This file is based on checkout of our SVN repository revision $Revision: 135 $
Jie Zheng
Chris Stoeckert
Elisabetta Manduchi
The ontology is built based on OBI Release 2013-10-25 (http://purl.obolibrary.org/obo/obi/2013-10-25/obi.owl)
Versions of ontologies used by BCGO
ChEBI: version 108
CL: 2013-10-15
CLO: 2013-11-06
GO: 2013-12-11
NCBITaxon: 2013-01-24
PATO: 2013-10-10
PR: 38.0. (date: 14:10:2013 12:13)
SO: May 11 15:18:44 PDT 2004. version: $Revision: 1.45 (14:04:2011 13:58)
UBERON: 2014-01-23
UO: 2013-06-27
EFO: version 2.36 (15th May 2013)
phalanx number
different_in_magnitude_relative_to
different_in_magnitude_relative_to
different_in_magnitude_relative_to
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
Description
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.
spatially_disjoint_from
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
database_cross_reference
database_cross_reference
curator note
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
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
preceding element is
has_obo_namespace
has_obo_namespace
subset_property
subset_property
pharyngeal arch number
Attribute slim
present_in_taxon
cell_quality
has_exact_synonym
has_exact_synonym
IEDB alternative term
An alternative term used by the IEDB.
IEDB
IEDB alternative term
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
axiom id
increased_in_magnitude_relative_to
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
derives from
sexually_homologous_to
homologous_to
has_narrow_synonym
has_narrow_synonym
is count of
has_broad_synonym
has_broad_synonym
Relational slim: types of quality that require an additional entity in order to exist
external_definition
never_in_taxon
abstract upper-level terms not directly useful for analysis
shorthand
shorthand
in_subset
in_subset
Scalar slim
has_specified_input
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
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
has_specified_input
see is_input_of example_of_usage
definition
textual definition
textual definition
definition
definition
definition
textual 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
definition
expand expression to
expand expression to
editor note
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
has curation status
has curation status
OBI_0000281
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
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_specified_output
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
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
has_specified_output
term 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 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
term editor
ray number
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
expand assertion to
has_alternative_id
has_alternative_id
taxon_notes
Source
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.
implements_design_pattern
has_relational_adjective
editor preferred label
editor preferred term
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 label
editor preferred term
example of usage
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 of usage
external_comment
axiom_lost_from_external_ontology
homology_notes
ISA alternative term
Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA alternative term
Person: Philippe Rocca-Serra
Person: Alejandra Gonzalez-Beltran
ISA tools project (http://isa-tools.org)
An alternative term used by the ISA tools project (http://isa-tools.org).
Disposition slim
Abnormal/normal slim
label
has_related_synonym
has_related_synonym
dubious_for_taxon
imported from
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
Value slim
Pathology slim
has_genetic_background_of
strain a has genetic backgroud as strain b is that strain a is derived from strain b and genetic make-up (all its alleles at all loci) of strain a is same to strain b except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. For example, the genetic background of the mutant strains NOD.129S7(B6)-Rag1tm1Mom/J (003729) and NOD.Cg-Rag1tm1Mom Prf1tm1Sdz/SzJ (004848) is NOD.
Person: Jie Zheng
produces_low_amount
Person: Jie Zheng
a produces b if some process that occurs_in a has_output b and amount of b is low relative to normal cases, where a and b are material entities. Examples: defective beta ccell line produces less amount of insulin
produces_high_amount
a produces b if some process that occurs_in a has_output b and amount of b is high relative to generally cases, where a and b are material entities.
Person: Jie Zheng
not_produce
Person: Jie Zheng
a produces_no b if some process that occurs_in a and has_no_output b, where a and b are material entities.
is part of
part of
part_of
domain of part of
has part
has_part
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
realized by
realized_by
realizes
participates in
participates_in
has participant
has_participant
is concretized as
concretizes
is immediately preceded by
immediately preceded by
immediately_preceded_by
immediately precedes
immediately_precedes
is preceded by
preceded by
preceded_by
precedes
is course of
course of
course_of
has course
has_course
occurs in
occurs_in
has site of
has_site_of
begins to exist during
begins_to_exist_during
ceases to exist during
ceases_to_exist_during
s depends on
s_depends_on
has granular part
has_granular_part
has granular process part
has_granular_process_part
is granular part of
granular part of
granular_part_of
is granular part of process
granular part of process
granular_part_of_process
is aggregate of
aggregate of
aggregate_of
is fiat part of
fiat part of
fiat_part_of
has participant beginning to exist
has_participant_beginning_to_exist
has participant ceasing to exist
has_participant_ceasing_to_exist
is function of
function of
function_of
is quality of
quality of
quality_of
is role of
role of
role_of
is located in
located in
located_in
is located at
located at
located_at
g depends on
g_depends_on
has function
has_function
has quality
has_quality
has role
has_role
has measurement unit label
A relation between a value specification and its unit of measurement.
has measurement unit label
is about
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
is about
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
denotes
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
person:Alan Ruttenberg
is quality measurement of
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
Alan Ruttenberg
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
is quality measurement of
m is a quality measurement of q at t when
q is a quality
there is a measurement process p that has specified output m, a measurement datum, that is about q
is duration of
Person:Alan Ruttenberg
is duration of
relates a process to a time-measurement-datum that represents the duration of the process
is_supported_by_data
Philly 2011 workshop
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
is_supported_by_data
OBI
OBI
has_specified_input
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
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
has_specified_input
see is_input_of example_of_usage
has_specified_output
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
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
has_specified_output
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
is_specified_output_of
PERSON:Bjoern Peters
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
is_specified_output_of
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.
achieves_planned_objective
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
supplies
A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
GROUP: Relations branch
supplies
has_supplier
A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
PERSON: Alan Rutternberg
PERSON: Cristian Cocos
PERSON: Frank Gibson
PERSON: Melanie Courtot
has_supplier
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.
objective_achieved_by
OBI
OBI
has value specification
has value specification
PERSON: James A. Overton
OBI
A relation between an information content entity and a value specification that specifies its value.
derives from
has_plasma_membrane_part
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
has_plasma_membrane_part
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
develops_from
RO:0002202
develops_from
develops into
capable_of
A relation between a material entity (such as a cell) and a process. This is a shortcut relation, translation rule for which is: capable_of P <-> bearer_of (some realized_by only P). Example: osteoclast capable of bone resorption.
http://purl.obolibrary.org/obo/BFO_0000053 some (http://purl.obolibrary.org/obo/BFO_0000054 only ?Y)
produces
Melissa Haendel
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
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
translates_to
Example: codon translates_to amino_acid.
Inverse of translation _of.
Wed Aug 19 00:11:53 PDT 2009
kareneilbeck
translation_of
Example: Polypeptide translation_of CDS.
Wed Aug 19 00:09:59 PDT 2009
X is translation of Y if X is translated by ribosome to create Y.
kareneilbeck
has_high_plasma_membrane_amount
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
has_low_plasma_membrane_amount
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
lacks_part
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
lacks_plasma_membrane_part
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
different_in_magnitude_relative_to
different_in_magnitude_relative_to
different_in_magnitude_relative_to
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
has_cross_section
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
has_cross_section
quality
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
increased_in_magnitude_relative_to
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
immediate_transformation_of
direct_transformation_of
http://semanticscience.org/resource/SIO_000658
immediate_transformation_of
immediately transforms from
has specified value
OBI
A relation between a value specification and a number that quantifies it.
PERSON: James A. Overton
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
mouse strain
Mus musculus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism.
Person: Jie Zheng
rat strain
Person: Jie Zheng
Rattus norvegicus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism.
insulin expressing cell
a cell that expresses a gene for insulin.
sequence feature quantification
UPenn Group
Person: Chris Stoeckert, Jie Zheng, Elisabetta Manduchi
A data transformation that attaches quantified values to specific sequence features, e.g. transcript, exon, etc.
high throughput sequence alignment
EFO_0004917 high throughput sequence alignment protocol
a data transformation that aligns sequencing reads to reference sequence.
Person: Chris Stoeckert, Jie Zheng
STOCK Tg(Ins1-EGFP/GH1)14Hara/Mmmh mouse strain
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=438
Person: Jie Zheng, Chris Stoeckert
A mouse strain generated from CD1 and Charles River mouse strains with enhanced green flourescent protein transgene driven by mouse insulin promoter. Genetic background of the strain is CD1. This mouse strain is generally used in development, endocrine deficiency and human disease research.
C57BL/6J mouse strain
A mouse strain that is a laboratory mouse generated from long inbreeding with nearly identical genotype. C57BL/6 mouse has a dark brown, nearly black coat, and an easily irritable temperament. It has a good reproductive performance and is the most widely used "genetic background" for genetically modified mice for use as models of human disease.
black 6
C57
http://en.wikipedia.org/wiki/C57BL/6
Person:Jie Zheng
C57 black 6
functional beta cell like cell
A cell that has all features and genetic signatures as functional beta cell. It may not be part of pancreas.
STOCK Sox17tm2(EGFP/cre)Mgn/Mmnc mouse strain
RES1681 mouse strain
Person: Jie Zheng, Chris Stoeckert
Sox17(GFPCre)Mgn mouse strain
Sox17tm1.3(Cre.GFP)Mgn mouse strain
A mouse strain that was generated by using a novel tag-and-exchange (RMCE) strategy to insert a Cre-GFP (Green fluorescent protein) fusion protein into a Sox17[LCA] allele thereby replacing Sox17 coding sequences. The Sox17-CreGFP mice may be used to track Sox17-expressing cells and their early progeny, or to conditionally inactivate genes in Sox17-expressing cells.
http://www.betacell.org/resource/view/resource_id/1681/
http://www.dkcoin.org/resources/view/id/2096/
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=36463
B6.129S6-Pdx1tm2Mgn/Mmnc mouse strain
Person: Jie Zheng, Chris Stoeckert
RES1301 mouse strain
A mouse strain contains a cyan fluorescent protein (CFP, Cerulean), tagged with 3 copies of an SV40 NLS knocked into the endogenous Pdx1 gene. This mouse strain enables prepancreatic endoderm to be easily identified in the developing mouse embryo and the isolation of Pdx1(+) cells by FACS.
http://www.betacell.org/resource/view/resource_id/1301/
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=36462
Pdx1(CFP)Mgn mouse strain
Pdx1CFP mouse strain
STOCK Ptf1atm1.1Mgn/Mmmh mouse strain
Ptf1atm1Mgn mouse strain
http://www.betacell.org/resource/view/resource_id/236/
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=29175
A mouse strain contains a yellow fluorescent protein (YFP), knocked into the endogenous ptf1a gene. This mouse strain may be used to visualize YFP expression from the ptf1a allele. Ptf1a is expressed in pancreatic buds beginning at E9.5 and plays a vital role in the growth and lineage specification of pancreatic multipotent progenitor cells (MPCs). Ptf1a is also expressed in the neuronal precursors of the cerebellum, spinal cord, and retina where it also performs fate determining roles.
ptf1aYFP mouse strain
RES236 mouse strain
Person: Jie Zheng, Chris Stoeckert
B6.129S-Neurog3tm1(EGFP)Khk/Mmcd mouse strain
http://www.betacell.org/resource/view/resource_id/176/
A mouse strain with targeted mutation at the Neurogenin 3 locus where EGFP replaces entire coding region of Neurogenin3. The basic phenotype is EGFP expression in developing endocrine cells of pancreas and in glandular regions of the stomach.
ngn3-EGFP mouse strain
RES176 mouse strain
Person: Jie Zheng
Insm1tm2Mgn mouse strain
RES661 mouse strain
Person: Jie Zheng, Chris Stoeckert
http://www.betacell.org/resource/view/resource_id/661/
http://www.betacell.org/resource/view/resource_id/661/ provide the definition of 'Insm1tm1.1Mgn mouse strain' which might be the early version of 'Insm1tm2Mgn mouse strain'. However, we are not clear the difference between two strains. We borrowed the definition of 'Insm1tm1.1Mgn mouse strain'. In the webpage, it has strain name 'Mouse Strain RES661' and common name 'lnsm1GFP.Cre mouse strain'. We added 'lnsm1GFP.Cre mouse strain' as alternative term which is true to 'Insm1tm2Mgn mouse strain' too .
A mouse strain contains a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of the Insm1 gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice.
Insm1GFP.Cre mouse strain
STOCK Tg(Tnpo1-EGFP)6729Hara/Mmmh mouse strain
http://www.betacell.org/resource/view/resource_id/188/
RES188 mouse strain
Person: Jie Zheng
MIP-GFP mouse strain
A mouse strain which is hemizygous and shows expression of EGFP in beta lineage cells of the pancreas.
129X1/SvJ mouse strain
A mouse strain that is a laboratory mouse generated from inbreeding. It has white-bellied, pink-eyed, light chinchilla (off-white) or albino or white-bellied, pink-eyed, light chinchilla (light tan). It has a good reproductive performance and is widely used in the production of targeted mutations due to the availability of multiple embryonic stem cell lines derived from them.
Person:Jie Zheng
http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
http://jaxmice.jax.org/strain/000691.html
129X1
129/SvJ
C3H mouse strain
A mouse strain that Inbred from F130 to F170 depending on substrain original generated from a cross of a Bagg albino female and a DBA male by Strong in 1920. It has Agouti coat color. Most substrains have a good reproductive performance. It is widely used in a wide variety of research areas including cancer, immunology and inflammation, sensorineural, and cardiovascular biology.
Person:Jie Zheng
http://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml
http://www.criver.com/EN-US/PRODSERV/BYTYPE/RESMODOVER/RESMOD/Pages/C3HMouse.aspx
black swiss mouse strain
Person: Jie Zheng
Sox17-expressing definitive endodermal cell
Person: Chris Stoeckert, Jie Zheng
Chris Stoeckert
Sox17 expressing cell from the embryo body proper
an endodermal cell that is part of the definitive endoderm and expresses a gene for SOX-17
Sox17-expressing Epcam+ pancreatic epithelial cell
an epithelial cell that is part of the ventral pancreatic bud, expresses a gene for SOX-17 and has Epcam in the plasma membrane.
Person: Chris Stoeckert, Jie Zheng
Sox17 expressing cell in ventral pancreatic bud
Chris Stoeckert
Pdx1-expressing foregut endodermal cell
Pdx1-expressing endoderm cell
an endodermal cell that is part of the foregut endoderm and expresses the gene for pancreas/duodenum homeobox protein 1
Person: Chris Stoeckert, Jie Zheng
Chris Stoeckert
Ptf1a-expressing multipotent pancreatic cell
Chris Stoeckert
Person: Chris Stoeckert, Jie Zheng
a non-terminally differentiated cell that is part of the pancreatic bud, participates in pancreas development and expresses the gene for pancreas transcription factor 1 subunit alpha.
Ptf1a-expressing cell
Ptf1a-lacking pancreatic progenitor cell
Ptf1a-null cell
Chris Stoeckert
a non-terminally differentiated cell that is part of the pancreatic bud but lacks pancreas transcription factor 1 subunit alpha.
Person: Chris Stoeckert, Jie Zheng
neurogenin-3-expressing endocrine progenitor cell
Chris Stoeckert
Ngn3-expressing cell
a non-terminally differentiated cell that participates in endocrine pancreas developement and expresses the gene for neurogenin-3.
Person: Chris Stoeckert, Jie Zheng
neurogenin-3-lacking pancreatic progenitor cell
Chris Stoeckert
a non-terminally differentiated cell that is part of the pancreas, participates in pancreas development and lacks neurogenin-3.
Ngn3-null cell
Person: Chris Stoeckert, Jie Zheng
Insm1-expressing endocrine progenitor cell
Chris Stoeckert
a non-terminally differentiated cell that participates in endocrine pancreas development and expresses a gene for insulinoma-associated protein 1
Person: Chris Stoeckert, Jie Zheng
Insm1 expressing pancreatic endocrine cell
Insm1-lacking endocrine progenitor cell
Chris Stoeckert
a non-terminally differentiated cell that is part of the endocrine pancreas and lacks insulinoma-associated protein 1
Person: Chris Stoeckert, Jie Zheng
Non-functional Insm1 expressing pancreatic endocrine cell
insulin-expressing immature beta cell
Chris Stoeckert
a type B pancreatic cell that is immature and expresses a gene for insulin
Person: Chris Stoeckert, Jie Zheng
insulin-expressing nascent beta cells
insulin-expressing mature beta cell
a type B pancreatic cell that is mature and expresses a gene for insulin
Chris Stoeckert
insulin-expressing mature beta cells
Person: Chris Stoeckert, Jie Zheng
Insm1-expressing Pdx1 high-positive pancreatic endocrine progenitor cell
A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a high level.
Person: Jie Zheng, Chris Stoeckert
Insm1-expressing Pdx1 low-positive pancreatic endocrine progenitor cell
Person: Jie Zheng, Chris Stoeckert
A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a low level.
Insm1tm2(GFP.Cre)Mgn/Pdx1tm2(CFP)Mgn mouse strain
A mouse strain that is the result of mating between a Insm1GFPCre/+ mouse and a Pdx1CFP/+ mouse both on a CD-1 background
Person: Chris Stoeckert, Anna Osipovich
differential expression software
GBCO
A software implementing a higher level analysis protocol of type differential expresssion.
B6.Cg-Tg(Ins1-EGFP)1Hara/J mouse strain
A mouse strain that is genetically modified expressing Enhanced Green Fluorescent Protein (EGFP) under the control of the mouse insulin 1 promoter. Fluorescence is detected in tissues where insulin I is normally expressed; fluorescent protein expression in pancreatic beta-cells is evident from embryonic day (E)13.5 through adulthood. The fluorescence expression pattern is similar to the patterns seen in two other strains STOCK Tg(Ins1-Cerulean)24Hara/J and STOCK Tg(Ins1-DsRed*T4)32Hara/J. This mutant mouse strain exhits normal glucose tolerance and pancreatic insulin levels and may be useful in studies of diabetes and pancreatic beta islet cell biology.
Person: Jie Zheng
http://jaxmice.jax.org/strain/006864.html
entity
entity
continuant
An 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.
a heart
a person
a symphony orchestra
continuant
endurant
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
a surgical operation as processual context for a nosocomical infection
occurrent
perdurant
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a heart
a leg
a person
a symphony orchestra
an organism
independent continuant
substantial entity
the bottom right portion of a human torso
the lawn and atmosphere in front of our building
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
dependent continuant
process
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
process
the life of an organism
the process of cell-division
the process of sleeping
temporal region
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].
An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
An occurrent that is part of time.
Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
temporal region
the duration of a surgical procedure
the moment of death
the time it takes to run a marathon
disposition
A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C.
disposition
the disposition of a patient with a weakened immune system to contract disease
the disposition of a vase to brake if dropped
the disposition of blood to coagulate
the disposition of metal to conduct electricity
the disposition of vegetables to decay when not refrigerated
realizable entity
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
realizable entity
the disposition of blood to coagulate
the disposition of metal to conduct electricity
the function of the reproductive organs
the role of being a doctor
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
quality
the ambient temperature of air
the circumference of a waist
the color of a tomato
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
mode
property
specifically dependent continuant
the color of a tomato
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the mass of a cloud
the role of being a doctor
the smell of mozzarella
trope
temporal instant
A connected temporal region comprising a single moment of time.
right now
temporal instant
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death
connected temporal region
A temporal region every point of which is mediately or immediately connected with every other point of which.
connected temporal region
the 1970s years
the time from the beginning to the end of a heart attack
the time taken up by cellular meiosis
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
the role of a biological grandfather as legal guardian in the context of a system of laws
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 person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
object boundary
An independent continuant that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object entities that exist at exactly the point where the object is separated off from the rest of the existing entities in the world.
Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
object boundary
substance boundary
the outer surface of a cell or cell wall
the surface of the earth
the surface of the interior of the stomach
the surface of the skin
site
An independent continuant consisting of a characteristic spatial shape in relation to some arrangement of other continuant entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site entities are entities that can be occupied by other continuant entities.
An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are sites) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
Maria's nostril or her intestines for a variety of bacteria
a particular room in a particular hospital
site
generically dependent continuant
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
a certain PDF file that exists in different and in several hard drives
generically dependent continuant
scattered temporal region
A temporal region every point of which is not mediately or immediately connected with every other point of which.
scattered temporal region
the time occupied by the individual games of the World Cup
the time occupied by the individual liaisons in a romantic affair
function
A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
function
the digestive function of the stomach to nutriate the body
the function of a birth canal to enable transport
the function of a computer program to compute mathematical equations
the function of a hammer to drive in nails
the function of a judge in a court of law
the function of an automobile to provide transportation
the function of reproduction in the transmission of genetic material
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
process boundary
A processual entity that is the fiat or bona fide instantaneous temporal process boundary.
birth
death
process boundary
the detaching of a finger in an industrial accident
the final separation of two cells at the end of cell-division
the forming of a synapse
the incision at the beginning of a surgery
the onset of REM sleep
temporal interval
A connected temporal region lasting for more than a single moment of time.
any continuous temporal duration during which a process occurs
temporal interval
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
material entity
lymphoblastoid cell line
lymphoblastoid cell line
embryonic stem cell line
embryonic stem cell line
CCE cell
CCE cell
gross anatomical part
Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
gross anatomical part
biotin
An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.
biotin
polynucleotide
A nucleobase-containing molecular entity with an oligomeric structure comprised of a linear sequence of 13 or more nucleotide residues.
polynucleotide
peptide
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
peptide
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acid
hydrogensulfite
A sulfur oxoanion that has formula HO3S.
hydrogensulfite
polysaccharide
A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
polysaccharide
2'-deoxyribonucleoside
2'-deoxyribonucleoside
pyrimidine 2'-deoxyribonucleoside
pyrimidine 2'-deoxyribonucleoside
N-glycosyl compound
A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond.
