquatica subsp. orientale (Sam.) Sam.
Francisella tularensis
Bacterium tularense
Brucella tularensis
Francisella tularense
Pasteurella tularensis
Iris <angiosperm>
Iris
Eleutherococcus gracilistylus
Acanthopanax gracilistylus
Acanthopanax gracilistylus W.W.Sm.
Eleutherococcus gracilistylus (W.W.Sm.) S.Y.Hu
Artemisia capillaris
Atractylodes macrocephala
Atractylodes macrocephala Koidz.
Atractylodes macrocephla
Morinda officinalis
ba ji
Polistes olivaceus
Plantago
Plantago L.
ribworts
Origanum majorana
Majorana hortensis
Origanum dubium
sweet marjoram
Citrus
Citrus limon
Citrus lemona
Citrus limonum
Citrus x limon
lemon
Citrus sinensis
Citrus x sinensis
Valencia orange
apfelsine
naranja
navel orange
sweet orange
Drynaria fortunei
Dermaptera
earwigs
Congiopodus peruvianus
Agriopus peruvianus
horsefish
Rhodophyta
Rhodophyceae
Rhodophycota
algae
red algae
rhodophytes
Symphytum officinale
boneset
common comfrey
slippery-root
Streptococcus mitis
Tannerella forsythia
Bacteroides forsythus
Tannerella forsythensis
Prevotella intermedia
Bacteroides intermedius
Bacteroides melaninogenicus subsp. intermedius
Prevotella intermedius
Prevotella nigrescens
Palmaria palmata
Dulse
Rhodymenia palmata
Human adenovirus 5
Adenovirus type 5
Human adenovirus type 5
Mastadenovirus 5
Mastadenovirus h5
adenovirus Ad5
adenovirus type 5 AD5
Burkholderia pseudomallei
Bacillus pseudomallei
Bacterium whitmori
Burkholderia pseudomallai
Loefflerella pseudomallei
Malleomyces pseudomallei
Pseudomonas pseudomallei
Asarum canadense
Asarum canadense L.
Pogostemon cablin
Pogostemon cablin (Blanco) Benth.
Pogostemon patchouly
Pogostemon patchouly Pellet.
patchouli
Anthoxanthum nitens
Hierochloe odorata
Hierochloe odorata (L.) Beauv.
vanilla grass
Pseudomonas aeruginosa
Bacillus aeruginosus
Bacillus pyocyaneus
Bacterium aeruginosum
Bacterium pyocyaneum
Micrococcus pyocyaneus
Peudomonas aeruginosa
Pseudomonas polycolor
Pseudomonas pyocyanea
probable synonym or variety: "Pseudomonas polycolor" Clara 1930
Laminariales
Dianthus superbus
Mycoplasma bovis
Bovine serotype 5
Mycoplasma agalactiae subsp. bovis
Mycoplasma agalactiae var. bovis
Mycoplasma bovimastitidis
Rhus aromatica
Euphrasia officinalis
Euphrasia officinalis L.
Scrophularia ningpoensis
Scrophularia ningpoensis Hemsl.
xuan shen
Crassostrea gigas
Crassotrea gigas
Ostrea gigas
Pacific oyster
Gentiana scabra
Mentha canadensis
Japanese mint
Mentha arvensis var. piperascens
Mentha haplocalix
Mentha haplocalyx
Mentha haplocalyx var. piperascens
Mentha sachalinensis
corn mint
Mentha pulegium
pennyroyoal
Phyllanthus niruri
Phyllanthus niruri L.
Spirodela polyrhiza
Spirodela polyrrhiza
great duckweed
Lophatherum gracile
Lophatherum gracile Brongn.
Phragmites australis
Phragmites australis (Cav.) Trin. ex Steud.
Phragmites communis
common reed
Mentha spicata
Mentha crispa var. crispata f. reticulata
Mentha viridis
spearmint
Vitis vinifera
Vitis vinifera subsp. vinifera
wine grape
Mangifera indica
Magnifera indica
mango
Galium aparine
Rubia tinctorum
dyer's madder
madder
Plantago major
cart-track plant
common plantain
white-man's-foot
Crataegus laevigata
Crataegus laevigata (Poir.) DC.
Auricularia auricula-judae
Auricularia auricula
Hirneola auricula-judae
ear fungus
wood ear
Archaeognatha
Microcoryphia
bristletails
Ephemeroptera
mayflies
Psocoptera
book lice
booklice
booklice and barklice
Strepsiptera
Strepsipteriformia
twisted-wing parasites
Trichoptera
caddisflies
Thysanura
Zygentoma
Zygoentomata
silverfish and firebrats
Chlorophyta
Chlorophycota
Chlorophyta sensu Bremer 1985
algae
green algae
Squalidae
dogfish sharks
Chlamydomonas
Chlamydomonas reinhardtii
Chlamydomonas reihhardtii
Chlamydomonas reinhardtii P.A.Dangeard
Chlamydomonas smithii
Chlamydomonas smithii R.W.Howshaw & H.Ettl
Chlamydonas reinhardtii
Sciurus carolinensis
Sciurus carolinensus
eastern gray squirrel
gray squirrel
Dipodidae
jerboas
Lobelia inflata
Indian-tobacco
Lobelia inflata L.
Takifugu rubripes
Fugu rubripes
Sphaeroides rubripes
Takifugu rubripes (Temminck & Schlegel, 1850)
Tetraodon rubripes
tiger puffer
torafugu
Diadema
Diadema setosum
Holothuria glaberrima
Sepia esculenta
golden cuttlefish
Angelica pubescens
Angelica pubescens Maxim.
du huo
Peucedanum praeruptorum
Peucedanum praeruptorum Dunn
bai hua qian hu
Glires
Rodents and rabbits
Simiiformes
Anthropoidea
Hominoidea
ape
apes
Viola philippica
Viola philippica Cav.
Viola yedoensis
Viola yedoensis Makino
Speranskia
Stillingia sylvatica
queen's-delight
Bambusa tuldoides
Bambusa textilis
Bambusa textilis McClure
Commiphora myrrha
myrrh
Burkholderia
Burkholderia Yabuuchi et al. 1993 emend. Gillis et al. 1995
Pseudomonas RNA homology group II
Convallaria majalis
Convallaria majali
lily-of-the-valley
Eriobotrya japonica
loquat
Rubus idaeus
European raspberry
Rubus idaeus L.
red raspberry
Prunus persica var. nucipersica
Prunus persica var nucipersica
Prunus persica var. nectarina
nectarine
Teleostei
teleost fishes
Lycopodium
Lycopodium clavatum
Lycopodium clavatum L.
stag's-horn clubmoss
Equisetum
horstails
scouring rushes
Equisetum arvense
Equisetum arvense L.
common horsetail
field horsetail
Equisetum hyemale
Dutch rush
Equisetum hiemale
Ananas nanus
Ananas nanus (L.B.Sm.) L.B.Sm.
Ziziphus jujuba
Chinese jujube
Zizyphus jujuba
common jujube
non Ziziphus jujuba (L.) Gaertn., nom. illeg.
Zanthoxylum bungeanum
Sichuan-pepper
Zanthoxylum bungei
hua jiao
Turnera diffusa
Dysphania ambrosioides
American wormseed
Chenopodium ambrosiodes
Chenopodium ambrosioides
Jerusalem-tea
epazote
Dioscorea villosa
Dioscorea villosa L.
Parvimonas micra
'Diplococcus glycinophilus'
Diplococcus glycinophilus
Micromonas micros
Peptococcus glycinophilus
Peptostreptococcus micros
Streptococcus anaerobius micros
Streptococcus micros
Eupatorium fortunei
Chinese eupatorium
Eupatorium fortunei Turcz.
pei lan
Viridiplantae
Chlorobionta
Chlorophyta/Embryophyta group
chlorophyte/embryophyte group
green plants
Eremothecium gossypii
Ashbya gossipii
Ashbya gossypii
Eremothecium gossypii (Ashby & Nowell) Kurtzman
Nematospora gossypii
Thuja occidentalis
Heteroptera
true bugs
Pinus <genus>
Pinus
Pinus strobus
Eastern white pine
Carnivora
carnivores
Stramenopiles
Chromophyta
heterokonts
Laminaria
Euglenozoa
Euglenozoans
Rubia cordifolia
Rubia cordiolia
Stemona sessilifolia
Stemona sessilifolia (Miq.) Miq.
Magnolia
Aromadendron
Dugandiodendron
Elmerrillia
Kmeria
Pachylarnax
Parakmeria
Talauma
Woonyoungia
Iris germanica
Iris x germanica
Iris x germanicum
flag
fleur-de-lis
Lithospermum erythrorhizon
Lithospermum erythrorhizon Siebold & Zucc.
Mentha x piperita
Mentha aquatica x Mentha spicata
Mentha piperita
Mentha x piperita L.
Mentha x piperita glacialis
Mentha x piperita var. officinalis
Mentha x piperita var. officinalis f. rubescens
peppermint
Eucalyptus globulus
Eucalyptus globus
blue gum
Persea americana
Persea americanum
avocado
Clematis
virgin's bower
Acrobeloides ellesmerensis
Eschscholzia californica
California poppy
Eschscholtzia californica
Eschscholzia californica Cham.
Papaver somniferum
Papaver somnifera
opium poppy
Senna obtusifolia
Cassia obtusifolia
Senna obtusifolia (L.) H.S.Irwin & Barneby
Sanguinaria canadensis
red puccoon
Cannabis sativa
hemp
marijuana
Humulus lupulus
European hop
common hop
Ficus <angiosperm>
Ficus
Ficus L. 1753
fig trees
figs
Morus alba
Morus acidosa
Morus sinensis
white mulberry
Urtica dioica
great nettle
stinging nettle
Morella cerifera
Morella cerifera (L.) Small
Myrica cerifera
Myrica cerifera L.
candleberry
southern bayberry
wax-myrtle
Quercus alba
Quercus alba L.
white oak
Phytolacca americana
American pokeweed
Phytolacca decandra
Virginia poke
common pokeberry
common pokeweed
red stem pokeweed
Anemopaegma
Zanthoxylum americanum
Zanthoxylum americanum Mill.
northern prickly-ash
toothache-tree
Zanthoxylum schinifolium
Sichuan-pepper
Zanthoxylum schinifolium Siebold & Zucc.
qing hua jiao
Polygala tenuifolia
Chinese senega-root
Polygala tenuifolia Willd.
yuan zhi
Rhabditella axei
Artemisia annua
sweet Annie
sweet wormwood
Saponaria officinalis
common soapwort
Dioscorea collettii var. hypoglauca
Dioscorea collettii var. hypoglauc
Dioscorea hypoglauca
Cucumis melo var. inodorus
Cucumis melo Inodorus Group
Cucumis melo subsp. melo var. inodorus
casaba melon
honeydew
honeydew melon
Ipomoea nil
Ipomoea nil (L.) Roth
Japanese morning glory
Pharbitis nil
qian niu
Paeonia lactiflora
Chinese peony
Paeonia albiflora
common garden peony
Diospyros kaki
Japanese persimmon
kaki
kaki persimmon
Podophyllum peltatum
Lablab purpureus
Dolichos lab lab
Dolichos lablab
Dolichos purpureus
antaque
banner bean
carmelita
frijol caballero
hyacinth bean
natoba
Santalum album
Santalum album L.
white sandalwood
Vitis
Haliotis diversicolor
Sulculus diversicolor
Rhamnus cathartica
Rhamnus catharticus
Rhamus cathartica
common buckthorn
Rumex
Rheum
Rheum x hybridum
Rheum x cultorum
garden rhubarb
non Rheum rhabarbarum L.
non Rheum rhaponticum L.
rhubarb
Actinidia
Actinidia Lindl.
Rhaponticum uniflorum
Rhaponticum uniflorum (L.) DC.
Actinidia deliciosa
Actinidia chinensis deliciosa
Actinidia chinensis var. deliciosa
Actinidia deliciosa (A.Chev.) C.F.Liang & A.R.Ferguson
Chinese gooseberry
kiwifruit
Carica papaya
Carica papaya L.
Carica payaya
mamon
papaya
Cucumis
Cucumis L.
Cucumis melo
Cucumis melo var. markuwa Markino
Cucurbita melo L.
Oriental melon
muskmelon
Cucumis sativus
Cucumis sativu
cucumber
cucumbers
Xanthium
Xanthium L.
Prunus armeniaca
Armeniaca vulgaris
Armeniaca vulgaris var. glabra
Armeniaca vulgaris var. meixianensis
Armeniaca vulgaris var. vulgaris
Prunus armeniaca var. Bergeron
Prunus armenica
apricot
Cucurbita
marrows
pumpkins
squashes
Cucurbita moschata
Canada pumpkin
Cucurbita moschata Duchesne
ayote
crookneck pumpkin
crookneck winter squash
cushaw squash
lacayote
Luffa aegyptiaca
Luffa aegyptiaca Mill.
Luffa cylindrica
Luffa cylindrica M.Roem.
dishcloth gourd
loofa
smooth loofah
sponge gourd
vegetable sponge
Momordica charantia
Mormordica charanti
balsam pear
bitter gourd
bitter melon
Trichosanthes kirilowii
Mongolian snake-gourd
Trichosanthes kirilowii Maxim.
Trichosanthin kirilowii
Trichosanthin kirilowii Maxim
gua lou
tian hua fen
Eupolyphaga sinensis
Eupolyphaga sinensis Walker
Lobelia chinensis
Lobelia chinensis Lour.
Populus trichocarpa
Populus balsamifera subsp. trichocarpa
black cottonwood
western balsam poplar
Arabidopsis thaliana
Arabidopsis thaliana (thale cress)
Arbisopsis thaliana
mouse-ear cress
thale cress
thale-cress
Armoracia rusticana
Armoracia lapathifolia
Armoracia laphatifolia
Armoracia rusticana P.Gaertn., B.Mey. & Scherb.
horseradish
Brassica
Brassica L.
Brassica nigra
Brassica nigra (L.) W. D.J.Koch
black mustard
Ovibos moschatus
Ovis moschatus
Capsella bursa-pastoris
Capsella bursapastoris
shepherd's purse
Raphanus sativus
radish
Sinapis alba
Brassica hirta
Sinabs alba
bai jie
white mustard
yellow mustard
Gruberia
Fragaria
Fragaria x ananassa
Fragaria ananassa
Fragaria chiloensis x Fragaria virginiana
Fragaria virginiana x Fragaria chiloensis
strawberry
Malus x domestica
Malus domestica
Malus pumila auct.
Malus pumila var. domestica
Malus sylvestris var. domestica
Pyrus malus
apple
apple tree
cultivated apple
Pimenta dioica
Jamaica-pepper
Pimenta dioica (L.) Merr.
allspice
malaqueta
Prunus
Prunus domestica
plum
Prunus persica
Amygdalus persica
Persica vulgaris
Prunus persica var densa
peach
Rosa
Rosa L.
Rosa x damascena
Rosa x damascena Mill.
damask rose
Apocynum venetum
Apocynum venetum L.
Agathosma
Agathosma Willd.
Prunus africana
Prunus africana (Hook.f.) Kalkman
Schlechtendalia chinensis
Melaphis chinensis
Schlectendalia chinensis
horned gall aphid
Albizia julibrissin
Albizia julibrissin Durazz.
Albizzia julibrissin
silk tree
Abrus precatorius
Abrus cyaneus
Indian licorice
crab's eye
crab's-eye
rosary pea
Arachis hypogaea
Arachis hypogea
goober
ground-nut
peanut
Cyamopsis tetragonoloba
Cyanopsis tetragonoloba
cluster bean
guar
Erythrina variegata
Erythrina indica
Indian coral tree
ci tong
dabdab
Cyathula officinalis
Cyathula officinalis K.C.Kuan
Glycine max
Glycine max; cv. Wye
soybean
soybeans
Diprotodontia
Betula pubescens
Betula alba
downy birch
Medicago sativa
Medicago sativa subsp. sativa
alfalfa
lucerne
Phaseolus
Gentiana lutea
yellow gentian
Salvia officinalis
Salvia officinalis L.
garden sage
Pueraria montana var. lobata
Pueraria lobata
Pueraria lobata var. chinensis
kudzu
kudzu vine
Anolis sagrei
brown anole
Sophora
Sophora japonica
Japanese pagoda tree
Styphnolobium japonicum
Vigna
Vigna Savi
Vigna radiata var. radiata
Phaseolus aureus
Phaseolus radiatus
golden gram
green gram
mung bean
Origanum
marjorams
oreganos
Scrophularia
Scrophularia L.
figworts
Salvia apiana
Salvia apiana Jeps.
Paullinia cupana
Paullinia cupana Kunth
guarana
Collinsonia canadensis
northern horse-balm
stoneroot
Hyssopus officinalis
hyssop
Lavandula angustifolia
Lavandula officinalis
lavender
Melissa officinalis
common balm
sweet balm
Nepeta cataria
catmint
catnip
Ocimum basilicum
Ocimum bascilicum
basil
sweet basil
Origanum vulgare
oregano
Prunella vulgaris
self-heal
Rosmarinus officinalis
rosemary
Vaccaria hispanica
Saponaria vaccaria
Vaccaria pyramidata
Vaccaria segetalis
bladder-soapwort
cow herb
Verbascum thapsus
Aaron's-rod
common mullein
flannel plant
velvet plant
Polygonatum biflorum
small Solomon's seal
Combretum indicum
Quisqualis indica
Rangoon-creeper
shi jun zi
Scutellaria barbata
Scutellaria barbata D.Don
Phoradendron
Rosa x centifolia
Burgundy rose
Rosa centifolia
Rosa x centifolia L.
Junonia coenia
Precis coenia
buckeye
peacock butterfly
Centipeda minima
Terminalia
Terminalia L.
Linum usitatissimum
Linum usitatissimum L.
flax
Geranium
Daucus carota
Daucus carota L.
Queen Anne's lace
carrot
carrots
Petroselinum crispum
Petroselinum crispum var. vulgare
Petroselinum hortense
Petroselinum sativum
parsley
Apium
Apium L.
Apium graveolens
Apium graveolans
Coriandrum sativum
coriander
Panax
Piper cubeba
Piper cubeba L.f.
Panax ginseng
Chinese ginseng
Korean ginseng
ginseng
hong shen
insam
ninjin
ren seng
Botryotinia fuckeliana
Botrytis cinerea
Sclerotinia fuckeliana
Dipsacus
Dipsacus L.
teasels
Tenodera sinensis
Chinese praying mantis
Tenodera aridifolia sinensis
Tenodera sinensis (Saussure, 1871)
Mammalia
mammals
Gymnema sylvestre
Capsicum
peppers
Capsicum annuum
Capsicum annuum L.
Capsicum annuum var. conoide
Capsicum annuum var. conoides
Capsicum capsicum
Capsicum conoide
Capsicum conoides
Solanum lycopersicum
Lycopersicon esculentum
Lycopersicon esculentum Mill.
Lycopersicon esculentum var. esculentum
Lycopersicon lycopersicum
Lycopersicum esculentum
Solanum esculentum
Solanum esculentum Dunal
Solanum lycopersicon
Solanum lycopersicum L.
tomato
Anthriscus cerefolium
Anthriscus cerefolium (L.) Hoffm.
chervil
Anethum graveolens
dill
Angelica
Angelica L.
Angelica archangelica
Angelica archangelica L.
wild parsnip
Schizopyrenida
Marrubium vulgare
white horehound
Leonurus
Leonurus L.
Leonurus japonicus
Chinese motherwort
Leonurus artemisia
Leonurus artemisia (Lour.) S.Y.Hu
Leonurus heterophyllus
Leonurus heterophyllus Sweet
Leonurus japonicus Houtt.
sagebrush motherwort
yi mu cao
Scutellaria
Olea europaea
Olea europaea L.
Olea europea
Olea europeae
Olea sativa
common olive
Atractylodes
Calendula officinalis
Calendula officianalis
Calendula ofiicinalis
common marigold
pot marigold
Centaurea
Chrysanthemum x morifolium
Chrysanthemum hortorum
Chrysanthemum morifolium
Dendranthema grandiflora
Dendranthema grandiflorum
Dendranthema morifolium
Dendranthema x grandiflorum
Dendranthema x morifolium
Dendrathema x grandiflorum
Dendrathemum grandiflorum
Dendronthema grandiform
florist's chrysanthemum
mum
Inula
Inula L.
Aggregatibacter
Sesamum indicum
Sesamum orientale
beniseed
gingelly
hu ma
koba
sesame
Pseudostellaria heterophylla
Pseudostellaria heterophylla (Miq.) Pax
hai er shen
Sambucus
Sambucus nigra
European elder
Viburnum
Viburnum L.
Arctium lappa
great burdock
Artemisia
Artemisia vulgaris
Artemisia vulgaris L.
common wormwood
mugwort
Carthamus tinctorius
Carthamnus tinctorius
safflower
Aconoidasida
Sigmodon hispidus
Sigmodon hispiedis
hispid cotton rat
Stephania tetrandra
Stephania tetrandra S.Moore
Hirudo nipponia
Ilex
Ilex L.
Cullen corylifolium
Psoralea corylifolia
Tabebuia impetiginosa
Tabebuia impetiginosa (Mart. ex DC.) Standl.
Citrus aurantium
Citrus x aurantium
Seville orange
bitter orange
sour orange
Aesculus hippocastanum
European horse chestnut
common horse chestnut
Uncaria
Uncaria rhynchophylla
Lobelia
Lobelia L.
Commiphora
Eucommia ulmoides
Eucommia almoides
Hamamelis virginiana
American witch-hazel
Hamamelis macrophylla
Euryale ferox
Nelumbo nucifera
Nelumbo nucifera Gaertn.
padma
sacred lotus
Verbena hastata
American blue vervain
Verbena hastata L.
simpler's-joy
wild hyssop
Camellia
Camellia sinensis
Camelia sinensis
Thea sinensis
black tea
Panax notoginseng
Panax pseudoginseng var. notoginseng
san-qi
sanchi ginseng
tienchi
Malva verticillata
Malva verticillata L.
Acorus
Acorus L.
Acorus calamus
Acorus calamus L.
flagroot
sweet flag
Dictyostelium discoideum
Avena sativa
Avena sativa L.
cultivated oat
oat
Coix lacryma-jobi
Coix lachryma jobi
Coix lachryma-jobi
Coix lacryma
Job's tears
Hordeum vulgare
Hordeum vulgare L.
Horedum vulgare
barley
Paeonia suffruticosa
Paeonia arborea
Paeonia moutan
moutan peony
tree peony
Mitchella repens
Hebanthe paniculata
Hebanthe paniculata Mart.
Pfaffia paniculata
Pfaffia paniculata (Mart.) Kuntze
Aralia racemosa
Oryza sativa
red rice
rice
Spatholobus suberectus
Spatholobus suberectus Dunn
Triticum aestivum
Canadian hard winter wheat
Tricum aestivum
Triticum aestivam
Triticum aestivum subsp. aestivum
Triticum aestivum8
Triticum vulgare
bread wheat
common wheat
wheat
Zea mays
Zea mays mays
Zea mays var. japonica
maize
Bambusa
Bambusa Schreb.
bamboos
Corydalis yanhusuo
Corydalis yanhusuo (Y.H.Chou & Chun C.Hsu) W.T.Wang
Ligustrum lucidum
Picrasma excelsa
Picrasma excelsa (Sw.) Planch.
Quassia excelsa
Quassia excelsa Sw.
Celosia argentea
Celosia argentea L.
red-spinach
silver cockscomb
Portulaca oleracea
Portulaca oleraceae
Ananas comosus
Ananas comosus var. comosus
pineapple
Solidago virgaurea
Glycyrrhiza
Glycyrrhiza L.
licorice
Dioscorea
Borderea
Dioscorea L.
Nanarepenta
Tamus
Allium
Allium L.
Polygonum
Polygonum L.
Allium cepa
Allium cepa L.
onion
Allium sativum
Allium sativa
Allium sativum L.
garlic
Sassafras albidum
Sassafras albidum (Nutt.) Nees
white sassafras
Actaea <angiosperm>
Actaea
Cimicifuga
Astragalus complanatus
Neopicrorhiza scrophulariiflora
Neopicrorhiza scrophulariiflora (Pennell) D.Y.Hong
Picrorhiza scrophulariiflora
Picrorhiza scrophulariiflora Pennell
Melilotus
Melilotus Mill.
Galega officinalis
goat's rue
Serenoa repens
saw palmetto
Fungi
fungi
Margaritifera
Elsholtzia splendens
Pneumocystis carinii
Pneumocystis carinii f. sp. carinii
Pneumocystis carinii f. sp. ratti
Pneumocystis carinii f. sp. rattus
Carum carvi
caraway
Foeniculum vulgare
Foeniculum vulgare Mill.
fennel
Levisticum officinale
Angelica dahurica
Centella asiatica
Asiatic pennywort
Centrella asiatica
gotu kola
ji xue cao
sheep-rot
thankuni
Glehnia littoralis
Glehnia littoralis F.Schmidt ex Miq.
Caesalpinia sappan
Caesalpinia sappan L.
Indian redwood
sappanwood
Perilla frutescens
Perilla frutescens (L.) Britton
Perrilla frutescens
beefsteak-mint
shiso-zoku
Neisseria gonorrhoeae
Diplococcus gonorrhoeae
Gonococcus neisseri
Merismopedia gonorrhoeae
Micrococcus der gonorrhoe
Micrococcus gonococcus
Micrococcus gonorrhoeae
Neisseria gonorrheae
Neisseria gonorrhoeae.
Nesseria gonorrhoeae
Juniperus monosperma
Juniperus monosperma (Engelm.) Sarg.
cherrystone juniper
one-seed juniper
Clematis armandii
Clematis armandi
Clematis armandii Franch.
Persicaria japonica
Persicaria japonica (Meisn.) H.Gross ex Nakai
Polygonum japonicum
Polygonum japonicum Meisn.
Polygonum japonicum var. japonicum
Schizosaccharomyces pombe
Schizosaccharomyces malidevorans
Schizosaccharomyces pombeP
fission yeast
Aconitum
Salvia hispanica
Salvia hispanica L.
Fucus vesiculosus
Saccharomyces
Pachytichospora
Saccharomyces cerevisiae
Candida robusta
Saccaromyces cerevisiae
Saccharomyces capensis
Saccharomyces italicus
Saccharomyces oviformis
Saccharomyces uvarum var. melibiosus
Saccharomyes cerevisiae
Sccharomyces cerevisiae
baker's yeast
brewer's yeast
lager beer yeast
yeast
Piper longum
Piper longum L.
Ligusticum
Ligusticum L.
lovage
Ligusticum sinense
Ligusticum chuanxiong
Liqusticum chuanxiong
Sichuan lovage
chuang-xiong
gaoben
Taraxacum
Baptisia tinctoria
Baptisia tinctoria (L.) R.Br.
horseflyweed
indigo-broom
rattleweed
yellow-broom
Erythrina crista-galli
Erythrina crista-galli L.
ceibo
cockspur coraltree
cry-baby tree
Glycyrrhiza glabra
Glycyrrhiza glabra L.
Sophora flavescens
Sophora falvescens
Alchemilla vulgaris
Satureja montana
Satureja montana L.
winter savory
Thymus vulgaris
Thymus vulgaris L.
garden thyme
thyme
Artemesia
Taraxacum officinale
Taraxacum officinalis
dandelion
Arisaema
Centaurea benedicta
Cnicus benedictus
blessed thistle
Eleutherococcus
Sargentodoxa cuneata
Sargentodoxa cuneata (Oliv.) Rehder & E.H.Wilson
Schisandra chinensis
Schisandra chinensis (Turcz.) Baill.
magnolia-vine
wu wei zi
Aspergillus
Trillium erectum
Trillium erectum L.
bethroot
birth root
stinking benjamin
wakerobin
Insecta
true insects
Aspergillus flavus
Petromyces flavus
Embioptera
Embiidina
web-spinners
Penicillium
Gentiana macrophylla
Crataegus pinnatifida
Chinese hawthorn
Crataegus pinnatifida Bunge
shan zha
Myristica fragrans
Myristica fragrans Houtt.
mace
nutmeg
Vanilla planifolia
Vanilla fragrans
Juglans regia
English walnut
Juglans regia L.
Cyperus rotundus
Cyperus rotundus L.
Capitellidae
Brassica rapa subsp. pekinensis
Brassica campestris (Pekinensis Group)
Brassica campestris ssp. pekinensis
Brassica campestris subsp. pekinensis
Brassica campestris var. pekinensis
Brassica pekinensis
Brassica rapa Chinese Cabbage Group
Brassica rapa ssp. pekinensis
Brassica rapa var. glabra
Chinese cabbage
bai cai
celery cabbage
pe-tsai
Neurospora crassa
Chrysonilia crassa
Mosla chinensis
Mosla chinensis Maxim.
Vincetoxicum stauntonii
Cynanchum stauntonii
Dipsacus asper
Dipsacus asper Wall.
Lycopus lucidus
di gua er miao
shiny bugleweed
shiro-ne
Vaccinium oxycoccos
European cranberry
Oxycoccus palustris
Vaccinium oxycoccus
Vaccinium palustre
mossberry
Chamaeleo
Cryptococcus neoformans
Filobasidiella neoformans
Filobaxidiella neoformans
Elymus repens
Agropyron repens
Agropyron repens for. repens
Elytrigia repens
Bupleurum chinense
Cuminum cyminum
cumin
Ferula
Ferula L.
Ferula assa-foetida
Ferula assa-foetida L.
asafoetida
Actinomyces gerencseriae
Actinomyces israelii serovar II
Ganoderma lucidum
Ganoderma lucidium
Betonica officinalis
Stachys minor
Stachys officinalis
Eclipta
Eclipta prostrata
Eclipta alba
Echinacea purpurea
Echinacea purpurea (L.) Moench
Rudbeckia purpurea L., nom. cons.
Caesalpinia
Caesalpinia L.
Dipteryx odorata
cumaru
sarrapia
tonga-bean
Eikenella corrodens
"Bacteroides corrodens" Eiken 1958 (in part)
"Ristella corrodens" (Eiken 1958) Prevot 1966
Bacteroides corrodens
Eikenella corrodens (Eiken 1958) Jackson and Goodman 1972
Ristella corrodens
Senna
Senna Mill.
Aloysia triphylla
Tenericutes
Actinomyces oris
Actinomyces naeslundii genospecies 2
Vitex
Vitex L.
Vitex agnus-castus
Vitex agnus-castus L.
chasteberry
chastetree
Lindera aggregata
Lindera strychnifolia
Ligusticum porteri
Ligusticum porteri J.M.Coult. & Rose
osha
Hansenia weberbaueriana
Notopterygium incisum
Notopterygium weberbauerianum
Candida albicans
Candida stellatoidea
Candida stellatoidea type I
Ceanothus americanus
Piper kadsura
Cladosporium
Sciuridae
Frangula purshiana
Rhamnus purshiana
cascara buckthorn
cascara sagrada
chittambark
Trichoderma harzianum
Hypocrea lixi
Hypocrea lixii
Trichoderma harizianum
Amoebozoa
Dioscorea alata
Dioscorea alata L.
Guyana arrowroot
greater yam
name-de-agua
ten-months yam
water yam
white yam
winged yam
yam
Inula helenium
Inula helenium L.
elecampane
tu mu xiang
velvet-dock
Stevia rebaudiana
Hirudinida
leeches
Yucca filamentosa
Adam's-needle
Yucca filamentosa L.
bear-grass
spoon-leaf yucca
Matricaria
Escherichia coli
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherchia coli
Eschericia coli
bacterium E3
Leishmania <genus>
Leishmania
Dioscorea oppositifolia
Dioscorea opposita
Dioscorea oppostifolia
non Dioscorea opposita auct.
Sambucus canadensis
American elderberry
Sambucus nigra canadensis
Sambucus nigra subsp. canadensis
Eleutherodactylus coqui
Eleutherodactylus coqui Thomas, 1966
Puerto Rican coqui
coqui
Parabasalia
Parabasalidea
parabasalians
parabasalids
Trichomonas vaginalis
Tritrichomonas vaginalis
Trifolium pratense
peavine clover
purple clover
red clover
rotklee
Naegleria gruberi
Xanthium sibiricum
Cirsium setosum
Breea setosa
Cephalanoplos setosum
Cephalonoplos setosum
Serratula setosa
Agrimonia eupatoria
Filipendula ulmaria
Fragaria vesca
European strawberry
alpine strawberry
wood strawberry
Burkholderia thailandensis
Burkholderia pseudomallei-like species
Juniperus communis
Juniperus communis L.
Juniperus comunis
common juniper
Platycladus orientalis
Thuja orientalis
Toxoplasma gondii
Garcinia
Plasmodium falciparum
Plasmodium (Laverania) falciparum
malaria parasite P. falciparum
Leonurus cardiaca
Isodon rubescens
Rabdosia rubescens
Ciliophora
Ciliata
ciliates
Aster tataricus
Tetrahymena
Iris domestica
Belamcanda chinensis
Typha angustifolia
narrow-leaf cattail
Anemarrhena asphodeloides
Ruscus aculeatus
Fritillaria
Tetrahymena thermophila
Euplotes
Euplotes aediculatus
Oxytricha
Murina
Taeniopygia guttata
Poephila guttata
Taenopygia guttata
zebra finch
Ptychopetalum olacoides
Vinca minor
Vinca minor L.
common periwinkle
running-myrtle
Chlorocebus pygerythrus
Cercopithecus aethiops pygerythrus
Cercopithecus pygerythrus
Chlorocebus aethiops pygerythrus
Cnidaria
Coelenterata
cnidarians
coelenterates
Hydra
Chlorohydra
Pelmatohydra
Scyphozoa
jellyfishes
Rumex acetosella
common sorrel
red sorrel
sheep sorrel
Lumbriculus variegatus
Trematoda
Schistosoma mansoni
Fasciola hepatica
Fasciolidae hepatica
liver fluke
Piscidia piscipula
Nematoda
Nemata
nematode
nematodes
roundworm
roundworms
Panagrellus
Panagrellus redivivus
Caenorhabditis briggsae
Caenorhabditis elegans
Rhabditis elegans
nematode
Ascaris
Calvatia fenzlii
Lasiosphaera fenzlii
Cynomorium songaricum
Yersinia <bacteria>
Yersinia
Yersinia pestis
Bacillus pestis
Bacterium pestis
Pasteurella pestis
Pestisella pestis
Yersinia pseudotuberculosis subsp. pestis
Yersinia pseudotuberculosis
Bacillus pseudotuberkulosis
Bacterium pseudotuberculosis
Pasteurella pseudotuberculosis
Shigella pseudotuberculosis
Epimedium
Epimedium L.
Epimedium koreanum
Epimedium grandiflorum subsp. koreanum
Epimedium grandiflorum subsp. koreanum (Nakai) Kitam.
Epimedium koreanum Nakai
Liquidambar formosana
Formosan gum
Annelida
annelid worms
segmented worms
Vincetoxicum
Vincetoxicum Wolf
Lumbricus terrestris
common earthworm
Pheretima sieboldi
earthworm
Actaea cimicifuga
Actaea simplex Prantl
Cimicifuga foetida
Actaea racemosa
Cimicifuga racemosa
Pyrola calliantha
Tilia x europaea
Tilia europaea
Mollusca
molluscs
mollusks
Gastropoda
gastropods
Tremella fuciformis
Amomum krervanh
Amomum kravanh
Astragalus membranaceus
Aplysia
Lithospermum canescens
Helix aspersa
Cantareus aspersa
Cantareus aspersus
Cornu aspersum
Cornu copiae von Born, 1778
Cryptomphalus aspersus
Helix (Cornu) aspersa
Helix (Cryptomphalus) aspersa
brown garden snail
Scutellaria baicalensis
Baikal skullcap
Scutellaria baicalensis Georgi
Hypericum perforatum
Hypericum perforatum L.
Acacia arabica
Nasturtium officinale
Nasturtium nasturtium-aquaticum (L.) H.Karst., nom. inval.
Roripa nasturtium-aquaticum
Rorippa nasturtium-aquaticum
Rorippa nasturtiumaquaticum
watercress
Cymbopogon citratus
lemon grass
Cephalopoda
cephalopods
Sepiidae
cuttlefish
cuttlefishes
Gleditsia sinensis
Grindelia camporum
Great Valley gumweed
Arthropoda
arthropods
Crustacea
crustaceans
Vibrio cholerae
Bacillo virgola del Koch
Bacillus cholerae
Bacillus cholerae-asiaticae
Kommabacillus
Liquidivibrio cholerae
Microspira comma
Pacinia cholerae-asiaticae
Spirillum cholerae
Spirillum cholerae-asiaticae
Vibrio choleae
Vibrio cholera
Vibrio cholerae-asiaticae
Vibrio comma
Larrea tridentata
creosote bush
Bixa orellana
Bixa orellana L.
achiote
annatto
arnatto
lipstick tree
roucou
urucum
lobster
Pleocyemata fam. gen. sp.
Pleocyemata gen. sp.
lobsters
Nephropidae
Homaridae
clawed lobsters
Lycopodium japonicum
Astacoidea
crayfish
Virgaviridae
Brachyura
short-tailed crabs
true crabs
Callinectes
Cryptotympana atrata
Cryptotympana pustulata
Zanthoxylum
Xanthoxylon
Xanthoxylum
Zanthoxyllum
Curculigo orchioides
Phellodendron amurense
Vaccinium corymbosum
American blueberry
highbush blueberry
Gasterosteus aculeatus
Gasterosteus aculeatus Linnaeus, 1758
three spined stickleback
three-spined stickleback
Trachelospermum jasminoides
Atractylodes lancea
Atractylodes lancea (Thunb.) DC.
Atryactylis lancea
Diploptera
Diploptera punctata
Pacific beetle cockroach
Orthoptera
Saltatoria
grasshoppers &c.
Gryllidae
crickets
Epalzeorhynchos kalopterus
Barbus kalopterus
Epalzeorhynchos kallopterus (Bleeker, 1851)
Epalzeorhynchos kalopterum
flying fox
Acheta domesticus
house cricket
Locusta migratoria
migratory locust
Schistocerca
Schistocerca americana
American grasshopper
Smilax glabra
Coleoptera
beetles
Tritonia diomedea
Tritonia diomedia
Lepidoptera
butterflies and moths
moths
Bombyx mori
Bombyx mori Linnaeus, 1758
domestic silkworm
silk moth
silkworm
Spodoptera frugiperda
fall armyworm
Chelidonium majus
Manduca
Manduca Hubner, 1807
Manduca sexta
Carolina sphinx
hornblower
tobacco hawkmoth
tobacco hornworm
tomato hornworm
Buddleja officinalis
Dictamnus dasycarpus
Homalomena occulta
Pulsatilla chinensis
Anemone chinensis
Anemone pulsatilla var. chinensis
Rubus chingii
Sophora tonkinensis
Diptera
flies
Culicidae
mosquitos
Aedes aegypti
Stegomyia aegypti
yellow fever mosquito
Aedes albopictus
Asian tiger mosquito
Stegomyia albopicta
forest day mosquito
Melia azedarach var. toosendan
Melia toosendan
Anopheles gambiae
African malaria mosquito
Anopheles gambia
Anopheles gambiae Giles, 1902
Anopheles gambiae sensu stricto
Drosophila <fruit fly, genus>
Drosophila
Drosophila Fallen, 1823
fruit flies
Drosophila melanogaster
Drosophila melangaster
fruit fly
Artemisia absinthium
Artemisia dracunculus
French tarragon
tarragon
Senna alexandrina
Cassia acutifolia
Cassia angustifolia
Cassia senna
Indian senna
casse
jalelo
Musca domestica
house fly
Hymenoptera
hymenopterans
Apis mellifera
Apis mellifica
European honey bee
Western honey bee
bee
honey bee
honeybee
Aspergillus fumigatus
Aspergillus fumigates
Neosartorya fumigata
Sartorya fumigata
Glycyrrhiza uralensis
Chinese licorice
Glycyrrhiza uralensis Fisch. ex DC.
gan zao
Rosa gallica
French rose
Rosa gallica L.
apothecary rose
red-rose-of-Lancaster
Rosa canina
dog briar
Rosa rugosa
Japanese rose
Rosa rugosa Thunb.
Turkestan rose
Rosa laevigata
Cherokee rose
Rosa laevigata Michx.
Agrimonia pilosa
long ya cao
xian he cao
Clematis chinensis
Allium schoenoprasum
Allium schoenoprasum L.
chive
Mantodea
mantids
Rubus occidentalis
Rubus occidentalis L.
black raspberry
non Rubus occidentalis H.Lev., nom. illeg.
Siphonaptera
fleas
Neuroptera
Planipennia
Hemiptera
bugs
Salix alba
Salix alba L.
white willow
Echinodermata
echinoderms
Dallia pectoralis
Alaska blackfish
Lactuca virosa
Lactuca virosa L.
Fallopia multiflora
Chinese knotweed
Fagopyrum multiflorum
Polygonum multiflorum
Reynoutria multiflora
fo ti
he shou wu
Sophora prostrata
Sophora prostata
Strongylocentrotus
Holothuroidea
Holothurioidea
holothurians
sea cucumbers
Chordata
chordates
Tunicata
Urochordata
tunicates
Ascidiacea
sea squirts
Vertebrata <Metazoa>
Vertebrata
vertebrates
Petromyzontidae
Petromyzonidae
lampreys
Myxinidae
hagfishes
Myxine glutinosa
Atlantic hagfish
common hagfish
hagfish
Chondrichthyes
cartilaginous fishes
fish
fishes
sharks
Elasmobranchii
elasmobranchs
sharks and rays
Discopyge ommata
Discopyge ommata Jordan & Gilbert, 1890
electric ray
ocellated electric ray
Torpedo
Torpedo marmorata
Torpedo marmorata Risso, 1810
Torpedo marmorata@
marbled electric ray
spotted torpedo
Cetraria islandica
Trigonella foenum-graecum
Trigonella foenum-graecum L.
fenugreek
Danio rerio
Brachidanio rerio
Brachydanio rerio
Brachydanio rerio frankei
Cyprinus rerio
Cyprinus rerio Hamilton, 1822
Danio frankei
Danio rerio (Hamilton, 1822)
Danio rerio frankei
leopard danio
zebra danio
zebra fish
zebrafish
Carassius auratus
Carassius carassius auratus
Cyprinus auratus
goldfish
Verbena officinalis
Verbena officinalis L.
common verbena
kumatsuzura
ma bian cao
pigeon's-grass
Astyanax mexicanus
Astyanax mexicanus (De Filippi, 1853)
Mexican tetra
blind cave fish
Electrophorus
Electrophorus electricus
electric eel
electric knifefish
Salmonidae
salmonids
Laminaria digitata
Imperata cylindrica
Capsicum chinense
Capsicum chinense Jacq.
Scotch bonnet
bonnet pepper
habanero
rocotillo
Fundulus heteroclitus
Atlantic killifish
killifish
mummichog
Oryzias latipes
Japanese medaka
Japanese rice fish
medaka
Wolfiporia cocos
Poria cocos
Haplochromis burtoni
Astatotilapia burtoni
Burton's mouthbrooder
Chromis burtoni
Eleutherococcus senticosus
Acanthopanax senticosus
Polygonatum odoratum
yu zhu
Lilium brownii
Hong Kong lily
ye bai he
Amphibia
amphibians
Caudata
Urodela
salamanders
Ambystoma mexicanum
Ambystoma mexicanum (Shaw & Nodder, 1798)
axolotl
Salamandridae
newts
Notophthalmus
Notopthalmus
Bassia scoparia
Bassia scorpia
Kochia densiflora
Kochia scoparia
burning bush
summer cypress
Notophthalmus viridescens
Notophthalmus viridiscens
Notopthalmus viridescens
Triturus viridescens
eastern newt
red-spotted newt
Pleurodeles
Triturus
Anura
Salientia
anurans
frogs
frogs & toads
frogs and toads
Xenopus <genus>
Xenopus
Xenopus borealis
Kenyan clawed frog
Marasbit clawed frog
Xenopus borealis Parker, 1936
Xenopus laevis borealis
Xenopus laevis
African clawed frog
Bufo laevis
Xenopus laevis (Daudin, 1802)
Xenopus leavis
clawed frog
common platanna
platanna
Xenopus (Silurana) tropicalis
Silurana tropicalis
Xenopus laevis tropicalis
Xenopus tropicalis
western clawed frog
Porphyromonas gingivalis
Bacteroides gingivalis
Lepidobatrachus laevis
Prevotella
Polygonum cuspidatum
Polygonum cuspidatum Willd. ex Spreng.
non Polygonum cuspidatum Siebold & Zucc., nom. illeg.
Oroxylum indicum
Oroxylum indicum (L.) Vent.
broken bones plant
kampong
midnight horror
tree of Damocles
Rana <genus>
Pseudorana
Rana
Rana catesbeiana
Aquarana catesbeiana
Lithobates catesbeianus
Rana catesbiana
bullfrog
bullfrogs
Arctostaphylos uva-ursi
Arctostaphylos uvaursi
bearberry
Rana pipiens
Lithobates pipiens
Pantherana pipiens
northern leopard frog
Testudines
Anapsida
Reptilia
Testudinata
anapsid reptiles
reptiles
turtles
Crocodylidae
Crocodilia
Crocodylia
Reptilia
crocodiles
crocodilians
reptiles
Lepidosauria
Reptilia
lepidosaurs
lizards
reptiles
Laurus nobilis
bay laurel
Viburnum opulus
European cranberrybush
Viburnum opulus L.
crampbark
guelder rose
Aconitum carmichaelii
Aconitum carmichaeli
Citrus reticulata
Citrus poonensis
mandarin orange
tangerine
Blattodea
Blattaria
Blattoptera
cockroaches
roaches
Magnolia denudata
Magnolia heptapeta
Magnolia heptapetala
haku-mokuren
lilytree
yu lan
Magnolia officinalis
Codonopsis pilosula
Campanumoea pilosula
Campanumoea pilosula Franch.
Codonopsis pilosella
Codonopsis pilosula (Franch.) Nannf.
Vigna umbellata
Phaseolus calcaratus
Phaseolus chrysanthos
Phaseolus chrysanthus
Vigna calcarata
mambi-bean
rice bean
Aves
birds
Saccharina japonica
Laminaria japonica
Anatidae
waterfowl
Anas
ducks
Pinus tabuliformis
Pinus tabulaeformis
southern Chinese pine
Musa x paradisiaca
Musa acuminata x Musa balbisiana
Musa lactan
Musa paradisiaca
Musa sapientum
Musa x sapientum
banana
Columbidae
pigeons
Bubalus bubalis
Bubalis arnee bubalis
Bubalis bubalis
Bubalus arnee
Bubalus arnee bubalis
Bubalus bubalus
domestic water buffalo
river buffalo
water buffalo
Numididae
guineafowls
Taraxacum mongolicum
Taraxacum monogolicum
Phasianidae
turkeys
Phasianidae gen. sp.
Phasianidae sp.
Gallus gallus
Gallus domesticus
Gallus gallus domesticus
bantam
chicken
chickens
Scrophularia nodosa
Scrophularia nodosa L.
figwort
Salmonella enterica subsp. enterica serovar Typhimurium
Bacillus typhimurium
Salmonella choleraesuis serotype typhimurium
Salmonella enterica 1,4,[5],12,:i:1,2
Salmonella enterica ser. typhimurium
Salmonella enterica serotype Typhimurium
Salmonella enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar 1,4,[5],12,:i:1,2
Salmonella typhi-murium
Salmonella typhimurium
Samonella typhimurium
Meleagris gallopavo
common turkey
turkey
wild turkey
Allium macrostemon
Allium macrostemon Bunge
Gastrodia elata
Gastrodia elata Blume
Juglans cinerea
Juglans cinerea L.
Spilanthes paniculata
Acmella paniculata
Serinus canaria
Canario raza
Serinus canarius
canary
common canary
Didelphidae
American opossums
opossums
Silybum marianum
Carduus marianus L.
holy thistle
lady's thistle
milk thistle
Macropus sp.
kangaroo
Daemonorops
Cola acuminata
Chimaphila umbellata
san xing xi dong cao
Coturnix japonica
Coturnix coturnix japonica
Japanese quail
Tupaia
Chiroptera
bats
Cnidium monnieri
Platycodon grandiflorus
Chinese-bellflower
Platycodon grandiflorum
balloon-flower
jie geng
Alpinia <angiosperm>
Alpinia
Zingiber officinale
ginger
Primates
Primata
primate
primates
Ehrlichia chaffeensis
Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001
Ehrlichia chaffensis
Platyrrhini
New World monkeys
monkey
monkeys
Callithrix
Cebuella
Lethenteron
Aotus trivirgatus
douroucouli
night monkey
northern night monkey
owl monkey
Cebus
capuchin monkeys
Cebus albifrons
brown pale-fronted capuchin
pale-fronted capuchin
white-fronted capuchin
Cebus apella
Tufted capuchin
black-capped capuchin
brown capuchin
brown-capped capuchin
Cebus capucinus
white-faced capuchin
white-faced sapajou
white-throated capuchin
Saimiri
Siamiri
squirrel monkeys
Saimiri sciureus
South American squirrel monkey
common squirrel monkey
Callicebus
titi monkeys
Cercopithecidae
Old World monkeys
monkey
monkeys
Chlorocebus aethiops
African green monkey
African green monkeys
Cercopithecus aethiops
Ceropithecus aethiops
green monkey
grivet
savanah monkey
vervet monkey
Erythrocebus patas
Cercopithecus patas
hussar
patas monkey
red guenon
Macaca
macaques
Macaca arctoides
bear macaque
stump-tailed macaque
Macaca fascicularis
Macaca cynomolgus
Macaca irus
crab eating macaque
crab-eating macaque
cynomolgus monkey
cynomolgus monkeys
long-tailed macaque
Macaca fuscata
Japanese macaque
Japanese monkey
Macaca mulatta
Rhesus monkey
rhesus macaque
rhesus macaques
rhesus monkeys
Macaca nemestrina
pig-tailed macaque
pigtail macaque
pigtail monkey
Burkholderia cenocepacia
Burkholderia cepacia genomovar III
Papio
baboons
Papio anubis
Anubis baboon
Doguera baboon
Kenya baboon
Papio cynocephalus anubis
Papio doguera
Papio hamadryas anubis
Papio hamadryas doguera
baboon
olive baboon
Pan troglodytes
Chimpansee troglodytes
chimpanzee
Homo sapiens
human
man
Canis lupus familiaris
Canis canis
Canis domesticus
Canis familiaris
dog
dogs
Ursus americanus
American black bear
Euarctos americanus
Persicaria tinctoria
Persicaria tinctorium
Polygonum tinctorium
Malva
Malva L.
Mustela lutreola
European mink
mink
Mustela putorius furo
Mustela furo
Mustela putoris furo
black ferret
domestic ferret
ferret
Felidae
cat family
Felis catus
Felis domesticus
Felis silvestris catus
cat
cats
domestic cat
Hydrangea arborescens
Hydrangea arborescens L.
Dryopteris crassirhizoma
Dryopteris crassirhizoma Nakai
Prunus japonica
Cerasus japonica
Prunus japonica Thunb.
Viola odorata
Viola odorata L.
Bacteroidetes
BCF group
Bacteroides-Cytophaga-Flexibacter group
CFB group
CFB group bacteria
Cytophaga-Flexibacter-Bacteroides phylum
Equidae
horses
Equus asinus
African ass
African wild ass
Somali wild ass
ass
domestic ass
donkey
Equus caballus
Equus ferus caballus
Equus przewalskii f. caballus
Equus przewalskii forma caballus
domestic horse
equine
horse
Lethenteron camtschaticum
Arctic lamprey
Entosphenus japonicus
Japanese lamprey
Lampetra camtschatica
Lampetra japonica
Lampreta japonica
Lethenteron japonicum
Petromyzon japonicus
Petromyzon marinus camtschaticus
Suidae
boars
pigs
Sus scrofa domesticus
Sus domestica
Sus domesticus
Sus scrofa domestica
domestic pig
Ruminantia
Artiodactyla
Matricaria chamomilla
Rangifer tarandus
caribou
reindeer
Tanacetum
Bos taurus
Bos Tauurus
Bos bovis
Bos primigenius taurus
bovine
cattle
cow
domestic cattle
domestic cow
Capra hircus
Capra aegagrus hircus
Carpa hircus
South African angora goat
domestic goat
goat
goats
Rehmannia glutinosa
Chinese foxglove
Ovis aries
Ovis ammon aries
Ovis orientalis aries
Ovis ovis
domestic sheep
lambs
sheep
wild sheep
Curcuma
Curcuma L.
Oryctolagus cuniculus
European rabbit
Japanese white rabbit
Lepus cuniculus
domestic rabbit
rabbit
rabbits
Rodentia
rodents
Urocitellus parryii
Arctic ground squirrel
Citellus parryii
Spermophilus parryi
Spermophilus parryii
planned process
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Bjoern Peters
Injecting mice with a vaccine in order to test its efficacy
branch derived
A processual entity that realizes a plan which is the concretization of a plan specification.
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
regulatory role
GROUP: Role branch
OBI, CDISC
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
regulatory role
chromatography column
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
Frank Gibson
chromatography column
http://en.wikipedia.org/wiki/Column_chromatography
pump valve switch
A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument
OBI
OBI Instrument branch
pump valve switch
xenotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
xenotransplantation
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
chromatography device
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
Frank Gibson
a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
chromatography device
chromatography instrument
http://en.wikipedia.org/wiki/Chromatography
mass spectrometer
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
Frank Gibson
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
http://en.wikipedia.org/wiki/Mass_spectrometry
mass spectrometer
obsolete_platform
OBI Instrument branch
OBI Instrument branch
suggested for deprecation https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
platform
liquid chromatography mass spectrometry platform
OBI Instrument branch
OBI instrument branch
A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
liquid chromatography mass spectrometry platform
microarray platform
OBI Instrument branch
OBI Instrument branch
A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
microarray platform
allotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
allotransplantation
is the transplantation of organs between members of the same species.
gamma counter
A Geiger counter
A processed material which measures gamma radiation
Frank Gibson
gamma counter
http://en.wikipedia.org/wiki/Gamma_counter
investigation
Could add specific objective specification
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
Bjoern Peters
OBI branch derived
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about some evaluant
OBI branch derived
PlanAndPlannedProcess Branch
assay
measuring
scientific observation
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
OBI branch derived
PlanAndPlannedProcess Branch
sample preparation for assay
study
reagent role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
reagent
reagent role
www.answers.com/topic/reagent; November 2008
Buffer, dye, a catalyst, a solvating agent.
GROUP: Role Branch
a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances
material processing
A cell lysis, production of a cloning vector, creating a buffer.
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
material processing
A planned process which results in physical changes in a specified input material
OBI branch derived
PERSON: Bjoern Peters
material transformation
transplantation
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application to replace an organ or tissue of an organism
transplantation
Bernoulli trial
Bernoulli trial
OBI branch derived
PlanAndPlannedProcess Branch
is an assay where the output data is a datum with one of two values denoted success and failure.
incubator
Frank Gibson
Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
http://www.medterms.com/script/main/art.asp?articlekey=18426
incubator
cell co-culturing
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
OBI branch derived
PlanAndPlannedProcess Branch
cell co-culturing
autotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
autotransplantation
is the transplantation of tissue from one part of \nthe body to another in the same individual. )
nuclear magnetic resonance assay
PlanAndPlannedProcess Branch
an assay used to identify the chemical structure of a compound or biological macromolecule using an NMR instrument.
nuclear magnetic resonance assay
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
OBI branch derived
PlanAndPlannedProcess Branch
imaging assay
microtiter plate
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
Melanie Courtot
http://en.wikipedia.org/wiki/Microtiter_plate
microplate
microtiter plate
radioactivity detection
An assay in which a material's radioactivity is measured.
Measurment of the radioactivity of a supernatant, as in chromium_release_assay.
OBI branch derived
PlanAndPlannedProcess Branch
radioactivity detection
enzymatic cleavage
OBI branch derived
PlanAndPlannedProcess Branch
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
enzymatic cleavage
enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
artificially induced nucleic acid hybridization
Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
OBI branch derived
PlanAndPlannedProcess Branch
artificially induced nucleic acid hybridization
www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
DNA extraction
DNA preparation
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
DNA extraction
OBI branch derived
PlanAndPlannedProcess Branch
protocol
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.
PlanAndPlannedProcess Branch
Protocol
a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
protocol
protein-protein interaction detection
20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays.
An assay with the objective to determine interactions between proteins, such as protein-protein binding.
protein-protein interaction detection
transcription factor binding site identification
OBI
Philippe Rocca-Serra
transcription factor binding site identification
a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors
histological sample preparation
OBI branch derived
PERSON:Bjoern Peters
histological sample preparation
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
mass analyzer
Frank Gibson
PERSON: Daniel Schober
http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
mass analyzer
ion source
Frank Gibson
http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source
The ion source of a Voyager-DE‚Ñ¢ STR Biospectrometry Workstation
ion source
ion detector
Frank Gibson
http://en.wikipedia.org/wiki/Mass_spectrometry#Detector
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
ion detector
metabolite profiling
OBI
Philippe Rocca-Serra
metabolite assay
metabolite profiling
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
record function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
record function
magnify function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
magnify function
contain function
A syringe, a beaker
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A contain function is a function to constrain a material entities location in space
contain function
heat function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A heat function is a function that increases the internal kinetic energy of a material
heat function
material separation function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
material separation function
ionize process
2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
Electrospray ionization in mass spectrometry
Person:Bjoern Peters
a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation.
ionize process
excitation function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
excitation function
freeze function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
freeze function
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
synthesizing function
perturb function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
http://en.wikipedia.org/wiki/Perturbation_biology
perturb function
mechanical function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
http://en.wikipedia.org/wiki/Mechanical_work
mechanical function
transfer function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A transfer function is a function to displace a material from one location to another.
transfer function
cool function
Daniel Schober
Frank Gibson
Melanie Courtot
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
cool function
isoelectric focusing device
Frank Gibson
sep:00097
An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated.
isoelectric focusing device
isoelectric focusing unit
information processor function
Frank Gibson
An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
data processor function
information processor function
signal conversion function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
transduction function
A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon.
signal conversion function
blot module
Frank Gibson
sep:00092
A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
blot module
signal amplification function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
signal amplification function
image acquisition function
Frank Gibson
An image acquisition function is a function to acquire an image of a material
image acquisition function
environment control function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
environment control function
gel dryer
Frank Gibson
sep:00094
A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
gel dryer
viral RNA extraction
Person:Bjoern Peters
The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
The extraction of RNA from an input material that specifically isolates viral RNA
viral RNA extraction
recombinant plasmid
GROUP: OBI Biomaterial Branch
PERSON: Bjoern Peters
PERSON: Kevin Clancy
PERSON: Melanie Courtot
a plasmid in which extraneous DNA has been inserted.
recombinant plasmid
cell cycle synchronization
Bjoern Peters and Nicole Washington
OBI PA
cell cycle synchronization
Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs.
a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
polymerase chain reaction
OBI Plan
adapted from wikipedai
polymerase chain reaction
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
PCR
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
measuring glucose concentration in blood serum
An assay that determines the concentration of glucose molecules in a blood serum sample
Person:Bjoern Peters
measuring glucose concentration in blood serum
syringe
OBI Instrument adapted from Wikipedia
Philippe Rocca-Serra
syringe
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
transcription profiling assay
OBI
Philippe Rocca-Serra
transcription profiling assay
An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
gene expression profiling
DNA sequence feature detection
An assay with the objective to determine a sequence feature of DNA
DNA sequence feature detection
OBI
Person:Bjoern Peters
Philippe Rocca-Serra
genotyping using an Affymetrix chip
should be a defined class where interpretation of data generated by assay qualifies a DNA sequence
genotyping assay
OBI Biomaterial
Philippe Rocca-Serra
genotyping assay
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
genotype profiling, SNP genotyping
DNA sequence variation detection
DNA sequence variation detection
OBI Biomaterial
Philippe Rocca-Serra
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.
analyte assay
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
analyte assay
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
mass measurement assay
Helen Parkinson
OBI
Philippe Rocca-Serra
The patients was weighed and mass was determined to be 47 kilograms
mass measurement assay
a process to determine the mass of an evaluant
intra cellular electrophysiology recording
An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular
PERSON: Frank Gibson
PERSON: Frank Gibson
intra cellular electrophysiology recording
packed column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218
A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube.
PERSON:Daniel Schober
WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
packed column
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
PERSON: Daniel Schober
PERSON: Helen Parkinson
PERSON: Melanie Courtot
PERSON:Frank Gibson
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
measure function
extracellular electrophysiology recording
An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data
PERSON: Frank Gibson
PERSON: Frank Gibson, Helen Parkinson
The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron
extracellular electrophysiology recording
material transformation objective
GROUP: OBI PlanAndPlannedProcess Branch
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
material transformation objective
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
manufacturing
GROUP: OBI PlanAndPlannedProcess Branch
Manufacturing implies reproducibility and responsibility AR
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
manufacturing
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
This includes a single scientist making a processed material for personal use.
column chromatography detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077
PERSON:Daniel Schober
There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles.
WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html>
chromatography detector, defined class/xps
column chromatography detector
organic acid column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099
An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
organic acid column
thermal conductivity detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084
PERSON:Daniel Schober
TCD, hot wire detector
The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity).
WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
thermal conductivity detector
protein column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
protein column
refactor as defined class
solvent mixer
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072
A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
check on definition !
solvent mixer
mass spectrometry assay
PRIDE: PRIDE:0000027
Philippe Rocca-Serra
This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
mass spectrometry
mass spectrometry assay
nano pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052
A pump system optimized for nano flow chromatography.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
nano pump system
manual injection system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
manual injection system
column connector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography device
column connector
solid NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
An NMR probe that is designed to hold a solid sample.
GROUP:<http://msi-ontology.sourceforge.net>
NMR device
PERSON:Daniel Schober
solid NMR probe
chromatography detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012
A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
chromatography detector
normal phase column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097
A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
normal phase column
NMR sample holder
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212
An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
GROUP:<http://msi-ontology.sourceforge.net>
NMR device
NMR sample holder
PERSON:Daniel Schober
chromatography instrument
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262
Any instrument that is used to carry out a chromatography experiment.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography device, defined class?
chromatography instrument
continuous wave NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned).
NMR instrument
PERSON:Daniel Schober
WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
continuous wave NMR instrument
fourier transformation NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation.
NMR instrument
PERSON:Daniel Schober
fourier transformation NMR instrument
nitrogen phosphorous detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089
PERSON:Daniel Schober
The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement.
WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
nitrogen phosphorous detector
cation exchange column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096
A cation exchange column is a chromatography column that is used in cation exchange chromatography.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
cation exchange column
direct detection NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
An NMR probe designed to allow the direct detection of acquisition nuclei.
GROUP:<http://msi-ontology.sourceforge.net>
NMR device
PERSON:Daniel Schober
direct detection NMR probe
rapid resolution column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102
A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
rapid resolution column
liquid chromatography autosampler
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061
Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
liquid chromatography autosampler
vacuum degasser
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053
A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/topics/vacuum.html>
vacuum degasser
capillary column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066
A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
capillary column
sample inlet
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
PERSON:Daniel Schober
The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head.
WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
chromatography device
sample inlet
NMR tube washing system
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204
An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
GROUP:<http://msi-ontology.sourceforge.net>
NMR instrument
NMR tube washing system
PERSON:Daniel Schober
NMR console
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015
A component of an NMR instrument that controls the activities of the other components.
GROUP:<http://msi-ontology.sourceforge.net>
NMR console
NMR instrument, TODO: same as or part of acquisition computer?
PERSON:Daniel Schober
dual loop autosampler
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063
A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate).
PERSON:Daniel Schober
WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149>
dual loop autosampler
variable wavelength detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079
A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
variable wavelength detector
sample injection system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057
An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography device
sample injection system
multiple wavelength detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078
A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
multiple wavelength detector
photoionization detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090
PERSON:Daniel Schober
PID
The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis.
WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
photoionization detector
gas generator
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033
An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html>
gas chromatography equipment
gas generator
column jacket
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography device
column jacket
electron capture detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085
ECD
PERSON:Daniel Schober
The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes.
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
electron capture detector
reversed phase column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106
A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
reversed phase column
injector lubricant
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118
A lubricant used in liquid chromatography that eases sample injector penetration.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
injector lubricant
isolation of cell population
Person: Bjoern Peters
a process in which a population of cells with certain characteristics is isolated from a larger population
isolation of cell population
removing CD4+ cells from PBMCs using magnetic beads.
chromatofocusing column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209
A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind.
PERSON:Daniel Schober
WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
chromatofocusing column
NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014
GROUP:<http://msi-ontology.sourceforge.net>
NMR instrument
NMR probe
PERSON:Daniel Schober
Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.\n alt The instrument that transmits and receives radiofrequency to and from the NMR sample.
NMR magnet
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185
A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.\n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.
GROUP:<http://msi-ontology.sourceforge.net>
NMR instrument
NMR magnet
PERSON:Daniel Schober
trap column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261
A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
trap column
flow probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes.
NMR device
PERSON:Daniel Schober
WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
flow probe
clinical chemistry assay
3/26/09: There needs to be a restriction set that specifies which type of evaluants are used in the assay, somewhere along the lines of 'sample derived of bodily fluid'
Person: Philippe Rocca-Serra
a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism.
adapted from Wikipedia
chemical pathology
clinical chemistry assay
detection of analyte in blood sample
flame ionization detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197
A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample.
FID
PERSON:Daniel Schober
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
flame ionization detector
vial
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117
A vial is a cylindrical container often made from glass tubing.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
vial
magic angle spinning rotor
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130
A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle.
MAS rotor
NMR instrument
PERSON:Daniel Schober
WEB:<http://www.freepatentsonline.com/4352066.html>
magic angle spinning rotor
splitless GC injector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060
Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent.
PERSON:Daniel Schober
WEB:<http://en.wikipedia.org/wiki/Gas_chromatography>
splitless GC injector
preparative autosampler
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062
For preparative LC with injection of sample volumes ranging from L to mL ranges.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
preparative autosampler
flow high resolution probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
GROUP:<http://msi-ontology.sourceforge.net>
Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
NMR probe
PERSON:Daniel Schober
flow HR-probe
flow high resolution probe
liquid chromatography valve
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html>
chromatography device
liquid chromatography valve
column cartridge
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055
A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography device, check on definition !
column cartridge
affinity column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094
An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
affinity column
gel filtration column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104
A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
gel filtration column
fraction collector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073
A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/topics/fraction/collector.html>
fraction collector
copy number variation profiling
CNV analysis
Philippe Rocca-Serra
copy number variation profiling
copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping.
in-line filter
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123
A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity.
PERSON:Daniel Schober
WEB:<http://www.appliedporous.com/frits-chromatography.htm>
in-line filter
imaging NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
An NMR probe that is designed for generating pictures from sample states via NMR imaging.
GROUP:<http://msi-ontology.sourceforge.net>
NMR device
PERSON:Daniel Schober
imaging NMR probe
gas chromatography equipment
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030
Any device used in a gas chromatography experiment.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
gas chromatography equipment
will become defined class/xps
syringe filter
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122
A small membrane filter of defined pore size, that filters samples from a syringe.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
syringe filter
column compartment
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068
For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
column compartment
capillary pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051
A pump system optimized for capillary chromatography.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
capillary pump system
evaporative light scattering detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082
PERSON:Daniel Schober
The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas.
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html>
evaporative light scattering detector
column cartridger
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054
A chromatography device where the column cartridge is inserted into and stabilised.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
check on definition !
column cartridger
nitrogen generator
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034
A gas generator that generates nitrogen gas.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
nitrogen generator
needle assembly
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
chromatography device, check on definition !
needle assembly
reverse transcribed polymerase chain reaction
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
Philippe Rocca-Serra
RT-PCR
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
reverse transcribed polymerase chain reaction
reverse transcription polymerase chain reaction
gas chromatography oven
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
gas chromatography equipment
gas chromatography oven
autosampler
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002
An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. \n alt The autosampler is an automatic sample changer device.
GROUP:<http://msi-ontology.sourceforge.net>
NMR instrument
PERSON:Daniel Schober
autosampler
isocratic pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049
A pump system optimized for isocratic chromatography.
PERSON:Daniel Schober
WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html>
isocratic pump system
flash pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048
Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
flash pump system
liquid NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
An NMR probe that is designed to hold a liquid sample.
GROUP:<http://msi-ontology.sourceforge.net>
NMR device
PERSON:Daniel Schober
liquid NMR probe
ion exchange column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105
An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
ion exchange column
anion trap column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277
An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
anion trap column
fluorescene detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080
A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html>
fluorescene detector
tecmag EAGLE probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
GROUP:<http://msi-ontology.sourceforge.net>
NMR probe
PERSON:Daniel Schober
The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers.
tecmag EAGLE probe
electrical conductivity detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239
PERSON:Daniel Schober
The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area.
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html>
electrical conductivity detector
NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059
An Instrument which is used to carry out a NMR analysis of some sample.
GROUP:<http://msi-ontology.sourceforge.net>
NMR instrument
NMR instrument
NMR instrument
PERSON:Daniel Schober
piston-seal
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116
PERSON:Daniel Schober
The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless.
WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
piston-seal
mass selective detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198
A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier.
PERSON:Daniel Schober
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
mass selective detector
mass spectrometry detector
spin column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232
A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
spin column
manufacturer role
GROUP: Role Branch
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
OBI
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
manufacturer role
transfer line
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system.
PERSON:Daniel Schober
WEB:<http://www.freepatentsonline.com/5702671.html>
chromatography device
transfer line
gradient pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050
A pump system optimized for gradient chromatography.
PERSON:Daniel Schober
WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html>
gradient pump system
high temperature column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233
A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
high temperature column
y-column connector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237
A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
y-column connector
refractive index detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081
For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html>
refractive index detector
anion exchange column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095
An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
anion exchange column
plunger column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108
A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
plunger column
flame photometric detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091
FPD
PERSON:Daniel Schober
The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected.
WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
flame photometric detector
chromatography pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046
Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
PERSON:Daniel Schober
WEB:<http://en.wikipedia.org/wiki/Column_chromatography>
chromatography pump system
chromatography detector filter
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121
An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography detector filter
cation trap column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278
A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
cation trap column
column adapter
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
An Adapter that enabled the connection of a column to additional devices.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography device
column adapter
pulsed amperometric detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240
A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC).
PAD
PERSON:Daniel Schober
WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L>
pulsed amperometric detector
ozone-induced chemiluminescence detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088
Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry.
PERSON:Daniel Schober
WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177>
ozone-induced chemiluminescence detector
chromatography consumable
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115
A chromatography consumable is a consumable that is used in a chromatography experiment.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
chromatography consumable
chromatography device
column frit
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density).
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/topics/radial/columns.html>
chromatography device
column frit
liquid chromatography column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227
A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
liquid chromatography column
detector lamp
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119
A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html>
detector lamp
chart recorder
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration.
chart recorder
chromatography device
open tubular column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219
An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube.
PERSON:Daniel Schober
WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
open tubular column
high resolution magic angle spin probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
GROUP:<http://msi-ontology.sourceforge.net>
NMR probe
PERSON:Daniel Schober
Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
high resolution MAS, hr-MAS
high resolution magic angle spin probe
hydrogen generator
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035
A gas generator that generates hydrogen gas.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
hydrogen generator
glass column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101
A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
glass column
auto injector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058
A gas chromatography device that can auto-inject a small number of samples an inlet.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
auto injector
guard column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
GROUP:<http://msi-ontology.sourceforge.net>
Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns.
PERSON:Daniel Schober
chromatography device
guard column
protein expression profiling
OBI branch derived
Phlippe Rocca-Serra
a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays
protein expression profiling
proteomic analysis
high resolution probe with automatic tuning and matching
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
GROUP:<http://msi-ontology.sourceforge.net>
High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
NMR probe
PERSON:Daniel Schober
The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems.
high resolution probe with automatic tuning and matching
fluorine-induced chemiluminescence detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087
A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator.
PERSON:Daniel Schober
WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm>
fluorine-induced chemiluminescence detector
size exclusion column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100
A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
size exclusion column
chromatography splitter
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html>
chromatography device
chromatography splitter
custom made column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234
A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
custom made column
gel permeation column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103
A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size.
PERSON:Daniel Schober
WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
gel permeation column
DNA sequencing
DNA sequencing
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
OBI Branch derived
Philippe Rocca-Serra
quaternary pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047
A pump system that pump and mix up to four different solvents in parallel.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
quaternary pump system
carbon nanotube column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107
Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well.
PERSON:Daniel Schober
WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
carbon nanotube column
hematology
OBI branch derived
Philippe Rocca-Serra
blood analysis, haematology
hematology
hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
column heater
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040
PERSON:Daniel Schober
The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure.
WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
column heater
DNA methylation profiling assay
DNA methylation profiling assay
OBI branch derived
Philippe Rocca-Serra
an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
acquisition computer
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
GROUP:<http://msi-ontology.sourceforge.net>
NMR instrument
PERSON:Daniel Schober
acquisition computer
gas chromatography detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083
A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors.
FID
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
chromatography detector, defined class/xps
gas chromatography detector
gas purifier
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems.
PERSON:Daniel Schober
WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html>
gas chromatography equipment
gas purifier
indirect detection probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
An NMR probe designed to allow the indirect detection of acquisition nuclei.
GROUP:<http://msi-ontology.sourceforge.net>
NMR device
PERSON:Daniel Schober
indirect detection probe
atomic emission detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086
AED
Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element.
PERSON:Daniel Schober
WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
atomic emission detector
specimen collection
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
Bjoern Peters
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
a planned process with the objective of obtaining specimen.
specimen creation
ELISA
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
ELISA
ELISA is an assay where an enzyme linked antibody is used to detect a plate bound material in a liquid (the evaluant) utilizing a chemiluminescent reaction. The detected signal is proxy for the concentration of an analyte in the evaluant.
Enzyme-Linked ImmunoSorbent Assay
IEDB
IEDB
It is possible to add further restrictions, such as utilizing a plate as part of the assay.
BrdU incorporation assay
A BrdU incorporation assay is an assay to detect actively replicating cells. BrdU is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication. Antibodies specific for BrdU can then be used to detect the incorporated chemical, thus indicating cells that were actively replicating their DNA.
BrdU incorporation assay
IEDB
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU.
wiki http://en.wikipedia.org/wiki/BrdU
intracellular cytokine staining assay
ICCS
ICS
IEDB
IEDB
Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
intracellular cytokine staining assay
MHC multimer staining assay
2/26/09 RESOLVE: Need to add a restriction for the 'MHC multimer' as a reagent used
An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer
IEDB
IEDB
MHC multimer staining assay
MHC tetramer assay
Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.
tritiated thymidine incorporation assay
2/26/09: RESOLVE: need to replace 'molecular entities' in the logical definition with 'tritiated thymidine'
A tritiated thymidine incorporation assay is an assay to detect actively replicating cells. Tritiated thymidine is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine can then be detected thus indicating cells that were actively replicating their DNA.
IEDB
IEDB
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity.
tritiated thymidine incorporation assay
nucleotide overhang cloning
Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
Helen Parkinson
Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
nucleotide overhang cloning
immunoprecipitation
OBI plan and planned process branch
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
Philippe Rocca-Serra
immunoprecipitation
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
recombination enzyme based cloning
a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector
recombination enzyme based cloning
MeDIP-SEQ assay
MeDIP-SEQ assay
Methylated DNA immunoprecipitation sequencing assay
PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
Philippe Rocca-Serra
adapted from wikipedia
is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
chain termination sequencing
Philippe Rocca-Serra
Sanger sequencing
adapted from wikipedia
chain termination sequencing
dye terminator sequencing
is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
Helicos sequencing
Helicos sequencing
Philippe Rocca-Serra
adapted from wikipedia
is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length.
true single molecule sequencing
decision tree induction objective
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
James Malone
decision tree induction objective
Edman degradation
Edman degradation
PMID 4773306. Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942-1010
adapted from Wikipedia (http://en.wikipedia.org/wiki/Edman_degradation)
is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.
SOLiD sequencing
PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
Philippe Rocca-Serra
SOLiD sequencing
adapted from Wikipedia and Applied Biosystems web site
laboratory animal care
a process that realizes an animal care protocol that specifies how animals are kept and maintained
laboratory animal care
library preparation
PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
Philippe Rocca-Serra
is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
library construction
library preparation
ChIP-seq assay
ChIP-seq assay
Philippe Rocca-Serra
adapted from Wikipedia
an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
chromatin immunoprecipitation sequencing assay
made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes
vaccine preparation
OBI
The production of B. pertussis vaccine.
vaccine preparation
vaccine preparation is a planned process with specified output a vaccine
glucose tolerance test
NuGO OBI plan branch
Philippe Rocca-Serra
glucose tolerance test
is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
DNA sequencing by ligation
DNA sequencing by ligation
PERSON: Philippe Rocca-Serra
is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
Solexa sequencing
Philippe Rocca-Serra
Solexa sequencing
adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
reversible terminator sequencing
pyrosequencing
Philippe Rocca-Serra
Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
pyrosequencing
DNA sequencing by synthesis
DNA sequencing by synthesis
PERSON: Philippe Rocca-Serra
PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25.
is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
restriction enzyme based cloning
Kevin Clancy, Bjoern Peters
restriction enzyme based cloning
restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector.
immune response assay
an assay with the objective to determine information about an immune response
immune response assay
material sampling process
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
material sampling process
bisulfite sequencing
8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing.
Philippe Rocca-Serra
adapted from Wikipedia
bisulfite sequencing
is a DNA sequencing which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
fluorescently labeled MHC multimer
A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand
fluorescently labeled MHC multimer
recombinant BAC cloning
Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material
http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome
recombinant BAC cloning
double blind study execution
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated
Person:Alan Ruttenberg
double blind study execution
http://clinicaltrials.gov/ct2/info/glossary#double
glucometer
A measurement device with the function to measure and record the level/amount of glucose in a blood sample
Diabetic patients use glucometers to determine their glucose levels
PERSON:Frank Gibson
PERSON:Helen Parkinson
glucometer
glucose meter
http://en.wikipedia.org/wiki/Glucose_meter
recombinant phage cloning
Helen Parkinson
Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
recombinant phage cloning
cross linking
A process in which bonds are created that link one polymer to another
PERSON: Chris Stoeckert
cross linking
cross linking can be used as a probe to link proteins together, to check protein protein interactions
http://en.wikipedia.org/wiki/Cross-link
prothrombin time assay
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
Person:Alan Ruttenberg
The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma.
WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06
prothrombin time assay
denaturing
Denaturing DNA in alcohol
Is a process in which the tertiary or secondary structure of a polymer is disrupted
denaturing
http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29
micro electrode
A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
Helen Parkinson, Jessica Turner, Dirk Derom
Jessica Turner, Dirk Derom
micro electrode
micro electrode measuring device
activated partial thromboplastin time (aPTT) assay
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms.
PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent.
Person:Alan Ruttenberg
WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06
activated partial thromboplastin time (aPTT) assay
single blind study execution
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated
Person:Alan Ruttenberg
http://clinicaltrials.gov/ct2/info/glossary#single
single blind study execution
thrombin time assay
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time
PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
Person:Alan Ruttenberg
WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06
thrombin time assay
recombinant YAC cloning
Helen Parkinson
Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
recombinant YAC cloning
treatment portion of study execution
09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A planned process, part of a study design execution, during which the treatment of subjects is ongoing
Person:Alan Ruttenberg
treatment portion of study execution
manufacturer
A person or organization that has a manufacturer role
unblinding process
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials
unblinding process
western blot analysis
PMID: 6266278. "Western blotting": electrophoretic transfer of proteins from sodium dodecyl sulfate--polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A. Anal Biochem. 1981 Apr;112(2):195-203
a western blot analysis is an assay which allows detection of protein present in a extract resolved on polyacrylamide gel by electrophoresis, transfered to a membrane made of nitrocellulose or polyvinylidene difluoride and immobilized using formaldehyde based cross linking. Specific proteins are probed using specific antibodies. detection is carried by staining with secondary antibody usually linked to biotin or to a reporter enzyme such as alkaline phosphatase or horseradish peroxidase. This means that several secondary antibodies will bind to one primary antibody and enhance the signal. Most commonly, a horseradish peroxidase-linked secondary is used to cleave a chemiluminescent agent, and the reaction product produces luminescence in proportion to the amount of protein. Detection can only be achieved by radio marking antibodies and using Phosphor imagers.
person: Philippe Rocca-Serra
protein immunoblotting
western blot analysis
wikipedia
Southern blot analysis
OBI & Wikipedia
PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3.
Person: Philippe Rocca-Serra
Southern blot
Southern blot analysis
Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
flow cytometry assay
An assay that uses a flow cytometer to detect fluorescence in individual particles that flow by a laser in solution.
PERSON:Randi Vita, Bjoern Peters
Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
flow cytometry assay
animal euthanization
A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject
Helen Parkinson and Melissa Haendel
Melissa Haendel
Rats were euthanized with CO2
animal euthanization
animal sacrifice
may later be refined with more specific list of organisms
surface plasmon resonance assay
IEDB
PERSON:Bjoern Peters
Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow.
SPR assay
surface plasmon resonance assay
calorimeter
A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
PERSON:Bjoern Peters
calorimeter
calorimetry instrument
http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm
positron emission tomography scanner
PERSON:Bjoern Peters
PET scanner
http://en.wikipedia.org/wiki/Positron_emission_tomography
positron emission tomography scanner
micromanipulator
PERSON:Bjoern Peters
http://en.wikipedia.org/wiki/Micromanipulator
micromanipulator
optical microscope
A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
PERSON:Bjoern Peters
optical microscope
vibration isolation table
A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor.
PERSON:Bjoern Peters
United States Patent 6877711
vibration isolation table
sterilization function
a function to remove viable organisms from an input material
sterilization function
oscilloscope
A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis).
PERSON:Bjoern Peters
http://en.wikipedia.org/wiki/Oscilloscope
oscilloscope
electrode puller
A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube.
PERSON:Bjoern Peters
electrode puller
http://faculty.plattsburgh.edu/donald.slish/Puller1.html
vibrotome
vibrotome
reagent application function
4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people?
A function that is realized when a reagent is automatically added to some research material.
An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
PERSON: Nicole Vasilevsky, Matthew Brush
PERSON: Nicole Vasilevsky, Matthew Brush
reagent application function
addition of molecular tracer function
A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen.
Immunohistochemical labeling of tissue sections by an autostainer staining system.
PERSON: Nicole Vasilevsky, Matthew Brush
PERSON: Nicole Vasilevsky, Matthew Brush
addition of molecular tracer function
computed tomography scanner
CT scanner
PERSON:Bjoern Peters
X-ray computed tomography scanner
computed tomography scanner
http://en.wikipedia.org/wiki/X-ray_computed_tomography
PCR instrument
03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent.
A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
PCR instrument
electron microscope
A microscope that produces an image of an object by targeting it with an electron beam
electron microscope
Faraday cage
A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
Faraday cage
Faraday shield
PERSON:Bjoern Peters
Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
isolation function? HP
specimen fixation function
EAGLE-I
a function that allows specific identification of individual speciment from one another.
e.g the function of a bar code reader used to read slide bar codes
specimen fixation function
cell transfer function
A cell harvester has a cell transfer function.
EAGLE-I
cell transfer function
is a transfer function that displaces cells from one place to another
angiograph
A device that records the patterns of pulse waves inside blood vessels.
PERSON: Erik Segerdell
angiograph
http://medical-dictionary.thefreedictionary.com/angiograph
capillary blotter
A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed.
PERSON: Erik Segerdell
capillary blotter
http://www.biometra.de/
bioreactor
A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT
PERSON: Erik Segerdell
bioreactor
http://en.wikipedia.org/wiki/Bioreactor
pH meter
A device that is used to measure the pH (acidity or alkalinity) of a liquid.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/PH_meter
pH meter
digital camera
An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
PERSON: Erik Segerdell
digital camera
http://en.wikipedia.org/wiki/Digital_camera
chip spotting device
A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray.
PERSON: Erik Segerdell
United States Patent 7416705
chip spotting device
RNA extraction/purification instrument
A device that is used to isolate and collect RNA for subsequent molecular analysis.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
RNA extraction/purification instrument
two-photon laser/detector
A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy
two-photon laser/detector
electrophoresis system
A device that moves charged particles through a medium by using an electric field induced by electrodes.
PERSON: Erik Segerdell
electrophoresis system
http://en.wikipedia.org/wiki/Category:Electrophoresis
PET synthesizer
A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
PET synthesizer
spinning-disk confocal microscope
A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Nipkow_disk
spinning-disk confocal microscope
DNA synthesizer
An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
DNA synthesizer
PERSON: Erik Segerdell
http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers
high performance liquid chromatography instrument
A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
PERSON: Erik Segerdell
high performance liquid chromatography instrument
http://en.wikipedia.org/wiki/High_performance_liquid_chromatography
microplate reader
A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Plate_reader
microplate reader
ELISA microplate reader
A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
ELISA microplate reader
PERSON: Erik Segerdell
PERSON: Erik Segerdell
spot cutter
A robotic device that is used to excise spots from gels.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
spot cutter
microwave synthesis system
A device that is used to apply microwave irradiation to chemical reactions.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Microwave_chemistry
microwave synthesis system
densitometer
A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface.
PERSON: Erik Segerdell
densitometer
http://en.wikipedia.org/wiki/Densitometer
automatic staining machine
A device that is used to automatically stain tissue sections on slides or tissue specimens.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
automatic staining machine
automatic tissue processor
A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
PERSON: Erik Segerdell
United States Patent 3762362
automatic tissue processor
stereo microscope
An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes.
Macro microscope
PERSON: Erik Segerdell
dissecting microscope
dissection microscope
http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope
stereo microscope
top loading balance
A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
top loading balance
perfusion station
A device or system in which perfusion units are integrated.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
perfusion station
SPECT scanner
A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required.
PERSON: Erik Segerdell
SPECT scanner
http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography
scintillation counter
A device that is used to measure ionizing radiation.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Scintillation_counter
scintillation counter
programmable array microscope
A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
PERSON: Erik Segerdell
Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8
programmable array microscope
cryostat
A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION
PERSON: Erik Segerdell
cryostat
http://en.wikipedia.org/wiki/Cryostat
microtome knife maker
A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
microtome knife maker
cryofixation device
A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy.
PERSON: Erik Segerdell
cryofixation device
http://en.wikipedia.org/wiki/Cryofixation
hybridization oven
A device that creates an appropriate environment for nucleic acid hybridization.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
hybridization oven
incubator shaker
An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
PERSON: Erik Segerdell
PERSON: Erik Segerdell
incubator shaker
small-animal image acquisition device
A device that is used to image small laboratory animals (e.g., rats and mice) in vivo.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
small-animal image acquisition device
infrared image acquisition device
An image acquisition device that is responsive to an infrared emissive target within a given field of view.
PERSON: Erik Segerdell
United States Patent 4107530
infrared image acquisition device
confocal microscope
A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
PERSON: Erik Segerdell
confocal microscope
http://en.wikipedia.org/wiki/Confocal_microscopy
patch clamp device
A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Patch_clamp
patch clamp device
gel imaging system
A device that is used to acquire images of laboratory gels.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
gel imaging system
protein separation apparatus
A device that is used for the separation of proteins.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
protein separation apparatus
multichannel electronic pipette
A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations.
PERSON: Erik Segerdell
http://www.faqs.org/patents/app/20090196797
multichannel electronic pipette
vitrification apparatus
A device that is used to effect the transition of a substance into a glass.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Glass_transition
vitrification apparatus
radiography instrument
An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Medical_radiography
radiography instrument
radiation measurement device
A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
radiation measurement device
lyophilizer
A device that is used to freeze dry material.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Freeze_drying
lyophilizer
tandem mass spectrometer
A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge.
PERSON: Erik Segerdell
http://goldbook.iupac.org/T06250.html
tandem mass spectrometer
microhardness tester
A hardness testing device that is used in light-optical microscopes.
PERSON: Erik Segerdell
United States Patent 4611487
microhardness tester
multimode microplate reader
A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
multimode microplate reader
mechanical balance
A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
PERSON: Erik Segerdell
http://www.britannica.com/EBchecked/topic/49765/balance
mechanical balance
computer cluster
A group of linked computers, working together closely so that in many respects they form a single computer.
PERSON: Erik Segerdell
computer cluster
http://en.wikipedia.org/wiki/Cluster_(computing)
microtome knife sharpener
A device that is used to sharpen knives used in microtomy.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
microtome knife sharpener
plate shaker
A device that provides shaking motion for microplates.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
plate shaker
coagulation analyzer
A device for automatically analyzing blood coagulation in a clinical laboratory.
PERSON: Erik Segerdell
United States Patent 5439646
coagulation analyzer
laser capture microdissection microscope
A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
PERSON: Erik Segerdell
http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine
laser capture microdissection microscope
liquid extraction robot
A liquid handling device that provides automatic liquid extraction.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
liquid extraction robot
ultrasound machine
A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Sonography
ultrasound machine
immunoblot scanner
A device that is used for the imaging of immunoblots.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
immunoblot scanner
microcentrifuge
A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Laboratory_centrifuge
microcentrifuge
electronic repeater pipette
A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations.
PERSON: Erik Segerdell
electronic repeater pipette
http://www.faqs.org/patents/app/20090196797
electron paramagnetic resonance spectrometer
An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.
PERSON: Erik Segerdell
electron paramagnetic resonance spectrometer
http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance
rocker
A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
PERSON: Erik Segerdell
PERSON: Erik Segerdell
rocker
analytical balance
A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy.
PERSON: Erik Segerdell
analytical balance
http://en.wikipedia.org/wiki/Weighing_scale
scanning force microscope
A microscope that forms images of surfaces using a physical probe that scans the specimen.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Scanning_probe_microscopy
scanning force microscope
pulsed-field gel electrophoresis system
A gel electrophoresis system that is used to separate very large molecules of DNA.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis
pulsed-field gel electrophoresis system
tissue embedding station
A device that is used to perform paraffin embedding of tissue specimens.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
tissue embedding station
bead array reader
A device that is used to acquire and image bead array data.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
bead array reader
real-time PCR machine
An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
real-time PCR machine
paraffin oven
A device that is used for the warming of paraffin embedding medium.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
paraffin oven
autoclave
A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents.
J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave
PERSON: Erik Segerdell
autoclave
microplate washer
A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
PERSON: Erik Segerdell
http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037
microplate washer
nucleic acid extraction/purification instrument
A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
nucleic acid extraction/purification instrument
ELISA microplate washer
A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
ELISA microplate washer
PERSON: Erik Segerdell
PERSON: Erik Segerdell
vacuum manifold
A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
vacuum manifold
DNA extraction/purification instrument
A device that is used to isolate and collect DNA for subsequent molecular analysis.
DNA extraction/purification instrument
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/DNA_extraction
multichannel pipette
A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
multichannel pipette
cell harvester
A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
PERSON: Erik Segerdell
PERSON: Erik Segerdell
cell harvester
portable fluorometer
A compact fluorometer that can be carried or moved with ease.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
portable fluorometer
gel electrophoresis system
A device that moves charged particles through a medium by using an electric field induced by electrodes.
PERSON: Erik Segerdell
electrophoresis system
gel electrophoresis system
http://en.wikipedia.org/wiki/Category:Electrophoresis
diffractometer
A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it.
PERSON: Erik Segerdell
diffractometer
http://en.wikipedia.org/wiki/Diffractometer
microdissection instrument
A device that is used for the dissection of tissues under magnification.
PERSON: Erik Segerdell
http://medical-dictionary.thefreedictionary.com/microdissection
microdissection instrument
micropipette puller
A device that is used to fabricate glass micropipettes.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Micropipette
micropipette puller
laser scanning confocal microscope
A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy
laser scanning confocal microscope
digital microscope
A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
PERSON: Erik Segerdell
digital microscope
http://en.wikipedia.org/wiki/Digital_microscope
freeze substitution system
A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins.
PERSON: Erik Segerdell
doi:10.1017/S143192760707866X
freeze substitution system
micropipette
A microinjection device that is used to measure very small volumes of liquids.
PERSON: Erik Segerdell
http://www.answers.com/topic/micropipette
micropipette
voltage clamp device
A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Voltage_clamp
voltage clamp device
vacuum oven
A device that heats materials in a vacuum.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
vacuum oven
slide warmer
A device that is used to heat microscope slides.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
slide warmer
capillary electrophoresis instrument
An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
PERSON: Erik Segerdell
capillary electrophoresis instrument
http://en.wikipedia.org/wiki/Capillary_electrophoresis
denaturing high-performance liquid chromatography instrument
A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis.
PERSON: Erik Segerdell
denaturing high-performance liquid chromatography instrument
doi:10.1385/1-59259-850-1:173
agarose gel electrophoresis system
A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
PERSON: Erik Segerdell
agarose gel electrophoresis system
http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis
balance
A measuring instrument that is used to determine the weight or mass of an object.
PERSON: Erik Segerdell
balance
http://en.wikipedia.org/wiki/Weighing_scale
scale
surface plasmon resonance instrument
A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Surface_plasmon_resonance
surface plasmon resonance instrument
protein sequencer
An device that is used to determine the order of amino acids in protein sequences.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
protein sequencer
X-ray source
A device that is used to generate X-rays.
PERSON: Erik Segerdell
X-ray source
http://en.wikipedia.org/wiki/X-ray_generator
x-ray generator
liquid chromatography instrument
A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
PERSON: Matthew Brush
PERSON: Matthew Brush
liquid chromatography instrument
SNP microarray
EFO_0002703 SNP array
Person: Helen Parkinson
a DNA microarray used to detect polymorphisms in DNA samples
SNP microarray
ChIP-chip assay
ChIP-on-chip assay
Person: James Malone
Philippe Rocca-Serra
WEB: http://en.wikipedia.org/wiki/ChIP-on-chip
an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis.
ChIP-chip assay
tiling microarray
EFO_0002704: tiling array
Person: Helen Parkinson
a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
genome tiling array
tiling microarray
DNA sequence data
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
A sequence data item that is about the primary structure of DNA
DNA sequence data
OBI call; Bjoern Peters
OBI call; Melanie Courtout
The part of a FASTA file that contains the letters ACTGGGAA
establishing cell line
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
PERSON:Matthew Brush
organism
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
GROUP: OBI Biomaterial Branch
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
organism
plant
virus
data transformation
Philippe Rocca-Serra
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
Branch editors
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
data transformation
differential expression analysis objective
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
differential expression analysis objective
descriptive statistical calculation objective
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
Elisabetta Manduchi
James Malone
Melanie Courtot
Monnie McGee
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
PERSON: Monnie McGee
descriptive statistical calculation objective
sequence analysis objective
James Malone
PERSON: James Malone
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
sequence analysis objective
data visualization
Generation of a heatmap from a microarray dataset
data encoding as image
data visualization
An planned process that creates images, diagrams or animations from the input data.
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
PERSON: Tina Boussard
Tina Boussard
visualization
data transformation objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
James Malone
PERSON: James Malone
data transformation objective
normalize objective
data normalization objective
Elisabetta Manduchi
Helen Parkinson
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
James Malone
PERSON: James Malone
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
data normalization objective
correction objective
PERSON: James Malone
PERSON: Melanie Courtot
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
James Malone
Type I error correction
correction objective
background correction objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
James Malone
background correction objective
curve fitting objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
James Malone
curve fitting objective
error correction objective
Application of a multiple testing correction method
PERSON: James Malone
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
James Malone, Helen Parkinson
error correction objective
comet assay
PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay.
PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review.
Philippe Rocca-Serra
SCGE assay
a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions.
comet assay
single cell gel electrophoresis assay
PCR-SSCP assay
PCR-SSCP assay
PERSON: Philippe Rocca-Serra
PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene?
PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases.
a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure.
polymerase chain reaction-single strand conformation polymorphism assay
extraction
A material separation in which a desired component of an input material is separated from the remainder
Person:Bjoern Peters
Philippe Rocca-Serra
extraction
nucleic acid extraction using phenol chloroform
filtration
OBI-Branch: adapted from wikipedia and wordnet
Philippe Rocca-Serra
filtration
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
centrifugation
Philippe Rocca-Serra
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
staining
Philippe Rocca-Serra
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
irradiation
Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
irradiation
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves
polymerization
OBI-Branch
Philippe Rocca-Serra
polymerization
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
PRS:22102008: need to import catalyst from CHEBI 35223
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
trypsination
OBI PA
Philippe Rocca-Serra
trypsination
The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483
trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity
enzymatic ligation
OBI-Branch
Philippe Rocca-Serra
enzymatic ligation
An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity
PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202.
electrocution
OBI branch
Philippe Rocca-Serra
electrocution
PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376.
electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process.
cervical dislocation
OBI branch
Philippe Rocca-Serra
cervical dislocation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax)
cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion
asphyxiation
OBI branch
Philippe Rocca-Serra
asphyxiation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms.
intentional overdosing
OBI Biomaterial
Philippe Rocca-Serra
intentional overdosing
intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death
lethal injection
decapitation
OBI-Branch
Philippe Rocca-Serra
decapitation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..)
immobilization
OBI-Branch
Philippe Rocca-Serra
immobilization
PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23.
immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum.
elution
Philippe Rocca-Serra
elution
wordnet.princeton.edu/perl/webwn
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
DNA Subtraction
OBI-Branch
Philippe Rocca-Serra
DNA Subtraction
PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81
a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library.
validation
Philippe Rocca-Serra
adapted from wordnet (wkipedia)
validation
PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results
electroporation
Philippe Rocca-Serra
WEB:http://en.wikipedia.org/wiki/Electroporation
electropermeabilization
electroporation
PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13.
a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA
analog-to-digital converter
A-D
A2D
An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal.
John Quinn
Melanie Courtot
The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection.
analog-to-digital converter
http://en.wiktionary.org/wiki/Analog-to-Digital_Converter
flow cytometer analyzer
An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis.
FACS Calibur, Luminex 100
John Quinn
flow cytometer analyzer
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
arc lamp
Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point.
John Quinn
The Jablochkoff Candle
arc lamp
http://en.wikipedia.org/wiki/Arc_lamp
argon ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes.
Daniel Schober
John Quinn
argon ion laser
argon ion laser in a cytometer
avalanche photodiode
An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand.
C30644E - InGaAs Avalanche Photodiode
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
avalanche photodiode
band pass filter
530/30 BP filter, 585/42 BP filter
A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others.
Person:John Quinn
band pass filter
http://en.wikipedia.org/wiki/Band_pass_filter
charge plate
John Quinn
LSR2 charge plate
Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
charge plate
dichroic filter
A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
Cy3 Dichroic Filter
John Quinn
dichroic filter
http://en.wikipedia.org/wiki/Dichroic_filter
dichroic mirror
A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
John Quinn
ViewLux Alexa 594 dichroic mirror
dichroic mirror
http://en.wikipedia.org/wiki/Dichroic_mirror
differential pressure gauge
John Quinn
LSR2 differential pressure gauge
Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
differential pressure gauge
diode laser
A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer.
Daniel Schober
FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc.
John Quinn
diode laser
dye laser
A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification.
Daniel Schober
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Rhodamine 101 dye laser used to irradiate cells in a flow cytometer.
dye laser
flow cell
flow cell
flow_cell
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
Biofilm Flow Cell
Person:John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
flow cytometer
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
FACS Calibur
John Quinn
flow cytometer
http://en.wikipedia.org/wiki/Flow_cytometer
fluid pressure regulator
LSR2 fluid pressure regulator
Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank.
Person: John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
fluid pressure regulator
gas laser
gas laser
http://en.wikipedia.org/wiki/Gas_laser
A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas.
Daniel Schober
John Quinn
helium-neon gas laser used to erradiate cells in a flow cytometer.
helium cadmium ion laser
A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer.
John Quinn
KIMMON HeCd 325nm laser
helium cadmium ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
helium neon ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
A helium neon laser can by used to irradiate cells in a flow cytometer.
A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm.
Daniel Schober
John Quinn
helium neon ion laser
ion laser
http://en.wikipedia.org/wiki/Ion_laser
2 Watt Lexel 88 Argon Ion laser
An ion laser is a gas laser which uses an ionized gas as its lasing medium.
Daniel Schober
John Quinn
ion laser
krypton ion laser
A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however.
Daniel Schober
John Quinn
Lexel 95L krypton laser
krypton ion laser
laser
http://en.wikipedia.org/wiki/Laser
A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer.
A laser is the most common way to irradiate a cell in a flow cytometer.
Daniel Schober
John Quinn
laser
light amplification by the stimulated emission of radiation
light source
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Elizabeth M. Goralczyk
John Quinn
Olga Tchuvatkina
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
light source
logarithmic voltage amplifier
A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale.
HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
logarithmic voltage amplifier
long pass filter
750 LP filter
A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm.
John Quinn
http://en.wikipedia.org/wiki/high-pass_filter
long pass filter
metal vapor laser
A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer.
Gold vapor laser, Helium-cadmium metal-vapor laser
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
metal vapor laser
mixed argon-krypton gas laser
A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer.
John Quinn
argon-krypton laser in a cytometer
http://www.eio.com/repairfaq/sam/laserarg.htm
mixed argon-krypton gas laser
multi-well plate
96 well plate, 48 multiwell plate
A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
FG this is synonymous with microtiter plate
John Quinn
http://www.nuncbrand.com/page.aspx?ID=301
multi-well plate
neodymium-YAG laser
A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer.
Daniel Schober
John Quinn
Neodymium-YAG Laser in DURIP99 System
neodymium-YAG laser
obscuration bar
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
Daniel Schober
John Quinn
obscuration bar
obscuration bar in a flow cytometer
optical filter
720 LP filter, 580/30 BP filter
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
John Quinn
http://en.wikipedia.org/wiki/Optical_filter
optical filter
optical subsystem
DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one.
John Quinn
Person: Daniel Schober
a device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles.
optical subsystem
optical subsystem of a cytometer
particle delivery vessel
FC 500 particle delivery vessel
FG: this should be delted - particle delivery is a role that an object can play
John Quinn
Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
particle delivery vessel
photodetector
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
A photomultiplier tube, a photo diode
John Quinn
http://einstein.stanford.edu/content/glossary/glossary.html
photodetector
photodiode
A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer.
Avalanche photodiode
John Quinn
http://cyto.mednet.ucla.edu/Protocols/flow.htm
photodiode
photomultiplier tube
A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect.
John Quinn
R9647 by manufactured by Hamamatsu
http://cyto.mednet.ucla.edu/Protocols/flow.htm
photomultiplier tube
piezo electric crystal
piezo electric crystal
think this is natural thing, not a device HP/JF
Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell.
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar
plate loader
measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future.
FC 500 plate loader
John Quinn
Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications.
http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf
plate loader
preamplifier
A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing.
Built in preamplifier in a Hamamatsu H9656 PMT
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
preamplifier
quartz cuvette flow chamber
A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells.
CVF-Q-10 flow chamber, CV-Q-10 flow chamber
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
quartz cuvette flow chamber
sheath tank
John Quinn
LSR2 sheath tank
Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
sheath tank
short pass filter
620 SP filter
A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm.
John Quinn
http://en.wikipedia.org/wiki/Low-pass_filter
short pass filter
solid state laser
A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser.
Daniel Schober
Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command
http://en.wikipedia.org/wiki/Solid-state_laser
solid state laser
flow cytometer sorter
A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest.
BioSorter2000, LSR2
John Quinn
Melanie Courtot
flow cytometer sorter
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
syringe pump
NE-1000 Single Syringe Pump
Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates.
Person:John Quinn
http://www.answers.com/topic/syringe, 2007-05-11
syringe pump
voltage amplifier
Frank Gibson
A voltage amplifier is a device that amplifies the voltage signal.
John Quinn
Linear amplifier, log amplifier, microwave amplifier
http://en.wiktionary.org/wiki/amplifier
voltage amplifier
DNA sequencer
genome sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
DNA sequencer
MO
Trish Whetzel
array scanner
GROUP: MGED Ontology
Throughput array plate scanner
microarry scanner
An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip
GenePix 4200A, GenePix4000B
Trish Whetzel
array scanner
arrayer
BioRobotics Microgrid II TAS, Affymetrix GMS 417
MO_697 arrayer
Trish Whetzel
a device which deposits biological material onto a substrate in a defined pattern.
arrayer
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
Person: Jennifer Fostel
Melanie Courtot
Trish Whetzel
centrifuge
http://en.wikipedia.org/wiki/Centrifuge
computer
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
Apple PowerBook, Dell OptiPlex
Melanie Courtot
Trish Whetzel
computer
http://en.wikipedia.org/wiki/Computer
heating block
A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay
An instrument used to heat and/or maintain material at a set temperature.
Daniel Schober
MO
heating block
homogenizer
A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Melanie Courtot
Trish Whetzel
homogenizer
http://en.wikipedia.org/wiki/Homogenizer
mortar, blender
hybridization chamber
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
Glass Array Hybridization Cassette
MO_563 hybridization_chamber
Trish Whetzel
hybridization chamber
hybridization station
A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
Labnet Problot12
MO_497 hybridization station
Trish Whetzel
hybridization station
liquid handler
Beckman BioMek 2000
MO_868 liquid_handler
a device that is used for automated liquid transfer and handling.
liquid handler
liquid_handling_instrument
oligonucleotide synthesizer
An instrument used to chemically synthesize oligonucleotides.
Automated Multiplex Oligonucleotide Synthesizer
MO
Trish Whetzel
oligonucleotide synthesizer
sonicator
An instrument that converts a variable electrical current to mechanical vibration of a metallic probe. The instrument is used for the lysis of cells, the mixing of compounds or solutions, or to create emulsions.
MO
Sonicator 3000
Trish Whetzel
sonicator
spectrophotometer
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
Helios Gamma Spectrophotometer
MO
Melanie Courtot
Trish Whetzel
spectrophotometer
thermal cycler
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
DNA_amplifier
MO
Melanie Courtot
PCR_machine
Piko(tm) 96-well Thermal Cycler
Polymerase_Chain_Reaction_ machine
Trish Whetzel
thermal cycler
thermocycler
vacuum dryer
An instrument which removes liquid by the application of negative pressure, i.e. vacuum.
MO
Model 777 Microarray Oven
Trish Whetzel
vacuum dryer
vortexer
A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
Melanie Courtot
Trish Whetzel
VWR Genie 2
http://en.wikipedia.org/wiki/Vortex_mixer
vortex_mixer
vortexer
microarray wash station
ArrayIt(r) Microarray Wash Station
MO_626 wash_station
Trish Whetzel
a device that is used to wash Affymetrix-type arrays.
microarray wash station
temperature control bath
Alan Ruttenburg
Daniel Schober
Frank Gibson
OBI Instrument branch
A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature).
VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
temperature control bath
molecular crosslinker
AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly.
MO ?? cannot be found in MO
Stratalinker
Trish Whetzel
a device that is able to chemically join two or more molecules.
molecular crosslinker
molecular crosslinker
image cytometer
An image_cytometer is an instrument for image-based study or measurement of cells.
Melanie Courtot
The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining.
http://web.mit.edu/solab/Research/ImageCytometry.html
image cytometer
cytometer
A cytometer is an instrument for counting and measuring cells.
Melanie Courtot
cytometer
http://medical.merriam-webster.com/medical/cytometer
gel tank
Person:Frank Gibson
CHEF gel box, slab gel box, capillary electrophoresis
Person:Kevin Clancy
a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
electrophoresis box
electrophoresis unit
gel tank
sep:00095
power supply
Frank Gibson
sep:00093
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
Daniel Schober
PERSON: Daniel Schober
PSU
electrical power supply
power pack
power supply
power supply unit
was power_pack, maps to SEP electrical_power_supply
fluorometer
Fluorimeter
fluorescence imager
spectrofluorometer
A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample.
Allyson Lister
Kevin Lister
OBI
fluorometer
laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
multispectral imaging flow cytometer
A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations.
MIFC
Melanie Courtot
http://www.amnis.com/
multispectral imaging flow cytometer
microarray
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
PERSON: Chris Stoeckert
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
Daniel Schober
microarray
DNA microarray
PERSON: Frank Gibson
Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
DNA Chip
DNA microarray
DNA-array
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
PERSON: Daniel Schober
protein microarray
PERSON: Daniel Schober
A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
Daniel Schober
The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
protein microarray
droplet sorter
OBI Instrument branch
OBI Instrument branch
droplet sorter
water bath
Daniel Schober
PERSON: Daniel Schober
A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
water bath
oil bath
Daniel Schober
PERSON: Daniel Schober
An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample).
An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period.
oil bath
digital-to-analog converter
Daniel Schober
PERSON: Daniel Schober
A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal.
A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound.
digital-to-analog converter
microtome
PERSON: Daniel Schober
PERSON: Phillippe Rocca-Serra
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
microtome
microscope
PERSON: Phillippe Rocca-Serra
wikipedia
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
microscope
animal cage
OBI biomaterial branch
PERSON: Phillippe Rocca-Serra
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
a processed material which has the function to define a bounded habitat which is amenable to keeping animals.
animal cage
laboratory cage
study design
A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
PERSON: Chris Stoeckert
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
study design
tumor grading
Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
OBI branch derived; submitted by MO
grading of tumor
tumor grading
performing a clinical assessment
clinical diagnosis
performing a clinical assessment
(maybe CIO)
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition.
collecting specimen from organism
IEDB
PERSON:Bjoern Peters
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
environmental material collection
Bjoern Peters, Alan Ruttenberg
IEDB
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
environmental material collection
environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
the researcher is very interested in the location
material component separation
Bjoern Peters
IEDB
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
material component separation
detection of label
Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present
OBI branch derived
PERSON:Bjoern Peters
detection of label
the detection of the amount of a label which is a proxy for the detection of the labeled biomaterial
histology
PRS:20090901: addition of alternative term = histopathology
histopathology
OBI branch derived
PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
histology
need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement
cell fixation
OBI branch derived
PERSON:Bjoern Peters
a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time
cell fixation
http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus
should include capturing what qualities are being preserved
we could generalize this for other input materials
excision
Alan Ruttenberg, Kevin Clancy
Cutting out the portion of a gel which contains a DNA fragment
excision
the use physical means to remove a portion of a substance from the rest
www.crohnsresource.com/glossary.jsp (via google define:resection)
non specific enzymatic cleavage
OBI branch derived
PERSON:Kevin Clancy
The use of agarase to digest an agar gel
a protocol application to digest the fraction of input material that is susceptible to that enzyme
non specific enzymatic cleavage
maintaining cell culture
This is a renamed of the manaintainig cell culture
OBI branch derived
PlanAndPlannedProcess Branch
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
maintaining cell culture
longitudinal mass measurement assay
A process in which the mass of a material is measured at two or more time points
Helen Parkinson
OBI branch derived
The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection
longitudinal mass measurement assay
artificially induced cell membrane lysis
---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined.
OBI branch derived
PlanAndPlannedProcess Branch
a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate
artificially induced cell membrane lysis
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent.
artificially induced reverse transcription
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
OBI branch derived
PERSON:Kevin Clancy
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
artificially induced reverse transcription
isolation of cell culture supernatant
OBI branch derived
PlanAndPlannedProcess Branch
Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube.
This does not apply to the case where the cells are lysed
a protocol which results in the separation of supernatant material from a cell culture
isolation of cell culture supernatant
experimental disease induction
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application to induce a specific disease in an organism
could be defined class
experimental disease induction
the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome.
ELISPOT assay
2/26/09: RESOLVE: we need to specify the produced substance that is desired to be detected. Analyte does not work, as this is not a concentration, and this is not present at the start of the assay.
ELISPOT assay
Enzyme-linked immunosorbent spot assay
An assay in which the number of cells producing a material in a larger cell population are stained and counted. This is done by visualizing and counting the number of spots present on a surface via an antibody specific for the produced material. Each spot represents one cell producing the material of interest.
Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell.
ELISPOT
IEDB
IEDB
artificially induced DNA repair
---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application to repair damaged DNA molecules
artificially induced DNA repair
the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands
cell permeabilization
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
Electroporation of HeLa cells to allow transfection with pUC19.
OBI branch derived
PERSON:Bjoern Peters
cell permeabilization
definition blessed by Jay, Alan, Randi
need to add output cell has_quality permeable
precipitation
OBI branch derived
PERSON:Kevin Clancy
The use of ethanol to precipitate DNA molecules from a solution containing DNA
a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate)
precipitation
establishing cell culture
OBI branch derived
PlanAndPlannedProcess Branch
establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density.
establishing cell culture
cell culture splitting
OBI branch derived
PlanAndPlannedProcess Branch
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
cell culture splitting
labeling
OBI branch derived
PERSON:Kevin Clancy
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
definition blessed by Allyson, Bjoern, Jay & Randi
labeling
the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future
artificially induced methylation
A planned process of adding methyl groups to polymers
OBI branch derived
PERSON:Kevin Clancy
artificially induced methylation
the use of enzymes to add methyl groups to DNA molecules
synthesis
synthesis
OBI branch derived
PERSON:Kevin Clancy
This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription
making cDNA from nucleotides using RNA as a template
synthesize
the construction of a biomaterial from simpler biomaterials
concentrate
Evaporation of the solution containing DNA to increase the concentration of the DNA molecules
OBI branch derived
PERSON:Kevin Clancy
a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material
concentrate
recombinant plasmid cloning
OBI branch derived
PERSON:Kevin Clancy
The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35.
recombinant plasmid cloning
the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial
genetic transformation
OBI branch derived
PERSON:Kevin Clancy
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
genetic modification
genetic transformation
the introduction. alteration or integration of genetic material into a cell or organism
lavage
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
OBI branch derived
PlanAndPlannedProcess Branch
This is not washing, in which case the material of interest is not the resulting fluid
lavage
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
preparative chromatography
OBI branch derived
PERSON:Kevin Clancy; Bjoern Peters
The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides.
preparative chromatography
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
sequencing assay
OBI branch derived
PlanAndPlannedProcess Branch
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has_output should be sequence of input; we don't have sequence well defined yet
sequencing assay
the use of a chemical or biochemical means to infer the sequence of a biomaterial
vector mediated amplification
vector mediated amplification
E coli expressing the gene for M avium p35 were cultured in order to produce p35.
OBI branch derived
PERSON:Kevin Clancy
The process of creating a copy of some biological entity in cell culture
DNA polymerase amplification
Philippe Rocca-Serra
DNA polymerase amplification
DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input
OBI branch derived
PERSON:Kevin Clancy
The use of taq polymerase to amplify a DNA fragment during a PCR.
specific enzymatic cleavage
OBI branch derived
PERSON:Kevin Clancy
The use of a protease to digest a protein into peptides
a protocol application to digest the fraction of input material that is susceptible to that enzyme
specific enzymatic cleavage
gradient separation
OBI branch derived
PERSON:Kevin Clancy
a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
gradient separation
the use of a sucrose gradient to isolate mitochondria
dialysis
OBI branch derived
PERSON:Kevin Clancy
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
electrophoresis
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers.
OBI branch derived
PERSON:Kevin Clancy
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
electrophoresis
DNA cleavage, restriction analysis
DNA cleavage, restriction analysis
PERSON:Kevin Clancy
restriction enzyme assay
the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
protease cleavage
OBI branch derived
PlanAndPlannedProcess Branch
enzymatic digestion
protease cleavage
protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments).
the use of trypsin to cleave pepsin into peptide fragments
enzymatic amplification
OBI branch derived
PERSON:Kevin Clancy
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
recombinant vector cloning
molecular cloning
OBI branch derived
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
recombinant vector cloning
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
OBI branch derived
PlanAndPlannedProcess Branch
RNA extraction
requested by Helen Parkinson for MO
nucleic acid extraction
OBI branch derived
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
PlanAndPlannedProcess Branch
a material separation to recover the nucleic acid fraction of an input material
nucleic acid extraction
requested by Helen Parkinson for MO. Could be defined class
immunogen
immunogen
IEDB
IEDB
a material entity bearing the immunogen role
disease
disease
IEDB
IEDB
placeholder to be imported from disease ontology
immunogen role
immunogen role
IEDB
IEDB
any entity capable of eliciting an immune response when introduced to components of the immune system
PATO quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.
trait
biological sex
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
viability
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
physical object quality
A quality which inheres in a continuant.
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
hermaphrodite
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
intersex
alive
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
phenotypic sex
organismal quality
A quality that inheres in an entire organism or part of an organism.
deletion
The point at which one or more contiguous nucleotides were excised.
deleted_sequence
nucleotide deletion
nucleotide_deletion
translocation
A region of nucleotide sequence that has translocated to a new position.
transchr
translocated sequence
simple_sequence_length_variation
SSLP
simple sequence length polymorphism
simple sequence length variation
sequence_length_variation
sequence length variation
insertion
The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
insertion
nucleotide insertion
nucleotide_insertion
SNP
SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
single nucleotide polymorphism
MNP
A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
multiple nucleotide polymorphism
copy_number_variation
A variation that increases or decreases the copy number of a given region.
CNP
CNV
copy number polymorphism
copy number variation
sequence_alteration
A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
partially characterised change in DNA sequence
partially_characterised_change_in_DNA_sequence
sequence alteration
transgenic_insertion
An insertion that derives from another organism, via the use of recombinant DNA technology.
transgenic insertion
SNV
SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist.
single nucleotide variant
substitution
Any change in genomic DNA caused by a single event.
complex_substitution
When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change.
complex substitution
point_mutation
A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
point mutation
transition
Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.
pyrimidine_transition
A substitution of a pyrimidine, C or T, for another pyrimidine.
pyrimidine transition
C_to_T_transition
A transition of a cytidine to a thymine.
C to T transition
C_to_T_transition_at_pCpG_site
C to T transition at pCpG site
The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.
T_to_C_transition
T to C transition
purine_transition
A substitution of a purine, A or G, for another purine.
purine transition
A_to_G_transition
A to G transition
A transition of an adenine to a guanine.
G_to_A_transition
A transition of a guanine to an adenine.
G to A transition
transversion
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.
pyrimidine_to_purine_transversion
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.
pyrimidine to purine transversion
C_to_A_transversion
A transversion from cytidine to adenine.
C to A transversion
C_to_G_transversion
C to G transversion
T_to_A_transversion
A transversion from T to A.
T to A transversion
T_to_G_transversion
A transversion from T to G.
T to G transversion
purine_to_pyrimidine_transversion
Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.
purine to pyrimidine transversion
A_to_C_transversion
A to C transversion
A transversion from adenine to cytidine.
A_to_T_transversion
A to T transversion
A transversion from adenine to thymine.
G_to_C_transversion
A transversion from guanine to cytidine.
G to C transversion
G_to_T_transversion
A transversion from guanine to thymine.
G to T transversion
indel
A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.
duplication
One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point.
nucleotide duplication
nucleotide_duplication
inversion
A continuous nucleotide sequence is inverted in the same position.
inversion
direct_tandem_duplication
A tandem duplication where the individual regions are in the same orientation.
direct tandem duplication
inverted_tandem_duplication
A tandem duplication where the individual regions are not in the same orientation.
inverted tandem duplication
mirror duplication
tandem_duplication
A duplication consisting of 2 identical adjacent regions.
erverted
tandem duplication
anatomical structure
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
biological structure
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
developmental stage
stage
material anatomical entity
Anatomical entity that has mass.
tissue
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
portion of tissue
simple tissue
tissue portion
germ layer
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[UBERONREF:0000002]
germinal layer
ectoderm
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
embryonic ectoderm
endoderm
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
This class was created automatically from a combination of ontologies
mesoderm
Taxon notes: sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates[UBERONREF:0000002]
The middle germ layer of the embryo, between the endoderm and ectoderm.
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
embryonic structure
Anatomical structure that is part of an embryo.
Note in FMA embryo is_a embryonic structure
developing embryonic structure
embryonic anatomical structure
neural crest
Editor note: consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). Taxon notes: A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]. Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
The neural crest, a transient component of the ectoderm, is located in between the neural tube and the epidermis (or the free margins of the neural folds) of an embryo during neural tube formation. Neural crest cells quickly migrate during or shortly after neurulation, an embryological event marked by neural tube closure.
embryonic tissue
A portion of tissue that is part of an embryo.
portion of embryonic tissue
developing anatomical structure
germ layer / neural crest
Case-control study
A case control study is an observational study that compares people with a specific disease or outcome of interest (cases) to people from the same population without that disease or outcome (controls), and which seeks to find associations between the outcome and prior exposure to particular risk factors. [Glossary of Terms in The Cochrane Collaboration]
Simona
Case-crossover study
A case-crossover study is an observational study that aims to answer the question, “Was this event triggered by something unusual that happened just before?” The key feature of the design is that each case serves as its own control. The method is analogous to a crossover experiment viewed retrospectively, except that the investigator does not control when a patient starts and stops being exposed to the potential trigger. Also, the exposure frequency is typically measured in only a sample of the total time when the patient was at risk of the injury or disease onset. Thus it usually resembles a case-control study more than a retrospective cohort study.
The simplest case-crossover design is closely analogous to a traditional matched-pair case-control design. In both designs, each case has a matched control. In a traditional matched-pair case-control study, the control is a different person at a similar time. In the matched-pair case-crossover design, the control is the same person at a different time [Annu Rev Public Health. 2000;21:193-221.]
Simona
Cohort study
A cohort study is an observational study in which a defined group of people (the cohort) is followed over time. The outcomes of people in subsets of this cohort are compared, to examine people who were exposed or not exposed (or exposed at different levels) to a particular intervention or other factor of interest. A prospective cohort study assembles participants and follows them into the future. A retrospective (or historical) cohort study identifies subjects from past records and follows them from the time of those records to the present. [Glossary of Terms in The Cochrane Collaboration]
Simona
Cross-sectional study
A cross-sectional study is an observational study measuring the distribution of some characteristic(s) in a population at a particular point in time. (Also called survey.) [adapted from: Glossary of Terms in The Cochrane Collaboration]
Simona
Interventional study
An interventional study is a quantitative study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes. Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioural treatments, process-of-care changes, preventive care, etc. [adapted from: WHO, available at: http://www.who.int/ictrp/en/]
Simona
Simona: to be reviewed
Observational study
An observational study is a quantitative study in which the investigators do not seek to intervene, and simply observe the course of events. [adapted from: Glossary of Terms in The Cochrane Collaboration]
Simona
Parallel group study
A parallel group study is an interventional study that compares across at least two allocation groups concurrently, each receiving a regimen of interventions (which can be "no intervention").
Simona
Simona: to be reviewed.
Qualitative human study
A qualitative study is an individual-human study whose primary mode of inquiry is qualitative.
Simona
Quantitative human study
A quantitative study is an individual-human study whose primary mode of inquiry is quantitative.
Simona
Crossover study
A crossover study is an interventional study where the population is a more than a single human subject, in which at least two regimens of interventions are given alternatingly. Upon completion of one regimen, participants are switched to the other. For example, for a comparison of regimens A and B, the participants are randomly allocated to receive them in either the order A, B or the order B, A.
Regimens are assigned to and data are analyzed within more than one participant at a time.
Simona
Simona: to be reviewed
N-of-1 crossover study
An N-of-1 crossover study is an interventional study where the population is a single human subject and in which at least two regimens of interventions are given alternatingly. Regimens are assigned to and data are analyzed within one participant at a time.
Simona
Simona: to be reviewed
Phase
Phase describes the level of a trial required of drugs before (and after) they are routinely used in clinical practice:
- Phase I trials assess toxic effects on humans (not many people participate in them, and usually without controls);
- Phase ll trials assess therapeutic benefit (usually involving a few hundred people, usually with controls, but not always);
- Phase III trials compare the new treatment against standard (or placebo) treatment (usually a full randomised controlled trial). At this point, a drug can be approved for community use.
- Phase IV monitors a new treatment in the community, often to evaluate longterm safety and effectiveness. [Glossary of Terms in The Cochrane Collaboration]
A trial can be of a combination phase (e.g., I/II).
The concept of phase is not applicable to trials studying certain interventions (e.g., device, procedure, behavioral)
Simona
Phase 0
A Phase 0 trial is an exploratory trial involving very limited human exposure, with no therapeutic or diagnostic intent (e.g., screening study, microdose study). [http://prsinfo.clinicaltrials.gov/definitions.html]
Simona
Phase 1
A Phase I trial assesses toxic effects on humans (not many people participate, and usually without controls) [Glossary of Terms in The Cochrane Collaboration]
Simona
Phase 2
A Phase ll trial assesses therapeutic benefit (usually involving a few hundred people, usually with controls, but not always) [Glossary of Terms in The Cochrane Collaboration]
Simona
Phase 3
A Phase III trial compares the new treatment against standard (or placebo) treatment (usually a full
randomised controlled trial). At this point, a drug can be approved for community use. [Glossary of Terms in The Cochrane Collaboration]
Simona
Phase 4
A Phase IV study monitors a new treatment in the community, often to evaluate longterm safety and effectiveness. [Glossary of Terms in The Cochrane Collaboration]
Simona
Single group study
A single group study is an interventional study that has only a single allocation group and no contemporaneuos comparison group.
A study in which an individual acts has his/her own comparison does not fall into this category, since an individual is not a group.
Simona
Simona: to be reviewed
Patent
A document describing the exclusive right granted by a government to an inventor to manufacture, use, or sell an invention for a certain number of years.
Academic Department
Association
A formal organization of people or groups of people around a subject or practice.
Special Libraries Association; Association for Computing Machinery(ACM); American Medical Informatics Association(AMIA)
Center
A place where a particular activity or service is concentrated.
Clinical Organization
Any organization with a significant clinical function as a matter of course and not just through occasional clinical roles
College
A primary academic unit within a University or a free-standing higher education organization without graduate degree programs
College of Arts & Sciences; Ivy Tech Community College
Committee
A group of people organized for a specific purpose (e.g., a reporting or advisory role), often with a charge and for a specific duration
Curriculum Steering Committee; PhD Advisory Committee
Company
A legally-recognized business organization
Consortium
Core Laboratory
A lab providing services such as training, protocols, or access to instruments or software
Department
Division
Extension Unit
A unit devoted primarily to extension activities, whether for outreach or research
Foundation
Funding Organization
A defined class of organizations that fund Grants
Government Agency
Hospital
Institute
An Institute normally has a research focus but may also fulfill instructional or outreach roles
Laboratory
An organizational unit (as opposed to the physical facility) that performs research, provides services, or processes materials
Library
Museum
Private Company
Program
An ongoing academic initiative not formalized with department or division status.
Publisher
Research Organization
Any organization (likely also asserted as another class of Organization) with a primary, ongoing research function, not just through occasional roles
School
Service Providing Lab
A laboratory that provides services
Student Organization
A student organization is an organization, operated by students at a university, whose membership normally consists only of students.
Team
An informal organization brought together for the purposes of a project or event
University
2-sample pooled t-test
'ACME'
The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe.
Average log expression across arrays (ALE)
ALL/AML data set
ANCOVA
The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR
'ANOVA'
ANNOVA
AP-MS data
ARACNE algorithm
ARR
AWS algorithm
Binning clustering method
BED file
BGL
BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering
Iterative Bayesian Model Averaging (BMA)
Base-Pair-Distance Kernel
BPMAP
BaldiLongT
Bayesian Model
CBS
The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm.
CBS algorithm
CDF
CEL
CHP file
CLR algorithm
CMA
CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting)
CRLMM algorithm
This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance.
Continuous Wavelet Transform (CWT)-based peak detection algorithm
Category analysis
PCMG
PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex.
Chi-square
distance calculation objective
BCRANK
BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list.
Cosmo
cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture
F test
Non-linear functional regression model
non-linear functional regression model with both additive and multiplicative error terms
Complex Estimation Algorithm
Discriminant Fuzzy Pattern Algorithm
A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High'
DFW
digital gene expression (DGE) datasets
Expectation-Maximization(EM) algorithm
Empirical Bayes rule
FACS ( fluorescence-activated cell sorter)
FACS data
FARMS
FASTA
FC
FCS
'FDR'
Fixed effect model
Firth's bias reduction procedure
Fischer's Exact Test
FoxDimmicT
GASSCO method
GEO data type
GEO Matrix Series file
Gamma Gamma Model
Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)
Gene Recommender algorithm
Gamma-Gamma hierarchical model
Gaussian locally weighted regression
Gene-Set Enrichment Analysis
Hexagon binning algorithm
Heterogeneous Error Model (HEM)
Hubert’s gamma
Hidden Markov Model
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
Hidden Variable Dynamic Modelling HVDM)
Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets.
HaarSeg algorithm
Hardy-Weinberg equilibrium
Hypergeometric probability
Iteratively ReWeighted Least Squares
ILLUMINA data
Jaccard’s index
KGML file
'KLD'
Kolmogorov Smirnov rank-sum based algorithm
KS measures how biased the ranks of a subset of items are among the ranks of the entire set
LC-MS data
Locally Moderated Weighted-t (LMW) method
Lognormal Normal Model
Lognormal Normal with Modied Variance Model
Langmuir Isotherm
Laplace mixture model
Library Search Algorithm
Loess algorithm
Logic regression
Median Average Difference Algorithm
MAGE-ML files
MAQC data
MATLAB language
Multivariate correlation estimator
Markov Chain Monte Carlo
MCR algorithm
minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples.
'MI'
mutual information matrix (MIM)
MMD
MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes),
Mahalanobis distance
Misclassification-Penalized Posteriors (MiPP)
Mixed model equations
'Needleman-Wunsch'
Nested Effects Models
This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing
Nonlinear Estimation by Iterative Partial Least Squares
Presence-Absence calls with Negative Probesets (PANP)
Pearson correlation estimator
'PLM'
it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis
Probe level Locally moderated Weighted median-t (PLW) method
PPC algorithm
Propagation of uncertainty in microarray analysis
Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions
Power Law Global Error Model (PLGEM) analysis method
PLIER (Probe Logarithmic Error Intensity Estimate) method
Radial basis function
R interface to boost graph library algorithm (RBGL)
Random effects model
Recursive Feature Elimination (RFE)
for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC)
Regression model
RMA
RMA+
RMA++
Rnw
Robust likelihood-based survival modeling
S-Score algorithm
Serial Analysis of Gene Expression (SAGE)
SAM
Note: It is unclear from just the label what is meant by a SAM algorithm. It may or may not be related to the SAM sequence alignment software described by the class SWO_0000077 (Allyson Lister)
SBMLR file
SBML model
SDF format
SNPRMA algorithm
Semantic Similarity Measures
SVDimpute algorithm
50-50 MANOVA algorithm
Classical multivariate analysis-of-variance tests perform poorly in cases with several highly correlated responses and the tests collapse when the number of responses exceeds the number of observations. This paper presents a new method which handles this problem. The dimensionality of the data is reduced by using principal component decompositions and the final tests are still based on the classical test statistics and their distributions. The methodology is illustrated with an example from the production of sausages with responses from near infrared reflectance spectroscopy. A closely related method for testing relationships in uniresponse regression with collinear explanatory variables is also presented. The new test, which is called the 50-50 F-test, uses the first k components to calculate SSMODEL. The next d components are not involved in SSERROR and they are called buffer components.
Langsrud, Ø. (2002), 50-50 Multivariate Analysis of Variance for Collinear Responses, The Statistician, 51, 305-317.
gene list
clustered data set
R data frame
R language
Signaling Pathway Impact Analysis (SPIA) algorithm
Similarity score
'Smith-Waterman'
Theodore Ts’o’s
Variance-stabilizing transformation (VST) algorithm
WilcEbam
Wilcoxon
Xba.CQV and Xba.regions
data annotation objective
annotation data packages
Associative T method
AvgNRRs
Bootstrap
cdt
chamber slide format
cls
Categorical (e.g tumor vs normal) class file format
http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29
Concordance
covdesc file
database creation objective
An objective in which the aim is to create a new database instance.
James Malone
PERSON: James Malone
cross validation objective
.data
dcf
design file
Dynamic programming algorithm
f-test
gct
Gene Cluster Text file format
http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29
Gene array analysis algorithm
gene expression analysis objective
gene expression dataset
gff format
Global test
global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments.
gmt format
gpr format
gtr
gxl format
Hierarchical clustering
Hypergeometric enrichment
image
Data containing moving pictures st
Iterative local regression and model selection
k-cores
k-means
k-nearest neighbour classification
Likelihood method
Linear modelling
lma
Local-pooled-error
log file
logicFS dataset
Logit-t algorithm
'MAS5'
mas5 format
M-estimation regression
meta data
microarray data
mrnet algorithm
Multinomial probit regression with Gaussian Process priors
Multiple testing
multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included.
Multivariate t mixture models
Negative binomial distribution
Neural networks models
newick
OMICS data
pair file
pedigree data file
Position weight matrix (PWM )
qPCR data
Quantile normalization
Quantile regression techniques
Rank-invariant set normalization
Rank product non-parametric method
.raw files
rda
.rma format
Sim method
sproc
sqlite
Statistical tests
Paired t-test , Paired L-statistic and Paired Lw-statistic with their FDRs
't-test'
Two-stage measurement error model
data rendering and visualization objective
Tweaked label. From 'data visualization objective' to 'data rendering and visualization objective'. Need to decide if we should separate rendering from visualization.
AMDIS
software license
Racket
Racket is a Scheme-based language interpreter and programming environment
Java
Spreadsheet
A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered.
XLS spreadsheet
A spreadsheet data format designed for Microsoft Excel.
XML spreadsheet
A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity.
Matlab m file
XML
Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C.
RDF
http://www.w3.org/TR/REC-rdf-syntax/
The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web.
RDF-XML
A serialisation of RDF into an XML format.
Image format
DWG
http://en.wikipedia.org/wiki/.dwg
DWG ("drawing") is a binary file format used for storing two and three dimensional design data and metadata
DXF
http://en.wikipedia.org/wiki/AutoCAD_DXF
DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs.
BMP
http://www.fileformat.info/format/bmp/egff.htm
The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter).
CGM
Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632.
http://en.wikipedia.org/wiki/Computer_Graphics_Metafile
Web page specification
Document exchange format
pdf
Portable Document Format
PDF is an open standard for document exchange.
TIFF
Tagged Image File Format
TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry.
JPEG
JPEG is a lossy file format for storing images
JPG
PNG
Portable Network Graphics
PNG is a bitmapped image format and video codec that employs lossless data compression.
GIF
The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia]
Graphics Interchange Format
Raster image format
A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel.
Vector image format
A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering.
SVG
Scalable Vector Graphics
AI
Adobe Illustrator format
PostScript
PostScript is a format used for describing documents.
tex
LaTeX format
tex is a format for documents written in the document markup language and document preparation system LaTeX.
Outline document format
A format specification for data used or produced by outliner software
OmniOutline format
A proprietary format for documents created and edited using OmniOutliner outliner software,
OPML
OPML (Outline Processor Markup Language) is an XML format for outlines
Outline Processor Markup Language
JPEG 2000
JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia]
Word processing document format
WordStar format
Microsoft Word doc
A file format for word processing documents for Microsoft Word.
Programming language format
.java file
James Malone
A source code file format which is specified to be used with the Java programming language.
.class file
A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine.
James Malone
CopasiML
.cps
An XML-based file format for use with the COPASI software.
SBML file
Systems Biology Markup Language
Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time.
http://sbml.org
OWL-XML
The Web Ontology Language (OWL) in XML serialization
OWL2-XML
Web Ontology Language version 2 in XML Serialization
OBO Flat File Format
OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies.
Text file format
ASCII format
Plain text file format
MAGE tab format
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files.
http://www.mged.org/mage-tab/
Tab delimited file format
PSI-MI format
Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012.
The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools.
PSI-MIF
SIF
http://wiki.cytoscape.org/GettingStarted and http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats, accessed 20 June 2012
SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces).
GML
GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages
http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012
XGMML
http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012
XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML.
BioPAX RDF/XML format
BioPAX Manchester OWL Syntax format
Creative Commons
Proprietary commercial software license
Mozilla Public License Version 1.1
GNU General Public License
Apache license v2
Academic License version 3
FreeBSD License
2 clause BSD License
Open source software license
License without restrictions on derivatives
MIT License
Lesser GNU Public License
The Artistic License 1.0
Eclipse Public License
Modified BSD License
3 clause BSD License
Latex Project Public License
Open Public License
http://wyatterp.com/opl.html
Mozilla Public License
annotation editing objective
entity
continuant
Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
dependent_continuant
Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.
disposition
Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
fiat_object_part
Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
function
Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
generically_dependent_continuant
Examples: a certain PDF file that exists in different and in several hard drives
independent_continuant
Synonyms: substantial entity
material_entity
Examples: collection of random bacteria, a chair, dorsal surface of the body
object
Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
object_aggregate
Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
object_boundary
Synonyms: substance boundary
one_dimensional_region
Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space
quality
Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
realizable_entity
Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity
role
Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university
site
Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
spatial_region
Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
specifically_dependent_continuant
Synonyms: property, trope, mode
three_dimensional_region
Examples: a cube-shaped part of space, a sphere-shaped part of space
two_dimensional_region
Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space
zero_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with no dimensions.
connected_spatiotemporal_region
Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus
connected_temporal_region
Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis
fiat_process_part
Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
occurrent
Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
process
Examples: the life of an organism, the process of sleeping, the process of cell-division
process_aggregate
Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
process_boundary
Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery
processual_context
Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.
processual_entity
Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird
scattered_spatiotemporal_region
Definition: A space time region [span:SpaceTimeRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
scattered_temporal_region
Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
spatiotemporal_instant
Examples: the space time region occupied by a single instantaneous temporal slice (part) of a process
spatiotemporal_interval
Definition: A connected space time region [span:ConnectedSpaceTimeRegion] that endures for more than a single moment of time.
spatiotemporal_region
Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
temporal_instant
Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death
temporal_interval
Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
temporal_region
Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
DeprecatedClass
DeprecatedClass
The class of deprecated classes.
agent
An agent
PERSON: Scott Hoffmann
Things that do stuff.
agent
group
A collection of individual agents.
A group
PERSON: Scott Hoffmann
group
organization
A kind of Agent corresponding to social instititutions such as companies, societies etc.
An organization
PERSON: Scott Hoffmann
organization
person
A person
An instance of a human being (Homo sapiens)
PERSON: Melissa Haendel
person
biosafety level 1
biosafety level 2
biosafety level 3
biosafety level 4
example to be eventually removed
failed exploratory term
Person:Alan Ruttenberg
The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
core
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
Alan Ruttenberg
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
defined class
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
Alan Ruttenberg
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
Alan Ruttenberg
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Alan Ruttenberg
Terms with this status should eventually replaced with a term from another ontology.
group:OBI
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI