John Judkins
VEuPathDB Ontology
The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.
Cristian Cocos
Jie Zheng
2019-12-16
Chris Stoeckert
BFO OWL specification label
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
Label used in EuPathDB
EuPathDB alternative term
definition shown on EuPathDB website
EuPathDB definition
Label of terms used in Amazonia data dictionary. It is in Spanish.
obsolete_Amazonia data dictionary label (es)
true
English label used in Amazonia project for display on the website
obsolete_Amazonia preferred label (en)
true
Spanish label used in Amazonia project for display on the website
obsolete_Amazonia preferred label (es)
true
label of term used in the ontology
obsolete_ontological label
true
Label of terms used in PRISM data dictionary. It is in English.
obsolete_PRISM data dictionary label (en)
true
English label used in Prism project for display on the website
obsolete_PRISM preferred label (en)
true
Term description provided by Amazonia group
obsolete_Amazonia description
true
Term description provided by PRISM group
PRISM description
Three options of term type:
- category: used for organize the filter in the website, not ontology term
- variable: term in the data dictionary of project. Should have mapped ontology term associate with it
- value: controlled vocubulary used for annotation of variable in the data dictionary. Should have mapped ontology term associate with it
obsolete_term type
true
specify ICEMR term original from which database
obsolete_resource ID
true
definition of term in ontology
obsolete_ontological definition
true
An annotation property used to specify the order of terms displayed on a website.
displayOrder
display order
Label of terms used in Indian data dictionary. It is in English.
obsolete_Indian data dictionary label (en)
true
English label used in Indian project for display on the website
obsolete_Indian preferred label (en)
true
Term description provided by Indian group
obsolete_Indian description
true
Translated English label of terms in Amazonia data dictionary.
obsolete_Amazonia data dictionary label (en)
true
In a data file, there is a column with name 'age'. It mapped to EuPath ontology term 'age at visit'. We can add 'implements variable' annotation with value 'age' to term 'age at visit'.
Column header for each variable from the original datasets (use format from datasets, not data dictionary).
column header
variable
The column order of variables in the original data files
colOrder
column order
The original file name for the data file the variable was found in, or a shortened version of the file name that contains all relevant information to identify the data file.
dataFile
data file
The highest level parent term (Household, Participant, Observation, Specimen) the variable falls under.
category
The variable description from the data dictionary. Useful for assigning display labels. To be provided either directly from the data provider in their codebook or filled out by ClinEpi Outreach before handing over to Ontology.
codebookDescription
codebook description
All possible responses and their mapped terms for each variable, from the data dictionary. Useful for value mapping.
codebookValues
codebook values
An annotation that specifies how a term is used in generation search filters on a website. It has five options:
category: a term to organize the variables for exploration on the website
variable: a variable in the dataset
variable, derived: one term that is calculated, using the data in two or more other variables
multifilter: any value below it in the hierarchy will be displayed as a multifilter
value: the value of a multifilter
termType
term type
editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred term
editor preferred term
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
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.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
definition
textual definition
textual definition
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
editor note
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
Person: Alejandra Gonzalez-Beltran
Person: Philippe Rocca-Serra
ISA tools project (http://isa-tools.org)
ISA alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC alternative term
IEDB alternative term
An alternative term used by the IEDB.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
temporal interpretation
temporal interpretation
https://code.google.com/p/obo-relations/wiki/ROAndTime
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.
An account of the content of the resource.
Description
Description
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.
A reference to a resource from which the present resource
is derived.
Source
Source
title
label
label
part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
X precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
http://purl.obolibrary.org/obo/ro.owl
precedes
B occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in; unfolds in; unfolds_in
http://purl.obolibrary.org/obo/ro.owl
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
no longer in use
obsolete_material may be used for
true
manifestation of
A relation between a medication material and a disease or symptom that it may treat.
may treat
A relation between a drug product and (one of) its active ingredient.
replaced with RO:0002248
obsolete_has active ingredient
true
has measurement unit label
has measurement unit label
is about
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
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.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
http://purl.obolibrary.org/obo/iao.owl
mentions
denotes
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.
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
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
person:Alan Ruttenberg
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
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
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
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.
Alan Ruttenberg
is quality measurement of
is duration of
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
is duration of
provides_service_consumer_with
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
provides_service_consumer_with
is_supported_by_data
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.
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
OBI
OBI
Philly 2011 workshop
is_supported_by_data
has_specified_input
see is_input_of example_of_usage
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.
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: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
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.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
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
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
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
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.
OBI
OBI
objective_achieved_by
is member of organization
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
Person:Alan Ruttenberg
Person:Helen Parkinson
Person:Alan Ruttenberg
Person:Helen Parkinson
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
is member of organization
has organization member
Relating an organization to a legal person or organization.
See tracker:
https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
Person: Jie Zheng
has organization member
has value specification
A relation between an information content entity and a value specification that specifies its value.
PERSON: James A. Overton
OBI
has value specification
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
concretizes
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
role of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
has role
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
derives from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
temporal relation
move to BFO?
Allen
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
starts
inverse of starts with
Chris Mungall
Allen
starts
A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has active ingredient
the relationship between a fraction and the number above the line
has numerator
the relationship between a fraction and the number below the line (or divisor)
has denominator
has measurement value
has measurement value
has specified value
A relation between a value specification and a number that quantifies it.
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.
PERSON: James A. Overton
OBI
has specified value
fracture (bone)
Fracture
burns
Burn
Foreign body
Bacterial infection of skin
Tree (organism)
Tree
shock
ICEMR protein array
shock
Soft tissue injury
Animal bite (morphologic abnormality)
Animal bite
Pyrexia of unknown origin
An identifier that denotes a group of organisms or groups of organisms based on common ancestors.
genetic clade of organism
clade name
entity
Entity
entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
Continuant
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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
occurrent
Occurrent
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
ic
IndependentContinuant
independent continuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
process
Process
process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
disposition
Disposition
disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
realizable
RealizableEntity
realizable entity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
quality
Quality
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
sdc
SpecificallyDependentContinuant
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
role
Role
role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student 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.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
site
Site
site
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
gdc
GenericallyDependentContinuant
generically dependent continuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
function
p-boundary
ProcessBoundary
process boundary
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
material
MaterialEntity
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
immaterial
ImmaterialEntity
immaterial entity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
liver cell line
fibroblast cell line
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
A monocarboxylic acid comprising 1,8-naphthyridin-4-one substituted by carboxylic acid, ethyl and methyl groups at positions 3, 1, and 7, respectively. An orally administered antibacterial, it is used in the treatment of lower urinary-tract infections due to Gram-negative bacteria, including the majority of E. coli, Enterobacter, Klebsiella, and Proteus species.
nalidixic acid
A triazole-based antifungal agent used for the treatment of esophageal candidiasis, invasive pulmonary aspergillosis, and serious fungal infections caused by Scedosporium apiospermum and Fusarium spp. It is an inhibitor of cytochrome P450 2C9 (CYP2C9) and CYP3A4.
voriconazole
A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively.
ciprofloxacin
An optically active form of dopa having L-configuration. Used to treat the stiffness, tremors, spasms, and poor muscle control of Parkinson's disease
L-dopa
A cinchona alkaloid that is cinchonidine in which the hydrogen at the 6-position of the quinoline ring is substituted by methoxy.
quinine
A chlorophenylethane that is 1,1,1-trichloro-2,2-diphenylethane substituted by additional chloro substituents at positions 4 of the phenyl substituents. It is a commonly used organochlorine insecticide.
DDT
An inorganic peroxide consisting of two hydroxy groups joined by a covalent oxygen-oxygen single bond.
hydrogen peroxide
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
Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6.
penicillin
An organochlorine compound that is dichloro-substituted acetamide containing a nitrobenzene ring, an amide bond and two alcohol functions.
chloramphenicol
Any of a group of aminoglycoside antibiotics produced by fermentation of some Micromonospora spp.
gentamycin
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
molecular entity
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
drug
A macrocyclic lactone with a ring of twelve or more members derived from a polyketide.
macrolide
A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group.
amoxicillin
A macrolide antibiotic used to treat potentially life-threatening fungal infections.
amphotericin B
A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-phenylacetamido group.
ampicillin
A macrolide antibiotic useful for the treatment of bacterial infections.
azithromycin
A carboxylic ester obtained by formal condensation of cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylic acid and [(2-methyl-1,1'-biphenyl)-3-yl]methanol.
bifenthrin
gamma-hexachlorocyclohexane
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
antimicrobial agent
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
metal atom
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
macromolecule
A macromolecule is a 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.
polymer
macromolecule
A carbamate ester obtained by the formal condensation of 1-naphthol with methylcarbamic acid.
carbaryl
bendiocarb
An organic thiophosphate that is O,O-diethyl hydrogen phosphorothioate in which the hydrogen of the hydroxy group has been replaced by a 3,5,6-trichloropyridin-2-yl group.
chlorpyrifos
An organic thiophosphate that is O,O-dimethyl hydrogen phosphorothioate in which the hydrogen of the hydroxy group has been replaced by a 3,5,6-trichloropyridin-2-yl group.
chlorpyrifos-methyl
An alkenyl phosphate that is the 2,2-dichloroethenyl ester of dimethyl phosphate.
dichlorvos
An organochlorine compound resulting from the epoxidation of the double bond of aldrin. It is the active metabolite of the proinsecticde aldrin.
dieldrin
A benzoylurea insecticide that is urea in which a hydrogen attached to one of the nitrogens is replaced by a 4-chlorophenyl group, and a hydrogen attached to the other nitrogen is replaced bgy a 2,6-difluorobenzoyl group.
diflubenzuron
A monocarboxylic acid amide that is N-methylacetamide in which one of the hydrogens of the methyl group attached to the carbonyl moiety is replaced by a (dimethoxyphosphorothioyl)sulfanediyl group.
dimethoate
An organic thiophosphate that is O,O-dimethyl O-phenyl phosphorothioate substituted by a methyl group at position 3 and a nitro group at position 4.
fenitrothion
An organic thiophosphate that is O,O-dimethyl hydrogen phosphorothioate in which the hydrogen atom of the hydroxy group is replaced by a 3-methyl-4-(methylsulfanyl)phenyl group. It exhibits acaricidal and insecticidal activities.
fenthion
methoprene
An organic cation that consists of 4,4'-bipyridine bearing two N-methyl substituents loctated at the 1- and 1'-positions.
paraquat
A cyclopropanecarboxylate ester in which the esterifying alcohol is 3-phenoxybenzyl alcohol and the cyclopropane ring is substituted with a 2,2-dichlorovinyl group and with gem-dimethyl groups.
permethrin
An organic thiophosphate that is ethyl mandelate in which the hydroxy group has been replaced by a (dimethoxyphosphorothioyl)sulfanediyl group.
phenthoate
A carbamate ester that is phenyl methylcarbamate substituted at position 2 by a propan-2-yloxy group.
propoxur
An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms.
triazoles
An aminoquinoline that is quinoline which is substituted at position 4 by a [5-(diethylamino)pentan-2-yl]amino group at at position 7 by chlorine. It is used for the treatment of malaria, hepatic amoebiasis, lupus erythematosus, light-sensitive skin eruptions, and rheumatoid arthritis.
chloroquine
A two-component mixture comprising trimethoprim and sulfamethoxazole.
co-trimoxazole
A drug used in the treatment of malaria. Antimalarials are usually classified on the basis of their action against Plasmodia at different stages in their life cycle in the human.
antimalarial
carbosulfan
famphur
fenamiphos
An organic thiophosphate that is O,O-dimethyl O-pyrimidin-4-yl phosphorothioate substituted by a methyl group at position 6 and a diethylamino group at position 2.
pirimiphos-methyl
profenofos
An organic sulfide that is diphenyl sulfide in which the hydrogen at the para position of each of the phenyl groups has been replaced by a (dimethoxyphosphorothioyl)oxy group.
temephos
An N-nitro compound consisting of 2-nitroguanidine having a (2-chloro-1,3-thiazol-5-yl)methyl group at position 1 and a methyl group at position 3.
clothianidin
A two-component mixture comprising spinosyn A and spinosyn D in a ratio of approximately 5:1. Obtained from the fermentation of the naturally occurring soil dwelling bacterium Saccharopolyspora spinosa, it is used for the topical treatment of head lice.
spinosad
An aromatic ether that consists of propylene glycol having a 2-pyridyl group at the O-1 position and a 4-phenoxyphenyl group at the O-3 position.
pyriproxyfen
A diastereoisomeric mixture comprising the enantiomeric pair (1R)-cis-(alphaS)- and (1S)-cis-(alphaR)-cyfluthrin in ratio 1:2 with the enantiomeric pair (1R)-trans-(alphaS)- and (1S)-trans-(alphaR)-cyfluthrin.
beta-cyfluthrin
Reaction product comprising equal quantities of CHEBI:39323 and CHEBI:39327.
lambda-cyhalothrin
A racemate comprising equimolar amounts of (1R)-cis-(alphaS)- and (1S)-cis-(alphaR)-cypermethrin.
alpha-cypermethrin
A diastereoisomeric mixture comprising the enantiomeric pair (1R)-cis-(alphaS)- and (1S)-cis-(alphaR)-cypermethrin in ratio approximately 2:3 with the enantiomeric pair (1S)-trans-(alphaR)- and (1R)-trans-(alphaS)-cypermethrin.
beta-cypermethrin
A member of the class of pyrroles that is 4-bromo-1H-pyrrole-3-carbonitrile which is substituted at positions 1, 2 and 5 by ethoxymethyl, p-chlorophenyl and trifluoromethyl groups, respectively. A proinsecticide used for termite control and crop protection against several insects and mite pests.
chlorfenapyr
An aromatic ether that is the 3-phenoxybenzyl ether of 2-(4-ethoxyphenyl)-2-methylpropan-1-ol.
etofenprox
tetramethrin
A carboxylic ester obtained by formal condensation between 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropanecarboxylic acid and (4-fluoro-3-phenoxyphenyl)(hydroxy)acetonitrile.
cyfluthrin
A carboxylic ester obtained by formal condensation between 3-(2-chloro-3,3,3-trifluoroprop-1-en-1-yl)-2,2-dimethylcyclopropanecarboxylic acid and cyano(3-phenoxyphenyl)methanol.
cyhalothrin
A carboxylic ester resulting from the formal condensation between 3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropanecarboxylic acid and the alcoholic hydroxy group of hydroxy(3-phenoxyphenyl)acetonitrile.
cypermethrin
A cyclopropanecarboxylate ester obtained by formal condensation between 3-(2,2-dibromovinyl)-2,2-dimethylcyclopropanecarboxylic acid and cyano(3-phenoxyphenyl)methanol. It is the active insecticide of the proinsecticide tralomethrin.
deltamethrin
A member of the class of triazoles that is propan-2-ol substituted at position 1 and 3 by 1H-1,2,4-triazol-1-yl groups and at position 2 by a 2,4-difluorophenyl group. It is an antifungal drug used for the treatment of mucosal candidiasis and for systemic infections including systemic candidiasis, coccidioidomycosis, and cryptococcosis.
fluconazole
A semisynthetic cyclic hexapeptide echinocandin antibiotic which exerts its effect by inhibiting the synthesis of 1,3-beta-D-glucan, an integral component of the fungal cell wall.
caspofungin
Any of several wide-spectrum macrolide antibiotics obtained from actinomycete Saccharopolyspora erythraea (formerly known as Streptomyces erythraeus).
erythromycin
A racemate comprising equimolar amounts of (R)- and (S)-fipronil.
fipronil
pivmecillinam hydrochloride
A semisynthetic echinocandin anti-fungal drug. It is active against Aspergillus and Candida species and is used for the treatment of invasive candidiasis.
anidulafungin
An imidazolidine that is N-nitroimidazolidin-2-imine bearing a (6-chloro-3-pyridinyl)methyl substituent at position 1.
imidacloprid
A cyclic hexapeptide echinocandin antibiotic which exerts its effect by inhibiting the synthesis of 1,3-beta-D-glucan, an integral component of the fungal cell wall. It is used as the sodium salt for the treatment of invasive candidiasis, and of aspergillosis in patients who are intolerant of other therapy.
micafungin
An N-arylpiperazine that is cis-ketoconazole in which the imidazol-1-yl group is replaced by a 1,2,4-triazol-1-yl group and in which the actyl group attached to the piperazine moiety is replaced by a p-[(+-)1-sec-butyl-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl]phenyl group. A potent P-glycoprotein and CYP3A4 inhibitor, it is used as an antifungal drug for the treatment of various fungal infections, including aspergillosis, blastomycosis, candidiasis, chromoblastomycosis, coccidioidomycosis, cryptococcosis, histoplasmosis, and sporotrichosis.
itraconazole
A racemate composed of (+)-(11R,2'S)- and (-)-(11S,2'R)-enantiomers of mefloquine. An antimalarial agent which acts as a blood schizonticide; its mechanism of action is unknown.
mefloquine
An N-arylpiperazine that consists of piperazine carrying two 4-substituted phenyl groups at positions 1 and 4. A triazole antifungal drug.
posaconazole
A racemate comprising equimolar amounts of (R) and (S)-malaoxon. It is the active insecticide of the proinsecticide malathion.
malaoxon
A racemate comprising equimolar amounts of (R) and (S)-malathion. It is a broad spectrum organophosphate proinsecticide used to control a wide range of pests including Coleoptera, Diptera, fruit flies, mosquitos and spider mites.
malathion
methoxychlor
A phosphonic ester that is dimethyl phosphonate in which the hydrogen atom attched to the phosphorous is substituted by a 2,2,2-trichloro-1-hydroxyethyl group.
trichlorfon
Chlorphoxim
An N-substituted diamine that is pentane-1,4-diamine substituted by a 6-methoxyquinolin-8-yl group at the N(4) position. It is a drug used in the treatment of malaria and Pneumocystis pneumonia.
primaquine
resmethrin
cell
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
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.
cell
cultured cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
cultured cell
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
erythrocyte
experimentally modified cell in vitro
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
experimentally modified cell in vitro
diastolic blood pressure
white blood cell count
respiration rate
partial pressure of blood oxygen (Po2)
A disease that involving errors in metabolic processes of building or degradation of molecules.
disease of metabolism
A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions.
disease by infectious agent
A fungal infectious disease that results_in infection of the keratinized layers located_in skin, located_in hair or located_in nail, which extends deeper into the epidermis, has_material_basis_in Fungi and results_in_formation_of skin lesions.
cutaneous mycosis
A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell).
sensory system disease
A respiratory system disease which involves the lower respiratory tract.
lower respiratory tract disease
An opportunistic mycosis that has_material_basis_in Penicillium marneffei, results_in systemic infection and has_symptom fever, has_symptom anemia, has_symptom weight loss, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom respiratory signs, and has_symptom skin lesions.
penicilliosis
A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread.
primary bacterial infectious disease
A skin disease that is characterized by a rash that results from a variety of causes including bacteria, viruses, toxins, drugs and autoimmune disorders.
exanthem
An autoimmune hypersensitivity disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the musculoskeletal system.
autoimmune disease of musculoskeletal system
An autoimmune hypersensitivity disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the skin and connective tissue.
autoimmune disease of skin and connective tissue
A disease of metabolism that has _material_basis_in enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to an endocrine organ disease, organ malfunction, inadequate intake, dietary deficiency, or malabsorption.
acquired metabolic disease
A cheilitis characterized by inflammation of one or both of the corners of the mouth.
angular cheilitis
An intestinal disease characterized by a protrusion of abdominal cavity contests through the inguinal canal.
inguinal hernia
A middle ear disease characterized by an inflammation of the mucosal lining of the mastoid antrum and the mastoid air cell system inside the mastoid process.
mastoiditis
A tooth disease characterized by a localized collection of pus associated with a tooth.
dental abscess
sensorineural hearing loss
A viral infectious disease that results in inflammation located in salivary gland, has material basis in Mumps virus, which is transmitted by droplet spread of saliva or mucus from the mouth, nose, or throat of an infected person, or transmitted by contaminated fomites. The infection has symptom fever, has symptom headache, has symptom muscle aches, has symptom tiredness, has symptom loss of appetite, has symptom swollen and tender salivary glands under the ears or jaw on one or both sides of the face.
mumps
A parotid disease characterized by the inflammation of one or both parotid glands.
parotitis
An upper respiratory tract disease which involves inflammation of the tonsils resulting from bacterial (Group A streptococcus) and viral (Epstein-Barr virus, adenovirus) infections. Symptoms include a severe sore throat (which may be experienced as referred pain to the ears), painful/difficult swallowing, coughing, headache, myalgia (muscle aches), fever and chills. Tonsillitis is characterized by signs of red, swollen tonsils which may have a purulent exudative coating of white patches (i.e. pus). Swelling of the cheeks and neck may occur.
tonsillitis
An upper respiratory tract disease which involves inflammation of the mucous membranes of the nose, throat, eyes, and eustachian tubes with watery then purulent discharge. This is an acute contagious disease caused by rhinoviruses, human parainfluenza viruses, human respiratory syncytial virus, influenza viruses, adenoviruses, enteroviruses, or metapneumovirus.
common cold
A kidney disease characterized by the failure of the kidneys to adequately filter waste products from the blood.
kidney failure
A otitis which involves inflammation of the middle ear.
otitis media
salivary gland disease
A viral infectious disease that results in infection located in mouth, has material basis in Human coxsackievirus A16, has material basis in Human enterovirus 71, has material basis in group B coxsackievirus, or has material basis in echoviruses, which are transmitted by ingestion of food contaminated with feces, transmitted by contact with pharyngeal secretions, or transmitted by droplet spread of oronasal secretions. The infection has symptom fever, has symptom sore throat, and has symptom lesions in the back area of the mouth, particularly the soft palate or tonsillar pillars.
herpangina
tooth disease
A lung disease characterized by inadequate gas exchange by the respiratory system.
respiratory failure
A primary bacterial infectious disease that results in prolonged contraction of skeletal muscle fibers, has material basis in Clostridium tetani, which produces tetanospasmin, a neurotoxin, which is carried to the brain and spinal cord, where it binds irreversibly to receptors inhibiting neurotransmission. Damaged upper motor neurons cannot control reflex responses to afferent sensory stimuli.
tetanus
A respiratory failure that results from diffuse injury to the endothelium of the lung (as in sepsis, chest trauma, massive blood transfusion, aspiration of the gastric contents, or pneumonia) and is characterized by pulmonary edema with an abnormally high amount of protein in the edematous fluid and by difficult rapid breathing and hypoxemia.
ICEMR protein array
adult respiratory distress syndrome
A lower respiratory tract disease that affects the airways leading into the lungs, which is caused due to inflammation of the bronchi and bronchioles, infection, or blockage.
bronchial disease
neutropenia
marasmus
A parasitic protozoa infectious disease characterized as a vector-borne infectious disease caused by the presence of protozoan parasites of the genus Plasmodium in the red blood cells, transmitted from an infected to an uninfected individual by the bite of anopheline mosquitoes, and characterized by periodic attacks of chills and fever that coincide with mass destruction of blood cells and the release of toxic substances by the parasite at the end of each reproductive cycle.
malaria
An intestinal infectious disease that involves inflammation of the intestines, especially colon, due to chemical irritants, bacteria, protozoa, or parasitic worms, which results in severe diarrhea with passage of mucus and blood.
dysentery
rectal disease
A nail disease characterized by often-tender bacterial or fungal hand infection or foot infection due to either bacteria or fungus (Candida albicans) where the nail and skin meet at the side or the base of a finger or toe nail. The infection can start suddenly (acute paronychia) or gradually (chronic paronychia). Puss is usually present, along with gradual thickening and browning discoloration of the nail plate.
paronychia
A cystitis characterized by a sudden onset or severe symptoms.
acute cystitis
A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea.
diarrhea
A primary bacterial infectious disease that is a communicable systemic illness, has_material_basis_in Salmonella enterica subsp enterica serovar Typhi, which is transmitted_by ingestion of food or water contaminated with the feces of an infected person. The infection has_symptom fever, has_symptom diarrhea, has_symptom prostration, has_symptom headache, has_symptom splenomegaly, has_symptom liver enlargement, has_symptom eruption of rose-colored spots, and has_symptom leukopenia.
typhoid fever
A disease by infectious agent that is carried out by a parasite which by definition is a pathogen that simultaneously injures and derives sustenance from its host.
parasitic infectious disease
A malaria that involves neurologic damage resulting from blockage of the blood vessels, caused due to the infection of the red blood cells by Plasmodium species.
ICEMR protein array
cerebral malaria
glossitis
A sensory system disease that is located_in the eye or the adnexa of the eye.
eye and adnexa disease
A primary bacterial infectious disease that is described as an acute, diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae, which is characterized by profuse watery diarrhea, vomiting, leg cramps, circulatory collapse and shock.
cholera
An opportunistic mycosis that involves fungal infection of the mouth, throat, skin, scalp, vagina, fingers, nails, bronchi, lungs, heart and brain by Candida species, of which Candida albicans is the most common. Systemic Candida infections are usually confined to severely immunocompromised persons.
candidiasis
A skin disease characterized by skin rash notable for pale red, raised and itchy bumps, located_in the upper dermis.
urticaria
A disease by infectious agent that results_in infection, has_material_basis_in Fungi, which pass the resistance barriers of the human or animal body.
fungal infectious disease
An autoimmune hypersensitivity disease that involves inflammation or pain in the muscles, joints, or fibrous tissue.
rheumatic disease
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
respiratory system disease
A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
integumentary system disease
lymphadenitis
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
musculoskeletal system disease
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
urinary system disease
A bowel dysfunction that is characterized by infrequent or difficult evacuation of feces.
constipation
dental caries
carbuncle
An upper respiratory tract disease involving inflammation of the throat or pharynx resulting from bacterial, viral, fungal infections or irritants like pollutants or chemical substances and smoking. The infection is often referred to as "sore throat". The symptoms include pain during swallowing, enlarged tonsils coated with a white discharge, runny nose, cough and slight fever.
pharyngitis
dyspepsia
A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen.
gastroenteritis
A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells.
anemia
A systemic mycosis that results_in fungal infection located_in human body of immunocompromised individuals, has_material_basis_in Fungi. The organisms invade via the respiratory tract, alimentary tract, or intravascular devices.
opportunistic mycosis
An endocrine system disease that is located_in the pancreas.
pancreas disease
A skin disease characterized by itchy, erythematous, vesicular, weeping and crusting patches of skin.
dermatitis
auditory system disease
A parasitic infectious disease that is caused by parasitic protozoa which are microorganisms classified as unicellular eukaryotes.
parasitic protozoa infectious disease
A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors. The disease has_symptom recurring periods of wheezing (a whistling sound while breathing), has_symptom chest tightness, has_symptom shortness of breath, has_symptom mucus production and has_symptom coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.
asthma
A disease of anatomical entity that is located_in the immune system.
immune system disease
A lung disease that is an inflammation of the bronchioles, the smallest air passages of the lungs. It is caused by viruses and bacteria. The disease has_symptom cough, has_symptom wheezing, has_symptom shortness of breath, has_symptom fever, has_symptom nasal flaring in infants and has_symptom bluish skin due to lack of oxygen.
bronchiolitis
gingivitis
anus disease
A bone disease that results_in inflammation of the located_in bone.
bone inflammation disease
periodontal disease
A skin disease where there is a diffuse infection of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin. Cellulitis can be caused by normal skin flora or by exogenous bacteria, and often occurs where the skin has previously been broken: cracks in the skin, cuts, blisters, burns, insect bites, surgical wounds, or sites of intravenous catheter insertion.
cellulitis
An integumentary system disease that is located_in skin.
skin disease
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
disease
A gastrointestinal system disease that is located_in the mouth.
mouth disease
Pyoderma is a skin infectious disease where the infection is pyogenic causing the formation of pus.
pyoderma
A dermatophytosis that results_in contagious fungal infection located_in scalp, located_in hair of head, located_in eyebrow or located_in eyelash, has_material_basis_in Ascomycota fungi that belong to a group called dermatophytes and has_symptom itching of the scalp, has_symptom pus filled lesions on the scalp, and has_symptom patches of hair loss, sometimes with a 'black dot' pattern.
tinea capitis
folliculitis
A rhinitis that is an allergic inflammation and irritation of the nasal airways involving sneezing, runny nose, nasal congestion, itching and tearing of the eyes caused by exposure to an allergen such as pollen, dust, mold, animal dander and droppings of cockroaches or house dust mites.
allergic rhinitis
pancreatitis
middle ear disease
A gastrointestinal system disease that is located_in the intestine.
intestinal disease
dental pulp disease
A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing.
pneumonia
An eye and adnexa disease that is located_in the eye.
eye disease
A conjunctival disease characterized by an inflammation of the conjunctiva, the outermost layer of the eye and the inner surface of the eyelids.
conjunctivitis
An arthritis that is an autoimmune disease which develops due to an infection located elsewhere in the body.
reactive arthritis
A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
connective tissue disease
A disease that manifests in a defined anatomical structure.
disease of anatomical entity
A disease of anatomical entity that has_material_basis_in hematopoietic cells.
hematopoietic system disease
peptic ulcer disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
gastrointestinal system disease
periodontitis
A mite infestation that is a contagious ectoparasite skin infection caused by human itch mite Sarcoptes scabiei type hominis, which burrows into the upper layer of the skin but never below the stratum corneum causing severe itching and a rash found on the hands, folds of the wrist, elbow or knee, penis, breast, and shoulder blades.
scabies
A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in joint and/or redness located_in skin over the joint.
arthritis
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
lung disease
A pyoderma consisting of three forms of skin lesions having either a thick, adherent, recurrent, dirty yellow crust with an erythematous margin (common or superficial impetigo) or lessions which are superficial, thin-walled, and bullous as found in bullous impetigo. The lesions in bullous (staphylococcal) impetigo, which are always caused by S aureus, are superficial, thin-walled, and bullous.
impetigo
An autoimmune disease of skin and connective tissue characterized by large blisters.
bullous pemphigoid
A viral infectious disease that results_in infection located_in nerve fiber, has_material_basis_in Human herpesvirus 3, which reactivates after appearing as chickenpox in childhood. The virus is transmitted_by direct contact with the rash, which can develop into chickenpox in newly-infected individuals. The infection has_symptom rash which is followed by blisters, has_symptom headache, has_symptom fever, has_symptom malaise, has_symptom itching, has_symptom burning pain, and has_symptom paresthesia.
herpes zoster
A viral infectious disease that results_in_formation_of lesions, located_in mouth, located_in face, located_in genitalia, or located_in hands, has_material_basis_in Human herpesvirus 1 or has_material_basis_in Human herpesvirus 2, which are transmitted_by direct contact with an active lesion or body fluid of an infected person.
herpes simplex
A viral infectious disease that results_in infection located_in skin, has_material_basis_in Measles virus, which is transmitted_by contact with oronasal secretions, or semen of an infected person. The infection has_symptom fever, has_symptom cough, has_symptom coryza, has_symptom conjunctivitis, and has_symptom maculopapular, erythematous rash.
measles
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
nervous system disease
A viral infectious disease that results_in infection located_in skin, has_material_basis_in Human herpesvirus 3, which is transmitted_by direct contact with secretions from the rash, or transmitted_by droplet spread of respiratory secretions. The infection has_symptom anorexia, has_symptom myalgia, has_symptom nausea, has_symptom fever, has_symptom headache, has_symptom sore throat, and has_symptom blisters.
chickenpox
viral exanthem
pyomyositis
A parasitic infectious disease that occurs when part of the body is infested with parasitic worms such as cestodes, nematodes and trematodes.
parasitic helminthiasis infectious disease
A parasitic protozoa infectious disease that involves infection caused by protozoan parasite of the genus Leishmania, which is transmitted by the bite of sand fly (subfamily Phlebotominae).
leishmaniasis
A leishmaniasis that involves skin infection caused by Leishmania species, resulting in one or more cutaneous lesions.
cutaneous leishmaniasis
A leishmaniasis that is the most severe form of the disease caused by protozoan parasites of the Leishmania genus, resulting in the infection of the internal organs such as liver, spleen and bone marrow. The symptoms include fever, weight loss, and an enlarged spleen and liver.
visceral leishmaniasis
A parasitic protozoa infectious disease that involves infection caused by the amoeba Entamoeba histolytica. Amebic invasion of the intestinal lining causes dysentery, colitis or diarrhea. The infection can also spread through the blood to the liver and, rarely, to the lungs, brain or other organs.
amebiasis
rectal prolapse
A disease by infectious agent that results in infection, has material basis in Viruses.
viral infectious disease
keratoconjunctivitis
An external ear disease that involves inflammation of the outer ear and ear canal. It can be caused by active bacterial or fungal infections.
otitis externa
A central nervous system disease that is characterized by an inflammation of the pia-arachnoid meninges. It can be caused by growth of bacteria, fungi, or parasites within the subarachnoid space or by the growth of bacteria or viruses within the meningeal or ependymal cells.
meningitis
A stomatitis characterized by the repeated formation of benign and non-contagious mouth ulcers.
aphthous stomatitis
A respiratory system disease which involves the upper respiratory tract.
upper respiratory tract disease
Hordeolum is a sequelae of infectious and parasitic disease consisting of an infection of the sebaceous glands at the base of the eyelashes. Styes are generally caused by a Staphylococcus aureus bacterial infection.
hordeolum
A glucose metabolism disease that is characterized by abnormally low levels of blood glucose.
ICEMR protein array
hypoglycemia
the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
clinical drug role
a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role
drug product
artemether
lumefantrine
A drug product in solution form for injection that has the chemical ingredient chloroquine and used in the treatment or prevention of malaria.
chloroquine injection
Chloroquine Injectable Solution
A drug product in tablet form for oral administration that has the chemical ingredient chloroquine and used in the treatment or prevention of malaria.
chloroquine tablets
Chloroquine Oral Tablet
geographic feature
An anthropogenic geographic feature is a geographic feature
resulting from the influence of human beings on nature.
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
An anthropogenic geographic feature is a geographic feature'resulting from the influence of human beings on nature.
anthropogenic geographic feature
A geographical feature associated with water.
hydrographic feature
Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation.
canal
A large expanse of saline water usually connected with an ocean.
sea
A body of water or other liquid of considerable size contained in a depression on a landmass.
lake
A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.
river
A watercourse which is linear and flows across the solid portion of a planetary surface.
Linear body of water flowing on the Earth's surface.
stream
An artificial body of water, often contained by a dam, constructed for the purpose of water storage.
reservoir
A point where groundwater or steam flows out of the ground, and is thus where the aquifer surface meets the ground surface or where there is a fissure.
spring
A flowing body of water.
watercourse
A body of water, usually of smaller size than a lake.
pond
A wetland ecosystem which includes communities of grasses, rushes, reeds, typhas, sedges, and other herbaceous plants (possibly with low-growing woody plants).
marsh
A spring that is produced by the emergence of geothermally-heated groundwater from the Earth's crust.
hot spring
A pond or lake used for the artificial culture of fish.
fishpond
An accumulation of water of varying size.
water body
Naturally formed, subterranean open area or chamber.
cave
A feature that has been constructed by deliberate human effort.
construction
A permanent walled and roofed construction.
building
An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.
farm
A landform that extends above the surrounding terrain in a limited area.
A landform that extends above the surrounding terrain in a limited area. A mountain is generally steeper than a hill, but there is no universally accepted standard definition for the height of a mountain or a hill although a mountain usually has an identifiable summit and a local relief of more than 300m.
mountain
Area of dry or relatively dry land surrounded by water or low wetland.
island
An area with a high density of trees. A small forest may be called a wood.
forested area
A landform elevated above the surrounding area.
elevation
An elevated and comparatively level expanse of land.
plateau
A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes.
solid astronomical body part
solid landform
A wetland ecosystem in which land mass is permanently inundated by shallow bodies of water, generally with a substantial number of hummocks, or dry-land protrusions.
swamp ecosystem
A paddy field for the cultivation of rice.
rice field
A speleothem projecting vertically upwards from a cave floor and formed by precipitation from drips.
stalagmite
A lake purposefully constructed.
artificial lake
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
biome
A reservoir constructed for the purpose of providing drinking water.
drinking water reservoir
The line of contact between a body of water and the land.
shoreline
The portion of the ground surface which lies below water.
bed
submerged bed
Incorporated populated place.
city
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
rock
Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.
soil
A significant accumulation of water which is part of a marine biome.
marine water body
Water that has been adversely affected in quality by anthropogenic influence.
waste water
An excreta material which is composed primarily of feces, an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation.
fecal material
An environmental material primarily composed of dihydrogen oxide in its liquid form.
liquid water
water
Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.
sediment
Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere.
dust
Water which contains a significant concentration of dissolved salts.
saline water
Water which has a low concentration of dissolved solutes, particularly that of sodium chloride.
fresh water
Wastewater that is contaminated with feces or urine,
sewage
A complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix; usually adhering to a substratum.
biofilm
wood
Water that is found on the surface of an astronomical object.
surface water
wastewater treatment plant
The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.
sludge
beach sand
The aerobically decomposed remnants of organic materials.
compost
A hospital is a building in which health care services are provided by specialized staff and equipment.
hospital
pond water
A portion of soil which is found in a forested area.
forest soil
A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process).
waste material
A material entity which determines an environmental system.
environmental feature
Drinking water is water which may be consumed by humans with no adverse effects on their health.
Water that is safe enough to be consumed by humans or used with low risk of immediate or long term harm.
http://en.wikipedia.org/wiki/Drinking_water
drinking water
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
manufactured product
tap water
bore hole water
A portion of soil which is part of a cropland or a rangeland biome.
farm soil
A portion of soil which is found in a grassland.
grassland soil
Soil in which trees from an orchard grow.
orchard soil
Soil which is found in a pasture and in which vegetation, such as the grass used for the grazing of ungulates, grows.
pasture soil
The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms.
rhizosphere
environmental material
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
Material in or on which organisms may live.
Environmental Material
CS20
NIAID GSCID-BRC
environmental material
Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.
aerosol
Anthropogenic material in or on which organisms may live.
anthropogenic environmental material
agricultural environmental material
A liquid or semi-liquid mixture of water and some combination of soil, silt, and clay.
mud
water well
A naturally occurring granular material composed of finely divided rock and mineral particles.
sand
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
Environmental material derived from living organisms.
organic material
A system which has the disposition to environ one or more material entities.
environmental system
A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface.
layer
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
environmental zone
A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls.
room
Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time.
concrete
Masonry cement is a substance used in construction that has the disposition to set and harden and thus may be used to bind materials together.
masonry cement
An exterior wall is a building wall which separates the interior of a building from the buildings surrounding environment.
exterior wall
A roof is the covering on the uppermost part of a building which provides protection from animals and weather, notably rain, but also heat, wind and sunlight. A roof is also the framing or structure which supports the covering
roof
building roof
Thatch is material composed of dry vegetation such as straw, water reed, sedge (Cladium mariscus), rushes, or heather.
thatch
A brick is a masonry unit which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete material, fire-hardened or air-dried.
brick
A tile is a manufactured piece of hard-wearing material such as ceramic, stone, metal, or even glass, generally used for covering roofs, floors, walls, showers, or other objects such as tabletops. Alternatively, tile can sometimes refer to similar units made from lightweight materials such as perlite, wood, and mineral wool, typically used for wall and ceiling applications.
tile
A fixture which is used primarily for the collection and, in some cases, disposal of human urine and feces.
toilet fixture
A pit latrine is a latrine which is constructed by digging a hole in the ground.
pit latrine
A toilet fixture which uses water to flush liquid and solid excreta into a sewage containment or processing facility through a drainpipe.
flush toilet fixture
A ventilated improved pit latrine is a pit latrine which includes a vent pipe fitted to the pit with a flyscreen covering the pipe's outlet. Air currents moving across the outlet of the vent pipe create a vaccum which draws odors out of the latrine's superstructure.
ventilated improved pit latrine
A covered pit latrine is a building which comprises a pit latrine sheltered by an outhouse.
covered pit latrine
A covered pit latrine with slab is a building which comprises a pit latrine with a slab floor sheltered by an outhouse.
covered pit latrine with slab floor
A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils.
composting toilet
Charcoal is a light, black residue, consisting of carbon and any remaining ash, obtained by removing water and other volatile constituents from animal and vegetation substances. Charcoal is usually produced by slow pyrolysis, the heating of wood or other substances in the absence of oxygen.
charcoal
A flat-wick lamp is a simple type of paraffin lamp, which burns paraffin drawn up through a wick by capillary action.
flat-wick lamp
A paraffin lantern is a lantern which houses a parrafin lamp in a structure of soldered or crimped-together sheet metal stampings and glass or other translucent material.
paraffin lantern
An electric lamp is a lamp which produces light from electricity.
electric lamp
A battery-powered electric lamp is an electric lamp which draws its power from a device composed of two or more electrochemical cells that convert stored chemical energy into electrical energy.
battery-powered electric lamp
A candle is a lamp composed of a wax within which an ignitable wick is embedded.
candle
A device capable of receiving and/or transmitting information encoded in electromagnetic radiation through wave modulation.
radio device
A cassette deck is a device capable of playing and recording audio compact cassettes.
cassette player
A television set is a device that combines a tuner, display, and loudspeakers for the purpose of converting digital or analog information signals into moving images and sound.
television set
A telephone is a telecommunications device which converts sound into electronic signals suitable for transmission via cables or other transmission media, and reconverts such signals into sound waves.
telephone
A mobile phone is a telephone which transmits sound information to a mobile phone network via radio transmissions.
mobile phone
A landline telephone is a telephone which is connected to a telephone network with wires through which electronic signals are carried.
landline telephone
A refrigerator is a device which consists of a thermally insulated compartment and a mechanical, chemical, or electronic heat pump that transfers heat from the inside of the fridge to its external environment such that the inside of the fridge is cooled to a temperature below the ambient temperature of the room
refrigerator
A table is a form of furniture with a flat horizontal upper surface used to support objects, for storage, show, and/or manipulation.
table
A chair is a piece of furniture with a raised surface commonly used to seat a single person.
chair
A piece of furniture is a movable object intended to support various human activities such as seating (e.g., chairs, stools and sofas) and sleeping (e.g., beds).
piece of furniture
A sofa is a bench which is partially or entirely upholstered, and often fitted with springs and tailored cushions.
sofa
A cabinet is a roughly cuboidal piece of furniture which is used to store miscellaneous items in compartments accessible through doors or drawers.
cabinet
A cupboard is a cabinet which is used indoors to store household objects such as food, crockery, textiles and liquor, and to protect them from dust and dirt
cupboard
A clock is an instrument which may indicate, keep, and/or co-ordinate time.
clock
A pressure lamp is a portable paraffin or oil lamp in which fuel is forced up into the mantle or burner by air pressure in the reservoir, which can be increased by pumping with a plunger.
pressure lamp
A spring which emits fresh water.
freshwater spring
river water
Rainwater is liquid water which has precipitated in the form of droplets through the condensation of atmospheric water vapour.
rainwater
A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails.
motor vehicle
A water truck is a truck which transports water.
water truck
A vehicle is a mobile machine which transports people or cargo.
vehicle
A bicycle is a human-powered, pedal-driven, single-track vehicle, having two wheels attached to a frame, one behind the other.
bicycle
A motorcycle is a two- or three-wheeled motor vehicle.
motorcycle
A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow.
lentic water body
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
human dwelling
A material part of an astronomical body.
astronomical body part
An environmental material which is in a solid state.
solid environmental material
An environmental system which includes both living and non-living components.
ecosystem
A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
wetland ecosystem
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
solid layer
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes.
liquid astronomical body part
A bodily fluid material which is composed primarily of excreta, bodily fluids consisting of matter which contains the waste products of biological processes, including urine or feces, discharged from an organism's body.
excreta material
An assay that enables the presence or the concentration of a substance in a material to be measured by exploiting the specific binding between an analyte and the corresponding detection antibody.
immunoassay
A relationship between persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption
family relationship
A material entity used to build a dwelling or part of a dwelling.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
building material
A material entity for accommodation, such as a building, part of a building, caravan, houseboat or other mobile home. A tent is not normally considered to be substantial.
false
Person: Jie Zheng, Chris Stoeckert
Penn Group
http://en.wikipedia.org/wiki/Dwelling
PRISM
obsolete_dwelling
true
A building material used in the construction of a roof.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
roof material
deprecated in favor of ENVO_01000472 'building roof'
obsolete_roof
true
A building material used in the construction of a floor
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
floor material
A building material used in the construction of a wall.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
wall material
A processed material shaped a small rectangular block typically made of clay mixed with sand and fired in a kiln or baked by the sun, used in building wall construction.
http://www.thefreedictionary.com/brick
wall brick
was ICEMR PRISM household, no longer used
obsolete_traditional house
true
was ICEMR household, no longer used
obsolete_modern house
true
A data item of a household's cumulative living standard represented in a numerical datum. The wealth index is calculated using easy-to-collect data on a household's ownership of selected assets, such as televisions and bicycles; materials used for housing construction; and types of water access and sanitation facilities.
Person: Jie Zheng, Chris Stoeckert
Penn Group
http://dhsprogram.com/topics/Wealth-Index.cfm
PRISM
numerical household wealth index
A processed material that is the bottom edge of a roof. The primary function of the eaves is to keep rain water off the walls and to prevent the ingress of water at the junction where the roof meets the wall. The secondary function is to control solar penetration; the eaves overhang can be designed to adjust the building's solar heat gain to suit the local climate, the latitude and orientation of the building, refer to passive solar building design. The eaves overhang may also shelter openings to ventilate the roof space.
Person: Jie Zheng, Chris Stoeckert
Penn Group
http://en.wikipedia.org/wiki/Eaves
PRISM
eaves
was ICEMR PRISM, no longer used
obsolete_open eaves
true
was ICEMR PRISM household, no longer used
obsolete_closed eaves
true
A brick with holes which is embedded in a wall to allow ventilation through it.
Person: Jie Zheng, Chris Stoeckert
Penn Group
http://en.wiktionary.org/wiki/air_brick
PRISM
air brick
A scalar measurements datum of resident in a dwelling.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
number of residents in a dwelling
An information content entity to indicate whether a household has electricity in a dwelling.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
household having electricity information
A material entity that consists of fuel mainly used for cooking.
Person: Jie Zheng, Chris Stoeckert
PRISM
Penn Group
PRISM
cooking fuel material
A material entity that consists of an energy source for lighting.
Person: Jie Zheng, Chris Stoeckert
PRISM
Penn Group
PRISM
obsolete_lighting material
true
number of rooms in a dwelling that are used for sleeping.
Person: Jie Zheng, Chris Stoeckert
number of bedrooms in a dwelling
PRISM
Penn Group
PRISM
number of rooms for sleeping in a dwelling
land area measured in acres: a scalar measurement datum of land measured in acres that may be of a particular type such as land owned by a household.
Person: Jie Zheng, Chris Stoeckert
Penn Group
Person: Chris Stoeckert
PRISM
land area measured in acres
A scalar measurement datum of meals per day in a household
Person: Jie Zheng, Chris Stoeckert
PRISM
Penn Group
PRISM
number of meals per day
A scalar measurement datum of days eating meat in a week in a household
Person: Jie Zheng, Chris Stoeckert
PRISM
Penn Group
PRISM
number of days eating meat in a week
how often problems satisfying food needs in a household
Person: Jie Zheng, Chris Stoeckert
PRISM
Penn Group
PRISM
frequency of not satisfying food needs
A length measurement datum of the distance in kilometers to from a dwelling to the nearest health facility.
Person: Jie Zheng, Chris Stoeckert
Penn Group
Person: Chris Stoeckert
PRISM
distance to health facility in km
replaced by EFO_0004950: date of birth
ICEMR protein array
obsolete_date of birth
true
A genotype information which is about the presence of certain genetic variants of glucose-6-phosphate dehydrogenase.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
glucose 6 phosphate dehydrogenase genotype
A genotype information which is about the presence and degree of alpha-thalassemia, a form of thalassemia involving the number of functional HBA1 and HBA2 genes.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
alpha thalassemia genotype
A genotype information which is about the presence of sickle-cell hemoglobin (HbS), an abnormal form of hemoglobin which is the oxygen-carrying protein within the red blood cells.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
sickle hemoglobin genotype
a diagnosis that is an assertion that a patient, who is the subject of a diagnostic process, has malaria
Person: John Judkins
EuPathDB
diagnosis of malaria
A phenotypic abnormality of the presence of bacteria in the blood.
http://en.wikipedia.org/wiki/Bacteremia
presence of bacteria in the blood
A diagnosis of malaria without evidence of complicated malaria.
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Grant Dorsey
PRISM
diagnosis of uncomplicated malaria
A phenotypic abnormality of the presence of a virus in the blood. It is a medical condition where viruses enter the bloodstream and hence have access to the rest of the body.
http://en.wikipedia.org/wiki/Viremia
presence of virus in the blood
A diagnosis of malaria with the presence of any danger signs including inability to sit up or stand, vomiting everything, unable to breastfeed or drink and lethargy or meeting criteria for severe malaria.
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Grant Dorsey
PRISM
diagnosis of complicated malaria
was ICEMR PRISM observation, no longer used
obsolete_diagnosis of complicated malaria with high parasite density
true
A diagnosis of complicated malaria with signs and symptoms, such as inability to sit up or stand, vomiting everything, unable to breastfeed or drink, lethargy, which are not listed as WHO criteria used to diagnose severe malaria.
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Grant Dorsey
PRISM
diagnoses of complicated malaria with danger signs
A diagnosis of complicated malaria based on WHO criteria that include the presence of parasite infections, most commonly P.falciparum, and any one or more of symptoms/signs of serious organ failures or abnormalities, including cerebral malaria, severe anemia, generalized convulsions, hypoglycemia, respiratory distress, fluid and electrolyte disturbances, acute renal failure, ARDS, circulatory collapse, abnormal bleeding, and Jaundice.
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Grant Dorsey
PRISM
diagnosis of severe malaria
a malaria characterized by serious organ failures or abnormalities including cerebral malaria, severe anemia, generalized convulsions, hypoglycemia, respiratory distress, fluid and electrolyte disturbances, acute renal failure, ARDS, circulatory collapse, abnormal bleeding, and jaundice.
Person: John Judkins
Centers for Disease Control and Prevention
severe malaria
A symptom or sign that is used for the diagnosis of severe malaria based on World Health Organization (WHO) criteria.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
severe malaria symptom or sign
A scalar measurement datum about the level of hemoglobin in the blood with a value in units of g/dl.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
ICEMR protein array
hemoglobin level in g per dL
A categorical measurement datum that indicates the presence of asexual parasites in blood cells by microscopy using a value of positive or negative.
Person: Jie Zheng, Chris Stoeckert
asexual parasites present by microscopy
Penn Group
PRISM
ICEMR protein array
blood smear reading as positive or negative
A planned process in which a patient is seen by a medical practitioner.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
clinical visit
A clinical visit that is primarily for a regular examination.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
routine clinical visit
a human being who bears a participant under investigation role
Person: John Judkins
human study subject
EuPathDB
human participant under investigation
A material entity whichis part of a dwelling for providing fresh air to the dwelling.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
dwelling ventilation
A geographical location which is part of Uganda.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
subcounty in Uganda
was ICEMR PRISM, no longer used
obsolete_CDC light trap assay
true
A role borne by some material entity which can be delivered/administrated into some organisms and the role is realized during clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
Person: Jie Zheng, Chris Stoeckert
Penn Group
medication role
quinine used in malaria medication
blood used in transfusion for replacement blood lost during surgery or due to a serious injury.
A material entity that is bearer of a medication role.
replaced by OBIB_0000029:medication material
Person: Jie Zheng, Chris Stoeckert
Penn Group
obsolete_medication material
true
A medication material intended to prevent or treat malaria.
Person: Jie Zheng, Chris Stoeckert
Penn Group
malaria medication
A medication material intended to prevent or treat a disease other than malaria.
Person: Jie Zheng, Chris Stoeckert
Penn Group
non-malaria medication
A drug product that has the chemical ingredient quinine and has antipyretic (fever-reducing), antimalarial, analgesic (painkilling), and anti-inflammatory properties.
Person: Jie Zheng, Chris Stoeckert
quinine
PRISM
http://en.wikipedia.org/wiki/Quinine
quinine drug product
A drug product that is the of combination artemether/lumefantrine (trade names Coartem and Riamet, Falcynate-LF). It is generally used for the treatment of acute uncomplicated Plasmodium falciparum malaria.
Person: Jie Zheng, Chris Stoeckert
artemether-lumefantrine
coartem
PRISM
http://en.wikipedia.org/wiki/Artemether/lumefantrine
artemether-lumefantrine drug product
A dependent continuant which is either disease or phenotypic abnormality.
clinical characteristics
An information content entity is about household.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
household information
A diagnosis of uncomplicated malaria that occurs with the first trimester of pregnancy.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
diagnosis of uncomplicated malaria in the 1st trimester of pregnancy
A diagnosis based on presence of asexual parasites by microscopy in the absence of subjective fever or documented elevated temperature
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Penn Group
PRISM
diagnosis of asymptomatic microscopic parasitemia
A diagnosis of malaria based on positive blood smear with subjective fever or elevated temperature resulting in antimalarial treatment.
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Penn Group
PRISM
diagnosis of symptomatic malaria
A time measurement datum that specifies the date of a clinical visit.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
clinical visit date
A scalar measurement datum that is the number of asexual parasites per ul in a specimen using microscopy.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
asexual parasite density in count per ul by microscope
An information content entity about dwelling.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
dwelling information
A symbol that denotes a specific household.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
household identifier
A symbol that denotes a specific human participant under investigation.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
ICEMR protein array
human study subject identifier
An information content entity which is about features of a human participant under investigation.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
ICEMR protein array
study participant information
elevated temperature or subjective fever
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
ICEMR protein array
febrile
A function to provide fresh air to a closed space.
ventilation function
A material entity in a dwelling that is designed, built, installed, selected, etc., to serve a specific function affording a convenience or service to people who are living in the dwelling.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
dwelling facility
A phenotypic abnormality of a subjective fever as reported by the study participant or their parent/guardian
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Grant Dorsey
PRISM
subjective fever
a febrile quality of an abnormally high temperature
Person: John Judkins
EuPathDB
elevated temperature
A scalar measurement datum that is about temperature.
temperature measurement datum
was in ICEMR, no longer used
A ventilation function to provide fresh air to a dwelling.
obsolete_dwelling ventilation function
true
an organism that is the bearer of a partipant under investigation role
Person: John Judkins
study subject
EuPathDB
participant under investigation
A role that inheres in a material entity that is realized in a building process in which the material entity will become part of a structure with a roof and walls standing more or less permanently in one place.
Person: Jie Zheng, Chris Stoeckert
Penn Group
building material role
A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a roof.
Person: Jie Zheng, Chris Stoeckert
Penn Group
roof material role
A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a wall.
Person: Jie Zheng, Chris Stoeckert
Penn Group
wall material role
A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a floor.
Person: Jie Zheng, Chris Stoeckert
Penn Group
floor material role
A role that inheres in a material entity that is realized in a process that provides a convenience or service to people who are living in a dwelling.
dwelling facility role
A temperature measurement datum that is about an organism.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
blood smear reading as positive or negative
organismal body temperature measurement datum
A processed material shaped a small rectangular block typically made of clay mixed with sand and fired in a kiln or baked by the sun, used in building floor construction.
http://www.thefreedictionary.com/brick
floor brick
An age since birth measurement datum at the time of a clinical visit.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
ICEMR protein array
age since birth at time of visit
An average value of asexual parasites counted per microliter of blood (i.e. malaria parasite density) across mulitiple clinical visits of a participant who was diagnosed with asymptomatic microscopic parasitemia.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average asexual parasite density of a participant with asymptomatic microscopic parasitemia
An average value of asexual parasites counted per microliter of blood (i.e. malaria parasite density) across mulitiple clinical visits of a participant who was diagnosed with malaria.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average asexual parasite density of a participant with malaria
An average value of female Anopheles mosquitoes collected across multiple collections (e.g. from one or more households on a number of nights).
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of female Anopheles per night
An average value of Anopheles mosquitoes tested for sporozoites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of female Anopheles tested for sporozoite
An average value of sporozoite positive female Anopheles mosquitoes across multiple collections (e.g. from a given household over a number of nights of collections).
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of sporozoite-positive female Anopheles
An average precentage value of female Anopheles mosquitoes tested as sporozoites-positive in all female mosquitoes tested for sporozoites across multiple collections.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average percent of female Anopheles with Plasmodium sporozoites
An age since birth measurement datum at the time of subject enrollment.
Person: Jie Zheng
Penn Group
PRISM
age since birth at time of enrollment
A data item of the total number of clinical visits by a participant in an investigation.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
number of clinical visits
A data item of the number of clinical visits during which the participant was diagnosed with malaria
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
number of clinical visits resulting in a malaria diagnosis
A data item of the number of clinical visits during which the participant was diagnosed with asymptomatic microscopic parasitemia.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
number of clinical visits resulting in an asymptomatic microscopic parasitemia diagnosis
A data item of the total number of clinical visits which were not sheduled routine visits.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
number of non-routine clinical visits
A data item of the total number of clinical visits which were sheduled routine visits.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
number of routine clinical visits
An information content entity that is about the type of sample/specimen collected during a clinical visit.
Person: Jie Zheng, Chris Stoeckert
PRISM
sample available information
A blood specimen that is located on a filter paper.
Person: Jie Zheng, Chris Stoeckert
Gruop: Penn group
blood specimen on filter paper
A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cell under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system.
Person: Jie Zheng, Chris Stoeckert
PBMC specimen
http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell
peripheral blood mononuclear cell specimen
A processed specimen consisting of red blood cells isolated from whole blood by centrifugation.
Person: Jie Zheng, Chris Stoeckert
RBC specimen
erythrocyte specimen
http://www.ruf.rice.edu/~bioslabs/studies/sds-page/gellab1.html
red blood cell specimen
An average value for female Anopheles mosquitoes tested positive for carrying Plasmodium parasites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of Plasmodium parasite-positive female Anopheles
An average value for female Anopheles mosquitoes tested for carrying Plasmodium parasites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of female Anopheles tested for Plasmodium parasite
An average percentage value for female Anopheles mosquitoes carrying Plasmodium parasites in all female mosquitoes tested for carrying Plasmodium parasites across multiple collections.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average percent of Plasmodium parasite-positive female Anopheles
A count of Anopheles mosquitoes collections performed (e.g. from a given household) in a given period.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
number of Anopheles collections
A sum value for all species of female Anopheles mosquitoes in a given collections.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
sum number of female Anopheles in a collection
A sum value for all female Anopheles funestus mosquitoes in a given collections.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
sum number of female Anopheles funestus in a collection
A sum value for all female Anopheles gambiae mosquitoes in a given collections.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
sum number of female Anopheles gambiae in a collection
A time datum for the duration of a patients participation in an investigation.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
participant observation duration time
An average value for the number of clinical visits of a patient based on calendar years
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of clinical visits per year
An average value for the number of clinical visits of a patient with asymptomatic microscopic parasitemia based on calendar years.
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of clinical visits with asymptomatic microscopic parasitemia diagnosis per year
An average value for the number of clinical visits of a patient with malaria based on calendar years
Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey
Penn Group
PRISM
average number of clinical visits with malaria diagnosis per year
A clinical visit date that specifies the date/time period of a routine clinical visit.
Person: Jie Zheng
Penn Group
PRISM
routine clinical visit date
A data item about a household's cumulative living standard represented in a categorical datum. The wealth index is calculated using data on a household's ownership of selected assets, such as televisions and bicycles; materials used for housing construction; and types of water access and sanitation facilities.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
http://dhsprogram.com/topics/Wealth-Index.cfm
PRISM
categorical household wealth index
An information content entity about items that a household owns such as a car, funiture, etc.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household asset information
An information content entity indicating whether a person was given antimalarial therapy outside the study since last seen as part of the study.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
antimalarial therapy given outside the study since last seen information
An information content entity indicating the cause of death for a participant in the study.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
cause of participant death
A clinical visit occuring because of a sickness.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
clinical visit when sick
A covered pit latrine that does not have a latrine slab.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
covered pit latrine without slab
A time measurement datum specifying the date of death
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
date of death
A time measurement datum that specified the date of participant first enrolled in a study
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
date of participant first enrolled in a study
A time measurement datum that specified the date of participant last seen in a study
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
date of participant last seen in a study
A time measurement datum measuring the number of days since a clinical visit took place which resulted in a malaria diagnosis.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
days since a clinical visit with a malaria diagnosis
A time measurement datum that measures the duration of having abdominal pain.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of abdominal pain
A time measurement datum that measures the duration of having anorexia.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of anorexia
A time measurement datum that measures the duration of having a cough.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of cough
A time measurement datum that measures the duration of having diarrhea.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of diarrhea
A time measurement datum that measures the duration of having fatigue.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of fatigue
A time measurement datum that measures the duration of having a headache.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of headache
A time measurement datum that measures the duration of having jaundice.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of jaundice
A time measurement datum that measures the duration of having joint pains.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of joint pains
A time measurement datum that measures the duration of having muscle aches.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of muscle aches
A time measurement datum that measures the duration of having seizures.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of seizures
A time measurement datum that measures the duration of having subjective fever.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of subjective fever
A time measurement datum that measures the duration of having vomiting.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
duration of vomiting
A household asset information indicating whether a member of a household has or owns an animal-drawn cart.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household animal-drawn cart asset
A household asset information indicating whether a member of a household has a bank account.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household bank account asset
A household asset information indicating whether a household has a bed.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household bed asset
A household asset information indicating whether a member of a household has or owns a bicycle.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household bicycle asset
A household asset information indicating whether a member of a household has or owns a boat without a motor.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household boat without a motor asset
A household asset information indicating whether a member of a household has or owns a car or truck.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household car asset
A household asset information indicating whether a household has a cassette player.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household cassette player asset
A household asset information indicating whether a household has a chair.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household chair asset
A household asset information indicating whether a household has a clock.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household clock asset
A household asset information indicating whether a household has a cupboard.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household cupboard asset
A household asset information indicating whether a household has electricity in their dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household electricity asset
A household asset information indicating whether a household has a land line or fixed location phone.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household fixed phone asset
A household asset information indicating whether a household has a mobile phone.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household mobile phone asset
A household asset information indicating whether a member of a household has or owns a boat with a motor.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household motorboat asset
A household asset information indicating whether a member of a household has or owns a motorcycle or motor scooter.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household motorcycle or scooter asset
A household asset information indicating whether a household has a radio.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household radio asset
A household asset information indicating whether a household has a refrigerator.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household refrigerator asset
A household asset information indicating whether a household has a sofa.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household sofa asset
A household asset information indicating whether a household has a table.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household table asset
A household asset information indicating whether a household has a television.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household television asset
A household asset information indicating whether a member of a household has or owns a watch.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
household watch asset
An information content entity indicating whether a malaria episode occurred
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
incident of malaria episode information
A material entity where a clinical visit took place.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
location of clinical visit
A material entity where a death occurred.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
location of death
An information content entity indicating whether medical care occurred outside the study clinic since last seen as part of the study.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
medical care outside the study clinic since last seen information
A time measurement datum of the days from the time of participant enrollment in a study until the current visit.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of days from time of participant enrollment in a study until current visit
A measurement datum of the number of female Anopheles funestus with a recent blood meal in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of fed female Anopheles funestus in a collection
A measurement datum of the number of female Anopheles gambiae with a recent blood meal in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of fed female Anopheles gambiae in a collection
A measurement datum of the number of female Anopheles dissected for parity in a given collection.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of female Anopheles dissected for parity in a collection
A measurement datum of the number of female Anopheles that have never layed eggs in a given collection.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of female null parous Anopheles in a collection
A measurement datum of the number of female Anopheles that have layed eggs before or are pregnant in a given collection.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of female parous Anopheles in a collection
A measurement datum of the number of gravid or semi-gravid female Anopheles funestus in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of gravid or semi-gravid Anopheles funestus in a collection
A measurement datum of the number of gravid or semi-gravid female Anopheles gambiae in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of gravid or semi-gravid female Anopheles gambiae in a collection
An average value for the number of insecticide treated mosquito net(s) per person.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of insecticide treated mosquito net(s) per person
A measurement datum of the number of female Anopheles that are not gambiae nor funestus in a given collection.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of non-gambiae or funestus female Anopheles species in a collection
A data item of the number of sleeping spaces in a dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of sleeping places in dwelling with a household
A measurement datum of the number of Anopheles funestus that could not be accessed in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of unassessable Anopheles funestus in a collection
A measurement datum of the number of Anopheles gambiae that could not be assessed in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of unassessable Anopheles gambiae in a collection
A measurement datum of the number of female Anopheles funestus without a recent blood meal in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of unfed female Anopheles funestus in a collection
A measurement datum of the number of female Anopheles gambiae without a recent blood meal in a given collection
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
number of unfed female Anopheles gambiae in a collection
An information content entity that indicates whether a plasma sample is lost or not.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
plasma sample lost information
A categorical measurement datum that indicates whether Plasmodium gametocytes were present in a specimen using microscopy.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
presence of Plasmodium gametocytes by microscopy
An information content entity indicating the reason why a participant withdrew from a study.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
reason for participant withdrawal
An information content entity that indicates whether a redraw of a symptom occurred after a clinical visit.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
redraw of a symptom after clinical visit information
A routine clinical visit in which a blood specimen was collected for a T-cell study.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
routine clinical visit for T-cell study
A routine clinical visit in which a blood specimen was collected by finger prick and sent for lab testing (e.g., blood smear, hemoglobin level measurement).
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
routine clinical visit with finger prick
A routine clinical visit in which a blood specimen was collected using venipuncture and sent for lab testing (e.g., blood smear, hemoglobin level measurement).
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
routine clinical visit with venipuncture
A routine clinical visit in which no routine assessment was done during the visit.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
routine clinical visit without any routine assessment done
An air brick with a screen that can prevent some insects get in the dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
screened air brick
An anemia with hemoglobin levels less than 5 gm/dL.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
ICEMR protein array
severe anemia
An information content entity indicating whether a person slept in an insecticide treated net the previous night.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
slept in an insecticide treated net last night information
A sum value for all female Anopheles examined for sporozoites in a given collection.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
sum number of female Anopheles examined for sporozoites in a collection
A sum value for all female Anopheles with Plasmodium sporozoites in a given collection.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
sum number of female Anopheles with Plasmodium sporozoites in a collection
A time measurement datum indicating when screening of a human study subject was perfomed.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
time of screening
A pit latrine that is not sheltered by an outhouse but has a latrine slab.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
uncovered pit latrine with slab
A pit latrine that is not sheltered by an outhouse and does not have a latrine slab.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
uncovered pit latrine without slab
An air brick without a screen to prevent insects from enetering the dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
unscreened air brick
Pain perceived to originate in the muscle.
PRISM
PRISM
Muscle aches
A light source that light is produced from solar energy.
Person: Jie Zheng, Chris Stoeckert
solar light source
drinking water that is obtained from a publicly accessible water well without a constructed barrier built around it to limit movement of waste or runoff into it
Person: John Judkins
EuPathDB
drinking water from open public well
drinking water that is obtained from a water well with a constructed barrier built around it to limit movement of waste or runoff into the well and the well is located in the yard of a dwelling
Person: John Judkins
EuPathDB
drinking water from open well in yard
drinking water accessed through a plumbing fixture located inside a human dwelling
Person: John Judkins
EuPathDB
drinking water from pipe into dwelling
drinking water obtained through a plumbing fixture located in the yard of a human dwelling
Person: John Judkins
EuPathDB
drinking water from pipe into yard
was ClinEpi household, no longer used
obsolete_drinking water from protected public well
true
from ClinEpi household, no longer used
obsolete_drinking water from freshwater spring
true
ClinEpi household, no longer used
obsolete_drinking water from protected well in yard
true
drinking water that is obtained from a freshwater spring without a constructed barrier built around it that would limit movement of waste or runoff into it
Person: John Judkins
EuPathDB
drinking water from unprotected freshwater spring
was ICEMR PRISM household, no longer used
obsolete_drinking water from water truck
true
A centrally registered identifier symbol assigned by the American Type Culture Collection (ATCC).
ATCC #
ATCC number
half life datum (t 1/2) for cleaning parasite
clearance half life
parasite clearance half life
a rate measurement datum that represents the number of parasite organisms removed from the bearer of a host role by means of the biological processes of the bearer of the host role
Person: John Judkins
clearance rate
EuPathDB
parasite clearance rate
a time measurement datum that is the result of measuring the time it takes for the biological processes of the bearer of a host role to remove parasite organisms within it, until such time as the organisms cannot be detected
Person: John Judkins
clearance time
EuPathDB
parasite clearance time
was in ICEMR Amazonia, no longer used
obsolete_symptomatic episode
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_chloroquine resistant
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_pyrimethamine and chloroquine resistant
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_pyrimethamine, mefloquine and chloroquine resistant
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_pyrimethamine resistant, chloroquine sensitive
true
was in ICEMR prism, no longer used
obsolete_record of unknown information
true
same as EUPATH_0000282: pyrimethamine, mefloquine and chloroquine resistant
obsolete_pyrimethamine,chloroquine, and mefloquine resistant
true
was in EuPathDB/PlasmoDB, no longer used
not responsive to SAG therapy
obsolete_sodium antimony gluconate resistant
true
was EuPathDB/PlasmoDB term, no longer used
Sensitive to SAG
obsolete_sodium antimony gluconate sensitive
true
was ICEMR PRISM observation, no longer used
obsolete_no malaria parasite infection diagnosis
true
A population of people who share a common ancestor on the patrilineal or matrilineal line.
haplogroup
a time measurement datum that represents the beginning of the first process in which a parasitemia is realized
Person: John Judkins
parasitemia start
EuPathDB
parasitemia start time
an information content entity that describes the success, failure, or indeterminacy of a treatment
Person: John Judkins
treatment outcome
EuPathDB
treatment outcome information
was in EuPathDB/PlasmoDB, no longer used
ETF
obsolete_early treatment failure
true
was in EuPathDB/PlasmoDB, no longer used
LCF
obsolete_late clinical failure
true
Shannon Takala Harrison: Also not sure about LF, it could either be late failure or lost to follow-up.
Term need for annotation NIH-10K experiment, treatment outcome
was in EuPathDB/PlasmoDB, no longer used
LF
obsolete_late failure
true
Shannon Takala Harrison: LOSS probably also means the patient was lost to follow-up.
Term need for annotation NIH-10K experiment, treatment outcome
no longer used
LOSS
obsolete_lost to follow-up
true
was in EuPathDB/PlasmoDB, no longer used
LPF
obsolete_late parasitological failure
true
was in EuPathDB/PlasmoDB, no longer used
LTF
obsolete_Late Treatment Failure
true
Shannon Takala Harrison: Not sure what NULL means; it could also indicate lost to follow-up.
Term need for annotation NIH-10K experiment, treatment outcome
was EuPathDB/PlasmoDB term, no longer used
NULL
obsolete_unknown outcome
true
was ICEMR Amazonia, no longer used
VIVAX
obsolete_have a subsequent P. vivax infection
true
was in EuPathDB/PlasmoDB, no longer used
WTH
obsolete_withdrew from the study
true
was ICEMR, no longer used
obsolete_summary information about a dwelling
true
an information content entity that is about a process in which a human being occupying a dwelling participates. It either specifies the bearer of the function that is realized in the process, or it specifies that the process does not occur in the dwelling or its yard.
Person: John Judkins
EuPathDB
information on dwelling facilities
a information content entity that is about a part of a dwelling
Person: John Judkins
EuPathDB
information on dwelling physical characteristics
an information content entity that is about a household and is an estimator of capabilities of household members to participate in processes that maintain their health, social status, and economic freedom
Person: John Judkins
EuPathDB
socioeconomic factor
a data item that is about an investigation and is the specified output of a data transformation that has only clinical visit data as input
Person: John Judkins
EuPathDB
aggregated clinical visit information
a genotype information that is about the genetic material of a human being
Person: John Judkins
EuPathDB
human genotype information
an information content entity that is about a part of a study design execution that is part of an investigation under which a human being is a participant
Person: John Judkins
EuPathDB
information on participant study details
an information content entity that is about a part of a health care encounter that occurs in a hospital facility
Person: John Judkins
EuPathDB
ICEMR protein array
hospitalization information
an information content entity that is about a sign or symptom of a patient
This should stay consistent w/OGMS's definitions, so this definition may need to be changed if OGMS changes their definitions of sign and symptom to information content entities.
Person: John Judkins
EuPathDB
ICEMR protein array
symptom or sign information
an information content entity that is about a clinical visit
Person: John Judkins
EuPathDB
information on observation details
an information content entity that specifies whether a clinical visit is scheduled or unscheduled
Person: John Judkins
EuPathDB
clinical visit type information
an entomological data item that results from either (a) counting insect collections from multiple catches of live specimens or (b) an averaging data transformation that has single catch entomological measurement data as input
Person: John Judkins
aggregated entomological measurement data
EuPathDB
aggregated entomological data item
an entomological data item that is the specified output of an assay that has a collection of insect specimens as specified input; this collection is the specified output of exactly one catch of live specimens
Person: John Judkins
individual entomological measurement data
EuPathDB
single catch entomological measurement datum
a clinical visit that realizes the concretization of a protocol specifying the time of the visit
Person: John Judkins
EuPathDB
scheduled clinical visit
a clinical visit that occurs at a time that is not mentioned in a protocol that directs the time of the visit
Person: John Judkins
EuPathDB
unscheduled clinical visit
an information content entity that is about a malaria diagnosis and describes the severity of the disease or the basis for the diagnosis
Person: John Judkins
EuPathDB
malaria severity and basis information
a diagnosis that is an assertion that a patient, who is the subject of a diagnostic process, has a disease other than malaria
Person: John Judkins
EuPathDB
diagnosis of disease other than malaria
an information content entity that is about a participant under investigation and specifies the hospital admitting the participant
Person: John Judkins
EuPathDB
hospital admission information
a time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's admission to a hospital
Person: John Judkins
EuPathDB
date of hospital admission
a time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's discharge from a hospital
Person: John Judkins
EuPathDB
date of hospital discharge
A diagnosis given at time of discharge.
ICEMR prism
diagnosis at discharge
an information content entity that is about a collection of Anopheles funestus
Person: John Judkins
EuPathDB
Anopheles funestus related information
an information content entity that is about a collection of Anopheles gambiae sensu lato
Person: John Judkins
EuPathDB, Wikipedia 'Sensu' entry
Anopheles gambiae sensu lato related information
an information content entity that is about a number of mosquitos that have given birth
Person: John Judkins
EuPathDB
mosquito parity information
an entomological data item that is the specified output of an analyte assay to determine whether a sporozoite is present in any insect in a collection of insects
Person: John Judkins
EuPathDB
sporozoite testing information
a data item that is the specified output of a data transformation that has only sporozoite testing information as input
Person: John Judkins
EuPathDB
aggregated sporozoite testing information
a data item that is about a collection of insects
Person: John Judkins
entomological measurement data
EuPathDB
entomological data item
was ICEMR PRISM, no longer used
obsolete_clinical visit information
true
One dimensional cartesian spatial coordinate datum refers to eastward-measured distance (or the x-coordinate). The terms easting and northing are geographic Cartesian coordinates for a point. Easting and northing coordinates are commonly measured in meters from a horizontal datum.
easting coordinate measurement datum
One dimensional cartesian spatial coordinate datum refers to the northward-measured distance (or the y-coordinate). The terms easting and northing are geographic Cartesian coordinates for a point. Easting and northing coordinates are commonly measured in meters from a horizontal datum.
northing coordinate measurement datum
A human waste disposal in a household.
human waste disposal in a household
A count of the total number of non-scheduled clinical visits in an investigation.
number of non-scheduled visits
A count of the total number of scheduled clinical visits in an investigation.
number of scheduled visits
An information content entity that is about malaria diagnosis and parasite status testing by blood smear or LAMP.
Person: Jie Zheng, Grant Dorsey
PRISM
malaria diagnosis and parasite status information
A dwelling information about animal living in a human dwelling.
dwelling animal information
An information content entity that is about human traveling.
human traveling information
An information content entity that is about vector control intervention towards interruption of transmission of infectious diseases.
vector control intervention information
An information content entity that is about employment.
employment information
An organism that raised by people and lives in a human dwelling.
domesticated animal in a human dwelling
An information content entity that is about when the bed net is last treated.
information on when bed net last treated
An information content entity that is about the highest level of schooling that a person has reached.
educational level information
A count of the total times of a person who infected with P. vivax in his lifetime.
Person: Chris Stoeckert, Jie Zheng
number of infections with P. vivax in lifetime
A count of the total times of a person who infected with P. vivax last year.
Person: Chris Stoeckert, Jie Zheng
number of infections with P. vivax in the last year
A count of the total times of a person who infected with P. falciparum in his lifetime.
Person: Chris Stoeckert, Jie Zheng
number of infections with P. falciparum in lifetime
A count of the total times of a person who infected with P. falciparum last year.
Person: Chris Stoeckert, Jie Zheng
number of infections with P. falciparum in the last year
A time measurement datum of days in a week at primary job.
number of days per week at primary job
A time measurement datum of days in a week at secondary job.
number of days per week at secondary job
"A human social role realized in a process that often performed in exchange for payment. Many people have multiple job roles, such as those of parent, homemaker, and employee."
https://en.wikipedia.org/wiki/Job
job role
A planned process that a person participates in exchange for payment. The job role born by the person is realized in the process.
economic activity
An economic activity that a person is involved in primarily.
primary economic activity
An economic activity that a person is not involved in primarily.
secondary economic activity
A textual entity that describes a person's primary economic activity.
primary economic activity description
A textual entity that describes a person's secondary economic activity.
secondary economic activity description
An information content entity about secondary economic activity a person participates in the last month.
secondary economic activity in last month
An information content entity that is about an activity that realizes a social role and is often performed for payment.
occupation
A time measurement datum about the pay period of primary economic activity.
primary economic activity pay period
A time measurement datum about the pay period of secondary economic activity.
secondary economic activity pay period
An information content entity about whether a person received payment from primary economic activity.
information on whether received payment from primary economic activity
An information content entity about whether a person received payment from secondary economic activity.
information on whether received payment from secondary economic activity
A data item of salary of primary job.
salary of primary economic activity
A data item of salary of other job.
salary of secondary economic activity
A time measurement datum about number of hours per day spend at primary economic activity.
number of hours per day at primary economic activity
A time measurement datum about number of hours per day spend at secondary economic activity.
number of hours per day at secondary economic activity
An environmental feature for disposing garbage.
garbage disposal
A textual entity about community where a person is living.
community name
A textual entity about community where a study taken place.
study location name
A malaria medication that is generally taken for initial treatment of malaria.
first line malaria medication
"A malaria medication that is given when first-line medication doesn't work, or stops working."
second line malaria medication
was in ICEMR Amazonia, no longer used
obsolete_information of whether malaria medication is given
true
a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage
Person: John Judkins
EuPathDB, BFO's 'relational quality' examples
marital status
a categorical value specification that specifies whether a human being plans to change within two years the dwelling which that human being occupies
Person: John Judkins
EuPathDB
information on whether a person plans to move
an information content entity that specifies the relationship between a participant under investigation and the head of the participant's household
Person: John Judkins
EuPathDB
relationship to head of Family
a time measurement datum that represents the time a human being resides in a human dwelling
Person: John Judkins
EuPathDB
years of living in the dwelling
a time measurement datum that is about a human being, has years as its unit, and represents the time interval that the human being has lived in a geographic location where the inhabitants share a common trait
Person: John Judkins
EuPathDB
years of living in the community
a count of the number of instances of a site, within a human dwelling and its yard, to which any resident of the dwelling has access
Person: John Judkins
EuPathDB
number of common areas in a dwelling
a scalar measurement datum that has the square meter as its measurement label and is the result of a measurement of area that is covered by a roof
Person: John Judkins
EuPathDB
covered area measured in square meter
An information content entity about where the kitchen is located inside or outside of a dwelling.
information on kitchen location
a scalar measurement datum that is the result of a measurement of area and has the square meter as its measurement label
Person: John Judkins
EuPathDB
total area measured in square meter
a categorical value specification that is about a dwelling and specifies whether (a) it is owned by an occupant of the dwelling or (b) a rental agreement exists such that an occupant has an obligation to pay rent to someone who does not occupy the dwelling
Person: John Judkins
EuPathDB
information on whether occupant owns or pays rent on dwelling
was ICEMR Amazonia, no longer used
obsolete_days of travel
true
was in ICEMR Amazonia, no longer used
obsolete_information of whether ship is taken during a trip
true
an information content entity that is about a geographic location in which part of a journey occurs
Person: John Judkins
EuPathDB
information on place visited during a trip
An information content entity about travel to any place more than 10 km away from where a person live.
information on travel in the last month
an information content entity that is about a patient diagnosed with malaria and describes geographic locations the patient visited
Person: John Judkins
EuPathDB
information on travel before malaria
A material entity that is used to make bed net.
bed net material
a time measurement datum that is about a human dwelling and specifies the most recent date on which the dwelling was fumigated, i.e. filled with pesticide
Person: John Judkins
EuPathDB
date of last fumigation
an information content entity that specifies the organization that administers insecticide to a collection of bed nets
Person: John Judkins
EuPathDB
information on organization responsible for treating bed nets
an information content entity that specifies whether a human participant under investigation is a contact for malaria, based on the partipant's association with sites in which malaria infections are known to occur
Person: John Judkins
EuPathDB
information on contact with malaria
an information content entity that is about a human participant under investigation and specifies whether the person is present for a scheduled clinical visit
Person: John Judkins
EuPathDB
information on participant status at visit
was ICEMR Amazonia, no longer used
obsolete_information of whether address has changed
true
a count of the number of instances of a domesticated animal that is raised in an agricultural setting to produce labor and commodities
Person: John Judkins
Wikipedia
number of livestock
a count of the number of instances of a domesticated animal that is kept for pleasure rather than utility
Person: John Judkins
EuPathDB
number of pets
was in ICEMR Amazonia, no longer used
obsolete_bed net treatment information
true
a count of the number of instances of a bed net to which insecticide was applied in the past six months
Person: John Judkins
EuPathDB
number of insecticide-treated bed nets treated less than 6 months ago
a count of the number of instances of a bed net to which insecticide was applied before the previous six months
Person: John Judkins
EuPathDB
number of insecticide-treated bed nets treated more than 6 months ago
a count of the number of instances of bed net to which long last insecticide is administered
Person: John Judkins
EuPathDB
number of long last insecticide-treated bed nets
a count of the number of instances of a bed net to which insecticide has not been applied
Person: John Judkins
EuPathDB
number of untreated bed net
no longer used
obsolete_blood pressure measurement datum
true
A categorical measurement datum about proximity to case dwelling.
proximity to case dwelling datum
no longer used
obsolete_information of whether a census form filled at enrollment
true
an organization that administrates a medical care center that provides healthcare services on an outpatient basis
Person: John Judkins
obsolete_clinic organization
true
A geographic location where the clinic is located.
clinic location
a textual entity that denotes a political entity that is a division of a state or territory of India
Person: John Judkins
EuPathDB
district of India name
A textual entity about a 'division' or 'ward' being a sub-division of a city.
division number
a categorical value specification that specifies whether a patient complies with a dose specification that specifies the dose of malaria medication to self-administer
Person: John Judkins
EuPathDB
information on whether antimalarial drugs taken as advised
an information content entity that specifies whether a participant under investigation self-administered antimalarial drugs in the past 2 weeks
Person: John Judkins
EuPathDB
information on whether took antimalarial drugs in last 2 weeks
an information content entity that is about a human participant under investigation that has a disease and specifies the disease
Person: John Judkins
EuPathDB
information on existing illness
an information content entity that is about a human participant under investigation and specifies whether the participant has a disease
Person: John Judkins
EuPathDB
information on whether has existing illness
a categorical value specification that is about a health care provider role that is realized in a treatment to alleviate symptoms of a fever. It either specifies whether this role is borne by a hospital or clinic, private practice, or the patient, or it specifies that this information is missing.
Person: John Judkins
EuPathDB
fever treatment provider information
A time measurement datum that measures the duration of having febrile.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
duration of being febrile
was ICEMR Amazonia, no longer used
obsolete_information of whether a person is family head
true
was ICEMR Amazonia, no longer used
obsolete_hospital registration number
true
an information content entity that specifies whether a human being is manifesting a disease
Person: John Judkins
EuPathDB
information on whether a person is sick now
"An information content entity is about who are indoor residents, such as only human, or human and animals."
indoor residents information
a measurement datum that approximates the temporal interval between applications of larvicide at the same site
Person: John Judkins
EuPathDB
frequency of larvicide in use
an information content entity that specifies any locations in which a diagnostic process has occurred in the past twelve months that resulted in a diagnosis of malaria
Person: John Judkins
EuPathDB
information on where malaria diagnosed in last 12 months
a count of the number of instances of a parasite in a life cycle stage in which reproduction is asexual
Person: John Judkins
EuPathDB, Centers for Disease Control and Prevention
number of asexual parasite
was ICEMR, no longer used
obsolete_number of sexual parasite
true
A data item of which parasite species detected in a blood specimen.
parasite species information
A country name denote where a person was born.
birth country name
an information content entity that is part of a diagnosis of malaria, resulting from a diagnostic process that occurred within the past year, and specifies the species of the infectious agent causing the malaria
Person: John Judkins
EuPathDB
information on malaria parasite infection diagnosis past year
A count of malaria diagnosis past year.
number of malaria diagnosis past year
A time measurement datum of number of months since malaria diagnosis.
number of months since malaria diagnosis
An information content entity about whether antimalarial drug treated last year
information on whether antimalarial drug treated last year
A time measurement datum about when the antimalarial drug used last year
antimalarial drug used date
An information content entity about what antimalarial drug used last year
information on antimalarial drug used last year
An information about who treated malaria last year
information on who treated malaria last year
A specimen that is used for DNA extraction and following PCR assay.
specimen used for DNA PCR
An organism identification assay that identifies the species of parasites by PCR.
parasite species identification by PCR assay
A textual entity that denotes the public health clinic/hospital that the human subject normally uses (for non malaria illness).
primary health center name
A data item of income level issued annually by the Department of Health and Human Services. Federal poverty levels are used to determine your eligibility for certain programs and benefits.
poverty line
An information that specifies a person has no illness.
no illness information
A laboratory test that can quickly establishing the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood.
falcivax rapid diagnostic test
"A laboratory test that is a rapid, sensitive malaria test that is able to differentiate between P. falciparum and other malaria parasites. "
optimal-IT rapid diagnostic test
A material entity that a person uses to deter mosquitoes from approaching or settling.
personal mosquito repellent
"An information content entity about a person's resident status, permanent or temporary."
resident status information
An information content entity about repellent sprayed in last 12 months in a dwelling.
information on mosquito repellent sprayed in last 12 months
A text entity denotes to a state where a person was born.
state name of birth
An information content entity that is about whether a person take fever suppressant.
take fever suppressant information
A text entity denotes to a taluk.
taluk name
A country name denote a geographic location that a person has visited.
visited country name
A text entity denotes to a district that a person has visited.
visited district name
A text entity denotes to a state that a person has visited.
visited state name
A taluk name denote a geographic location that a person has visited.
visited taluk name
A village name denote a geographic location that a person has visited.
visited village name
An information content entity about whether a person travelled in last 14 days.
traveled information in last 14 days
An information content entity about healthcare that is private or public.
healthcare information
A text entity denotes to a village.
village name
A text entity of a zone number denotes to a geographic location.
location zone number
deprecated in favor of GENEPIO_0000092 'read coverage'
obsolete_average mapping coverage
true
a data item that is about a sequencing assay and is the ratio of the count of mapped reads to the total count of reads
Person: John Judkins
EuPathDB
proportion mapped reads
was in EuPathDB/PlasmoDB, no longer used
obsolete_number mapped reads
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_average read length
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_unstranded unique average mapping coverage
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_unstranded unique proportion mapped reads
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_unstranded unique number mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_unstranded unique average read length
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_unstranded non unique average mapping coverage
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_unstranded non unique proportion mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_unstranded non unique number mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_unstranded non unique average read length
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_first strand unique average mapping coverage
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_first strand unique proportion mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_first strand unique number mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_first strand unique average read length
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_first strand non unique unstranded unique average mapping coverage
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_first strand non unique unstranded unique proportion mapped reads
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_first strand non unique unstranded unique number mapped reads
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_first strand non unique unstranded unique average read length
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand unique unstranded non unique average mapping coverage
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand unique unstranded non unique proportion mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand unique unstranded non unique number mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand unique unstranded non unique average read length
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand non unique first strand unique average mapping coverage
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand non unique first strand unique proportion mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand non unique first strand unique number mapped reads
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_second strand non unique first strand unique average read length
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29444.aspx
obsolete_Candida albicans strain 12C
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29445.aspx
obsolete_Candida albicans strain L26
true
A diagnosis based on parasites detected by microscopy (parasite density > 0) or LAMP assay (LAMP result is positive) in the absence of febrile (subjective fever and temperature>=38).
diagnosis of asymptomatic parasitemia
A diagnosis based on presence of parasites by LAMP assay when microscopy result was negative in the absence of subjective fever or documented elevated temperature.
Person: Grant Dorsey, Jie Zheng
diagnosis of submicroscopic parasitemia
A data item of the number of clinical visits during which the participant was diagnosed with asymptomatic parasitemia.
Person: Jie Zheng, Shon cade, Grant Dorsey
PRISM
number of clinical visits resulting in an asymptomatic parasitemia diagnosis
a presence of parasite that indicates whether parasites too small to be seen under light microscopy are present in a specimen. It is the specified output of a loop-mediated isothermal amplification assay
Person: Jie Zheng, Grant Dorsey, John Judkins
presence of submicrosopic parasites by LAMP
Penn group
PRISM
presence of submicrosopic parasites by loop-mediated isothermal amplification assay
An information content entity is about blood smear not performed.
Person: Jie Zheng, Grant Dorsey
PRISM
information on blood smear not performed
A laboratory finding about parasite present which is negative in both blood smear and LAMP assay.
Person: Jie Zheng, Grant Dorsey
PRISM
negative blood smear and negative LAMP
An information content entity is about parasite status with negative blood smear and LAMP test is not performed.
Person: Jie Zheng, Grant Dorsey
PRISM
information on negative blood smear and LAMP not done
An average value for the number of clinical visits of a patient with asymptomatic parasitemia based on calendar years.
Person: Jie Zheng, Shon cade, Grant Dorsey
PRISM
average number of clinical visits with asymptomatic parasitemia diagnosis per year
A count of the number of courses of antibiotics received by the human or animal.
Person: Daniel Beiting, Jie Zheng
microbiome
number of courses of antibiotics given
A symbol that denotes a specific family, rather than the physical home in which they live.
Person: Daniel Beiting, Jie Zheng
microbiome
family identifier
A symbol denotes a physical structure/home/dwelling, rather than the human inhabitants.
Person: Daniel Beiting, Jie Zheng
microbiome
dwelling identifier
An information content entity that idicates whether the hive was treated with tetracyline to prevent infection with the bacterial pathogen Paenibacillus larvae.
Person: Daniel Beiting, Jie Zheng
microbiome
information on whether hive treated with tetracyline
An information indicates that samples from child or from the mother, or both.
Person: Daniel Beiting, Jie Zheng
microbiome
information on whether specimen from mother or child
A number of courses of antibiotics given to a mother during delivery.
Person: Daniel Beiting, Jie Zheng
microbiome
number of courses of antibiotics received by mom prior to delivery
A region of the 16S rRNA gene that was PCR amplified and sequenced.
replaced by: SO_0001000: rRNA_16S
Person: Daniel Beiting, Jie Zheng
microbiome
false
obsolete_16S rRNA gene region for sequencing
true
An organism that realizes host role in laboratory.
lab host
was EuPathDB/PlasmoDB term, no longer used
obsolete_bronchial wash specimen
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_bronchoalveolar lavage fluid specimen
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_lung aspirate specimen
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_lung lesion specimen
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_lung mold bronch specimen
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_lung nodule specimen
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_TGH specimen
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_TGH mold iso specimen
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_number of contigs
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_number of genes called
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_number of bases
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_lesion on arm specimen
true
A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized.
https://en.wikipedia.org/wiki/Common_name
common name of organism
An information content entity specify any molecular data associated with specimen source is available.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on availability of molecular data
An information content entity indicates whether the specimen collection is original collection or follow up collection from same study subject.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on original or follow up specimen collection
An information content entity specifies whether study subject signed informed consent for data collection and usage.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on informed consent for data collection and usage
deprecated in favor of HP_0003111 'Abnormality of ion homeostasis'
Person: Jie Zheng, Chris Stoeckert, John Judkins
ICEMR protein array
obsolete_electrolyte disturbances
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29447.aspx
obsolete_Candida albicans strain P37005
true
A categorical measurement datum that indicates whether Plasmodium falciparum were present in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of Plasmodium falciparum
A categorical measurement datum that indicates whether gametocyte were present in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of gametocyte
A categorical measurement datum that indicates whether Plasmodium knowlesi were present in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of Plasmodium knowlesi
A categorical measurement datum that indicates whether Plasmodium malariae were present in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of Plasmodium malariae
A categorical measurement datum that indicates whether Plasmodium ovale were present in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of Plasmodium ovale
A categorical measurement datum that indicates whether parasite were present in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of parasite
A categorical measurement datum that indicates whether Plasmodium vivax were present in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of Plasmodium vivax
A time measurement datum measuring the number of days from the first specimen collection to current specimen collection from same study subject.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
days of follow up specimen collection
A scalar measurement datum that is about gametocyte density measured using microscopy.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
gametocyte density by microscope
A scalar measurement datum that is about gametocyte density measured by RT-PCR.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
gametocyte density by RT-PCR
An assay that detects parasite gametocyte in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
gametocyte detection assay
A protocol that specifies how to measure the density of parasite gametocyte.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
gametocyte detection protocol
a site in which a global positioning system receiver produces a data item specifying the location of the site
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
location where GPS coordinates were taken
An information content entity specify any host genetics data associated with specimen source is available.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on availabilty of host genetics data
An information content entity specify any immune response data associated with specimen source is available.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on availability of immune response data
An information content entity specify any parasite genetics data associated with specimen source is available.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on availability of parasite genetics data
An information content entity specify any molecular data other than host genetics, parasite genetics, and immune response, associated with specimen source is available.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on availability of other molecular data
A centrally registered identifier symbol assigned to a research project by Institutional Review Board (IRB). The IRB is a committee established to review and approve applications for research projects involving human subjects. The primary purpose of the IRB is to protect the rights and welfare of the human subjects.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
IRB number
A scalar measurement datum that is about parasite density measured by PCR.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
parasite density by PCR
A scalar measurement datum that is about parasite density measured by microscope.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
parasite density by microscope
An assay that detects parasite in a specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
parasite detection assay
An assay that detects parasite in a specimen using PCR.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
parasite detection by PCR assay
A categorical measurement datum that indicates whether asexual parasite were present in a specimen using PCR.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
presence of asexual parasite by PCR
A categorical measurement datum that is the result of rapid diagnosis test using a value of positive or negative.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
rapid diagnosis test result as positive or negative
The site where specimen collection taken place.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
location of specimen collection
a research organization that is located in an area where malaria is endemic and is one of many centers established by the National institute of Allergy and Infectious Diseases with the following aims: to design and conduct multidisciplinary research on the epidemiology, transmission, and pathogenesis of malaria in its specific region, to design and conduct special projects to capitalize on new opportunities and emerging public health needs, and to build clinical research capacity and improve malaria control and prevention
Person: Jie Zheng, Chris Stoeckert, John Judkins
National Institute of Allergy and Infectious Diseases
ICEMR protein array
ICEMR organization
An assay that detects body temperature of an organism.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
organismal body temperature measurement assay
An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
malaria rapid diagnosis test
gametocyte density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium falciparum
Person: Jie Zheng, Chris Stoeckert, John Judkins
EuPathDB
ICEMR protein array
Plasmodium falciparum gametocyte density by microscope
gametocyte density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium vivax
Person: Jie Zheng, Chris Stoeckert, John Judkins
EuPathDB
ICEMR protein array
Plasmodium vivax gametocyte density by microscope
A gametocyte density by RT-PCR that is about Plasmodium vivax.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
Plasmodium vivax gametocyte density by RT-PCR
parasite density by PCR that is the output of an assay that realizes a measurand role that inheres in Plasmodium vivax
Person: Jie Zheng, Chris Stoeckert, John Judkins
EuPathDB
ICEMR protein array
Plasmodium vivax parasite density by PCR
parasite density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium falciparum
Person: Jie Zheng, Chris Stoeckert, John Judkins
EuPathDB
ICEMR protein array
Plasmodium falciparum parasite density by microscope
parasite density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium vivax
Person: Jie Zheng, Chris Stoeckert, John Judkins
EuPathDB
ICEMR protein array
Plasmodium vivax parasite density by microscope
parasite density by PCR that is the output of an assay that realizes a measurand role that inheres in Plasmodium falciparum
Person: Jie Zheng, Chris Stoeckert, John Judkins
EuPathDB
ICEMR protein array
Plasmodium falciparum parasite density by PCR
An information content entity specifies whether study subject signed informed consent for future use of specimen.
Person: Jie Zheng, Chris Stoeckert
ICEMR protein array
information on informed consent for future use of specimen
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29449.aspx
obsolete_Candida albicans strain 19F
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29434.aspx
obsolete_Candida albicans strain P78048
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29450.aspx
obsolete_Candida albicans strain P37037
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29451.aspx
obsolete_Candida albicans strain P37039
true
was in EuPathDB/PlasmoDB, no longer used
obsolete_Candida albicans strain SC5314
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29435.aspx
obsolete_Candida albicans strain P57072
true
was in EuPath/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29441.aspx
obsolete_Candida albicans strain P76055
true
was EuPathDB/PlasmoDB term, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29442.aspx
obsolete_Candida albicans strain P76067
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29439.aspx
obsolete_Candida albicans strain P57055
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29443.aspx
obsolete_Candida albicans strain P78042
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29436.aspx
obsolete_Candida albicans strain P34048
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29453.aspx
obsolete_Candida albicans strain P87
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29452.aspx
obsolete_Candida albicans strain GC75
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29438.aspx
obsolete_Candida albicans strain P75016
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29440.aspx
obsolete_Candida albicans strain P75063
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29446.aspx
obsolete_Candida albicans strain P94015
true
was in EuPathDB/PlasmoDB, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29448.aspx
obsolete_Candida albicans strain P60002
true
was EuPathDB/PlasmoDB term, no longer used
https://www.beiresources.org/Catalog/Fungi/NR-29437.aspx
obsolete_Candida albicans strain P75010
true
A genotype information of parasite organism.
parasite organism genotype information
deprecated in favor of APOLLO_SV_00000232 'clade name'
obsolete_genetic clade of organism
true
was EuPathDB/PlasmoDB term, no longer used
obsolete_NLST Clade of organism
true
a data item that is about some virulence and is the count of infectious agents that kill half of a collection of human beings infected with the agents
Person: John Judkins
Wikipedia: LD50
virulence score (LDt50)
a data item that is about some virulence and is the proportion of the number of human beings with a disease (caused by the bearer of the virulence) that die of the disease
Person: John Judkins
virulence score (slope)
A centrally registered identifier symbol assigned by the BEI Resources (https://www.beiresources.org/) to cultures and reagents for microbiology and infectious diseases research.
BEI repository identifier
A measurement datum of vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly.
vertical distance below a surface measurement datum
An age since birth measurement datum measured in days.
age in days
age since birth in days
An information content entity about whether child exposed to antibiotics.
information on whether child exposed to antibiotics
a health care encounter in which a health care provider assists a mother in the birth of a child
Person: John Judkins
baby's delivery
EuPathDB
mode of baby delivery
A medication material that is used in the treatment and prevention of bacterial infections. It may either kill or inhibit the growth of bacteria.
https://en.wikipedia.org/wiki/Antibiotics
antibiotics
An information content entity about whether bee colony treated with tetracycline.
information on whether bee colony treated with tetracycline
main source of nutrition for a child
child's diet
main source of nutrition for a child for each month
child's diet by month
An information content entity about any drug used by a participant under investigation and the frequency of usage.
drug usage information
An information content entity about environmental material, environmental feature, environmental system, etc.
environment information
household information that specifies whether the household relocated during its time under investigation
Person: John Judkins
EuPathDB
information on whether a family moved
an information content entity that is about the bearer of a host role
Person: John Judkins
EuPathDB
host information
the diet of an animal that is the bearer of a host role
Person: John Judkins
EuPathDB
type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
host's diet
An organism that has host role
host organism
a categorical value specification that is about a collection of bee larvae and specifies whether tetracycline was administered to the larvae
Person: John Judkins
EuPathDB
information on whether bee larvae treated with tetracycline
mass measurement datum is about a host that measured at specimen collection process
host mass measurement datum at specimen collection
same as EUPATH_0000496
obsolete_information of specimen obtained from the mother or chid
true
a count that is about a dwelling and is also the result of counting the instances of a child that occupies the dwelling
Person: John Judkins
EuPathDB
number of child occupants in a dwelling
An environmental feature for disposing human waste.
human waste disposal
a ratio that is about a dwelling, is expressed as a percent, has a count of adult occupants of the dwelling as the numerator, and has a count of all occupants of the dwelling as the denominator
Person: John Judkins
EuPathDB
percent adult occupants in a dwelling
a ratio that is about a dwelling, is expressed as a percent, has a count of male occupants of the dwelling as the numerator, and has a count of all occupants of the dwelling as the denominator
Person: John Judkins
EuPathDB
percent male occupants in a dwelling
a categorical value specification that specifies whether a mother received an antimicrobial agent
Person: John Judkins
EuPathDB
information on whether antibiotics given to mom
an information content entity that is about an antimicrobial agent given to a mother and specifies the agent by chemical compound
Person: John Judkins
EuPathDB
information on class of antibiotics given to mom
an information content entity that specifies the trimester of a pregnancy for which a mother receives an antimicrobial agent
Person: John Judkins
EuPathDB
information on trimester antibiotics given to mom
An information content entity about presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present.
environmental pets or farm animals information
a protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial
Person: John Judkins
EuPathDB
sequencing protocol
An information content entity about In which batch were samples sequenced together.
sequencing batch information
an information content entity that is about an investigation and has as parts only the most significant information content entities that result from the investigation
Person: John Judkins
EuPathDB
summary information of investigation
a symbol that denotes the bearer of a participant under investigation role
Person: John Judkins
EuPathDB
participant identifier
an information content entity that is about weight loss occurring in a three-month period
Person: John Judkins
EuPathDB
information on weight loss in last three months
a protocol such that, if it is concretized and its concretization is realized, its concretization is realized in a planned process that has as its objective collecting a specimen
Person: John Judkins
EuPathDB
specimen collection protocol
an information content entity about the bearer of a specimen role
Person: John Judkins
EuPathDB
specimen information
symptom or sign information that results from an examination of either the skin of the patient or a process in which the skin participates
Person: John Judkins
EuPathDB
skin symptom or sign information
an information content entity that is about a specimen collection process
Person: John Judkins
EuPathDB
specimen source information
an information content entity that specifies whether an animal is also human
Person: John Judkins
EuPathDB
information specifying human or animal
a specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts
Person: John Judkins
EuPathDB
specimen collection time post infection
skin symptom or sign information that is about the thickness of the ear of the patient
Person: John Judkins
EuPathDB
ear thickness
skin symptom or sign information that specifies the rate at which water passes through the epidermis of the patient into the air
Person: John Judkins
EuPathDB
transepidermal water loss
was microbiomeDB, no longer used
obsolete_site of ear swabbed
true
a categorical measurement datum that is about the skin of a human being and specifies whether the skin is either dry, moist, or sebaceous
Person: John Judkins
EuPathDB
skin type swabbed
a categorical value specification that is about a portion of skin that has a disorder hypothesized to be clinically significant. It specifies the degree to which a portion of skin is clinically abnormal.
Person: John Judkins
EuPathDB
skin pathology score
a count of the number of instances of a treatment
Person: John Judkins
EuPathDB
number of treatments
skin symptom or sign information that is about increased thickness of the skin
Person: John Judkins
EuPathDB
degree of skin thickening
skin symptom or sign information that specifies the size of a disorder on the skin of a patient
Person: John Judkins
EuPathDB
lesion size
skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
axillary lesion score before treatment
skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
axillary lesion score during treatment
skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
axillary lesion score after treatment
skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
groin lesion score before treatment
skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
groin lesion score during treatment
skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
groin lesion score after treatment
skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
pinna lesion score before treatment
skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
pinna lesion score during treatment
skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion
Person: John Judkins
EuPathDB
pinna lesion score after treatment
treatment outcome information that specifies whether the treatment of a skin lesion was successful
Person: John Judkins
EuPathDB
information on whether skin lesion cured after treatment
a time measurement datum that represents the time interval between the first appearance of a skin lesion and the time it is swabbed for specimen collection
Person: John Judkins
EuPathDB
skin lesion duration
a categorical value specification that specifies the degree of erythema
Person: John Judkins
EuPathDB
NCIT & HP ontologies, EuPathDB
degree of skin redness
skin symptom or sign information that specifies the area of a part of a patient's skin that participates in an inflammation process
Person: John Judkins
EuPathDB
degree of skin inflammation
a measurement datum that is a measurement of the hydration of the outer epidermis
Person: John Judkins
Pubmed 2459872 & https://academic.oup.com/jn/article/134/8/2110S/4688890
corneometry
an information content entity that specifies the degree to which alopecia has been realized in a patient
Person: John Judkins
EuPathDB
degree of hairloss
a skin symptom or sign information that specifies whether the patient has atopic dermatitis
Person: John Judkins
EuPathDB
information on whether affected by atopic dermatitis
A diagnosis given at time of hospitalization.
ICEMR prism
diagnosis at hospitalization
a population that is the bearer of a study group role
Person: John Judkins
EuPathDB
study group
a symbol that denotes a cage that has the function to keep an animal that is the bearer of a participant under investigation role
Person: John Judkins
EuPathDB
animal cage number for experiment
a symbol that denotes a cage that has the function to keep a mouse that is the bearer of a participant under investigation role
Person: John Judkins
EuPathDB
mouse cage number
Deprecated in favor of CHEBI:38068
obsolete_antimalarial
true
A human waste disposal that has the function of disposing of waste material produced by a human child
Person: John Judkins
EuPathDB
human child waste disposal
Assay that subjects a stool sample to a test for microorganisms.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
stool test for microorganisms
A biological process that breeds a plant or animal by natural processes from the parent stock.
Term added for annotation of a Crypto SNP dataset but the term is not used.
Person: Jie Zheng
propagation
A genotype information which is about cluster of differentiation 36 (CD36) gene, which encodes an integral membrane protein in many cell types and a member of the scavenger receptor family that imports fatty acids into cells (Canton et al., 2013). CD36 is also an endothelial receptor for binding of erythrocytes infected with P. falciparum.
Grant Dorsey: The human CD36 antigen is an integral membrane protein in many cell types and a member of the scavenger receptor family that imports fatty acids into cells (Canton et al., 2013). CD36 is also an endothelial receptor for binding of erythrocytes infected with P. falciparum; this cytoadhesion is believed to be an important feature of the virulence of falciparum malaria, due both to its prevention of clearance of infected erythrocytes by the spleen and to local effects of cytoadhering parasites (Newbold et al., 1999). Importantly, expression of CD36 is low in the brain, even in the setting of cerebral malaria (Silamut et al., 1999), suggesting that binding to CD36 is most relevant in non-cerebral forms of severe malaria. CD36 is also believed to be an important macrophage pattern recognition receptor that mediates innate recognition and clearance of infected erythrocytes (Cabrera et al., 2014). Considering our current understanding, CD36 expression might be seen to contribute to malaria severity, by mediating cytoadherence, or to help control malaria, via immune effects. Results with murine malaria models have been complex; mice with decreased CD36-mediated cytoadherence had decreased growth of P. berghei (Fonager et al., 2012), but CD36-deficient mice had increased risk of fatal P. chabaudi malaria (Patel et al., 2007). Considering human populations, many CD36 polymorphisms, including nonsense mutations that prevent production of the molecule, are common, particularly in African populations (Aitman et al., 2000). However, attempts to identify associations between common polymorphisms and malaria risk have led to inconsistent results, with evidence for enhancement of(Aitman et al., 2000; Omi et al., 2002), no effect (Fry et al., 2009), or protection from (Das et al., 2009; Omi et al., 2003; Pain et al., 2001; Sinha et al., 2008) severe malaria with different polymorphisms.
CD3T188G is a polymophism on the human CD36 gene.
cluster of differentiation 36 genotype
An information content entity is about a process.
information on process
A planned process that an organism exposed to that are not one of the variables under study.
MO_55 EnvironmentalHistory
environmental history
A treatment to alleviate the signs and symptoms associated with malaria.
malaria treatment
A time measurement datum of duration of an individual acquires, develops, or first experiences a condition or symptoms of a disease or disorder.
time to onset
A time measurement datum that specifies when the DNA was extracted
DNA extraction date
The measurement datum generated by Inverse polymerase chain reaction (Inverse PCR).
iPCR datum
A time measurement datum of duration of the observation at the end of an observation period.
end of observation period
A time measurement datum of a person first diagnosed as malaria
time to first malaria diagnosis
A time measurement datum of the duration for reinfection.
time to reinfection
A genotype information about 60 kDa glycoprotein (gp60) gene.
gp60 genotype
A specimen collection time measurement datum in year.
specimen collection time in year
An information content entity of multiple blood smear results during an observation period.
information on blood smear result
An organism that has pathogen role.
pathogen organism
A quality inheres in parasite organism.
parasite phenotype
A genotype information of fungus.
fungal organism genotype information
A Fungus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred Fungus
fungal strain
A Candida albicans that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred Candida albicans
Candida albicans strain
A parasite that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred parasite organisms
parasite strain
a time measurement datum specifying the date of a clinical visit scheduled for sixty days after a treatment
Date of observation
EuPathDB
60 day follow-up date
Administering substance in vivo where an antibiotic substance is administered to a living organism.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Antibiotic administration before stool collection
Penn Group
GEMS
antibiotic administration process
An information content entity that is about a subject pairing of two participants for a case-control study design
Person: John Judkins, Chris Stoeckert
Matched case
EuPathDB
information on case matching
An immediate clinical history that is about a treatment for diarrhea
Previous diarrheal care
diarrheal treatment immediate history
an information content entity that is about a realization of diarrhea
John Judkins
Diarrheal episodes
EuPathDB
information on diarrheal episode
Treatment whose aim is to restore the normal hydration state of a living organism.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Rehydration therapy
EuPathDB
Penn Group
GEMS
rehydration treatment
environmental system associated with the dwelling used by humans.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
environment associated with human dwelling
study participant information that specifies details of the study design execution in which the human participant under investigation is participating
John Judkins
Administrative information
EuPathDB
study participant administrative information
An information content entity that mentions an eligiblity criterion
Person: John Judkins
Eligibility criteria
EuPathDB
information on eligibility criterion
an information content entity that is about a human being in the community of a human participant under investigation and identifies the relationship between them both
John Judkins
Individuals related to participant
EuPathDB
information on relation to participant
A data item that is about a quality of a fecal specimen
Person: John Judkins
Stool characteristics
EuPathDB
fecal specimen data item
Specimen collection process aimed at collecting a stool sample.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
stool collection process
an information content entity that specifies an antibiotic that is administered to a human participant under investigation, which precedes stool collection from the participant
Person: John Judkins
Antibiotic administered before stool collection
EuPathDB
information specifying antibiotic administered before stool collection
Organization that undertakes a clinical study at some point in time.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
study center
Site where a human life process ended.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
place of death
A mass measurement datum that is the result of measuring the combined mass of a human participant under investigation and a caretaker of that participant
Person: John Judkins
Weight of caretaker + child
EuPathDB
caretaker and participant combined mass measurement datum
A mass measurement datum that is the result of measuring the mass of a caretaker of a human participant under investigation
Person: John Judkins
Weight of caretaker alone
EuPathDB
caretaker of participant mass measurement datum
an average value that is the specified output of a data transformation that has as input only length measurement data about height
John Judkins
Height; mean
EuPathDB
mean height
A center value that is the specified output of a median calculation that has as input only length measurement data about height
Person: John Judkins
Height; median
EuPathDB
median height
a length measurement datum that is the result of the first in a series of assays measuring the length around the same upper arm, such that the measurement is taken midway along the upper arm
John Judkins
MUAC, 1st
The Mother and Child Health and Education Trust
first mid-upper arm circumference datum
a length measurement datum that is the result of the second in a series of assays measuring the length around the same upper arm, such that the measurement is taken midway along the upper arm
John Judkins
MUAC, 2nd
The Mother and Child Health and Education Trust
second mid-upper arm circumference datum
A length measurement datum that is the result of the third in a series of assays measuring the length around the same upper arm, such that the measurement is taken midway along the upper arm
Person: John Judkins
MUAC, 3rd
EuPathDB
third mid-upper arm circumference datum
An average value of two or more mid-upper arm circumference data of the same human participant under investigation
Person: John Judkins, Chris Stoeckert
MUAC; mean
EuPathDB
mean mid-upper arm circumference
A center value of one or more mid-upper arm circumference data of the same human participant under investigation
Person: John Judkins, Chris Stoeckert
MUAC; median
EuPathDB
median mid-upper arm circumference
A temperature measurement datum that is about the temperature of an axilla
John Judkins
Axillary temperature
EuPathDB
axillary temperature measurement datum
a rate measurement datum that is about a human participant under investigation and is the specified output of the first of a series of countings of instances of the participant's respiration
John Judkins
Respiratory rate 1
Respiratory rate per minute, 1st
EuPathDB
first respiratory rate measurement datum
a rate measurement datum that is about a human participant under investigation and is the specified output of the second of a series of countings of instances of the participant's respiration
John Judkins
Respiratory rate 2
Respiratory rate per minute, 2nd
EuPathDB
second respiratory rate measurement datum
an average value that is the specified output of a data transformation that has two or more respiratory rates of the same human participant under investigation as specified input
John Judkins
Respiratory rate, mean
EuPathDB
average respiratory rate
Container used by humans to drink water.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
water container
Information Content entity that is a boolean-valued measurement datum, outcome of a chlorine testing assay that aims at testing a body of drinking water for a specified minimum concentration of Chlorine.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
chlorine test result
Site where humans wash their hands.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
hand washing location
An information content entity that specifies whether a human participant under investigation is currently a medication-taking patient
Person: John Judkins, Jie Zheng
Currently receiving medication
EuPathDB
indicator of whether receiving medication
A time measurement datum of the date encompassing a defecation
Person: John Judkins
Date stool passed
EuPathDB
defecation date
a quality of water composition, shape, or structure that inheres in fecal material
John Judkins
Stool consistency
Wikipedia: Bristol stool scale
stool consistency
A time measurement datum of the date of the first in a series of antibiotic administrations to a human participant under investigation
Person: John Judkins
Date of first antibiotic administration
EuPathDB
date of first antibiotic administration
A time measurement datum of the time of the first in a series of antibiotic administrations to a human participant under investigation
Person: John Judkins
Time of first antibiotic administration
EuPathDB
time of first antibiotic administration to human participant under investigation
A time measurement datum that is the result of measuring the duration of a diarrheal episode
Person: John Judkins, Chris Stoeckert
Diarrheal episode duration
EuPathDB
diarrheal episode time measurement datum
Measurement datum resulted from the volume measurement process of an entire stool.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
stool volume in ml
a time measurement datum of the date at which a dehydration treatment is administered
John Judkins
Person: John Judkins
EuPathDB
date of rehydration
a time measurement datum of the time of day at which a dehydration treatment is administered
John Judkins
Time of rehydration
EuPathDB
time of rehydration
A symptom at enrollment information about a symptom that was experienced within seven days prior to the time of enrollment
Person: John Judkins
Symptoms in the last 7 days
EuPathDB
symptom in last seven days information
A symptom or sign information that is about a symptom experienced after a disease course has started
Person: John Judkins
Symptoms since illness began
EuPathDB
symptom since illness began information
Process of feeding of babies and young children with milk from a woman's breast.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
breastfeeding process
Child study subject identifier received upon enrolling into a healthcare study for the first time.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
Penn Group
GEMS
child study subject identifier at first enrollment
An information content entity that is about a treatment for diarrhea, given to a participant under investigation, that precedes any treatment for diarrhea given to the participant as part of a clinical visit.
Person: John Judkins
Diarrhea treatment before visit
EuPathDB
information on diarrhea treatment before clinical visit
an information content entity that specifies how the money was raised to cover the cost of a health care encounter
John Judkins
Money source for expenses before visit
EuPathDB
information on raising money for health care encounter
A diarrheal treatment immediate history that is about the person or place from which the treatment is sought
Person: John Judkins
Previously sought care
EuPathDB
information on where diarrheal treatment sought
A categorical value specification that specifies whether the value of an anthropometric information content entity lies outside a specified range
Person: John Judkins
Anthropometry flag
EuPathDB
anthropometric value range specification
An information content entity that is about a treatment for diarrhea that is administered in a health care facility
Person: John Judkins
Diarrhea treatment given in health center
EuPathDB
information on diarrhea treatment in health care facility
An information content entity that is about a treatment provided by a health care prescription for a human participant under investigation for diarrhea
Person: John Judkins
Diarrhea treatment by prescription at home
EuPathDB
information on diarrhea treatment by prescription
A diagnosis of a human participant under investigation, two months before the participant's follow-up visit
Person: John Judkins
Previous diagnosis at 60 day follow-up visit
EuPathDB
diagnosis previous to two month follow-up
Information on case matching that denotes the sex of the case subject
Person: John Judkins
Sex, matched case
EuPathDB
information on sex of matched case
The date of birth of a case subject in a case-control study
Person: John Judkins
Date of birth, matched case
EuPathDB
date of birth of matched case
A categorical value specification that specifies whether a human participant under investigation meets requirements for human subject enrollment
Person: John Judkins
Eligibility for enrollment
EuPathDB
indicator of participant eligibility for enrollment
a categorical measurement datum that is about a maximum fever temperature in Celsius and specifies whether its value is at least 37.5
John Judkins
Fever at episode, temperature >37.5C
EuPathDB
presence of maximum fever temperature of at least 37.5 degrees
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Adenovirus
John Judkins
Adenovirus ELISA performed
EuPathDB
information on whether Adenovirus ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Astrovirus
John Judkins
Astrovirus ELISA performed
EuPathDB
information on whether Astrovirus ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Rotavirus
John Judkins
Rotavirus ELISA performed
EuPathDB
information on whether Rotavirus ELISA performed
a categorical value specification that specifies whether a modified acid fast staining method was performed
John Judkins
modified acid fast staining method performed
EuPathDB
information on whether modified acid fast staining method performed
a categorical value specifiction that specifies whether a reverse transcription polymerase chain reaction assay was performed with the objective of determining whether a specimen contains Norovirus
John Judkins
Norovirus RT-PCR performed
EuPathDB
information on whether Norovirus RT-PCR performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Cryptosporidium
John Judkins
Cryptosporidium ELISA performed
EuPathDB
information on whether Cryptosporidium ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Entamoeba histolytica
John Judkins
Entamoeba histolytica ELISA performed
EuPathDB
information on whether Entamoeba histolytica ELISA performed
a categorical value specification that specifies whether an enzyme linked immunosorbent assay was performed with the objective of determining whether a specimen contains Giardia
John Judkins
Giardia ELISA performed
EuPathDB
information on whether Giardia ELISA performed
a categorical measurement datum that specifies whether Adenovirus was detected by an enzyme-linked immunosorbent assay
John Judkins
Adenovirus, by ELISA
EuPathDB
presence of Adenovirus by ELISA
a categorical measurement datum that specifies whether Aeromonas was detected by differential medium assay
John Judkins
Aeromonas, by bacteriology
EuPathDB
presence of Aeromonas by differential medium assay
a categorical measurement datum that specifies whether Ascaris lumbricoides was detected by a microscopy assay
John Judkins
Ascaris lumbricoides, by microscopy
EuPathDB
presence of Ascaris lumbricoides by microscopy
a categorical measurement datum that specifies whether Astrovirus was detected by an enzyme-linked immunosorbent assay
John Judkins
Astrovirus, by ELISA
EuPathDB
presence of Astrovirus by ELISA
a categorical measurement datum that specifies whether Endolimax nana was detected by microsopy
John Judkins
Endolimax nana, by microscopy
EuPathDB
presence of Endolimax nana by microscopy
a categorical measurement datum that specifies whether Enterobius vermicularis was detected by microsopy
John Judkins
Enterobius vermicularis, by microscopy
EuPathDB
presence of Enterobius vermicularis by microscopy
a categorical measurement datum that specifies whether Hymenolepis diminuta was detected by differential medium assay
John Judkins
Hymenolepis diminuta, by microscopy
EuPathDB
presence of Hymenolepis diminuta by microscopy
a categorical measurement datum that specifies whether Hymenolepis nana was detected by microscopy
John Judkins
Hymenolepis nana, by microscopy
EuPathDB
presence of Hymenolepis nana by microscopy
a categorical measurement datum that specifies whether Ancylostomatoidea was detected by microscopy
John Judkins
Hookworm, by microscopy
EuPathDB
presence of Ancylostomatoidea by microscopy
a categorical measurement datum that specifies whether Iodamoeba butschlii was detected by microscopy
John Judkins
Iodamoeba butschlii, by microscopy
EuPathDB
presence of Iodamoeba butschlii by microscopy
a categorical measurement datum that specifies whether Entamoeba coli was detected by microscopy
John Judkins
Entamoeba coli, by microscopy
EuPathDB
presence of Entamoeba coli by microscopy
a categorical measurement datum that specifies whether Norovirus was detected by a reverse transcription polymerase chain reaction assay
John Judkins
Norovirus, by RT-PCR
EuPathDB
presence of Norovirus by RT-PCR
a categorical measurement datum that specifies whether Norovirus GI was detected by a reverse transcription polymerase chain reaction assay
John Judkins
Norovirus GI, by RT-PCR
EuPathDB
presence of Norovirus GI by RT-PCR
a categorical measurement datum that specifies whether Norovirus GII was detected by a reverse transcription polymerase chain reaction assay
John Judkins
Norovirus GII, by RT-PCR
EuPathDB
presence of Norovirus GII by RT-PCR
a categorical measurement datum that specifies whether Entamoeba histolytica was detected by an enzyme-linked immunosorbent assay
projects using equivalent term that has different ID
John Judkins
Entamoeba histolytica, by ELISA
EuPathDB
obsolete_presence of Entamoeba histolytica by ELISA
true
a categorical measurement datum that specifies whether Plesiomonas shigelloides was detected by differential medium assay
John Judkins
Plesiomonas shigelloides, by bacteriology
EuPathDB
presence of Plesiomonas shigelloides by differential medium assay
a categorical measurement datum that specifies whether Rotavirus detected by an enzyme-linked immunosorbent assay
John Judkins
Rotavirus, by ELISA
EuPathDB
presence of Rotavirus by ELISA
a categorical measurement datum that specifies whether Schistosoma was detected by microscopy
John Judkins
Schistosoma, by microscopy
EuPathDB
presence of Schistosoma by microscopy
a categorical measurement datum that specifies whether Shigella was detected by differential medium assay
John Judkins
Shigella, by bacteriology
EuPathDB
presence of Shigella by differential medium assay
a categorical measurement datum that specifies whether Strongyloides stercoralis was detected by a microscopy assay
John Judkins
Strongyloides stercoralis, by microscopy
EuPathDB
presence of Strongyloides stercoralis by microscopy
a categorical measurement datum that specifies whether Taenia was detected by a microscopy assay
John Judkins
Taenia, by microscopy
EuPathDB
presence of Taenia by microscopy
a categorical measurement datum that specifies whether Vibrio was detected by differential medium assay
John Judkins
Vibrio, by bacteriology
EuPathDB
presence of Vibrio by differential medium assay
a categorical measurement datum that specifies whether Yersinia enterocolitica was detected by differential medium assay
John Judkins
Yersinia enterocolitica, by bacteriology
EuPathDB
presence of Yersinia enterocolitica by microscopy
a categorical measurement datum that specifies whether the objective of an assay to detect bacteria was achieved
John Judkins
Any bacteria, by any method
EuPathDB
presence of bacteria
a categorical measurement datum that specifies whether the objective of an assay to detect a pathogen organism was achieved
John Judkins
Any pathogen, by any method
EuPathDB
presence of pathogen
a categorical measurement datum that specifies whether an assay achieves its objective to detect a virus
John Judkins
Any virus, by any method
EuPathDB
presence of virus
a presence of parasite that specifies that a parasite was detected by the modified acid fast staining method
John Judkins
Any parasites, by modified acid stain microscopy
EuPathDB
presence of parasite by modified acid stain microscopy
a categorical measurement datum that specifies whether Campylobacter was detected by differential medium assay
John Judkins
Campylobacter, by bacteriology
EuPathDB
presence of Campylobacter by differential medium assay
a categorical measurement datum that specifies whether Campylobacter was detected by an enzyme-linked immunosorbent assay
John Judkins
Campylobacter, by ELISA
EuPathDB
presence of Campylobacter by ELISA
a categorical measurement datum that specifies whether Cryptosporidium was detected by an enzyme-linked immunosorbent assay
John Judkins
Cryptosporidium, by ELISA
EuPathDB
presence of Cryptosporidium by ELISA
a categorical measurement datum that specifies whether Cryptosporidium was detected by the modified acid fast staining method
John Judkins
Cryptosporidium, by modified acid stain microscopy result
EuPathDB
presence of Cryptosporidium by modified acid stain microscopy
a categorical measurement datum that specifies whether Giardia was detected by an enzyme-linked immunosorbent assay
John Judkins
Giardia, by ELISA
EuPathDB
presence of Giardia by ELISA
a categorical measurement datum that specifies whether Isospora was detected by a microscopy assay
John Judkins
Isospora, by microscopy
EuPathDB
presence of Isospora by microscopy
Information on process that is about breastfeeding
Person: John Judkins and Chris Stoeckert
Breastfeeding
EuPathDB
information on breastfeeding process
Any measurement of the calories (usually large calories, kilogram calories, dietary calories, or nutritional calories) consumed by an organism. a large calorie is the amount of energy needed to raise the temperature of one kilogram of water by one degree celsius, a measure of the energy which an organism can derive by metabolizing the source of those calories, i.e., a food, a drink, or both.
Person: John Judkins
Calories
EuPathDB
calorie intake measurement
An information content entity that is about an acute manifestation of a lower respiratory tract disease
Person: John Judkins
ALRI episodes
EuPathDB
information on acute lower respiratory tract disease
a laboratory test that has a blood specimen as specified input
John Judkins
Blood test
EuPathDB
blood test
a laboratory test that has a urine specimen as specified input
John Judkins
Urine test
EuPathDB
urine test
An information content entity that is about a microscopy assay
Person: John Judkins
Microscopy
EuPathDB
information on microscopy assay
Charcoal as a cooking fuel
Person: John Judkins
Charcoal
EuPathDB
charcoal cooking fuel
An information content entity that mentions drinking water piped into a dwelling
Person: John Judkins
Piped into house
EuPathDB
information on drinking water piped into dwelling
An information content entity that mentions drinking water obtained through a plumbing fixture located in the yard of a human dwelling
Person: John Judkins
Piped into yard
EuPathDB
information on drinking water piped into yard
drinking water that is derived from rainwater
John Judkins
Rainwater
EuPathDB
drinking water derived from rainwater
Drinking water that is derived from bore hole water
John Judkins
Bore hole
EuPathDB
drinking water derived from bore hole water
A symptom since illness began information that mentions respiratory distress
Person: John Judkins
Difficulty breathing
EuPathDB
respiratory distress since illness began information
A symptom since illness began information that mentions convulsion
Person: John Judkins
Convulsion
EuPathDB
convulsion since illness began information
information on raising money for health care encounter that specifies that less money was spent on food to cover healthcare costs
John Judkins
Cutting down expenses from meal
EuPathDB
information on cutting food expenses to pay for health care
information on raising money for health care encounter that specifies that less money was spent on goods or services other than food to cover healthcare costs
John Judkins
Cutting down from other expenses
EuPathDB
information on cutting non-food expenses to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs was derived from savings
John Judkins
Using savings
EuPathDB
information on using savings to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs was borrowed
John Judkins
Borrowing
EuPathDB
information on borrowing to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs derived from money obtained through the sale of assets
John Judkins
Selling assets
EuPathDB
information on selling assets to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs was donated but not by any member of the patient's household
John Judkins
Asking for donations outside the household
EuPathDB
information on asking for donations outside the household to pay for health care
information on raising money for health care encounter that specifies that the money to cover healthcare costs was donated by a friend or relative of the patient
John Judkins
Paid by relative or friend
EuPathDB
information on health care paid for by relative or friend
A symptom or sign information that mentions rectal prolapse
Person: John Judkins
Rectal prolapse
EuPathDB
rectal prolapse information
A symptom or sign information that mentions pedal edema
Person: John Judkins
Bipedal edema
EuPathDB
pedal edema symptom information
A symptom or sign information that mentions flaky paint dermatosis
Person: John Judkins
Skin has 'flaky paint' appearance
EuPathDB
flaky paint dermatosis information
a diagnosis that is an assertion that a patient who is the subject of a diagnostic process has diarrhea
John Judkins
Diarrhea
EuPathDB
diagnosis of diarrhea
a categorical measurement datum that specifies whether Vibrio cholerae O1 was detected by differential medium assay
John Judkins
Vibrio cholerae O1, by bacteriology
EuPathDB
presence of Vibrio cholerae O1 by differential medium assay
a categorical measurement datum that specifies whether the Vibrio cholerae Inaba serotype was detected by differential medium assay
John Judkins
Vibrio cholerae O1, serotype Inaba, by bacteriology
EuPathDB
presence of Vibrio cholerae Inaba by differential medium assay
a categorical measurement datum that specifies whether the Vibrio cholerae Ogawa serotype was detected by differential medium assay
John Judkins
Vibrio cholerae O1, serotype Ogawa, by bacteriology
EuPathDB
presence of Vibrio cholerae Ogawa by differential medium assay
a categorical measurement datum that specifies whether Vibrio cholerae O139 was detected by differential medium assay
John Judkins
Vibrio cholerae O139, by bacteriology
EuPathDB
presence of Vibrio cholerae O139 by differential medium assay
a categorical measurement datum that specifies whether Salmonella typhi was detected by differential medium assay
John Judkins
Salmonella typhi, by bacteriology
EuPathDB
presence of Salmonella typhi by differential medium assay
a categorical measurement datum that specifies whether a Salmonella serotype other than typhi was detected by differential medium assay
John Judkins
Salmonella non-typhi, by bacteriology
EuPathDB
presence of Salmonella by differential medium assay
a categorical measurement datum that specifies whether Sapovirus was detected by a reverse transcription polymerase chain reaction assay
John Judkins
Sapovirus, by RT-PCR
EuPathDB
presence of Sapovirus by RT-PCR
a categorical measurement datum that specifies whether a species of Campylobacter other than Campylobacter jejuni or Campylobacter coli was detected by differential medium assay
John Judkins
Campylobacter (non-jejuni or coli), by bacteriology
EuPathDB
presence of non-jejuni non-coli Campylobacter by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 4b was detected by differential medium assay
John Judkins
Shigella flexneri serotype 4B, by bacteriology
EuPathDB
presence of Shigella flexneri 4b by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 5b was detected by differential medium assay
John Judkins
Shigella flexneri serotype 5B, by bacteriology
EuPathDB
presence of Shigella flexneri 5b by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 6 was detected by differential medium assay
John Judkins
Shigella flexneri serotype 6, by bacteriology
EuPathDB
presence of Shigella flexneri 6 by differential medium assay
a categorical measurement datum that specifies whether Vibrio cholerae was detected by differential medium assay
John Judkins
Vibrio cholerae, by bacteriology
EuPathDB
presence of Vibrio cholerae by differential medium assay
a categorical measurement datum that specifies whether Campylobacter coli was detected by differential medium assay
John Judkins
Campylobacter coli, by bacteriology
EuPathDB
presence of Campylobacter coli by differential medium assay
a categorical measurement datum that specifies whether Campylobacter jejuni was detected by differential medium assay
John Judkins
Campylobacter jejuni, by bacteriology
EuPathDB
presence of Campylobacter jejuni by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri was detected by differential medium assay
John Judkins
Shigella flexneri, by bacteriology
EuPathDB
presence of Shigella flexneri by differential medium assay
a categorical measurement datum that specifies whether Shigella boydii was detected by differential medium assay
John Judkins
Shigella boydii, by bacteriology
EuPathDB
presence of Shigella boydii by differential medium assay
a categorical measurement datum that specifies whether Shigella dysenteriae was detected by differential medium assay
John Judkins
Shigella dysenteriae, by bacteriology
EuPathDB
presence of Shigella dysenteriae by differential medium assay
a categorical measurement datum that specifies whether Vibrio parahaemolyticus was detected by differential medium assay
John Judkins
Vibrio parahaemolyticus, by bacteriology
EuPathDB
presence of Vibrio parahaemolyticus by differential medium assay
a categorical measurement datum that specifies whether Shigella sonnei was detected by differential medium assay
John Judkins
Shigella sonnei, by bacteriology
EuPathDB
presence of Shigella sonnei by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 4a was detected by differential medium assay
John Judkins
Shigella flexneri serotype 4A, by bacteriology
EuPathDB
presence of Shigella flexneri 4a by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 4c was detected by differential medium assay
John Judkins
Shigella flexneri serotype 4C, by bacteriology
EuPathDB
presence of Shigella flexneri 4c by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 5a was detected by differential medium assay
John Judkins
Shigella flexneri serotype 5A, by bacteriology
EuPathDB
presence of Shigella flexneri 5a by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype X was detected by differential medium assay
John Judkins
Shigella flexneri serotype X, by bacteriology
EuPathDB
presence of Shigella flexneri X by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype Y was detected by differential medium assay
John Judkins
Shigella flexneri serotype Y, by bacteriology
EuPathDB
presence of Shigella flexneri Y by differential medium assay
a categorical measurement datum that specifies whether Astrovirus was detected by a reverse transcription polymerase chain reaction assay
John Judkins
Astrovirus, by RT-PCR
EuPathDB
presence of Astrovirus Y by RT-PCR
a categorical measurement datum that specifies whether Ancylostoma duodenale was detected by a real time polymerase chain reaction assay
John Judkins
Ancylostoma duodenale, by Real Time PCR
EuPathDB
presence of Ancylostoma duodenale by qPCR
a categorical measurement datum that specifies whether Ascaris lumbricoides was detected by a real time polymerase chain reaction assay
John Judkins
Ascaris lumbricoides, Real Time PCR
EuPathDB
presence of Ascaris lumbricoides by qPCR
a categorical measurement datum that specifies whether Escherichia coli was detected by differential medium assay
projects using equivalent term that has different ID
John Judkins
E. coli, by bacteriology
EuPathDB
obsolete_presence of Escherichia coli by differential medium assay
true
a categorical measurement datum that specifies whether Helicobacter pylori was detected by immunoassay
John Judkins
Helicobacter pylori, Immunoassay
EuPathDB
presence of Helicobacter pylori by immunoassay
a categorical measurement datum that specifies whether Ancylostomatoidea was detected by a real time polymerase chain reaction assay
John Judkins
Hookworm, Real Time PCR
EuPathDB
presence of Ancylostomatoidea by qPCR
a categorical measurement datum that specifies whether Necator americanus was detected by a real time polymerase chain reaction assay
John Judkins
Necator americanus, Real Time PCR
EuPathDB
presence of Necator americanus by qPCR
a categorical measurement datum that specifies whether Shigella dysenteriae serotype 1 was detected by differential medium assay
John Judkins
Shigella dysenteriae serotype 1, by bacteriology
EuPathDB
presence of Shigella dysenteria 1 by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 7 was detected by differential medium assay
John Judkins
Shigella flexneri serotype 7, by bacteriology
EuPathDB
presence of Shigella flexneri 7 by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 1a was detected by differential medium assay
John Judkins
Shigella flexneri serotype 1A, by bacteriology
EuPathDB
presence of Shigella flexneri 1a by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 1b was detected by differential medium assay
John Judkins
Shigella flexneri serotype 1B, by bacteriology
EuPathDB
presence of Shigella flexneri 1b by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 2a was detected by differential medium assay
John Judkins
Shigella flexneri serotype 2A, by bacteriology
EuPathDB
presence of Shigella flexneri 2a by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 2b was detected by differential medium assay
John Judkins
Shigella flexneri serotype 2B, by bacteriology
EuPathDB
presence of Shigella flexneri 2b by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 3a was detected by differential medium assay
John Judkins
Shigella flexneri serotype 3A, by bacteriology
EuPathDB
presence of Shigella flexneri 3a by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 3b was detected by differential medium assay
John Judkins
Shigella flexneri serotype 3B, by bacteriology
EuPathDB
presence of Shigella flexneri 3b by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 3c was detected by differential medium assay
John Judkins
Shigella flexneri serotype 3C, by bacteriology
EuPathDB
presence of Shigella flexneri 3c by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 7a was detected by differential medium assay
John Judkins
Shigella flexneri serotype 7A, by bacteriology
EuPathDB
presence of whether Shigella flexneri 7a by differential medium assay
A mass measurement datum of the mass of a fecal specimen
Person: John Judkins
Stool weight
EuPathDB
fecal specimen mass measurement datum
a categorical measurement datum that specifies whether Strongyloides stercoralis was detected by a real time polymerase chain reaction assay
John Judkins
Strongyloides stercoralis, by qPCR
EuPathDB
presence of Strongyloides stercoralis by qPCR
A time measurement datum of the date encompassing a stool test for microorganisms
Person: John Judkins
Test date
EuPathDB
stool test for microorganisms date
a categorical measurement datum that specifies whether Vibrio cholerae O1 biovar El Tor was detected by differential medium assay
John Judkins
Vibrio cholerae O1 El Tor, by bacteriology
EuPathDB
presence of Vibrio cholerae O1 El Tor by differential medium assay
a data item that is the specified output of a differential medium assay that has the objective of determining whether a specimen contains Vibrio cholerae serogroup O1
John Judkins
Vibrio cholerae 01, by bacteriology
EuPathDB
data about Vibrio cholerae O1 by differential medium assay
a data item that is the specified output of a differential medium assay that has the objective of determining whether a specimen contains Vibrio cholerae serogroup O139
John Judkins
Vibrio cholerae O139, by bacteriology
EuPathDB
data about Vibrio cholerae O139 by differential medium assay
An information content entity that is about a dead human participant under investigation and specifies the process which caused the death of the participant
Person: John Judkins
Cause of death
EuPathDB
information on cause of death
a domesticated animal that is raised in an agricultural setting to produce labor and commodities
John Judkins
Livestock
Wikipedia
livestock animal
a categorical value specification that specifies that a bed net is not used
John Judkins
None
EuPathDB
no use of bed net
a categorical value specification that specifies that a bed net is used, but it is not treated with insecticide
John Judkins
Untreated
EuPathDB
bed net not treated
a categorical value specification that specifies that a bed net is used, but it was last treated earlier than six months ago
John Judkins
Regular ITN treated >6 months ago
EuPathDB
bed net treated over six months ago
a categorical value specification that specifies that a bed net is used, and it was last treated more recently than six months previous
John Judkins
Regular ITN treated <6 months ago
EuPathDB
bed net treated within past six months
a categorical value specification that specifies that a bed net is used, and it was treated with long last insecticide
John Judkins
Long-lasting ITN
EuPathDB
bed net treated with long last insecticide
an information content entity that is about a human participant under investigation and specifies that the participant received treatment, for a fever, that was provided at a clinic within the past two weeks
John Judkins
Clinic
EuPathDB
information specifying fever treated at clinic in past 2 weeks
an information content entity that is about a human participant under investigation and specifies that the participant received treatment, for a fever, that was provided by a self-employed health care provider within the past two weeks
John Judkins
Private practice
EuPathDB
information specifying fever treated by private practicioner in past 2 weeks
an information content entity that is about a human participant under investigation and specifies that the participant received treatment, for a fever, that was self-provided within the past two weeks
John Judkins
Self-treated
EuPathDB
information specifying fever self-treated in past 2 weeks
an information content entity that is about a human participant under investigation and specifies that the participant had a fever within the past two weeks but did not receive treatment for the fever
John Judkins
Not treated
EuPathDB
no treatment for fever
a data item that is the specified output of a microscopy assay that has a sample of blood as specified input and indicates that the sample does not contain Plasmodium
John Judkins
Negative
EuPathDB
no Plasmodium by microscopy
a data item that is the specified output of a microscopy assay that has a sample of blood as specified input and indicates that the sample contains Plasmodium falciparum
John Judkins
Plasmodium falciparum
EuPathDB
presence of Plasmodium falciparum by microscopy
a data item that is the specified output of a microscopy assay that has a sample of blood as specified input and indicates that the sample contains Plasmodium vivax
John Judkins
Plasmodium vivax
EuPathDB
presence of Plasmodium vivax by microscopy
a data item that is the specified output of a microscopy assay that has a sample of blood as specified input and indicates that the sample contains Plasmodium malariae
John Judkins
Plasmodium malariae
EuPathDB
presence of Plasmodium malariae by microscopy
a categorical value specification that specifies whether a microscopy assay was performed
John Judkins
Microscopy performed
EuPathDB
microscopy assay performed
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium falciparum
John Judkins
Plasmodium falciparum
EuPathDB
Plasmodium falciparum diagnosis within past year
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium vivax
John Judkins
Plasmodium vivax
EuPathDB
Plasmodium vivax diagnosis within past year
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium malariae
John Judkins
Plasmodium malariae
EuPathDB
information on Plasmodium malariae diagnosis within past year
an information content entity that is about a human participant under investigation and specifies that the participant remembers being diagnosed, within the past year, with a disease by Plasmodium, but does not remember the species of Plasmodium
John Judkins
Can't remember
EuPathDB
forgot which Plasmodium species in diagnosis within past year
information on antimalarial drug used last year that specifies artesunate as the drug administered as the most recent treatment
John Judkins
Artesunate
EuPathDB
information specifying Artesunate as antimalarial drug as most recent treatment within past year
an information content entity that is about a human participant under investigation who, within one year previous, was administered an antimalarial drug to alleviate symptoms of malaria. This information content entity specifies that the participant does not remember which drug was administered.
John Judkins
Can't remember
EuPathDB
forgot which antimalarial in most recent treatment
information on antimalarial drug used last year that specifies a combination of aretesunate, pyrimethamine, and sulphadox as the drugs administered as the most recent treatment
John Judkins
Artesunate/pyrimethamine/sulphadoxine
EuPathDB
artesunate/pyrimethamine/sulphadoxine combination as most recent malaria treatment
information on antimalarial drug used last year that specifies chloroquine or primaquine as the drugs administered as the most recent treatment
John Judkins
Chloroquine/primaquine
EuPathDB
chloroquine or primaquine as most recent malaria treatment
information on antimalarial drug used last year that specifies pyrimethamine or sulphadoxine as the drugs administered as the most recent treatment
John Judkins
Pyrimethamine/sulphadoxine
EuPathDB
pyrimethamine or sulphadoxine as most recent malaria treatment
information on antimalarial drug used last year that specifies quinine or quinidine as the drugs administered as the most recent treatment
John Judkins
Quinine/quinidine
EuPathDB
quinine or quinidine as most recent malaria treatment
information on antimalarial drug used last year that specifies tetracycline or doxycycline as the drugs administered as the most recent treatment
John Judkins
Tetracycline/doxycycline
EuPath
tetracycline or doxycycline as most recent malaria treatment
an information content entity that is about a human participant under investigation and specifies that the participant received treatment for malaria in a clinic, within the past year
John Judkins
Clinic/hospital
EuPathDB
information on whether treated in clinic
a categorical value specification that specifies whether the bearer of an organization health care role, which administered a treatment to alleviate an episode of malaria, was a private practice
John Judkins
Private doctor
EuPathDB
information on whether treated by private practice
A categorical value specification that specifies whether a treatment to alleviate an episode of malaria was self-administered
Person: John Judkins
Self-treated
EuPathDB
indicator of self-treated malaria
an information content entity that is about a human participant under investigation who, within one year previous, was administered an antimalarial drug to alleviate symptoms of malaria. This information content entity specifies that the participant does not remember the geographic location where this treatment was provided.
John Judkins
Can't remember
EuPathDB
forgot where treatment within past year occurred
a presence of parasite that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that no Plasmodium was detected
John Judkins
Negative
EuPathDB
no Plasmodium by blood sample PCR
a presence of Plasmodium falciparum that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium falciparum was detected
John Judkins
Plasmodium falciparum
EuPathDB
presence of Plasmodium falciparum by blood sample PCR
a presence of Plasmodium falciparum that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium vivax was detected
John Judkins
Plasmodium vivax
EuPathDB
presence of Plasmodium vivax by blood sample PCR
a presence of Plasmodium malariae that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium malariae was detected
John Judkins
Plasmodium malariae
EuPathDB
presence of Plasmodium malariae by blood sample PCR
a presence of Plasmodium ovale that is the specified output of a parasite detection by PCR assay, has a blood specimen as specified input, and specifies that Plasmodium ovale was detected
John Judkins
Plasmodium ovale
EuPathDB
presence of Plasmodium ovale by blood sample PCR
a presence of Plasmodium falciparum that is the specified output of a falcivax rapid diagnostic test and specifies that Plasmodium falciparum was detected
John Judkins
Plasmodium falciparum
EuPathDB
presence of Plasmodium falciparum by falcivax
a presence of Plasmodium vivax that is the specified output of a falcivax rapid diagnostic test and specifies that Plasmodium vivax was detected
John Judkins
Plasmodium vivax
EuPathDB
presence of Plasmodium vivax by falcivax
a presence of parasite that is the specified output of a falcivax rapid diagnostic test and indicates that no Plasmodium was detected
John Judkins
Negative
EuPathDB
no presence of Plasmodium by falcivax
a categorical value specification that specifies whether a falcivax rapid diagnostic test was performed
John Judkins
FalciVax RDT performed
EuPathDB
information on whether falcivax performed
a presence of Plasmodium falciparum that is the specified output of a optimal-IT rapid diagnostic test and specifies that Plasmodium falciparum was detected
John Judkins
Plasmodium falciparum
EuPathDB
presence of Plasmodium falciparum by optimal-IT
a presence of parasite that is the specified output of a optimal-IT rapid diagnostic test and specifies that an antigen common to multiple Plasmodium species was detected
John Judkins
Pan Plasmodium
EuPathDB
presence of pan-Plasmodium antigen by optimal-IT
a presence of parasite that is the specified output of an optimal-IT rapid diagnostic test and specifies that no Plasmodium was detected
John Judkins
Negative
EuPathDB
no Plasmodium by optimal-IT
a categorical value specification that specifies whether an optimal-IT rapid diagnostic test was performed
John Judkins
OptiMAL RDT performed
EuPathDB
information on whether optimal-IT performed
an information content entity that is about a human participant under investigation and specifies that the participant does not remember using a personal mosquito repellent
John Judkins
Can't remember
EuPathDB
forgot whether used personal mosquito repellent
an information content entity that specifies that a human participant under investigation does not remember whether insecticide was applied in the previous 12 months
John Judkins
Can't remember
EuPathDB
no knowledge of insecticide spraying in last 12 months
healthcare information that specifies that the organization that typically provides the healthcare is funded by a government rather than funded independently
John Judkins
Public
EuPathDB
public healthcare information
healthcare information that specifies that the organization that typically provides the healthcare is funded independently of any government
John Judkins
Private
EuPathDB, New Oxford American Dictionary entry for 'private'
private healthcare information
water accessed through a plumbing fixture located inside a human dwelling
John Judkins
Indoor plumbing
EuPathDB
water piped into dwelling
water derived from water that is part of either a stream or a river
John Judkins
Stream/river
EuPath
stream water
a blood specimen that is located in a vacutainer
John Judkins
Vacutainer sample
EuPathDB
blood specimen in vacutainer
a time measurement datum of the day that encompasses a process that has as specified output a data item about a household
John Judkins
Household data collection date
EuPathDB
household data collection date
a categorical value specification that specifies whether there exists some quality of a patient, material entity that is part of a patient, or processual entity that a patient participates in, that is both observed in a physical examination and deemed by the clinician to be of clinical significance
John Judkins
Any signs
EuPathDB, based on definition for 'sign' in OGMS
information on whether participant has sign
a categorical value specification that specifies whether there exists some quality of a patient that is observed by the patient or some processual entity experienced by the patient that is hypothesized by the patient to be a realization of a disease
John Judkins
Any symptoms
EuPathDB, based on definition for 'sign' in OGMS
information on whether participant has symptom
a categorical value specification that specifies whether a human participant under investigation was febrile in the previous 48 hours
John Judkins
Fever in last 48 hours
EuPathDB
information on whether had fever in last 48 hours
a categorical value specification that specifies whether medication to treat malaria was administered in the past two weeks to a human participant under investigation
John Judkins
Malaria medication in last 2 weeks
EuPathDB
information on whether given malaria medication in past 2 weeks
a categorical value specification that specifies whether a human participant under investigation was febrile in the previous two weeks
John Judkins
Fever in last 2 weeks
EuPathDB
information on whether had fever in last two weeks
a clinical history that is about a human participant under investigation and contains only statements about health-relevant qualities that come into existence after the enrollment of the participant in the study
John Judkins
Immediate clinical history
immediate clinical history
EuPathDB
immediate clinical history
a geographic location that is either a city or an area containing settlements where the inhabitants share a common trait
John Judkins
Community
Wikipedia
community
a wall material used to build an exterior wall
John Judkins
External wall material
EuPathDB
external wall material
a wall material used to build a wall between rooms
John Judkins
Internal wall material
EuPathDB
internal wall material
a count of the number of beds in the dwelling of a household that have a bed net hung over them
John Judkins
Beds with bednet (#)
EuPathDB
count of beds with bednet
a household asset information indicating whether a household has a freezer
John Judkins
Freezer
EuPathDB
household freezer asset
a household asset information indicating whether a household has an electrical appliance that has the function of mixing food or drink
John Judkins
Blender
EuPathDB
household blender asset
a household asset information indicating whether a household has an appliance that has a heating element as part and has the function of heating food or drink
John Judkins
Electric stove
EuPathDB
household electric stove asset
a household asset information indicating whether a household has an appliance that has the function of heating food or drink through the combustion of natural gas
John Judkins
Gas stove
EuPathDB
household gas stove asset
a household asset information indicating whether a household has an appliance that has the function of heating food or drink through the combustion of kerosene
John Judkins
Kerosene stove
EuPathDB
household kerosene stove asset
a household asset information indicating whether a household has an appliance that has the function of heating food or drink through the combustion of coal
John Judkins
Coal stove
EuPathDB
household coal stove asset
a household asset information indicating whether a household has a television set that is capable of producing grayscale images but not color images
John Judkins
Black and white TV
EuPathDB
household black and white television asset
a household asset information indicating whether a household has a television set that is capable of producing color images
John Judkins
Color TV
EuPathDB
household color television asset
a household asset information indicating whether a household has a device capable of playing DVDs
John Judkins
DVD
EuPathDB
household DVD player asset
a household asset information indicating whether a household has a sound system
John Judkins
Stereo
EuPathDB
househould sound system asset
a household asset information indicating whether a household has cows
John Judkins
Cows
EuPathDB
household cows asset
a household asset information indicating whether a household has goats
John Judkins
Goats
EuPathDB
household goats asset
a household asset information indicating whether a household has sexually immature domesticated birds
John Judkins
Chicks
EuPathDB
household chicks asset
a household asset information indicating whether a household has domesticated female birds
John Judkins
Hens
EuPathDB
household hens asset
a household asset information indicating whether a household has roosters
John Judkins
Roosters
EuPathDB
household roosters asset
a household asset information indicating whether a household has turkeys
John Judkins
Turkeys
EuPathDB
household turkeys asset
a household asset information indicating whether a household has ducks
John Judkins
Ducks
EuPathDB
household ducks asset
a household asset information indicating whether a household has small parrots with long tails
John Judkins
Parakeets
EuPathDB
household parakeets asset
a household asset information indicating whether a household has parrots
John Judkins
Parrots
EuPathDB
household parrots asset
a household asset information indicating whether a household has monkeys
John Judkins
Monkeys
EuPathDB
household monkeys asset
a household asset information indicating whether a household has pigs
John Judkins
Pigs
EuPathDB
household pigs asset
a household asset information indicating whether a household has rabbits
John Judkins
Rabbits
EuPathDB
household rabbits asset
a household asset information indicating whether a household has dogs
John Judkins
Dogs
EuPathDB
household dogs asset
a household asset information indicating whether a household has cats
John Judkins
Cats
EuPathDB
household cats asset
a household asset information indicating whether a household has turtles
John Judkins
Turtles
EuPathDB
household turtles asset
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's most recent malaria episode
John Judkins
Traveled in the 2 weeks before most recent malaria episode
EuPath
traveled within two weeks earlier than most recent malaria episode
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's second most recent malaria episode
John Judkins
Traveled in the 2 weeks before second most recent malaria episode
EuPath
traveled within two weeks earlier than second most recent malaria episode
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's third most recent malaria episode
John Judkins
Traveled in the 2 weeks before third most recent malaria episode
EuPath
traveled within two weeks earlier than third most recent malaria episode
a categorical value specification that specifies whether a human participant under investigation had traveled within the two weeks previous to the time of the participant's fourth most recent malaria episode
John Judkins
Traveled in the 2 weeks before fourth most recent malaria episode
EuPath
traveled within two weeks earlier than fourth most recent malaria episode
a time measurement datum of the duration of the most recent journey of a human participant under investigation
John Judkins
Length of most recent trip (days)
EuPathDB
duration of most recent trip
a time measurement datum of the duration of the second most recent journey of a human participant under investigation
John Judkins
Length of second most recent trip (days)
EuPathDB
duration of second most recent trip
a time measurement datum of the duration of the third most recent journey of a human participant under investigation
John Judkins
Length of third most recent trip (days)
EuPathDB
duration of third most recent trip
a time measurement datum of the duration of the fourth most recent journey of a human participant under investigation
John Judkins
Length of fourth most recent trip (days)
EuPathDB
duration of fourth most recent trip
an information content entity that specifies which rivers were visited during the most recent journey of a human participant under investigation
John Judkins
River traveled on most recent trip
EuPathDB
rivers traveled on most recent trip
human traveling information that specifies the community to which a human participant under investigation has most recently traveled
John Judkins
Community visited on most recent trip
EuPathDB
community visited on most recent trip
human traveling information that specifies the community to which a human participant under investigation has traveled the second most recently
John Judkins
Community visited on second most recent trip
EuPathDB
community visited on second most recent trip
human traveling information that specifies the community to which a human participant under investigation has traveled the third most recently
John Judkins
Community visited on third most recent trip
EuPathDB
community visited on third most recent trip
human traveling information that specifies the community to which a human participant under investigation has traveled the fourth most recently
John Judkins
Community visited on fourth most recent trip
EuPathDB
community visited on fourth most recent trip
a time measurement datum of the time since the beginning of the most significant occupation of a human participant under investigation
John Judkins
Length of main occupation (years)
EuPathDB
duration of current main occupation
a time measurement datum of the time since the beginning of the second most significant occupation of a human participant under investigation
John Judkins
Length of secondary occupation (years)
EuPathDB
duration of current secondary occupation
a categorical value specification that specifies whether a human participant under investigation was on the property of the participant's household at the time of a scheduled clinical visit
John Judkins
Present at visit
EuPathDB
information on whether participant present for clinical visit
human travel informaton that is about a human participant under investigation and specifies both method and geographic location of the most recent journey taken by the participant
John Judkins
Most recent travel
EuPathDB
information on most recent travel
human travel information that is about a human participant under investigation and specifies both method and geographic location of the second most recent journey taken by the participant
John Judkins
Second most recent travel
EuPathDB
information on second most recent travel
a categorical value specification that specifies whether the collection of a specimen from a human participant under investigation was prompted by a sign that the participant was febrile
John Judkins
Reason for specimen collection
EuPathDB
information on whether specimen collection prompted by sign of fever
an information content entity that is about a human participant under investigation from which the collection of a specimen was not prompted by a sign that the partipant was febrile. This information content entity specifies that which prompted the specimen collection
John Judkins
Other reason for specimen collection
EuPathDB
reason besides fever for specimen collection
a time measurement datum of the last time insecticide was applied to the bednets used by a household
John Judkins
Last bednet treatment
EuPath
time of most recent bednet treatment
an information content entity that is about the relocation of the household of a human participant under investigation
John Judkins
Relocation details
EuPathDB
relocation information
a time measurement datum of the time point at which a human subject enrollment is complete
John Judkins
Enrollment time
EuPath
time of participant first enrolled in a study
a categorical measurement datum that specifies whether a bacterium was detected by a microscopy assay
John Judkins
Bacteria, microscopy
EuPathDB
presence of bacteria by microscopy
a scalar measurement datum of the concentration of bicarbonate in blood that is a specified output of a blood test
John Judkins
Bicarbonate (mmol/L)
EuPathDB
blood bicarbonate concentration
A data item that is about a child infected with malaria and is the sum of the blantyre coma eye movement score, the blantyre coma motor response score, and the blantyre coma verbal response score for the same child during the same infection
Person: John Judkins
Blantyre coma score - total
Wikipedia
Blantyre coma score sum
a scalar measurement datum of the concentration of urea in blood that is the specified output of a blood test
John Judkins
BUN (mg/dL)
EuPathDB
blood urea concentration
a scalar measurement datum of the concentration of creatine in blood that is the specified output of a blood test
John Judkins
Creatinine (mg/dL)
EuPathDB
blood creatine concentration
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a second time while in hospital
John Judkins
Take second antimalarial medication
EuPathDB
information on whether second antimalarial taken
a categorical value specification that specifies whether a human participant under investigation was discharged from hospital
John Judkins
Discharged
EuPathDB
information on whether discharged from hospital
gametocyte density by microscope that is the output of an assay that realizes a measurand role that inheres in Plasmodium
John Judkins
Gametocyte density, microscopy (per uL blood)
EuPathDB
Plasmodium gametocyte density by microscope
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a third time while in hospital
John Judkins
Take third antimalarial medication
EuPathDB
information on whether third antimalarial taken
A hemoglobin level in g per dl that is the specified output of an assay that occurs in a hospital facility
Person: John Judkins
Hemoglobin, from hospital
EuPathDB
hemoglobin concentration measured in hospital
a categorical value specification that specifies whether a human participant under investigation moved to a different dwelling in the previous twelve months
John Judkins
Moved in last 12 months
EuPathDB
information on whether moved in past twelve months
a categorical value specification that specifies whether a human participant under investigation moved to a different dwelling in the previous month
John Judkins
Moved in last month
EuPathDB
information on whether moved in past month
A parasitemia measurement that is the specified output of a microscopy assay in which a blood specimen is evaluated to determine the fraction of red blood cells infected with plasmodium falciparum
Person: John Judkins
P. falciparum parasitemia, microscopy
EuPathDB
Plasmodium falciparum parasitemia measurement datum
A parasitemia measurement that is the specified output of a microscopy assay in which a blood specimen is evaluated to determine the fraction of red blood cells infected with plasmodium malariae
Person: John Judkins
P. malariae parasitemia, microscopy
EuPathDB
Plasmodium malariae parasitemia measurement datum
A parasitemia measurement that is the specified output of a microscopy assay in which a blood specimen is evaluated to determine the fraction of red blood cells infected with plasmodium vivax
Person: John Judkins
P. vivax parasitemia, microscopy
EuPathDB
Plasmodium vivax parasitemia measurement datum
a falcivax rapid diagnostic test that occurs in a hospital facility
John Judkins
Parasite species, FalciVax RDT from hospital
EuPathDB
falcivax rapid diagnostic test in hospital
A categorical measurement datum that specifies whether Plasmodium was detected by a microscopy assay that has as part a thick smear technique
Person: John Judkins
Parasite species, microscopy - thick smear
EuPathDB
presence of Plasmodium by thick smear microscopy assay
A categorical measurement datum that specifies whether Plasmodium was detected by a microscopy assay that has as part a thin smear technique
Person: John Judkins
Parasite species, microscopy - thin smear
EuPathDB
presence of Plasmodium by thin smear microscopy assay
a categorical value specification that specifies whether a human participant under investigation is receiving treatment to alleviate symptoms of malaria
John Judkins
Initiated antimalarial treatment
EuPathDB
information on whether antimalarial treatment initiated
A relocation information on a human participant under investigation who moved to a different dwelling within one month previous. this information specifies the subnational region from which the participant moved.
Person: John Judkins
State moved from in last month
EuPathDB
subnational region relocated from within past month
human traveling information that specifies which subnational regions a human participant under investigation had visited within one month previous
John Judkins
State visited in last month
EuPath
subnational region visited within past month
A relocation information on a human participant under investigation who moved to a different dwelling within twelve months previous. this information specifies subnational regions from which the participant moved.
Person: John Judkins
States moved from in last 12 months
EuPathDB
subnational region relocated from within past 12 months
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a fourth time while in hospital
John Judkins
Take fourth antimalarial medication
EuPathDB
information on whether fourth antimalarial taken
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a fifth time while in hospital
John Judkins
Take fifth antimalarial medication
EuPathDB
information on whether fifth antimalarial taken
human traveling information that specifies which subnational regions a human participant under investigation had visited within twelve months previous
John Judkins
States visited in last 12 months
EuPath
subnational region visited within past 12 months
a time measurement datum of the date during which a treatment starts
John Judkins
Treatment start date
EuPath
treatment start date
a time measurement datum of the time point at which a treatment starts
John Judkins
Treatment start time
EuPath
treatment start time
a time measurement datum specifying the time (of day) of a clinical visit scheduled for sixty days after a treatment
John Judkins
Time of observation
EuPathDB
60-day follow-up observation time
a scalar measurement datum of the mass concentration of bilirubin in blood that is a specified output of a blood test
John Judkins
Total bilirubin (mg/dL)
EuPathDB
blood bilirubin concentration
a categorical value specification that is about a human participant under investigation and specifies whether the participant had traveled within twelve months previous
John Judkins
Traveled in last 12 months
EuPathDB
information on participant travel in the last twelve months
a categorical value specification that specifies whether a human participant under investigation self-identifies as a member of a tribe
John Judkins
Tribal affilliation
EuPathDB
information on whether participant is member of tribe
a categorical value specification that specifies whether the life-death temporal boundary of a human participant under investigation occurred during a health care encounter in a hospital facility
John Judkins
Died
EuPathDB
information on whether participant died in hospital
A passage history record is a data item recording in sequential order the hosts in which the strain has been previously subcultured in.
passage history record
A mushroom (or toadstool) is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground on soil or on its food source.
mushroom
mushroom (food source)
infant formula
liquid
liquid (food source)
A solid product is a hard or soft product capable of retaining its own shape at room temperature (20 degrees C.). A soft product that is spreadable or formable is considered semisolid.
food (solid)
A reference to a place on the Earth, by its name or by its geographical location.
http://purl.obolibrary.org/obo/gaz.owl
geographic location
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
average mapping coverage
read coverage
A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
subnational region
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
The covalent alteration of one or more amino acid residues within a histone protein.
histone modification
A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism.
ICEMR protein array
Renal insufficiency
A phenotypic abnormality.
Phenotypic abnormality
Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose.
Epistaxis
An eye that is more deeply recessed into the plane of the face than is typical.
Deeply set eye
Abnormal alignment, positioning, or spacing of the teeth, i.e., misaligned teeth.
Misalignment of teeth
A state of unease characterized by diffuse motor activity or motion subject to limited control, nonproductive or disorganized behavior, and subjective distress.
Restlessness
Yellow pigmentation of the skin due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.
ICEMR protein array
Jaundice
Abnormal excessive perspiration (sweating) despite the lack of appropriate stimuli like hot and humid weather.
Hyperhidrosis
Abnormally pale skin.
Pallor
Pruritus is an itch or a sensation that makes a person want to scratch. This term refers to an abnormally increased disposition to experience pruritus.
Pruritus
A state of disinterestedness, listlessness, and indifference, resulting in difficulty performing simple tasks or concentrating.
Lethargy
Complete absence of wakefulness and content of conscience, which manifests itself as a lack of response to any kind of external stimuli.
ICEMR protein array
Coma
Abnormal increased size of the spleen.
Splenomegaly
An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects.
ICEMR protein array
Abnormal bleeding
Dehydration
Elevated body temperature due to failed thermoregulation.
Fever
Excessive thirst manifested by excessive fluid intake.
Polydipsia
Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.
Vomiting
A sensation of unease in the stomach together with an urge to vomit.
Nausea
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen.
Abdominal pain
Difficulty in breathing. The physical presentation of respiratory distress is generally referred to as labored breathing, while the sensation of respiratory distress is called shortness of breath or dyspnea.
Respiratory distress
Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.
Headache
Very rapid breathing.
Tachypnea
Abnormality of the homeostasis (concentration) of a monoatomic ion.
electrolyte disturbances
Abnormal blood ion concentration
Abnormality of ion homeostasis
Genital ulcers
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back.
Back pain
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the lower back.
Low back pain
Reduced consciousness/confusion
Malnutrition
Loss of consciousness
Excessive wrinkled skin
An abnormal accumulation of excess fluid in the lower extremity resulting in swelling of the feet and extending upward to the lower leg.
Pedal edema
Cognitive, psychiatric or memory anomaly.
Abnormality of higher mental function
Increased size of the parotid gland.
Enlargement of parotid gland
A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity.
Abdominal colic
An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.
Pain
Pain in the ear can be a consequence of otologic disease (primary or otogenic otalgia), or can arise from pathologic processes and structures other than the ear (secondary or referred otalgia).
Ear pain
Ear pain
The state in which profound and widespread reduction of effective tissue perfusion leads first to reversible, and then if prolonged, to irreversible cellular injury.
Shock
A dermatosis characterized by generalized shiny, enamel-like, hyperpigmented scales in an irregular pattern. The scales may peel or desquamate, rather like old, sun-baked blistered paint, often with areas of underlying hypopigmentation. This has led to the terms peeling paint or flaky paint dermatosis (See the Figure in PMID:24285001).
Flaky paint dermatosis
Fluid accumulation in the lungs.
Pulmonary edema
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest.
Chest pain
An acute hypersensitivity reaction due to exposure to a previously encountered antigen.
Anaphylactic shock
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the eye.
Ocular pain
A small elevation of the skin containing cloudy or purulent material usually consisting of necrotic inflammatory cells.
Pustule
Warts, benign growths on the skin or mucous membranes that cause cosmetic problems as well as pain and discomfort. Warts most often occur on the hands, feet, and genital areas.
Verrucae
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
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."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
action specification
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
GROUP: IAO
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
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
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.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154).
PERSON: James A. Overton
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.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
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.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
1
1
scalar measurement datum
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
scalar measurement datum
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
2013-05-30 Alan Ruttenberg: 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
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
directive information entity
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and 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.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
OBI_0000270
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
curation status specification
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
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.
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
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
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
plan specification
measurement datum
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,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
OBI_0000305
group:OBI
measurement datum
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
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
text
textual entity
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
PERSON: Lawrence Hunter
document
publication
A journal article or book
A document that has been accepted by a publisher
PERSON: Lawrence Hunter
publication
publication about an investigation
Most scientific journal articles
A publication that is about an investigation
PERSON: Lawrence Hunter
scientific publication
publication about an investigation
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
one dimensional cartesian spatial coordinate datum
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
time measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
time measurement datum
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
Person:Alan Ruttenberg
Person:Chris Stoeckart
email address
documenting
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
a planned process in which a document is created or added to by including the specified input in it.
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
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
assigning a centrally registered identifier
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Alan Ruttenberg
Person:Bjoern Peters
Person:Melanie Courtot
assigning a CRID
assigning a centrally registered identifier
centrally registered identifier symbol
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID symbol
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
centrally registered identifier
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier
centrally registered identifier registry
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID registry
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier registry
A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
identifier
proper name
The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done.
obsolete follow-up visit
A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
pathogen role
A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time.
infection prevalence
An infection bearing the primary infection role.
primary infection
A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
infection
human pathogenicity disposition
A disposition to initiate processes that result in a disorder in a human organism.
Human Pathogenicity of Suspected Organism(s) in Specimen
CS19
NIAID GSCID-BRC
human pathogenicity disposition
Hymenolepis nana
Viruses
Viruses
Adenoviridae
Rotavirus
Entamoeba coli
Endolimax nana
typhus group
Euteleostomi
bony vertebrates
Euteleostomi
Norovirus GI
Norovirus GII
Dengue virus
Vibrio cholerae O1
Shigella flexneri 2b
Norovirus
Clostridioides difficile
Shigella flexneri 4c
Shigella flexneri X variant
Campylobacter
Campylobacter coli
Campylobacter jejuni
Bacteria
eubacteria
Bacteria
Helicobacter pylori
Archaea
Archaea
Eukaryota
eucaryotes
eukaryotes
Eukaryota
Euarchontoglires
Euarchontoglires
Tetrapoda
tetrapods
Tetrapoda
Amniota
amniotes
Amniota
Opisthokonta
Opisthokonta
Bilateria
Bilateria
Ancylostomatoidea
Trichuris trichiura
Chikungunya virus
Shigella flexneri 1a
Astroviridae
Mammalia
mammals
Mammalia
Shigella flexneri 1b
Shigella flexneri 3a
Shigella flexneri 5a
Shigella flexneri Y
Shigella flexneri 2a
Shigella flexneri 3b
Cyclospora
Chilomastix mesnili
Fungi
Ancylostoma duodenale
Enterobius vermicularis
Necator americanus
Candida albicans
Escherichia coli
Isospora
Giardia
Entamoeba histolytica
Cryptosporidium
Plasmodium
Salmonella
Schistosoma
Shigella
Taenia
Shigella boydii
Hymenolepis diminuta
Shigella dysenteriae
Shigella flexneri
Shigella sonnei
Strongyloides stercoralis
Ascaris lumbricoides
Yersinia enterocolitica
Aeromonas
Vibrio
Vibrio cholerae
Vibrio parahaemolyticus
Plesiomonas shigelloides
Balantioides coli
Vertebrata <Metazoa>
Vertebrata
vertebrates
Vertebrata <Metazoa>
Bacteroides fragilis
Sapovirus
Homo sapiens
human
human being
man
Homo sapiens
Canis lupus familiaris
Shigella flexneri 4a
A species of nonpathogenic parasitic amoeba. Transmission of I. butschlii is by a fecal-oral route and infection is usually asymptomatic.
Iodamoeba butschlii
A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).
Fungus
A note acknowledging a source of information or quoting a passage.
Reference
A sterile liquid preparation infused into a vein. IV fluid is prescribed as a replacement of fluid, electrolytes, calories, vitamins, and other nutritional substances. In addition, IV fluids are used to administer blood products and medications such as chemotherapy. Examples of IV fluids include Normal Saline, Ringers Solution, and Lactated Ringers Solution. (NCI)
IV Fluid
A type of dog known for its special or distinctive characteristics.
Dog Breed
A blood smear technique used to make a thick blood smear on a microscope slide which is generally used to look for blood parasites such as those causing malaria.
Thick Smear Technique
A blood smear technique used to make a thin blood smear on a microscope slide which is generally used to look for blood parasites such as those causing malaria.
Thin Smear Technique
A data transformation that add two or more numbers, magnitudes, quantities, or particulars as determined by or as if by the mathematical process of addition.
tracker: https://github.com/obcs/obcs/issues/7
Person: Jie Zheng
http://dictionary.reference.com/browse/summing
PRISM
summing data transformation
A data item that is produced as the output of a summing data transformation and represents the total value of the input data.
Tracker:https://github.com/obcs/obcs/issues/7
Person: Jie Zheng
Jie Zheng
sum value
A material entity that is bearer of a medication role.
medication material
A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets.
buffy coat specimen
A scalar measurement datum that is the output of a volume measurement assay that has a blood specimen as evaluant.
blood specimen volume
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'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.)
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.
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
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
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
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Bjoern Peters
OBI branch derived
Could add specific objective specification
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
study
investigation
evaluant role
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
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)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
evaluant role
reporting party role
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
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
MO:submitter mapped to this term. So, alternative term 'submitter' was added.
Jennifer Fostel
reporting party
submitter
OBI
reporting party role
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
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.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
study assay
any method
assay
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
PlanAndPlannedProcess Branch
study
OBI branch derived
sample preparation for assay
culture medium
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
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.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
material transformation
OBI branch derived
material processing
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.
participant under investigation role
responsible party role
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Person: Jennifer Fostel
responsible party
OBI
responsible party role
principal investigator role
a responsible party role played by a person responsible for the overall conduct of a study
Person: Jennifer Fostel
principal investigator
CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
principal investigator role
specimen role
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
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.
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.
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.
GROUP: Role Branch
OBI
specimen role
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
population
investigation agent role
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
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.
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.
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)
GROUP: Role Branch
investigator
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
study person role
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)
investigation agent role
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
organization
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.
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
GROUP: OBI
organization
protocol
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.
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.
PlanAndPlannedProcess Branch
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
study protocol
protocol
drawing a conclusion based on data
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.
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
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
Bjoern Peters
drawing a conclusion based on data
planning
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
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
planning
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
extract
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
PERSON: Philippe Rocca-Serra
extracted material
GROUP: OBI Biomatrial Branch
extract
averaging objective
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.
Elisabetta Manduchi
James Malone
PERSON: Elisabetta Manduchi
averaging objective
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.
genotyping assay
assay objective
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)
PPPB branch
PPPB branch
assay objective
material transformation objective
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.
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
artifact creation objective
GROUP: OBI PlanAndPlannedProcess Branch
material transformation objective
study design execution
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that realizes the concretization of 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.
branch derived
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.
study design execution
A sequencing assay which determines information on the sequence of a DNA molecule.
DNA sequencing assay
DNA sequencing assay
material separation objective
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.
PPPB branch
PPPB branch
material separation objective
a portion of urine collected from an organism
urine specimen
a material entity derived from a portion of blood collected from an organism
blood specimen
specimen collection process
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
A planned process with the objective of collecting a 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.
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.
label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
Bjoern Peters
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
ICEMR protein array
specimen collection process
specimen collection process
An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
enzyme-linked immunosorbent assay
sample from organism
a material obtained from an organism in order to be a representative of the whole
5/29: This is a helper class for now
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.
sample from organism
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
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
portioning objective
average value
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
PERSON: James Malone
PERSON: Monnie McGee
arithmetic mean
average value
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
whole organism preparation
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
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).
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
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
Bjoern Peters
Bjoern Peters
specimen collection objective
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
host role
material sample role
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.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
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.
material sample role
material sample
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.
A material entity that has the material sample role
OBI: workshop
sample population
sample
material sample
material maintenance objective
An objective specification maintains some or all of the qualities of a material over time.
PERSON: Bjoern Peters
PERSON: Bjoern Peters
material maintenance objective
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
ICEMR protein array
informed consent process
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
A medical organization at which sick or injured people are given clinical care
hospital
a information content entity created to indicate that information about something is not available to the person recording it.
record of missing knowledge
a record indicating that the biological sex of an organism is not known.
record of unknown sex
An assay, based on the PCR, that amplifies and simultaneously quantifies 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.
real time polymerase chain reaction assay
sequence feature annotation
Information about a sequence region
Bjoern Peters
Bjoern Peters
place holder for sequence ontology term
sequence feature annotation
infectious agent
is a material entity bearing the disposition to infect an organism
IEDB
IEDB
Suspected Organism(s) in Specimen
CS17, CS18
NIAID GSCID-BRC
infectious agent
A measurement datum that is reported on a categorical scale
categorical measurement datum
service consumer role
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
Person:Helen Parkinson
OBI
service consumer role
service provider role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
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
PERSON:Helen Parkinson
service provider role
an intervention design in which the treatment is the administration of a compound
compound treatment design
A specimen that has been intentionally physically modified.
processed specimen
A device that can be used to restrict the location of material entities over time
container
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
device
sequence data
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
Person:Chris Stoeckert
GROUP: OBI
sequence data
The directed combination of a material entity with a specimen.
administration of material to specimen
individual organism identifier
a CRID symbol used to distinguish one individual organism from another.
PERSON: Chris Stoeckert, Jie Zheng
MO_169 Individual
Specimen Source ID
CS1
NIAID GSCID-BRC
individual organism identifier
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.
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.
PERSON: Alan Ruttenberg
OBI group
age measurement assay
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
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
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
MO_178 Age
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
discussed on Nov 15, dev call
All subtype will be defined by textual definition now.
Specimen Source Age - Value
CS6
NIAID GSCID-BRC
age 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.
age since birth measurement datum
The time it takes for 50% of a class of stochastic processes to occur.
half life datum (t 1/2)
service
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
Carlo; Matt
OBI workshop San Diego 2011
service
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
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
selectively maintained organism
A genotyping assay that uses a high througput sequencer
genotyping by high throughput sequencing assay
A genotyping assay that uses an array
genotyping by array assay
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.
genotype information
A study design that assays differences between distinct species.
species comparison design
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
genetic characteristics information
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
genotyping design
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
strain comparison design
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).
PERSON: Chris Stoeckert, Jie Zheng
MO_954 organism_part
Specimen Type
CS16
NIAID GSCID-BRC
tissue specimen
material maintenance service
model organism colony maintanance
A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Matthew Brush
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
material maintenance service
sequence assembly algorithm
An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Assembly Method
SA6
NIAID GSCID-BRC
NIAID GSCID-BRC
sequence assembly algorithm
material service
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Carlo Torniai
material service
material analysis service
Services performing DNA sequencing or Cell Analysis
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Matthew Brush
material analysis service
A scalar measurement datum that represents the number of events occuring over a time interval
rate measurement datum
material storage service
A service that offers liquid nitrogen stroage.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
PERSON: Carlo Torniai
PERSON: Matthew Brush
PERSON: Matthew Brush
material storage service
A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance.
data maintenance service
GenBank ID
A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
GenBank Record ID
SA10
NIAID GSCID-BRC
NIAID GSCID-BRC
GenBank ID
investigation description
A textual entity that describes an investigation.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
study description
Project Description
CP3
NIAID GSCID-BRC
NIAID GSCID-BRC
investigation description
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
Person: Chris Stoeckert, Jie Zheng
specimen ID
NIAID GSCID-BRC metadata working group
Specimen ID
CS15
NIAID GSCID-BRC
ICEMR protein array
NIAID GSCID-BRC
specimen identifier
PubMed ID
A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
Person: Chris Stoeckert, Jie Zheng
PMID
PubMed Identifier
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
Publication Citation
CP12
NIAID GSCID-BRC
NIAID GSCID-BRC
PubMed ID
average depth of sequence coverage
An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Genome Coverage
SA7
NIAID GSCID-BRC
NIAID GSCID-BRC
average depth of sequence coverage
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
Person: Chris Stoeckert, Jie Zheng
collection date
NIAID GSCID-BRC metadata working group
Specimen Collection Date
CS10
NIAID GSCID-BRC
ICEMR protein array
NIAID GSCID-BRC
specimen collection time measurement datum
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
Person: Chris Stoeckert, Jie Zheng
latitude
NIAID GSCID-BRC metadata working group
Specimen Collection Location - Latitude
CS11
NIAID GSCID-BRC
ICEMR protein array
NIAID GSCID-BRC
latitude coordinate measurement datum
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
Person: Chris Stoeckert, Jie Zheng
longitude
NIAID GSCID-BRC metadata working group
Specimen Collection Location - Longitude
CS12
NIAID GSCID-BRC
ICEMR protein array
NIAID GSCID-BRC
longitude coordinate measurement datum
investigation title
A textual entity that denotes an investigation.
Person:Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
study title
Project Title
CP1
NIAID GSCID-BRC
NIAID GSCID-BRC
investigation title
organism identification objective
A biological feature identification objective to identify the organism species in a specimen.
Person: Chris Stoeckert, Jie Zheng
Penn Group
organism identification objective
organism identification assay
An assay that identifies the organism species in a specimen.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Organism Detection Method
CS21
NIAID GSCID-BRC
NIAID GSCID-BRC
organism identification assay
sequence annotation algorithm
An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
sequence annotation algorithm
Bioinformatics Resource Center
An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
Person: Chris Stoeckert, Jie Zheng
BRC
Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
Bioinformatics Resource Center
CP20
NIAID GSCID-BRC
NIAID GSCID-BRC
Bioinformatics Resource Center
country name
A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Website: http://en.wikipedia.org/wiki/Country
Specimen Collection Location - Country
CS14
NIAID GSCID-BRC
ICEMR protein array
NIAID GSCID-BRC
country name
investigation identifier
A CRID symbol used to identify an investigation.
Person: Chris Stoeckert, Jie Zhneg
NIAID GSCID-BRC metadata working group
Project ID
CP2
NIAID GSCID-BRC
NIAID GSCID-BRC
investigation identifier
grant identifier
A CRID symbol used to identify a grant.
Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Supporting Grants/Contract ID
CP11
NIAID GSCID-BRC
NIAID GSCID-BRC
grant identifier
grant
A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
Discussed on Feb 13, 2012 dev call. Details see the tracker:
https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
Group: OBI
OBI
AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178
grant
contact representative role
A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
Discussed on May 7, 2012 dev call
propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ?
Whether it works for communicating author in manuscript or not?
Tracker:
https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178
Person: Chris Stoeckert
NIAID GSCID-BRC
contact representative role
specimen collector role
An Investigation agent role borne by a person or organization which
is realized in a specimen collection process.
Person: Jie Zheng, Chris Stoeckert
Penn Group
NIAID GSCID-BRC
specimen collector role
A material entity comprised of cultured cells and the media in which they are being propagated or stored.
cell culture
organization of specimen provider principal investigator
An organization that is the affiliation of the principal investigator providing the specimens for the investigation
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sample Provider PI's Institution
CP14
NIAID GSCID-BRC
NIAID GSCID-BRC
organization of specimen provider principal investigator
organization of Bioinformatics Resource Center contact person
An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Bioinformatics Resource Center Contact's Institution
CP22
NIAID GSCID-BRC
NIAID GSCID-BRC
organization of Bioinformatics Resource Center contact person
target material in specimen specification
Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome.
A plan specification which specifies the type of material that will be assayed in an investigation.
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Target Material
CP6
NIAID GSCID-BRC
NIAID GSCID-BRC
target material in specimen specification
Bioinformatics Resource Center contact person
A person who is the contact representative of a Bioinformatics Resource Center
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Bioinformatics Resource Center Contact Name
CP21
NIAID GSCID-BRC
NIAID GSCID-BRC
Bioinformatics Resource Center contact person
specimen-based scope of investigation specification
Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic.
A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection.
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sample Scope
CP5
NIAID GSCID-BRC
NIAID GSCID-BRC
specimen-based scope of investigation specification
specimen repository organization
An organization that provides a service to store and distribute specimens
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Specimen Repository
CS22
NIAID GSCID-BRC
NIAID GSCID-BRC
specimen repository organization
email address of Bioinformatics Resource Center contact person
An email address of the person who is contact representative of a Bioinformatics Resource Center
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Bioinformatics Resource Center Contact's email
CP23
NIAID GSCID-BRC
NIAID GSCID-BRC
email address of Bioinformatics Resource Center contact person
sequencing facility contact person
A person who is the contact representative at the sequencing facility
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sequencing Facility Contact Name
CP17
NIAID GSCID-BRC
NIAID GSCID-BRC
sequencing facility contact person
specimen provider principal investigator
A person who is a principal investigator and provides the specimen
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sample Provider Principal Investigator (PI) Name
CP13
NIAID GSCID-BRC
NIAID GSCID-BRC
specimen provider principal investigator
email address of specimen collector
An email address of the person collecting the specimen
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Specimen Collector's email
CS27
NIAID GSCID-BRC
NIAID GSCID-BRC
email address of specimen collector
sequencing facility organization
An organization that provides sequence determination service
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sequencing Facility
CP16
NIAID GSCID-BRC
NIAID GSCID-BRC
sequencing facility organization
specification of data to be generated in an investigation
Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype
An objective specification which indicates the type of data that will be generated and submitted to a database.
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Project Objectives
CP9
NIAID GSCID-BRC
NIAID GSCID-BRC
specification of data to be generated in an investigation
organization of specimen collector
An organization that is the affiliation of the person collecting the specimen
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Specimen Collector's Institution
CS26
NIAID GSCID-BRC
NIAID GSCID-BRC
organization of specimen collector
email address of sequencing facility contact person
An email address of the contact representative at the sequencing facility
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sequencing Facility Contact's email
CP19
NIAID GSCID-BRC
NIAID GSCID-BRC
email address of sequencing facility contact person
specimen collector
A person who collects the specimen
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Specimen Collector Name
CS25
NIAID GSCID-BRC
NIAID GSCID-BRC
specimen collector
investigation assay specification
Some examples of Project Method are Sequence, Array, Mass Spectrometry
A plan specification which indicates the assay type used to obtain data.
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Project Method
CP8
NIAID GSCID-BRC
NIAID GSCID-BRC
investigation assay specification
organization of sequencing facility contact person
An organization that is the affiliation of the contact representative at the sequencing facility
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sequencing Facility Contact's Institution
CP18
NIAID GSCID-BRC
NIAID GSCID-BRC
organization of sequencing facility contact person
comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Comments
CS24
NIAID GSCID-BRC
ICEMR protein array
NIAID GSCID-BRC
comment on investigation
target capture specification
Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey
A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen.
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Target Capture
CP7
NIAID GSCID-BRC
NIAID GSCID-BRC
target capture specification
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Specimen Repository Sample ID
CS23
NIAID GSCID-BRC
NIAID GSCID-BRC
specimen identifier assigned by specimen repository
specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sample ID - Sequencing Facility
SA1
NIAID GSCID-BRC
NIAID GSCID-BRC
specimen identifier assigned by sequencing facility
sample preparation for sequencing assay
A sample preparation for assay that preparation of nucleic acids for a sequencing assay
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Nucleic Acid Preparation Method
SA3
NIAID GSCID-BRC
NIAID GSCID-BRC
sample preparation for sequencing assay
email address of specimen provider principal investigator
An email address of the principal investigator providing the specimens for the investigation
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Sample Provider PI's email
CP15
NIAID GSCID-BRC
NIAID GSCID-BRC
email address of specimen provider principal investigator
sequencing service
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
Person: Jie Zheng
Adpated from 'DNA sequencing service'
NIAID GSCID-BRC
sequencing service
conclusion based on data
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".
An information content entity that is inferred from 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.
Group:2013 Philly Workshop group
Group:2013 Philly Workshop group
conclusion based on data
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
A value specification that is specifies one category out of a fixed number of nominal categories
categorical value specification
1
1
scalar value specification
A value specification that consists of two parts: a numeral and a unit label
PERSON:Bjoern Peters
scalar value specification
value specification
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
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.
PERSON:Bjoern Peters
value specification
grant agency
An organization that provides funding support for projects such as investigations.
PERSON: Jie Zheng, Chris Stoeckert
funding organization
NIAID GSCID-BRC metadata working group
Grant Agency
CP10
NIAID GSCID-BRC
NIAID GSCID-BRC
grant agency
'funding organization'
http://vivoweb.org/ontology/core#FundingOrganization
sequence annotation
A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
PERSON: Jie Zheng, Chris Stoeckert
NIAID GSCID-BRC metadata working group
Annotation Method
SA9
NIAID GSCID-BRC
NIAID GSCID-BRC
sequence annotation
sequence annotation provider
A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence.
PERSON: Jie Zheng, Chris Stoeckert
NIAID GSCID-BRC metadata working group
Annotation Provider
SA8
NIAID GSCID-BRC
NIAID GSCID-BRC
sequence annotation provider
sequence assembly name
A textual entity that is used to denote a sequence assembly.
PERSON: Jie Zheng, Chris Stoeckert
NIAID GSCID-BRC metadata working group
Assembly Name
SA5
NIAID GSCID-BRC
NIAID GSCID-BRC
sequence assembly name
sequence annotation reporting role
A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence.
PERSON: Jie Zheng, Chris Stoeckert
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC
sequence annotation reporting role
A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.
Illumina HiSeq 2000
An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
microscopy assay
A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material
medication time value specification
A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment
medication dose value specification
A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design.
case role in case-control study
A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design.
control role in case-control study
A specimen that is derived from cerbrospinal fluid.
cerebrospinal fluid specimen
cerebrospinal fluid specimen
A specimen that is derived from feces.
feces specimen
A specimen that is derived from sputum.
sputum specimen
sputum specimen
A specimen that is derived from bone marrow.
bone marrow specimen
bone marrow specimen
A specimen that is derived from pleural fluid.
pleural fluid specimen
pleural fluid specimen
A specimen that is derived from lung.
lung specimen
lung specimen
A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants.
case-control study design
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
blood plasma specimen
organism
animal
fungus
plant
virus
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.
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
WEB: http://en.wikipedia.org/wiki/Organism
Specimen Source Species
CS3, CS4
NIAID GSCID-BRC
organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
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
GROUP: OBI Biomaterial Branch
Specimen Category
CS2
NIAID GSCID-BRC
specimen
cultured cell population
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).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
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.
PERSON:Matthew Brush
cell culture sample
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
data transformation
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.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Philippe Rocca-Serra
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
James Malone
PERSON: James Malone
data transformation objective
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
James Malone
PERSON: James Malone
averaging data transformation
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
observation design
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.
pool of specimens
extraction
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
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.
Person:Bjoern Peters
Philippe Rocca-Serra
extraction
storage
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
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
Philippe Rocca-Serra
OBI-Branch
storage
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.
light source
study design
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.
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
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
Project Relevance
CP4
ICEMR protein array
NIAID GSCID-BRC
study design
an eligibility criterion (rule) is_a selection criterion which
defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
eligibility criterion
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
human subject enrollment
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
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
PERSON:Bjoern Peters
IEDB
collecting specimen from organism
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
administering substance in vivo
material component separation
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
Bjoern Peters
IEDB
material component separation
maintaining cell culture
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
PlanAndPlannedProcess Branch
OBI branch derived
maintaining cell culture
establishing cell culture
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).
PERSON:Matthew Brush
PERSON:Matthew Brush
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.
establishing cell culture
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
the use of a chemical or biochemical means to infer the sequence of a biomaterial
has_output should be sequence of input; we don't have sequence well defined yet
PlanAndPlannedProcess Branch
OBI branch derived
Sequencing Technology
SA4
NIAID GSCID-BRC
sequencing assay
sequencing assay
sequencing assay
nucleic acid extraction
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.
a material separation to recover the nucleic acid fraction of an input material
PlanAndPlannedProcess Branch
OBI branch derived
requested by Helen Parkinson for MO. Could be defined class
Nucleic Acid Extraction Method
SA2
NIAID GSCID-BRC
nucleic acid extraction
infection
the detrimental process in which an infectious agent colonizes or replicates in a host environment
IEDB
IEDB
infection process
A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
lymph node cell specimen
disposition to infect an organism
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
IEDB
IEDB
disposition to infect an organism
pathologic process
abnormal, harmful processes caused by or associated with a disease
IEDB
IEDB
pathologic process
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
ICEMR protein array
clinical finding
A series of statements representing health-relevant qualities of a patient and of a patient's family.
clinical history
A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
ICEMR protein array
laboratory finding
A clinically abnormal phenotype.
clinical phenotype
disease
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
Specimen Source Disease
CS9
NIAID GSCID-BRC
disease
A measurement assay that has as input a patient-derived specimen and as output a data itme that is about a quality of the specimen.
A measurement assay that has as input a patient-derived specimen, and as output a result that represents a quality of the specimen.
laboratory test
The representation of a conclusion of a diagnostic process.
ICEMR protein array
diagnosis
TODO: Define.
physical examination finding
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate the signs and symptoms of a disorder or pathological process
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
treatment
A microbial phenotype related to the resistance or sensitivity of a microbe to antimicrobial agents that kill (microbiocidal) or inhibit growth (microbiostatic) of a microbe.
antimicrobial agent resistance phenotype
A social role inhering in a human being.
human social role
A facility that is run by a hospital organization and is the bearer of a hospital function.
hospital facility
health care facility
A life cycle stage of a parasite.
Life cycle stage of a parasite.
parasite lifecycle stage
An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class.
An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class.
parasite organism
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
age
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
concentration of
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.
Specimen Source Gender
CS5
ICEMR protein array
NIAID GSCID-BRC
biological sex
A 1-D extent quality which is equal to the distance between two points.
length
A physical quality of the thermal energy of a system.
temperature
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
female
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
male
A quality denoting the lack of an entity.
absent
A quality inhering in a bearer by virtue of the bearer's existence.
present
A quality inhering in a bearer by virtue of the bearer's having susceptibilty toward an external stimulus.
susceptible toward
A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus.
resistant to
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
quality of a single physical entity
A biological sex quality inhering in a population of multiple sexes.
mixed sex
A quality inhering in a population by virtue of the proportion of its members that are ill at a given time.
morbidity
A structural quality inhering in a cell or blood vessel or capillary by virtue of the bearer's being in a rigid state of fullness resulting from pressure of the contents against the wall or membrane.
turgor
A turgor which is relatively low.
decreased turgor
A biological sex quality inhering in an individual or a population that undergo sexual reproduction.
mating type
organismal quality
A quality that inheres in an entire organism or part of an organism.
Specimen Source Health Status
CS8
NIAID GSCID-BRC
organismal quality
A viviparous organism having never given birth.
nulliparous
A material entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people.
household
A document authored by a health care provider that specifies how to realize some health care process for a particular patient.
Un document créé par un fournisseur de soin indiquant comment réaliser une partie d'un processus de santé pour un patient particulier.
health care prescription
prescription de santé
A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
fruit
A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
flower
An anatomical entity that is or was part of a plant.
plant anatomical entity
protein
antithrombin III is a protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
protein
social role
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.
primary structure of sequence macromolecule
sequence
region
A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
chromosome_arm
SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ.
simple_sequence_length_variation
A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
microsatellite
sequence_assembly
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
sequence_assembly
A region of sequence implicated in an experimental result.
experimental_result_region
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
A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
rRNA_16S
A genome is the sum of genetic material within a cell or virion.
genome
A genotype is a variant genome, complete or incomplete.
genotype
assembly
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
assembly
A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
reference_genome
A collection of one or more sequences of an individual.
variant_collection
A sequence variant where the structure of the gene is changed.
gene_variant
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
variant_frequency
A quality inhering in a variant by virtue of its phenotype.
variant_phenotype
A continuous nucleotide sequence is inverted in the same position.
inversion
A chromosomal inversion that does not include the centromere.
paracentric_inversion
a count is a data item denoted by an integer and represented the number of instances or occurences of an entity
count
Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data.
threshold cycle
A general symptom that is characterized as an act, instance, or result of being bled or the process by which something is bled: as a the escape of blood from vessels.
bleeding
joint pain
A sensation perception where there is an unpleasant sensation that usually indicates the body is threatened or damaged. The sensation may be sharp or dull, short-lived or chronic, intermittent or continual, confined to one area or spread over the entire body.
pain
seizure
Wasting is a nutrition, metabolism, and development symptom characterized by the unintended loss of weight and lean body tissue characteristic of many diseases (as cancer, tuberculosis, and AIDS).
wasting
dry mouth
underweight
Anorexia is a nutrition, metabolism, and development symptom characterized by a loss of appetite especially when prolonged.
anorexia
ICEMR protein array
convulsion
Dizziness is a neurological and physiological symptom characterized by a sensation of unsteadiness accompanied by a feeling of movement within the head.
dizziness
Cough is a respiratory system and chest symptom characterized by an explosive expulsion of air from the lungs acting as a protective mechanism to clear the air passages or as a symptom of pulmonary disturbance.
cough
respiratory distress
abscess
septicemia
chills
Fatigue is a neurological and physiological symptom characterized by a weariness or exhaustion from labor, exertion, or stress.
fatigue
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
zone of skin
An organ that is capable of transducing sensory stimulus to the nervous system.
sense organ
Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
lymph node
The head is the anterior-most division of the body [GO].
head
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
anatomical structure
Anatomical structure that performs a specific function or group of functions [WP].
organ
A multicellular structure that is a part of an organ.
organ part
A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
larval stage
A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis.
pupal stage
An anatomical structure that develops from the endoderm and the mesoderm.
mixed endoderm/mesoderm-derived structure
A spatiotemporal region encompassing some part of the life cycle of an organism.
life cycle stage
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
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
oral cavity
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity
excreta
A fluid that is composed of blood plasma and erythrocytes.
blood
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
mucosa
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.
organism substance
Anatomical entity that has mass.
material anatomical entity
Anatomical entity that has no mass.
immaterial anatomical entity
Anatomical structure that is an individual member of a species and consists of more than one cell.
multicellular organism
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
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
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
simple columnar epithelium
Compound organ that contains one or more macroscopic anatomical spaces.
cavitated compound organ
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
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
heart
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
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
cornea
An organ that detects light.
eye
Blood analogue used by all arthropods and most mollusks that have an open circulatory system. In these animals there is no distinction between blood and interstitial fluid. The liquid fills all of the interior (the hemocoel) of the body and surrounds all cells.
hemolymph
saliva-secreting exocrine glands of the oral cavity[GO]
saliva-secreting gland
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
midgut
The caudalmost subdivision of a digestive tract.
hindgut
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
Transudate contained in the pleural cavity.
pleural fluid
Excretion that is the output of a kidney
urine
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control
diaphragm
Muscle tissue that consists primarily of skeletal muscle fibers.
skeletal muscle tissue
A pouch in the digestive tract that connects 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
Anatomical cavity bounded by visceral and parietal peritoneum
peritoneal cavity
Mucosal layer that lines the intestine.
intestinal mucosa
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
cerebrospinal fluid
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].
muscle organ
A muscular organ in the floor of the mouth.
tongue
the smooth stratified squamous epithelium that covers the outer surface of the cornea
corneal epithelium
A skeletal muscle organ that is part of the trunk region.
skeletal muscle of trunk
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
aqueous humor of eyeball
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
saliva
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
Organism substance that is composed of sperm cells suspended in seminal fluid.
semen
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
Portion of semisolid bodily waste discharged through the anus[MW,modified]
feces
Respiration organ that develops as an oupocketing of the esophagus.
lung
the organ that functions to filter blood and to store red corpuscles and platelets
spleen
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
An organ that aids digestion and stores bile produced by the liver[WP].
gall bladder
A paired organ of the urinary tract which has the production of urine as its primary function.
kidney
the middle layer of the heart, comprised mainly of striated cardiac muscle fibers
myocardium
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
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
Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.
thymus
the soft tissue that fills the cavities of bones
bone marrow
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
muscle tissue
An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail
tail
an organ that functions as a secretory or excretory organ
gland
Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians.
gill
A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle.
larva
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
anatomical cavity
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
surface structure
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
A gland that is part of a digestive tract [Automatically generated definition].
gland of digestive tract
Any muscle organ that is part of a thorax [Automatically generated definition].
thoracic segment muscle
An anatomical structure that develops (entirely or partially) from the endoderm.
endoderm-derived structure
An anatomical structure that develops (entirely or partially) from the mesoderm.
mesoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
ectoderm-derived structure
Organ that is part of the hematopoietic system.
hemopoietic organ
the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi
respiratory tract epithelium
A proximal-distal subdivision of the digestive tract.
subdivision of digestive tract
A part of a wall of an organ that forms a layer.
organ component layer
An organ that is part of a immune system [Automatically generated definition].
immune organ
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
muscle structure
The avian beak is an external anatomical structure, in the head region, that is adapted for feeding self and young, catching prey, probing, etc. It encompasses, but is not restricted to, the maxilla, mandible, maxillary ramaphotheca, mandibular ramaphotheca, nostril, nasal fossa, nasal bones, egg tooth and rictus[GO]. The beak, bill or rostrum is an external anatomical structure of birds which is used for eating and for grooming, manipulating objects, killing prey, probing for food, courtship and feeding young. .
beak
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
abdomen element
An organ or element 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 region element
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
thoracic segment organ
An epithelium that lines the nasal cavity.
nasal cavity epithelium
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
endo-epithelium
The laminar structure of the heart
heart layer
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
bodily fluid
Any gland that is part of the digestive system.
digestive system gland
A pouched enlargement of the gullet of many birds that serves as a receptacle for food and for its preliminary maceration.
crop
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
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
transudate
An organism containing a developing embryo, fetus, or unborn offspring within the body.
ICEMR protein array
gravid organism
Branch or outpocketing of the digestive tract.
digestive tract diverticulum
sac
An anatomical structure that has more than one cell as a part.
multicellular anatomical structure
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
oral gland
An anatomical structure that develops from the neural crest.
neural crest-derived structure
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
ecto-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
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
subdivision of organism along main body axis
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
digestive system element
Any structure that is placed on one side of the left-right axis of a bilaterian.
lateral structure
A epithelium that is part of a camera-type eye.
eye epithelium
A viscus that is part of a abdomen.
abdominal viscera
A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence.
prime adult stage
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
bladder organ
Any region of epithelium that is part of a skin region.
skin epithelium
sensory organ epithelium
nose epithelium
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.
Specimen Source Age - Unit
CS7
NIAID GSCID-BRC
time unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
temperature unit
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
microgram
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
nanogram
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
A time unit which is equal to 60 seconds.
minute
A time unit which is equal to 3600 seconds or 60 minutes.
hour
A time unit which is equal to 24 hours.
day
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
A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.
year
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
concentration unit
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
volume unit
A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance.
parts per notation unit
A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6].
parts per million
A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9].
parts per billion
A unit which is a standard measure of the influence exerted by some mass.
density unit
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
dimensionless unit
A dimensionless ratio unit which denotes numbers as fractions of 100.
percent
A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry.
pi
A dimensionless unit which denotes a simple count of things.
count unit
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
ratio
A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator).
fraction
A dimensionless count unit which denotes the number of molecules.
molecule count
A dimensionless percent unit which denotes the homogeneity of a biomaterial.
purity percentage
A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture).
confluence percentage
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
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
pH
A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance.
liter per kilogram
A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg.
milliliter per kilogram
A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg.
microliter per kilogram
A concentration unit which denotes the average cell number in a given volume.
cell concentration unit
A unit of cell concentration which is equal to one cell in a volume of 1 milliliter.
cells per milliliter
A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume.
catalytic (activity) concentration unit
A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter.
katal per cubic meter
A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter.
katal per liter
A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution.
volume per unit volume
A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution.
milliliter per cubic meter
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
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
gram per deciliter
A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters.
milligram per liter
A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters.
microgram per milliliter
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
microgram per liter
A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject.
dose unit
A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject.
milligram per square meter
a path that is located in gross anatomical part of an organism (e.g., human) and is used for administering a vaccine, a drug, fluid, poison, or other substance into the body.
route of administration
An antibody function (or antigen binding function) is an infection-fighting protein molecule in blood or secretory fluids that tags, neutralizes, and helps destroy pathogenic microorganisms such as bacteria, viruses and toxins.
antibody
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
injury
A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured.
replicate
Regular course of eating and drinking adopted by a person or animal. This does not include DIET THERAPY, a specific diet prescribed in the treatment of a disease.
The customary allowance of food and drink taken by a person or an animal from day to day, particularly one especially planned to meet specific requirements of the individual, including or excluding certain items of food; a prescribed course of eating and drinking in which the amount and kind of food, as well as the times at which it is to be taken, are regulated for therapeutic purposes or selected with reference to a particular state of health.
diet
The number of PLATELETS per unit volume in a sample of venous BLOOD.
The number of PLATELETS per unit volume in a sample of venous BLOOD.
platelet count
The number of times the HEART VENTRICLES contract per unit of time, usually per minute.
heart rate
The volume of packed RED BLOOD CELLS in a blood specimen. The volume is measured by centrifugation in a tube with graduated markings, or with automated blood cell counters. It is an indicator of erythrocyte status in disease. For example, ANEMIA shows a low value; POLYCYTHEMIA, a high value.
hematocrit
The point in time at which an individual was born.
The point in time at which an individual was born.
ICEMR protein array
date of birth
date of birth
The age at which death occurs.
age at death
quantification of the content of parasites in the blood, used as a measurement of parasite load in the organism and an indication of the degree of an active parasitic infection
parasitemia measurement
a categorical measurement datum that specifies whether Adenovirus was detected in feces by enzyme-linked immunosorbent assay
John Judkins
Adenovirus, by ELISA
VEuPathDB
presence of Adenovirus in feces by enzyme-linked immunosorbent assay
a categorical measurement datum that specifies whether Ascaris lumbricoides was detected in feces by a microscopy assay
John Judkins
Ascaris lumbricoides, by microscopy
VEuPathDB
presence of Ascaris lumbricoides in feces by microscopy assay
a categorical measurement datum that specifies whether Astrovirus was detected in feces by an enzyme-linked immunosorbent assay
John Judkins
Astrovirus, by ELISA
VEuPathDB
presence of Astrovirus in feces by enzyme-linked immunosorbent assay
a categorical measurement datum that specifies whether Trichuris trichiura was detected in feces by an enzyme-linked immunosorbent assay
John Judkins
Trichuris trichiura, by microscopy
VEuPathDB
presence of Trichuris trichiura by microscopy
a categorical measurement datum that specifies whether Balantioides coil was detected in feces by a microscopy assay
John Judkins
Balantidium coli, by microscopy
VEuPathDB
presence of Balantidium coli in feces by microscopy assay
a categorical measurement datum that specifies whether Escherichia coli was detected by differential medium assay
John Judkins
Escherichia coli, by bacteriology
VEuPathDB
presence of Escherichia coli by differential medium assay
a categorical measurement datum that specifies whether Chilomastix mesnili was detected in feces by a microscopy assay
John Judkins
Chilomastix mesnili, by microscopy
VEuPathDB
presence of Chilomastix mesnili in feces by microscopy assay
a categorical measurement datum that specifies whether Cyclospora was detected in feces by microscopy
John Judkins
Cyclospora, by microscopy
VEuPathDB
presence of Cyclospora by microscopy
a categorical measurement datum that specifies whether Entamoeba histolytica was detected in feces by an enzyme-linked immunosorbent assay
John Judkins
Entamoeba histolytica, by ELISA
VEuPathDB
presence of Entamoeba histolytica by ELISA
a categorical measurement datum that specifies whether Salmonella was detected in feces by a differential medium assay
John Judkins
Salmonella, by bacteriology
VEuPathDB
presence of Salmonella in feces by differential medium assay
a categorical measurement datum that specifies whether bacteria were detected in an organism identification assay
John Judkins
Any bacteria, by any method
VEuPathDB
presence of bacteria by assay
a categorical measurement datum that specifies whether a pathogen organism was detected in an organism identification assay
John Judkins
Any pathogen, by any method
VEuPathDB
presence of pathogen by assay
a categorical measurement datum that specifies whether a virus was detected in an organism identification assay
John Judkins
Any virus, by any method
VEuPathDB
presence of virus by assay
a categorical measurement datum that specifies whether Cryptosporidium was detected in feces by an enzyme-linked immunosorbent assay
John Judkins
Cryptosporidium, by ELISA
VEuPathDB
presence of Cryptosporidium in feces by enzyme-linked immunosorbent assay
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Blastocystis in a feces specimen
John Judkins
Blastocystis Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Blastocystis in stool
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Clostridium difficile in a feces specimen
John Judkins
Clostridium difficile Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Clostridium difficile in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Entamoeba in a feces specimen
John Judkins
Entamoeba Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Entamoeba in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Hymenolepis nana in a feces specimen
John Judkins
Hymenolepis nana Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Hymenolepis nana in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Mycobacterium tuberculosis in a feces specimen
John Judkins
Mycobacterium tuberculosis Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Mycobacterium tuberculosis in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Plesiomonas in a feces specimen
John Judkins
Plesiomonas Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Plesiomonas in feces
a categorical measurement datum that specifies whether a Vibrio serogroup other than O1 or O139 was detected in feces by differential medium assay
John Judkins
Vibrio cholerae non-O1/O139, by bacteriology
VEuPathDB
presence of Vibrio cholerae non-(O1 or O139) in feces by differential medium assay
a categorical measurement datum that specifies whether a species of Vibrio other than cholerae or parahaemolyticus was detected in feces by differential medium assay
John Judkins
Vibrio (other species), by bacteriology
VEuPathDB
presence of Vibrio non-(cholerae or parahaemolyticus) in feces by differential medium assay
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Cryptosporidium hominis in a feces specimen
John Judkins
Cryptosporidium hominis Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Cryptosporidium hominis in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Cryptosporidium parvum in a feces specimen
John Judkins
Cryptosporidium parvum Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Cryptosporidium parvum in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Cyclospora in a feces specimen
John Judkins
Cyclospora Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Cyclospora in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Enterocytozoon bieneusi in a feces specimen
John Judkins
Enterocytozoon bieneusi Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Enterocytozoon bieneusi in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Entamoeba histolytica in a feces specimen
John Judkins
Entamoeba histolytica Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Entamoeba histolyica in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Encephalitozoon intestinalis in a feces specimen
John Judkins
Encephalitozoon intestinalis Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Encephalitozoon intestinalis in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Giardia in a feces specimen
John Judkins
Giardia Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Giardia in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Helicobacter pylori in a feces specimen
Person: John Judkins
Helicobacter pylori Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Helicobacter pylori in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Isospora in a feces specimen
Person: John Judkins
Isospora Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Isospora in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Necator in a feces specimen
Person: John Judkins
Necator Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Necator in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Rotavirus in a feces specimen
Person: John Judkins
Rotavirus Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Rotavirus in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Salmonella in a feces specimen
Person: John Judkins
Salmonella Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Salmonella in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Sapovirus in a feces specimen
Person: John Judkins
Sapovirus Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Sapovirus in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Strongyloides in a feces specimen
Person: John Judkins
Strongyloides Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Strongyloides in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Trichuris in a feces specimen
Person: John Judkins
Trichuris Ct value, by TAC result
VEuPathDB
TaqMan threshold cycle for Trichuris in feces
the threshold cycle that is the specified output of a fluorogenic PCR assay that has the objective of determining the number of Vibrio cholerae in a feces specimen
Person: John Judkins
Vibrio cholerae Ct value, by TAC result
VEuPathDB
TaqMan threshold value for Vibrio cholerae in feces
a categorical measurement datum that specifies whether Shigella dysenteriae serotype 1 was detected by differential medium assay
Person: John Judkins
Shigella dysenteriae serotype 1, by bacteriology result
VEuPathDB
presence of Shigella dysenteria serotype 1 by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 7 was detected by differential medium assay
Person: John Judkins
Shigella flexneri serotype 7, by bacteriology result
VEuPathDB
presence of Shigella flexneri serotype 7 by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 1a was detected in feces by differential medium assay
Person: John Judkins
Shigella flexneri serotype 1A, by bacteriology
VEuPathDB
presence of Shigella flexneri serotype 1a in feces by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 1b was detected in feces by differential medium assay
Person: John Judkins
Shigella flexneri serotype 1B, by bacteriology
VEuPathDB
presence of Shigella flexneri serotype 1b in feces by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 2a was detected in feces by differential medium assay
Person: John Judkins
Shigella flexneri serotype 2A, by bacteriology
VEuPathDB
presence of Shigella flexneri serotype 2a in feces by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 2b was detected in feces by differential medium assay
Person: John Judkins
Shigella flexneri serotype 2B, by bacteriology
VEuPathDB
presence of Shigella flexneri serotype 2b in feces by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 3a was detected in feces by differential medium assay
Person: John Judkins
Shigella flexneri serotype 3A, by bacteriology
VEuPathDB
presence of Shigella flexneri serotype 3a in feces by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 3b was detected in feces by differential medium assay
Person: John Judkins
Shigella flexneri serotype 3B, by bacteriology
VEuPathDB
presence of Shigella flexneri serotype 3b in feces by differential medium assay
a categorical measurement datum that specifies whether Shigella flexneri serotype 3c was detected in feces by differential medium assay
Person: John Judkins
Shigella flexneri serotype 3C, by bacteriology
VEuPathDB
presence of Shigella flexneri serotype 3c in feces by differential medium assay
the threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the number of Plasmodium vivax in a blood specimen
Person: John Judkins
Plasmodium vivax Ct value, by qPCR
VEuPathDB
qPCR threshold cycle for Plasmodium vivax in blood
the threshold cycle that is the specified output of a real time polymerase chain reaction assay that has the objective of determining the amount of Plasmodium falciparum in a blood specimen
Person: John Judkins
Plasmodium falciparum Ct value, by qPCR
VEuPathDB
qPCR threshold cycle for Plasmodium falciparum in blood
A categorical household wealth index representing the bottom third of values for the numerical household wealth index.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
bottom household wealth index
A categorical household wealth index representing the middle third of values for the numerical household wealth index.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
middle household wealth index
A categorical household wealth index representing the top third of values for the numerical household wealth index.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
top household wealth index
A information content entity created to indicate the lack of air bricks in the dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
no airbrick
A information content entity indicating that the household eats in restaurants.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
record of eating in restaurants
A information content entity indicating that the household does not cook in the dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
record of no cooking at home
An information content entity indicates no toilet facility in the dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
record of no toilet facility
An information content entity indicating that a household uses a neighbours' toilet facility.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
record of using neighbours' toilet
A time of screening occurring during the initial human subject enrollment period.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
time of screening during initial enrollment
A time of screening occuring after the initial enrollment period had ended and the study had begun.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
time of screenng after initial enrollment
PRISM
unknown withdrawal reason
PRISM
withdrew due to death
PRISM
inability to comply with protocol
PRISM
moved out of area
PRISM
reached 11 years of age
PRISM
unable to be located for over 120 days
PRISM
withdrawal of all children under care
PRISM
withdrawal of informed consent
PRISM
unknown cause of death
PRISM
complications of HIV
PRISM
diarrheal illness
PRISM
suicide
PRISM
Bwindi Hospital
PRISM
Jinja Hospital
PRISM
Kauka Health Centre
PRISM
Kihihi Health Centre IV
PRISM
Nagongera Health Centre IV
PRISM
Tororo District Hospital
PRISM
record of unknown death location
A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.
Uganda
example to be eventually removed
example to be eventually removed
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
term created to ease viewing/sort terms for development purpose, and will not be included in a release
PERSON:Alan Ruttenberg
organizational term
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
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
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
axiom holds for all times
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times