N-glycosyl compound
benzopyrrole
benzopyrrole
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
deoxyribonucleoside
deoxyribonucleoside
chemical entity
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
organic heterocyclic compound
A cyclic compound having as ring members atoms of carbon and at least of one other element.
organic heterocyclic compound
hydroxides
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
hydroxides
indoles
Any compound containing an indole skeleton.
indoles
ion
A molecular entity having a net electric charge.
ion
agarose
A polysaccharide that has formula C24H38O19.
agarose
molecule
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
molecule
organic heteromonocyclic compound
organic heteromonocyclic compound
oxide
An oxide is a chemical compound of oxygen with other chemical elements.
oxide
oxygen molecular entity
oxygen molecular entity
pyrimidine nucleoside
pyrimidine nucleoside
sulfur molecular entity
sulfur molecular entity
oxolanes
Any oxacycle having an oxolane (tetrahydrofuran) skeleton.
oxolanes
organic heterobicyclic compound
organic heterobicyclic compound
phosphorus atom
A pnictogen that has formula P.
phosphorus atom
atom
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
atom
primary amide
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
primary amide
organosulfur compound
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
organosulfur compound
polyatomic anion
An anion consisting of more than one atom.
polyatomic anion
heteroorganic entity
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
heteroorganic entity
chalcogen molecular entity
Any p-block molecular entity containing a chalcogen.
chalcogen molecular entity
main group element atom
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
main group element atom
sulfur oxoacid derivative
sulfur oxoacid derivative
sulfur oxoanion
sulfur oxoanion
organosulfonic acid
An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon.
organosulfonic acid
carboxylic acid
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
carboxylic acid
main group molecular entity
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
main group molecular entity
cyclic compound
Any molecule that consists of a series of atoms joined together to form a ring.
cyclic compound
organic aromatic compound
organic aromatic compound
heteromonocyclic compound
heteromonocyclic compound
heteropolycyclic compound
heteropolycyclic compound
heterobicyclic compound
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
heterobicyclic compound
p-block molecular entity
A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element.
p-block molecular entity
biomacromolecule
A macromolecule formed by a living organism.
biomacromolecule
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
ribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
ribonucleic acid
organic cyclic compound
Any organic molecule that consists of atoms connected in the form of a ring.
organic cyclic compound
heteroarene
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
heteroarene
nucleoside
An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents.
nucleoside
organonitrogen compound
Any heteroorganic entity containing at least one carbon-nitrogen bond.
organonitrogen compound
oxoanion
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
oxoanion
carbon oxoacid
carbon oxoacid
polyatomic entity
Any molecular entity consisting of more than one atom.
polyatomic entity
polyatomic ion
An ion consisting of more than one atom.
polyatomic ion
carbonyl compound
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
carbonyl compound
organochalcogen compound
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
organochalcogen compound
organooxygen compound
An organochalcogen compound containing at least one carbon-oxygen bond.
organooxygen compound
heteroatomic molecular entity
A molecular entity consisting of two or more chemical elements.
heteroatomic molecular entity
carboxamide
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
carboxamide
cyanine dye
Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole.
cyanine dye
phosphorus-32 atom
The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
phosphorus-32 atom
phosphorus-33 atom
The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
phosphorus-33 atom
Cy3 dye
Cy3 dye
Cy5 dye
Cy5 dye
organonitrogen heterocyclic compound
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
organonitrogen heterocyclic compound
oxacycle
Any organic heterocyclic compound containing at least one ring oxygen atom.
oxacycle
organosulfur heterocyclic compound
organosulfur heterocyclic compound
organic heteropentacyclic compound
organic heteropentacyclic compound
organic heteropolycyclic compound
organic heteropolycyclic compound
azabicycloalkane
azabicycloalkane
thiabicycloalkane
thiabicycloalkane
diazines
Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure).
diazines
double-stranded DNA
double-stranded DNA
5-bromo-2'-deoxyuridine
5-bromo-2'-deoxyuridine
A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
organic molecular entity
Any molecular entity that contains carbon.
organic molecular entity
nitrogen molecular entity
nitrogen molecular entity
biotins
Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton.
biotins
Alexa Fluor 532
Alexa Fluor 532
An organosulfonic acid that has formula C34H33N3O11S2.
Alexa Fluor 546
Alexa Fluor 546
An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3.
heterocyclic compound
A cyclic compound having as ring members atoms of at least two different elements.
heterocyclic compound
nucleobase-containing molecular entity
Any compound that has a nucleobase as a part.
nucleobase-containing molecular entity
pyrimidine deoxyribonucleoside
A deoxyribonucleoside containing a pyrimidine base.
pyrimidine deoxyribonucleoside
organic molecule
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
organic molecule
cell line cell
cell line cell
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
immortal cell line cell
immortal cell line cell
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
cell line
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
cell line
immortal stem cell line cell
a cell line that is derived from stem cell
immortal stem cell line cell
immortal neuron cell line cell
a immortal electrically responsive cell line cell that is derived from neuron
immortal neuron cell line cell
immortal animal cell line cell
a immortal eukaryotic cell line that is derived from animal cell
immortal animal cell line cell
immortal hematopoietic cell line cell
a immortal animal cell line that is derived from hematopoietic cell
immortal hematopoietic cell line cell
immortal neural cell line cell
a immortal animal cell line that is derived from neural cell
immortal neural cell line cell
immortal somatic cell line cell
a cell line that is derived from somatic cell
immortal somatic cell line cell
immortal mouse embryo-derived cell line cell
An immortal embryo-derived cell line cell that derives from mouse.
immortal mouse embryo-derived cell line cell
3T3-L1 cell
3T3-L1 cell
Ainv15 cell
Ainv15 cell
BETA-TC-3 cell
BETA-TC-3 cell
CGR8 cell
CGR8 cell
Daudi cell
Daudi cell
H9 cell
H9 cell
JURKAT cell
JURKAT cell
K 562 cell
K 562 cell
PANC-1 cell
PANC-1 cell
Raji cell
Raji cell
SW480 cell
SW480 cell
immortal cell line
A cell line that is expected to be capable of indefinite propagation in an vitro culture.
immortal cell line
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FMA:68646
GO:0005623
KUPO:0000002
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
VHOG:0001533
WBbt:0004017
XAO:0003012
cell
native cell
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
CARO:0000013
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
cell
cell in vivo
cultured cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.
cell
female germ cell
Female germ cell is a germ cell that supports female gamete production.
MA:0000388
VHOG:0001530
cell
ncithesaurus:Egg
oocyte
A female germ cell that has entered meiosis.
BTO:0000964
CALOHA:TS-0711
FBbt:00004886
FMA:18644
WBbt:0006797
cell
oogonium
stem cell
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
CALOHA:TS-2086
FMA:63368
cell
hematopoietic stem cell
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
BTO:0000725
CALOHA:TS-0448
FMA:70337
FMA:86475
HSC
Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.
VHOG:0001485
blood forming stem cell
cell
colony forming unit hematopoietic
hemopoietic stem cell
erythroid progenitor cell
A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).
BFU-E
BTO:0004911
CFU-E
blast forming unit erythroid
burst forming unit erythroid
cell
colony forming unit erythroid
erythroid stem cell
germ line cell
A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
Originally this term had some plant germ line cell children.
cell
monoblast
A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.
CALOHA:TS-1195
CFU-M
FMA:83553
Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.
cell
colony forming unit macrophage
colony forming unit monocyte
monocyte stem cell
multi fate stem cell
A stem cell that can give rise to multiple lineages of cells.
FMA:84789
cell
multi-fate stem cell
multifate stem cell
multipotent cell
multipotent stem cell
common myeloid progenitor
A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1.
BTO:0004730
CFU-GEMM
CFU-S
CMP
CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.
cell
colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
common myeloid precursor
multipotential myeloid stem cell
myeloid stem cell
pluripotent stem cell (bone marrow)
megakaryocyte-erythroid progenitor cell
A progenitor cell committed to the megakaryocyte and erythroid lineages.
CFU-EM
CFU-MegE
MEP
MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.
Meg/E progenitor
cell
colony forming unit erythroid megakaryocyte
megakaryocyte/erythrocyte progenitor
megakaryocyte/erythroid progenitor cell
common lymphoid progenitor
A oligopotent progenitor cell committed to the lymphoid lineage.
CL:0000044
CLP
CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative.
ELP
cell
committed lymphopoietic stem cell
common lymphocyte precursor
common lymphocyte progenitor
common lymphoid precursor
early lymphocyte progenitor
lymphoid stem cell
lymphopoietic stem cell
non-terminally differentiated cell
A precursor cell with a limited number of potential fates.
BTO:0000125
FMA:84782
blast cell
cell
define using PATO mulit-potent or oligopotent?
myoblast
A precursor cell of the myogenic lineage that develops from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes.
BTO:0000222
CALOHA:TS-0650
FBbt:00005083
FMA:70335
VHOG:0001529
cell
fibroblast
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
BTO:0000452
CALOHA:TS-0362
FMA:63877
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
VHOG:0001482
cell
epithelial cell
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
BTO:0000414
CALOHA:TS-2026
CARO:0000077
FBbt:00000124
FMA:66768
WBbt:0003672
cell
epitheliocyte
blood vessel endothelial cell
An endothelial cell that lines the vasculature.
cell
cuboidal endothelial cell of vascular tree
columnar/cuboidal epithelial cell
cell
squamous epithelial cell
CALOHA:TS-1249
cell
blood cell
A cell found predominately in the blood.
FMA:62844
cell
epithelial cell of pancreas
An epithelial cell of the pancreas.
BTO:0000028
cell
pancreatic epithelial cell
pancreas epithelial cell
T cell
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
BTO:0000782
CALOHA:TS-1001
CL:0000804
CL:0000812
FMA:62870
T lymphocyte
T-cell
T-lymphocyte
VHOG:0001479
cell
immature T cell
mature T cell
granulocyte
A leukocyte with abundant granules in the cytoplasm.
BTO:0000539
BTO:0001026
CALOHA:TS-0422
FMA:62854
cell
granular leucocyte
granular leukocyte
polymorphonuclear leukocyte
endothelial cell
An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
BTO:0001176
CALOHA:TS-0278
FMA:66772
From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].
cell
endotheliocyte
neurectodermal cell
Ectoderm destined to be nervous tissue.
cell
neurectoderm cell
mesenchymal cell
A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
BMSC
BTO:0002625
BTO:0003298
CFU-F
CL:0002452
FMA:70546
MSC
Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.
bone marrow stromal cells
cell
colony-forming unit-fibroblast
marrow stromal cells
mesenchymal precursor cell
mesenchymal progenitor cells
mesenchymal stem cell
mesenchymal stromal cell
mesenchymal stromal cells
stem cells, mesenchymal
fat cell
A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
BTO:0000443
CALOHA:TS-0012
CL:0000450
FMA:63880
adipocyte
adipose cell
cell
pigment cell
A pigment cell is a cell that contains pigment granules.
VHOG:0001678
cell
chromatocyte
chromatophore
melanocyte
A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
BTO:0000847
CALOHA:TS-0613
CL:0000572
FMA:70545
VHOG:0001679
cell
melanophore
glandular epithelial cell
A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
CALOHA:TS-2085
FMA:86494
cell
secretory cell
A cell that specializes in controlled release of one or more substances.
BTO:0003659
FMA:86916
cell
exocrine cell
A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
FMA:16014
cell
protein secreting cell
cell
endocrine cell
A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
FMA:83809
cell
endocrinocyte
enteroendocrine cell
An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
BTO:0003865
FMA:62930
cell
peptide hormone secreting cell
cell
insulin secreting cell
BTO:0000783
cell
type B pancreatic cell
A cell that secretes insulin and is located towards the center of the islets of Langerhans.
B-cell of pancreatic islet
BTO:0000783
EV:0200009
FMA:70586
MA:0002419
Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression.
beta cell
beta cell islet
beta cell of pancreatic islet
cell
insulin-secreting cell
ncithesaurus:Beta_Cell
pancreatic B cell
pancreatic B-cell
pancreatic beta cell
pancreatic islet core
type B enteroendocrine cell
glucagon secreting cell
A cell that secretes glucagon.
FMA:84045
cell
glucagon-secreting cell
pancreatic A cell
A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
BTO:0000990
FMA:70585
alpha cell of iselt of Langerhans
cell
pancreatic alpha cell
somatostatin secreting cell
cell
pancreatic D cell
A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
BTO:0000803
D-cell of pancreatic islet
FMA:70587
cell
delta cell of islet
delta cell of pancreatic islet
pancreatic D-cell
pancreatic delta cell
somatostatin-secreting pancreatic cell
metabolising cell
A cell whose primary function is intermediary metabolism.
cell
hepatocyte
BTO:0000575
CALOHA:TS-0454
FMA:14515
Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.
The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
cell
contractile cell
A cell whose primary function is to shorten.
cell
muscle cell
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
BTO:0000888
BTO:0000902
CALOHA:TS-2032
FBbt:00005074
FMA:67328
WBbt:0003675
cell
muscle fiber
myocyte
skeletal muscle cell
A somatic cell located in skeletal muscle.
BTO:0004392
CALOHA:TS-2158
FMA:9727
cell
electrically active cell
A cell whose function is determined by the generation or the reception of an electric signal.
cell
lining cell
A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.
boundary cell
cell
barrier cell
A cell whose primary function is to prevent the transport of stuff across compartments.
cell
motile cell
A cell that moves by its own activities.
cell
ectodermal cell
A cell of the outer of the three germ layers of the embryo.
FMA:72549
cell
ectoderm cell
mesodermal cell
A cell of the middle germ layer of the embryo.
FMA:72554
cell
mesoblast
mesoderm cell
endodermal cell
A cell of the inner of the three germ layers of the embryo.
FMA:72555
cell
endoderm cell
anucleate cell
A cell that lacks a nucleus.
FMA:68647
cell
non-nucleated cell
single nucleate cell
A cell with a single nucleus.
cell
erythrocyte
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
BTO:0000424
CALOHA:TS-0290
FMA:81100
RBC
cell
red blood cell
platelet
A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
BTO:0000132
CALOHA:TS-0803
FMA:62851
Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF.
anucleate thrombocyte
blood platelet
cell
enucleate thrombocyte
B cell
A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
B lymphocyte
B-cell
B-lymphocyte
BTO:0000776
CALOHA:TS-0068
FMA:62869
VHOG:0001480
cell
eukaryotic cell
cell
stuff accumulating cell
A cell that is specialised to accumulate a particular substance(s).
cell
oxygen accumulating cell
cell
migratory neural crest cell
A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
FMA:86667
cell
skeletal muscle stem cell
A multifate stem cell found in skeletal muscle than can differentiate into many different cell types. Distinct cell type from satellite cell.
FMA:86767
cell
electrically responsive cell
A cell whose function is determined by its response to an electric signal.
cell
polyploid cell
A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
cell
endopolyploid cell
cell
white fat cell
CALOHA:TS-1119
FMA:83434
Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole.
cell
white adipocyte
white adipose cell
white fat cell
dendritic cell
A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
BTO:0002042
CALOHA:TS-0194
FMA:83036
cell
interdigitating cell
veiled cell
biogenic amine secreting cell
cell
serotonin secreting cell
5-HT secreting cell
5-Hydroxytryptamine secreting cell
A cell type that secretes 5-Hydroxytryptamine (serotonin).
cell
type D enteroendocrine cell
A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.
D cell
FMA:62935
cell
cardiac muscle myoblast
A precursor cell destined to differentiate into cardiac muscle cell.
CL:0000714
FMA:84797
cell
melanoblast
A cell that originates from the neural crest and differentiates into a pigment cell.
BTO:0003217
Derived from UBERON:0002342 neural crest.
FMA:83377
cell
lymphocyte
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
BTO:0000775
CALOHA:TS-0583
Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)
FMA:62863
VHOG:0001535
cell
proerythroblast
An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
FMA:83518
cell
pronormoblast
rubriblast
animal cell
cell
basophilic erythroblast
A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
FMA:83505
basophilic normoblast
cell
early erythroblast
early normoblast
prorubricyte
polychromatophilic erythroblast
A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
FMA:83506
cell
intermediate erythroblast
intermediate normoblast
polychromatic erythroblast
polychromatic normoblast
polychromatophilic normoblast
rubricyte
orthochromatic erythroblast
FMA:84646
The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
acidophilic erythroblast
cell
eosinophilic erythroblast
late erythoblast
orthochromatic normoblast
pyknotic eto enrythroblast
megakaryocyte progenitor cell
BTO:0001164
CALOHA:TS-0610
CFU-Meg
FMA:84235
Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.
Meg-CFC
MkP
The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
cell
colony-forming unit-megakaryocyte
megacaryoblast
megacaryocyte progenitor cell
megakaryoblast
megakaryocytic progenitor cell
promegacaryocyte
promegakaryocyte
megakaryocyte
A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm.
BTO:0000843
CALOHA:TS-0611
FMA:83555
Megakaryocytes are reportedly CD181-positive and CD182-positive.
cell
megacaryocyte
megalocaryocyte
megalokaryocyte
granulocyte monocyte progenitor cell
A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.
CFU-C , Colony forming unit in culture
CFU-GM
GMP
Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.
cell
colony forming unit granulocyte macrophage
granulocyte-macrophage progenitor
granulocyte/monocyte precursor
granulocyte/monocyte progenitor
reticulocyte
An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
BTO:0001173
CALOHA:TS-0864
cell
promonocyte
A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules.
BTO:0004657
FMA:83551
Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.
cell
angioblastic mesenchymal cell
A mesenchymal stem cell capable of developing into blood vessel endothelium.
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.
angioblast
cell
chondroplast
monocyte
BTO:0000876
CALOHA:TS-0638
FMA:62864
Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
cell
experimentally modified cell in vitro
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12
cell
germ cell
BTO:0000535
The reproductive cell in multicellular organisms.
VHOG:0001534
WBbt:0006796
cell
acinar cell
A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
FMA:83625
acinic cell
acinous cell
cell
natural killer cell
A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
BTO:0000914
BTO:0004716
CALOHA:TS-0664
FMA:63147
FMA:83601
NK cell
VHOG:0001697
cell
large granular lymphocyte
null cell
muscle precursor cell
cell
PP cell
A cell that stores and secretes pancreatic polypeptide hormone.
FMA:62938
FMA:83409
cell
type F enteroendocrine cell
neurecto-epithelial cell
BTO:0004301
Epithelial cells derived from neural plate and neural crest.
FMA:70557
The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).
cell
neuroepithelial cell
somatic stem cell
A stem cell that can give rise to cell types of the body other than those of the germ-line.
CALOHA:TS-2086
FMA:63368
cell
striated muscle cell
BTO:0002916
CALOHA:TS-2157
FMA:86936
Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
cell
leukocyte
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
BTO:0000751
CALOHA:TS-0549
FMA:62852
cell
immune cell
leucocyte
white blood cell
cardiac muscle cell
BTO:0001539
CALOHA:TS-0115
Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
FMA:14067
FMA:83808
This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.
cardiac muscle fiber
cardiac myocyte
cardiocyte
cardiomyocyte
cell
heart muscle cell
myeloid cell
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
BTO:0001441
CALOHA:TS-0647
cell
erythroid lineage cell
A immature or mature cell in the lineage leading to and including erythrocytes.
CALOHA:TS-0290
CL:0002156
FMA:62845
FMA:83516
Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.
cell
erythropoietic cell
erythroblast
A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
BTO:0001571
CALOHA:TS-0289
FMA:83504
cell
normoblast
myeloid leukocyte
A cell of the monocyte, granulocyte, or mast cell lineage.
cell
basophil
Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
BTO:0000129
CALOHA:TS-0073
FMA:62862
Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive.
basophilic leucocyte
basophilic leukocyte
cell
polymorphonuclear leucocyte
polymorphonuclear leukocyte
eosinophil
Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive.
BTO:0000399
CALOHA:TS-0279
Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte.
FMA:62861
cell
eosinocyte
eosinophilic granulocyte
eosinophilic leucocyte
eosinophilic leukocyte
polymorphonuclear leucocyte
polymorphonuclear leukocyte
neutrophil
Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
BTO:0000130
CALOHA:TS-0688
FMA:62860
PMN
cell
neutrocyte
neutrophil leucocyte
neutrophil leukocyte
neutrophilic leucocyte
neutrophilic leukocyte
poly
polymorphonuclear leucocyte
polymorphonuclear leukocyte
polymorphonuclear neutrophil
polynuclear neutrophilic leucocyte
polynuclear neutrophilic leukocyte
pro-NK cell
A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative.
Most markers only described for human pro NK cells.
NKP
cell
natural killer cell progenitor
null cell
preNK cell
pro-natural killer cell
pro-B cell
A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs.
BTO:0003104
Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative.
cell
pre-B cell (Philadelphia nomenclature)
pre-pro B cell
pro-B lymphocyte
pro-B-cell
pro-B-lymphocyte
progenitor B cell
progenitor B lymphocyte
progenitor B-cell
progenitor B-lymphocyte
pro-T cell
A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.
DN1 cell
DN1 thymocyte
TN1 cell
cell
pro-T lymphocyte
progenitor T cell
myeloblast
BTO:0000187
FMA:83524
The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow.
cell
promyelocyte
A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative.
CALOHA:TS-0825
FMA:83530
cell
hematopoietic multipotent progenitor cell
A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
BTO:0000725
CALOHA:TS-0448
MPP
Markers differ between mouse and human.
cell
hemopoietic progenitor cell
lymphoid lineage restricted progenitor cell
A progenitor cell restricted to the lymphoid lineage.
BTO:0004731
CALOHA:TS-2025
FMA:70338
Note that this is a class of cell types, not an identified single cell type.
cell
lymphoid progenitor cell
myeloid lineage restricted progenitor cell
A progenitor cell restricted to the myeloid lineage.
BTO:0004730
CALOHA:TS-2099
FMA:70339
Note that this is a class of cell types, not an identified single cell type.
cell
myeloid progenitor cell
mononuclear cell
A leukocyte with a single non-segmented nucleus in the mature form.
BTO:0000878
CALOHA:TS-0768
FMA:86713
cell
peripheral blood mononuclear cell
lymphocyte of B lineage
A lymphocyte of B lineage is a lymphocyte that expresses CD19 on the cell surface. An additional defining characteristic is the commitment to express an immunoglobulin complex.
Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells).
cell
hematopoietic cell
A cell of a hematopoietic lineage.
BTO:0000574
CALOHA:TS-2017
FMA:70366
FMA:83598
cell
haematopoietic cell
haemopoietic cell
hemopoietic cell
CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor
CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid
Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617).
cell
CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor
Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617).
cell
CD34-positive, CD38-positive common lymphoid progenitor
A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive.
CD10-positive common lymphocyte precursor
CD10-positive common lymphocyte progenitor
CD10-positive common lymphoid precursor
These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617).
cell
CD34-positive, CD38-negative hematopoietic stem cell
CALOHA:TS-0448
CD133-positive hematopoietic stem cell
CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive.
Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617).
FMA:86475
cell
CD34-positive, CD38-positive common myeloid progenitor
A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative.
CD71-positive common myeloid precursor
Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617).
cell
CD7-negative lymphoid progenitor cell
CD7-negative lymphoid precursor
CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative.
These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617).
cell
cell in vitro
'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells.
2012-01-12T09:58:38Z
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
cell
haendel
bone cell
2011-11-16T04:28:16Z
A connective tissue cell found in bone.
adiehl
cell
macrophage dendritic cell progenitor
2010-01-19T02:51:58Z
A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages.
MDP
cell
tmeehan
hematopoietic lineage restricted progenitor cell
2010-01-06T03:43:20Z
A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.
cell
tmeehan
hematopoietic oligopotent progenitor cell
2010-01-06T03:43:27Z
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.
cell
tmeehan
CD34-positive, CD38-negative multipotent progenitor cell
2010-01-12T11:14:15Z
A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative.
Cell markers are associated with human hematopoietic multipotent progenitor cells.
cell
tmeehan
type A enterocrine cell
2010-09-10T10:48:54Z
An enterocrine cell that produces glucagon.
FMA:62939
cell
tmeehan
endo-epithelial cell
2010-06-29T03:38:14Z
An epithelial cell derived from endoderm.
FMA:69075
cell
tmeehan
ecto-epithelial cell
2010-06-29T03:38:22Z
An epithelial cell derived from ectoderm.
FMA:69074
cell
tmeehan
meso-epithelial cell
2010-06-29T03:49:14Z
Epithelial cell derived from mesoderm or mesenchyme.
FMA:69076
cell
epithelial mesenchymal cell
tmeehan
nongranular leukocyte
2010-07-22T11:30:33Z
A leukocyte that lacks granules.
FMA:62855
agranular leukocyte
cell
tmeehan
bone marrow cell
2010-07-22T04:48:15Z
A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells.
BTO:0004850
FMA:83621
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
cell
tmeehan
endothelial cell of vascular tree
2010-08-24T02:06:40Z
An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels.
BTO:0001854
CALOHA:TS-1106
FMA:67755
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
cell
cubodial endothelial cell of vascular tree
tmeehan
vascular endothelial cell
granulocytopoietic cell
2010-08-30T12:54:27Z
A cell involved in the formation of a granulocyte.
FMA:83519
cell
tmeehan
myelocyte
2010-08-30T01:08:19Z
A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses.
BTO:0000734
FMA:83525
cell
tmeehan
monopoietic cell
2010-08-30T01:27:48Z
A cell involved in the formation of a monocyte (monopoiesis).
FMA:83552
cell
tmeehan
epithelial cell of tracheobronchial tree
2010-09-02T02:09:14Z
An epithelial cell of the tracheobronchial tree.
CL:1000407
FMA:66816
cell
tmeehan
nucleate cell
2010-09-07T03:32:33Z
A cell containing at least one nucleus.
FMA:67513
cell
tmeehan
epithelial cell of thymus
2010-09-13T02:34:22Z
An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies.
CALOHA:TS-1040
CL:1000459
FMA:72208
cell
epithelial cell of thymus gland
epithelial reticular cell
epithelial reticular cell of thymus
thymic epithelial cell
tmeehan
connective tissue cell
2010-09-15T03:01:54Z
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
CALOHA:TS-2096
CL:1000406
FMA:63875
cell
tmeehan
embryonic cell
2010-09-15T03:39:21Z
A cell of the embryo.
CALOHA:TS-0263
FMA:82840
FMA:82841
WBbt:0007028
cell
tmeehan
embryonic stem cell
2010-09-15T03:44:35Z
A stem cell of embryonic origin.
BTO:0001086
CALOHA:TS-0263
ESC
FMA:82841
This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive.
cell
tmeehan
bronchial epithelial cell
2010-09-20T02:00:00Z
An epithelial cell of the bronchus.
BTO:0002922
cell
tmeehan
preadipocyte
2010-09-20T02:31:53Z
An undifferentiated fibroblast that can be stimulated to form a fat cell.
BTO:0001107
cell
tmeehan
progenitor cell of endocrine pancreas
2010-09-21T04:41:06Z
A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1.
cell
pancreatic endocrine progenitor
pancreatic islet progenitor cell
tmeehan
medullary thymic epithelial cell
2010-09-23T03:17:14Z
An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output.
BTO:0004563
cell
mTEC
tmeehan
respiratory epithelial cell
2010-09-23T04:38:49Z
An endo-epithelial cell of the respiratory tract.
BTO:0004533
airway epithelial cell
cell
tmeehan
somatic cell
2010-09-24T09:44:42Z
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
BTO:0001268
FMA:72300
WBbt:0008378
cell
tmeehan
cardiocyte
2010-12-07T09:37:22Z
A cell located in the heart, including both muscle and non muscle cells.
BTO:0001539
CALOHA:TS-0115
FMA:83808
FMA:84791
From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.
cell
heart cell
tmeehan
aortic endothelial cell
2011-02-28T03:54:42Z
An arterial endothelial cell that is part of the aorta endothelium.
BTO:0003245
CALOHA:TS-0047
cell
tmeehan
embryonic blood vessel endothelial progenitor cell
2011-02-28T04:20:39Z
An endothelial progenitor cell that participates in angiogenesis during development.
See CL:0002619.
cell
tmeehan
epithelial cell of lower respiratory tract
2011-06-21T12:29:31Z
cell
tmeehan
ghrelin secreting cell
A cell that secretes ghrelin, the peptide hormone that stimulates hunger.
cell
pancreatic epsilon cell
Ghrelin secreting cells found in the found in the exocrine pancreas.
In mammals the endocrine pancreas is called the Islets of Langerhans.
cell
pancreatic e cell
hepatoblast
Multi fate stem cell that gives rise to to both hepatocytes and cholangiocytes as descendants.
premigratory neural crest cell
2012-06-27T08:27:35Z
Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.
cell
haendel
hematopoietic precursor cell
Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
cardiac myoblast
endothelial cell of artery
A blood vessel endothelial cell that is part of an arterial endothelium.
BTO:0004758
CL:0002542
FMA:67761
KUPO:0001095
arterial endothelial cell
cell
epithelial cell of gall bladder
An epithelial cell that is part of the gallbladder.
FMA:67780
cell
bone marrow hematopoietic cell
CALOHA:TS-2109
Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.
bone marrow hematopoietic cells
bone marrow poietic cells
neutrophillic cytoplasm
2010-05-25T01:36:34Z
Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions.
cell
tmeehan
acidophilic cytoplasm
2009-12-22T04:23:25Z
Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions.
cell
eosinophilic
tmeehan
basophilic cytoplasm
2009-12-22T04:24:54Z
Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions.
cell
tmeehan
polychromatophilic cytoplasm
2009-12-28T04:25:23Z
Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions.
cell
tmeehan
increased nucleus size
2009-12-23T10:53:24Z
A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.
cell
tmeehan
soil
Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m.
soil
environmental material
Material in or on which organisms may live.
environmental material
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.
massively parallel signature sequencing
biopsy
Specimen creation of a sample of tissue from a living body for diagnostic purposes.
biopsy
Fetus
Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus.
Fetus
geographical location
A reference to a place on the Earth, by its name or by its geographical location.
chromatin
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
chromatin
euchromatin
A dispersed and relatively uncompacted form of chromatin.
euchromatin
heterochromatin
A compact and highly condensed form of chromatin.
heterochromatin
osteoblast differentiation
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
osteoblast differentiation
ameboidal cell migration
Cell migration that is accomplished by extension and retraction of a pseudopodium.
ameboidal cell migration
cytokine production
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
cytokine production
serotonin secretion
The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.
serotonin secretion
somatic diversification of immune receptors
The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences.
somatic diversification of immune receptors
natural killer cell mediated immunity
The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines.
natural killer cell mediated immunity
hematopoietic progenitor cell differentiation
The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
hematopoietic progenitor cell differentiation
immune system process
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
immune system process
lymphocyte mediated immunity
Any process involved in the carrying out of an immune response by a lymphocyte.
lymphocyte mediated immunity
T cell mediated immunity
Any process involved in the carrying out of an immune response by a T cell.
T cell mediated immunity
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus.
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
leukocyte differentiation
The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
leukocyte differentiation
somatic diversification of immune receptors via germline recombination within a single locus
The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus.
somatic diversification of immune receptors via germline recombination within a single locus
myeloid leukocyte differentiation
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
myeloid leukocyte differentiation
regulation of immune system process
Any process that modulates the frequency, rate, or extent of an immune system process.
regulation of immune system process
regulation of leukocyte activation
Any process that modulates the frequency, rate, or extent of leukocyte activation.
regulation of leukocyte activation
peptide secretion
The controlled release of a peptide from a cell or a tissue.
peptide secretion
circulatory system process
A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
circulatory system process
molecular_function
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
molecular_function
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
catalytic activity
RNA-directed DNA polymerase activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
RNA-directed DNA polymerase activity
cellular_component
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
cellular_component
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
nucleus
nucleolus
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
nucleolus
cytoplasm
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoplasm
vacuole
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
vacuole
ribosome
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
ribosome
nucleobase-containing compound metabolic process
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase-containing compound metabolic process
DNA metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
DNA metabolic process
DNA replication
DNA replication
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
DNA packaging
Any process in which DNA and associated proteins are formed into a compact, orderly structure.
DNA packaging
chromatin remodeling
Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
chromatin remodeling
cellular aromatic compound metabolic process
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
cellular aromatic compound metabolic process
transport
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
transport
ion transport
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
ion transport
serotonin transport
The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems.
serotonin transport
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
immune response
organelle organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
organelle organization
cell cycle
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
cell cycle
endomitotic cell cycle
A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
endomitotic cell cycle
meiosis
A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle. A meiotic cell cycle is the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations.
meiosis
female meiosis
A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle in the female germline.
female meiosis
gamete generation
The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.
gamete generation
blood coagulation
The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
blood coagulation
blood circulation
The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
blood circulation
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
metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process
biosynthetic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
biosynthetic process
macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
macromolecule biosynthetic process
protein secretion
The controlled release of proteins from a cell.
protein secretion
detection of chemical stimulus
The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal.
detection of chemical stimulus
detection of carbohydrate stimulus
The series of events in which a carbohydrate stimulus is received by a cell and converted into a molecular signal.
detection of carbohydrate stimulus
detection of hexose stimulus
The series of events in which a stimulus from a hexose is received and converted into a molecular signal.
detection of hexose stimulus
response to carbohydrate
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus.
response to carbohydrate
response to hexose
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus.
response to hexose
hormone transport
The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
hormone transport
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
cellular process
gene expression
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
gene expression
protein transport
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
protein transport
oxygen transport
The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
oxygen transport
peptide transport
The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
peptide transport
monoamine transport
The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
monoamine transport
cytoplasmic membrane-bounded vesicle
A membrane-bounded vesicle found in the cytoplasm of the cell.
cytoplasmic membrane-bounded vesicle
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organization
somatic recombination of immunoglobulin gene segments
The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus.
somatic recombination of immunoglobulin gene segments
cell migration
The orderly movement of a cell from one site to another, often during the development of a multicellular organism or multicellular structure.
cell migration
stem cell division
The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.
stem cell division
regulation of nucleobase-containing compound metabolic process
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase-containing compound metabolic process
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of metabolic process
B cell mediated immunity
Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells.
B cell mediated immunity
immunoglobulin complex
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
immunoglobulin complex
B cell receptor complex
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
B cell receptor complex
antigen processing and presentation
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
antigen processing and presentation
reproductive process
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
reproductive process
sarcomere
The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
sarcomere
peptide hormone secretion
The regulated release of a peptide hormone from a cell.
peptide hormone secretion
insulin secretion
The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
insulin secretion
lymphocyte differentiation
The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
lymphocyte differentiation
myeloid cell differentiation
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
myeloid cell differentiation
secretory granule
A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
secretory granule
cell differentiation
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
cell differentiation
neuron differentiation
The process in which a relatively unspecialized cell acquires specialized features of a neuron.
neuron differentiation
T cell differentiation
T cell differentiation
The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
erythrocyte differentiation
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
erythrocyte differentiation
megakaryocyte differentiation
The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
megakaryocyte differentiation
monocyte differentiation
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte.
monocyte differentiation
macrophage differentiation
The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
macrophage differentiation
chromosome condensation
The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
chromosome condensation
apoptotic chromosome condensation
The compaction of chromatin during apoptosis.
apoptotic chromosome condensation
osteoclast differentiation
The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
osteoclast differentiation
ribonucleoprotein complex
A macromolecular complex containing both protein and RNA molecules.
ribonucleoprotein complex
granulocyte differentiation
The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
granulocyte differentiation
epithelial cell differentiation
The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
epithelial cell differentiation
pancreas development
The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
pancreas development
endocrine pancreas development
The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.
endocrine pancreas development
regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolic process
cytoplasmic vesicle
A vesicle formed of membrane or protein, found in the cytoplasm of a cell.
cytoplasmic vesicle
vesicle
Any small, fluid-filled, spherical organelle enclosed by membrane or protein.
vesicle
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
developmental process
secretion by cell
The controlled release of a substance by a cell.
secretion by cell
macromolecular complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
macromolecular complex
immunoglobulin V(D)J recombination
The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined.
immunoglobulin V(D)J recombination
response to monosaccharide
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus.
response to monosaccharide
detection of monosaccharide stimulus
The series of events in which a stimulus from a monosaccharide is received and converted into a molecular signal.
detection of monosaccharide stimulus
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolic process
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
cellular macromolecule biosynthetic process
ghrelin secretion
The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone.
ghrelin secretion
regulation of molecular function, epigenetic
Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.
regulation of molecular function, epigenetic
T cell receptor complex
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
T cell receptor complex
response to chemical
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
response to chemical
melanosome
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
melanosome
immunoglobulin complex, circulating
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
immunoglobulin complex, circulating
DNA polymerase complex
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
DNA polymerase complex
azurophil granule
Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
azurophil granule
MHC protein complex
A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
MHC protein complex
MHC class II protein complex
A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
MHC class II protein complex
amide transport
The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
amide transport
myeloid dendritic cell differentiation
The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin.
myeloid dendritic cell differentiation
macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
macromolecule metabolic process
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
organelle
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
intracellular organelle
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-bounded organelle
intracellular non-membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
intracellular non-membrane-bounded organelle
protein complex
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
protein complex
receptor complex
Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
receptor complex
sequence-specific DNA binding
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
sequence-specific DNA binding
regulation of DNA methylation
Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
regulation of DNA methylation
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolic process
primary metabolic process
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
primary metabolic process
cellular biosynthetic process
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
cellular biosynthetic process
cellular macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
cellular macromolecule metabolic process
organelle part
Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane.
organelle part
intracellular part
Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
intracellular part
membrane part
Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
membrane part
cytoplasmic part
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoplasmic part
intracellular organelle part
A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane.
intracellular organelle part
contractile fiber part
Any constituent part of a contractile fiber, a fiber composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
contractile fiber part
plasma membrane part
Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
plasma membrane part
cell part
Any constituent part of a cell, the basic structural and functional unit of all organisms.
cell part
single-organism process
A biological process that involves only one organism.
single-organism process
single organism reproductive process
A biological process that directly contributes to the process of producing new individuals, involving a single organism.
single organism reproductive process
single-multicellular organism process
A biological process occurring within a single, multicellular organism.
single-multicellular organism process
single-organism metabolic process
A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism.
single-organism metabolic process
single-organism cellular process
Any process that is carried out at the cellular level, occurring within a single organism.
single-organism cellular process
single-organism transport
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism.
single-organism transport
single-organism developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism.
single-organism developmental process
innate immune response
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
innate immune response
leukocyte activation
A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor.
leukocyte activation
fat cell differentiation
The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
fat cell differentiation
regulation of T cell differentiation
Any process that modulates the frequency, rate or extent of T cell differentiation.
regulation of T cell differentiation
regulation of cell differentiation
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
regulation of cell differentiation
regulation of lymphocyte differentiation
Any process that modulates the frequency, rate or extent of lymphocyte differentiation.
regulation of lymphocyte differentiation
heterocycle metabolic process
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
heterocycle metabolic process
lymphocyte activation
A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor.
lymphocyte activation
hormone secretion
The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.
hormone secretion
secretion
The controlled release of a substance by a cell or a tissue.
secretion
somatic stem cell division
The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line.
somatic stem cell division
oogenesis
The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
oogenesis
multicellular organismal reproductive process
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
multicellular organismal reproductive process
anatomical structure development
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
anatomical structure development
cellular developmental process
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
cellular developmental process
cell motility
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
cell motility
regulation of immune response
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
regulation of immune response
regulation of biological process
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
regulation of biological process
regulation of developmental process
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
regulation of developmental process
regulation of cellular process
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular process
regulation of body fluid levels
Any process that modulates the levels of body fluids.
regulation of body fluid levels
multicellular organismal movement
Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism.
multicellular organismal movement
response to stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
response to stimulus
regulation of DNA metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
regulation of DNA metabolic process
regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen compound metabolic process
establishment of localization
The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
establishment of localization
regulation of lymphocyte activation
Any process that modulates the frequency, rate or extent of lymphocyte activation.
regulation of lymphocyte activation
chromosome organization
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information.
chromosome organization
detection of glucose
The series of events in which a glucose stimulus is received by a cell and converted into a molecular signal.
detection of glucose
cardiac muscle cell differentiation
The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
cardiac muscle cell differentiation
heart contraction
The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body.
heart contraction
chondroblast differentiation
The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes.
chondroblast differentiation
biological regulation
Any process that modulates a measurable attribute of any biological process, quality or function.
biological regulation
regulation of biological quality
Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
regulation of biological quality
glucagon secretion
The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans).
glucagon secretion
somatostatin secretion
The regulated release of somatostatin from secretory granules in the D cells of the pancreas.
somatostatin secretion
organic substance transport
The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
organic substance transport
organic substance metabolic process
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic substance metabolic process
nitrogen compound transport
The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
nitrogen compound transport
extracellular vesicular exosome assembly
The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.
extracellular vesicular exosome assembly
regulation of primary metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
regulation of primary metabolic process
nucleic acid metabolic process
Any cellular metabolic process involving nucleic acids.
nucleic acid metabolic process
organic cyclic compound metabolic process
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
organic substance biosynthetic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic substance biosynthetic process
regulation of leukocyte differentiation
Any process that modulates the frequency, rate or extent of leukocyte differentiation.
regulation of leukocyte differentiation
catalytic complex
A protein complex which is capable of catalytic activity.
catalytic complex
regulation of multicellular organismal development
Any process that modulates the frequency, rate or extent of multicellular organismal development.
regulation of multicellular organismal development
measurement unit label
2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.
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 data item label that 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
2013-09-23 OBI call: Simplify definition by removing following part -
When the objective specification is part of a plan specification, the concretization of the plan specification is realized in a planned process in which the bearer tries to control the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an
non realizable information entity which can serve as that proper part
of a plan towards which the realization of the plan is directed."
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.
objective specification
the objective of a ChIP assay is to identify protein and DNA interaction
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
action specification
data item label
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
datum label
An information content entity that is part of some data item and is used to partially define the denotation of that data item.
GROUP: IAO
data item label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
software
GROUP: OBI
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
Software is a plan specification composed of a series of instructions that can be
interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
software
information carrier
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
A quality of an information bearer that imparts the information content
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
PERSON: Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
information carrier
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.
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 that reliably tends to produce (approximately) truthful statements.
Data items include counts of things, analyte concentrations, and statistical summaries.
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
symbol
20091104, MC: this needs work and will most probably change
A written proper name such as “OBI”; a serial number such as “12324X”; a stop sign.
An information content entity that is a mark or character used as a conventional representation of another entity.
PERSON: Jonathan Rees
based on Oxford English Dictionary
symbol
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 material entity and stands in relation of aboutness to some entity
information content entity
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
scalar measurement datum
10 feet. 3 ml.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
scalar measurement datum
directive information entity
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be
concretized and realized by an actor" with alternative term "instruction".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.
Philly2013 - AR: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
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
directive information entity
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
report
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on
something that has completed." Should it be restricted to those things
that are completed? For example, a progress report is (usually) about
something that definitely has *not* been completed, or may include
(only) projections. I think the definition would not suffer if the
whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-03-16: work has been done on this term 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.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
An information content entity assembled by an author for the purpose of providing information for an audience, and that is meant to provide an accurate account of something that happened.
GROUP: OBI
OBI_0000099
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
PERSON:Chris Stoeckert
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
journal article, patent application, grant progress report, case report (not patient record)
report
data set
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
OBI_0000042
data set
group:OBI
person:Allyson Lister
person:Chris Stoeckert
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
OBI_0000030
group:OBI
image
person:Alan Ruttenberg
person:Allyson
person:Chris Stoeckert
data about an ontology part
Person:Alan Ruttenberg
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
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
To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes.
a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified.
plan specification
measurement data item
2/2/2009 is_specified_output of some assay?
A data item that is a recording of the output of an assay.
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
OBI_0000305
group:OBI
measurement datum
measurement data item
person:Chris Stoeckert
material information bearer
A material entity in which a concretization of an information content entity inheres.
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. Additional examples: a hard drive, a brain.
GROUP: IAO
material information bearer
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
textual entity
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
textual entity
figure
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Any picture, diagram or table
PERSON: Lawrence Hunter
figure
time measurement datum
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A scalar measurement datum that is the result of measuring a temporal interval
Person:Alan Ruttenberg
time measurement datum
documenting
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Copying the readout from an instrument into a spreadsheet.
a planned process in which input information is used to create or add to a report
documenting
wikipedia http://en.wikipedia.org/wiki/Documenting
CRID
centrally registered identifier
A symbol that is sufficient to look up information about the corresponding entity from its CRID (centrally registered identifier) registry.
CRID
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
PubMed identifier “PMID:12345”
CRID registry
A data set that consists of CRIDs (centrally registered identifier) and additional information about their corresponding entities, that were recorded in the dataset through an assigning a centrally registered identifier process.
centrally registered identifier registry
CRID registry
IAO call, 20101124: PubMed registry is an instance of CRID registry
PubMed and GenBank both have CRID registries as parts of their database systems.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
obese
a status with body weight that is grossly above the average, acceptable or desirable weight, usually due to accumulation of excess fat tissue in the body
chewing
chewing
"The process of biting and mashing food with the teeth prior to swallowing." [NBO:GVG]
Mus musculus
Mus musculus
Rattus
Rattus
Rattus norvegicus
Rattus norvegicus
Viruses
Viruses
Euteleostomi
Euteleostomi
Bacteria
Bacteria
Archaea
Archaea
Eukaryota
Eukaryota
Euarchontoglires
Euarchontoglires
Teleostei
Teleostei
Amniota
Amniota
Sauria
Sauria
Murinae
Murinae
Vertebrata <Metazoa>
Vertebrata <Metazoa>
Gnathostomata <vertebrate>
Gnathostomata <vertebrate>
Danio rerio
Danio rerio
Serpentes
Serpentes
Aves
Aves
Homo sapiens
Homo sapiens
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
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
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
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
biological feature identification objective
material supplier role
Jackson Labs is an organization which provide mice as experimental material
Supplier role is a special kind of service, e.g. biobank
material provider role
supplier
PERSON:Jennifer Fostel
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
material supplier role
reference substance role
reference substance
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
OBI
Person:Jennifer Fostel
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
reference substance role
waiting
BP: I have doubts about the utility of this.
OBI branch derived
PERSON:Alan Ruttenberg
We need a better handling/modeling of time (January 2008)
not actively doing anything to a material for a duration of time.
waiting
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
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
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
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
study
Bjoern Peters
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core
editor = PRS
OBI branch derived
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
evaluant role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
GROUP: Role Branch
OBI
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
evaluant role
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
reporting party role
MO:submitter mapped to this term. So, alternative term 'submitter' was added.
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
reporting party
submitter
Jennifer Fostel
OBI
The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
a study personnel role played by a party who reports the outcome of a study component
reporting party role
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
any method
study assay
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
OBI branch derived
PlanAndPlannedProcess Branch
assay
measuring
scientific observation
diagnosis textual entity
Jennifer Fostel
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
diagnosis textual entity
culture medium
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178
Modification made by JZ.
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
OBI
Person: Jennifer Fostel, Jie Zheng
culture medium
reagent role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
PERSON:Matthew Brush
reagent
(copied from ReO)
Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.
Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.
In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
Buffer, dye, a catalyst, a solvating agent.
PERSON:Matthew Brush
reagent role
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
A planned process which results in physical changes in a specified input material
OBI branch derived
PERSON: Bjoern Peters
material processing
material transformation
protocol testing objective
Jennifer Fostel
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
protocol testing objective
participant under investigation role
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study.
Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study.
Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
OBI
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
Following OBI call November 2012,26th:
1. it was decided there was no need for moving the children class and making them siblings of study subject role.
2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study
This note closes the issue and validates the class definition to be part of the OBI core
editor = PRS
GROUP: Role Branch
participant under investigation role
measured expression level
OBI Data Transformation branch
A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
measured expression level
person:Chris Stoeckert
biological vector role
6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning
Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
GROUP: Role Branch
OBI and Wikipedia
a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
biological vector role
specimen role
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
GROUP: Role Branch
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.
OBI
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.
parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.
specimen role
sequence feature identification objective
Jennifer Fostel
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
sequence feature identification objective
intervention design
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
OBI branch derived
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
Philppe Rocca-Serra
intervention design
worker role
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker
OBI
Person:Jennifer Fostel
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
worker role
molecular feature identification objective
Jennifer Fostel
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
molecular feature identification objective
complete nutrient role
A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment.
complete nutrient
Person: Jennifer Fostel
Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
complete nutrient role
cDNA library
GROUP: PSI
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
PMID:6110205. collection of cDNA derived from mouse splenocytes.
PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction
cDNA library
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
protocol optimization objective
Jennifer Fostel
Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
protocol optimization objective
biological replicate role
a reference participant role realized by equivalent treatment of participants
biological replicate
A member of a dose-time group; a patient in a given arm of a trial
OBI
Person:Jennifer Fostel
biological replicate role
investigation agent role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
investigation agent role
investigator
study person role
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
GROUP: Role Branch
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
OBI
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
nutrient role
19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment.
nutrient
GROUP: Role branch
Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
Wikipedia, feb 29, 2008
a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.
nutrient role
methodology testing objective
Jennifer Fostel
Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
methodology testing objective
cellular feature identification objective
Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
Jennifer Fostel
cellular feature identification objective
reference subject role
reference participant
Jennifer Fostel
OBI
Saline treated rat; one of three identically-treated subjects
a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
reference subject role
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
software testing objective
Jennifer Fostel
Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
software testing objective
organization
GROUP: OBI
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
organization
feed role
a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment.
feed
OBI
Person: Jennifer Fostel
Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
feed role
technical replicate role
technical replicate
technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
Aliquots of a tissue subjected to parallel assays
Person: Jennifer Fostel
technical replicate role
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
DNA extraction
OBI branch derived
PlanAndPlannedProcess Branch
organism feature identification objective
Jennifer Fostel
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
organism feature identification objective
protocol
study protocol
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
PlanAndPlannedProcess Branch
protocol
adding a material entity into a target
BP
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
branch derived
adding a material entity into a target
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
analyte role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
GROUP: Role Branch
Glucose in blood (measured in an assay to determine the concentration of glucose).
OBI
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
analyte role
disease stage
PERSON: Bjoern peters
Stage II breast cancer, The timepoint of recovery from a disease
a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
disease stage
intraperitoneal injection
BP
is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
intraperitoneal injection
material to be added role
9 March 09 from discussion with PA branch
OBI
Role Branch
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
drawing a conclusion based on data
Bjoern Peters
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
planning
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
Bjoern Peters
Bjoern Peters
Plans and Planned Processes Branch
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
planning
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
An ion source is a device that is part of a mass
spectrometer that ionizes the material under analysis. The ions are
then transported by magnetic or electric fields to the mass analyzer.
Techniques for ionization have been key to determining what types of
samples can be analyzed by mass spectrometry. Electron ionization and
chemical ionization are used for gases and vapors. In chemical
ionization sources, the material is ionized by chemical ion-molecule
reactions during collisions in the source. Two techniques often used
with liquid and solid biological samples include electrospray
ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser
desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp
(Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson
(Editor) (ISBN 0-941901-31-9))).
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
An ion detector is a device that measures and records
the charge induced or current produced when an ion passes by or hits a
surface. In a scanning instrument the signal produced in the detector
during the course of the scan versus where the instrument is in the
scan (at what m/Q) will produce a mass spectrum, a record of ions as a
function of m/Q.
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
ion detector
light emission function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
light emission 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
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
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
filter function
Frank Gibson
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
filter 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
ionization function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
The ion source in amass spectrometer
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
http://en.wikipedia.org/wiki/Ionization
ionization 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
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
image acquisition function
Frank Gibson
An image acquisition function is a function to acquire an image of a material
image acquisition function
image creation device
Frank Gibson
sep:00096
An image creation device is a device which captures a digitized image of an object
image acquisition device
image creation device
solid support function
Daniel Schober
Frank Gibson
Melanie Courtot
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support 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
sort function
Daniel Schober
Frank Gibson
Melanie Courtot
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
sort function
PCR product
GROUP: OBI BIomaterial Branch
GROUP: OBI BIomaterial Branch
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
PCR product
We are using PCR and not the written out words, as this is the most common used.
is double stranded DNA that is the specified output of a polymerase chain reaction
nucleic acid template role
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid template role
cloning vector role
PERSON: Helen Parkinson
pBluescript plays the role of a cloning vector
a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
cloning vector role
polymerase chain reaction
OBI Plan
adapted from wikipedai
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.
polymerase chain reaction
cloning insert role
Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
GROUP: Role branch
OBII and Wikipedia
cloning insert role
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
reverse transcriptase
group:OBI
person:Melanie Courtot
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase
activity)
reverse transcriptase
syringe
OBI Instrument adapted from Wikipedia
Philippe Rocca-Serra
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
syringe
extract
GROUP: OBI Biomatrial Branch
PERSON: Philippe Rocca-Serra
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extract
extracted material
transcription profiling assay
OBI
Philippe Rocca-Serra
transcription profiling
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
transcription profiling assay
averaging objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
averaging objective
injection
OBI Biomaterial
Philippe Rocca-Serra
Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
injection
injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
enzyme
GROUP:OBI
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything
that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
person: Melanie Courtot
(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)
enzyme
intraperitoneal administration
Person:Bjoern Peters
Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
The administration of a substance into the peritoneum of an organism
intraperitoneal administration
plasmid
group:OBI
person:Melanie Courtot
plasmid
plasmid = DNA and has_quality circular and has_function
(is_realized_as some gene expression) GO:0010467
adding material objective
BP
creating a mouse infected with LCM virus
adding material objective
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
genotyping assay
OBI Biomaterial
Philippe Rocca-Serra
SNP analysis
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
an assay which generates data about a genotype from a specimen of genomic DNA. A variety of
techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
genotype profiling, SNP genotyping
genotyping assay
analyte measurement objective
PERSON: Bjoern Peters
PPPB branch
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
assay objective
PPPB branch
PPPB branch
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
analyte assay
PERSON:Bjoern Peters
PERSON:Helen Parkinson
PERSON:Philippe Rocca-Serra
PERSON:Alan Ruttenberg
GROUP:OBI Planned process branch
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum
and
('has measurement unit label' some 'measurement unit label') and
('is quality measurement of' some 'molecular concentration'))
2013-09-23: simplify equivalent axiom
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.
analyte assay
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
target of material addition role
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
GROUP: Role Branch
OBI
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
target of material addition role
normalized data set
PERSON: James Malone
PERSON: Melanie Courtot
A data set that is produced as the output of a normalization data transformation.
normalized data set
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
consume data function
PERSON: Daniel Schober
PERSON: Frank Gibson
PERSON: Melanie Courtot
Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
consume data function
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.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation 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 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.
manufacturing
manufacturing objective
GROUP: OBI PlanAndPlannedProcess Branch
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
is the objective to manufacture a material of a certain function (device)
manufacturing objective
study design execution
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
a planned process that realizes the concretization of a study design
branch derived
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
study design execution
reverse transcribed polymerase chain reaction
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group.
Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW.
Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
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
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
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
nucleotide sequencing
DNA methylation profiling assay
DNA methylation profiling
DNA methylation profiling assay
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J.
Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979
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.
material separation objective
PPPB branch
PPPB branch
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
material separation objective
clustered data set
A clustered data set is the output of a K means clustering data transformation
AR thinks could be a data item instead
PERSON: James Malone
PERSON: Monnie McGee
data set with assigned discovered class labels
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
clustered data set
differential expression analysis data transformation
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
James Malone
Melanie Courtot
Monnie McGee
WEB:
differential expression analysis data transformation
urine specimen
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
a portion of urine collected from an organism
are we happy calling collection of urine a material separation?
urine specimen
material combination
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
bp
bp
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
material combination
device setting
Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
PERSON: Frank Gibson
a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
device setting
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
A planned process with the objective of collecting a specimen.
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.
specimen collection
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
error correction data transformation
EDITORS
Monnie McGee
An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
James Malone
error correction data transformation
sample from organism
5/29: This is a helper class for now
a material obtained from an organism in order to be a representative of the whole
sample from organism
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
center value
PERSON: James Malone
PERSON: Monnie McGee
median
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
center value
portioning objective
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
The objective to obtain multiple aliquots of an enzyme preparation.
portioning objective
average value
PERSON: James Malone
PERSON: Monnie McGee
arithmetic mean
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
average value
whole organism preparation
A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
putting a mouse in the blender. Not: putting a mouse on a scale
whole organism preparation
separation into different composition objective
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
The objective to obtain cells contained in a sample of blood.
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
separation into different composition objective
specimen collection objective
A objective specification to obtain a material entity for potential use as an input during an investigation.
Bjoern Peters
Bjoern Peters
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
specimen collection objective
material combination objective
PPPB branch
bp
is an objective to obtain an output material that contains several input materials.
material combination objective
454 Genome Sequence 20
454 Genome Sequence 20
GS 20
PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults.
Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are
controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
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
ABI 377 automated sequencer
ABI 377 automated sequencer
Applied Biosystems
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
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.
animal feeding
Bjoern Peters
In an investigation, this will typically be part of an animal care process
animal feeding
animal feeding is a process in which animals are provided with food
branch derived
giving crickets to a snake.
chain termination sequencing
PMID: 271968. DNA sequencing with chain-terminating inhibitors.
Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7.
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
AB SOLiD System
AB SOLiD System
Applied Biosystems
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
Helicos sequencing
Helicos sequencing
PMID: 18388294. Single-molecule DNA sequencing of a viral genome.
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9.
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
454 Genome Sequencer FLX
454 GS FLX
454 Genome Sequencer FLX
GS-FLX
PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B.
J Biotechnol. 2008 Aug 31;136(1-2):3-10.
Philippe Rocca-Serra
adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are
controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
Illumina Genome Analyzer II
Illumina Corporation
Illumina Genome Analyzer II
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
Philippe Rocca-Serra
is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
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
is a DNA sequencing which allows sequence identification by relying on the following steps:
1. Primers hybridize to the P1 adapter sequence within the library template.
2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction.
3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length.
4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles
Li-Cor 4300 DNA Analysis System
Li-Cor 4300 DNA Analysis System
OBI and Li-Cor
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
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
PMID: 19275939
ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.
Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.
Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9.
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
HeliScope Single Molecule Sequencer
HeliScope Single Molecule Sequencer
Philippe Rocca-Serra
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
paired-end library
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
Philippe Rocca-Serra
adapted from information provided by Solid web site
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
mate-paired library
paired-end library
paired-end tag (PET) library
DNA sequencing by ligation
DNA sequencing by ligation
PERSON: Philippe Rocca-Serra
PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding.
McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y,
Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22.
is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
Solexa sequencing
PMID: 18987734
Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9.
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
host role
30 Mar09 submitted by vaccine community
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
GROUP: Role Branch
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
OBI
host role
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
http://en.wikipedia.org/wiki/Host_(biology)
pyrosequencing
Philippe Rocca-Serra
Pyrosequencing sheds light on DNA sequencing.
PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review.
Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template.
ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
pyrosequencing
recombinant vector
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
recombinant vector
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.
single fragment library
Philippe Rocca-Serra
fragment library
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
single fragment library
cloning vector
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
cloning vector
material sample role
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
material sample role
material sample
A material entity that has the material sample role
OBI: workshop
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
material sample
sample
sample population
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.
An assay 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.
PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J.
Genome Res. 2009 Jul 6.
Philippe Rocca-Serra
adapted from Wikipedia
bisulfite sequencing
study design independent variable
2009-03-16: work has been done on this term 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 thisdefinition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
study factor
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
independent variable
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
experimental factor
study design independent variable
multiple testing correction objective
A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
Application of the Bonferroni correction
http://en.wikipedia.org/wiki/Multiple_Testing_Correction
multiple comparison correction objective
multiple testing correction objective
transcription factor binding site
PLace_holder for sequence ontology term
SO:0000235
transcription factor binding site
purification objective
10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality
BP
PERSON:Bjoern Peters
The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
isolation objective
purification objective
the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
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
material maintenance objective
An objective specification maintains some or all of the qualities of a material over time.
PERSON: Bjoern Peters
material maintenance objective
PERSON: Bjoern Peters
amplified DNA
Alan Ruttenberg
Amplied DNA created by PCR
DNA that has been produced in an enzymatic amplification process
PERSON: Alan Ruttenberg
amplified DNA
primary structure of DNA macromolecule
BP et al
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
placeholder for SO
primary structure of DNA macromolecule
DNA residue methylation
DNA residue methylation
a quality of a DNA residue that has a methyl group attached to it
measurement device
A device in which a measure function inheres.
A ruler, a microarray scanner, a Geiger counter.
GROUP:OBI Philly workshop
OBI
measurement device
high molecular weight DNA extract
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
OBI
PERSON:Chris Stoeckert
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
high molecular weight DNA extract
material maintenance
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance
primary structure of RNA molecule
Person:Bjoern Peters
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
primary structure of RNA molecule
polyA RNA extraction
A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
polyA RNA extraction
organellar RNA extraction
A RNA extraction process in which the desired output material is RNA in the organelle(s).
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
organellar RNA extraction
record of missing knowledge
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
Bjoern Peters
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
a information content entity created to indicate that information about something is not available to the person recording it.
record of missing knowledge
total RNA extraction
A RNA extraction process in which total cellular and organelle RNA are extracted.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
total RNA extraction
record of unknown sex
A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
Bjoern Peters
I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement.
a record indicating that the biological sex of an organism is not known.
record of unknown sex
cytoplasmic RNA extraction
A RNA extraction process in which the desired output material is RNA in the cytoplasm.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
cytoplasmic RNA extraction
nuclear RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
nuclear RNA extract
polyA RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3’ end are purified.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
UPenn Group
polyA RNA extract
pre-mortem specimen
Bjoern Peters
a specimen that was taken from a live organism
material obtained through a liver biopsy from a human patient
pre-mortem specimen
MO_705 premortem
cytoplasmic RNA extract
A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
cytoplasmic RNA extract
RNA extract
Group: UPenn Group
PERSON: Chris Stoeckert
PERSON: Jie Zheng
RNA extract
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
nuclear RNA extraction
A RNA extraction process in which the desired output material is RNA in the nucleus.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
nuclear RNA extraction
real time polymerase chain reaction assay
A laboratory technique based on the PCR, which is used to
amplify and simultaneously quantify a specific DNA
molecule based on the use of complementary probes/primers. It enables
both detection and quantification (as absolute number of copies or relative
amount when normalized to DNA input or additional normalizing genes) of one
or more specific sequences in a DNA sample.
Q-PCR
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
kinetic polymerase chain reaction
person: Bjoern Peters
person: Melanie Courtot
qPCR
quantitative real time polymerase chain reaction
real time PCR
real time polymerase chain reaction assay
protein extract
OBI & wikipedia
PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE.
J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
Person: Philippe Rocca-Serra
a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,
protein extract
total RNA extract
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
Extraction of total RNA from cells with Qiagen mini RNeasy kit.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
total RNA extract
organellar RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
Extraction of organellar RNA from plant cells using organellar RNA binding protein.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
organellar RNA extract
post mortem specimen
Bjoern Peters
a specimen that was taken from a dead organism
post mortem specimen
the spleen taken from a dead mouse
MO_416 postmortem
sequence feature annotation
Bjoern Peters
Bjoern Peters
Information about a sequence region
place holder for sequence ontology term
sequence feature annotation
labeled DNA extract
Group: OBI group
Group: OBI group
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
Added duirng Mar 1, 2010 dev call
a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
labeled DNA extract
freezing storage
2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance"
A process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities
Freezing a pellet for later assay
OBI
Person: Alan Ruttenberg
freezing storage
MO_481 frozen_storage
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
labeled RNA extract
Group: OBI group
Group: OBI group
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
Added duirng Mar 1, 2010 dev call
a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
labeled RNA extract
frozen specimen
A specimen that has been frozen in order to store it.
Frozen blood plasma
MO_610 frozen_sample
Person:Alan Ruttenberg
frozen specimen
labeled specimen
A specimen that has been modified in order to be able to detect it in future experiments
OBI group
added during call 3/1/2010
labeled specimen
lyophilization storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a storage process with input material entity and output freeze dried material for long time storage
can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
lyophilization storage
study intervention
GROUP: OBI
PERSON: Bjoern Peters
study intervention
the part of the execution of an intervention design study which is varied between two or more subjects in the study
material separation device
A device with a separation function realized in a planed process
flow cytometer
material separation device
intramuscular injection
intramuscular injection
is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
service provider role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
PERSON:Helen Parkinson
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
service provider role
paraffin specimen
MO_990 paraffin_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
liver tissue embedded in paraffin
paraffin specimen
compound treatment design
MO_555 compound_treatment_design
PERSON: Bjoern Peters
This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
an intervention design in which the treatment is the administration of a compound
compound treatment design
processed specimen
A specimen that has been intentionally physically modified.
Bjoern Peters
Bjoern Peters
processed specimen
A tissue sample that has been sliced and stained for a histology study.
A tissue sample that has been sliced and stained for a histology study.
A blood specimen that has been centrifuged to obtain the white blood cells.
subcutaneous injection
PERSON: Melanie Courtot
is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe
subcutaneous injection
lyophilized specimen
MO_589 freeze_dried_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
freezing dried DNA
lyophilized specimen
container
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A device that can be used to restrict the location of material entities over time
PERSON: Bjoern Peters
container
device
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform.
2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:
(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.
(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.
(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.
In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
OBI development call 2012-12-17.
PERSON: Helen Parkinson
device
instrument
dose specification
a directive information entity that describes the dose that will be administered to a target
a protocol specifying to administer 1 ml of vaccine to a mouse
dose specification
fresh specimen
MO_730 fresh_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a liver freshly removed from a rat
a specimen that is output of a specimen creation process used for an investigation without storage.
fresh specimen
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
GROUP: OBI
Person:Chris Stoeckert
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
sequence data
paraffin storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
need to specify paraffin or wax is one of specified input of the process
paraffin storage
agar stab specimen
MO_971 agar_stab
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a process that cell culture inoculated into agar for long term storage.
agar stab specimen
growth condition intervention design
A study design in which the independent variable is the environmental condition in which the specimen is growing
MO_588 growth_condition_design
PERSON: Bjoern Peters
growth condition intervention design
intravenous injection
PERSON: Melanie Courtot
intravenous injection
is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe
administration of material to specimen
Bjoern Peters
Bjoern Peters
Staining cells in a tissue slice with a dye.
The directed combination of a material entity with a specimen.
administration of material to specimen
growth environment
OBI group
PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
Right now this may be incomplete. Should also cover e.g. sound, light as well.
The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
growth environment
agar stab storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
a storage process with input cell culture and agar and output agar stab for long time storage
agar stab storage
need to specify that agar is one of input for this process
image creation
A planned process that captures an image of an object.
PERSON: Jie Zheng
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
image acquisition
image creation
nucleic acid extract
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
PERSON: Jie Zheng
UPenn Group
nucleic acid extract
feature extraction
A planed process with objective of obtaining quantified values from an image.
MO_928: feature_extraction
PERSON: Jie Zheng
feature extraction
array image creation
An image creation process that generate an image from the array.
MO_929: image_acquisition
PERSON: Jie Zheng
array image acquisition
array image creation
light emission device
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
OBI
Person:Helen Parkinson
a device which has a function to emit light.
light emission device
perturbation device
A homogenizer is a perturbation device.
A perturbation device is a device which is designed to perform a perturb function
Helen Parkinson
OBI Vancouver workshop 2010
PERSON: Helen Parkinson
perturbation device
environmental control device
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
Helen Parkinson
OBI
environmental control device
DNA extract
DNA extract
Group: UPenn group
Person: Jie Zheng
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
array manufacturer role
a manufacturer role which is played by the person or organization that manufactured the array
MO_695 array_manufacturer
PERSON: Chris Stoeckert, Jie Zheng
array manufacturer role
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
spike-in quality control role
MO_937 spike_quality_control
PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
spike-in quality control role
individual organism identifier
PERSON: Chris Stoeckert, Jie Zheng
MO_169 Individual
a CRID symbol used to distinguish one individual organism from another.
individual organism identifier
dye swap quality control role
MO_524 dye_swap_quality_control
PERSON: Chris Stoeckert, Jie Zheng
a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes
dye swap quality control role
labeled nucleic acid extract
MO_221 labeledExtract
Person: Jie Zheng
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
labeled extract
labeled extract
labeled nucleic acid extract
cell culture expansion
BP:
add it as subclass of 'cell culturing'
JZ:
No 'cell culturing' in OBI
Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process.
MO_758 grow
PERSON: Chris Stoeckert, Jie Zheng
a processual entity that results in the increase of cell numbers
cell culture expansion
including grow of yeast and bacteria
gene knock out
MO_771 gene_knock_out
PERSON: Chris Stoeckert, Jie Zheng
a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
gene knock out
gene knock in
PERSON: Chris Stoeckert, Jie Zheng
MO_437 gene_knock_in
WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
gene knock in
chromosomal substitution
A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'.
MO_995 chromosomal_substitution
PERSON: Chris Stoeckert, Jie Zheng
chromosomal substitution
genetically modified material
GROUP: OBI
PERSON: Jie Zheng
a material entity, organism or cell, that is the output of a genetic transformation process.
genetically modified material
term is proposed by BP on Oct 25, 2010 dev call
transfection
MO_366 transfection
PERSON: Chris Stoeckert, Jie Zheng
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
transfection
genetic transformation objective
suggested to be added by BP and AR during Oct 25, 2010 dev call
Person: Jie Zheng
Person: Jie Zheng
a material transformation objective aims to create genetically modified organism or cell
genetic transformation objective
induced mutation
MO_564 induced_mutation
PERSON: Chris Stoeckert, Jie Zheng
a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
induced mutation
age since planting measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call.
Term proposed by Bjoern on Nov 8, 2010 dev call
Supported by Alan on Nov 15, 2010 dev call
MO_495 planting
PERSON:Chris Stoeckert, Jie Zheng
age since planting measurement datum
age since hatching measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
MO_745 hatching
PERSON:Chris Stoeckert, Jie Zheng
age since hatching measurement datum
age measurement assay
An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
OBI group
PERSON: Alan Ruttenberg
This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
age measurement assay
age since egg laying measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
MO_767 egg laying
PERSON:Chris Stoeckert, Jie Zheng
age since egg laying measurement datum
assay validation objective
GROUP: Penn Group
PERSON: Chris Stoeckert, Jie Zheng
an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
assay validation objective
age since germination measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
MO_590 germination
PERSON:Chris Stoeckert, Jie Zheng
age since germination measurement datum
validation by reverse transcription PCR design
MO_986 reverse_transcription_PCR_quality_control
PERSON: Chris Stoeckert, Jie Zheng
a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
validation by reverse transcription PCR design
age since eclosion measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
MO_876 eclosion
PERSON:Chris Stoeckert, Jie Zheng
age since eclosion measurement datum
age since sowing measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
MO_748 sowing
PERSON:Chris Stoeckert, Jie Zheng
age since sowing measurement datum
age since coitus measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
MO_783 coitus
PERSON:Chris Stoeckert, Jie Zheng
age since coitus measurement datum
validation by real time PCR design
MO_434 real_time_PCR_quality_control
PERSON: Chris Stoeckert, Jie Zheng
a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
validation by real time PCR design
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
In MageTab file, we use
initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.)
Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
MO_178 Age
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
discussed on Nov 15, dev call
All subtype will be defined by textual definition now.
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet.
life of bearer doesn't imply organism
this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature
age as a quality is dubious; we plan to revisit
stages in development are currently handled with controlled vocabulary, such as 2-somite stage
age measurement datum
age since fertilization measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
Definition of fertilization comes from GO.
MO_701 fertilization
PERSON:Chris Stoeckert, Jie Zheng
age since fertilization measurement datum
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
MO_710 birth
PERSON:Chris Stoeckert, Jie Zheng
age since birth measurement datum
reverse transcription polymerase chain reaction assay
GROUP: Penn Group
PERSON: Chris Stoeckert, Jie Zheng
an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
reverse transcription polymerase chain reaction assay
selective organism creation objective
PERSON: Chris Stoeckert, Jie Zheng
WEB: wikipedia
http://en.wikipedia.org/wiki/Cultivar
http://en.wikipedia.org/wiki/Ecotype
http://en.wikipedia.org/wiki/Strain_%28biology%29
an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
selective organism creation objective
RNA sequencing
BP 12/21:Created based on a request from Melanie
Bjoern Peters
Bjoern Peters
RNA sequencing
RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
cultivar
ecotype
strain
selectively maintained organism
operator variation design
Person: Chris Stoeckert, Jie Zheng
A study design that assesses the operator performance and relation to data consistency and quality.
MO_519 operator_variation_design
operator variation design
comparative genome hybridization by array design
Person: Chris Stoeckert, Jie Zheng
A study design that detects genomic copy number variations using microarray technology.
MO_856 comparative_genome_hybridization_design
comparative genome hybridization by array design
in vivo design
Person: Chris Stoeckert, Jie Zheng
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
MO_454 in_vivo_design
in vivo design
cell component comparison design
A study design that compares samples from different cell components.
Person: Chris Stoeckert, Jie Zheng
MO_1019 cell_component_comparison_design
cell component comparison design
ex vivo design
Person: Chris Stoeckert, Jie Zheng
A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
MO_808 ex_vivo_design
ex vivo design
normalization testing design
Person: Chris Stoeckert, Jie Zheng
A study design that tests different normalization procedures.
MO_729 normalization_testing_design
normalization testing design
genetic population background information
Group: OBI group
Group: OBI group
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
proposed and discussed on San Diego OBI workshop, March 2011
environmental history design
MO_698 environmental_history_design
Person: Chris Stoeckert, Jie Zheng
A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
environmental history design
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
epigenetic modification identification objective
transcription profiling by tiling array assay
Person: James Malone
An assay in which the transcriptome of a biological sample is analysed using a tiling path array.
EFO_0002769 transcription profiling by tiling array
transcription profiling by tiling array assay
array platform variation design
Person: Chris Stoeckert, Jie Zheng
A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
MO_899 array_platform_variation_design
array platform variation design
translational bias design
Person: Chris Stoeckert, Jie Zheng
A study design that characterizes the association of transcripts and translation machinery.
MO_939 translational_bias_design
translational bias design
DNA methylation profiling by high throughput sequencing assay
EFO_0002761 methylation profiling by high throughput sequencing
Group: ArrayExpress production team, James Malone, Helen Parkinson
Philippe Rocca-Serra
An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
DNA methylation profiling by high throughput sequencing assay
RNA-seq assay
An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
JZ: should be inferred as 'DNA sequencing'. Will check in the future.
EFO_0002770 transcription profiling by high throughput sequencing
PERSON: James Malone
RNA-seq assay
an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.
WEB: http://en.wikipedia.org/wiki/RNA-Seq
transcription profiling by high throughput sequencing
in vitro design
Person: Chris Stoeckert, Jie Zheng
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
MO_347 in_vitro_design
in vitro design
transcription profiling by array design
MO_533 transcript_identification_design
Person: Chris Stoeckert, Jie Zheng
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
transcription profiling by array design
disease state design
Person: Chris Stoeckert, Jie Zheng
A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
MO_902 disease_state_design
disease state design
wild type organism genotype information
C57BL/6J wild type
Group: OBI group
Group: OBI group
a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
proposed and discussed on San Diego OBI workshop, March 2011
wild type organism genotype information
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
Group: OBI group
Group: OBI group
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
genotype information
RNA stability design
Person: Chris Stoeckert, Jie Zheng
A study design that examines the stability and/or decay of RNA transcripts.
MO_553 RNA_stability_design
RNA stability design
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
species comparison design
A study design that assays differences between distinct species.
Person: Chris Stoeckert, Jie Zheng
MO_675 species_design
species comparison design
organism development design
Person: Chris Stoeckert, Jie Zheng
A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
MO_892 development_or_differentiation_design
organism development design
family history design
Person: Chris Stoeckert, Jie Zheng
A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
MO_544 family_history_design
family history design
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Group: Penn Group
Person: Chris Stoeckert, Jie Zheng
transcription profiling identification objective
quality control testing design
Person: Chris Stoeckert, Jie Zheng
A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
MO_981 quality_control_testing_design
quality control testing design
clinical history design
Person: Chris Stoeckert, Jie Zheng
A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
MO_832 clinical_history_design
clinical history design
allele information
MO_58 Allele
Person: Chris Stoeckert, Jie Zheng
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
allele information
discussed on San Diego OBI workshop, March 2011
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
post-transcriptional modification design
Person: Chris Stoeckert, Jie Zheng
A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
MO_392 cellular_modification_design
post transcription modification design?
or more clear RNAi design / antibody targeting design?
need to check the use cases
post-transcriptional modification design
genetic alteration information
Group: OBI group
Group: OBI group
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
genetic alteration information
proposed and discussed on San Diego OBI workshop, March 2011
cellular process design
Person: Chris Stoeckert, Jie Zheng
A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
MO_810 cellular_process_design
cellular process design
wild type allele information
MO_605 genotype
Person: Chris Stoeckert, Jie Zheng
an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
discussed on San Diego OBI workshop, March 2011
wild type allele information
injury design
Person: Chris Stoeckert, Jie Zheng
A study design in which the response of an organism(s) to injury or damage is studied.
MO_726 injury_design
injury design
organism status comparison design
Person: Chris Stoeckert, Jie Zheng
A study design that compares samples from live and dead organisms.
MO_841 organism_status_design
organism status comparison design
comparative genomic hybridization by array assay
Philippe Rocca-Serra
An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
EFO_0000749: comparative genomic hybridization by array
Person: James Malone
array CGH
comparative genomic hybridization by array assay
stimulus or stress design
Person: Chris Stoeckert, Jie Zheng
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
MO_568 stimulus_or_stress_design
stimulus or stress design
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
MO_933 binding_site_identification_design
Person: Chris Stoeckert, Jie Zheng
protein and DNA interaction identification objective
protocol optimization design
Person: Chris Stoeckert, Jie Zheng
A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
MO_934 optimization_design
protocol optimization design
genetic characteristics information
MO definition:
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
examples in ArrayExpress
wild_type
MutaMouse (CD2F1 mice with lambda-gt10LacZ integration)
AlfpCre; SNF5 flox/knockout
p53 knock out
C57Bl/6 gp130lox/lox MLC2vCRE/+
fer-15; fem-1
df/df
pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
MO_66 IndividualGeneticCharacteristics
Person: Chris Stoeckert, Jie Zheng
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
genetic characteristics information
imprinting design
Person: Chris Stoeckert, Jie Zheng
A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.
MO_914 imprinting_design
imprinting design
cell cycle design
Person: Chris Stoeckert, Jie Zheng
A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
MO_822 cell_cycle_design
cell cycle design
cell type comparison design
Person: Chris Stoeckert, Jie Zheng
A study design that compares cells of different type, for example different cell lines.
MO_764 cell_type_comparison_design
cell type comparison design
dose response design
Person: Chris Stoeckert, Jie Zheng
A study design that examines the relationship between the size of the administered dose and the extent of the response.
MO_485 dose_response_design
dose response design
organism part comparison design
A study design that compares tissues, regions, organs within or between organisms
Person: Chris Stoeckert, Jie Zheng
MO_953 organism_part_comparison_design
organism part comparison design
protein binding site identification design
A study design that investigates protein binding sites on nucleic acids.
MO_933 binding_site_identification_design
Person: Chris Stoeckert, Jie Zheng
protein binding site identification design
sex comparison design
A study design that assays differences associated with an organism's sex, gender or mating type.
Person: Chris Stoeckert, Jie Zheng
MO_575 sex_design
sex comparison design
transcription profiling by tiling array design
MO_507 tiling_path_design
Person: Chris Stoeckert, Jie Zheng
A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.
transcription profiling by tiling array design
cell differentiation design
Person: Chris Stoeckert, Jie Zheng
A study design that assays events associated with cell development or differentiation.
MO_892 development_or_differentiation_design
cell differentiation design
transcription profiling design
A study design that identifies forms and abundance of transcripts in the genome.
MO_533 transcript_identification_design
Person: Chris Stoeckert, Jie Zheng
transcription profiling design
operon identification design
Person: Chris Stoeckert, Jie Zheng
A study design that identifies locations and members of operons in a genome.
MO_772 operon_identification_design
operon identification design
all pairs design
Person: Chris Stoeckert, Jie Zheng
A study design in which all specimens are compared to every other specimen.
MO_565 all_pairs
all pairs design
genotyping design
Person: Chris Stoeckert, Jie Zheng
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
MO_560 genotyping_design
genotyping design
individual genetic characteristics comparison design
Person: Chris Stoeckert, Jie Zheng
A study design where genotype, haplotype, or other individual genetic characteristics are compared.
MO_527 individual_genetic_characteristics_design
individual genetic characteristics comparison design
pathogenicity design
Person: Chris Stoeckert, Jie Zheng
A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
MO_807 pathogenicity_design
pathogenicity design
genetic modification design
Person: Chris Stoeckert, Jie Zheng
A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
MO_447 genetic_modification_design
genetic modification design
transcription profiling by array assay
An assay in which the transcriptome of a biological sample is analysed using array technology.
Person: James Malone
EFO_0002768: transcription profiling by array
transcription profiling by array assay
strain comparison design
Person: Chris Stoeckert, Jie Zheng
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
MO_462 strain_or_line_design
strain comparison design
cell specimen
A specimen primarily composed of cells collected from a multicellular organism or a cell culture
MO_612 cell
PERSON: Chris Stoeckert, Jie Zheng
cell specimen
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
MO_95 BiosourceType
PERSON: Chris Stoeckert, Jie Zheng
specimen with known storage state
lowess group transformation
A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
MO_861 lowess_group_normalization
Person: Elisabetta Manduchi
lowess group transformation
lowess transformation
A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.
MO_720 lowess_normalization
Person: Elisabetta Manduchi
lowess transformation
tissue specimen
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
MO_954 organism_part
PERSON: Chris Stoeckert, Jie Zheng
tissue specimen
lowess global transformation
A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
MO_692 lowess_global_normalization
Person: Elisabetta Manduchi
lowess global transformation
cell collecting
A planned process that collects cells from culture.
MO_982 harvest
PERSON: Chris Stoeckert, Jie Zheng
cell collecting
linear amplification
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
MO_997 linear_amplification
PERSON: Chris Stoeckert, Jie Zheng
linear amplification
atmosphere
A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
MO_219 atmosphere
PERSON: Chris Stoeckert, Jie Zheng
atmosphere
dissection
A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
EFO_0003856 dissection
MO_374 dissect
PERSON: Chris Stoeckert, Jie Zheng
dissection
purification
A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
MO_406 purify
PERSON: Chris Stoeckert, Jie Zheng
purification
specimen with pre- or post-mortem status
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
MO_84 OrganismStatus
PERSON: Chris Stoeckert, Jie Zheng
organizational term, used in description of specimen that is created from known pre- or post-mortem status
specimen with pre- or post-mortem status
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
MO_738 timepoint
Person: Chris Stoeckert
sampling time measurement datum
time point
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
binding
9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
A peptide binding to an MHC molecule to form a complex.
IEDB
PERSON: Bjoern Peters, Randi Vita
The process of material entities forming complexes.
binding
cap analysis of gene expression
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
Takahashi H, Lassmann T, Murata M, Carninci P.
Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005.
PMID: 22362160
An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
CAGE
PERSON:Philippe Rocca-Serra; Marcus Chibucos
PMID:14663149
cap analysis of gene expression
immunoprecipitation assay
An assay with the objective to determine presence of an analyte by mixing a solution of antigen and antibody and separating out bound antigen:antibody complexes using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies.
Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum.
IEDB
PERSON:Bjoern Peters, Randi Vita
immunoprecipitation assay
chromatin interaction analysis by paired-end tag sequencing
ChIA-PET assay
An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
ENCODE project
Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262]
ChIA-PET
chromatin interaction analysis by paired-end tag sequencing
http://en.wikipedia.org/wiki/ChIA-PET
structural analysis by paired-end tag sequencing
Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419]
ENCODE project
An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants.
DNA-PET assay
DNA-PET
Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419]
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
structural analysis by paired-end tag sequencing
transcript analysis by paired-end tag sequencing
An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions.
RNA-PET
RNA-PET assay
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
ENCODE project
Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299]
Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299]
transcript analysis by paired-end tag sequencing
transcription start site identification objective
Person: Chris Stoeckert, Jie Zheng
A transcription profiling identification objective that aims to characterize the transcription start sites of genes.
Penn Group
transcription start site identification objective
paired-end library preparation
ENCODE project
Person: Venkat Malladi, Jie Zheng
A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
Venkat Malladi, Jie Zheng
paired-end library preparation
DNase I hypersensitive sites sequencing assay
DNase-seq assay
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
DNase-Seq
ENCODE project
DNase I hypersensitive sites sequencing assay
Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541]
http://en.wikipedia.org/wiki/DNase-Seq
An assay to identify the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I.
protein and RNA interaction identification objective
JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'.
A sequence feature identification objective that aims to characterize the interactions between protein and RNA.
Person: Jie Zheng
Jie Zheng
protein and RNA interaction identification objective
RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay
Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659]
RIP-seq
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
RIP-seq assay
Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659]
An assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs).
ENCODE project
RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay
cross-linking immunoprecipitation high-throughput sequencing assay
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
HITS-CLIP
An assay that employs UV-crosslinking between RNA and the protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput used for screening for RNA sequences that interact with a particular RNA-binding protein.
Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288]
CLIP-seq assay
ENCODE project
CLIP-seq
Licatalosi et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27 456: 464-469 [PMID:18978773]
cross-linking immunoprecipitation high-throughput sequencing assay
formaldehyde-assisted isolation of regulatory elements assay
An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity.
http://en.wikipedia.org/wiki/FAIRE-Seq
Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877–85. [PMID:17179217]
ENCODE project
FAIRE-seq
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
FAIRE-seq assay
formaldehyde-assisted isolation of regulatory elements assay
methylation-sensitive restriction enzyme sequencing assay
Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]
MRE-seq assay
MRE-seq
An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA.
Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
ENCODE project
methylation-sensitive restriction enzyme sequencing assay
reduced representation bisulfite sequencing assay
ENCODE project
RRBS
A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol that enriches CG-rich parts of the genome.
Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174]
Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174]
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
RRBS assay
reduced representation bisulfite sequencing assay
shotgun bisulfite-seq assay
Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030].
A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
WGSBS
ENCODE project
Shotgun bisulfite sequencing
Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]
shotgun bisulfite-seq assay
whole-genome shotgun bisulfite sequencing
RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
ENCODE project
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248]
An assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization
of their transcripts using high throughput sequencing.
RAMPAGE
Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248]
RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
conclusion based on data
Group:2013 Philly Workshop group
An information content entity that is inferred from data.
Group:2013 Philly Workshop group
conclusion based on data
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting.
The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
cell freezing medium
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
PERSON: Matthew Brush
cell freezing medium
multiplex ligation-mediated amplification
Multiplex ligation-dependent probe amplification
A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation.
LMA
Chris Stoeckert, Jie Zheng
MLPA
multiplex ligation-mediated amplification
web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification
Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/
DNA replication identification objective
A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time.
Group: Penn Group
Chris Stoeckert, Jie Zheng
DNA replication identification objective
chromosome conformation identification objective
A molecular feature identification objective that aims to determine spatial organization of chromatin.
Chris Stoeckert, Jie Zheng
Group: Penn Group
chromosome conformation identification objective
Carbon-copy chromosome conformation capture assay
An assay that is used to analyze the organization of chromosomes at the genome-wide scale.
5C
Carbon-copy chromosome conformation capture assay
ENCODE project
Venkat Malladi, Chris Stoeckert, Jie Zheng
"Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]"
5C assay
van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094]
DNA replication timing by sequencing assay
Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280]
Repli-seq
ENCODE project
Venkat Malladi, Chris Stoeckert, Jie Zheng
An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing.
DNA replication timing by sequencing assay
Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139–144. [PMID:19966280]
Repli-seq assay
microRNA profiling by high throughput sequencing assay
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
miRNA-seq
microRNA-seq assay
A RNA-seq assay in which high throughput sequencing technology is used to analyse the microRNA component of the transcriptome.
ENCODE project
microRNA profiling by high throughput sequencing assay
http://www.ebi.ac.uk/efo/EFO_0002896
microRNA-seq
Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating
specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). [PMID: 21731767]
protein sequencing by tandem mass spectrometry assay
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
protein sequencing by tandem mass spectrometry assay
A sequencing assay in which amino acid sequences of proteins is determined using multiple rounds of mass spectrometry and molecule fragmentation.
ENCODE project
Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305]
Hunt et al. Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A. 1986;83(17): 6233–6237. [PMID:3462691]
micrococcal nuclease digestion followed by high throughput sequencing assay
micrococcal nuclease digestion followed by high throughput sequencing assay
ENCODE project
Johnson et al. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006 Dec;16(12):1505-16. [PMID:17038564]
JZ: should be inferred as 'DNA sequencing'. Will check in the future.
MNase-seq
Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607]
MNase-seq assay
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
An assay to identify nucleosome positioning by genome wide sequencing of regions senstative to digestion by micrococal nuclease
chromatin immunoprecipitation with exonuclease sequencing assay
A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]
ENCODE project
ChIP-exo assay
chromatin immunoprecipitation with exonuclease sequencing assay
Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]
microRNA profiling assay
microRNA profiling assay
ENCODE project
microRNA expression assay
A transcription profiling assay in which aims to quantify the microRNA species within a biological sample.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
Kolbert et al. Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues. PLoS One. 2013;8(1):e52517 [PMID: 23382819]
miRNA expression assay
scalar value specification
1
1
scalar value specification
A value specification that consists of two parts: a numeral and a unit label
PERSON:Bjoern Peters
value specification
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
value specification
PERSON:Bjoern Peters
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
molecular-labeled material
PERSON:Matthew Brush
OBI developer call, 3-12-12
a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
molecular-labeled material
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')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
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
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
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.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
specimen
obsolete_immortal cell line culture
1
A cell line that is expected to be capable of indefinite propagation in an vitro culture.
PERSON:Matthew Brush
PERSON:Matthew Brush
permanent cell line
immortal cell line sample
2013-08-09 MHB: Replaced with cell line class from CLO, follwoing outcome of Spring 2013 CLO alignment work. Subclass axioms were: 'has grain' some 'immortal cell line cell' and 'has grain' only 'immortalcell line cell'
MHB 3-5-13: This OBI class was formerly called 'immortalized cell line culture', but label changed and definition updated following CLO alignment work in spring of 2013.
http://purl.obolibrary.org/obo/CLO_0009828
obsolete_immortal cell line culture
cultured cell population
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
PERSON:Matthew Brush
PERSON:Matthew Brush
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
cultured cell population
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
cell culture sample
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948).
A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
organ section
GROUP: OBI Biomaterial Branch
PERSON: Philippe Rocca-Serra
A liver slice used in a perfusion experiment.
Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
GROUP: CEBS
PERSON: Helen Parkinson
organ section
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 planned process that 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
feature extraction objective
Elisabetta Manduchi
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
James Malone
TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
feature extraction objective
linlog transformation
Philippe Rocca-Serra
A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
Elisabetta Manduchi
PMID: 16646782
This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782.
linlog transformation
loess global transformation
Philippe Rocca-Serra
A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess global transformation
loess group transformation
Philippe Rocca-Serra
A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess group transformation
loess scale group transformation
A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess scale group transformation
total intensity transformation single
Philippe Rocca-Serra
A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
OTHER: Adjusted from MGED Ontology
This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
total intensity transformation single
total intensity transformation paired
Philippe Rocca-Serra
A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
Elisabetta Manduchi
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
OTHER: Adjusted from MGED Ontology
This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays.
total intensity transformation paired
quantile transformation
A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
This 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.
quantile 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
dye swap merge
A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
Elisabetta Manduchi
James Malone
PERSON: Elisabetta Manduchi
PERSON: James Malone
dye swap merge
moving average
Philippe Rocca-Serra
A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
Elisabetta Manduchi
Helen Parkinson
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
The moving average is often used to handle data from tiling arrays.
moving average
replicate analysis
A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
Elisabetta Manduchi
Helen Parkinson
PERSON: Helen Parkinson
PERSON:Elisabetta Manduchi
Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data.
replicate analysis
loess transformation
Philippe Rocca-Serra
A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess transformation
multiple testing correction method
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
Monnie McGee
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
multiple testing correction method
multiple testing procedure
data transformation objective
Modified definition in 2013 Philly OBI workshop
An objective specification to transformation input data into output data
James Malone
PERSON: James Malone
data transformation objective
normalize objective
data normalization objective
Elisabetta Manduchi
Helen Parkinson
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
A normalization objective is a data transformation objective where the aim is to remove
systematic sources of variation to put the data on equal footing in order
to create a common base for comparisons.
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
normalization data transformation
James Malone
A normalization data transformation is a data transformation that has objective normalization.
PERSON: James Malone
normalization data transformation
averaging data transformation
James Malone
An averaging data transformation is a data transformation that has objective averaging.
PERSON: James Malone
averaging data transformation
class discovery data transformation
James Malone
clustering data transformation
unsupervised classification data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
PERSON: James Malone
class discovery data transformation
center calculation objective
PERSON: James Malone
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
James Malone
center calculation objective
class discovery objective
PERSON: Elisabetta Manduchi
PERSON: James Malone
clustering objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
James Malone
class discovery objective
discriminant analysis objective
unsupervised classification objective
center calculation data transformation
James Malone
A center calculation data transformation is a data transformation that has objective of center calculation.
PERSON: James Malone
center calculation data transformation
scaling objective
Person:Helen Parkinson
Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
is a data transformation 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
Awaiting English definition from Monnie McGee
James Malone
scaling objective
scaling data transformation
A scaling data transformation is a data transformation that has objective scaling.
James Malone
PERSON: James Malone
scaling data transformation
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
pool of specimens
GROUP: CEBS
PERSON: Jennifer Fostel
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
pool of specimens
genetically modified organism
PERSON: Philippe Rocca-Serra
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis.
Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
OBI Biomaterial
an organism that is the output of a genetic transformation process
genetically modified organism
extraction
A material separation in which a desired component of an input material is separated from the remainder
Person:Bjoern Peters
Philippe Rocca-Serra
nucleic acid extraction using phenol chloroform
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity.
'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
centrifugation
Philippe Rocca-Serra
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
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
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
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.
staining
washing
OBI-Branch
Philippe Rocca-Serra
PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
washing
washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
irradiation
Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/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
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
enzymatic ligation
OBI-Branch
Philippe Rocca-Serra
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.
enzymatic ligation
storage
OBI-Branch
Philippe Rocca-Serra
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
storage
cell lysis
BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process.
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
cell lysis
cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock.
immobilization
OBI-Branch
Philippe Rocca-Serra
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.
immobilization
nucleic acid hybridization
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
hybridization assay
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
nucleic acid hybridization
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
flow cell
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
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
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
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
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
DNA 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
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
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses.
TW: This is required by MO.
FG & DS: Capture as function.
All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class.
The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation.
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses.
TW: This is required by MO.
FG: Or as function.
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
A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, 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
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
cytometer
A cytometer is an instrument for counting and measuring cells.
Melanie Courtot
cytometer
http://medical.merriam-webster.com/medical/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
droplet sorter
OBI Instrument branch
OBI Instrument branch
A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original
sample for particles of interest based on qualities determined by gating) or disposal.
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
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
study design
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
loop design
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
MO_912
PMID: 12933549
Philippe Rocca-Serra on behalf of MO
loop design
reference design
A reference experiment design type is where all samples are compared to a common reference.
MO_699
PMID: 12933549
Philippe Rocca-Serra on behalf of MO
reference design
dye swap design
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
MO_858
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
Philippe Rocca-Serra on behalf of MO
dye swap design
replicate design
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
MO_885
Philippe Rocca-Serra on behalf of MO
replicate design
self vs self design
A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared.
MO_490
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
Philippe Rocca-Serra on behalf of MO
self vs self design
time series design
Groups of assays that are related as part of a time series.
MO_887
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
Philippe Rocca-Serra on behalf of MO
time series 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
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
killing
Philippe Rocca-Serra
A protocol application in which an organism is intentionally put to death
CEBS, Biomaterial_branch
Jennifer Fostel
Terminal sacrifice of animals by cervical dislocation at the end of an investigation.
death status type
difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing.
euthanisia
killing
life termination
sacrifice
administering substance in vivo
1
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
A process by which a substance is intentionally given to an organism
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
Person:Bjoern Peters
Bjoern Peters
Different routes and means of administration should go as children underneath this
IEDB
administering substance in vivo
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
exposure of material to environment
Alan says there will be problmes, e.g. with selection by survival
Bjoern Peters
IEDB
Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input.
exposure of material to environment
acclimatization
A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment.
CEBS, Biomaterial_branch
Jennifer Fostel
acclimatization
placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
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
pooling specimens
2
OBI branch derived
PlanAndPlannedProcess Branch
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
physical combination of several instances of like material
pooling specimens
sample pooling
material portioning
OBI branch derived
PERSON:Bjoern Peters
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
aliquoting
apportioning
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
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
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
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
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
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
establishing cell culture
PERSON:Matthew Brush
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
establishing cell culture
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
PERSON:Matthew Brush
addition of molecular label
labeling
OBI developer call, 3-12-12
PERSON:Matthew Brush
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+.
a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
addition of molecular label
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
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
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
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
vector mediated amplification
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
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
phage display library
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction
WEB: http://www.immuneepitope.org/home.do
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
display library
phage display library
cell lysate
The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
lysed material
GROUP: PSI
PERSON: Susanna Sansone
PRS:22-02-2008: is a material which has output_role during lysis protocol-application.
old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process
a cell lysate is a material entity which is output of a cell lysis process
cell lysate
lysate
infection
IEDB
IEDB
infection
the detrimental process in which an infectious agent colonizes or replicates in a host environment
adaptive immune receptor
IEDB
IEDB
adaptive immune receptor
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
disease
IEDB
IEDB
disease
placeholder to be imported from disease ontology
disposition to infect an organism
IEDB
IEDB
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
disposition to infect an organism
material to be added
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
A mixture of peptides that is being added into a cell culture.
IEDB
a material that is added to another one in a material combination process
material to be added
target of material addition
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
A cell culture into which a mixture of peptides is being added.
A material entity into which another is being added in a material combinatino process
IEDB
target of material addition
pathologic process
IEDB
IEDB
abnormal, harmful processes caused by or associated with a disease
pathologic process
clinical history
A series of statements representing health-relevant qualities of a patient and of a patient's family.
clinical history
phenotype
phenotype
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
disease course
disease course
The totality of all processes through which a given disease instance is realized.
treatment
treatment
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.
PATO:0000001
PATO:0000072
quality
trait
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
PATO:0000011
quality
composition
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
PATO:0000025
PATO:0002015
compositionality
content
quality
structure, composition
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.
PATO:0000047
quality
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
PATO:0000051
quality
shape
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATO:0000052
PATO:0001647
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
quality
relational shape quality
qualitative
PATO:0000068
TODO: define this or obsolete it and move children somewhere else.
quality
deviation(from_normal)
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
PATO:0000069
quality
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
PATO:0000117
quality
structure
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATO:0000141
PATO:0001452
quality
relational structural quality
temperature
A physical quality of the thermal energy of a system.
PATO:0000146
quality
time
A quality in which events occur in sequence.
PATO:0000165
quality
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.
PATO:0000169
quality
maturity
A quality of a single physical entity which is held by a bearer when the latter exhibits complete growth, differentiation, or development.
PATO:0000261
quality
female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
PATO:0000383
quality
male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
PATO:0000384
quality
circular
A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
PATO:0000411
quality
round
rounded
normal
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
PATO:0000461
average
quality
increased size
A size quality which is relatively high.
PATO:0000586
PATO:0001202
big
enlarged
expanded
great
large
quality
elliptic
A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
PATO:0000947
ellipse-shaped
ellipsoid
elliptical
oval
ovoid
quality
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATO:0001018
PATO:0002079
Wikipedia:Physical_property
quality
relational physical quality
physical object quality
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
PATO:0001241
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
monadic quality of an object
monadic quality of continuant
multiply inhering quality of a physical entity
quality
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
snap:Quality
bacterial mating type
A mating type that indicates whether the F plasmid has integrated into the chromosome.
PATO:0001335
quality
yeast mating type
A yeast mating type.
PATO:0001337
quality
mixed sex
A biological sex quality inhering in a population of multiple sexes.
For example a mixture of females and male or males and hermaphrodites.
PATO:0001338
quality
biomaterial purity
A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial.
PATO:0001339
quality
hermaphrodite
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
PATO:0001340
intersex
quality
a mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating.
PATO:0001341
a
quality
Saccharomyces cerevisiae mating type
A S. cerevisiae mating type.
PATO:0001342
quality
Schizosaccharomyces pombe mating type
A S. pombe mating type determined by the gene configuration on the mat1 locus.
PATO:0001343
quality
alpha mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids.
PATO:0001344
alpha
quality
h minus
A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus.
M
PATO:0001345
h -
quality
h plus
A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus.
P
PATO:0001346
h+
quality
F mating type
A bacterial mating type indicating the presence of F plasmid in a bacterial cell.
PATO:0001347
quality
F minus mating type
A bacterial mating type indicating the absence of F plasmid in a bacterial cell.
F-
PATO:0001348
quality
ploidy
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
PATO:0001374
quality
haploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
PATO:0001375
quality
polyploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
PATO:0001377
quality
aneuploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes.
PATO:0001385
quality
euploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.
PATO:0001393
quality
diploid
A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father.
PATO:0001394
The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fracton of cells that are polyploidy.
quality
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
PATO:0001396
quality
cellular potency
A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types.
PATO:0001397
quality
unipotent
A cellular potency that is the capacity to produce only one differentiated cell type.
PATO:0001400
Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells.
quality
oligopotent
A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity.
Less potent than multipotent, often thought of as precursor or progenitor cell status.
PATO:0001401
quality
multipotent
A cellular potency that is the capacity to form multiple differentiated cell types.
PATO:0001402
quality
nucleate quality
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
PATO:0001404
quality
anucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
PATO:0001405
quality
mononucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
PATO:0001407
quality
striated
A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel.
PATO:0001410
quality
alive
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
PATO:0001421
quality
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
PATO:0001422
quality
immature
A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development.
PATO:0001501
quality
underdeveloped
mature
A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development.
PATO:0001701
quality
concave
A shape quality in a bearer by virtue of the bearer's curving inward.
PATO:0001857
quality
cylindrical
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
PATO:0001203
PATO:0001873
quality
rod-like
rod-shaped
tubulate
discoid
A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter.
PATO:0001874
disc-shaped
disk-shaped
quality
phenotypic sex
PATO:0001894
quality
mating type
A biological sex quality inhering in an individual or a population that undergo sexual reproduction.
PATO:0001895
quality
frozen
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
PATO:0001985
quality
organismal quality
A quality that inheres in an entire organism or part of an organism.
PATO:0001995
quality
population quality
A quality that inheres in an entire population or part of a population.
PATO:0002003
quality
concavity
PATO:0002005
Surface shape that refers to the inward or outward curvature of the surface.
quality
2-D shape
2-D projection
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
PATO:0002006
cross-sectional
quality
convex 3-D shape
A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png
PATO:0002007
Use this term or an is_a child of this term when the entire shape of the object is known.
quality
biconcave
A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces.
PATO:0002039
quality
affinity
2009-09-18T01:16:16Z
A molecular quality that arises from the molecular attraction exerted between two atoms or compounds.
George Gkoutos
PATO:0002070
quality
basophilic
2009-10-05T12:05:23Z
An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions.
PATO:0002094
george
quality
molecular quality
2010-03-10T03:18:15Z
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
George Gkoutos
PATO:0002061
PATO:0002182
quality
relational molecular quality
3-D shape
2010-10-05T12:31:16Z
A shape that inheres in a 3 dimensional entity.
PATO:0002266
george
quality
increased quality
2011-06-16T06:39:43Z
A quality that has a value that is increased compared to normal or average.
George Gkoutos
PATO:0002300
quality
increased object quality
2011-06-16T06:54:01Z
A quality of an object that has a value that is increased compared to normal or average.
George Gkoutos
PATO:0002305
quality
superelliptic
2011-10-12T12:45:16Z
A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
George Gkoutos
Lamé curve
PATO:0002318
quality
transversely striated
2013-09-15T12:29:15Z
A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer.
PATO:0002478
gkoutos
quality
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
protein
CD19 molecule
A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction.
CD19 molecule
CD34 molecule
A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved.
CD34 molecule
CD4 molecule
A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
CD4 molecule
receptor-type tyrosine-protein phosphatase C
A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (PF00041) followed by two copies of the Protein-tyrosine phosphatase (PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule.
receptor-type tyrosine-protein phosphatase C
integrin alpha-M
An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1.
integrin alpha-M
receptor-type tyrosine-protein phosphatase C isoform CD45RA
A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C).
receptor-type tyrosine-protein phosphatase C isoform CD45RA
CD3 epsilon
A CD3 subunit that is a translation product of the human CD3E gene or a 1:1 ortholog thereof.
CD3 epsilon
neural cell adhesion molecule 1
A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof.
neural cell adhesion molecule 1
CD2 molecule
A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof.
CD2 molecule
T-cell surface glycoprotein CD8 alpha chain
A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.
T-cell surface glycoprotein CD8 alpha chain
chemokine receptor CCR1/3/1L
A rhodopsin-like G-protein coupled receptor that is a translation product of the CCR1, CCR3, or CCR1L1 genes (the last found so far only in mouse).
chemokine receptor CCR1/3/1L
chemokine receptor CCR1
A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof.
chemokine receptor CCR1
chemokine receptor CCR3
A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof.
chemokine receptor CCR3
membrane-spanning 4-domains subfamily A member 1
A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof.
membrane-spanning 4-domains subfamily A member 1
CD44 molecule
A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof.
CD44 molecule
carcinoembryonic antigen-related cell adhesion molecule 8
A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof.
carcinoembryonic antigen-related cell adhesion molecule 8
CD69 molecule
A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets.
CD69 molecule
ectonucleotide pyrophosphatase/phosphodiesterase family member 3
A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof.
ectonucleotide pyrophosphatase/phosphodiesterase family member 3
endoglin
A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof.
endoglin
immunoglobulin gamma Fc receptor II/III/IV
A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III.
immunoglobulin gamma Fc receptor II/III/IV
interleukin-2 receptor subunit beta
A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof.
interleukin-2 receptor subunit beta
ADP-ribosyl cyclase 1
ADP-ribosyl cyclase 1
An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof.
cadherin-5
A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.
cadherin-5
alpha-(1,3)-fucosyltransferase FUT4
A fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof.
alpha-(1,3)-fucosyltransferase FUT4
low affinity immunoglobulin gamma Fc region receptor II
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof.
low affinity immunoglobulin gamma Fc region receptor II
low affinity immunoglobulin gamma Fc region receptor III
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof.
low affinity immunoglobulin gamma Fc region receptor III
tumor-associated calcium signal transducer 1
A tumor-associated calcium signal transducer that is a translation product of the human TACSTD1 gene or a 1:1 ortholog thereof.
tumor-associated calcium signal transducer 1
prominin-1
A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof.
prominin-1
5'-nucleotidase
5'-nucleotidase
A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof.
CD59-like glycoprotein
A protein that is a translation product of the CD59 or closely related gene. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues.
CD59-like glycoprotein
CD7 molecule
A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof.
CD7 molecule
T-cell surface glycoprotein CD5
A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.
T-cell surface glycoprotein CD5
Thy-1 membrane glycoprotein
A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof.
Thy-1 membrane glycoprotein
interleukin-3 receptor class 2 alpha chain
A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof.
interleukin-3 receptor class 2 alpha chain
interleukin-5 receptor subunit alpha
A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof.
interleukin-5 receptor subunit alpha
interleukin-7 receptor subunit alpha
A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof.
interleukin-7 receptor subunit alpha
KLRB1-like protein
A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat.
KLRB1-like protein
leukosialin
A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof.
leukosialin
CD14 molecule
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
CD14 molecule
CD33 molecule
A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof.
CD33 molecule
neprilysin
A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof.
neprilysin
paired box protein PAX-5
A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof.
paired box protein PAX-5
signal transducer CD24
A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof.
signal transducer CD24
transcription factor PU.1
A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof.
transcription factor PU.1
transferrin receptor protein 1
A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof.
transferrin receptor protein 1
tumor necrosis factor ligand superfamily member 5
A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof.
tumor necrosis factor ligand superfamily member 5
urokinase plasminogen activator surface receptor
A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof.
urokinase plasminogen activator surface receptor
mast/stem cell growth factor receptor
A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof.
mast/stem cell growth factor receptor
vascular endothelial growth factor receptor 2
A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof.
vascular endothelial growth factor receptor 2
lymphocyte antigen 6G
A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof.
lymphocyte antigen 6G
lymphocyte antigen 76
A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof.
lymphocyte antigen 76
CD9 molecule
A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof.
CD9 molecule
CCAAT/enhancer-binding protein alpha
A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof.
CCAAT/enhancer-binding protein alpha
DNA nucleotidylexotransferase
A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof.
DNA nucleotidylexotransferase
high affinity immunoglobulin epsilon receptor subunit alpha
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof.
high affinity immunoglobulin epsilon receptor subunit alpha
erythroid transcription factor
A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof.
erythroid transcription factor
endothelial transcription factor GATA-2
A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof.
endothelial transcription factor GATA-2
glucagon
A protein that is a translation product of the human GCG gene or a 1:1 ortholog thereof.
glucagon
insulin
A protein that is a translation product of the human INS gene or a 1:1 ortholog thereof.
insulin
insulinoma-associated protein 1
A protein that is a translation product of the human INSM1 gene or a 1:1 ortholog thereof.
insulinoma-associated protein 1
insulin gene enhancer protein ISL-1
A protein that is a translation product of the human ISL1 gene or a 1:1 ortholog thereof.
insulin gene enhancer protein ISL-1
transcription factor MafA
A protein that is a translation product of the human MAFA gene or a 1:1 ortholog thereof.
transcription factor MafA
neurogenin-3
A protein that is a translation product of the human NEUROG3 gene or a 1:1 ortholog thereof.
neurogenin-3
pancreas/duodenum homeobox protein 1
A protein that is a translation product of the human PDX1 gene or a 1:1 ortholog thereof.
pancreas/duodenum homeobox protein 1
pancreas transcription factor 1 subunit alpha
A protein that is a translation product of the human PTF1A gene or a 1:1 ortholog thereof.
pancreas transcription factor 1 subunit alpha
transcription factor SOX-17
A protein that is a translation product of the human SOX17 gene or a 1:1 ortholog thereof.
transcription factor SOX-17
T-cell acute lymphocytic leukemia protein 1
A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof.
T-cell acute lymphocytic leukemia protein 1
DNA ligase
A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof.
DNA ligase
molecular label role
a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
molecular label role
molecular label
molecular label
a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
ICR
region
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
region
sequence
polypeptide
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
polypeptide
protein
sequence_feature
An extent of biological sequence.
located sequence feature
located_sequence_feature
sequence feature
sequence_feature
read
A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
read
miRNA
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
miRNA
micro RNA
microRNA
pseudogene
A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog).
pseudogene
polymer_attribute
An attribute to describe the kind of biological sequence.
polymer_attribute
pseudogenic_region
A non-functional descendent of a functional entity.
pseudogenic region
pseudogenic_region
SRP_RNA
7S RNA
SRP RNA
SRP_RNA
The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
signal recognition particle RNA
ncRNA
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
ncRNA
noncoding RNA
transcript
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
transcript
gene
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
gene
QTL
A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
QTL
quantitative trait locus
transgene
A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
transgene
circular
A quality of a nucleotide polymer that has no terminal nucleotide residues.
circular
BAC_end
A region of sequence from the end of a BAC clone that may provide a highly specific marker.
BAC end
BAC end sequence
BAC_end
BES
protein_coding_gene
protein coding gene
protein_coding_gene
ncRNA_gene
ncRNA gen
ncRNA gene
ncRNA_gene
non-coding RNA gene
miRNA_gene
miRNA gene
miRNA_gene
scRNA_gene
scRNA gene
scRNA_gene
snoRNA_gene
snoRNA gene
snoRNA_gene
snRNA_gene
snRNA gene
snRNA_gene
tRNA_gene
tRNA gene
tRNA_gene
biological_region
A region defined by its disposition to be involved in a biological process.
biological region
biological_region
YAC_end
A region of sequence from the end of a YAC clone that may provide a highly specific marker.
YAC end
YAC_end
heritable_phenotypic_marker
A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.
heritable phenotypic marker
heritable_phenotypic_marker
phenotypic marker
rRNA_gene
A gene that encodes for ribosomal RNA.
rRNA gene
rRNA_gene
RNase_P_RNA_gene
A gene that encodes an RNase P RNA.
RNase P RNA gene
RNase_P_RNA_gene
RNase_MRP_RNA_gene
A gene that encodes a RNase_MRP_RNA.
RNase MRP RNA gene
RNase_MRP_RNA_gene
lincRNA_gene
A gene that encodes large intervening non-coding RNA.
lincRNA gene
lincRNA_gene
telomerase_RNA_gene
A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
TERC
Telomerase RNA component
telomerase RNA gene
telomerase_RNA_gene
pseudogenic_gene_segment
A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.
pseudogenic_gene_segment
gene_segment
A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
gene segment
gene_segment
uterine cervix
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
uterine cervix
islet of Langerhans
Regions of the pancreas that contain its endocrine (i.e., hormone-producing) cells.
islet of Langerhans
pituitary gland
The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
pituitary gland
zone of skin
A sub-region of the skin. Note the distinct between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
zone of skin
endocrine pancreas
The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO].
endocrine pancreas
sense organ
An organ that is capable of detection of chemical stimulus involved in sensory perception of smell.
sense organ
tube
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
tube
lymph node
Oval or bean shaped bodies (1 - 30 mm in diameter) located along the lymphatic system. Lymph nodes are garrisons of B, T, and other immune cells. Lymph nodes are found all through the body, and act as filters or traps for foreign particles. They contain white blood cells that use oxygen to process. Thus they are important in the proper functioning of the immune system. The lymph node is surrounded by a fibrous capsule, and inside the lymph node the fibrous capsule extends to form trabeculae. The substance of the lymph node is divided into the outer cortex and the inner medulla surrounded by the former all around except for at the hilum, where the medulla comes in direct contact with the surface. Thin reticular fibers, elastin and reticular fibers form a supporting meshwork called reticular network (RN) inside the node, within which the white blood cells (WBCs), most prominently, lymphocytes are tightly packed as follicles in the cortex. Elsewhere, there are only occasional WBCs. The RN provides not just the structural support, but also provide surface for adhesion of the dendritic cells, macrophages and lymphocytes. It allows for exchange of material with blood through the high endothelial venules and provides the growth and regulatory factors necessary for activation and maturation of immune cells[WP].
lymph node
head
The head is the anterior-most division of the body [GO].
head
serous membrane
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
serous membrane
dorsal root ganglion
dorsal root ganglion
ganglion on the dorsal root of each spinal nerve that is one of a series of ganglia lodging cell bodies of sensory neurons[BTO]. Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves[..]. one on the posterior root of each spinal nerve, composed of unipolar nerve cell bodies of the sensory neurons of the nerve[TFD].
ganglion
A biological tissue mass, most commonly a mass of nerve cell bodies.
ganglion
large intestine
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
large intestine
anatomical structure
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
anatomical structure
organ
Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions[GO].
organ
organ segment
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball[FMA].
organ segment
organ part
anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA].
organ part
respiratory tract
anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
respiratory tract
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
embryo stage
segment of respiratory tract
An organ segment that is part of a respiratory tract [Automatically generated definition].
segment of respiratory tract
regional part of nervous system
An anatomical structure that is part of a nervous system [Automatically generated definition].
regional part of nervous system
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the endoderm and the mesoderm.
mixed endoderm/mesoderm-derived structure
post-embryonic stage
post-embryonic stage
stage succeeding embryo, including mature structure
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
life cycle stage
juvenile stage
juvenile stage
post-juvenile adult stage
The stage of being a sexually mature adult animal.
post-juvenile adult stage
lung epithelium
lung epithelium
the epithelial layer of the lung.
respiratory tube
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
respiratory tube
neuron projection bundle
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
neuron projection bundle
neural nucleus
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO)
neural nucleus
intestine
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
intestine
segment of colon
An organ segment that is part of a colon [Automatically generated definition].
segment of colon
blood
Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid).
blood
gyrus
A ridge on the cerebral cortex. It is generally surrounded by one or more sulci .
gyrus
preputial gland
An exocrine gland that are located in front of the genitals of some mammals (including mice) and produce pheromones[WP].
preputial gland
prefrontal cortex
The anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas.nnThis brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals.nnThe most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes).nnMany authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. - definition adapted from Wikipedia
prefrontal cortex
portion of organism substance
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
portion of organism substance
material anatomical entity
Anatomical entity that has mass.
material anatomical entity
multi-cellular organism
Anatomical structure that is an individual member of a species and consists of more than one cell.
multi-cellular organism
testis
gonad of a male animal, produces and releases sperm.
testis
organism subdivision
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
organism subdivision
anatomical cluster
Anatomical group that has its parts adjacent to one another.
anatomical cluster
extraembryonic structure
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
extraembryonic structure
tissue
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
tissue
anatomical group
Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.
anatomical group
multi-tissue structure
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
multi-tissue structure
epithelium
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
epithelium
simple columnar epithelium
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
simple columnar epithelium
simple squamous epithelium
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
simple squamous epithelium
cavitated compound organ
Compound organ that contains one or more macroscopic anatomical spaces.
cavitated compound organ
unilaminar epithelium
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
unilaminar epithelium
embryo
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
embryo
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.
germ layer
ectoderm
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
ectoderm
endoderm
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
endoderm
mesoderm
The middle germ layer of the embryo, between the endoderm and ectoderm.
mesoderm
stomach
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
stomach
aorta
Artery carrying blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation
aorta
heart
a myogenic muscular organ found in the cardiovascular system. It is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions. The vertebrate heart is composed of cardiac muscle, which is an involuntary striated muscle tissue found only in this organ, and connective tissue. Primitive fish have a four-chambered heart; however, the chambers are arranged sequentially so that this primitive heart is quite unlike the four-chambered hearts of mammals and birds. The first chamber is the sinus venosus, which collects de-oxygenated blood, from the body, through the hepatic and cardinal veins. From here, blood flows into the atrium and then to the powerful muscular ventricle where the main pumping action takes place. The fourth and final chamber is the conus arteriosus which contains several valves and sends blood to the ventral aorta. The ventral aorta delivers blood to the gills where it is oxygenated and flows, through the dorsal aorta, into the rest of the body. (In tetrapods, the ventral aorta has divided in two; one half forms the ascending aorta, while the other forms the pulmonary artery. In the adult fish, the four chambers are not arranged in a straight row but, instead, form an S-shape with the latter two chambers lying above the former two. This relatively simpler pattern is found in cartilaginous fish and in the more primitive ray-finned fish. In teleosts, the conus arteriosus is very small and can more accurately be described as part of the aorta rather than of the heart proper. The conus arteriosus is not present in any amniotes which presumably having been absorbed into the ventricles over the course of evolution. Similarly, while the sinus venosus is present as a vestigial structure in some reptiles and birds, it is otherwise absorbed into the right atrium and is no longer distinguishable[WP].
heart
brain
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
brain
cerebral cortex
The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
cerebral cortex
retina
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
retina
eye
An organ that detects light.
eye
femur
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
femur
skeletal joint
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
skeletal joint
pons
Brainstrem structure that has as its parts the pontine tegmentum and basal part of pons[FMA].
pons
gonad
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
gonad
female gonad
Ovum-producing female reproductive organ.
female gonad
uterus
a major female hormone-responsive reproductive sex organ of most mammals including humans. One end, the cervix, opens into the vagina, while the other is connected to one or both fallopian tubes, depending on the species. It is within the uterus that the fetus develops during gestation, usually developing completely in placental mammals such as humans and partially in marsupials such as kangaroos and opossums. Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused[WP].
uterus
vagina
a fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
vagina
seminal vesicle
Either of a pair of glandular pouches that lie one on either side of the male reproductive tract and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct.
seminal vesicle
epidermis
The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA].
epidermis
adipose tissue
Connective tissue composed of adipocytes.
adipose tissue
axon tract
A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
axon tract
yolk sac
Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes.
yolk sac
salivary gland
saliva-secreting exocrine glands of the oral cavity[GO]. The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research[WP].
salivary gland
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.
anatomical entity
urine
Excretion in liquid state processed by the kidney.[FMA]
urine
calcareous tooth
Organ with a cavity which consist of dentine surrounded by enamel. Examples: incisor, molar.
calcareous tooth
diaphragm
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control
diaphragm
parathyroid gland
The parathyroid gland is an organ specialised for secretion of parathyroid hormone[GO]. Parathyroid glands control the amount of calcium in the blood and within the bones[WP].
parathyroid gland
cardiac muscle tissue
Muscle composed of cardiac muscle cells that is part of the heart[ZFA]. involuntary striated muscle found in the walls of the heart, specifically the myocardium[Wikipedia]. Tissue which consists of cardiac myocytes surrounded by cardiac endomysium. Examples: Cardiac muscle tissue proper, conducting tissue of heart[FMA].
cardiac muscle tissue
skeletal muscle tissue
Striated muscle tissue under control of the somatic nervous system. It is one of three major muscle types, the others being cardiac and smooth muscle. As its name suggests, most skeletal muscle is attached to bones by bundles of collagen fibers known as tendons. Skeletal muscle is made up of individual components known as muscle fibers. These fibers are formed from the fusion of developmental myoblasts. The myofibers are long, cylindrical, multinucleated cells composed of actin and myosin myofibrils repeated as a sarcomere, the basic functional unit of the cell and responsible for skeletal muscle's striated appearance and forming the basic machinery necessary for muscle contraction. The term muscle refers to multiple bundles of muscle fibers held together by connective tissue[WP].
skeletal muscle tissue
smooth muscle tissue
Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. Tissue which consists of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Examples: Arrector muscle of hair, Muscularis mucosae.
smooth muscle tissue
caecum
Pouch, connecting the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
caecum
vermiform appendix
a blind-ended tube connected to the cecum, from which it develops embryologically[WP].
vermiform appendix
colon
Last portion of the digestive system in most vertebrates; it extracts water and salt from solid wastes before they are eliminated from the body[WP] In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]. In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-050120-6'>Wallace et al, 2005.</a>
colon
ascending colon
Organ part which is continuous with the cecum proximally and the transverse colon distally.[FMA]
ascending colon
sigmoid colon
sigmoid colon
the part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
pyloric antrum
Pyloric antrum (antrum, lesser cul-de-sac) is the initial portion of the pyloric part of the stomach. It is near the bottom of the stomach on the left side of the pyloric sphincter, which separates the stomach and the duodenum. It may temporarily become partially or completely shut off from the remainder of the stomach during digestion by peristaltic contraction of the prepyloric sphincter; it is demarcated, sometimes, from the second part of the pyloric part of the stomach by a slight groove. [WP,unvetted].
pyloric antrum
adrenal cortex
Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted].
adrenal cortex
urinary bladder
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
urinary bladder
pancreas
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans[PMID].
pancreas
myometrium
middle layer of the uterine wall consisting of smooth muscle cells and supporting stromal and vascular tissue.
myometrium
epididymis
A narrow, tightly-coiled tube connecting the efferent ducts from the rear of each testicle to its vas deferens.
epididymis
seminiferous tubule of testis
Seminiferous tubules are located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa. The epithelium of the tubule consists of sustentacular or Sertoli cells, which are tall, columnar type cells that line the tubule. In between the Sertoli cells are spermatogenic cells, which differentiate through meiosis to sperm cells. There are two types: convoluted and straight. convuluted towards the lateral side and straight as the tubule comes medially to form ducts which will exit the testis. [WP,unvetted].
seminiferous tubule of testis
white adipose tissue
Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified]
white adipose tissue
brown adipose tissue
A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified]
brown adipose tissue
gastrocnemius
A muscle of the shank. In mammals it has two heads[Kardong]. It runs from its two heads just above the knee to the heel, and is involved in standing, walking, running and jumping. Along with the soleus muscle it forms the calf muscle. [WP].
gastrocnemius
soleus muscle
a powerful muscle in the back part of the lower leg (the calf). It runs from just below the knee to the heel, and is involved in standing and walking. It is closely connected to the gastrocnemius muscle and some anatomists consider them to be a single muscle, the triceps surae. Its name is derived from the solefish whose shape it resembles. The soleus is located in the superficial posterior compartment of the leg. Not all mammals have a soleus muscle; one familiar species that lacks the soleus is the dog.
soleus muscle
bone element
Skeletal element that is composed of bone tissue.
bone element
knee joint
The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation. Since in humans the knee supports nearly the whole weight of the body, it is the joint most vulnerable both to acute injury and the development of osteoarthritis. [WP,unvetted].
knee joint
thoracic aorta
The thoracic aorta is contained in the posterior mediastinal cavity. It begins at the lower border of the fourth thoracic vertebra where it is continuous with the aortic arch, and ends in front of the lower border of the twelfth thoracic vertebra, at the aortic hiatus in the diaphragm where it becomes the abdominal aorta. At its commencement, it is situated on the left of the vertebral column; it approaches the median line as it descends; and, at its termination, lies directly in front of the column. The vessel describes a curve which is concave forward; as the branches given off from it are small, its diminution in size is insignificant. It has a radius of approximately 1.16 cm. [WP,unvetted].
thoracic aorta
abdominal aorta
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
abdominal aorta
lower respiratory tract
The segment of respiratory tract from the trachea to the lungs[WP,modified]
lower respiratory tract
muscle organ
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Nonparenchymatous organ that primarily consists of skeletal muscle tissue aggregated into macroscopic fasciculi by connective tissue; together with other muscles, it constitutes the muscular system. Examples: biceps, diaphragm, masseter, right third external intercostal muscle, external oblique, levator ani, serratus anterior[FMA].
muscle organ
artery
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
artery
vein
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
vein
mandible
A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton.
mandible
tongue
A muscular organ in the floor of the mouth.
tongue
submandibular gland
The paired submandibular glands (submaxillary glands) are salivary glands located beneath the floor of the mouth. In humans, they account for 70% of the salivary volume and weigh about 15 grams. [WP,unvetted].
submandibular gland
muscle of trunk
Muscle organ which is a part of the trunk. Examples: external intercostal muscle, external oblique, levator ani.
muscle of trunk
autonomic ganglion
autonomic ganglion
ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
sympathetic ganglion
Sympathetic ganglia are the ganglia of the sympathetic nervous system. They deliver information to the body about stress and impending danger, and are responsible for the familiar fight-or-flight response. They are located close to and on either side of the spinal cord in long chains. [WP,unvetted].
sympathetic ganglion
paravertebral ganglion
Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord.
paravertebral ganglion
parasympathetic ganglion
Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands.
parasympathetic ganglion
lacrimal gland
The lacrimal glands are paired almond-shaped glands, one for each eye, that secrete the aqueous layer of the tear film. They are situated in the upper, outer portion of each orbit. Inflammation of the lacrimal glands is called dacryoadenitis[WP].
lacrimal gland
sebaceous gland
A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP].
sebaceous gland
major salivary gland
major salivary gland
the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands.
parotid gland
The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted].
parotid gland
frontal cortex
Anterior portion of the frontal cortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally.
frontal cortex
parietal lobe
Parietal lobe is the one of five lobes of the cerebral hemisphere which occupies the dorsal-posterior portion of the hemisphere. It is bounded by the central sulcus on its anterior border and and by the longitudinal cerebral fissure on its medial border. Posteriorly it shares an arbitrary border with the occipital lobe.
parietal lobe
caudate nucleus
Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species.
caudate nucleus
globus pallidus
Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle.
globus pallidus
amygdala
Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM).
amygdala
midbrain
Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
midbrain
medulla oblongata
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
medulla oblongata
thalamus
A midline paired symmetrical structure within the brains of vertebrates, including humans. It is situated between the cerebral cortex and midbrain, both in terms of location and neurological connections. Its function includes relaying sensation, special sense and motor signals to the cerebral cortex, along with the regulation of consciousness, sleep and alertness. The thalamus surrounds the third ventricle. It is the main product of the embryonic diencephalon.
thalamus
hypothalamus
A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia].
hypothalamus
subthalamic nucleus
The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO].
subthalamic nucleus
mammary gland
The specialized accessory gland of the skin of female mammals that secretes milk. In the human female, it is a compound tubuloalveolar gland composed of 15 to 25 lobes arranged radially about the nipple and separated by connective and adipose tissue, each lobe having its own excretory (lactiferous) duct opening on the nipple. The lobes are subdivided into lobules, with the alveolar ducts and alveoli being the secretory portion of the gland[BTO]. The mouse forms five to six pairs of mammary glands that extend from the neck to the groin.
mammary gland
endothelium of artery
An endothelium that is part of an artery [Automatically generated definition].
endothelium of artery
preoptic area
Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus[ZFA].
preoptic area
Ammon's horn
A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum.
Ammon's horn
blood vessel
A vessel through which blood circulates in the body.
blood vessel
endothelium
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
endothelium
placenta
organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
placenta
superior cervical ganglion
Trunk ganglion which is bilaterally paired and located at the anterior end of the sympathetic ganglion chain.
superior cervical ganglion
olfactory epithelium
Epithelium inside the nasal cavity that is responsible for detecting odors[WP].
olfactory epithelium
gray matter of neuraxis
Heterogeneous cluster of neural somas in the brain and the spinal cord.
gray matter of neuraxis
hindbrain
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
hindbrain
epithelium of bronchus
An epithelium that is part of a bronchus [Automatically generated definition].
epithelium of bronchus
striated muscle tissue
Tissue which consists of striated muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue, Cardiac muscle tissue[FMA].
striated muscle tissue
cerebellum
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
cerebellum
thyroid gland
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
thyroid gland
lung
Respiration organ present in all air-breathing animals whose principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere[WP]. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax[GO].
lung
embryonic structure
Anatomical structure that is part of an embryo.
embryonic structure
ciliary ganglion
The ciliary ganglion is a parasympathetic ganglion located in the posterior orbit. It measures 1P2 millimeters in diameter and contains approximately 2,500 neurons (adapted from Wikipedia)
ciliary ganglion
umbilical vein
The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted].
umbilical vein
hypodermis
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
hypodermis
viscus
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. // An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.
viscus
spleen
Organ found in virtually all vertebrate animals with important roles in regard to red blood cells and the immune system. In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron. It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells.
spleen
liver
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
liver
small intestine
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
small intestine
gallbladder
a small organ that aids digestion and stores bile produced by the liver[WP]. Organ with organ cavity which is continuous proximally with the cystic duct and distally terminates in the fundus of the gallbladder[FMA].
gallbladder
kidney
A paired organ which has the production of urine as its primary function.
kidney
duodenum
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
duodenum
ileum
The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum. [WP,unvetted].
ileum
medulla of thymus
Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size.
medulla of thymus
bronchus
A portion of the airway that connects to the lungs[GO].
bronchus
spinal cord
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
spinal cord
vomeronasal organ
The vomeronasal organ (VNO), or Jacobson's organ, is an auxiliary olfactory sense organ that is found in many animals. It was discovered by Ludwig Jacobson in 1813. During embryological development, it forms from the nasal (olfactory) placode, at the anterior edge of the neural plate. It is a chemoreceptor organ which is completely separated from the nasal cavity the majority of the time, being enclosed in a separate bony or cartilaginous capsule which opens into the base of the nasal cavity. It is a tubular crescent shape and split into two pairs, separated by the nasal septum. It is the first processing stage of the accessory olfactory system, after which chemical stimuli go to the accessory olfactory bulb, then to targets in the amygdala and hypothalamus. The vomeronasal organ is mainly used to detect pheromones, chemical messengers that carry information between individuals of the same species, hence is sometimes referred to as the 'sixth sense. ' The VNO has two separate types of neuronal receptors, V1R and V2R, which are seven-transmembrane receptors that are coupled to G proteins. The receptors are distinct from each other and form the large family of receptors in the main olfactory system. Evidence shows that the VNO responds to nonvolatile cues which stimulate the receptor neurons. Information is then transferred to the accessory olfactory bulb as well as other centres of the brain such as the anterior part of the hypothalamus. Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans is widely controversial, though most studies agree the organ regresses during fetal development. [WP,unvetted].
vomeronasal organ
olfactory bulb
A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]. Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract. In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb[WP].
olfactory bulb
telencephalic ventricle
A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere
telencephalic ventricle
nucleus of brain
Nucleus of neuraxis which is located within the brain. Example: pontobulbar nucleus, globose nucleus[FMA]. brain structure consisting of a relatively compact cluster of neurons. It is one of the two most common forms of nerve cell organization, the other being layered structures such as the cerebral cortex or cerebellar cortex. In anatomical sections, a nucleus shows up as a region of gray matter, often bordered by white matter. The vertebrate brain contains hundreds of distinguishable nuclei, varying widely in shape and size. A nucleus may itself have a complex internal structure, with multiple types of neurons arranged in clumps (subnuclei) or layers.[Wikipedia]
nucleus of brain
white matter
Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.
white matter
umbilical cord
The connecting cord from the developing embryo to the placenta.
umbilical cord
corpus callosum
The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provides communications between the right and left cerebral hemispheres[GO].
corpus callosum
neural crest
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
neural crest
atrioventricular node
Subdivision of conducting system of heart which is located in the muscular part of the interatrial septum that is continuous with the atrioventricular bundle.[FMA]
atrioventricular node
peritoneum
A serous membrane that lines the peritoneal cavity[VHOG,modified].
peritoneum
exocrine gland
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
exocrine gland
prostate gland
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
prostate gland
endocrine gland
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
endocrine gland
adrenal gland
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
adrenal gland
thymus
Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.
thymus
bone marrow
bone marrow
flexible tissue found in the hollow interior of bones. In adults, marrow in large bones produces new blood cells[WP].
tonsil
Portion of lymphoid tissue on either side of the throat.
tonsil
connective tissue
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
connective tissue
muscle tissue
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
muscle tissue
immune system
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
immune system
pericardium
The outer membrane/wall of the developing heart, surrounding the myocardium.
pericardium
skin gland
A gland that is part of a skin of body [Automatically generated definition].
skin gland
basal ganglion
basal ganglion
one of a group of nuclei in the brains of vertebrates, situated at the base of the forebrain and strongly connected with the cerebral cortex, thalamus and other areas.ganglion in the head. The main components of the basal ganglia are the striatum, pallidum, substantia nigra, and subthalamic nucleus[WP]. Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF].
limb bone
A bone that is part of a limb [Automatically generated definition].
limb bone
striatum
A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO].
striatum
intercerebral commissure
Class of unpaired telencephalic white matter structures consisting of fiber pathways which project across the midsagittal plane and which serve to interconnect telencephalic structures lying within the contralateral cerebral hemisphere[FMA].
intercerebral commissure
endochondral bone
Replacement bone that forms within cartilage.
endochondral bone
gland
A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO].
gland
digit
digit
one of several most distal parts of a limb, such as fingers or toes, present in many vertebrates[WP].
regional part of brain
A multi-tissue structure that is part of a brain [Automatically generated definition].
regional part of brain
regional part of cerebral cortex
A regional part of brain that is part of a cerebral cortex [Automatically generated definition].
regional part of cerebral cortex
cerebral peduncle
The cerebral peduncle, by most classifications, is everything in the mesencephalon except the tectum. The region includes the midbrain tegmentum, crus cerebri, substantia nigra and pretectum. By this definition, the cerebral peduncles are also known as the basis pedunculi, while the large ventral bundle of efferent fibers is referred to as the crus cerebri or the pes pedunculi There are numerous nerve tracts located within this section of the brainstem. Of note, in the cerebral peduncular loop fibers from motor areas of the brain project to the cerebral peduncle and then project to various thalamic nuclei. In as much as the peduncles are an anatomic landmark, for details regarding the function of this area interested readers are referred to the individual referenced articles. On a broad scale, though, this area contains many nerve tracts conveying motor information to and from the brain to the rest of the body. Important fibers running through the cerebral peduncles include the corticospinal tract and the corticobulbar tract, among others. [WP,unvetted].
cerebral peduncle
regional part of midbrain tegmentum
A multi-tissue structure that is part of a midbrain tegmentum.
regional part of midbrain tegmentum
regional part of metencephalon
A regional part of brain that is part of a metencephalon [Automatically generated definition].
regional part of metencephalon
ventral tegmental area
A group of neurons located close to the midline on the floor of the midbrain. The VTA, the origin of dopaminergic cell bodies that comprise the mesocorticolimbic dopamine system, is widely implicated in the drug and natural reward circuitry of the brain, cognition, motivation, drug addiction, and several psychiatric disorders. The VTA contains neurons that project to numerous areas of the brain, from the prefrontal cortex (PFC) to the caudal brainstem and everywhere in between. [WP,unvetted].
ventral tegmental area
regional part of forebrain
A regional part of brain that is part of a forebrain [Automatically generated definition].
regional part of forebrain
regional part of diencephalon
A regional part of brain that is part of a diencephalon [Automatically generated definition].
regional part of diencephalon
regional part of telencephalon
A regional part of brain that is part of a telencephalon [Automatically generated definition].
regional part of telencephalon
cingulate gyrus
A gyrus in the medial part of the brain. It partially wraps around the corpus callosum and is limited above by the cingulate sulcus. The cortical part of the cingulate gyrus is referred to as cingulate cortex.[Wikipedia]. The cingulate gyrus receives inputs from the anterior nucleus of the thalamus and the neocortex, as well as from somatosensory areas of the cerebral cortex. It projects to the entorhinal cortex via the cingulum. It functions as an integral part of the limbic system, which is involved with emotion formation and processing, learning, and memory. Also, executive control needed to suppress inappropriate unconscious priming is known to involve the anterior cingulate gyrus. It is also involved in respiratory control.
cingulate gyrus
lobe parts of cerebral cortex
lobe parts of cerebral cortex
surface structure
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
surface structure
compound organ
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
compound organ
trachea
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
trachea
skull
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
skull
reproductive organ
An organ involved in reproduction
reproductive organ
female reproductive organ
A female organ involved in reproduction
female reproductive organ
male reproductive organ
A male organ involved in reproduction
male reproductive organ
endoderm of foregut
An endoderm that is part of a foregut [Automatically generated definition].
endoderm of foregut
mesentery of oesophagus
A mesentery that is part of a esophagus [Automatically generated definition].
mesentery of oesophagus
gland of diencephalon
A gland that is part of a diencephalon [Automatically generated definition].
gland of diencephalon
ganglion of peripheral nervous system
A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
ganglion of peripheral nervous system
gland of gut
A gland that is part of a digestive tract [Automatically generated definition].
gland of gut
facial bone
A bone that is part of a facial skeleton [Automatically generated definition].
facial bone
hindlimb bone
A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)
hindlimb bone
respiratory system artery
An artery that is part of a respiratory system [Automatically generated definition].
respiratory system artery
arterial blood vessel
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
arterial blood vessel
limb long bone
A long bone that is part of a limb [Automatically generated definition].
limb long bone
hindlimb long bone
A long bone that is part of a hindlimb [Automatically generated definition].
hindlimb long bone
respiratory system arterial blood vessel
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
respiratory system arterial blood vessel
limb joint
Any joint that is part of a (free) limb.
limb joint
neural tissue
Portion of tissue which consists of neurons, neuroglia and vasculature. Examples: Neural tissue of brain, neural tissue of peripheral ganglion, neural tissue of nerve[FMA].
neural tissue
mouth mucosa
A mucous membrane that lines the mouth.
mouth mucosa
thoracic segment muscle
A muscle organ that is part of a thorax [Automatically generated definition].
thoracic segment muscle
fallopian tube
Two very fine tubes lined with ciliated epithelia, leading from the ovaries of female mammals into the uterus, via the utero-tubal junction[WP]. Embryos have two pairs of ducts to let gametes out of the body; one pair (the Mullerian ducts) develops in females into the Fallopian tubes, uterus and vagina, while the other pair (the Wolffian ducts) develops in males into the epididymis and vas deferens.
fallopian tube
epithelial tube
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
epithelial tube
endothelial tube
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
endothelial tube
pancreatic bud
The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. In humans, an embryonic structure that is an outgrowth of the duodenum during embryogenesis - joins together to form the adult pancreas[WP].
pancreatic bud
ventral pancreatic bud
pancreatic bud that gives rise to the major pancreatic duct.
ventral pancreatic bud
sex gland
any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction
sex gland
brain ventricle
brain ventricle
one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid
anatomical conduit
anatomical conduit
any opening in the body.
endoderm-derived structure
An anatomical structure that develops (entirely or partially) from the endoderm.
endoderm-derived structure
mesoderm-derived structure
An anatomical structure that develops (entirely or partially) from the mesoderm.
mesoderm-derived structure
ectoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
ectoderm-derived structure
hemopoietic organ
Organ that is part of the hematopoietic system.
hemopoietic organ
hindlimb zeugopod muscle
A muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition].
hindlimb zeugopod muscle
aortic arch
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]
aortic arch
bone of free limb or fin
A bone that is part of an appendage [Automatically generated definition].
bone of free limb or fin
cavity lining
cavity lining
blood vessel endothelium
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
blood vessel endothelium
arterial system endothelium
An endothelium that is part of an arterial system [Automatically generated definition].
arterial system endothelium
dentary
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].
dentary
dermal skeletal element
dermal skeletal element
dermis-derived entity that is made of skeletal tissue.
skeletal element
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
skeletal element
respiratory tract epithelium
An epithelium that is part of a respiratory tract [Automatically generated definition].
respiratory tract epithelium
respiratory system epithelium
An epithelium that is part of a respiratory system [Automatically generated definition].
respiratory system epithelium
lower respiratory tract epithelium
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
lower respiratory tract epithelium
aorta endothelium
An endothelium that is part of an aorta [Automatically generated definition].
aorta endothelium
cardiovascular system endothelium
An endothelium that is part of the cardiovascular system.
cardiovascular system endothelium
subdivision of digestive tract
A proximal-distal subdivision of the digestive tract.
subdivision of digestive tract
organ component layer
Organ component which is a part of a wall of an organ.
organ component layer
mucosa of tongue
A mucosa that is part of a tongue [Automatically generated definition].
mucosa of tongue
immune organ
An organ that is part of a immune system [Automatically generated definition].
immune organ
reproductive structure
An anatomical structure that is part of the reproductive system.
reproductive structure
multi cell component structure
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
multi cell component structure
abdomen organ
An organ that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
abdomen organ
trunk organ
An organ that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
trunk organ
embryonic tissue
A portion of tissue that is part of an embryo.
embryonic tissue
male preputial gland
One of the sebaceous glands of the corona and neck of the glans penis.
male preputial gland
dorsal telencephalic commissure
dorsal telencephalic commissure
the fiber tracts that connect the dorsal region of the two cerebral hemispheres and span the longitudinal fissure, including the corpus callosum and hippocampal commissure[MP].
female reproductive gland
A sex gland that is part of a female reproductive system.
female reproductive gland
male reproductive gland
A sex gland that is part of a male reproductive system.
male reproductive gland
definitive endoderm
definitive endoderm
extraembryonic membrane
Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
extraembryonic membrane
segment of aorta
Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle.
segment of aorta
occipital region
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
occipital region
duct of male reproductive system
Any of the ducts that are part of a male reproductive system.
duct of male reproductive system
endo-epithelium
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
endo-epithelium
brain commissure
A commissure that is part of a brain.
brain commissure
heart layer
heart layer
the laminar structure of the heart
urinary system structure
An anatomical structure that is part of a excretory system.
urinary system structure
diencephalic nucleus
A nucleus of brain that is part of a diencephalon.
diencephalic nucleus
adrenal/interrenal gland
This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]
adrenal/interrenal gland
squamous epithelium
an epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
squamous epithelium
digestive gland
A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion.
digestive gland
circulatory organ
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood[GO].
circulatory organ
tracheobronchial tree
the structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells.
tracheobronchial tree
outer epithelial layer
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. The epidermis of a more complex invertebrate is just one-layer deep, and may be protected by a non-cellular cuticle. The epidermis of a higher vertebrate has many layers, and the outer layers are reinforced with keratin and then die[WP].
outer epithelial layer
epithelial sac
An epithelial tube that is open at one end only.
epithelial sac
ciliated columnar epithelium
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
ciliated columnar epithelium
nucleus of thalamus
A nucleus of brain that is part of a thalamus.
nucleus of thalamus
external nose
Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae.
external nose
dermal bone
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
dermal bone
telencephalic nucleus
A nucleus of brain that is part of a telencephalon.
telencephalic nucleus
acinus
An acinus refers to any cluster of cells that resembles a many-lobed 'berry,' such as a raspberry (acinus is Latin for berry). The berry-shaped termination of an exocrine gland, where the secretion is produced is acinar in form, as is the alveolar sac containing multiple alveoli in the lungs.
acinus
digestive tract diverticulum
Branch or outpocketing of the digestive tract.
digestive tract diverticulum
sac
sac
multicellular anatomical structure
An anatomical structure that has more than one cell as a part.
multicellular anatomical structure
oral gland
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
oral gland
male accessory sex gland
Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
male accessory sex gland
neural crest-derived structure
An anatomical structure that develops from the neural crest.
neural crest-derived structure
structure with developmental contribution from neural crest
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
germ layer / neural crest
germ layer / neural crest
ecto-epithelium
Epithelium that derives from the ectoderm. Examples: epithelium of acinus of lactiferous duct, subscapular lens epithelium, epithelium of posterior surface of cornea.
ecto-epithelium
pseudostratified ciliated columnar epithelium
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
pseudostratified ciliated columnar epithelium
bone of appendage girdle complex
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
bone of appendage girdle complex
synovial limb joint
Any synovial joint that is part of a (free) limb.
synovial limb joint
cell part cluster of neuraxis
A multi cell component structure that is part of a central nervous system.
cell part cluster of neuraxis
gray matter of telencephalon
A portion of gray matter of neuraxis that is part of a telencephalon.
gray matter of telencephalon
meso-epithelium
Epithelium that derives from the mesoderm. [Automatically generated definition].
meso-epithelium
bone of jaw
bone of jaw
hemopoietic tissue
Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue
hemopoietic tissue
subdivision of uterine tube
subdivision of uterine tube
subdivision of tube
subdivision of tube
digestive system organ
digestive system organ
sex-specific anatomical structure
A part of the body present only in a specific gender.
sex-specific anatomical structure
male anatomical structure
A part of the body present only in males.
male anatomical structure
female anatomical structure
A part of the body present only in females.
female anatomical structure
length unit
A unit which is a standard measure of the distance between two points.
length unit
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
mass unit
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
temperature unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
temperature unit
substance unit
A unit which is a standardised quantity of an element or compound with uniform composition.
substance unit
meter
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
meter
kilogram
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
kilogram
second
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
second
kelvin
A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water.
kelvin
mole
A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12.
mole
centimeter
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
centimeter
millimeter
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
millimeter
micrometer
A length unit which is equal to one millionth of a meter or 10^[-6] m.
micrometer
nanometer
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
nanometer
gram
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
gram
milligram
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
milligram
microgram
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
microgram
nanogram
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
nanogram
picogram
A mass unit which is equal to 10^[-12] g.
picogram
degree Celsius
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
degree Celsius
millisecond
A time unit which is equal to one thousandth of a second or 10^[-3] s.
millisecond
microsecond
A time unit which is equal to one millionth of a second or 10^[-6] s.
microsecond
minute
A time unit which is equal to 60 seconds.
minute
hour
A time unit which is equal to 3600 seconds or 60 minutes.
hour
day
A time unit which is equal to 24 hours.
day
week
A time unit which is equal to 7 days.
week
month
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
month
year
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
year
micromole
A substance unit equal to a millionth of a mol or 10^[-6] mol.
micromole
nanomole
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
nanomole
picomole
A substance unit equal to 10^[-12] mol.
picomole
femtomole
A substance unit equal to 10^[-15] mol.
femtomole
attomole
A substance unit equal to 10^[-18] mol.
attomole
base unit
A unit which is one of a particular measure to which all measures of that type can be related.
base unit
concentration unit
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
concentration unit
mass density unit
A density unit which is a standard measure of the mass of a substance in a given volume.
mass density unit
unit of molarity
A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution.
unit of molarity
molar
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
molar
millimolar
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
millimolar
micromolar
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
micromolar
picomolar
A unit of molarity which is equal to 10^[-12] M.
picomolar
volume unit
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
volume unit
cubic centimeter
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
cubic centimeter
milliliter
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
milliliter
liter
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
liter
microliter
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
microliter
nanoliter
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
nanoliter
picoliter
A volume unit which is equal to 10^[-12] L.
picoliter
femtoliter
A volume unit which is equal to 10^[-15] L.
femtoliter
radiation unit
A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source.
radiation unit
activity (of a radionuclide) unit
A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance.
activity (of a radionuclide) unit
curie
An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps).
curie
roentgen
An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs.
roentgen
Roentgen equivalent man
A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem.
Roentgen equivalent man
disintegrations per minute
An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute.
disintegrations per minute
counts per minute
An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute.
counts per minute
light unit
A unit which is a standard measure of the intensity of light.
light unit
mass percentage
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
mass percentage
mass volume percentage
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
mass volume percentage
volume percentage
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
volume percentage
gram per liter
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
gram per liter
milligram per milliliter
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
milligram per milliliter
dimensionless unit
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
dimensionless unit
percent
A dimensionless ratio unit which denotes numbers as fractions of 100.
percent
count unit
A dimensionless unit which denotes a simple count of things.
count unit
degree Fahrenheit
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
degree Fahrenheit
pH
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
pH
volume per unit volume
A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution.
volume per unit volume
milliliter per liter
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
milliliter per liter
gram per deciliter
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
gram per deciliter
deciliter
A volume unit which is equal to one tenth of a liter or 10^[-1] L.
deciliter
colony forming unit per milliliter
A colony forming unit which a measure of viable bacterial numbers in one milliliter.
colony forming unit per milliliter
bit
An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1).
bit
acute lymphoblastic leukemia
acute lymphoblastic leukemia
acute myeloid leukemia
acute myeloid leukemia
acute promyelocytic leukemia
acute promyelocytic leukemia
asthma
asthma
Burkitts lymphoma
Burkitts lymphoma
cancer
cancer
chronic myelogenous leukemia
chronic myelogenous leukemia
colorectal adenocarcinoma
colorectal adenocarcinoma
diabetes mellitus
diabetes mellitus
disease
disease
family history
family history
insulinoma
insulinoma
leukemia
leukemia
neoplasm
neoplasm
experiment performer
experiment performer
type I diabetes mellitus
type I diabetes mellitus
type II diabetes mellitus
type II diabetes mellitus
lymphoid neoplasm
lymphoid neoplasm
data analyst
data analyst
investigator
investigator
submitter
submitter
myeloid neoplasm
myeloid neoplasm
mouse prenatal
mouse prenatal
Theiler stage 11
Theiler stage 11
Theiler stage 17
Theiler stage 17
Theiler stage 21
Theiler stage 21
Theiler stage 22
Theiler stage 22
Theiler stage 24
Theiler stage 24
Theiler stage 26
Theiler stage 26
Theiler stage 28
Theiler stage 28
International Unit
International Unit
mouse postnatal
mouse postnatal
Theiler stage 27
Theiler stage 27
Theiler stage 1
Theiler stage 1
Theiler stage 2
Theiler stage 2
Theiler stage 3
Theiler stage 3
Theiler stage 4
Theiler stage 4
Theiler stage 5
Theiler stage 5
Theiler stage 6
Theiler stage 6
Theiler stage 7
Theiler stage 7
Theiler stage 8
Theiler stage 8
Theiler stage 9
Theiler stage 9
Theiler stage 10
Theiler stage 10
Theiler stage 12
Theiler stage 12
Theiler stage 13
Theiler stage 13
Theiler stage 14
Theiler stage 14
Theiler stage 15
Theiler stage 15
Theiler stage 16
Theiler stage 16
Theiler stage 18
Theiler stage 18
Theiler stage 19
Theiler stage 19
Theiler stage 20
Theiler stage 20
Theiler stage 23
Theiler stage 23
Theiler stage 25
Theiler stage 25
Feature Extraction Software
Feature Extraction Software
Obsolete Class
Obsolete Class
embryonic day 15.5
15.5 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 16.5
16.5 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 8.5
Person: Chris Stoeckert, Jie Zheng
8.5 days after fertilization
embryonic day 17.5
Person: Chris Stoeckert, Jie Zheng
17.5 days after fertilization
embryonic day 8.25
8.25 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 18.5
Person: Chris Stoeckert, Jie Zheng
18.5 days after fertilization
embryonic day 8
8 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 18
18 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 11.5
Person: Chris Stoeckert, Jie Zheng
11.5 days after fertilization
postnatal day 0
Person: Jie Zheng
0 day after birth
embryonic day 12.5
12.5 days after fertilization
Person: Chris Stoeckert, Jie Zheng
postnatal day 4
4 days after birth
Person: Jie Zheng
embryonic day 9.5
Person: Chris Stoeckert, Jie Zheng
9.5 days after fertilization
postnatal day 12
12 days after birth
Person: Jie Zheng
embryonic day 10.5
Person: Chris Stoeckert, Jie Zheng
10.5 days after fertilization
postnatal day 60
Person: Jie Zheng
60 days after birth
embryonic day 13.5
Person: Chris Stoeckert, Jie Zheng
13.5 days after fertilization
embryonic day 14.5
Person: Chris Stoeckert, Jie Zheng
14.5 days after fertilization
postnatal day 1
Person: Jie Zheng
1 day after birth
example to be eventually removed
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
failed exploratory term
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.
metadata complete
organizational term
PERSON:Alan Ruttenberg
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."
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.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
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.
pending final vetting
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
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 imported
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.
term split
to be replaced with external ontology term
Alan Ruttenberg
Terms with this status should eventually replaced with a term from another ontology.
group:OBI
to be replaced with external ontology term
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
requires discussion
Helicos
Helicos
Philippe Rocca-Serra
Roche
Philippe Rocca-Serra
Roche
Illumina
Illumina
Philippe Rocca-Serra
Li-Cor
Li-Cor
Philippe Rocca-Serra
Applied Biosystems
Applied Biosystems
Philippe Rocca-Serra
Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations"
Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO"
Institute for Formal Ontology and Medical Information Science (IFOMIS)
Barry Smith: "Basic Tools of Formal Ontology"
Pierre Grenon
Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE"
Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain"
Barry Smith: "Beyond Concepts: Ontology as Reality Representation"
Barry Smith: "Against Fantology"
Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization"