Chris Stoeckert
Cristian Cocos
Jie Zheng
John Judkins
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.
VEuPathDB Ontology
2022-02-15
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
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
obsolete EuPathDB alternative term
true
definition shown on EuPathDB website
obsolete EuPathDB definition
true
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
obsolete PRISM description
true
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
obsolete column order
true
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
Annotation property that records the ontology term IRI originally used in the study.
VEuPathDB team
replaces
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
replaces
An annotation property to specify the value code used in the dataset.
obsolete datafile value
true
Annotation property that specifies units that are associated with a variable (if any) in a human-readable format. Use abbreviations.
VEuPathDB team
unitLabel
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
unit label
Annotation property that specifies the ontology term IRI of unit, generally from the unit ontology (UO).
VEuPathDB team
unitIRI
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
unit IRI
Annotation property that specifies which dataset a term belongs to.
VEuPathDB team
dataSet
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
dataSet
Annotation property that indicates terms that were assessed longitudinally / repeatedly over time.
VEuPathDB team
repeated
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
repeated
Annotation property that specifies important terms to be highlighted.
VEuPathDB team
is_featured
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
is featured
Annotation property that indicates that the term is hidden from the UI and download files.
VEuPathDB team
hidden
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
hidden
Annotation property that identifies terms that are on the log scale or natural log scale, as opposed to on the linear scale.
VEuPathDB team
scale
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
scale
Annotation property that specifies terms that are related to time, to be used in visualizations looking at data over time. Also to be used in subsetting tab histograms (to indicate that the data range should not include the origin)
VEuPathDB team
is_temporal
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
is temporal
Annotation property that specifies key terms with longitudinal/repeated measures in the studies.
VEuPathDB team
mergeKey
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
merge key
Annotation property that specifies default minimum value for each term's range. Useful to ensure that histograms for related terms have the same x-axis range
VEuPathDB team
defaultDisplayRangeMin
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
default display range min
Annotation property that specifies the default maximum value for each term's range. Useful to ensure that histograms for related terms have the same x-axis range
VEuPathDB team
defaultDisplayRangeMax
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
default display range max
Annotation property that specifies the bin width for each term's histogram.
VEuPathDB team
defaultBinWidth
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
default bin width
Annotation property used to annotate numeric terms as strings. Numeric terms annotated as strings will ALWAYS be ordinal. Study specific.
VEuPathDB team
forceStringType
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/185
force string type
Term ID as previously used by VectorBase
obsolete sourced by VectorBase ID
true
editor preferred term
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 term
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
GROUP:OBI
OBI_0000277
in branch
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition
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
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.obofoundry.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 https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
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
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
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
is denotator type
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
expand expression to
ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand expression to
expand assertion to
ObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
expand assertion to
first order logic expression
PERSON:Alan Ruttenberg
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
Alan Ruttenberg
antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID digit count
has ID range allocated
Datatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
Person:Alan Ruttenberg
has ID range allocated to
has ID policy for
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Person:Alan Ruttenberg
has ID policy for
has ID prefix
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
Person:Alan Ruttenberg
has ID prefix
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)
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
PERSON:Alan Ruttenberg
Add as annotation triples in the granting ontology
is allocated id range
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
has ontology root term
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
#40
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
may be identical to
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
https://github.com/geneontology/go-ontology/issues/15532
https://github.com/information-artifact-ontology/ontology-metadata/issues/32
GO ontology
scheduled for obsoletion on or after
has axiom id
Person:Alan Ruttenberg
Person:Alan Ruttenberg
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
term replaced by
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
NIAID GSCID-BRC 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
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
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
title
label
a core relation that holds between a part and its whole
part_of
part of
a core relation that holds between a whole and its part
has_part
has part
is realized by
realized_in
realized in
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.
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
occurs in
[copied from inverse property 'occurs in'] 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
contains process
executed by
executes
A relation between a medication material and a disease or symptom that it may treat.
no longer in use
obsolete material may be used for
true
obsolete manifestation of
true
A relation between a medication material and a disease or symptom that it may treat.
obsolete may treat
true
A relation between a drug product and (one of) its active ingredient.
obsolete has active ingredient
true
has measurement unit label
This document is about information artifacts and their representations
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
mentions
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.
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
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
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
has coordinate unit label
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
is quality measured as
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
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_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
has_specified_output
The inverse property of is_specified_output_of
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
is_manufactured_by
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Alan Ruttenberg
Liju Fan
has_make
has_manufacturer
is_manufactured_by
is_specified_output_of
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
provisions
A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use
5/11/2020: A prior definition contained reference to transfer of ownership. ("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"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship.
GROUP: Relations branch
supplies
provisions
has_supplier
A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
PERSON: Alan Rutternberg
PERSON: Cristian Cocos
PERSON: Frank Gibson
PERSON: Melanie Courtot
has_supplier
objective_achieved_by
This relation obtains between an 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
specifies value of
A relation between a value specification and an entity which the specification is about.
specifies value of
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
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
characteristic of
Inverse of characteristic_of
has characteristic
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
A relationship between a generically dependent continuant and a specifically 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. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
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
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
function of
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
role of
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has function
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
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
derives from
a relation between two distinct material entities, the old entity and the new 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
derives into
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
location of
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
located in
before or simultaneous with
before
immediately preceded by
starts during
happens during
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
overlaps
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
has component
temporally related to
inverse of starts with
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
inverse of has active ingredient
active ingredient in
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
characteristic of part of
A mereological relationship or a topological relationship
mereotopologically related to
has member is a mereological relation between a collection and an item.
has member
This relation groups causal relations between material entities and causal relations between processes
causally related to
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
causally upstream of or within
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
causal relation between processes
depends on
c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
is substance that treats
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 x coordinate value
has specified numeric 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 numeric value
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
OBI
has specified value
Tree (organism)
Tree
Migrant
Acute pulmonary edema
A taxonomy identifier that denotes a group of organisms or groups of organisms based on common ancestors.
clade name
A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval.
mortality rate
A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions.
employment status data item
Any strain of Staphylococcus aureus that has tested resistant (R) to at least one of methicillin, oxacillin or cefoxitin by standard susceptibility testing methods.
methicillin-resistant Staphylococcus aureus
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
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
per discussion with Barry Smith
continuant
Continuant
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
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]
occurrent
Occurrent
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
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.
per discussion with Barry Smith
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]
ic
IndependentContinuant
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
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
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]
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
per discussion with Barry Smith
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
t-region
TemporalRegion
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
per discussion with Barry Smith
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
2d-s-region
TwoDimensionalSpatialRegion
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
st-region
SpatiotemporalRegion
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
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.
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
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])
(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]
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
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]
realizable
RealizableEntity
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
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
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]
0d-s-region
ZeroDimensionalSpatialRegion
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
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
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]
sdc
SpecificallyDependentContinuant
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
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 (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
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.
per discussion with Barry Smith
(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]
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
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
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]
fiat-object-part
FiatObjectPart
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
1d-s-region
OneDimensionalSpatialRegion
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
object-aggregate
ObjectAggregate
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
3d-s-region
ThreeDimensionalSpatialRegion
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
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
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]
object
Object
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
gdc
GenericallyDependentContinuant
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.
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
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]
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
p-boundary
ProcessBoundary
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
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]
1d-t-region
OneDimensionalTemporalRegion
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
material
MaterialEntity
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
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
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]
cf-boundary
ContinuantFiatBoundary
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
immaterial
ImmaterialEntity
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
1d-cf-boundary
OneDimensionalContinuantFiatBoundary
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
process-profile
ProcessProfile
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
r-quality
RelationalQuality
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.
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
2d-cf-boundary
TwoDimensionalContinuantFiatBoundary
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
requested by Melanie Courtot
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
0d-t-region
ZeroDimensionalTemporalRegion
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
history
History
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
liver cell line
fibroblast cell line
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
chemokine ligand 10
A member of the class of fluorenes that is 9-(p-chlorobenzylidene)-9H-fluorene which is substitutec by chlorine at positions 2 and 7, and by a 2-(dibutylamino)-1-hydroxyethyl group at position 4. An antimalarial drug used in combination with artemether for the treatment of multi-drug resistant strains of falciparum malaria.
lumefantrine
A straight-chain, sixteen-carbon, saturated long-chain fatty acid.
hexadecanoic acid
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 long-chain fatty acid that is a C20, polyunsaturated fatty acid having four (Z)-double bonds at positions 5, 8, 11 and 14.
arachidonic acid
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
A synthetic monocyclic beta-lactam antibiotic (monobactam), used primarily to treat infections caused by Gram-negative bacteria. It inhibits mucopeptide synthesis in the bacterial cell wall, thereby blocking peptidoglycan crosslinking.
aztreonam
An octadec-9-enoic acid in which the double bond at C-9 has Z (cis) stereochemistry.
oleic acid
A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O).
urea
An inorganic peroxide consisting of two hydroxy groups joined by a covalent oxygen-oxygen single bond.
hydrogen peroxide
A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.
carbon dioxide
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
carbohydrate
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
An organic thiophosphate that is O,O-dimethyl O-phenyl phosphorothioate substituted by a chloro group at position 3 and a nitro group at position 4. It is a potent cholinesterase inhibitor and used as an insecticide for the control of a wide range of insects.
chlorthion
A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.
creatinine
A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin.
bilirubin IXalpha
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 octadecadienoic acid in which the two double bonds are at positions 9 and 12 and have Z (cis) stereochemistry.
linoleic acid
The carbon oxoanion resulting from the removal of a proton from carbonic acid.
hydrogencarbonate
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
An elemental molecule consisting of two hydrogens joined by a single bond.
dihydrogen
An artemisinin derivative that is artemisinin in which the lactone has been converted to the corresponding lactol methyl ether. It is used in combination with lumefantrine as an antimalarial for the treatment of multi-drug resistant strains of falciparum malaria.
artemether
A cephalosporin compound having acetoxymethyl and [2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino side groups.
cefotaxime
Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group.
benzoic acids
An insecticide compound naturally occurring in plants.
phytogenic insecticide
A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy.
cephalosporin
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
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
An icosanoid comprising icosanoic acid having one C=C bond at any position.
icosenoic acid
A substance used to destroy fungal pests.
fungicide
A glycosyl compound resulting from the attachment of a glycosyl group to a non-acyl group RO-, RS-, RSe-, etc. The bond between the glycosyl group and the non-acyl group is called a glycosidic bond. By extension, the terms N-glycosides and C-glycosides are used as class names for glycosylamines and for compounds having a glycosyl group attached to a hydrocarbyl group respectively. These terms are misnomers and should not be used. The preferred terms are glycosylamines and C-glycosyl compounds, respectively.
glycoside
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
Strictly, a substance intended to kill members of the class Insecta. In common usage, any substance used for preventing, destroying, repelling or controlling insects.
insecticide
A molecular entity having a net electric charge.
ion
juvenile hormone mimic
Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
lactam
A macrocyclic lactone with a ring of twelve or more members derived from a polyketide.
macrolide
A class of neuro-active insecticides that act at the nicotinic acetylcholine receptor.
neonicotinoid insectide
Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.
pesticide
Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
phosphate
pyrethroid insecticide
A class of aromatic heterocyclic compounds each of which contains a benzene ring ortho fused to carbons 2 and 3 of a pyridine ring.
quinolines
A quinoline having a chloro group at the 7-position and an aryl amino group at the 4-position.
amodiaquine
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
An oxopurine that is the final oxidation product of purine metabolism.
uric acid
Any member of a group of fat-soluble hydroxy seco-steroids that exhibit biological activity against vitamin D deficiency. Vitamin D can be obtained from sun exposure, food and supplements and is biologically inactive and converted into the biologically active calcitriol via double hydroxylation in the body.
vitamin D
A linolenic acid with cis-double bonds at positions 9, 12 and 15. Shown to have an antithrombotic effect.
alpha-linolenic acid
A 9-octadecenoic acid and the trans-isomer of oleic acid.
elaidic acid
A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile.
vancomycin
A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
acrylamide
A C18, omega-6 acid fatty acid comprising a linolenic acid having cis- double bonds at positions 6, 9 and 12.
gamma-linolenic acid
A hexadec-9-enoic acid in which the double bond at position C-9 has cis configuration.
palmitoleic acid
A C20 striaght-chain saturated fatty acid which forms a minor constituent of peanut (L. arachis) and corn oils. Used as an organic thin film in the production of liquid crystals for a wide variety of technical applications.
icosanoic acid
A C18 straight-chain saturated fatty acid component of many animal and vegetable lipids. As well as in the diet, it is used in hardening soaps, softening plastics and in making cosmetics, candles and plastics.
octadecanoic acid
A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring.
tobramycin
A C24 straight-chain saturated fatty acid.
tetracosanoic acid
A straight-chain, fourteen-carbon, long-chain saturated fatty acid mostly found in milk fat.
tetradecanoic acid
A straight-chain, C22, long-chain saturated fatty acid.
docosanoic acid
A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-phenylacetamido group.
ampicillin
A third-generation cephalosporin compound having 2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetylamino and [(2-methyl-5,6-dioxo-1,2,5,6-tetrahydro-1,2,4-triazin-3-yl)sulfanyl]methyl side-groups.
ceftriaxone
A macrolide antibiotic useful for the treatment of bacterial infections.
azithromycin
A hexitol produced by a variety of organisms including bacteria, fungi, lichens and plants.
mannitol
Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.
photon
A straight-chain, twelve-carbon medium-chain saturated fatty acid with strong bactericidal properties; the main fatty acid in coconut oil and palm kernel oil.
dodecanoic acid
A C10, straight-chain saturated fatty acid.
decanoic acid
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 chemical entity constituting the smallest component of an element having the chemical properties of the element.
atom
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
antimicrobial agent
A substance (or active part thereof) that kills or slows the growth of bacteria.
antibacterial agent
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
aromatic compound
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
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
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
amino-acid residue
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.
macromolecule
A carbamate ester obtained by the formal condensation of 1-naphthol with methylcarbamic acid.
carbaryl
An alkenyl alcohol with a structure based on a C8 unbranched chain with the hydroxy group at C-2 and unsaturation at C-1-C-2. It is a major volatile compound present in many mushrooms and fungi.
oct-1-en-3-ol
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
A third-generation cephalosporin antibiotic with methoxymethyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamino substituents at positions 3 and 7, respectively, of the cephem skeleton. Given by mouth as its proxetil ester prodrug, it is used to treat acute otitis media, pharyngitis, and sinusitis.
cefpodoxime
hemoglobin
Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids.
fatty acid
A first-generation cephalosporin antibiotic with a methyl substituent at position 3, and a (2R)-2-amino-2-cyclohexa-1,4-dien-1-ylacetamido substituent at position 7, of the cephem skeleton.
cephradine
A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon.
beta-lactam
An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce.
antifungal agent
An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms.
triazoles
A phosphorus oxoanion that is the conjugate base of phosphoric acid.
phosphate ion
Any C22 polyunsaturated fatty acid containing six double bonds.
docosahexaenoic acid
Any straight-chain, C20 polyunsaturated fatty acid having five C=C double bonds.
icosapentaenoic acid
A drug used to treat or prevent bacterial infections.
antibacterial drug
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 multi-component mixture comprising mostly of colistin A (R = Me) and B (R = H), with small amounts of colistin C and other polymyxins, produced by certain strains of Bacillus polymyxa var. colistinus. An antibiotic, it is used as its sulfate salt (for oral or topical use) or as the sodium salt of the N-methylsulfonic acid derivative (the injectable form) in the treatment of severe Gram-negative infections, partiularly those due to Pseudomonas aeruginosa.
colistin
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
Derivatives of carbamic acid with insecticidal properties of general formula ROC(=O)NR(1)R(2), where ROH is an alcohol, oxime, or phenol and R(1) is hydrogen or methyl. Like organophosphate insecticides, they are cholinesterase inhibitors, but carbamate insecticides differ in action from the organophosphates in that the inhibitory effect on cholinesterase is generally brief.
carbamate insecticide
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
The active insecticidal constituents of Chrysanthemum cinerariifolium flowers.
pyrethrins
pyrethroid ester insecticide
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
pyrethroid ether insecticide
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 tetracosenoic acid having a cis-double bond at position 15.
(15Z)-tetracosenoic acid
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 liquid that can dissolve other substances (solutes) without any change in their chemical composition.
solvent
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
A monocarboxylic acid amide that is lysergamide in which one of the hydrogens attached to the amide nitrogen is substituted by a 1-hydroxypropan-2-yl group (S-configuration). An ergot alkaloid that has a particularly powerful action on the uterus, its maleate (and formerly tartrate) salt is used in the active management of the third stage of labour, and to prevent or treat postpartum of postabortal haemorrhage caused by uterine atony: by maintaining uterine contraction and tone, blood vessels in the uterine wall are compressed and blood flow reduced.
ergometrine
Any of several wide-spectrum macrolide antibiotics obtained from actinomycete Saccharopolyspora erythraea (formerly known as Streptomyces erythraeus).
erythromycin
A semisynthetic penicillin antibiotic carrying a 3-(2-chlorophenyl)-5-methylisoxazole-4-carboxamido group at position 6.
cloxacillin
A retinoid consisting of 3,7-dimethylnona-2,4,6,8-tetraen-1-ol substituted at position 9 by a 2,6,6-trimethylcyclohex-1-en-1-yl group (geometry of the four exocyclic double bonds is not specified).
retinol
A racemate comprising equimolar amounts of (R)- and (S)-fipronil.
fipronil
A penicillanic acid ester that is the [(2,2-dimethylpropanoyl)oxy]methyl ester and prodrug of mecillinam.
pivmecillinam
An icosatrienoic acid having three cis double bonds at positions 8, 11 and 14.
all-cis-icosa-8,11,14-trienoic acid
The all-cis-isomer of a C22 polyunsaturated fatty acid having five double bonds in the 7-, 10-, 13-, 16- and 19-positions.
(7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid
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 aminoquinoline that is chloroquine in which one of the N-ethyl groups is hydroxylated at position 2. An antimalarial with properties similar to chloroquine that acts against erythrocytic forms of malarial parasites, it is mainly used as the sulfate salt for the treatment of lupus erythematosus, rheumatoid arthritis, and light-sensitive skin eruptions.
hydroxychloroquine
An imidazolidine that is N-nitroimidazolidin-2-imine bearing a (6-chloro-3-pyridinyl)methyl substituent at position 1.
imidacloprid
A straight-chain, monounsaturated, 16-carbon fatty acid with a trans-double bond at position C-9; the trans-isomer of palmitoleic acid and predominant trans-16:1 isomer in cheeses from goat and ewe milk. Major dietary sources are partly hydrogenated vegetable oils.
palmitelaidic acid
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
chemical substance
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 is an equimolar mixture of a pair of enantiomers.
racemate
Any straight-chain, C22 fatty acid having four C=C double bonds.
docosatetraenoic acid
A synthetic galactosylfructose disaccharide used in the treatment of constipation and hepatic encephalopathy.
lactulose
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
The all-cis-isomer of a C22 polyunsaturated fatty acid having five double bonds in the 4-, 7-, 10-, 13- and 16-positions. It is a member of n-6 PUFA and a product of linoleic acid metabolism.
(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid
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
A chemosterilant intended to sterilize insects.
insect sterilant
methoxychlor
Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen.
azole
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
A member of the class of imidazoles substituted at C-1, -2 and -5 with 2-hydroxyethyl, nitro and methyl groups respectively. It has activity against anaerobic bacteria and protozoa, and has a radiosensitising effect on hypoxic tumour cells. It may be given by mouth in tablets, or as the benzoate in an oral suspension. The hydrochloride salt can be used in intravenous infusions. Metronidazole is a prodrug and is selective for anaerobic bacteria due to their ability to intracellularly reduce the nitro group of metronidazole to give nitroso-containing intermediates. These can covalently bind to DNA, disrupting its helical structure, inducing DNA strand breaks and inhibiting bacterial nucleic acid synthesis, ultimately resulting in bacterial cell death.
metronidazole
A 20-carbon, polyunsaturated fatty acid having two double bonds at unspecified positions.
icosadienoic acid
An octadecadienoic acid containing two E (trans) double bonds at positions 9 and 12.
linoelaidic acid
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
Any antifungal agent used to prevent or treat fungal infections in humans or animals.
antifungal drug
(R)-salbutamol
resmethrin
An organic heterotricyclic compound that is 4,9-dihydro-10H-benzo[4,5]cyclohepta[1,2-b]thiophen-10-one which is substituted at position 4 by a 1-methylpiperidin-4-ylidene group. A blocker of histamine H1 receptors with a stabilising action on mast cells, it is used (usually as its hydrogen fumarate salt) for the treatment of asthma, where it may take several weeks to exert its full effect.
ketotifen
The representation of a negative conclusion of a diagnostic process for the COVID-19 coronavirus disease.
negative COVID-19 diagnosis conclusion
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
cell
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
native cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
cultured cell
A leukocyte with abundant granules in the cytoplasm.
granulocyte
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
erythrocyte
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
monocyte
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
leukocyte
Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
basophil
Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
neutrophil
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
cell in vitro
The minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
diastolic blood pressure
The amount of hemoglobin in a specific volume of blood, expressed as grams per deciliter of whole blood in humans.
blood hemoglobin level
The number of white blood cells in a specified volume of blood.
white blood cell count
A measurement relating body weight to height in an organism; typically calculated as the weight of an individual divided by the height of that individual squared. For quadrupeds, the square of body height is often replaced by the square of body length.
body mass index (BMI)
Fraction of forced vital capacity that is exhaled in a specific number of seconds.
forced expiratory volume
The number of breaths taken by an organism per unit of time.
respiration rate
The force per unit area attributable to the oxygen, the chemical element with atomic number 8 which is the essential agent in the respiration of plants and animals, dissolved in a specified volume of blood, defined as the force per unit area exerted by oxygen in a mixture of gases in equilibrium with such a sample of blood at the same temperature.
partial pressure of blood oxygen (Po2)
urine protein level
A disease that involving errors in metabolic processes of building or degradation of molecules.
disease of metabolism
A bacterial infectious disease has_material_basis_in Bacteria.
bacterial sepsis
A viral infectious disease that results_in infection located_in joint, has_material_basis_in Chikungunya virus, which is transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom arthralgia, and has_symptom maculopapular rash.
chikungunya
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
A tuberculosis that occurs at body sites other than the lung.
extrapulmonary tuberculosis
An autoimmune 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 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
A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function.
bone disease
A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment.
physical disorder
A physical disorder characterized by incomplete closure of the neural tube.
neural tube defect
An autoimmune disease of skin and connective tissue that is characterized by subepidermal blistering especially in the lower abdomen, groin, and flexor surfaces of the extremities, creating tense blisters that do not break easily.
pemphigoid
An inner ear disease that is characterized by hearing loss resulting from damage to the cochlea, auditory nerve and/or brainstem.
sensorineural hearing loss
A bone inflammation disease that has_material_basis_in infection located_in bone or located_in bone marrow.
osteomyelitis
A viral infectious disease that results in inflammation located in salivary gland, has_material_basis_in Mumps rubulavirus, 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
A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
bacterial infectious disease
An upper respiratory tract disease which is characterized by inflammation of the tonsils resulting from bacterial (Group A streptococcus) and viral (Epstein-Barr virus, adenovirus) infections. Symptoms include a severe sore throat, painful or difficult swallowing, coughing, headache, myalgia, fever and chills.
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
A mouth disease located_in the salivary gland.
salivary gland disease
A viral infectious disease that results in infection located in mouth, has_material_basis_in Human coxsackievirus A16, Human enterovirus 71, group B coxsackievirus, or 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
A mouth disease located_in the teeth.
tooth disease
A blood protein disease that is characterized by low number of red blood cells, repeated infections, and periodic episodes of pain, resulting from atypical hemoglobin molecules called hemoglobin S, which can distort red blood cells into a sickle, or crescent, shape.
sickle cell anemia
fetal erythroblastosis
A lung disease that is characterized by a newborn breathing in a mixture of meconium and amniotic fluid into the lungs around the time of delivery.
meconium aspiration syndrome
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
An opportunistic mycosis that is located in lungs, but can also occur in eyes, ears, skin, thyroid, pituitary, palate, parathyroid, esophagus, pleura, heart, liver, spleen, small intestine, adrenals, kidneys, bone marrow, and lymph nodes, has_material_basis_in Pneumocystis jirovecii that effects interstitial and alveolar tissues and has symptom nonproductive cough, has symptom shortness of breath, and has symptom fever.
pneumocystosis
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.
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
A nutritional deficiency disease that is characterized by inadequate dietary protein and calories, which can have profound systemic effects including decreased metabolism, altered tissue distribution, compromised immunity, and impaired growth, and has_material_basis_in dietary deprivation.
protein-energy malnutrition
A viral infectious disease that results in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted by Aedes mosquito bite. The infection has symptom fever, has symptom severe headache, has symptom severe pain behind the eyes, has symptom joint pain, has symptom muscle and bone pain, has symptom rash, and has symptom mild bleeding.
dengue disease
neutropenia
A protein-energy malnutrition that is characterized by severe caloric deprivation, has_symptom emaciation, decreased height and weight gain, and decreased metabolism with hypothermia, bradycardia, and constipation, and has_material_basis_in severe caloric deprivation.
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
A viral infectious disease that results_in infection located_in upper respiratory tract or located_in lower respiratory tract, has_material_basis_in Human respiratory syncytial virus, which is transmitted_by droplet spread of nasal secretions from an infected person while coughing or sneezing, or transmitted_by contaminated fomites. The infection has_symptom runny nose, has_symptom fever, has_symptom cough, has_symptom wheezing, and has_symptom respiratory distress.
respiratory syncytial virus infectious disease
rectal disease
A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
cardiovascular system 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 typhus that has_material_basis_in Orientia tsutsugamushi, which is transmitted by trombiculid mites (Leptotrombidium deliense). The infection has symptom fever, has symptom headache, has symptom muscle pain, has symptom cough, has symptom maculopapular rash, has symptom eschar, has symptom splenomegaly and has symptom lymphadenopathy.
scrub typhus
A parasitic helminthiasis infectious disease that involves infection of the intestine, urinary tract, skin, liver and spleen caused by multiple species of the trematode fluke of the genus Schistosoma. The symptoms include fever, chills, nausea, abdominal pain, diarrhea, malaise, myalgia, liver and spleen enlargement, rash and hematuria.
schistosomiasis
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.
cerebral malaria
glossitis
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 thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism.
pleural disease
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
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
A lymph node disease that is characterized by an acute or chronic inflammation of one or more lymph nodes.
lymphadenitis
A pleural disease that is characterized as an abnormal collection of air in the pleural space between the lung and the chest wall.
pneumothorax
congenital heart disease
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 brain disease that is characterized by the occurrance of at least two unprovoked seizures resulting from a persistent epileptogenic abnormality of the brain that is able to spontaneously generate paroxysmal activity and typically manifested by sudden brief episodes of altered or diminished consciousness, involuntary movements, or convulsions.
epilepsy
A hepatitis that involves viral infection causing inflammation of the liver.
viral hepatitis
A brain disease that is caused by damage to the motor control centers of the developing brain during pregnancy, during childbirth or after birth, which affects muscle movement and balance.
cerebral palsy
A candidiasis that refers to a heterogeneous group of disorders characterized by recurrent or persistent superficial fungal infections located_in skin, located_in mucous membrane, or located_in nail due to T-cell defects, has-agent Candida species and has_symptom scaling of skin lesions, has_symptom thickening of nails, has_symptom swollen periungal tissue, and has_symptom scarring of the scalp.
chronic mucocutaneous candidiasis
A bowel dysfunction that is characterized by infrequent or difficult evacuation of feces.
constipation
A teeth hard tissue disease that is characterized by damage to a tooth that can happen when decay-causing bacteria in your mouth make acids that attack the tooth’s surface, or enamel.
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
A primary bacterial infectious disease that involves systemic infection, has_material_basis_in Leptospira, which is transmitted by contact with water, food, or soil containing urine from the infected animals. The infection has symptom jaundice, has symptom chills, has symptom fever, has symptom muscle pain, and has symptom hepatomegaly.
leptospirosis
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
A skin disease characterized by itchy, erythematous, vesicular, weeping and crusting patches of skin.
dermatitis
A sensory system disease that is characterized by auditory dysfunction located_in the auditory system.
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 disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
endocrine system 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.
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
A tuberculosis that is a contagious disease located_in lungs. The infection has_symptom fever, has_symptom cough, has_symptom difficulty in breathing, has_symptom inflammatory infiltrations, has_symptom formation of tubercles, has_symptom caseation, has_symptom pleural effusion, and has_symptom fibrosis.
pulmonary tuberculosis
gingivitis
anus disease
A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
central nervous system disease
A bone disease that results_in inflammation of the located_in bone.
bone inflammation disease
A mouth disease that is relating to or affecting the structures surrounding and supporting the teeth.
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 soft tissue infectious disease that involves accumulation of pus in the pleural cavity as a result of infection within the lung (pneumonia) or a lung abscess spreading into the space. The symptoms include cough, fever, chest pain, sweating and shortness of breath.
pleural empyema
A primary bacterial infectious disease that is located_in lungs, located_in lymph nodes, located_in pericardium, located_in brain, located_in pleura or located_in gastrointestinal tract, has_material_basis_in Mycobacterium tuberculosis, which is transmitted_by droplets released into the air when an infected person coughs or sneezes.
tuberculosis
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
liver disease
An integumentary system disease that is located_in nail.
nail disease
A dermatitis that is characterized by a pyogenic infection 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
A upper respiratory infectious disease which involves irritation and inflammation of the mucous membrane of the nose due to viruses, bacteria or irritants. The inflammation results in generation of excessive amounts of mucus leading to runny nose, as well as nasal congestion and post-nasal drip.
rhinitis
A pancreas disease that is characterized by inflammation of the pancreas.
pancreatitis
middle ear disease
A nutrition disease that is characterized by deficiency of a nutritional element, such as a vitamin, mineral, carbohydrate, protein, fat, or general energy content.
nutritional deficiency disease
A viral infectious disease that results in destruction of immune system, leading to life-threatening opportunistic infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted by sexual contact, transmitted by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted by congenital method, and transmitted by contaminated needles. The virus infects helper T cells (CD4+ T cells) which are directly or indirectly destroyed, macrophages, and dendritic cells. The infection has symptom diarrhea, has symptom fatigue, has symptom fever, has symptom vaginal yeast infection, has symptom headache, has symptom mouth sores, has symptom muscle aches, has symptom sore throat, and has symptom swollen lymph glands.
human immunodeficiency virus infectious 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 bronchial disease that is an inflammation of the bronchial tubes. It is caused by bacteria and viruses. The disease has_symptom cough with mucus, has_symptom shortness of breath, has_symptom low fever and has_symptom chest tightness.
bronchitis
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 Human immunodeficiency virus infectious disease that results_in reduction in the numbers of CD4-bearing helper T cells below 200 per microliter of blood or 14% of all lymphocytes thereby rendering the subject highly vulnerable to life-threatening infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted_by sexual contact, transmitted_by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted_by congenital method, and transmitted_by contaminated needles. Opportunistic infections are common in people with AIDS.
acquired immunodeficiency syndrome
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
An immune system disease that is located_in the lymphatic system.
lymphatic system disease
peptic ulcer disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
gastrointestinal system disease
An arthritis that involves infection by a pathogen located_in joint.
septic arthritis
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 marrow disease characterized by an increased number of red blood cells in the bloodstream resulting in thicker blood and reduced blood flow.
polycythemia
A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in 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
A pemphigoid that is 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
perinatal necrotizing enterocolitis
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
A mouth disease located_in the lip.
lip disease
rectal prolapse
A disease by infectious agent that results in infection, has_material_basis_in Viruses.
viral infectious disease
A central nervous system disease that is located_in the brain.
brain 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 bacterial conjuctivitis that is characterized by pain and tenderness in the eyeball and conjuctival discharge.
ophthalmia neonatorum
bacterial conjunctivitis
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.
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
a portion of cream that is the bearer of a clinical drug role
drug cream
a portion of lotion that is the bearer of a drug role
drug lotion
a portion of solution that is the bearer of a clinical drug role
drug solution
a portion of suspension that is the bearer of a clinical drug role
drug suspension
a solid object typically of discoid, spheroid, or elliptic-cylindrical shape or approximations thereof, that bears a clinical drug role.
drug tablet
an object that is the bearer of a drug role and is comprised of a solid shell of elliptical-cylindrical shape and another object contained in the shell that has a scattered molecular aggregate as a proper part
drug capsule
amoxicillin suspension
Folic acid tablet
Clotrimazole skin cream
Nystatin suspension
Gentamicin injectable solution
Dexamethasone injection
Chloramphenicol solution for otic and ophthalmic administration
Ceftriaxone injectable solution
Metronidazole solution
prednisolone tablet
salbutamol suspension
Dornase Alfa
Sodium Chloride Nasal Solution
Acetaminophen Oral Solution
Ascorbic Acid Oral Tablet
Ibuprofen Oral Suspension
Ambroxol Oral Solution
Azithromycin Oral Suspension
Cefixime Oral Suspension
Cetirizine Oral Solution
Chloroquine Injectable Solution
Chloroquine Oral Tablet
Chlorpheniramine Oral Solution
Ciprofloxacin Oral Suspension
Clotrimazole Topical Solution
Diazepam Oral Tablet
Dicyclomine Oral Solution
Domperidone Oral Solution
Glycerin Rectal Suppository
Hydroxyzine Oral Solution
Mebendazole Oral Suspension
Naproxen Oral Suspension
Nitrazepam Oral Tablet
Ondansetron Oral Solution
Oxycodone Oral Tablet
Vitamin K 1 Injectable Solution
Potassium Chloride Oral Solution
Riboflavin Oral Tablet
Simethicone Oral Solution
Theophylline Oral Solution
Povidone Topical Solution
xylometazoline Nasal Solution
Tobramycin Ophthalmic Solution
Ketoconazole Medicated Shampoo
Betamethasone Topical Cream
Calamine Topical Lotion
Miconazole Topical Cream
Permethrin Topical Cream
Silver Sulfadiazine Topical Cream
Lactulose Oral Solution
amlexanox Oral Paste
montelukast Oral Tablet
nitazoxanide Oral Solution
Ranitidine Oral Solution
Miconazole Oral Gel
Tetracycline Topical Lotion
moxifloxacin Ophthalmic Solution
artesunate Injectable Solution
Gentamicin Sulfate (USP) / Hydrocortisone Topical Ointment
Erythromycin Oral Solution
desloratadine Oral Solution
Amoxicillin / Clavulanate Oral Solution
Mefenamate Oral Suspension
fexofenadine Oral Suspension
Floxacillin Oral Solution
Acyclovir Oral Solution
Fluconazole Oral Solution
Guaifenesin / Pseudoephedrine / Triprolidine Oral Solution
Sulfamethoxazole / Trimethoprim Oral Solution
artemether / lumefantrine Oral Tablet
Ciprofloxacin Otic Solution
Benzoate / Salicylic Acid Topical Cream
Zinc Sulfate 20 MG Oral Tablet
Gentamicin Otic Solution
A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
data use permission
An exposure to pyrethroid insecticide.
exposure to pyrethroid insecticide
administrative region
A primary administrative division of a country, such as a state in the United States.
first-order administrative region
A subdivision of a first-order administrative division.
second-order administrative region
A subdivision of a second-order administrative division.
third-order administrative region
A subdivision of a third-order administrative division.
fourth-order administrative region
A political association with effective dominion over a geographic area.
national geopolitical entity
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.
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
Place or area with clustered or scattered buildings and a permanent human population.
populated place
An accumulation of water of varying size.
water body
Naturally formed, subterranean open area or chamber.
cave
A construction that has been assembled by deliberate human effort.
human 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.
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 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
A two-dimensional continuant fiat boundary which is located between a landmass and a water body.
shoreline
The portion of the ground surface which lies below water.
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
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
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
Hay is grass, legumes or other herbaceous plants that have been cut, dried, and stored for use as animal fodder, particularly for grazing livestock such as cattle, horses, goats, and sheep.
hay
Drinking water is water which may be consumed by humans with no adverse effects on their health.
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
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
environmental material
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
surface layer
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
A well which provides access to groundwater held in an aquifer.
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.
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 is a construction which is part of a building.
building part
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
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 thatched building roof is a building roof that is built by thatching (or out of thatch).
thatched building roof
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 landmass which is part of a planet.
planetary landmass
An environmental system which can sustain and allow the growth of an ecological population.
habitat
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 village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement.
village
A material part of an astronomical body.
astronomical body part
eaves
An environmental system determined by an animal.
animal-associated environment
A material which is composed primarily of one or more pure metals and which shows their properties.
metallic material
An environmental system which includes both living and non-living components.
ecosystem
Manure which is composed primarily of the feces of poultry.
poultry manure
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 process during which materials deemed to be waste are transported away from a site.
waste disposal process
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
surface of an astronomical body
A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water.
land
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
A clinical assay that is performed as a preliminary procedure, such as a test or examination, to detect the most characteristic sign or signs of a disorder or a condition that may require further investigation.
patient screening
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 surgical technique involving a large incision through the abdominal wall to gain access into the abdominal cavity.
laparotomy
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.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Dwelling
Penn Group
PRISM
obsolete dwelling
true
A building material used in the construction of a roof.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
roof material
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
obsolete wall brick
true
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
http://en.wikipedia.org/wiki/Eaves
Penn Group
PRISM
obsolete eaves
true
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
obsolete household having electricity information
true
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
A scalar measurement datum of land such as land owned by a household.
Person: Jie Zheng, Chris Stoeckert
Penn Group
Person: Chris Stoeckert
PRISM
land area measurement datum
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
A categorical measurement datum that specifies how frequently the food needs of a household were not met.
Person: Jie Zheng, Chris Stoeckert
PRISM
Penn Group
PRISM
frequency of not satisfying food needs
A length measurement datum of the distance from a dwelling to the nearest health facility.
Person: Jie Zheng, Chris Stoeckert
Person: Chris Stoeckert
Penn Group
obsolete distance to health facility
true
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 represents one of the following conclusions about a patient: that the patient has malaria, asymptomatic parasitemia, or no parasitemia.
Person: John Judkins
EuPathDB
malaria-related diagnosis
A phenotypic abnormality of the presence of bacteria in the blood.
not in use; will replace w/Bacteremia from HP if equivalent term needed
http://en.wikipedia.org/wiki/Bacteremia
obsolete presence of bacteria in the blood
true
A diagnosis of malaria without evidence of complicated malaria.
Person: Jie Zheng, Chris Stoeckert, Grant Dorsey
Grant Dorsey
PRISM
obsolete diagnosis of uncomplicated malaria
true
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.
not in use; will replace w/Viremia from HP if equivalent term needed
http://en.wikipedia.org/wiki/Viremia
obsolete presence of virus in the blood
true
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
obsolete diagnoses of complicated malaria with danger signs
true
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
obsolete severe malaria
true
Symptom or sign information 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 information
A scalar measurement datum about the level of hemoglobin in the blood.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
ICEMR protein array
obsolete hemoglobin level
true
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
obsolete clinical visit
true
A clinical visit that is primarily for a regular examination.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
obsolete routine clinical visit
true
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.
PRISM
obsolete dwelling ventilation
true
A fourth-order administrative region of Uganda.
Person: Jie Zheng, Chris Stoeckert
VEuPathDB
PRISM
subcounty of 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
obsolete medication role
true
blood used in transfusion for replacement blood lost during surgery or due to a serious injury.
quinine used in malaria medication
A material entity that is bearer of a medication role.
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
obsolete quinine drug product
true
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
http://en.wikipedia.org/wiki/Artemether/lumefantrine
PRISM
obsolete artemether-lumefantrine drug product
true
A dependent continuant which is either disease or phenotypic abnormality.
obsolete clinical characteristics
true
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
obsolete diagnosis of uncomplicated malaria in the 1st trimester of pregnancy
true
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
obsolete diagnosis of asymptomatic microscopic parasitemia
true
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 output of a microscopy assay on a specimen and is expressed as a ratio of asexual parasites to either the quantity of specimen or number of leukocytes within it.
Person: Jie Zheng, Chris Stoeckert, John Judkins
Penn Group
PRISM
asexual parasite density by microscope
An information content entity about dwelling.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
obsolete dwelling information
true
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.
obsolete ventilation function
true
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
obsolete dwelling facility
true
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
obsolete elevated temperature
true
A scalar measurement datum that is about temperature.
obsolete temperature measurement datum
true
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
yes
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
yes
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
yes
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
yes
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.
yes
obsolete dwelling facility role
true
A temperature measurement datum that is about an organism.
Person: Jie Zheng, Chris Stoeckert
Penn Group
PRISM
obsolete organismal body temperature measurement datum
true
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
obsolete floor brick
true
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
obsolete age since birth at time of visit
true
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 percentage 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
obsolete age since birth at time of enrollment
true
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
obsolete number of non-routine clinical visits
true
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
obsolete number of routine clinical visits
true
An information content entity that is about the type of sample/specimen collected during a clinical visit.
Person: Jie Zheng, Chris Stoeckert
PRISM
obsolete sample available information
true
A blood specimen that is located on a filter paper.
Chris Stoeckert
Jie Zheng
Filter paper sample
Penn Group
obsolete blood specimen on filter paper
true
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
obsolete peripheral blood mononuclear cell specimen
true
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
obsolete red blood cell specimen
true
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
obsolete average number of Plasmodium parasite-positive female Anopheles
true
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
obsolete average number of female Anopheles tested for Plasmodium parasite
true
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
obsolete average percent of Plasmodium parasite-positive female Anopheles
true
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
obsolete routine clinical visit date
true
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
obsolete antimalarial therapy given outside the study since last seen information
true
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
obsolete cause of participant death
true
A clinical visit occuring because of a sickness.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete clinical visit when sick
true
A covered pit latrine that does not have a latrine slab.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete covered pit latrine without slab
true
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
obsolete days since a clinical visit with a malaria diagnosis
true
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
obsolete household bed asset
true
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
obsolete household bicycle asset
true
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
obsolete household cassette player asset
true
A household asset information indicating whether a household has a chair.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household chair asset
true
A household asset information indicating whether a household has a clock.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household clock asset
true
A household asset information indicating whether a household has a cupboard.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household cupboard asset
true
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
obsolete household electricity asset
true
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
obsolete household fixed phone asset
true
A household asset information indicating whether a household has a mobile phone.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household mobile phone asset
true
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
obsolete household motorcycle or scooter asset
true
A household asset information indicating whether a household has a radio.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household radio asset
true
A household asset information indicating whether a household has a refrigerator.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household refrigerator asset
true
A household asset information indicating whether a household has a sofa.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household sofa asset
true
A household asset information indicating whether a household has a table.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household table asset
true
A household asset information indicating whether a household has a television.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete household television asset
true
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
obsolete incident of malaria episode information
true
A material entity where a clinical visit took place.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete location of clinical visit
true
A material entity where a death occurred.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete location of death
true
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
obsolete medical care outside the study clinic since last seen information
true
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
obsolete number of insecticide treated mosquito net(s) per person
true
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
obsolete plasma sample lost information
true
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
obsolete redraw of a symptom after clinical visit information
true
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
obsolete routine clinical visit for T-cell study
true
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
obsolete routine clinical visit with finger prick
true
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
obsolete routine clinical visit with venipuncture
true
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
obsolete routine clinical visit without any routine assessment done
true
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
obsolete screened air brick
true
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
obsolete uncovered pit latrine with slab
true
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
obsolete uncovered pit latrine without slab
true
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
obsolete unscreened air brick
true
Pain perceived to originate in the muscle.
PRISM
PRISM
obsolete Muscle aches
true
A light source that light is produced from solar energy.
Person: Jie Zheng, Chris Stoeckert
obsolete solar light source
true
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
VEuPathDB
obsolete drinking water from open public well
true
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
VEuPathDB
obsolete drinking water from open well in yard
true
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
VEuPathDB
obsolete drinking water from unprotected freshwater spring
true
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).
obsolete ATCC number
true
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
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
VEuPathDB
obsolete single catch entomological measurement datum
true
a clinical visit that realizes the concretization of a protocol specifying the time of the visit
Person: John Judkins
VEuPathDB
obsolete scheduled clinical visit
true
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
VEuPathDB
obsolete unscheduled clinical visit
true
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 that is documented during the discharge process.
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
obsolete entomological data item
true
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.
obsolete easting coordinate measurement datum
true
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.
obsolete northing coordinate measurement datum
true
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.
obsolete dwelling animal information
true
An information content entity that is about human traveling.
replaced with OMRSE:00000142
obsolete human traveling information
true
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.
obsolete educational level information
true
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
obsolete job role
true
A planned process that a person participates in exchange for payment. The job role born by the person is realized in the process.
obsolete economic activity
true
An economic activity that a person is involved in primarily.
obsolete primary economic activity
true
An occupation that a person is not involved in primarily.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/289
secondary occupation
A textual entity that describes a person's primary economic activity.
obsolete primary economic activity description
true
A textual entity that describes a person's secondary economic activity.
obsolete secondary economic activity description
true
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.
Jie Zheng
Chris Stoeckert
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether person received payment from primary economic activity
An information content entity about whether a person received payment from secondary economic activity.
Jie Zheng
Chris Stoeckert
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether person 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.
obsolete garbage disposal
true
A textual entity about community where a person is living.
obsolete community name
true
A textual entity about community where a study taken place.
obsolete study location name
true
A malaria medication that is generally taken for initial treatment of malaria.
obsolete first line malaria medication
true
"A malaria medication that is given when first-line medication doesn't work, or stops working."
obsolete second line malaria medication
true
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
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether person plans to move
An information content entity that specifies the relationship between a person and the head of their household.
Person: John Judkins, Chris Stoeckert
EuPathDB
relationship to head of household
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.
Person: John Judkins
EuPathDB
area measurement datum
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
VEuPathDB
obsolete information on place visited during a trip
true
An information content entity about travel to any place more than 10 km away from where a person lives.
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
yes
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
VEuPathDB
obsolete information on contact with malaria
true
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
VEuPathDB
obsolete information on participant status at visit
true
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.
obsolete proximity to case dwelling datum
true
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.
obsolete clinic location
true
A second-order administrative region of India.
Person: John Judkins
VEuPathDB
district of India
A textual entity about a 'division' or 'ward' being a sub-division of a city.
obsolete division number
true
a categorical value specification that specifies whether a patient complies with a dose specification that specifies the dose of malaria medication to self-administer
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant taking antimalarial drugs as advised
an information content entity that specifies whether a participant under investigation self-administered antimalarial drugs in the past 2 weeks
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant taking 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
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant having 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
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether 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
VEuPathDB
obsolete information on where malaria diagnosed in last 12 months
true
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
obsolete number of asexual parasite
true
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
Jie Zheng
Chris Stoeckert
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant treated antimalarial drugs 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.
VEuPathDB
obsolete parasite species identification by PCR assay
true
A textual entity that denotes the public health clinic/hospital that the human subject normally uses (for non malaria illness).
obsolete primary health center name
true
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.
obsolete information that there is no illness
true
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.
obsolete falcivax rapid diagnostic test
true
A laboratory test that is a rapid, sensitive malaria test that is able to differentiate between P. falciparum and other malaria parasites.
VEuPathDB
obsolete optimal-IT rapid diagnostic test
true
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 third-order administrative region of India.
Person: John Judkins
VEuPathDB
taluk of India
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 first-order administrative region of Mali.
Person: John Judkins
VEuPathDB
region of Mali
A text entity of a zone number denotes to a geographic location.
obsolete location zone number
true
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
John Judkins
VEuPathDB
obsolete proportion mapped reads
true
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).
obsolete diagnosis of asymptomatic parasitemia
true
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
obsolete diagnosis of submicroscopic parasitemia
true
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
obsolete information on blood smear not performed
true
A presence of parasite that indicates that no parasite was detected in a specimen, either by loop-mediated isothermal amplification or blood smear.
Person: Jie Zheng, Grant Dorsey, John Judkins
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
obsolete information on whether hive treated with tetracyline
true
An information indicates that samples from child or from the mother, or both.
Person: Daniel Beiting, Jie Zheng
microbiome
obsolete information on whether specimen from mother or child
true
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.
Person: Daniel Beiting, Jie Zheng
microbiome
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
obsolete common name of organism
true
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
Person: Jie Zheng, Chris Stoeckert, John Judkins
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
VEuPathDB
obsolete gametocyte detection assay
true
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
obsolete parasite detection assay
true
An assay that detects parasite in a specimen using PCR.
Person: Jie Zheng, Chris Stoeckert
VEuPathDB
obsolete parasite detection by PCR assay
true
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
obsolete organismal body temperature measurement assay
true
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
obsolete malaria rapid diagnosis test
true
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
obsolete genetic clade of organism
true
multilocus sequence type clade name
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.
Jie Zheng
Chris Stoeckert
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
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.
Jie Zheng
Chris Stoeckert
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
yes
host organism
a categorical value specification that is about a collection of bee larvae and specifies whether tetracycline was administered to the larvae
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
An information content entity which indicates that samples are from the child or from the mother, or both.
Jie Zheng
Daniel Beiting, Jie Zheng
microbiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/194
indicator of whether specimen from mother or child
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 information content entity about disposal of human excreta material.
Person: John Judkins
Waste disposal
information on disposal of human excreta material
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
Jie Zheng
Chris Stoeckert
Person: John Judkins
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether antibiotics given to mother of participant
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
obsolete sequencing protocol
true
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
obsolete participant identifier
true
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
obsolete specimen collection protocol
true
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
obsolete specimen collection time post infection
true
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 that is documented during the admission process.
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
VEuPathDB
obsolete mouse cage number
true
obsolete antimalarial
true
An information content entity about disposal of excreta material produced by a child.
Person: John Judkins
Child waste disposal
EuPathDB
information on disposal of child excreta material
Assay that subjects a feces specimen to a test for microorganisms.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
stool test for microorganisms
Penn Group
GEMS
obsolete feces microbiology assay
true
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
obsolete propagation
true
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.
not used
MO_55 EnvironmentalHistory
obsolete environmental history
true
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.
obsolete pathogen organism
true
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
obsolete Candida albicans strain
true
A parasite that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred parasite organisms
parasite strain
A data item that indicates whether some organism is present in a specimen.
"Present" in this definition means 'located in' or 'part of' the specimen.
presence of organism in specimen
An information content entity that is about some quality, risk, or access to health care that inheres in a human being and is deemed clinically significant by the World Health Organization, which uses this entity to categorize each of their individual core health indicators, based on the type of quality, risk, or access.
Person: John Judkins
WHO 2018 Global Reference List of 100 Core Health Indicators
World Health Organization core health indicator subdomain
An information content entity that is about data collected at the household level on multiple occasions.
household repeated measure
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.
VEuPathDB
yes
groin lesion score
Skin symptom or sign information that is about a lesion on an axilla of a patient and specifies the extent of damage to the tissue.
VEuPathDB
yes
axillary lesion score
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.
VEuPathDB
yes
pinna lesion score
A mosquito feeds on a human whereby the human acquires the blood host role for the mosquito blood meal.
A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism.
obsolete blood meal source role
true
A time measurement datum that is about the duration of exposure to an insecticide that results in the death of 50% of a population of insects.
Person: John Judkins
LT50
VBcv:0000732
lethal insecticide time 50
A clinical finding of a death that has been confirmed to be likely caused by COVID-19.
death confirmed likely from COVID
VEuPathDB
finding of death from COVID-19
An information content entity that is about a treatment.
treatment information
An information content entity identifying an assay and specifying whether it was performed.
information on whether assay performed
An assay that detects parasite organisms in a specimen that are in the sporozoite stage.
Person: John Judkins
VEuPathDB
obsolete sporozoite detection assay
true
An information content entity about the groups of participants that are randomized to receive an intervention in a trial.
VEuPathDB
study cluster information
A 16S rRNA sequencing assay in which primers target the V1-V2 portion of the 16s gene.
Person: John Judkins, Wojtek Bażant
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284
MicrobiomeDB
16S rRNA sequencing assay targeting V1-V2 region
16S rRNA sequencing assay in which primers target the V1-V3 portion of the 16s gene
Person: John Judkins, Wojtek Bażant
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284
MicrobiomeDB
16S rRNA sequencing assay targeting V1-V3 region
16S rRNA sequencing assay in which primers target the V2 portion of the 16s gene
Person: John Judkins, Wojtek Bażant
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284
MicrobiomeDB
16S rRNA sequencing assay targeting V2 region
16S rRNA sequencing assay in which primers target the V3-V4 portion of the 16s gene
Person: John Judkins, Wojtek Bażant
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284
MicrobiomeDB
16S rRNA sequencing assay targeting V3-V4 region
16S rRNA sequencing assay in which primers target the V3-V5 portion of the 16s gene
Person: John Judkins, Wojtek Bażant
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284
MicrobiomeDB
16S rRNA sequencing assay targeting V3-V5 region
16S rRNA sequencing assay in which primers target the V4 portion of the 16s gene
Person: John Judkins, Wojtek Bażant
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/284
MicrobiomeDB
16S rRNA sequencing assay targeting V4 region
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
A data transformation of metagenome input sequence data involving mapping to genes with full Enzyme Commision (EC) number enzyme classifications and calculation of pathways.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
metagenome pathway and function analysis
A data item that is the output of a metagenome pathway and function analysis for the number of copies of genes annotated at the finest (4th level) EC classification.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
4th level EC metagenome abundance data
A data item that is the output of a metagenome pathway and function analysis for the number of copies of a pathway defined by EC classifications.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
metagenome enzyme pathway abundance data
A data item that is the output of a metagenome pathway and function analysis for gene coverage in a pathway defined by EC classifications.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
metagenome enzyme pathway coverage data
A data transformation of input sequence data to obtain the fraction of relative abundance of organisms.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative taxonomic abundance analysis
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of kingdom.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative abundance of kingdom data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of phylum.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative abundance of phylum data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of class.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative abundance of class data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of order.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative abundance of order data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of family.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative abundance of family data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of genus.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative abundance of genus data
A data item that is the output of a relative taxonomic abundance analysis for organisms grouped at the level of species.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
relative abundance of species data
A data transformation of input sequence data to obtain a mean species diversity.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
alpha diversity taxonomic analysis
A data item that is the output of an alpha diversity taxonomic analysis based on the Shannon index of diversity.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
Shannon-indexed alpha diversity data
A data item that is the output of an alpha diversity taxonomic analysis based on the inverse Simpson index of diversity.
Person: John Judkins
MicrobiomeDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/208
inverse Simpson-indexed alpha diversity data
A taxon detected by sequence match that indicates whether a plant taxon was detected.
Person: John Judkins
MicrobiomeDB
plant taxon detected by sequence match
A taxon detected by sequence match that indicates whether an animal taxon was detected.
Person: John Judkins
MicrobiomeDB
animal taxon detected by sequence match
A taxon detected by sequence match that indicates whether a protist taxon was detected.
Person: John Judkins
MicrobiomeDB
protist taxon detected by sequence match
A data item that indicates whether a method applied to data coming from a sequencing assay of the sample has detected a taxon through identifying sequences associated with organisms of a particular taxonomic grouping.
Person: John Judkins
MicrobiomeDB
taxon detected by sequence match
A taxon detected by sequence match that indicates whether a fungal taxon was detected.
Person: John Judkins
MicrobiomeDB
fungal taxon detected by sequence match
12.34 CPM (copies per million reads)
A data item of the normalized number of sequences that match a specific taxon.
Person: John Judkins
taxon-specific sequence matches
MicrobiomeDB
normalized number of taxon-specific sequence matches
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
obsolete antibiotic administration process
true
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 quality 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
obsolete study center
true
Site where a human life process ended.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert
place of death
Penn Group
GEMS
location 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
obsolete axillary temperature measurement datum
true
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
yes
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
Jie Zheng
Chris Stoeckert
Person: John Judkins, Jie Zheng
Currently receiving medication
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant 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
A measurement datum that results from measuring the volume of feces excreted during an instance of defecation.
Person: Cristian Cocos, Jie Zheng, Chris Stoeckert, John Judkins
stool volume measurement datum
Penn Group
GEMS
feces volume measurement datum
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 that precedes any treatment for diarrhea given to the same person during 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
Jie Zheng
Person: John Judkins
Eligibility for enrollment
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant eligible 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
Jie Zheng
Chris Stoeckert
John Judkins
Adenovirus ELISA performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Astrovirus ELISA performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Rotavirus ELISA performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether Rotavirus ELISA performed
a categorical value specification that specifies whether a modified acid fast staining method was performed
Jie Zheng
Chris Stoeckert
John Judkins
modified acid fast staining method performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Norovirus RT-PCR performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Cryptosporidium ELISA performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Entamoeba histolytica ELISA performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Giardia ELISA performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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 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 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
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 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 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.
VEuPathDB
obsolete blood test
true
A laboratory test that has a urine specimen as specified input.
John Judkins
VEuPathDB
obsolete urine test
true
An information content entity that is about a microscopy assay
Person: John Judkins
VEuPathDB
obsolete information on microscopy assay
true
A scalar measurement datum of the concentration of Ferritin in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood Ferritin concentration
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 scalar measurement datum of the concentration of retinol in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood retinol concentration
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
obsolete information on drinking water piped into dwelling
true
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
obsolete information on drinking water piped into yard
true
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 bipedal edema
Person: John Judkins
Bipedal edema
EuPathDB
bipedal edema symptom or sign 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 at discharge that is an assertion that a patient has diarrhea.
Person: John Judkins
VEuPathDB
diagnosis of diarrhea at discharge
A diagnosis at discharge that is an assertion that a patient has dysentery.
Person: John Judkins
VEuPathDB
diagnosis of dysentery at discharge
A diagnosis at discharge that is an assertion that a patient has pneumonia or lower respiratory tract disease.
Person: John Judkins
VEuPathDB
diagnosis of pneumonia of lower repiratory tract disease at discharge
A diagnosis at discharge that is an assertion that a patient has malaria.
Person: John Judkins
VEuPathDB
diagnosis of malaria at discharge
A diagnosis at discharge that is an assertion that a patient has nutritional deficiency disease.
Person: John Judkins
VEuPathDB
diagnosis of nutritional deficiency disease at discharge
A diagnosis at discharge that is an assertion that a patient has typhoid fever.
Person: John Judkins
VEuPathDB
diagnosis of typhoid fever at discharge
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 non-typhi 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 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
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
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 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 cycle for Vibrio cholerae in feces
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
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
Person: John Judkins
Shigella dysenteriae serotype 1, by bacteriology
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
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 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 result
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 result
EuPathDB
data about Vibrio cholerae O139 by differential medium assay
A treatment information that mentions a medication that treats diarrhea.
information on diarrhea treatment
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
(Fever treatment location) 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
(Plasmodium species, by microscopy) 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 species, by microscopy) 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 species, by microscopy) 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 species, by microscopy) Plasmodium malariae
EuPathDB
presence of Plasmodium malariae by microscopy
a categorical value specification that specifies whether a microscopy assay was performed
Jie Zheng
Chris Stoeckert
John Judkins
Microscopy performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether 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 species in last year) 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 species in last year) 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 species in last year) Plasmodium malariae
EuPathDB
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
(Plasmodium species in last year) 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
(Antimalarial medications used) 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
Jie Zheng
Chris Stoeckert
John Judkins
Clinic/hospital
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Private doctor
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether treated by private practice
A categorical value specification that specifies whether a treatment to alleviate an episode of malaria was self-administered
Jie Zheng
Person: John Judkins
(Where treated) Self-treated
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether malaria self-treated
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.
Jie Zheng
Chris Stoeckert
John Judkins
(Where treated) Can't remember
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant forgot treatment location within past year
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
(Plasmodium species, by qPCR) 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 species, by qPCR) 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 species, by qPCR) 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 species, by qPCR) 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 species, by FalciVax RDT) 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 species, by FalciVax RDT) 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
(Plasmodium species, by FalciVax RDT) Negative
EuPathDB
no presence of Plasmodium by falcivax
a categorical value specification that specifies whether a falcivax rapid diagnostic test was performed
Jie Zheng
Chris Stoeckert
John Judkins
FalciVax RDT performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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 species, by OptiMAL RDT) 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
(Plasmodium species, by OptiMAL RDT) Negative
EuPathDB
no Plasmodium by optimal-IT
a categorical value specification that specifies whether an optimal-IT rapid diagnostic test was performed
Jie Zheng
Chris Stoeckert
John Judkins
OptiMAL RDT performed
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
(Personal mosquito repellent) Can't remember
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
information on participant forgetting 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
(Sprayed in the last 12 months) 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.
Chris Stoeckert
Jie Zheng
Vacutainer sample
VEuPathDB
obsolete blood specimen in vacutainer
true
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
Jie Zheng
Chris Stoeckert
John Judkins
Any signs
EuPathDB, based on definition for 'sign' in OGMS
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Any symptoms
EuPathDB, based on definition for 'sign' in OGMS
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant has symptom
a categorical value specification that specifies whether a human participant under investigation was febrile in the previous 48 hours
Jie Zheng
Chris Stoeckert
John Judkins
Fever in last 48 hours
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant 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 first-order administrative region of India.
Person: John Judkins
VEuPathDB
state of India
a categorical value specification that specifies whether a human participant under investigation was febrile in the previous two weeks
Jie Zheng
Chris Stoeckert
John Judkins
Fever in last 2 weeks
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant 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 scalar measurement datum of the concentration of alanine aminotransferase in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood alanine aminotransferase concentration
A scalar measurement datum of the concentration of alkaline phosphatase in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood alkaline phosphatase concentration
A diagnosis at discharge that is an assertion that a patient has chikungunya.
Person: John Judkins
VEuPathDB
diagnosis of chikungunya at discharge
A diagnosis at discharge that is an assertion that a patient has dengue disease.
Person: John Judkins
VEuPathDB
diagnosis of dengue disease at discharge
A diagnosis at discharge that is an assertion that a patient has a gastrointestinal infection.
Person: John Judkins
VEuPathDB
diagnosis of gastrointestinal infection at discharge
A diagnosis at discharge that is an assertion that a patient has leptospirosis.
Person: John Judkins
VEuPathDB
diagnosis of leptospirosis at discharge
A scalar measurement datum of the concentration of phosphate in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood phosphate concentration
A diagnosis at discharge that is an assertion that a patient has scrub typhus.
Person: John Judkins
VEuPathDB
diagnosis of scrub typhus at discharge
A scalar measurement datum of the concentration of urea in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood urea concentration
A scalar measurement datum of the concentration of uric acid in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood uric acid concentration
A diagnosis at discharge that is an assertion that a patient has viral hepatitis.
Person: John Judkins
VEuPathDB
diagnosis of viral hepatitis at discharge
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
number 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
Jie Zheng
Chris Stoeckert
John Judkins
Present at visit
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
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 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
A measurement datum of the total area of a land lot on which a dwelling is built.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/149
dwelling lot area measurement datum
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 nitrogen in blood that is the specified output of a blood test.
John Judkins
BUN (mg/dL)
EuPathDB
blood urea nitrogen concentration
A scalar measurement datum of the concentration of creatinine in blood that is a specified output of a blood test.
Person: John Judkins
Creatinine (mg/dL)
VEuPathDB
blood creatinine concentration
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a second time while in hospital
Jie Zheng
Chris Stoeckert
John Judkins
Take second antimalarial medication
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant taking second antimalarial medication
a categorical value specification that specifies whether a human participant under investigation was discharged from hospital
Jie Zheng
Chris Stoeckert
John Judkins
Discharged
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant 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
Jie Zheng
Chris Stoeckert
John Judkins
Take third antimalarial medication
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant taking third antimalarial medication
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
Jie Zheng
Chris Stoeckert
John Judkins
Moved in last 12 months
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant 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
Jie Zheng
Chris Stoeckert
John Judkins
Moved in last month
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant 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
Jie Zheng
Chris Stoeckert
John Judkins
Initiated antimalarial treatment
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant taking initial antimalarial medication
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
Jie Zheng
Chris Stoeckert
John Judkins
Take fourth antimalarial medication
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant taking fourth antimalarial medication
a categorical value specification that specifies whether a human participant under investigation was administered malaria medication a fifth time while in hospital
Jie Zheng
Chris Stoeckert
John Judkins
Take fifth antimalarial medication
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant taking fifth antimalarial medication
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
Jie Zheng
Chris Stoeckert
John Judkins
Tribal affilliation
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of 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
Jie Zheng
Chris Stoeckert
John Judkins
Died
EuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/142
indicator of whether participant died in hospital
A diagnosis that is an assertion that a patient has diarrhea.
Person: John Judkins
VEuPathDB
diagnosis of diarrhea
A diagnosis that is an assertion that a patient has pneumonia.
Person: John Judkins
VEuPathDB
diagnosis of pneumonia
A diagnosis that is an assertion that a patient has upper respiratory tract disease.
Person: John Judkins
VEuPathDB
diagnosis of upper respiratory tract disease
A diagnosis that is an assertion that a patient has malaria.
Person: John Judkins
VEuPathDB
diagnosis of malaria
A third-order administrative region of Thailand.
Person: John Judkins
VEuPathDB
subdistrict of Thailand
A second-order administrative region of Thailand.
Person: John Judkins
VEuPathDB
district of Thailand
A first-order administrative region of Thailand.
Person: John Judkins
VEuPathDB
province of Thailand
A fifth-order administrative region of Uganda.
Person: John Judkins
VEuPathDB
parish of Uganda
Assay that subjects a urine specimen to a test for microorganisms.
John Judkins
urine microbiology test
VEuPathDB
obsolete urine microbiology assay
true
Assay that subjects an induced sputum specimen to a test for microorganisms.
John Judkins
induced sputum microbiology test
VEuPathDB
obsolete induced sputum microbiology assay
true
Assay that subjects a pleural fluid specimen to a test for microorganisms.
John Judkins
pleural fluid microbiology test
VEuPathDB
obsolete pleural fluid microbiology assay
true
Assay that subjects a endotracheal aspirate specimen to a test for microorganisms.
John Judkins
endotracheal aspirate microbiology test
VEuPathDB
obsolete endotracheal aspirate microbiology assay
true
A laboratory test that has an induced sputum specimen as specified input.
John Judkins
VEuPathDB
obsolete induced sputum test
true
A laboratory test that has a endotracheal aspirate specimen as specified input.
John Judkins
VEuPathDB
obsolete endotracheal aspirate test
true
A scalar measurement datum of the concentration of C-reactive protein in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood C-reactive protein concentration
A diagnosis at discharge that is an assertion that a patient has pneumonia.
Person: John Judkins
VEuPathDB
diagnosis of pneumonia at discharge
A diagnosis at discharge that is an assertion that a patient has bronchiolitis.
Person: John Judkins
VEuPathDB
diagnosis of bronchiolitis at discharge
A diagnosis at discharge that is an assertion that a patient has lower respiratory tract disease.
Person: John Judkins
VEuPathDB
diagnosis of lower respiratory tract disease at discharge
A diagnosis at discharge that is an assertion that a patient has seizure.
Person: John Judkins
VEuPathDB
diagnosis of seizure at discharge
A diagnosis at discharge that is an assertion that a patient has chronic mucocutaneous candidiasis.
Person: John Judkins
VEuPathDB
diagnosis of chronic mucocutaneous candidiasis at discharge
A diagnosis at discharge that is an assertion that a patient has anemia.
Person: John Judkins
VEuPathDB
diagnosis of anemia at discharge
A diagnosis at discharge that is an assertion that a patient has neonatal sepsis.
Person: John Judkins
VEuPathDB
diagnosis of neonatal sepsis at discharge
A diagnosis at discharge that is an assertion that a patient has anemia and heart failure.
Person: John Judkins
VEuPathDB
diagnosis of anemic heart failure at discharge
A diagnosis at discharge that is an assertion that a patient has osteomyelitis.
Person: John Judkins
VEuPathDB
diagnosis of osteomyelitis at discharge
A diagnosis at discharge that is an assertion that a patient has asthma.
Person: John Judkins
VEuPathDB
diagnosis of asthma at discharge
A diagnosis at discharge that is an assertion that a patient has otitis media.
Person: John Judkins
VEuPathDB
diagnosis of otitis media at discharge
A diagnosis at discharge that is an assertion that a patient has neonatal asphyxia.
Person: John Judkins
VEuPathDB
diagnosis of neonatal asphyxia at discharge
A diagnosis at discharge that is an assertion that a patient has pneumocystosis.
Person: John Judkins
VEuPathDB
diagnosis of pneumocystosis at discharge
A diagnosis at discharge that is an assertion that a patient has cellulitis.
Person: John Judkins
VEuPathDB
diagnosis of cellulitis at discharge
A diagnosis at discharge that is an assertion that a patient has pneumothorax.
Person: John Judkins
VEuPathDB
diagnosis of pneumothorax at discharge
A diagnosis at discharge that is an assertion that a patient has cerebral palsy.
Person: John Judkins
VEuPathDB
diagnosis of cerebral palsy at discharge
A diagnosis at discharge that is an assertion that a patient has congenital heart disease.
Person: John Judkins
VEuPathDB
diagnosis of congenital heart disease at discharge
A diagnosis at discharge that is an assertion that a patient has physical disorder.
Person: John Judkins
VEuPathDB
diagnosis of physical disorder at discharge
A diagnosis at discharge that is an assertion that a patient has protein-energy malnutrition.
Person: John Judkins
VEuPathDB
diagnosis of protein-energy malnutrition at discharge
A diagnosis at discharge that is an assertion that a patient has pleural empyema.
Person: John Judkins
VEuPathDB
diagnosis of pleural empyema at discharge
A diagnosis at discharge that is an assertion that a patient has pulmonary tuberculosis.
Person: John Judkins
VEuPathDB
diagnosis of pulmonary tuberculosis at discharge
A diagnosis at discharge that is an assertion that a patient has epilepsy.
Person: John Judkins
VEuPathDB
diagnosis of epilepsy at discharge
A diagnosis at discharge that is an assertion that a patient has septic arthritis.
Person: John Judkins
VEuPathDB
diagnosis of septic arthritis at discharge
A diagnosis at discharge that is an assertion that a patient has bacterial sepsis.
Person: John Judkins
VEuPathDB
diagnosis of bacterial sepsis at discharge
A diagnosis at discharge that is an assertion that a patient has fever-induced seizures.
Person: John Judkins
VEuPathDB
diagnosis of seizure precipitated by febrile infection at discharge
A diagnosis at discharge that is an assertion that a patient has sickle cell anemia.
Person: John Judkins
VEuPathDB
diagnosis of sickle cell anemia at discharge
A diagnosis at discharge that is an assertion that a patient has gastroenteritis.
Person: John Judkins
VEuPathDB
diagnosis of gastroenteritis at discharge
A diagnosis at discharge that is an assertion that a patient has parasitic helminthiasis infectious disease.
Person: John Judkins
VEuPathDB
diagnosis of parasitic helminthiasis infectious disease at discharge
A diagnosis at discharge that is an assertion that a patient has human immunodeficiency virus infectious disease.
Person: John Judkins
VEuPathDB
diagnosis of human immunodeficiency virus infectious disease at discharge
A diagnosis at discharge that is an assertion that a patient has urinary system disease.
Person: John Judkins
VEuPathDB
diagnosis of urinary system disease at discharge
A diagnosis at discharge that is an assertion that a patient has immunosuppression.
Person: John Judkins
VEuPathDB
diagnosis of immunosuppression at discharge
A diagnosis at discharge that is an assertion that a patient has upper respiratory tract disease.
Person: John Judkins
VEuPathDB
diagnosis of upper respiratory tract disease at discharge
A diagnosis at hospitalization that is an assertion that a patient has pulmonary tuberculosis.
Person: John Judkins
VEuPathDB
diagnosis of pulmonary tuberculosis at hospitalization
A diagnosis at hospitalization that is an assertion that a patient has extrapulmonary tuberculosis.
Person: John Judkins
VEuPathDB
diagnosis of extrapulmonary tuberculosis at hospitalization
A diagnosis at hospitalization that is an assertion that a patient has severe anemia.
Person: John Judkins
VEuPathDB
diagnosis of severe anemia at hospitalization
A diagnosis at discharge that is an assertion that a patient has bronchiolitis or respiratory syncytial virus infectious disease at hospitalization.
Person: John Judkins
VEuPathDB
diagnosis of bronchiolitis or respiratory syncytial virus infectious disease at hospitalization
A diagnosis at hospitalization that is an assertion that a patient has asthma.
Person: John Judkins
VEuPathDB
diagnosis of asthma at hospitalization
A diagnosis at hospitalization that is an assertion that a patient has measles.
Person: John Judkins
VEuPathDB
diagnosis of measles at hospitalization
A diagnosis at hospitalization that is an assertion that a patient has bronchitis.
Person: John Judkins
VEuPathDB
diagnosis of bronchitis at hospitalization
A diagnosis at hospitalization that is an assertion that a patient has malaria.
Person: John Judkins
VEuPathDB
diagnosis of malaria at hospitalization
A diagnosis at hospitalization that is an assertion that a patient has global developmental delay or cerebral palsy .
Person: John Judkins
VEuPathDB
diagnosis of global developmental delay or cerebral palsy at hospitalization
A diagnosis that is an assertion that a patient has meningitis.
Person: John Judkins
VEuPathDB
diagnosis of meningitis at hospitalization
A fourth-order administrative region of Bangladesh.
Person: John Judkins
VEuPathDB
union council of Bangladesh
An information content entity about the multiple households that share a location and a common trait such as infrastructure.
VEuPathDB
community information
A scalar measurement datum of the concentration of Activin A in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood Activin A concentration
A scalar measurement datum of the concentration of icosanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk arachidic acid concentration
A scalar measurement datum of the concentration of arachidonic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk arachidonic acid concentration
A scalar measurement datum of the concentration of docosanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk docosanoic acid concentration
A scalar measurement datum of the concentration of decanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk decanoic acid concentration
A scalar measurement datum of the concentration of all-cis-icosa-8,11,14-trienoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk all-cis-icosa-8,11,14-trienoic acid concentration
A scalar measurement datum of the concentration of docosahexaenoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk docosahexaenoic acid concentration
A scalar measurement datum of the concentration of (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk (7Z,10Z,13Z,16Z,19Z)-docosapentaenoic acid concentration
A scalar measurement datum of the concentration of (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoic acid concentration
A scalar measurement datum of the concentration of docosatetraenoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk docosatetraenoic acid concentration
A scalar measurement datum of the concentration of icosadienoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk icosadienoic acid concentration
A scalar measurement datum of the concentration of icosapentaenoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk icosapentaenoic acid concentration
A scalar measurement datum of the concentration of icosenoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk icosenoic acid concentration
A scalar measurement datum of the concentration of elaidic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk elaidic acid concentration
A scalar measurement datum of the concentration of gamma-linolenic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk gamma-linolenic acid concentration
A scalar measurement datum of the concentration of dodecanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk dodecanoic acid concentration
A scalar measurement datum of the concentration of tetracosanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk tetracosanoic acid concentration
A scalar measurement datum of the concentration of linoelaidic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk linoelaidic acid concentration
A scalar measurement datum of the concentration of linoleic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk linoleic acid concentration
A scalar measurement datum of the concentration of tetradecanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk myristic acid concentration
A scalar measurement datum of the concentration of (15Z)-tetracosenoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk nervonic acid concentration
A scalar measurement datum of the concentration of oleic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk oleic acid concentration
A scalar measurement datum of the concentration of palmitelaidic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk palmitelaidic acid concentration
A scalar measurement datum of the concentration of hexadecanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk hexadecanoic acid concentration
A scalar measurement datum of the concentration of palmitoleic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk palmitoleic acid concentration
A scalar measurement datum of the concentration of octadecanoic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk octadecanoic acid concentration
A scalar measurement datum of the concentration of interferon gamma in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interferon gamma concentration
A scalar measurement datum of the concentration of interleukin-10 in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-10 concentration
A scalar measurement datum of the concentration of interleukin-1 beta in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-1 beta concentration
A scalar measurement datum of the concentration of interleukin-4 in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-4 concentration
A scalar measurement datum of the concentration of interleukin-5 in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-5 concentration
A scalar measurement datum of the concentration of interleukin-6 in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-6 concentration
A scalar measurement datum of the concentration of interleukin-7 in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-7 concentration
A scalar measurement datum of the concentration of interleukin-8 in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-8 concentration
A scalar measurement datum of the concentration of tumor necrosis factor in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood tumor necrosis factor concentration
A scalar measurement datum of the concentration of eotaxin resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk eotaxin concentration
A scalar measurement datum of the concentration of granulocyte colony-stimulating factor resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk granulocyte colony-stimulating factor concentration
A scalar measurement datum of the concentration of granulocyte-macrophage colony-stimulating factor resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk granulocyte-macrophage colony-stimulating factor concentration
A scalar measurement datum of the concentration of interleukin-12 complex resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-12 complex concentration
A scalar measurement datum of the concentration of interleukin-13 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-13 concentration
A scalar measurement datum of the concentration of interleukin-15 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-15 concentration
A scalar measurement datum of the concentration of interleukin-17A resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-17A concentration
A scalar measurement datum of the concentration of interleukin-1 receptor antagonist protein resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-1 receptor antagonist protein concentration
A scalar measurement datum of the concentration of interleukin-2 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-2 concentration
A scalar measurement datum of the concentration of interleukin-9 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-9 concentration
A scalar measurement datum of the concentration of chemokine ligand 10 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk chemokine ligand 10 concentration
A scalar measurement datum of the concentration of C-C motif chemokine 2 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk C-C motif chemokine 2 concentration
A scalar measurement datum of the concentration of C-C motif chemokine 3 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk C-C motif chemokine 3 concentration
A scalar measurement datum of the concentration of platelet-derived growth factor complex resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk platelet-derived growth factor complex concentration
A scalar measurement datum of the concentration of C-C motif chemokine 5 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk C-C motif chemokine 5 concentration
A scalar measurement datum of the concentration of pro-epidermal growth factor resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk pro-epidermal growth factor concentration
A scalar measurement datum of the concentration of endotoxin in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood endotoxin concentration
A scalar measurement datum of the concentration of lactadherin resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk lactadherin concentration
A scalar measurement datum of the concentration of vitamin D in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood vitamin D concentration
A scalar measurement datum of the concentration of granulocyte colony-stimulating factor in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood granulocyte colony-stimulating factor concentration
A scalar measurement datum of the concentration of interferon gamma resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interferon gamma concentration
A scalar measurement datum of the concentration of interleukin-10 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-10 concentration
A scalar measurement datum of the concentration of interleukin-17A in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-17A concentration
A scalar measurement datum of the concentration of interleukin-1 beta resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-1 beta concentration
A scalar measurement datum of the concentration of interleukin-4 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-4 concentration
A scalar measurement datum of the concentration of interleukin-5 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-5 concentration
A scalar measurement datum of the concentration of interleukin-6 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-6 concentration
A scalar measurement datum of the concentration of interleukin-7 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-7 concentration
A scalar measurement datum of the concentration of interleukin-8 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk interleukin-8 concentration
A scalar measurement datum of the concentration of C-C motif chemokine 4 resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk C-C motif chemokine 4 concentration
A scalar measurement datum of the concentration of tumor necrosis factor resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk tumor necrosis factor concentration
A scalar measurement datum of the concentration of alpha-linolenic acid resulting from a clinical laboratory test on a milk specimen.
Person: John Judkins
VEuPathDB
milk alpha-linolenic acid concentration
A scalar measurement datum of the concentration of interleukin-2 in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood interleukin-2 concentration
A laboratory test that has a feces specimen as specified input.
John Judkins
VEuPathDB
obsolete feces test
true
Assay that subjects a cerebrospinal fluid specimen to a test for microorganisms.
John Judkins
cerebrospinal fluid microbiology test
VEuPathDB
obsolete cerebrospinal fluid microbiology assay
true
A laboratory test that has a cerebrospinal fluid specimen as specified input.
John Judkins
VEuPathDB
obsolete cerebrospinal fluid test
true
A second-order administrative region of Ethiopia.
Person: John Judkins
VEuPathDB
zone of Ethiopia
A fourth-order administrative region of Ethiopia.
Person: John Judkins
subdistrict of Ethiopia
VEuPathDB
kebele of Ethiopia
A third-order administrative region of Ethiopia.
Person: John Judkins
VEuPathDB
woreda of Ethiopia
An information content entity that specifies whether a blood smear has been performed.
Person: John Judkins
indicator of whether blood smear performed
A role of a material entity realized in drawing an arthropod in the direction of the material.
attractant
IRO:0000034
obsolete arthropod attractor role
true
An infusion material extracted from alfalfa.
IRO:0001059
alfalfa infusion
A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin.
BG-lure
IRO:0001060
obsolete BG-lure scent dispenser
true
An infusion material extracted from hay.
hay or grass infusion
IRO:0000037
hay infusion
An information content entity that specifies that no attractant was used in an anthropod trap
no attractant used
IRO:0000153
information specifying no arthropod attractor used
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant.
new jersey trap catch
IRO:0000031
Cire. N. J. agrie. Exp. Stn. 1942 No.421 pp.8
obsolete New Jersey light trap
true
An arthropod trap that is designed to collect gravid female arthropods or their eggs.
gravid trap catch
IRO:0000030
obsolete gravid trap
true
A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods.
EVS light trap
EVS trap catch
IRO:0000029
VSMO:0001295
obsolete encephalitis virus surveillance trap
true
A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods.
BG-Counter trap catch
IRO:0000143
obsolete BG-Counter
true
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce.
CDC light trap catch
IRO:0000163
obsolete Centers for Disease Control and Prevention light trap
true
An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current.
BG-Sentinal trap catch
VSMO:0001906
IRO:0000028
obsolete BG-Sentinel trap
true
An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container.
barrier catch
IRO:0000017
obsolete barrier trap
true
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter.
OVI light-suction trap
IRO:0000154
Parasites Vectors 8, 239 (2015)
obsolete Onderstepoort Veterinary Institute light-suction trap
true
An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity.
resting box catch
IRO:0000021
Proceedings of the Eighty-Second Annual Meeting of the New Jersey Mosquito Control Association, Inc. 1989, pp 53-57.
obsolete resting box trap
true
An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap.
shannon trap catch
IRO:0000191
The American Journal of Tropical Medicine and Hygiene, Volume s1-19, Issue 2, 1 Mar 1939, p. 131 - 140
obsolete Shannon trap
true
An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive.
sticky trap catch
IRO:0000128
obsolete sticky trap
true
An arthropod trap, consisting of a pit dug under the shelter of a plant, designed to provide a space for arthropods to rest and be collected.
artificial pit shelter
IRO:0000005
obsolete artificial pit shelter
true
An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity.
resting bucket catch
IRO:0000141
Kreppel et al. Parasites & Vectors (2015) 8:462
obsolete resting bucket
true
An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods.
mosquito magnet pro catch
IRO:0000022
obsolete Mosquito Magnet trap
true
An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized.
knockdown collection
IRO:0000014
38th Report East Malling Research Station 1949-50 , 1951, p.148
obsolete knockdown arthropod specimen collection process
true
A gravid trap consisting of an arthropod attractant and adhesive surface.
MosquiTRAP catch
IRO:0000140
obsolete MosquiTRAP
true
An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected.
sticky resting bucket catch
IRO:0000142
obsolete sticky resting bucket
true
A light trap designed to be placed inside a building.
indoor light trap catch
MIRO:30000009
obsolete light trap for indoor use
true
A knockdown arthropod specimen collection process in which the pesticide is pyrethrum.
pyrethrum spray catch
MIRO:30000023
obsolete knockdown arthropod specimen collection by pyrethrum spray
true
An arthropod trap that uses light as an attractant.
light trap catch
MIRO:30000065
obsolete light trap
true
An arthropod specimen collection process meant to collect live specimens.
catch of live specimens
MIRO:30000045
obsolete live arthropod specimen collection process
true
An arthropod specimen collection process in which the arthropods are in the larval stage.
collection of larvae
MIRO:30000022
obsolete larval specimen collection process
true
An arthropod specimen collection by aspiration that occurs in the daytime.
MIRO:30000007
obsolete daytime arthropod specimen collection by aspiration
true
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human.
man biting catch
MIRO:30000017
obsolete human-biting arthropod specimen collection by aspiration
true
An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females.
ovitrap catch
oviposition trap
MIRO:30000016
VSMO:0001501
obsolete ovitrap
true
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building.
man biting catch - indoors
MIRO:30000019
obsolete human-biting indoor arthropod specimen collection by aspiration
true
An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building.
man biting catch - outdoors
MIRO:30000018
obsolete human-biting outdoor arthropod specimen collection by aspiration
true
A live arthropod specimen collection process that involves the use of an aspirator, a device which is brought to an arthropod and causes the arthropod to be drawn by suction into a container.
catch by aspiration
MIRO:30000043
obsolete arthropod specimen collection by aspiration
true
An arthropod specimen collection by aspiration that catches specimens resting inside an animal house.
animal shed resting catch
MIRO:30000027
obsolete arthropod resting in animal house specimen collection by aspiration
true
An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity.
outdoors shelter catch
MIRO:30000024
obsolete arthropod resting outdoors specimen collection by aspiration
true
An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building.
outlet window trap catch
MIRO:30000020
Bull World Health Organ. 1948; 1(2): 253–296.
obsolete outlet window trap
true
A live arthropod specimen collection process in which the arthropods are in the adult stage.
collection of adults
MIRO:30000052
obsolete adult arthropod specimen collection process
true
An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal.
animal biting catch
MIRO:30000012
obsolete animal-biting arthropod specimen collection by aspiration
true
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture.
outdoors shelter catch - artificial
MIRO:30000026
obsolete arthropod resting outdoors on artificial support specimen collection by aspiration
true
A light trap designed to be placed outside a building.
outdoor light trap catch
MIRO:30000010
obsolete light trap for outdoor use
true
A device designed to catch arthropods.
trap catch
MIRO:30000011
obsolete arthropod trap
true
A specimen collection process that has the objective of collecting arthropods as specimens.
collection of arthropods
field population catch
VSMO:0001445
MIRO:30000044
obsolete arthropod specimen collection process
true
An animal-biting arthropod specimen collection by aspiration that occurs outside a building.
animal biting catch - outdoors
MIRO:30000014
obsolete animal-biting outdoor arthropod specimen collection by aspiration
true
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant.
outdoors shelter catch - natural
MIRO:30000025
obsolete arthropod resting outdoors on natural support specimen collection by aspiration
true
An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment.
aquatic environment catch
MIRO:30000048
obsolete aquatic arthropod specimen collection process
true
A count of the traps deployed in a study design execution.
number of traps
VBcv:0001122
number of traps
An arthropod specimen collection process that occurs while the arthropods land on a surface.
collection of landing insects
VSMO:0001457
For example, while they are landing on a human bait.
obsolete landing arthropod specimen collection process
true
A device that consists of a network of mesh and is designed to capture adult arthropods.
VSMO:0001522
Can be successfully used to catch resting or flying adult arthropods. The net typically is mounted on a frame that is attached to a handle to increase the reach. [ISBN:9781402066658]
obsolete hand-held sweep net
true
An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage.
trap for emerging adult arthropods
VSMO:0001352
American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389
obsolete trap for emerging adult arthropods
true
The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658]
A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan.
CDC gravid trap
J Am Mosq Control Assoc. 1988 Dec;4(4):536-8.
VSMO:0001510
obsolete Centers for Disease Control and Prevention gravid trap
true
An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller.
trap containing small non-human animal bait
VSMO:0001595
Small non-human animals used as bait include chickens and other birds, rabbits, rodents, and dogs.
obsolete arthropod trap containing small non-human animal bait
true
A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan.
collection of larvae from dippers
collection of pupae from dippers
dipper for immatures
MIRO:30000063
MIRO:30000064
VSMO:0001479
A dipper is a commonly used tool for collecting larvae and pupae from their aquatic development sites. Dippers vary in size, shape and the material they are constructed from. A variety of utensils have been used as dippers, e.g. soup ladles, rectangular enamel pie dishes, photographic trays, frying pans, plastic or enamel bowls, household metal strainers and spoons. Volumes of water collected by the dipper can vary from 100 ml to more than 1 liter depending on the specific dipper used. Dippers can be equipped with plastic or metal screen bottoms, or customized with long handles to increase their reach. [ISBN:9781402066658]"
obsolete dipper for arthropod immatures
true
An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity.
collection of resting insects capable of flight
VSMO:0000514
obsolete resting flight-capable arthropod specimen collection process
true
An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die.
VSMO:0001649
For example, Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes." [ISBN:9781402066658]
obsolete free-standing window trap
true
A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity.
trap or shelter for resting adult arthropods
VSMO:0001355
Most commonly used to collect mosquitoes.
obsolete device for resting of adult arthropods for collection
true
A material entity that has an arthropod attractor role.
arthropod attractor
An arthropod specimen collection by aspiration that catches specimens resting inside a human house.
obsolete arthropod resting in human house specimen collection by aspiration
true
An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal.
obsolete baited net trap
true
A processed material that results from the suspension of plant material in a solvent for enough time to allow compounds to be extracted from the plant material into the solvent.
infusion
This label distinguishes the infused material from the infusion process that produces it. -JJ
infused material
An arthropod specimen collection process in which the arthropods are in the pupal stage.
collection of pupae
MIRO:30000050
obsolete pupal specimen collection process
true
An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity.
obsolete resting arthropod trap
true
A time measurement datum that measures a temporal interval of insecticide exposure.
Person: Chris Stoeckert
duration time of insecticide exposure
A light source that provides UV light for use in a distant area using a delivery system.
Jie Zheng
obsolete UV light source
true
A light source that provides visible light for use in a distant area using a delivery system.
Jie Zheng
obsolete visible light source
true
This species is not in NCBITaxon so is assigned a EUPATH ID.
Psorophora johnstonii
This species is not in NCBITaxon so is assigned a EUPATH ID.
Psorophora mathesoni
This species is not in NCBITaxon so is assigned a EUPATH ID.
Psorophora mexicana
This subspecies is not in NCBITaxon so is assigned a EUPATH ID.
Toxorhynchites rutilus rutilus
This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID.
Aedes atlanticus-tormentor morphological group
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes fijiensis
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes hodgkini
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes hokkaidensis
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes idahoensis
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes juppi
Person: John Judkins
obsolete Aedes ledgeri
true
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes mathesoni
This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID.
VBsp:0000997
Aedes mathesoni complex
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes subdentatus
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes tricholabis
This subspecies is not in NCBITaxon so is assigned a EUPATH ID.
Aedes vexans arabiensis
This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID.
Aedes vexans sensu lato
This subspecies is not in NCBITaxon so is assigned a EUPATH ID.
Aedes vexans vexans
This species is not in NCBITaxon so is assigned a EUPATH ID.
Aedes washinoi
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles barberi
This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID.
Anopheles culicifacies AD subgroup
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles distinctus
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles flavicosta
Person: John Judkins
obsolete Anopheles franciscanus
true
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles georgianus
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles listeri
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles natalensis
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles perplexens
This taxonomic label is not in NCBITaxon, so this term is assigned a EUPATH ID.
Anopheles sinensis sensu lato
This species is not in NCBITaxon so is assigned a EUPATH ID.
Anopheles umbrosus
Person: John Judkins
obsolete Culex aurantapex
true
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex chorleyi
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex cinerellus
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex cuyanus
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex inconspicuosus
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex lineata
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex peringueyi
Person: John Judkins
obsolete Culex rubinotus
true
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex salisburiensis
Person: John Judkins
obsolete Culex stigmatosoma
true
This species is not in NCBITaxon so is assigned a EUPATH ID.
Culex trifoliatus
This species is not in NCBITaxon so is assigned a EUPATH ID.
Mimomyia hispida
Person: John Judkins
obsolete Mimomyia mediolineata
true
Person: John Judkins
obsolete Mimomyia mimomyiaformis
true
This species is not in NCBITaxon so is assigned a EUPATH ID.
Sergentomyia theodori
This species is not in NCBITaxon so is assigned a EUPATH ID.
Uranotaenia hopkinsi
This species is not in NCBITaxon so is assigned a EUPATH ID.
Uranotaenia mashonaensis
This species is not in NCBITaxon so is assigned a EUPATH ID.
Wyeomyia haynei
A data item that is about resistance to an insecticide.
Person: John Judkins
obsolete insecticide resistance datum
true
A scalar measurement datum of the concentration of an insecticide.
Person: John Judkins
insecticide concentration datum
An insecticide concentration datum expressed as a percent.
Person: John Judkins
VEuPathDB
insecticide concentration in percent
An insecticide concentration datum that has a parts per notation unit.
Person: John Judkins
VEuPathDB
insecticide concentration in parts per notation unit
An insecticide concentration datum that has an area density unit.
Person: John Judkins
VEuPathDB
insecticide concentration in area density unit
An insecticide concentration datum that has a mass density unit.
Person: John Judkins
VEuPathDB
insecticide concentration in mass density unit
An insecticide concentration datum that has a unit of mass unit per standard assay bottle, which is 250 ml.
Person: John Judkins
VEuPathDB
insecticide concentration in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 50% of a population of insects.
Person: John Judkins
LC50
VBcv:0000726
lethal insecticide concentration 50
A lethal insecticide concentration 50, expressed as a percent.
Person: John Judkins
LC50 in percent
VEuPathDB
lethal insecticide concentration 50 in percent
A lethal insecticide concentration 50 that has a parts per notation unit.
Person: John Judkins
LC50 in parts per million or billion
VEuPathDB
lethal insecticide concentration 50 in parts per notation unit
A lethal insecticide concentration 50 that has an area density unit.
Person: John Judkins
LC50 in mass per area
VEuPathDB
lethal insecticide concentration 50 in area density unit
A lethal insecticide concentration 50 that has a mass density unit.
Person: John Judkins
LC50 in mass per volume
VEuPathDB
lethal insecticide concentration 50 in mass density unit
A lethal insecticide concentration 50 that has a unit of mass unit per standard assay bottle, which is 250 ml.
Person: John Judkins
LC50 in mass per standard assay bottle
VEuPathDB
lethal insecticide concentration 50 in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 95% of a population of insects.
Person: John Judkins
LC95
VBcv:0000728
lethal insecticide concentration 95
A lethal insecticide concentration 95, expressed as a percent.
Person: John Judkins
LC95 in percent
VEuPathDB
lethal insecticide concentration 95 in percent
A lethal insecticide concentration 95 that has a parts per notation unit.
Person: John Judkins
LC95 in parts per million or billion
VEuPathDB
lethal insecticide concentration 95 in parts per notation unit
A lethal insecticide concentration 95 that has an area density unit.
Person: John Judkins
LC95 in mass per area
VEuPathDB
lethal insecticide concentration 95 in area density unit
A lethal insecticide concentration 95 that has a mass density unit.
Person: John Judkins
LC95 in mass per volume
VEuPathDB
lethal insecticide concentration 95 in mass density unit
A lethal insecticide concentration 95 that has a unit of mass unit per standard assay bottle, which is 250 ml.
Person: John Judkins
LC95 in mass per standard assay bottle
VEuPathDB
lethal insecticide concentration 95 in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 99% of a population of insects.
Person: John Judkins
LC99
VBcv:0000729
lethal insecticide concentration 99
A lethal insecticide concentration 99, expressed as a percent.
Person: John Judkins
LC99 in percent
VEuPathDB
lethal insecticide concentration 99 in percent
A lethal insecticide concentration 99 that has a parts per notation unit.
Person: John Judkins
LC99 in parts per million or billion
VEuPathDB
lethal insecticide concentration 99 in parts per notation unit
A lethal insecticide concentration 99 that has an area density unit.
Person: John Judkins
LC99 in mass per area
VEuPathDB
lethal insecticide concentration 99 in area density unit
A lethal insecticide concentration 99 that has a mass density unit.
Person: John Judkins
LC99 in mass per volume
VEuPathDB
lethal insecticide concentration 99 in mass density unit
A lethal insecticide concentration 99 that has a unit of mass unit per standard assay bottle, which is 250 ml.
Person: John Judkins
LC99 in mass per standard assay bottle
VEuPathDB
lethal insecticide concentration 99 in mass per standard assay bottle
A data item that is about the concentration of an insecticide that kills 90% of a population of insects.
Person: John Judkins
LC90
VBcv:0000727
lethal insecticide concentration 90
A lethal insecticide concentration 90, expressed as a percent.
Person: John Judkins
LC90 in percent
VEuPathDB
lethal insecticide concentration 90 in percent
A time measurement datum that is about the duration of exposure to an insecticide that results in the death of 90% of a population of insects.
Person: John Judkins
LT90
VBcv:0000733
lethal insecticide time 90
A time measurement datum that is about the duration of exposure to an insecticide that results in the death of 95% of a population of insects.
Person: John Judkins
LT95
VBcv:0000734
lethal insecticide time 95
A time measurement datum specifying the time at which half of a population of insects has died as a result of exposure to insecticide.
Person: John Judkins
KDT50
PMC2459197
VBcv:0000714
median knockdown time
A lethal insecticide concentration 90 that has a parts per notation unit.
Person: John Judkins
LC90 in parts per million or billion
VEuPathDB
lethal insecticide concentration 90 in parts per notation unit
A lethal insecticide concentration 90 that has an area density unit.
Person: John Judkins
LC90 in mass per area
VEuPathDB
lethal insecticide concentration 90 in area density unit
A lethal insecticide concentration 90 that has a mass density unit.
Person: John Judkins
LC90 in mass per volume
VEuPathDB
lethal insecticide concentration 90 in mass density unit
A lethal insecticide concentration 90 that has a unit of mass unit per standard assay bottle, which is 250 ml.
Person: John Judkins
LC90 in mass per standard assay bottle
VEuPathDB
lethal insecticide concentration 90 in mass per standard assay bottle
A data item that specifies the proportionality of the mean enzymatic activity of a field-collected population of specimens compared to that of a reference population.
Person: John Judkins
VEuPathDB
ratio of specimen population mean enzymatic activity to that of reference specimen population
A data item that specifies the proportionality of the median enzymatic activity of a field-collected population of specimens compared to that of a reference population.
Person: John Judkins
VEuPathDB
ratio of specimen population median enzymatic activity to that of reference specimen population
A data item that specifies the fraction of a population exhibiting higher enzymatic activity than the 99th percentile of a reference population.
Person: John Judkins
VEuPathDB
population fraction with greater enzymatic activity than 99th percentile of reference population
A count of the specimens involved in an assay.
Person: John Judkins
VEuPathDB
number of input specimens to assay
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014F.
VEuPathDB
prevalence of Kdr L1014F
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr S989P.
VEuPathDB
prevalence of Kdr S989P
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1011M.
VEuPathDB
prevalence of Kdr I1011M
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1011V.
VEuPathDB
prevalence of Kdr I1011V
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014S.
VEuPathDB
prevalence of Kdr L1014S
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr L1014C.
VEuPathDB
prevalence of Kdr L1014C
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr V1016G.
VEuPathDB
prevalence of Kdr V1016G
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr V1016I.
VEuPathDB
prevalence of Kdr V1016I
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr I1532T.
VEuPathDB
prevalence of Kdr I1532T
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534C.
VEuPathDB
prevalence of Kdr F1534C
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534L.
VEuPathDB
prevalence of Kdr F1534L
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr F1534S.
VEuPathDB
prevalence of Kdr F1534S
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr N1575Y.
VEuPathDB
prevalence of Kdr N1575Y
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Kdr D1763Y.
VEuPathDB
prevalence of Kdr D1763Y
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in AChE1 G119S.
VEuPathDB
prevalence of AChE1 G119S
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Gste2 L119F.
VEuPathDB
prevalence of Gste2 L119F
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Rdl A296G.
VEuPathDB
prevalence of Rdl A296G
A data item that is the output of an assay to quantify the frequency of genetic variation resulting in Rdl A296S.
VEuPathDB
prevalence of Rdl A296S
Number of mosquito collections in a survey dataset.
A count of collections of specimens that have only arthropods as their members.
Person: John Judkins
VEuPathDB
number of entomology collections
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr L1014 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr L1014
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr S989 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr S989
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr I1011 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr I1011
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr V1016 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr V1016
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr I1532 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr I1532
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr F1534 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr F1534
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr N1575 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr N1575
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Kdr D1763 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Kdr D1763
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at AChE1 G119 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type AChE1 G119
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at AChE1 F290 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type AChE1 F290
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at AChE1 F331 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type AChE1 F331
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Gste2 I114 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Gste2 I114
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Gste2 L119 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Gste2 L119
A data item that is the output of an assay to quantify the frequency of the reference sequence amino acid at Rdl A296 or is calculated from data items of the frequency of a variant at that position.
VEuPathDB
prevalence of wild type Rdl A296
An arthropod specimen collection process in which the arthropods are in the embryo stage.
collection of eggs
MIRO:30000049
obsolete egg specimen collection process
true
An arthropod specimen collection process in which the arthropods are in the larval stage and a trap is used to collect the specimens.
collection of larvae from traps
MIRO:30000062
larval specimen collection process from traps
A data item that is the specified output of an organism identification assay.
species assay result
VBcv:0000961
obsolete organism identification datum
true
A data item that is about the concentration of an insecticide that kills 100% of a population of insects.
Person: John Judkins
LC100
VEuPathDB
lethal insecticide concentration 100
A lethal insecticide concentration 100, expressed as a percent.
Person: John Judkins
LC100 in percent
VEuPathDB
lethal insecticide concentration 100 in percent
A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net.
Person: John Judkins
VEuPathDB
obsolete well net for arthropod immatures
true
An arthropod specimen collection process that has the objective of collecting gravid female arthropods.
Person: John Judkins
VEuPathDB
obsolete gravid female arthropod specimen collection process
true
An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected.
Person: John Judkins
VEuPathDB
obsolete arthropod collection process with automated identification
true
An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap.
Person: John Judkins
VEuPathDB
obsolete flying adult arthropod collection process by passive interception
true
A chemical substance manufactured by BioGents that is designed to attract mosquitoes by mimicking the scent of human skin.
BG-Lure
An identifier that encodes a geographic location into a short string of letters and digits.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash code
A geohash code encoding of geospatial location using 1 character.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 1
A geohash code encoding of geospatial location using 2 characters.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 2
A geohash code encoding of geospatial location using 3 characters.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 3
A geohash code encoding of geospatial location using 4 characters.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 4
A geohash code encoding of geospatial location using 5 characters.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 5
A geohash code encoding of geospatial location using 6 characters.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 6
A geohash code encoding of geospatial location using 7 characters.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 7
A geohash code encoding of geospatial location using 32 characters.
Jie Zheng
Bob MacCallum
https://en.wikipedia.org/wiki/Geohash
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/122
VectorBase
geohash 32
An information content entity that either specifies the process by which latitude and longitude data were obtained, or specifies that it is missing knowledge.
Person: John Judkins
VEuPathDB
geolocation provenance information
An objective specification to obtain geolocation data whose value has a particular degree of precision.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126
geolocation precision objective specification
A geolocation precision objective specification of zero decimal places.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126
geolocation precision objective of zero decimal places
A geolocation precision objective specification of one decimal place.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126
geolocation precision objective of one decimal place
A geolocation precision objective specification of two decimal places.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126
geolocation precision objective of two decimal places
A geolocation precision objective specification of three decimal places.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126
geolocation precision objective of three decimal places
A geolocation precision objective specification of four decimal places.
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/126
geolocation precision objective of four decimal places
A manufactured product that is a 3rd generation Indoor Residual Spraying (3GIRS) micro-encapsulated formulation of an existing organophosphate insecticide, Pirimiphos-methyl, co-developed through a partnership between Syngenta and IVCC.
https://www.ivcc.com/market-access/actellic-300cs
Actellic-300cs insecticide
A count of the number of copies of the interspecific chromosomal inversion (2La) in Anopheles gambiae complex.
2La is located on chromosome arm 2L:20524058-42165532 (approximate location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: Sharakhov, I.V., White, B.J., Sharakhova, M.V., Kayondo, J., Lobo, N.F., Santolamazza, F., Della Torre, A., Simard, F., Collins, F.H. and Besansky, N.J., 2006. Breakpoint structure reveals the unique origin of an interspecific chromosomal inversion (2La) in the Anopheles gambiae complex. Proceedings of the National Academy of Sciences, 103(16), pp.6258-6262. PMID: 16606844
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117
number of copies of the 2La Anopheles gambiae complex chromosomal inversion
A measurement datum of the number of copies of the chromosomal inversion 2Rb in Anopheles gambiae.
2Rb is located on chromosome arm 2R:19023925-26758676 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: Lobo, N.F., Sangaré, D.M., Regier, A.A., Reidenbach, K.R., Bretz, D.A., Sharakhova, M.V., Emrich, S.J., Traore, S.F., Costantini, C., Besansky, N.J. and Collins, F.H., 2010. Breakpoint structure of the Anopheles gambiae 2R b chromosomal inversion. Malaria journal, 9(1), pp.1-9. PMID:20974007
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117
number of copies of the 2Rb Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the trans-specific inversion 2Rc in Anopheles gambiae.
2Rc is located on chromosome arm 2R:26780000-31450000 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: White, B.J., Cheng, C., Sangaré, D., Lobo, N.F., Collins, F.H. and Besansky, N.J., 2009. The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae. Genetics, 183(1), pp.275-288. PMID:19581444
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117
number of copies of the 2Rc Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the chromosomal inversion 2Rd in Anopheles gambiae.
2Rd is located on chromosome arm 2R:31480000-42600000 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: George, P., Sharakhova, M.V. and Sharakhov, I.V., 2010. High‐resolution cytogenetic map for the African malaria vector Anopheles gambiae. Insect molecular biology, 19(5), pp.675-682. PMID:20609021
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117
number of copies of the 2Rd Anopheles gambiae complex chromosomal inversion
A measurement datum of the number of copies of the inversion 2Rj in Anopheles gambiae.
2Rj is located on chromosome arm 2R:3656857-14459087 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: Coulibaly, M.B., Lobo, N.F., Fitzpatrick, M.C., Kern, M., Grushko, O., Thaner, D.V., Traoré, S.F., Collins, F.H. and Besansky, N.J., 2007. Segmental Duplication Implicated in the Genesis of Inversion 2 Rj of Anopheles gambiae. PLoS One, 2(9), p.e849. PMID:17786220
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117
number of copies of the 2Rj Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the chromosomal inversion 2Rk in Anopheles gambiae.
2Rk is described in: Mario Coluzzi, Adriana Sabatini, Alessandra della Torre, Maria Angela Di Deco, Vincenzo Petrarca. A polytene chromosome analysis of the Anopheles gambiae species complex. PMID: 12364623
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117
number of copies of the 2Rk Anopheles gambiae complex chromosomal inversion
A count of the number of copies of the trans-specific inversion 2Ru in Anopheles gambiae.
2Ru is located on chromosome arm 2R:31480000-35500000 (location in the AgamP3 assembly; GenBank: GCF_000005575.2) as described in: White, B.J., Cheng, C., Sangaré, D., Lobo, N.F., Collins, F.H. and Besansky, N.J., 2009. The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae. Genetics, 183(1), pp.275-288. PMID:19581444
Person: John Judkins
VEuPathDB
https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/117
number of copies of the 2Ru Anopheles gambiae complex chromosomal inversion
An information content entity that is about data collected at the community level (e.g., village) on multiple occasions.
community repeated measure
Information about a female insect regarding when and if it had a blood meal.
Person: John Judkins
VEuPathDB
female insect feeding status
A female insect feeding status about a gravid female insect.
Person: John Judkins
VEuPathDB
gravid female insect feeding status
A gravid female insect feeding status of having a visible blood meal.
Person: John Judkins
VEuPathDB
fed gravid female insect status
A gravid female insect feeding status of not having a visible blood meal.
Person: John Judkins
VEuPathDB
unfed gravid female insect status
A female insect feeding status of not having a visible blood meal.
Person: John Judkins
VEuPathDB
unfed female insect status
A female insect feeding status of having a visible blood meal.
Person: John Judkins
VEuPathDB
fed female insect status
A data item that is the output of an assay to quantify the frequency of the genetic variation resulting in cytochrome P450 CYP4J5 L43F associated with pyrethroid resistance and located in the 2La inversion of Anopheles gambiae.
VEuPathDB
prevalence of Cyp4J5 L43F
A scalar measurement datum of the concentration of hydroxychloroquine in blood that is a specified output of a blood test.
Person: John Judkins
VEuPathDB
blood hydroxychloroquine concentration
A second-order administrative region of Uganda.
Person: John Judkins
VEuPathDB
district of Uganda
A first-order administrative region of Uganda.
Person: John Judkins
VEuPathDB
region of Uganda
A laboratory test that has a saliva specimen as specified input.
John Judkins
VEuPathDB
obsolete saliva test
true
A fourth-order administrative region of Tanzania.
Person: John Judkins
VEuPathDB
ward of Tanzania
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 (whole organism)
infant formula
A chemical food component in liquid form.
liquid
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)
One of the large, unbroken masses of land into which the Earth's surface is divided.
continent
A reference to a place on the Earth, by its name or by its geographical location.
geographic location
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
read coverage
A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
subnational region
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
molecular_function
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
catalytic activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
RNA-directed DNA polymerase activity
Catalysis of the reaction: acetylcholine + H2O = choline + acetate.
acetylcholinesterase activity
Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
glutathione transferase activity
The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs.
parturition
The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
respiratory gaseous exchange by respiratory system
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
biological_process
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
gene expression
The covalent alteration of one or more amino acid residues within a histone protein.
histone modification
Catalysis of the hydrolysis of any ester bond.
hydrolase activity, acting on ester bonds
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
B cell receptor complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
protein-containing complex
A process that modulates the rate or extent of water loss from an organism via the skin.
regulation of water loss via skin
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
DNA polymerase activity
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
T cell receptor complex
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
immunoglobulin complex, circulating
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
DNA polymerase complex
A nonsteroidal regulator, composed of two covalently linked inhibin beta-A subunits (sometimes known as activin beta-A or activin/inhibin beta-A).
activin A complex
A protein complex that is composed of an interleukin-12 alpha (p35, product of the IL12A gene) and an interleukin-12 beta subunit (p40, product of the IL12B gene) and is secreted into the extracellular space.
interleukin-12 complex
Catalysis of the hydrolysis of a carboxylic ester bond.
carboxylic ester hydrolase activity
A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain.
ferritin complex
The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.
immunoglobulin-mediated neutralization
A protein complex consisting of two chains of platelet-derived growth factor (PDGF) subunits. PDGF dimers bind to PDGF receptors in the plasma membrane and induce receptor dimerisation and activation. PDGFs are involved in a wide variety of signalling processes. PDGFs are found in all vertebrates where at least 2 different chains (A and B) exist. In human (and other mammals), four types of PDGF chains (A, B, C, and D) are known which form five different dimers (AA, AB, BB, CC and DD).
platelet-derived growth factor complex
An abnormality of the urinary system.
Abnormality of the urinary system
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.
Renal insufficiency
A phenotypic abnormality.
Phenotypic abnormality
The presence of any abnormality of the genitourinary system.
Abnormality of the genitourinary system
Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth.
Abnormal oral cavity morphology
Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation.
Hydrocephalus
An abnormality of the face.
Abnormality of the face
Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose.
Epistaxis
Any abnormality of the eye, including location, spacing, and intraocular abnormalities.
Abnormality of the eye
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.
Tooth malposition
An abnormality of the nervous system.
Abnormality of the nervous system
An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities.
Behavioral abnormality
A state of unease characterized by diffuse motor activity or motion subject to limited control, nonproductive or disorganized behavior, and subjective distress.
Restlessness
The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine).
Hematuria
An abnormality of the skin.
Abnormality of the skin
Yellow pigmentation of the skin due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.
Jaundice
An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body.
Edema
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
Laminar thickening of skin.
Thickened skin
An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities.
Abnormality of prenatal development or birth
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.
Coma
A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age.
Global developmental delay
Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm.
Failure to thrive
Smaller than normal size according to sex and gestational age related norms, defined as a weight below the 10th percentile for the gestational age.
Small for gestational age
An abnormality of fetal movement.
Prenatal movement abnormality
An abnormality of the integument, which consists of the skin and the superficial fascia.
Abnormality of the integument
An abnormality of the hair.
Abnormal hair morphology
A noncongenital process of hair loss, which may progress to partial or complete baldness.
Alopecia
The birth of a baby of less than 37 weeks of gestational age.
Premature birth
Any abnormality of the cardiovascular system.
Abnormality of the cardiovascular system
The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction.
Congestive heart failure
Necrosis of the myocardium caused by an obstruction of the blood supply to the heart and often associated with chest pain, shortness of breath, palpitations, and anxiety as well as characteristic EKG findings and elevation of serum markers including creatine kinase-MB fraction and troponin.
Myocardial infarction
An abnormality of the spleen.
Abnormality of the spleen
Abnormal increased size of the spleen.
Splenomegaly
An abnormality of the birth process.
Abnormal delivery
Reduction of total body weight.
Weight loss
An abnormality of the hematopoietic system.
Abnormality of blood and blood-forming tissues
An abnormality of leukocytes.
Abnormal leukocyte morphology
An abnormal decreased number of leukocytes in the blood.
Leukopenia
An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects.
Abnormal bleeding
A kind of anemia in which the volume of the red blood cells is normal.
Normocytic anemia
Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
Acute kidney injury
Abnormality of metabolism/homeostasis
Abnormal acid accumulation or depletion of base.
Acidosis
Metabolic acidosis (MA) is characterized by a fall in blood pH due to a reduction of serum bicarbonate concentration. This can occur as a result of either the accumulation of acids (high anion gap MA) or the loss of bicarbonate from the gastrointestinal tract or the kidney (hyperchloremic MA). By definition, MA is not due to a respirary cause.
Metabolic acidosis
Dehydration
Body temperature elevated above the normal range.
Fever
Excessive thirst manifested by excessive fluid intake.
Polydipsia
An abnormal increase in the number of leukocytes in the blood.
Leukocytosis
An abnormality of the viscera of the abdomen.
Abnormality of the abdominal organs
Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.
Vomiting
Abnormally increased frequency of loose or watery bowel movements.
Diarrhea
Difficulty in swallowing.
Dysphagia
Nausea is a commonly encountered symptom that has been defined as an unpleasant painless subjective feeling that one will imminently vomit. Vomiting has been defined as the forceful expulsion of the contents of the stomach, duodenum, or jejunum through the oral cavity. While nausea and vomiting are often thought to exist on a temporal continuum, this is not always the case. There are situations when severe nausea may be present without emesis and less frequently, when emesis may be present without preceding nausea.
Nausea and 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
Reduced body temperature due to failed thermoregulation.
Hypothermia
An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles.
Abnormality of the respiratory system
Any structural anomaly of the lung.
Abnormal lung morphology
Difficult or labored breathing. Dyspnea is a subjective feeling only the patient can rate, e.g., on a Borg scale.
Dyspnea
Respiratory distress is objectively observable as the physical or emotional consequences from the experience of dyspnea. 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
Lack of breathing with no movement of the respiratory muscles and no exchange of air in the lungs. This term refers to a disposition to have recurrent episodes of apnea rather than to a single event.
Apnea
Abnormally increased level of blood lactate (2-hydroxypropanoic acid). Lactate is produced from pyruvate by lactate dehydrogenase during normal metabolism. The terms lactate and lactic acid are often used interchangeably but lactate (the component measured in blood) is strictly a weak base whereas lactic acid is the corresponding acid. Lactic acidosis is often used clinically to describe elevated lactate but should be reserved for cases where there is a corresponding acidosis (pH below 7.35).
Increased serum lactate
Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.
Headache
An abnormality of the vasculature.
Abnormality of the vasculature
An abnormality of the immune system.
Abnormality of the immune system
Very rapid breathing.
Tachypnea
An anomaly of the rhythm or depth of breathing.
Abnormal pattern of respiration
Abnormal respiratory system physiology
An increased amount of bilirubin in the blood.
Hyperbilirubinemia
An abnormality of the composition of urine or the levels of its components.
Abnormality of urine homeostasis
Abnormality of the homeostasis (concentration) of a monoatomic ion.
Abnormal blood ion concentration
Genital ulcers
Pain in muscle.
Myalgia
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
The presence of free hemoglobin in the urine.
Hemoglobinuria
Death within the first 28 days of life.
Neonatal death
Death of the fetus in utero after at least 20 weeks of gestation.
Stillbirth
Abnormally low body weight.
Decreased body weight
An abnormality of temperature homeostasis.
Abnormality of temperature regulation
Reduced consciousness/confusion
A deficiency in the intake of energy and nutrients.
Malnutrition
A reduced desire to eat.
Poor appetite
A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus before the 20th week of pregnancy.
Spontaneous abortion
Loss of consciousness
Excessive wrinkled skin
A tumor (abnormal growth of tissue) of the skin.
Neoplasm of the skin
Stridor is a high pitched sound resulting from turbulent air flow in the upper airway.
Stridor
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
Redness of the skin, caused by hyperemia of the capillaries in the lower layers of the skin.
Erythema
A functional abnormality of the immune system.
Abnormality of immune system physiology
An abnormality of the gastrointestinal tract.
Abnormality of the gastrointestinal tract
Abnormal functionality of the cardiovascular system.
Abnormal cardiovascular system physiology
The presence of hemorrhage within the body.
Internal hemorrhage
An abnormality of the regulation of body fluids.
Abnormality of fluid regulation
Any morphological abnormality of the skin.
Abnormality of skin morphology
Any abnormality of the physiological function of the skin.
Abnormality of skin physiology
The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes.
Inflammatory abnormality of the skin
Vascular skin abnormality
Abnormality of the urinary system physiology
An abnormality of the skin that is not localized to any one particular region.
Generalized abnormality of skin
Cognitive, psychiatric or memory anomaly.
Abnormality of higher mental function
A subjective manifestation of disease localized to the abdomen.
Abdominal symptom
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
Number of leukocytes per volume of blood beyond normal limits.
Abnormal leukocyte count
Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it.
Feeding difficulties
An abnormal functionality of the kidney.
Abnormal renal physiology
An anomaly in the processes involved in the maintenance of an internal equilibrium.
Abnormal homeostasis
An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.
Pain
A functional anomaly of the nervous system.
Abnormal nervous system physiology
Abnormal functionality of the gastrointestinal tract.
Functional abnormality of the gastrointestinal tract
A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.
Cough
Respiratory failure in the newborn.
Neonatal asphyxia
Abnormality of the digestive system
A functional anomaly of the digestive system.
Abnormality of digestive system physiology
A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual.
Constitutional symptom
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
A high-pitched whistling sound associated with labored breathing.
Wheezing
An anomalous (adventitious) sound produced by the breathing process.
Abnormal breath sound
Widening of the nostrils upon inhalation as a manifestation of respiratory distress.
Nasal flaring
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
An abnormal level of an analyte measured in the blood.
Abnormal circulating metabolite concentration
Health status of a family member with respect to the disease being investigated in a proband.
Health status
Any form of seizure occurring at the time of a fever (temperature at or above 38.0 degrees Celcius) without infection of the central nervous system, and without an alternative cause such as severe metabolic derangement, occurring at any age.
Seizure precipitated by febrile infection
A palpable swelling in both feet and ankles caused by palpable swelling caused by an increase in interstitial fluid volume (excess fulid).
Bipedal edema
A cough with a characteristic sound that has been compared to a seal's bark.
Barking cough
Relative coldness of a body part to palpitation, often acccompanied by feelings of coldness.
Coldness
Systemic inflammatory response to infection in newborn babies.
Neonatal sepsis
Pulmonary hemorrhage is a bleeding within the lungs. Older children and adults may spit blood or bloody sputum. Neonates, infants and young children usually do not spit up blood. Anemia, pulmonary infiltrates, increasingling bloody return on BAL and the presence of hemosiderin-laden macrophages in broncho-alveolar lavage (BAL) fluid or lung biopsy can diagnose lung bleeding. Alveolar macrophages contain phagocytosed red blood cells and stain positive for hemosiderin, a product of hemoglobin degradation, after about 48-72 hours following pulmonary hemorraghe. Previous or recurrent bleeding can thus be distinguished from fresh events. A differentiation into local or diffuse is of importance. Also differentiate if pulmonary hemorrhage is due to a primary lung disorder or a manifestation of a systemic disease.
Pulmonary hemorrhage
Pain in head and neck region
Painful or difficult urination.
Dysuria
Fluid accumulation in the lungs.
Pulmonary edema
Pregnancy-induced hypertension in association with significant amounts of protein in the urine.
Preeclampsia
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest.
Chest pain
An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively.
Abnormality of the lymphatic system
Systemic inflammatory response to infection.
Sepsis
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
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.
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://github.com/information-artifact-ontology/IAO/issues/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
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
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
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
person:Alan Ruttenberg
person:Allyson
person:Chris Stoeckert
OBI_0000030
group:OBI
image
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
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
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
journal article, newspaper story, book, etc.
A document that is the output of a publishing process.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
PERSON: Lawrence Hunter
published document
Revisit the term in Octorber 2020. Improve the defintion.
publication
1
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
Alan Ruttenberg
AR notes: We need to discuss whether it should include site.
cartesian spatial coordinate datum
http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
1
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
Alan Ruttenberg
one dimensional cartesian spatial coordinate datum
A scalar measurement datum that is the result of measurement of length quality
Alan Ruttenberg
length measurement datum
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
A scalar measurement datum that is the result of measurement of mass quality
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
mass 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 https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Alan Ruttenberg
Person:Chris Stoeckart
email address
A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
Person: Jie Zheng
https://en.wikipedia.org/wiki/Publishing
VEuPathDB
publishing process
A document that is in preparation for submission to be published.
PERSON: Jie Zheng
EFO_0001795 in preparation
VEuPathDB
document in preparation for publication
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
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
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
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
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
identifier
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
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
ontology module
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
base ontology module
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
editors ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
main release ontology module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
bridge ontology module
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
import ontology module
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
subset ontology module
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
curation subset ontology module
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
exclusion subset ontology module
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
external import ontology module
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
species subset ontology module
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
reasoned ontology module
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
generated ontology module
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
template generated ontology module
taxonomic bridge ontology module
taxonomic bridge ontology module
ontology module subsetted by expressivity
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.
Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).
An ontology is OBO Basic if and only if it has the following characteristics:
DAG
Unidirectional
No Dangling Clauses
Fully Asserted
Fully Labeled
No equivalence axioms
Singly labeled edges
No qualifier lists
No disjointness axioms
No owl-axioms header
No imports
obo basic subset ontology module
ontology module subsetted by OWL profile
ontology module subsetted by OWL profile
EL++ ontology module
EL++ ontology module
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
A material entity with a pathogenic disposition.
pathogen
A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
endotoxin
A material entity bearing an antibacterial disposition.
antibacterial
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
A process that attenuates an immune response.
immunosuppression
A protein modification that effectively either removes neutral hydrogen atoms (proton and electron), or adds oxygen atoms to a residue with or without the removal of hydrogen atoms.
oxidized residue
A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.
iodoacetamide derivatized amino-terminal residue
Culex pseudovishnui
Culex vishnui
Rattus
Rattus norvegicus
Rattus rattus
Rodentolepis nana
Viruses
Anopheles punctipennis
Cytomegalovirus
Mansonia bonneae
Hepatitis B virus
Ochlerotatus hendersoni
Adenoviridae
Aedini
Anopheles jeyporiensis
Culex atratus
Culex cedecei
Culex iolambdis
Culex mulrennani
Culex peccator
Rusa timorensis
Pardalotus striatus
Iodamoeba
Rotavirus
Anopheles lesteri
Alphavirus
Eastern equine encephalitis virus
Western equine encephalitis virus
Flaviviridae
Flavivirus
Butorides virescens
Entamoeba coli
Endolimax nana
Saint Louis encephalitis virus
West Nile virus
Hepacivirus C
Human coronavirus 229E
Mononegavirales
Paramyxoviridae
Anopheles fluviatilis
Asio otus
Loxigilla noctis
Melanospiza bicolor
Human respirovirus 3
fluviatilis species complex
Anopheles fluviatilis S
Anopheles fluviatilis T
Anopheles minimus
Measles morbillivirus
Pneumoviridae
Human orthopneumovirus
Ochlerotatus diantaeus
Orthomyxoviridae
Influenza A virus
Anopheles pretoriensis
Anopheles rufipes
Anopheles theileri
typhus group
Influenza B virus
Influenza C virus
Zenaida auriculata
La Crosse virus
Human immunodeficiency virus 1
Euteleostomi
Chromadorea
Protomacleaya
Ochlerotatus theobaldi
Caliciviridae
Norwalk virus
Anopheles neomaculipalpus
Escherichia phage MS2
Picornaviridae
Enterovirus
Ochlerotatus atlanticus
Ochlerotatus increpitus
Ochlerotatus sierrensis
Ochlerotatus spencerii
Ochlerotatus thelcter
Ochlerotatus thibaulti
Ochlerotatus tortilis
Psorophora longipalpus
Psorophora pygmaea
Psorophora signipennis
Culiseta particeps
Psorophora discolor
Ochlerotatus mitchellae
Ecdysozoa
Lophotrochozoa
Human poliovirus 1
Human poliovirus 1 strain Sabin
Human poliovirus 2
Human poliovirus 3
Anopheles claviger
Ochlerotatus cantans
Ochlerotatus caspius
Aedes cinereus
Ochlerotatus detritus
Aedes geniculatus
Ochlerotatus rusticus
Ochlerotatus sticticus
Setophaga striata
Aedes vexans nipponii
Proteobacteria
Norovirus GI
Norovirus GII
Gammaproteobacteria
Anopheles pampanai
Firmicutes
Coquillettidia richiardii
Armigeres subalbatus
Dengue virus
Human respirovirus 1
Staphylococcus
Vibrio cholerae O1
Staphylococcus aureus
Respiratory syncytial virus
Staphylococcus epidermidis
Anopheles nitidus
Ochlerotatus fulvus
Shigella flexneri 2b
Ochlerotatus caballus
Anopheles argyropus
Blastocystis
Streptococcus
Human mastadenovirus F
Streptococcus pneumoniae
Streptococcus pyogenes
Melopsittacus undulatus
Streptococcus sp. 'group G'
Phlebotomus <genus>
Phlebotomus perniciosus
Rhodnius
Rhodnius prolixus
Phlebotomus similis
Citrobacter freundii complex
Enterococcus
Enterococcus faecalis
Enterococcus faecium
Pseudomonas stutzeri group
Protoculex
Ochlerotatus tormentor
Anopheles pseudowillmori
Anopheles hyrcanus
Anopheles dravidicus
Anopheles crawfordi
Enterovirus C
Parechovirus
Anopheles coustani
Anopheles mattogrossensis
Orthopodomyia
Orthopodomyia alba
Uranotaenia <genus>
Uranotaenia sapphirina
Aedeomyia
Giardia intestinalis assemblage B
Aedes japonicus
Aedes japonicus japonicus
Phlebotomus galilaeus
Aedes aegypti aegypti
Norovirus
Anopheles sawadwongporni
Anopheles vagus
Anopheles willmori
Boreoeutheria
Culex stigmatosoma
Mansonia <mosquitos,genus>
Aedes <subgenus>
Clostridioides difficile
Anopheles maculipalpis
Bocaparvovirus
Clostridium tetani
Anopheles dissidens
Anopheles saeungae
Anopheles wejchoochotei
Anopheles coluzzii
Anopheles demeilloni
Anopheles hancocki
Anopheles marshallii
Collessius pseudotaeniatus
Phagomyia cogilli
Candida <clade Candida/Lodderomyces clade>
Culiseta fumipennis
Psittaculidae
Acartomyia zammitii
Trichoglossus moluccanus
Galloanserae
Uranotaenia balfouri
Treponema
Anopheles maculipennis sensu lato BTLHVDV-2014
Culiseta incidens
Anopheles pulcherrimus
Columba oenas
Treponema pallidum subsp. pallidum
Shigella flexneri 4c
Human metapneumovirus
Anopheles leesoni
Anopheles parensis
Culex annulirostris
Culex sitiens
Culex palpalis
Culex rubinotus
Aedeomyia africana
Corynebacterium
Wyeomyia
Wyeomyia smithii
Culiseta
Culiseta impatiens
Passeroidea
Mycobacteriaceae
Aedes aegypti formosus
Culicoides pulicaris
Culicoides impunctatus
Mycobacterium tuberculosis
Terrabacteria group
Aedeomyia furfurea
Coquillettidia chrysosoma
Aedes hirsutus
Culex duttoni
Culex simpsoni
Culex thalassius
Culex vansomereni
Mimomyia splendens
Motacilla flava
Dobrotworskyius
Aedeomyia venustipes
Coquillettidia linealis
Culiseta inconspicua
Culex globocoxitus
Aedes alboannulatus
Aedes rubrithorax
Aedes macmillani
Aedes tremulus
Aedes wattensis
Aedes mallochi
Ochlerotatus sagax
Ochlerotatus vittiger
Tripteroides atripes
Tripteroides tasmaniensis
Polylepidomyia
Culex cylindricus
Nocardia
Rotavirus G
Anopheles peryassui
Anopheles nili
Anopheles moucheti
Eubacteriales
Lactobacillales
Respirovirus
Clostridioides
Aedes bahamensis
Aedes polynesiensis
Yersiniaceae
Anopheles incertae sedis
Anopheles atropos
Anopheles punctimacula
Uranotaenia lowii
Ochlerotatus <genus>
Meliphagoidea
Shigella flexneri X variant
Campylobacter
Campylobacter coli
Anopheles maculatus sensu lato 4821
Anopheles minimus sensu lato 1775
Anopheles barbirostris sensu lato 245
Campylobacter jejuni
Betainfluenzavirus
Gammainfluenzavirus
sundaicus species complex
Anopheles epiroticus
Bacteria
Balantioides
Anopheles peditaeniatus
Anopheles messeae x Anopheles daciae
Ochlerotatus fulvus pallens
Psorophora horrida
Catageiomyia
Ochlerotatus dupreei
Aedes fowleri
Aedes sudanensis
Fornicata
Anopheles coluzzii x Anopheles gambiae
Helicobacter
Anopheles nigerrimus
Mycoplasma
Helicobacter pylori
Mycoplasma pneumoniae
Sylvioidea
Campylobacterales
Archaea
Anopheles culicifacies D
Anopheles pharoensis
Achromobacter
Anopheles mascarensis
Anopheles plumbeus
Ochlerotatus canadensis
Ochlerotatus trivittatus
Ochlerotatus stimulans
Ochlerotatus grossbecki
Ochlerotatus intrudens
Sergentomyia <subgenus>
crucians species complex
Culex pipiens molestus
Cryptosporidium hominis
Shewanella putrefaciens
Negarnaviricota
Polyploviricotina
Orthocoronavirinae
Embecovirus
Anopheles pullus
Chryseobacterium indologenes
Mansoniini
Riboviria
Orthoparamyxovirinae
Orthorubulavirus
Human orthorubulavirus 2
Human orthorubulavirus 4
Culex aurantapex
Mimomyia mimomyiaformis
Mimomyia mediolineata
Ancylostomatoidea
Culex australicus
unclassified Streptococcus
Metamonada
Anopheles dthali
Anopheles superpictus
Phlebotomus mascittii
Mansonia dyari
Anthochaera
Anthochaera carunculata
Anthochaera chrysoptera
Phylidonyris novaehollandiae
Cryptococcus neoformans var. grubii VNI
Platycercus elegans
Severe acute respiratory syndrome coronavirus 2
Sar
Human poliovirus 3 strain Sabin
Orthornavirae
Kitrinoviricota
Pisuviricota
Pisoniviricetes
Revtraviricetes
Anopheles sergentii
Rotavirus A P4
Eukaryota
Aedes ledgeri
Human coronavirus NL63
Anopheles franciscanus
Acinetobacter lwoffii
Cronobacter sakazakii
Betaproteobacteria
Anolis
Anolis carolinensis
Culex spissipes
Culex taeniopus
Pseudomonas
Aedes atropalpus
Pseudomonas aeruginosa
Rotavirus A
Salmonella enterica
Culicoides obsoletus
Culicoides scoticus
Culicoides dewulfi
Human coronavirus HKU1
Phlebotomus papatasi
Burkholderia cepacia
Pseudomonas fluorescens
Culex decens
Anopheles koliensis
Anopheles merus
Anopheles nuneztovari
Anopheles punctulatus
Anopheles stephensi
Anopheles notanandai
Pseudomonas putida
Ardea cinerea
Strigiformes
Aedeomyia catasticta
Aedes fumidus
Anopheles jamesii
Anopheles pallidus
Lutzia fuscana
Culex gelidus
Lophoceraomyia
Culex infantulus
Culex nigropunctatus
Culex rubithoracis
Ficalbiini
Ficalbia minima
Mansonia annulifera
Mansonioides
Mansonia <mosquitos,subgenus>
Mansonia uniformis
Mimomyia <genus>
Mimomyia <subgenus>
Mimomyia chamberlaini
Ochlerotatus sollicitans
Enterocytozoon bieneusi
Laurasiatheria
Euarchontoglires
Glires
Simiiformes
Pseudomonas stutzeri
Human coronavirus OC43
Aedes pseudoscutellaris
Culex brevipalpis
Heizmannia <genus>
Heizmannia discrepans
Verrallina <genus>
Verrallina indica
Aedes vittatus
Anopheles philippinensis
Anopheles indefinitus
Burkholderia
Kingella
Tetrapoda
Amniota
Theria <mammals>
Pseudoficalbia
Uranotaenia recondita
Uranotaenia <subgenus>
Orthopodomyia anopheloides
Uranotaenia atra
Malaya genurostris
Uranotaenia bicolor
Anopheles splendidus
Heizmannia chandi
Anopheles aitkenii
Tripteroides aranoides
Culex minor
Sauria
Ochlerotatus communis
Ochlerotatus abserratus
Ochlerotatus aurifer
Ochlerotatus cantator
Ochlerotatus excrucians
Ochlerotatus taeniorhynchus
Psorophora ciliata
Culiseta morsitans
Culiseta minnesotae
Culiseta melanura
Coquillettidia
Coquillettidia perturbans
Toxorhynchites rutilus septentrionalis
Human bocavirus
Entamoebidae
Opisthokonta
Culiseta annulata
Bilateria
Ancylostomatidae
Protostomia
Neoptera
Phlebotomus tobbi
Carnivora
Alveolata
Cricetidae
Muroidea
Neotominae
Streptococcus sp. 'group C'
Rickettsieae
Anopheles tenebrosus
Anopheles ziemanni
Culex fuscocephala
Culex malayi
Culex hutchinsoni
Culex minutissimus
Culex pallidothorax
Rhinoskusea
Ochlerotatus wardi
Culex whitmorei
Macleaya <mosquitos>
Anopheles melas
Anopheles quadriannulatus
Anopheles sundaicus
Rotavirus G4
Enterobacter cloacae complex
Pecora
Rattus tanezumi
Trichuris trichiura
Motacillidae
Plasmodium ovale
Culex pluvialis
H1N1 swine influenza virus
Streptococcus sp. 'group A'
Mycobacteroides abscessus
Oryzomys palustris
Chikungunya virus
Streptococcus pneumoniae D39
Shigella flexneri 1a
Culicoides chiopterus
Anopheles annulipes
Aedes iyengari
Verrallina lugubris
Ochlerotatus portonovoensis
Feliformia
Caniformia
Anopheles rampae
Culex pipiens pipiens
Culex restuans
Culex salinarius
Medicago sativa
Anolis sagrei
Astroviridae
Thraupidae
Sigmodontinae
Stenotrophomonas
Stenotrophomonas maltophilia
Anopheles leucosphyrus
dirus species complex
Anopheles longipalpis
Cronobacter
Anopheles atroparvus
Anopheles labranchiae
Anopheles maculipennis
Anopheles messeae
Shigella flexneri 1b
Plasmodium (Plasmodium)
Ceratopogonidae
Culicoides <genus>
Culicoides punctatus
Culicoidea
Chironomoidea
Rhodnius robustus complex
Rhodnius robustus I
Rhodnius robustus II
Rhodnius robustus III
Rhodnius robustus IV
Culex univittatus
Pneumocystis jirovecii
Culex mimeticus
Eimeriorina
Neotoma floridana
Peromyscus gossypinus
Sigmodon hispidus
Culex erraticus
Culex erythrothorax
Culex nigripalpus
Culex pilosus
Culex territans
Lutzia tigripes
Culex torrentium
Shigella flexneri 3a
Shigella flexneri 5a
Shigella flexneri Y
Anopheles aquasalis
Shigella flexneri 2a
Hirundo rustica
Anopheles darlingi
Anopheles konderi
Shigella flexneri 3b
Culicomorpha
Culicinae
Manorina melanocephala
Cyclospora
Anopheles <subgenus>
Anopheles <series>
maculipennis group
maculipennis subgroup
Legionella
punctipennis group
freeborni species complex
maculipennis species complex
Cellia
Neocellia
Neomyzomyia
Pyretophorus
leucosphyrus subgroup
punctulatus species complex
gambiae species complex
Nyssorhynchus
albimanus section
argyritarsis section
oswaldoi series
oswaldoi subgroup
Chilomastix
Aedes ochraceus
Culex poicilipes
Dikarya
Anopheles campestris
Anthus pratensis
Vibrio cholerae O139
Toxorhynchites
Ochlerotatus punctor
Picornavirales
Moraxellaceae
Acinetobacter
Anopheles pseudopunctipennis
Acinetobacter baumannii
Acinetobacter calcoaceticus
Chilomastix mesnili
Moraxella
Fungi
Pneumocystis
Moraxella nonliquefaciens
Pseudomonas luteola
Moraxella catarrhalis
Neisseriaceae
Ptilotula penicillata
Neisseria
Cystoisospora belli
Urva auropunctata
Neisseria meningitidis
Anopheles baimaii
Passer domesticus
Ascomycota
Saccharomycetales
Pichia kudriavzevii
crucians subgroup
Anopheles bradleyi
Anopheles earlei
Anopheles walkeri
Aedes mcintoshi
Aedes cumminsii
Sylvilagus palustris
Alcaligenaceae
Aspergillus parasiticus
Tyto alba guttata
Aedes notoscriptus
Ancylostoma duodenale
Enterobius vermicularis
Necator americanus
Anopheles pseudojamesi
Bordetella
Culex pipiens complex
Bordetella pertussis
Culex coronator
Deinocerites cancer
Culex <subgenus>
Culiciomyia
Eumelanomyia
Lutzia <mosquitos>
Maillotia
Melanoconion
Aedimorphus
Stegomyia
Finlaya
Mucidus
Ochlerotatus <subgenus>
Sabethini
Culicini
Toxorhynchites rutilus
Tripteroides <genus>
triannulatus group
Enterobacteriaceae
Salmonella enterica subsp. enterica serovar Paratyphi A
Citrobacter
Culex modestus
Citrobacter freundii
Enterobacter
Candida albicans
Klebsiella aerogenes
Enterobacter cloacae
Toxostoma
Escherichia
Culex theileri
Escherichia coli
Culex nebulosus
Human rotavirus P6
Isospora
Aedes alternans
Klebsiella
Klebsiella oxytoca
Pentatrichomonas hominis
Klebsiella pneumoniae
Giardia <diplomonads>
Giardia intestinalis
Entamoeba
Entamoeba histolytica
Anopheles barbirostris subgroup clade III
Citrobacter braakii
Apicomplexa
Eimeriidae
Cryptosporidium
Cryptosporidium parvum
Plasmodium
Toxostoma rufum
albitarsis series
albitarsis group
Anopheles albitarsis
Anopheles braziliensis
Anopheles deaneorum
Anopheles marajoara
Laticorn
Arribalzagia
Myzorhynchus
Anopheles triannulatus
Avaritia
Culicoides <subgenus>
Proteus <enterobacteria>
Plasmodium falciparum
Proteus mirabilis
Nycticorax caledonicus
Plasmodium vivax
Plasmodium malariae
Aedes koreicus
Encephalitozoon intestinalis
Salmonella
Aedes mascarensis
leucosphyrus species complex
Anopheles balabacensis
barbirostris group
barbirostris subgroup
coustani group
hyrcanus group
lesteri subgroup
umbrosus group
Anopheles bancroftii
Myzomyia
funestus group
minimus group
Anopheles flavirostris
Anopheles karwari
Anopheles kochi
Anopheles longirostris
Anopheles subpictus
Anopheles tessellatus
Anopheles annularis group
Anopheles annularis
Anopheles hinesorum
Anopheles farauti No. 4
Salmonella enterica subsp. enterica
Larroussius
Paraphlebotomus
Sergentomyia <genus>
Sergentomyia minuta
Phlebotomus perfiliewi
Chryseobacterium
Apansporoblastina
Serratia
Serratia liquefaciens
Serratia marcescens
Platyhelminthes
Enterobacter asburiae
Schistosoma
Shigella
Cyclophyllidea
Taenia
Shigella boydii
Hymenolepididae
Hymenolepis diminuta
Shigella dysenteriae
Shigella flexneri
Nematoda
Anopheles funestus
Anopheles vaneedeni
Rhabditida
Shigella sonnei
Strongyloides
Strongyloides stercoralis
Ascaris
Ascaris lumbricoides
Spirurina
Yersinia <enterobacteria>
Yersinia enterocolitica
Anopheles culicifacies A
culicifacies species complex
Aeromonas
Zika virus
Aeromonas hydrophila
Ochlerotatus camptorhynchus
Biomphalaria glabrata
Coquillettidia metallica
Vibrio
Ochlerotatus flavescens
Ochlerotatus dorsalis
Orthopodomyia signifera
Arthropoda
Vibrio cholerae
Coquillettidia fuscopennata
Coquillettidia maculipennis
Mansonia africana
Oculeomyia
Culex annulioris
Vibrio parahaemolyticus
Streptococcus anginosus group
Vibrio cholerae O1 biovar El Tor
Aedes metallicus
Anopheles farauti
Alphacoronavirus
Betacoronavirus
Ixodes scapularis
Aedes w-albus
Culex bitaeniorhynchus
Plesiomonas
Plesiomonas shigelloides
Anopheles rivulorum
Culiseta inornata
Rotavirus G8
Pasteurellaceae
Nematocera
Chironomidae
Culicidae
Aedes <genus>
Balantioides coli
Aedes aegypti
Aedes albopictus
Aedes simpsoni
Ochlerotatus triseriatus
Aedes vexans
Anopheles <genus>
Anopheles gambiae
saccharomyceta
Anopheles quadrimaculatus
Anopheles albimanus
Anopheles dirus
Anopheles freeborni
Anopheles hermsi
Anopheles arabiensis
Culex <genus>
Culex pipiens
Culex quinquefasciatus
Culex tarsalis
Culex tritaeniorhynchus
Psorophora
Psorophora ferox
Simuliidae
Phlebotominae
Lutzomyia longipalpis
Rotavirus G1
Haemophilus
Anopheles sacharovi
Haemophilus haemolyticus
Haemophilus influenzae
Haemophilus parainfluenzae
Rotavirus G3
Aggregatibacter aphrophilus
Haemophilus parahaemolyticus
Ochlerotatus fitchii
Ochlerotatus implicatus
Ochlerotatus riparius
Anopheles maculatus group
Anopheles maculatus
nivipes species complex
Anopheles sinensis
Ochlerotatus incertae sedis
Ochlerotatus melanimon
Ochlerotatus nigromaculis
Ochlerotatus squamiger
Lontra canadensis
Vertebrata <vertebrates>
Orientia tsutsugamushi
Streptococcus viridans
Burkholderiales
Chlamydia
Bacteroides fragilis
Anura
Chlamydia pneumoniae
Dryophytes cinereus
Corynebacteriales
Iguania
Iguana iguana
Ochlerotatus bancroftianus
Achromobacter xylosoxidans
Wyeomyia vanduzeei
Wyeomyia mitchellii
Phlebotomus neglectus
Phlebotomus sergenti
Sergentomyia dentata
Culex neavei
Ochlerotatus annulipes
Culiseta ochroptera
Anopheles crucians
Mansonia titillans
Psorophora columbiae
Psorophora confinnis
Psorophora cyanescens
Psorophora howardii
Coereba flaveola
Culex thriambus
Aves
Burkholderia cepacia complex
Burkholderia multivorans
Alauda arvensis
Neognathae
Cygnus olor
Ardeidae
Nycticorax
Nycticorax nycticorax
Columbidae
Columba
Columba livia
Columba palumbus
Galliformes
Gallus gallus
Salmonella enterica subsp. enterica serovar Typhi
Ochlerotatus campestris
Acinetobacter calcoaceticus/baumannii complex
Bacilli
Anopheles squamosus
Culex antennatus
Passeriformes
Gymnorhina tibicen
Enterobacterales
Meliphagidae
Artiodactyla
Turdus merula
Psittaciformes
Metatheria
Didelphidae
Didelphis
Trichosurus
Eutheria
Dasypus novemcinctus
Anopheles aconitus
Anopheles varuna
minimus species complex
Giardia intestinalis assemblage A
Culex perexiguus
Phlebotomus simici
Phlebotomus alexandri
Sergentomyia fallax
Platyrrhini
Sapovirus
Burkholderia cenocepacia
Homo sapiens
Canidae
Canis lupus familiaris
Vulpes vulpes
Procyon lotor
Felidae
Felis catus
Bacteroidetes
Equus caballus
Ochlerotatus infirmatus
Suidae
Shigella dysenteriae 1
Shigella flexneri 4a
Cervidae
Odocoileus virginianus
Bovidae
Cardinalis cardinalis
Human poliovirus 2 strain Sabin
Bos taurus
Capra hircus
Ovis aries
Caprinae
Leporidae
Lepus europaeus
Oryctolagus cuniculus
Sylvilagus
Toxostoma curvirostre
Sylvilagus floridanus
Rodentia
A condition of the newborn characterized by the destruction of red blood cells initiated by the transmission of anti-A or anti-B antibodies from a mother to the child via the placenta against A or B antigens of the newborn's blood.
ABO Hemolytic Disease of the Newborn
The presence of more than one fungal and/or bacterial organism in a culture.
Mixed Flora
A measurement of the total number of induced abortions experienced by a female subject.
Number of Induced Abortions
A measurement of the total number of spontaneous abortions (in which the fetus is less than 20 weeks gestational age) experienced by a female subject.
Number of Spontaneous Abortions
The gestational age of the subject at birth.
Gestational Age at Birth
A 10-item, self-rating questionnaire designed to screen postpartum women for indications of depression.
Edinburgh Postnatal Depression Scale
A measurement of the distance between the pubic symphysis and the top of the palpable uterus.
Fundal Height
A respiratory infectious disorder that leads to an acute illness that requires medical attention.
Severe Acute Respiratory Infection
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 variation from processes or procedures defined in a protocol. Deviations usually do not preclude the overall evaluability of subject data for either efficacy or safety, and are often acknowledged and accepted in advance by the sponsor. (CDISC Glossary)
Protocol Deviation
A subtype of Staphylococcus characterized by an inability to produce free plasma coagulase.
Coagulase-Negative Staphylococcus
Beginning hour of sleep.
Hour Of Sleep
A period of three months; especially one of the three three-month periods into which human pregnancy is divided.
Trimester
A genus of single-stranded positive sense RNA viruses containing a single RNA molecule. The viral particles are not enveloped and are icosahedral in structure.
Rhinovirus
The numerical identifier of the visit.
Visit Number
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
Findings observed at the end of a pregnancy.
Pregnancy Outcome
The sounds of the fetal heart.
Fetal Heart Tone
A tightening of the involuntary smooth muscles of the uterus.
Uterine Contraction
Hemorrhage from the vagina that may range from light spotting to heavy flow during pregnancy.
Vaginal Bleeding during Pregnancy
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
adverse event
A study design that starts with an exposure and moves forward to the outcome of interest, even if the data are collected retrospectively. As an example, a group of patients who have variable exposure to a risk factor of interest can be followed over time for an outcome.
Yongqun He
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
cohort study design
A study design in which patients are randomly assigned to two or more interventions.
Yongqun He
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
randomized controlled trial design
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
summing data transformation
http://dictionary.reference.com/browse/summing
PRISM
summing data values
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
PRISM
sum value
A material entity that is bearer of a medication role.
Person: Chris Stoeckert, Jie Zheng
Penn Group
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.
Person: Jie Zheng, Chris Stoeckert
http://en.wikipedia.org/wiki/Buffy_coat
buffy coat specimen
Volume of blood collected in milliliters
A scalar measurement datum that is the output of a volume measurement assay that has a blood specimen as evaluant.
need volume measurement assay from OBI first
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
OBIB
NCI BBRB
blood specimen volume
A count that is about the aggregate of individuals who have been recruited to participate in a study.
Alice Nzinga
count of current total human study participant
A study design in which all participants or a representative subset of participants are examined at only a single time for characteristics of a interest (e.g. a specific disease).
Alice Nzinga
cross sectional study design
planned process
planned process
Injecting mice with a vaccine in order to test its efficacy
A process 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
reference substance role
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
Person:Jennifer Fostel
reference substance
OBI
reference substance role
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
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
reagent role
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
reagent
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO)
Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.
Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.
In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
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
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study.
Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study.
Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
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.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
OBI
Following OBI call November 2012,26th:
1. it was decided there was no need for moving the children class and making them siblings of study subject role.
2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study
This note closes the issue and validates the class definition to be part of the OBI core
editor = PRS
participant under investigation 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
intervention design
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Philppe Rocca-Serra
OBI branch derived
intervention design
filter paper
A device manufacture with the intent to provide a porous unsized paper used for filtering.
Frank Gibson
sep:00107
filter paper
study group role
The group of randomized participants that are assigned to a treatment arm of the trial
a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
Jennifer Fostel
study group population
study group role
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
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
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms:
http://code.google.com/p/popcomm-ontology/
PERSON: Philippe Rocca-Serra
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
population
imaging assay
An assay that produces a picture of an entity.
PlanAndPlannedProcess Branch
OBI branch derived
imaging assay
chromatin immunoprecipitation
Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method.
An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics.
Bjoern Peters, Randi Vita, James A. Overton
ChIP
OBI
chromatin immunoprecipitation
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
reference subject role
Saline treated rat; one of three identically-treated subjects
a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
Jennifer Fostel
reference participant
OBI
reference subject role
enzymatic cleavage
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
a material processing that digests the fraction of input material that is susceptible to that enzyme
PlanAndPlannedProcess Branch
OBI branch derived
enzymatic cleavage
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
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
PlanAndPlannedProcess Branch
OBI branch derived
DNA extraction
organism feature identification objective
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
Jennifer Fostel
organism feature identification objective
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
adding a material entity into a target
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
BP
branch derived
adding a material entity into a target
analyte role
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
analyte role
material to be added role
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
Role Branch
OBI
9 March 09 from discussion with PA branch
material to be added role
interpreting 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
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
light emission function
magnify function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
magnify function
contain function
A syringe, a beaker
A contain function is a function to constrain a material entities location in space
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
contain function
heat function
A heat function is a function that increases the internal kinetic energy of a material
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
heat function
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
material separation function
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
synthesizing function
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
Frank Gibson
filter function
electricity supply function
the function of supplying current during a neuroscience experiment.
An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
Daniel Schober
Frank Gibson
Melanie Courtot
power supply
electricity supply function
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
Daniel Schober
Frank Gibson
Melanie Courtot
cool function
image acquisition function
An image acquisition function is a function to acquire an image of a material
Frank Gibson
image acquisition function
solid support function
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
Daniel Schober
Frank Gibson
Melanie Courtot
solid support function
environment control function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
environment control function
primer role
a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer
primer role
PCR product
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
is double stranded DNA that is the specified output of a polymerase chain reaction
We are using PCR and not the written out words, as this is the most common used.
GROUP: OBI BIomaterial Branch
GROUP: OBI BIomaterial Branch
PCR product
nucleic acid template role
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid template role
polymerase chain reaction
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
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.
OBI Plan
PCR
adapted from wikipedai
polymerase chain reaction
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase
activity)
person:Melanie Courtot
group:OBI
reverse transcriptase
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
enzyme
(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything
that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
person: Melanie Courtot
GROUP:OBI
enzyme
polyacrylamide gel
Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
PERSON: Jie Zheng
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
polyacrylamide gel
adding material objective
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
BP
adding material objective
genotyping assay
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
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.
Philippe Rocca-Serra
SNP analysis
genotype profiling
OBI Biomaterial
genotyping assay
analyte measurement objective
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
PERSON: Bjoern Peters
PPPB branch
analyte measurement objective
agarose gel
Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
agarose gel
analyte assay
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Alan Ruttenberg
Bjoern Peters
Helen Parkinson
Philippe Rocca-Serra
Alan Ruttenberg
Bjoern Peters
Helen Parkinson
OBI Planned process branch
Philippe Rocca-Serra
analyte assay
target of material addition role
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
GROUP: Role Branch
OBI
target of material addition role
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
PERSON: Daniel Schober
PERSON: Helen Parkinson
PERSON: Melanie Courtot
PERSON:Frank Gibson
measure function
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
manufacturing
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
GROUP: OBI PlanAndPlannedProcess Branch
manufacturing
manufacturing objective
is the objective to manufacture a material of a certain function (device)
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
GROUP: OBI PlanAndPlannedProcess Branch
manufacturing 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 carries out 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
reverse transcribed polymerase chain reaction
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group.
Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW.
Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
Philippe Rocca-Serra
RT-PCR
reverse transcription polymerase chain reaction
reverse transcribed polymerase chain reaction
manufacturer role
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
GROUP: Role Branch
OBI
manufacturer role
DNA sequencing assay
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
Philippe Rocca-Serra
nucleotide sequencing
url:https://en.wikipedia.org/wiki/DNA_sequencing
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
urine specimen
a portion of urine collected from an organism
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
are we happy calling collection of urine a material separation?
urine specimen
material combination
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
bp
bp
material combination
blood specimen
blood drawn from a human for glucose assay
a material entity derived from a portion of blood collected from an organism
Bjoern Peters
Bjoern Peters
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
specimen collection process
enzyme-linked immunosorbent assay
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
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.
IEDB
ELISA
IEDB
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
center value
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
PERSON: James Malone
PERSON: Monnie McGee
median
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
whole organism preparation
putting a mouse in the blender. Not: putting a mouse on a scale
A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
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
immunoprecipitation
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
Philippe Rocca-Serra
OBI plan and planned process branch
immunoprecipitation
host role
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
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
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
GROUP: Role Branch
30 Mar09 submitted by vaccine community
OBI
http://en.wikipedia.org/wiki/Host_(biology)
host role
restriction enzyme
The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
an enzyme that has a specific target cleavage sites within nucleic acids
Kevin Clancy, Bjoern Peters
5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
restriction enzyme
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
independent variable specification
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
experimental factor
independent variable
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
study factor
study design independent variable
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
amplified DNA
Amplied DNA created by PCR
DNA that has been produced in an enzymatic amplification process
PERSON: Alan Ruttenberg
Alan Ruttenberg
amplified DNA
informed consent process
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.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
Person:Alan Ruttenberg
http://clinicaltrials.gov/ct2/info/glossary#informed
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
informed consent process
primary structure of DNA macromolecule
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
placeholder for SO
BP et al
primary structure of DNA macromolecule
measurement device
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
GROUP:OBI Philly workshop
OBI
measurement device
manufacturer
A person or organization that has a manufacturer role
manufacturer
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
record of missing knowledge
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
a information content entity created to indicate that information about something is not available to the person recording it.
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
Bjoern Peters
record of missing knowledge
complementary nucleotide probe role
A primer in a PCR reaction. A probe on an Affymetrix chip.
A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
PERSON:Bjoern Peters
complementary nucleotide probe role
record of unknown sex
A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
a record indicating that the biological sex of an organism is not known.
I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement.
Bjoern Peters
record of unknown sex
96-well neutralization assay
A serum neutralization of viral infectivity assay which is performed in a 96-well plate.
Bjoern Peters
Melanie Courtot
microneutralization assay
96-well neutralization assay
serum neutralization of viral infectivity assay
An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
Bjoern Peters
Melanie Courtot
influenza neutralization assay
url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/
serum neutralization of viral infectivity assay
RNA extract
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
Group: UPenn Group
RNA extract
real time polymerase chain reaction assay
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.
Bjoern Peters
Melanie Courtot
Q-PCR
kinetic polymerase chain reaction
qPCR
quantitative real time polymerase chain reaction
url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
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
real time reverse-transcription polymerase chain reaction assay
An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay.
Bjoern Peters
Melanie Courtot
RRT-PCR
RT-rt PCR
qRT-PCR
real time reverse-transcription polymerase chain reaction assay
cytometric bead array assay
Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture.
An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest.
IEDB
Luminex assay
IEDB
cytometric bead array assay
infectious agent
is a material entity bearing the disposition to infect an organism
IEDB
IEDB
infectious agent
study intervention
the part of the execution of an intervention design study which is varied between two or more subjects in the study
PERSON: Bjoern Peters
GROUP: OBI
study intervention
material separation device
flow cytometer
A device with a separation function realized in a planed process
material separation device
categorical measurement datum
A measurement datum that is reported on a categorical scale
Bjoern Peters
nominal mesurement datum
Bjoern Peters
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
compound treatment design
an intervention design in which the treatment is the administration of a compound
This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
PERSON: Bjoern Peters
MO_555 compound_treatment_design
compound treatment design
processed specimen
A tissue sample that has been sliced and stained for a histology study.
A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
Bjoern Peters
Bjoern Peters
A tissue sample that has been sliced and stained for a histology study.
processed specimen
container
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
PERSON: Bjoern Peters
container
device
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform.
2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:
(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.
(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.
(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.
In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
PERSON: Helen Parkinson
instrument
OBI development call 2012-12-17.
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
administration of material to specimen
Staining cells in a tissue slice with a dye.
The directed combination of a material entity with a specimen.
Bjoern Peters
Bjoern Peters
administration of material to specimen
image acquisition
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
A planned process that captures an image of an object.
PERSON: Jie Zheng
image acquisition
image creation
nucleic acid extract
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
PERSON: Jie Zheng
UPenn Group
nucleic acid extract
DNA extract
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
Person: Jie Zheng
Group: UPenn group
DNA extract
electrophoresis system
A device that moves charged particles through a medium by using an electric field induced by electrodes.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Category:Electrophoresis
electrophoresis system
nucleic acid sequencer
An device that is used to determine the order of nucleotides in nucleic acid sequences.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
nucleic acid sequencer
gel electrophoresis system
An electrophoresis system in which an electric field is applied to a gel matrix
PERSON: Erik Segerdell
https://en.wikipedia.org/wiki/Gel_electrophoresis
gel electrophoresis system
protein sequencer
An device that is used to determine the order of amino acids in protein sequences.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
protein sequencer
individual organism identifier
a CRID symbol used to distinguish one individual organism from another.
PERSON: Chris Stoeckert, Jie Zheng
MO_169 Individual
individual organism identifier
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.
age measurement datum
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
PERSON:Chris Stoeckert, Jie Zheng
MO_710 birth
age since birth measurement datum
reverse transcription polymerase chain reaction assay
An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
Chris Stoeckert
Jie Zheng
Penn Group
reverse transcription polymerase chain reaction assay
half life datum (t 1/2)
The time it takes for 50% of a class of stochastic processes to occur.
Bjoern Peters
t 1/2
Bjoern Peters
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
selective organism creation objective
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.
PERSON: Chris Stoeckert, Jie Zheng
WEB: wikipedia
http://en.wikipedia.org/wiki/Cultivar
http://en.wikipedia.org/wiki/Ecotype
http://en.wikipedia.org/wiki/Strain_%28biology%29
selective organism creation objective
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
cultivar
ecotype
strain
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
selectively maintained organism
SNP microarray
A DNA microarray used to detect polymorphisms in DNA samples
Person: Helen Parkinson
EFO_0002703 SNP array
SNP microarray
ChIP-chip by SNP array assay
A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin
ArrayExpress production team
EFO:0002764
ChIP-chip by SNP array assay
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
Group: OBI group
genetic population background information
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
epigenetic modification identification objective
genotyping by high throughput sequencing assay
A genotyping assay that uses a high througput sequencer
James Malone
EFO:0002771
genotyping by high throughput sequencing assay
genotyping by array assay
A genotyping assay that uses an array
ArrayExpress production team
EFO:0002767
genotyping by array assay
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
Group: OBI group
Group: OBI group
genotype information
species comparison design
A study design that assays differences between distinct species.
Person: Chris Stoeckert, Jie Zheng
MO_675 species_design
species comparison design
allele information
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
discussed on San Diego OBI workshop, March 2011
Person: Chris Stoeckert, Jie Zheng
MO_58 Allele
allele information
wild type allele information
an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
discussed on San Diego OBI workshop, March 2011
Person: Chris Stoeckert, Jie Zheng
MO_605 genotype
wild type allele information
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
Person: Chris Stoeckert, Jie Zheng
MO_933 binding_site_identification_design
protein and DNA interaction identification objective
genetic characteristics information
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
Person: Chris Stoeckert, Jie Zheng
MO_66 IndividualGeneticCharacteristics
MO definition:
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
examples in ArrayExpress
wild_type
MutaMouse (CD2F1 mice with lambda-gt10LacZ integration)
AlfpCre; SNF5 flox/knockout
p53 knock out
C57Bl/6 gp130lox/lox MLC2vCRE/+
fer-15; fem-1
df/df
pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
genetic characteristics information
genotyping design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
Person: Chris Stoeckert, Jie Zheng
MO_560 genotyping_design
genotyping design
strain comparison design
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Person: Chris Stoeckert, Jie Zheng
MO_462 strain_or_line_design
strain comparison design
cell specimen
A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
MO_612 cell
cell specimen
specimen from organism
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
tissue specimen
MO_954 organism_part
specimen from organism
linear amplification
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
PERSON: Chris Stoeckert, Jie Zheng
MO_997 linear_amplification
linear amplification
fluorescence detection assay
Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
An assay in which a material's fluorescence is determined.
IEDB
IEDB
fluorescence detection assay
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
Person: Chris Stoeckert
time point
MO_738 timepoint
sampling time measurement datum
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 Algorithm
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
rate measurement datum
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
A scalar measurement datum that represents the number of events occuring over a time interval
PERSON: Bjoern Peters, Randi Vita
IEDB
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
DNA sequence data
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
OBI call; Bjoern Peters
OBI call; Melanie Courtout
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
DNA sequence data
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
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
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
NIAID GSCID-BRC
specimen identifier
1
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.
Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/
Person: Chris Stoeckert, Jie Zheng
PMID
PubMed Identifier
Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
Publication Citation
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
Depth of Coverage - Average
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
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
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
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
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.
Chris Stoeckert
Jie Zheng
NIAID GSCID-BRC metadata working group
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
Annotation Algorithm
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
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
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
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
grant ID
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
assay array
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
Penn Group
assay array
cell culture
A material entity comprised of cultured cells and the media in which they are being propagated or stored.
PERSON:Matthew Brush
OBI-CLO Alignment Working Group (Spring 2013)
A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
categorical value specification
A value specification that is specifies one category out of a fixed number of nominal categories
PERSON:Bjoern Peters
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
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
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
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
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
taxonomic diversity assessment by targeted gene survey
PMID:20679230
PMID:25367129
An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity.
Philippe Rocca-Serra
environmental gene survey
targeted gene survey
targeted gene survey DNA barcoding
OBI
taxonomic diversity assessment by targeted gene survey
biodiversity assessment objective
biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level
PERSON:Philippe Rocca-Serra
PRS for OBI
biodiversity assessment objective
microarray assay
Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray.
An analyte assay where binding of the analyte to immobilized matrix is measured.
IEDB
IEDB
microarray assay
Illumina HiSeq 2000
Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380
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.
PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng
HiSeq 2000
http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
Illumina HiSeq 2000
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
OBIB, OBI
Biobank
collection of specimens
physical store
a freezer. a humidity controlled box.
A container with an environmental control function.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
Chris Stoeckert
Duke Biobank, OBIB
physical store
microscopy assay
Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy.
An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
ImmPort
PMID:21685355
microscopy assay
temperature value specification
A value specification that specifies the temperature of some thing.
Chris Stoeckert
OBI
temperature value specification
temperature measurement assay
An assay to determine the temperature of an evaluant.
Bjoern Peters
Chris Stoeckert
OBI
temperature measurement assay
venereal disease research laboratory test
An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood.
Bjoern Peters
Chris Stoeckert
James Overton
Randi Vita
VDRL test
OBI
https://github.com/obi-ontology/obi/issues/825
NCI BBRB
venereal disease research laboratory test
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
Person: Alan Ruttenberg, Jie Zheng
https://en.wiktionary.org/wiki/measurand
https://github.com/obi-ontology/obi/issues/778
measurand role
defined population inclusion criterion
inclusion based on age, sex, and living region (rural area or specified city).
An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
Chris Stoeckert, Mathias Brochhausen
MIABIS 2.0
920
MIABIS 2.0
defined population inclusion criterion
differential medium assay
an organism identification assay that uses a differential medium to achieve its objective
John Judkins
bacteriological assay
EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm
differential medium assay
medication time value specification
A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material
John Judkins
medication timepoint
OBI
VEuPathDB
medication time value specification
medication dose value specification
A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment
John Judkins
medication dose
OBI
VEuPathDB
medication dose value specification
case role in case-control study
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.
John Judkins, Bjoern Peters
OBI
case role in case-control study
control 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.
John Judkins, Bjoern Peters
OBI
control role in case-control study
cerebrospinal fluid specimen
A specimen that is derived from cerbrospinal fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
cerebrospinal fluid specimen
feces specimen
A specimen that is derived from feces.
Chris Stoeckert
stool specimen
Chris Stoeckert, Penn Medicine Biobank
feces specimen
digestive system fluid or secretion specimen
A specimen that is derived from digestive system fluid or secretion.
Chris Stoeckert
gastric fluid specimen
Chris Stoeckert, Penn Medicine Biobank
digestive system fluid or secretion specimen
milk specimen
A specimen that is derived from milk.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
milk specimen
saliva specimen
A specimen that is derived from saliva.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
saliva specimen
sputum specimen
A specimen that is derived from sputum.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
sputum specimen
bone marrow specimen
A specimen that is derived from bone marrow.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
bone marrow specimen
pleural fluid specimen
A specimen that is derived from pleural fluid.
Chris Stoeckert
Chris Stoeckert, Penn Medicine Biobank
pleural fluid specimen
lung specimen
A specimen that is derived from lung.
Chris Stoeckert
Chris Stoeckert, NCI BBRB
lung specimen
swab specimen
A specimen that is stored on a swab as the output of a collecting specimen with swab process.
Chris Stoeckert
OBIB/OBI
https://github.com/obi-ontology/obi/issues/910
OBIB
swab specimen
collecting specimen with swab
A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
Chris Stoeckert
OBIB
https://github.com/obi-ontology/obi/issues/910
OBIB
collecting specimen with swab
nasopharyngeal swab specimen
A specimen that is collected with a swab from the surface of a nasopharynx.
Chris Stoeckert
Chris Stoeckert, OBIB
nasopharyngeal swab specimen
oropharyngeal swab specimen
A specimen that is collected with a swab from the surface of a oropharynx.
Chris Stoeckert
Chris Stoeckert, OBIB
oropharyngeal swab specimen
whole metagenome sequencing assay
A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.
Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.).
Rebecca Jackson
WMS
Bjoern Peters
Michelle Giglio
https://github.com/obi-ontology/obi/issues/1056
whole metagenome sequencing assay
case-control study design
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.
John Judkins, Bjoern Peters
Wikipedia, OBI
case-control study design
Giemsa stain assay
Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs
An assay that uses a Giemsa stain to characterize cells.
Chris Stoeckert
Jie Zheng
https://github.com/obi-ontology/obi/issues/1093
VEuPathDB
Giemsa stain assay
1
individual organism specimen
A specimen composed of an individual organism to be studied in an investigation.
Person: Jie Zheng
EFO_0000542 individual
https://github.com/obi-ontology/obi/issues/1092
individual organism specimen
blood microbiology assay
An organism identification assay that identifies a microorganism in a blood specimen.
John Judkins
https://github.com/obi-ontology/obi/issues/1064
blood microbiology assay
case series study design
PMID: 22213493
A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included.
http://orcid.org/0000-0002-8844-9165
https://www.ncbi.nlm.nih.gov/pubmed/22213493
case series design
glass bottle
A container with a narrow neck that is made of glass.
VEuPathDB
VEuPathDB
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
glass bottle
glass bottle coated with insecticides
A glass bottle that coated with material designed to control insects.
VEuPathDB
VEuPathDB
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
glass bottle coated with insecticides
nested polymerase chain reaction
A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction.
Jie Zheng
nested-PCR
nested PCR
https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
nested polymerase chain reaction
counter current immunoelectrophoresis
An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions.
Jie Zheng
http://www.ispybio.com/search/protocols/ie%20protocol2.pdf
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
counter current immunoelectrophoresis
ligase detection reaction
A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product.
Jie Zheng
LDR
MIRO:20000103
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
ligase detection reaction
loop-mediated isothermal amplification
An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR.
Jie Zheng
LAMP
https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
loop-mediated isothermal amplification
detection of pathogenic organisms objective
An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms.
Jie Zheng
VEuPathDB
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
detection of pathogenic organisms objective
insecticide resistance detection objective
An organism feature identification objective that aims to detect insecticide resistance of an insect.
Jie Zheng
VEuPathDB
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance detection objective
arthropod meal of blood specimen
A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito.
A specimen of the blood ingested by an arthropod.
The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human.
Chris Stoeckert
Jie Zheng
blood meal
VEuPathDB
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
arthropod meal of blood specimen
polymerase chain reaction assay
An assay that uses polymerase chain reaction technique to amplify DNA.
VEuPathDB
VEuPathDB
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
polymerase chain reaction assay
restriction fragment length polymorphism assay
An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences.
VEuPathDB
RFLP
restriction fragment length polymorphism
restriction fragment length polymorphism analysis
https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
restriction fragment length polymorphism assay
DNA fingerprinting assay
An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA.
VEuPathDB
DNA finger printing
DNA fingerprint
DNA fingerprinting
DNA profiling
VEuPathDB
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
DNA fingerprinting assay
insecticide resistance assay
An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population.
VEuPathDB
resistance identification/monitoring
MIRO:20000001
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance assay
insecticide resistance by monitoring known mutations assay
An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes.
VEuPathDB
monitoring known mutations
MIRO:20000096
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by monitoring known mutations assay
insecticide resistance by detecting enzyme activity assay
An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes.
VEuPathDB
metabolic resistance assay
MIRO:20000003
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by detecting enzyme activity assay
insecticide resistance bioassay
An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism.
VEuPathDB
bioassay
MIRO:20000058
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance bioassay
insecticide resistance by detecting alpha esterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase.
VEuPathDB
alpha esterase activity assay
IRO:0000149
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by detecting alpha esterase activity assay
insecticide resistance by detecting beta esterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase.
VEuPathDB
beta esterase activity assay
IRO:0000150
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by detecting beta esterase activity assay
insecticide resistance by detecting acetylcholinesterase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase.
VEuPathDB
AChE activity assay
AChE assay
acetylcholinesterase assay
MIRO:20000010
MIRO:20000084
MIRO:20000086
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by detecting acetylcholinesterase activity assay
insecticide resistance by detecting glutathione S-transferase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST).
VEuPathDB
GST related assay
MIRO:20000083
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by detecting glutathione S-transferase activity assay
insecticide resistance by detecting carboxylic ester hydrolase activity assay
An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate.
VEuPathDB
pNPA assay
MIRO:20000019
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by detecting carboxylic ester hydrolase activity assay
insecticide resistance by detecting mixed-function oxidase assay
An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present.
VEuPathDB
mixed-function oxidase assay
MIRO:20000062
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by detecting mixed-function oxidase assay
direct insecticide resistance bioassay
An insecticide resistance bioassay without the use of any synergist.
VEuPathDB
direct bioassay
MIRO:20000044
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
direct insecticide resistance bioassay
topical application insecticide resistance bioassay
An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect.
VEuPathDB
topical application assay
IRO:0000155
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
topical application insecticide resistance bioassay
direct insecticide resistance diagnostic assay
A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population.
VEuPathDB
diagnostic test
MIRO:20000075
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
direct insecticide resistance diagnostic assay
insecticide resistance dose response assay
A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance.
VEuPathDB
dose response test
MIRO:20000076
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance dose response assay
insecticide resistance time response assay
A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide.
VEuPathDB
time response test
MIRO:20000013
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance time response assay
Centre for Disease Control and Prevention bottle bioassay
A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations.
VEuPathDB
CDC bottle bioassay
MIRO:20000009
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
Centre for Disease Control and Prevention bottle bioassay
WHO cone kit diagnostic assay
A direct insecticide resistance diagnostic assay uses WHO cone kit.
VEuPathDB
cone DT
MIRO:20000039
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
WHO cone kit diagnostic assay
WHO paper kit diagnostic assay
A direct insecticide resistance diagnostic assay uses WHO paper kit.
VEuPathDB
WHO paper kit DT
MIRO:20000041
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
WHO paper kit diagnostic assay
WHO larvicide diagnostic assay
A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide.
VEuPathDB
WHO larvicide DT
MIRO:20000049
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
WHO larvicide diagnostic assay
insecticide resistance dose response by bottle assay
An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides.
VEuPathDB
bottle bioassay DR test
MIRO:20000011
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance dose response by bottle assay
insecticide resistance dose response by survival of larvae assay
An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide.
VEuPathDB
WHO larvicide DR test
MIRO:20000050
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance dose response by survival of larvae assay
insecticide resistance dose response by WHO paper kit assay
An insecticide resistance dose response assay using WHO paper kit.
VEuPathDB
WHO paper kit DR test
MIRO:20000048
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance dose response by WHO paper kit assay
insecticide resistance time response by bottle assay
An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist.
VEuPathDB
bottle bioassay TR test
MIRO:20000030
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance time response by bottle assay
insecticide resistance time response by WHO paper kit assay
An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist.
VEuPathDB
WHO paper kit TR test
MIRO:20000036
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance time response by WHO paper kit assay
insecticide resistance by amplification refractory mutation system assay
An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations.
VEuPathDB
ARMS
Amplification Refractory Mutation System
IRO:0000006
PMID: 18428319
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by amplification refractory mutation system assay
insecticide resistance by primer introduced restriction analysis PCR assay
An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes.
VEuPathDB
PIRA-PCR
Primer Introduced Restriction Analysis PCR
polymerase chain reaction-primer-introduced restriction analysis
IRO:0000007
PMID: 8339229
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by primer introduced restriction analysis PCR assay
insecticide resistance by nested polymerase chain reaction assay
An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique.
VEuPathDB
gene mutation detection by nested PCR
IRO:0000127
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by nested polymerase chain reaction assay
insecticide resistance by ligase detection reaction assay
An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix.
VEuPathDB
MIRO:20000103
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by ligase detection reaction assay
insecticide resistance by ligase detection reaction-fluorescent microsphere assay
An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction.
VEuPathDB
gene mutation detection by LDR-FMA
ligase detection reaction-fluorescent microsphere assay
IRO:0000151
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by ligase detection reaction-fluorescent microsphere assay
insecticide resistance by PCR amplification of specific alleles assay
An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles.
VEuPathDB
PASA
PCR amplification of specific alleles
allele-specific amplification and amplification refractory mutation system
PMID: 1734929
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by PCR amplification of specific alleles assay
insecticide resistance by fluorogenic PCR assay
An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation.
VEuPathDB
MIRO:20000102
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by fluorogenic PCR assay
insecticide resistance by PCR-RELP assay
An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay.
VEuPathDB
PCR-RFLP
MIRO:20000113
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by PCR-RELP assay
insecticide resistance by short interspersed elements PCR assay
An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs).
VEuPathDB
Short Interspersed Elements PCR
IRO:0000013
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
insecticide resistance by short interspersed elements PCR assay
pathogen detection assay
An organism identification assay that aims to detect pathogens.
VEuPathDB
pathogen detection method
IRO:0000137
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
pathogen detection assay
VectorTest assay
A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip.
VEuPathDB
VectorTest
IRO:0000138
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
VectorTest assay
pathogen detection by Rapid Analyte Measurement Platform assay
A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances.
VEuPathDB
Rapid Analyte Measurement Platform
IRO:0000164
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
pathogen detection by Rapid Analyte Measurement Platform assay
pathogen detection by loop-mediated isothermal amplification assay
A pathogen detection assay that is based on loop-mediated isothermal amplification.
VEuPathDB
Loop-mediated isothermal amplification
IRO:0000165
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
pathogen detection by loop-mediated isothermal amplification assay
blood meal assay
An assay that analyzes the specimen taken from blood meal fed organism, such as insect.
VEuPathDB
blood meal analysis
IRO:0000135
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
blood meal assay
blood meal by counter current immunoelectrophoresis assay
A blood meal assay that uses a counter current immunoelectrophoresis technique.
VEuPathDB
CIE
countercurrent immunoelectrophoresis
IRO:0000136
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
blood meal by counter current immunoelectrophoresis assay
DNA based blood meal finger printing assay
A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect.
VEuPathDB
DNA based blood meal finger printing
VEuPathDB
VSMO:0001307
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
DNA based blood meal finger printing assay
organism identification by size assay
An organism identification assay that is based on the size of organism.
VEuPathDB
by size
IRO:0000145
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by size assay
organism identification by cross mating assay
An organism identification assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced.
VEuPathDB
cross mating experiment
MIRO:30000036
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by cross mating assay
organism identification by cytological chromosome examination assay
An organism identification assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species.
VEuPathDB
cytological chromosome examination
MIRO:30000037
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by cytological chromosome examination assay
organism identification by isoenzyme electrophoresis assay
An organism identification assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species.
VEuPathDB
isoenzyme electrophoresis
MIRO:30000038
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by isoenzyme electrophoresis assay
organism identification by morphological examination assay
An organism identification assay that is based on examination of morphology and the use of specific "taxonomic keys" to determine the species of the specimen.
VEuPathDB
morphological examination
MIRO:30000039
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by morphological examination assay
organism identification by PCR assay
An organism identification assay that is based on PCR.
VEuPathDB
PCR-based species identification
MIRO:30000040
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by PCR assay
organism identification by specific DNA hybridization assay
An organism identification assay that is based on DNA hybrdization.
VEuPathDB
species specific DNA hybridization
MIRO:30000041
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by specific DNA hybridization assay
organism identification by salinity tolerance assay
An organism identification assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species.
VEuPathDB
salinity tolerance tests
MIRO:30000042
https://github.com/obi-ontology/obi/issues/1117
VEuPathDB
organism identification by salinity tolerance assay
induced sputum specimen
A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
John Judkins
PMC3297553
induced sputum specimen
passage process
A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number.
John Judkins
https://en.wikipedia.org/wiki/Serial_passage
https://www.merriam-webster.com/dictionary/passage
passage process
passage history record
A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process.
John Judkins
https://en.wikipedia.org/wiki/Serial_passage
https://www.merriam-webster.com/dictionary/passage
passage history record
16s ribosomal gene sequencing assay
An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.
Michelle Giglio
Rebecca Jackson
Suvarna Nadendla
16S rRNA sequencing assay
PMID:31450270
CFDE
16s ribosomal gene sequencing assay
amplicon sequencing assay
A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.
Michelle Giglio
Rebecca Jackson
Suvarna Nadendla
PMID:29628929
PMID:31450270
CFDE
amplicon sequencing assay
karyotype information
A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell.
Jie Zheng
EFO_0004426 karyotype
https://github.com/obi-ontology/obi/issues/1097
VEuPathDB
karyotype information
partial karyotype information
A karyotype information that is about the structural variation of partial genome rather than whole genome.
Jie Zheng
VEuPathDB
https://github.com/obi-ontology/obi/issues/1097
VEuPathDB
partial karyotype information
full karyotype information
A karyotype information that is about the structural variation of the whole genome.
Jie Zheng
OBI group
https://github.com/obi-ontology/obi/issues/1097
full karyotype information
tracheal aspirate specimen
A specimen that is collected with a suctioning tube from the trachea.
Asiyah Yu Lin ORCID:0000-0003-2620-0345
tracheal wash specimen
PMID:25338241
tracheal aspirate specimen
mid-turbinate nasal swab specimen
A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity.
Asiyah Yu Lin ORCID:0000-0003-2620-0345
https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633
mid-turbinate nasal swab specimen
nasal aspirate specimen
A specimen that is collected with a suctioning tube from the nasal cavity.
Asiyah Yu Lin ORCID:0000-0003-2620-0345
nasal wash specimen|nasopharyngeal aspirate
Asiyah Yu Lin ORCID:0000-0003-2620-0345
nasal aspirate specimen
lower respiratory tract aspirate specimen
A specimen that is collected with a suctioning tube from the lower respiratory tract.
Asiyah Yu Lin ORCID:0000-0003-2620-0345
lower respiratory tract wash specimen
Asiyah Yu Lin ORCID:0000-0003-2620-0345
lower respiratory tract aspirate specimen
upper respiratory specimen
A specimen that is derived from the upper respiratory tract
Asiyah Yu Lin ORCID:0000-0003-2620-0345
Asiyah Yu Lin ORCID:0000-0003-2620-0345
upper respiratory specimen
lower respiratory tract specimen
A specimen that is derived from the lower respiratory tract.
Asiyah Yu Lin ORCID:0000-0003-2620-0345
Asiyah Yu Lin ORCID:0000-0003-2620-0345
lower respiratory tract specimen
anterior nasal swab specimen
A specimen that is derived from the anterior nasal wall
Asiyah Yu Lin ORCID:0000-0003-2620-0345
Asiyah Yu Lin ORCID:0000-0003-2620-0345
anterior nasal swab specimen
aspiration specimen collection
Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue.
Asiyah Yu Lin|ORCID:0000-0003-2620-0345
aspiration procedure
https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15631
aspiration specimen collection
surveillance process
An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity.
Chris Stoeckert
Shane Babcock, OBI
https://github.com/obi-ontology/obi/issues/1181
IDO, VEuPathDB
surveillance process
cluster study group role
A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound.
A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
Chris Stoeckert, Brianna Lindsay
cluster study arm
ClinEpiDB
cluster study group role
compound study group role
A compound study group consisting of geographically proximate households that share a common water source.
A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
Chris Stoeckert, Brianna Lindsay
compound study arm
ClinEpiDB
compound study group role
ultraviolet light source
A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system.
Person: Jie Zheng
UV light source
Person: Jie Zheng
https://github.com/obi-ontology/obi/issues/1200
VEuPathDB
ultraviolet light source
visible light source
A light source that provides visible light for use in a distant area using a delivery system.
Person: Jie Zheng
Person: Jie Zheng
https://github.com/obi-ontology/obi/issues/1200
VEuPathDB
visible light source
solar light source
A light source that light is produced from solar energy.
Person: Chris Stoeckert
Person: Jie Zheng
Person: Chris Stoeckert
Person: Jie Zheng
https://github.com/obi-ontology/obi/issues/1200
VEuPathDB
solar light source
adult arthropod specimen collection process
A live arthropod specimen collection process in which the arthropods are in the adult stage.
John Judkins
collection of adults
MIRO:30000052
https://github.com/obi-ontology/obi/issues/1217
adult arthropod specimen collection process
animal-biting arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal.
John Judkins
animal biting catch
MIRO:30000012
https://github.com/obi-ontology/obi/issues/1217
animal-biting arthropod specimen collection by aspiration
animal-biting outdoor arthropod specimen collection by aspiration
An animal-biting arthropod specimen collection by aspiration that occurs outside a building.
John Judkins
animal biting catch - outdoors
MIRO:30000014
https://github.com/obi-ontology/obi/issues/1217
animal-biting outdoor arthropod specimen collection by aspiration
aquatic arthropod specimen collection process
An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment.
John Judkins
aquatic environment catch
MIRO:30000048
https://github.com/obi-ontology/obi/issues/1217
aquatic arthropod specimen collection process
arthropod resting in animal house specimen collection by aspiration
An arthropod specimen collection by aspiration that catches specimens resting inside an animal house.
John Judkins
animal shed resting catch
MIRO:30000027
https://github.com/obi-ontology/obi/issues/1217
arthropod resting in animal house specimen collection by aspiration
arthropod resting outdoors on artificial support specimen collection by aspiration
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture.
John Judkins
outdoors shelter catch - artificial
MIRO:30000026
https://github.com/obi-ontology/obi/issues/1217
arthropod resting outdoors on artificial support specimen collection by aspiration
arthropod resting outdoors on natural support specimen collection by aspiration
An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant.
John Judkins
outdoors shelter catch - natural
MIRO:30000025
https://github.com/obi-ontology/obi/issues/1217
arthropod resting outdoors on natural support specimen collection by aspiration
arthropod resting outdoors specimen collection by aspiration
An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity.
John Judkins
outdoors shelter catch
MIRO:30000024
https://github.com/obi-ontology/obi/issues/1217
arthropod resting outdoors specimen collection by aspiration
arthropod specimen collection by aspiration
A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container.
John Judkins
catch by aspiration
MIRO:30000043
https://github.com/obi-ontology/obi/issues/1217
arthropod specimen collection by aspiration
arthropod specimen collection process
A specimen collection process that has the objective of collecting arthropods as specimens.
John Judkins
collection of arthropods
field population catch
MIRO:30000044
https://github.com/obi-ontology/obi/issues/1217
arthropod specimen collection process
human-biting arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human.
John Judkins
man biting catch
MIRO:30000017
https://github.com/obi-ontology/obi/issues/1217
human-biting arthropod specimen collection by aspiration
human-biting indoor arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building.
John Judkins
man biting catch - indoors
MIRO:30000019
https://github.com/obi-ontology/obi/issues/1217
human-biting indoor arthropod specimen collection by aspiration
human-biting outdoor arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building.
John Judkins
man biting catch - outdoors
MIRO:30000018
https://github.com/obi-ontology/obi/issues/1217
human-biting outdoor arthropod specimen collection by aspiration
knockdown arthropod specimen collection by pyrethrum spray
A knockdown arthropod specimen collection process in which the pesticide is pyrethrum.
John Judkins
pyrethrum spray catch
MIRO:30000023
https://github.com/obi-ontology/obi/issues/1217
knockdown arthropod specimen collection by pyrethrum spray
knockdown arthropod specimen collection process
An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized.
John Judkins
knockdown collection
IRO:0000014
https://github.com/obi-ontology/obi/issues/1217
knockdown arthropod specimen collection process
live arthropod specimen collection process
An arthropod specimen collection process meant to collect live specimens.
John Judkins
catch of live specimens
MIRO:30000044
VSMO:0001445
https://github.com/obi-ontology/obi/issues/1217
live arthropod specimen collection process
arthropod trap
A device designed to catch arthropods.
John Judkins
MIRO:30000011
https://github.com/obi-ontology/obi/issues/1217
arthropod trap
artificial pit shelter
An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected.
John Judkins
IRO:0000005
https://github.com/obi-ontology/obi/issues/1217
artificial pit shelter
baited net trap
An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal.
John Judkins
https://github.com/obi-ontology/obi/issues/1217
baited net trap
barrier trap
An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container.
John Judkins
IRO:0000017
https://github.com/obi-ontology/obi/issues/1217
barrier trap
BG-Counter
A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods.
John Judkins
IRO:0000143
https://github.com/obi-ontology/obi/issues/1217
BG-Counter
BG-Sentinel trap
An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current.
John Judkins
IRO:0000028
VSMO:0001906
https://github.com/obi-ontology/obi/issues/1217
BG-Sentinel trap
Centers for Disease Control and Prevention light trap
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant.
This trap is also designed to be lightweight and operate in environments in which electricity may be scarce.
John Judkins
CDC light trap
IRO:0000163
https://github.com/obi-ontology/obi/issues/1217
Centers for Disease Control and Prevention light trap
dipper for arthropod immatures
A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan.
John Judkins
dipper for immatures
VSMO:0001479
https://github.com/obi-ontology/obi/issues/1217
dipper for arthropod immatures
encephalitis virus surveillance trap
A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods.
John Judkins
EVS trap
IRO:0000029
VSMO:0001295
https://github.com/obi-ontology/obi/issues/1217
encephalitis virus surveillance trap
gravid trap
An arthropod trap that is designed to collect gravid female arthropods or their eggs.
John Judkins
IRO:0000030
https://github.com/obi-ontology/obi/issues/1217
gravid trap
light trap
An arthropod trap that uses light as an attractant.
John Judkins
MIRO:30000065
https://github.com/obi-ontology/obi/issues/1217
light trap
light trap for indoor use
A light trap designed to be placed inside a building.
John Judkins
indoor light trap
MIRO:30000009
https://github.com/obi-ontology/obi/issues/1217
light trap for indoor use
light trap for outdoor use
A light trap designed to be placed outside a building.
John Judkins
outdoor light trap
MIRO:30000010
https://github.com/obi-ontology/obi/issues/1217
light trap for outdoor use
Mosquito Magnet trap
An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods.
John Judkins
IRO:0000022
https://github.com/obi-ontology/obi/issues/1217
Mosquito Magnet trap
MosquiTRAP
A gravid trap consisting of an arthropod attractant and adhesive surface.
John Judkins
IRO:0000140
https://github.com/obi-ontology/obi/issues/1217
MosquiTRAP
New Jersey light trap
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant.
John Judkins
New Jersey trap
IRO:0000031
https://github.com/obi-ontology/obi/issues/1217
New Jersey light trap
Onderstepoort Veterinary Institute light-suction trap
A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter.
John Judkins
OVI light-suction trap
IRO:0000154
Parasites Vectors 8, 239 (2015)
https://github.com/obi-ontology/obi/issues/1217
Onderstepoort Veterinary Institute light-suction trap
outlet window trap
An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building.
John Judkins
outlet window trap
MIRO:30000020
https://github.com/obi-ontology/obi/issues/1217
outlet window trap
ovitrap
An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females.
John Judkins
oviposition trap
MIRO:30000016
VSMO:0001501
https://github.com/obi-ontology/obi/issues/1217
ovitrap
resting arthropod trap
An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity.
John Judkins
https://github.com/obi-ontology/obi/issues/1217
resting arthropod trap
resting box trap
An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity.
John Judkins
resting box catch
IRO:0000021
https://github.com/obi-ontology/obi/issues/1217
resting box trap
resting bucket
An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host).
John Judkins
resting bucket catch
IRO:0000141
https://github.com/obi-ontology/obi/issues/1217
resting bucket
Shannon trap
An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap.
John Judkins
shannon trap catch
IRO:0000191
https://github.com/obi-ontology/obi/issues/1217
Shannon trap
sticky resting bucket
An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected.
John Judkins
sticky resting bucket catch
IRO:0000142
https://github.com/obi-ontology/obi/issues/1217
sticky resting bucket
sticky trap
An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive.
John Judkins
sticky trap catch
IRO:0000128
https://github.com/obi-ontology/obi/issues/1217
sticky trap
population based design
A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
Chris Stoeckert
https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design
#1090
population based design
endotracheal tube specimen
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea.
John Judkins ORCID:0000-0001-6595-0902
https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3
endotracheal tube specimen
endotracheal aspirate specimen
A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube.
John Judkins ORCID:0000-0001-6595-0902
https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3
endotracheal aspirate specimen
altitude measurement datum
A length measurement datum between a point at sea or ground level and some point above it.
Chris Stoeckert
Adapted from https://www.merriam-webster.com/dictionary/altitude
altitude measurement datum
duration of specimen collection
Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration.
A time measurement datum that is the count of collection cycles over which a specimen collection process occurs.
specimen collection duration
VEuPathDB
specimen collection duration
prevalence of pathogen in specimens
prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR
A data item that is the frequency of detection of a specified pathogenic organism in collected specimens.
Chris Stoeckert
prevalence of pathogen
VEuPathDB
prevalence of pathogen in specimens
prevalence of blood meal specimens from a host organism
prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal.
A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens.
Chris Stoeckert
host blood index
VEuPathDB
prevalence of blood meal specimens from a host organism
presence of blood from host organism in blood meal specimen
presence of blood meal host organism indicated by boolean values of yes or no.
A data item that indicates whether blood in a blood meal specimen came from a specified host organism.
Chris Stoeckert
presence of blood meal host organism
VEuPathDB
presence of blood from host organism in blood meal specimen
blood meal source organism
An organism that is the source of a blood meal.
Chris Stoeckert
blood meal host organism
VEuPathDB
blood meal source organism
blood meal source role
A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal.
A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism.
Will deprecate this term in VEuPathDB ontology once in OBI.
Chris Stoeckert
http://purl.obolibrary.org/obo/EUPATH_0000791
blood meal source role
arthropod attractor role
A role of a material entity realized in drawing an arthropod in the direction of the material.
John Judkins
attractant
IRO:0000034
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
arthropod attractor role
arthropod collection process with automated identification
An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
arthropod collection process with automated identification
gravid female arthropod specimen collection process
An arthropod specimen collection process that has the objective of collecting gravid female arthropods.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
gravid female arthropod specimen collection process
resting flight-capable arthropod specimen collection process
An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity.
John Judkins
VSMO:0000514
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
resting flight-capable arthropod specimen collection process
daytime arthropod specimen collection by aspiration
An arthropod specimen collection by aspiration that occurs in the daytime.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
daytime arthropod specimen collection by aspiration
arthropod resting in human house specimen collection by aspiration
An arthropod specimen collection by aspiration that catches specimens resting inside a human house.
John Judkins
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
arthropod resting in human house specimen collection by aspiration
landing arthropod specimen collection process
An arthropod specimen collection process that occurs while the arthropods land on a surface.
John Judkins
collection of landing insects
VSMO:0001457
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
landing arthropod specimen collection process
flying adult arthropod collection process by passive interception
An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap.
John Judkins
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
flying adult arthropod collection process by passive interception
device for collection of resting adult arthropods
A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity.
John Judkins
VSMO:0001355
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
device for collection of resting adult arthropods
well net for arthropod immatures
A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net.
John Judkins
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
well net for arthropod immatures
arthropod trap containing small non-human animal bait
An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller.
John Judkins
trap containing small non-human animal bait
VSMO:0001595
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
arthropod trap containing small non-human animal bait
trap for emerging adult arthropods
An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage.
John Judkins
American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389
VSMO:0001352
https://github.com/obi-ontology/obi/issues/1302
VEuPathDB
trap for emerging adult arthropods
barcode target locus role
An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR.
Chris Stoeckert https://orcid.org/0000-0002-5714-991X
VEuPathDB
https://github.com/obi-ontology/obi/issues/1325
barcode target locus role
oligonucleotide primer set
A processed material that consists of oligonucleotides that bear a primer role.
Chris Stoeckert https://orcid.org/0000-0002-5714-991X
VEuPathDB
https://github.com/obi-ontology/obi/issues/1325
oligonucleotide primer set
fluorogenic PCR assay
A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores.
John Judkins
TaqMan
MIRO:20000102
https://github.com/obi-ontology/obi/issues/1320
fluorogenic PCR assay
genotyping by PCR assay
genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci.
A genotyping assay that uses polymerase chain reaction.
Chris Stoeckert, ORCID:0000-0002-5714-991X
Jie Zheng, ORCID:0000-0002-2999-0103
VEuPathDB
https://github.com/obi-ontology/obi/issues/1348
VEuPathDB
genotyping by PCR assay
coma severity assay
Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale.
A physical examination of individual that has the objective to determine the severity of coma in a patient.
John Judkins
https://github.com/obi-ontology/obi/issues/1357
John Judkins
coma severity assay
Plasmodium gametocyte detection assay
An assay that detects Plasmodium gametocytes in a specimen.
Chris Stoeckert
Jie Zheng
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
Plasmodium gametocyte detection assay
malaria rapid diagnosis assay
An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood.
Chris Stoeckert
Jie Zheng
malaria rapid diagnosis test
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
malaria rapid diagnosis assay
parasite detection assay
An assay that detects parasite in a specimen.
Chris Stoeckert
Jie Zheng
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
parasite detection assay
feces microbiology assay
An assay that detects microorganisms in a feces specimen.
John Judkins
stool test for microorganisms
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
feces microbiology assay
blood assay
An assay that has a blood specimen as evaulant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
blood assay
falcivax rapid diagnostic test
A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
falcivax rapid diagnostic test
optimal-IT rapid diagnostic test
A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
optimal-IT rapid diagnostic test
urine assay
An assay that has a urine specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
urine assay
parasite species identification by PCR assay
An organism identification assay that identifies the species of parasites by PCR.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
parasite species identification by PCR assay
parasite detection by PCR assay
An assay that detects parasite in a specimen using PCR.
Chris Stoeckert
Jie Zheng
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
parasite detection by PCR assay
free-standing window trap
Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658]
An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die.
VEuPathDB
VSMO:0001649
free-standing window trap
BG-lure scent dispenser
A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin.
VEuPathDB
BG-lure
IRO:0001060
BG-lure scent dispenser
hand-held sweep net
A device that consists of a network of mesh and is designed to capture adult arthropods.
VEuPathDB
VSMO:0001522
hand-held sweep net
Centers for Disease Control and Prevention gravid trap
The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658]
A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan.
VEuPathDB
CDC gravid trap
VSMO:0001510
Centers for Disease Control and Prevention gravid trap
egg specimen collection process
An arthropod specimen collection process in which the arthropods are in the embryo stage.
VEuPath
collection of eggs
MIRO:30000049
https://github.com/obi-ontology/obi/issues/1322
egg specimen collection process
larval specimen collection process
An arthropod specimen collection process in which the arthropods are in the larval stage.
VEuPath
collection of larvae
MIRO:30000022
https://github.com/obi-ontology/obi/issues/1322
larval specimen collection process
pupal specimen collection process
An arthropod specimen collection process in which the arthropods are in the pupal stage.
VEuPath
collection of pupae
MIRO:30000050
https://github.com/obi-ontology/obi/issues/1322
pupal specimen collection process
blood specimen in vacutainer
A blood specimen that is located in a vacutainer.
John Judkins
Vacutainer sample
VEuPathDB
blood specimen in vacutainer
blood specimen on filter paper
A blood specimen that is located on a filter paper.
Chris Stoeckert
Jie Zheng
Filter paper sample
Penn Group
blood specimen on filter paper
proportion mapped reads
A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads.
John Judkins
VEuPathDB
proportion mapped reads
antibiotic administration process
Administering substance in vivo where an antibiotic substance is administered to a living organism.
Chris Stoeckert
Cristian Cocos
Jie Zheng
Penn Group
antibiotic administration process
insecticide resistance datum
A data item that is about resistance to an insecticide.
John Judkins
VEuPathDB
insecticide resistance datum
organism identification datum
A data item that is the specified output of an organism identification assay.
John Judkins
VEuPathDB
organism identification datum
easting coordinate measurement datum
A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection.
Easting and northing coordinates are commonly measured in meters from a horizontal datum.
John Judkins
https://en.wikipedia.org/wiki/Grid_reference_system
easting coordinate measurement datum
northing coordinate measurement datum
A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection.
Easting and northing coordinates are commonly measured in meters from a horizontal datum.
John Judkins
https://en.wikipedia.org/wiki/Grid_reference_system
northing coordinate measurement datum
clinical study center
Organization that undertakes a clinical study at some point in time.
Chris Stoeckert
Cristian Cocos
Jie Zheng
Penn Group
clinical study center
sequencing protocol
A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial.
John Judkins
VEuPathDB
sequencing protocol
specimen collection protocol
A protocol that specifies processes to fulfill a specimen collection objective.
John Judkins
VEuPathDB
specimen collection protocol
participant identifier
A symbol that denotes a participant under investigation.
John Judkins
VEuPathDB
participant identifier
axillary temperature measurement datum
A temperature measurement datum that is about an axilla.
John Judkins
VEuPathDB
axillary temperature measurement datum
organismal body temperature measurement datum
A temperature measurement datum that is about an organism.
Chris Stoeckert
Jie Zheng
Penn Group
organismal body temperature measurement datum
common name of organism
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.
John Judkins
https://en.wikipedia.org/wiki/Common_name
common name of organism
age since birth at time of enrollment
An age since birth measurement datum at the time of subject enrollment.
Jie Zheng
Penn Group
age since birth at time of enrollment
age since birth at time of visit
An age since birth measurement datum at the time of a clinical visit.
Chris Stoeckert
Grant Dorsey
Jie Zheng
Shon Cade
Penn Group
age since birth at time of visit
entomological data item
A data item that is about a collection of insects.
John Judkins
entomological measurement datum
VEuPathDB
entomological data item
temperature measurement datum
A scalar measurement datum that is the result of measuring temperature.
John Judkins
VEuPathDB
temperature measurement datum
organismal body temperature measurement assay
An assay that detects body temperature of an organism.
Chris Stoeckert
Jie Zheng
VEuPathDB
https://github.com/obi-ontology/obi/issues/1322
organismal body temperature measurement assay
specimen collection time post infection
A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts.
Chris Stoeckert, ORCID: 0000-0002-5714-991X
VEuPathDB, EUPATH:0000613
https://github.com/obi-ontology/obi/issues/1286
specimen collection time post infection
laboratory-based population
Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033)
A population where the collection of individuals is located and maintained in a laboratory, research, or production facility.
Chris Stoeckert, ORCID: 0000-0002-5714-991X
VEuPathDB
https://github.com/obi-ontology/obi/issues/1370
laboratory-based population
cerebrospinal fluid assay
An assay that has a cerebrospinal fluid specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
cerebrospinal fluid assay
endotracheal aspirate assay
An assay that has an endotracheal aspirate specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
endotracheal aspirate assay
induced sputum assay
An assay that has an induced sputum specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
induced sputum assay
lung assay
An assay that has a lung specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
lung assay
milk assay
An assay that has a milk specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
milk assay
feces assay
An assay that has a feces specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
feces assay
umbilical cord blood assay
An assay that has an umbilical cord blood specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
umbilical cord blood assay
saliva assay
An assay that has a saliva specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
saliva assay
cerebrospinal fluid microbiology assay
An organism identification assay that has a cerebrospinal fluid specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
cerebrospinal fluid microbiology assay
endotracheal tube aspirate microbiology assay
An organism identification assay that has an endotracheal aspirate specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
endotracheal tube aspirate microbiology assay
induced sputum microbiology assay
An organism identification assay that has an induced sputum specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
induced sputum microbiology assay
blood assay datum
A data item that is the specified output of a blood assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
blood assay datum
blood microbiology datum
An organism identification assay that is the specified output of a blood microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
blood microbiology datum
feces assay datum
A data item that is the specified output of a feces assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
feces assay datum
feces microbiology datum
An organism identification assay that is the specified output of a feces microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
feces microbiology datum
urine assay datum
A data item that is the specified output of a urine assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
urine assay datum
urine microbiology datum
An organism identification assay that is the specified output of a urine microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
urine microbiology datum
induced sputum assay datum
A data item that is the specified output of a induced sputum assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
induced sputum assay datum
induced sputum microbiology datum
An organism identification assay that is the specified output of an induced sputum microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
induced sputum microbiology datum
cerebrospinal fluid assay datum
A data item that is the specified output of a cerebrospinal fluid assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
cerebrospinal fluid assay datum
cerebrospinal fluid microbiology datum
An organism identification assay that is the specified output of a cerebrospinal fluid microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
cerebrospinal fluid microbiology datum
endotracheal aspirate assay datum
An organism identification assay that is the specified output of an endotracheal aspirate assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
endotracheal aspirate assay datum
endotracheal tube aspirate microbiology datum
An organism identification assay that is the specified output of an endotracheal tube aspirate microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
endotracheal tube aspirate microbiology datum
lung microbiology datum
An organism identification assay that is the specified output of a lung microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
lung microbiology datum
nasopharyngeal or oropharyngeal swab microbiology datum
An organism identification assay that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
nasopharyngeal or oropharyngeal swab microbiology datum
pleural fluid microbiology datum
An organism identification assay that is the specified output of a pleural fluid microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
pleural fluid microbiology datum
umbilical cord blood microbiology datum
An organism identification assay that is the specified output of an umbilical cord blood microbiology assay.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
umbilical cord blood microbiology datum
bacteria in blood datum
A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
bacteria in blood datum
bacteria in feces datum
A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
bacteria in feces datum
bacteria in induced sputum datum
A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
bacteria in induced sputum datum
bacteria in endotracheal tube aspirate datum
A endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
bacteria in endotracheal tube aspirate datum
bacteria in lung datum
A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
bacteria in lung datum
bacteria in nasopharyngeal or oropharyngeal swab datum
A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
bacteria in nasopharyngeal or oropharyngeal swab datum
bacteria in pleural fluid datum
A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
bacteria in pleural fluid datum
eukaryota in umbilical cord blood datum
A umbilical cord blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1428
eukaryota in umbilical cord blood datum
lung microbiology assay
An organism identification assay that has a lung specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
lung microbiology assay
pleural fluid microbiology assay
An organism identification assay that has a pleural fluid specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
pleural fluid microbiology assay
umbilical cord blood microbiology assay
An organism identification assay that has an umbilical cord blood specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
umbilical cord blood microbiology assay
nasopharyngeal or oropharyngeal swab microbiology assay
An organism identification assay that has a nasopharyngeal or oropharyngeal swab specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
nasopharyngeal or oropharyngeal swab microbiology assay
urine microbiology assay
An organism identification assay that has a urine specimen as evaluant.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1429
urine microbiology assay
multiplex real time polymerase chain reaction assay
A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle.
John Judkins
multiplexed real time polymerase chain reaction assay
VEuPathDB
https://github.com/obi-ontology/obi/issues/1431
multiplex real time polymerase chain reaction assay
multiplex real time reverse-transcription polymerase chain reaction assay
A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle.
John Judkins
multiplexed real time reverse-transcription polymerase chain reaction assay
VEuPathDB
https://github.com/obi-ontology/obi/issues/1431
multiplex real time reverse-transcription polymerase chain reaction assay
mosquito membrane feeding device
A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1439
mosquito membrane feeding device
mosquito membrane feeding assay
Testing the effectiveness of drugs or antibodies against parasite transmission.
An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them.
John Judkins
VEuPathDB
https://github.com/obi-ontology/obi/issues/1439
mosquito membrane feeding assay
modified acid-fast stain microscopy assay
A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating.
John Judkins
NCIT:C85736
https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html
https://github.com/obi-ontology/obi/issues/1444
modified acid-fast stain microscopy assay
antibodies from lymphocyte secretions assay
PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes.
An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells.
John Judkins
ALS assay
antibodies from lymphocyte supernatant assay
OBI
VEuPathDB
https://github.com/obi-ontology/obi/issues/1443
antibodies from lymphocyte secretions assay
blood plasma specimen
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
PERSON: Maura Gasparetto
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
plasma
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood plasma specimen
blood serum specimen
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
PERSON: Maura Gasparetto
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood serum 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
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
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
bronchial alveolar lavage
solution containing lung derived T cells, eosinophils, and TNFa.
Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
PERSON: Bjoern Peters
BAL
GROUP: IEDB
bronchial alveolar lavage
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
center calculation objective
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
James Malone
PERSON: James Malone
center calculation objective
center calculation data transformation
A center calculation data transformation is a data transformation that has objective of center calculation.
James Malone
PERSON: James Malone
center calculation data transformation
observation design
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
Philippe Rocca-Serra
OBI branch derived
observation design
pool of specimens
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
PERSON: Jennifer Fostel
GROUP: CEBS
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
filtration
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
Philippe Rocca-Serra
OBI-Branch: adapted from wikipedia and wordnet
filtration
centrifugation
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
Philippe Rocca-Serra
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
staining
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
Philippe Rocca-Serra
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
polymerization
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
PRS:22102008: need to import catalyst from CHEBI 35223
Philippe Rocca-Serra
OBI-Branch
polymerization
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
nucleic acid hybridization
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
hybridization assay
nucleic acid hybridization
light source
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Elizabeth M. Goralczyk
John Quinn
Olga Tchuvatkina
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
light source
multi-well plate
96 well plate, 48 multiwell plate
A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
FG this is synonymous with microtiter plate
John Quinn
http://www.nuncbrand.com/page.aspx?ID=301
multi-well plate
DNA sequencer
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Trish Whetzel
MO
DNA sequencer
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
Melanie Courtot
Person: Jennifer Fostel
Trish Whetzel
http://en.wikipedia.org/wiki/Centrifuge
centrifuge
hybridization chamber
Glass Array Hybridization Cassette
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
Trish Whetzel
MO_563 hybridization_chamber
hybridization chamber
gel tank
CHEF gel box, slab gel box, capillary electrophoresis
A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
Person:Frank Gibson
Person:Kevin Clancy
electrophoresis box
electrophoresis unit
sep:00095
gel tank
power supply
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
Daniel Schober
Frank Gibson
PSU
electrical power supply
power pack
power supply unit
PERSON: Daniel Schober
sep:00093
was power_pack, maps to SEP electrical_power_supply
power supply
microscope
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
PERSON: Phillippe Rocca-Serra
wikipedia
microscope
animal cage
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
A processed material which has the function to define a bounded habitat which is amenable to keeping animals.
PERSON: Phillippe Rocca-Serra
laboratory cage
OBI biomaterial branch
animal cage
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.
study design
eligibility criterion
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
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.
Person: Philippe Rocca-Serra
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
eligibility criterion
human subject enrollment
enlisting familiy members of HIV patients into a study
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.
As with group assignment, should the specified output here be an organism which bears a role
Bjoern Peters
IEDB
criteria come from plan / clinical trial branch
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
1
administering substance in vivo
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
Different routes and means of administration should go as children underneath this
Update the definition based on the discussion. Details see the tracker:
https://sourceforge.net/p/obi/obi-terms/738/
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
Bjoern Peters
Person:Bjoern Peters
IEDB
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
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
PERSON:Bjoern Peters
aliquoting
apportioning
OBI branch derived
material portioning
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
artificially induced reverse transcription
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
PERSON:Kevin Clancy
OBI branch derived
artificially induced reverse transcription
'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
lavage
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
This is not washing, in which case the material of interest is not the resulting fluid
PlanAndPlannedProcess Branch
OBI branch derived
lavage
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
PlanAndPlannedProcess Branch
OBI branch derived
sequencing assay
specific enzymatic cleavage
The use of a protease to digest a protein into peptides
an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material
PERSON:Kevin Clancy
OBI branch derived
specific enzymatic cleavage
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
PERSON:Kevin Clancy
OBI branch derived
dialysis
electrophoresis
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
PERSON:Kevin Clancy
OBI branch derived
Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers.
electrophoresis
DNA cleavage, restriction analysis
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence
PERSON:Kevin Clancy
restriction enzyme assay
DNA restriction enzyme digestion
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
PERSON:Kevin Clancy
OBI branch derived
enzymatic amplification
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
PlanAndPlannedProcess Branch
OBI branch derived
requested by Helen Parkinson for MO
RNA extraction
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
assay bead
Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules.
DS: Probably better modeled as a role.
OBI
bead
assay bead
infection process
the detrimental process in which an infectious agent colonizes or replicates in a host environment
IEDB
IEDB
infection process
adaptive immune receptor
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
IEDB
IEDB
adaptive immune receptor
lymph node cell specimen
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.
IEDB
IEDB
lymph node cell specimen
organ harvesting
The process of removing an organ from its source organism
IEDB
IEDB
organ harvesting
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
bodily fluid specimen
A specimen that is derived from some bodily fluid
Christian Stoeckert ORCID:0000-0002-5714-991X
Mark A. Miller ORCID:0000-0001-9076-6066
Christian Stoeckert ORCID:0000-0002-5714-991X
Mark A. Miller ORCID:0000-0001-9076-6066
bodily fluid specimen
umbilical cord blood specimen
A specimen that is derived from some umbilical cord blood
Christian Stoeckert ORCID:0000-0002-5714-991X
Mark A. Miller ORCID:0000-0001-9076-6066
Christian Stoeckert ORCID:0000-0002-5714-991X
Mark A. Miller ORCID:0000-0001-9076-6066
umbilical cord blood specimen
erythrocyte specimen
A specimen that is derived from some erythrocytes
Christian Stoeckert ORCID:0000-0002-5714-991X
Mark A. Miller ORCID:0000-0001-9076-6066
Christian Stoeckert ORCID:0000-0002-5714-991X
Mark A. Miller ORCID:0000-0001-9076-6066
erythrocyte specimen
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
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.
laboratory finding
A clinically abnormal phenotype.
clinical phenotype
A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen.
clinical laboratory test
The totality of all processes through which a given disease instance is realized.
disease course
The representation of a conclusion of a diagnostic process.
diagnosis
TODO: Define.
physical examination finding
A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism.
congenital disorder
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
treatment
A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
health care process
A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
health care encounter
A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
diagnostic process
A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
clinical data item
A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
medication role
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
An azole compound resistance phenotype where an organism or cell is resistant to one or more azole compounds.
resistant to azole
A social role inhering in a human being.
human social role
A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
patient role
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function.
hospital facility
A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
residence function
A role in human social processes that, if realized, is realized when the bearer provides labor or services in exchange for a wage or salary as specified by some deontic declaration.
job role
health care facility
A deontic document act that concludes an inpatient encounter.
patient discharge
An information content entity that is about human travel.
human traveling information
A planned process in which the bearer of an employer role provides wages or salary to the bearer of an employee roll in fullfillment of the arrangements specified in some declaration
employment process
A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter.
admission process
A social identity information content entity that is about whether some person identifies as some ethnicity.
ethnic identity information content entity
A social identity information content entity that is about whether some person identifies as some gender.
gender identity information content entity
A data item that is about a person's job role and/or its realization.
job role data item
A socio-economic data item that is about a person and their completion of an education program (and its type), where that education progam is the last one in a sequence (of education programs) that the person has completed, where each education program completed except the last one is a pre-requisite to the education program completed after it.
highest level of education data item
A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone.
caregiver role
A relational quality that inheres within two or more 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 structured interview intended to capture detailed information about all foods and beverages (and possibly, dietary supplements) consumed by the respondent in the past 24 hours, most commonly, from midnight to midnight the previous day. A key feature of the 24HR is that, when appropriate, the respondent is asked for more detailed information than first reported. For example, a respondent reporting chicken for dinner or a sandwich for lunch would be asked about the preparation method and type of bread. This open-ended response structure is designed to prompt respondents to provide a comprehensive and detailed report of all foods and beverages consumed. A 24h can also be filled at home by the responder, and be checked during an interview to further improve it with additional details
24-hour dietary recall
A biological process that consists on the tear of the amniotic sac, causing the amniotic fluid to flow out through the vagina. It usually happens shortly before the birth, the expectant mother feels wetness and notices a clear odorless fluid.
Um processo biológico que consiste na ruptura do saco amniótico, fazendo com que o líquido amniótico flua para fora através da vagina. Geralmente acontece pouco antes do nascimento, a gestante sente umidade e percebe um líquido claro e inodoro.
ruptura de membranas
rupture of membranes
TO DO
TO DO
história obstétrica
obstetric history
A scalar measurement that refers to the diameter of the opening of the cervix measured during the cervical dilation process.
Uma medida escalar que se refere ao diâmetro da abertura do colo do útero medida durante o processo de dilatação cervical.
cervix diameter measurement datum
medida do diâmetro do colo do útero
A time measurement datum that is the result of measurement of the gestational age of a pregnant organism.
Um dado de medida de tempo que é o resultado da medição da idade gestacional de um organismo grávido.
gestational age measurement datum
idade gestacional medida
A human parturition where the birth of a baby happens with less than 37 weeks gestational age.
Um parto onde o nascimento de um bebê acontece com menos de 37 semanas da idade gestacional.
parto prematuro
preterm labour
A parasite lifecycle stage of sporozoa consisting of a zygote enclosed by cyst wall.
oocyst stage
A life cycle stage where a cell differentiates into male or female sexual forms.
gametocyte stage
A parasite lifecycle stage of some sporozoans where cells divide through sporogony producing daughter cells called sporozoites that infect new hosts.
sporozoite stage
A 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.
parasite organism
A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes
Plasmodium gametocyte
A time quality inhering in a bearer by virtue of how long the bearer has existed.
age
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
fluorescence
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
concentration of
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.
biological sex
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
morphology
qualitative
The number of entities of this type that are part of the whole organism.
amount
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
size
A 1-D extent quality which is equal to the distance between two points.
length
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
mass
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 of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
physical quality
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
A quality which inheres in a continuant.
physical object quality
A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
area
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
An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring.
reproductive quality
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
phenotypic sex
A biological sex quality inhering in an individual or a population that undergo sexual reproduction.
mating type
A quality that inheres in an entire organism or part of an organism.
organismal quality
A quality that inheres in an entire population or part of a population.
population quality
A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism.
virulence
A viviparous organism having never given birth.
nulliparous
A structural quality which is held by a bearer where a localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part is present.
lesioned
An organismal quality of having successfully reproduced.
parous
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms
An organismal 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 collection of organisms that consists of two or more organisms from at least two species.
multi-species collection of organisms
A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism.
number of generations of multicellular organism
A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations.
parasite isolate population
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 growth phenotype which describes the resistance of individuals or populations after exposure to voriconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow.
resistance to voriconazole
A growth phenotype which describes the resistance of individuals or populations after exposure to posaconazole. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow.
resistance to posaconazole
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
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
protein
A type II interferon that is a translation product of the human IFNG gene or a 1:1 ortholog thereof. The core domain structure consists of an Interferon gamma domain (Pfam:PF00714) that is four-helical cytokine domain with an additional helix in one of the crossover connections. It is a cytokine produced by lymphocytes activated by specific antigens or mitogens that has important immunoregulatory functions.
interferon gamma
A tumor necrosis factor, TNF-like that is a translation product of the human TNF gene or a 1:1 ortholog thereof. Tumour necrosis factor alpha (TNF) is a pleiotropic cytokine that mediates apoptosis, cell proliferation, immunomodulation, inflammation, viral replication, allergy, arthritis, septic shock, insulin resistance, autoimmune diseases, and other pathological conditions. TNF transduces these cellular responses through two distinct receptors: type I, which are expressed on all cell types, and type II, which are expressed only on cells of the immune system and endothelial cells.
tumor necrosis factor
An interleukin-1 that is a translation product of the human IL1B gene or a 1:1 ortholog thereof.
interleukin-1 beta
A protein that is a translation product of the human IL1RN gene or a 1:1 ortholog thereof.
interleukin-1 receptor antagonist protein
An interleukin-17 that is a translation product of the human IL17A gene or a 1:1 ortholog thereof. The active product is a proinflammatory cytokine produced by activated T cells. This cytokine regulates the activities of NF-kappaB and mitogen-activated protein kinases.
interleukin-17A
A protein that is a translation product of the human IL7 gene or a 1:1 ortholog thereof.
interleukin-7
A protein that is a translation product of the human IL13 gene or a 1:1 ortholog thereof. Interleukin-13 is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related.
interleukin-13
A protein that is a translation product of the human IL15 gene or a 1:1 ortholog thereof.
interleukin-15
A protein that is a translation product of the human IL2 gene or a 1:1 ortholog thereof. Interleukin-2 has a dual role in maintaining tolerance and contributing to immunity.
interleukin-2
A protein that is a translation product of the human IL4 gene or a 1:1 ortholog thereof.
interleukin-4
A protein that is a translation product of the human IL5 gene or a 1:1 ortholog thereof.
interleukin-5
A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof.
interleukin-6
A protein that is a translation product of the human CXCL8 gene or a 1:1 ortholog thereof.
interleukin-8
A protein that is a translation product of the human IL9 gene or a 1:1 ortholog thereof.
interleukin-9
A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof. Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds.
interleukin-10
A protein with core architecture consisting of a Small cytokines (intecrine/chemokine), interleukin-8 like (Pfam:PF00048) domain.
C/C-C motif small inducible chemokine
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
CD14 molecule
A C/C-C motif small inducible chemokine that is a translation product of the CCL3, CCL3L1/CCL3L3, or CCL4 gene.
C-C motif chemokine 3/4
A C/C-C motif small inducible chemokine that is a member of a subfamily that includes eotaxin.
eotaxin-like cytokine
A C/C-C motif small inducible chemokine that is a translation product of the human CCL5 gene or a 1:1 ortholog thereof.
C-C motif chemokine 5
An eotaxin-like cytokine that is a translation product of the human CCL2 gene or a 1:1 ortholog thereof.
C-C motif chemokine 2
A C-C motif chemokine 3/4 that is a translation product of the human CCL3 gene or a 1:1 ortholog thereof.
C-C motif chemokine 3
A C-C motif chemokine 3/4 that is a translation product of the human CCL4 gene or a 1:1 ortholog thereof.
C-C motif chemokine 4
An eotaxin-like cytokine that is a translation product of the human CCL11 gene or a 1:1 ortholog thereof.
eotaxin
A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof.
C-reactive protein
A protein that is a translation product of the human CSF2 gene or a 1:1 ortholog thereof.
granulocyte-macrophage colony-stimulating factor
A protein that is a translation product of the human CSF3 gene or a 1:1 ortholog thereof.
granulocyte colony-stimulating factor
A protein that is a translation product of the human EGF gene or a 1:1 ortholog thereof.
pro-epidermal growth factor
A protein that is a translation product of the human MFGE8 gene or a 1:1 ortholog thereof.
lactadherin
A serpin that is a translation product of the human SERPINA1 gene or a 1:1 ortholog thereof.
alpha-1-antitrypsin
A protein that is a translation product of the Escherichia coli K-12 aspC gene or a 1:1 ortholog thereof.
aspartate aminotransferase
A protein that is a translation product of the Escherichia coli K-12 phoA gene or a 1:1 ortholog thereof.
alkaline phosphatase
A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof.
alanine aminotransferase
An acetylcholinesterase that is a translation product of the Anopheles gambiae Ace gene or a 1:1 ortholog thereof.
insect-type acetylcholinesterase
A voltage-gated sodium channel subunit alpha that is a translation product of the fruit fly para gene or a 1:1 ortholog thereof.
sodium channel protein para
A sodium channel protein para sequence variant at position 1016 that has a Gly residue at the position equivalent to Val-1016 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr V1016G
A protein that is a translation product of the fruit fly Rdl gene or a 1:1 ortholog thereof.
gamma-aminobutyric acid receptor subunit beta
A sodium channel protein para sequence variant at position 1011 that has a Met residue at the position equivalent to Ile-1011 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr I1011M
A sodium channel protein para sequence variant at position 1011 that has a Val residue at the position equivalent to Ile-1011 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr I1011V
A sodium channel protein para sequence variant at position 989 that has a Pro residue at the position equivalent to Ser-989 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr S989P
A sodium channel protein para sequence variant at position 1014 that has a Ser residue at the position equivalent to Leu-1014 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr L1014S
A sodium channel protein para sequence variant at position 1532 that has a Thr residue at the position equivalent to Ile-1532 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr I1532T
A sodium channel protein para sequence variant at position 1534 that has a Cys residue at the position equivalent to Phe-1534 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr F1534C
A sodium channel protein para sequence variant at position 1534 that has a Leu residue at the position equivalent to Phe-1534 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr F1534L
A sodium channel protein para sequence variant at position 1534 that has a Ser residue at the position equivalent to Phe-1534 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr F1534S
A sodium channel protein para sequence variant at position 1575 that has a Tyr residue at the position equivalent to Asn-1575 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr N1575Y
A sodium channel protein para sequence variant at position 1763 that has a Tyr residue at the position equivalent to Asp-1763 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr D1763Y
A sodium channel protein para sequence variant at position 1016 that has an Ile residue at the position equivalent to Val-1016 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr V1016I
An insect-type acetylcholinesterase sequence variant at position 119 that has a Ser residue at the position equivalent to Gly-119 of the amino acid sequence represented by UniProtKB:P04058-1.
AChE1 G119S
A gamma-aminobutyric acid receptor subunit beta sequence variant at position 296 that has a Gly residue at the position equivalent to Ala-296 of the amino acid sequence represented by UniProtKB:P25123-1.
Rdl A296G
A gamma-aminobutyric acid receptor subunit beta sequence variant at position 296 that has a Ser residue at the position equivalent to Ala-296 of the amino acid sequence represented by UniProtKB:P25123-1.
Rdl A296S
A glutathione S-transferase epsilon that is a translation product of the Anopheles funestus GSTe2 gene or a 1:1 ortholog thereof.
glutathione S-transferase epsilon 2
A glutathione S-transferase epsilon 2 sequence variant at position 119 that has a Phe residue at the position equivalent to Leu-119 of the amino acid sequence represented by UniProtKB:V9QKI4-1.
Gste2 L119F
A sodium channel protein para sequence variant at position 1014 that has a Cys residue at the position equivalent to Leu-1014 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr L1014C
A sodium channel protein para sequence variant at position 1014 that has a Phe residue at the position equivalent to Leu-1014 of the amino acid sequence represented by UniProtKB:Q94615-1.
Kdr L1014F
social role
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
region
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
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
Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.
cytosolic_16S_rRNA
A genome is the sum of genetic material within a cell or virion.
genome
A genotype is a variant genome, complete or incomplete.
genotype
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
a subject pairing is a planned process which executes a pairing rule and results in the creation of sets of 2 subjects meeting the pairing criteria
subject pairing
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
Prostration is a general symptom characterized by complete physical or mental exhaustion.
prostration
seizure
dry mouth
Anorexia is a nutrition, metabolism, and development symptom characterized by a loss of appetite especially when prolonged.
anorexia
convulsion
Dizziness is a neurological and physiological symptom characterized by a sensation of unsteadiness accompanied by a feeling of movement within the head.
dizziness
septicemia
chills
Malaise is a neurological and physiological symptom characterized as an indefinite feeling of debility or lack of health often indicative of or accompanying the onset of an illness.
malaise
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
End of the life of an organism.
death stage
An section of a respiratory tract.
proximo-distal subdivision of respiratory tract
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
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
respiratory tube
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
A portion of organism substance that is produced by exocrine glands.
secretion of exocrine gland
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 which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
organism subdivision
Anatomical group that has its parts adjacent to one another.
anatomical cluster
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
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 major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
dorsum
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
The part of the forelimb extending from the shoulder to the autopod[cjm].
arm
Skeletal element that is composed of bone tissue.
bone element
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
upper respiratory tract
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
lower respiratory tract
An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
nasal cavity
A muscular organ in the floor of the mouth.
tongue
The section of the pharynx that lies above the soft palate.
nasopharynx
The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.
oropharynx
The part of the ear that projects from the head, connecting to the external acoustic meatus.
pinna
The small curved bones that extends horizontally along the lateral wall of the nasal passage.
turbinate bone
The smooth stratified squamous epithelium that covers the outer surface of the cornea.
corneal epithelium
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
aqueous humor of eyeball
The mucous membrane that lines the nasal cavity[MP].
nasal cavity mucosa
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
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
milk
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 outpocketing of the esophagus.
lung
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
viscus
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
Replacement bone that forms within cartilage.
endochondral bone
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
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
trachea
A gland that is part of a digestive tract [Automatically generated definition].
gland of digestive tract
A bone that is part of a head [Automatically generated definition].
head bone
A bone that is part of a facial skeleton [Automatically generated definition].
facial bone
One of the conchae of the ethmoid bone, which occupy the caudal part of the nasal fossae and form the lateral and superior portions of the turbinate bones in mammals[MP]. The ethmoturbinals are associated with the cribiform plate. They are covered with olfactory epithelium. Primarily, they serve to increase the surface area over which olfactory receptor neurons can come in contact with respiratory air. These olfactory receptor nerves then synapse with the mitral cells of the olfactory lobes through the cribiform plate in the manner described above[Palaeos].
nasal concha of ethmoid bone
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
This begins with the newly hatched first-instar larva, through its maturation to the end of the last larval stage. An example of this process is found in Drosophila melanogaster.
instar larval stage
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
skeletal element
A mucosa that is part of a gastrointestinal system.
gastrointestinal system mucosa
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 or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
thoracic cavity 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
zone of bone organ
The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.
middle nasal concha
The laminar structure of the heart.
heart layer
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
ocular refractive media
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
A portion of organism substance that secreted_by a respiratory system.
respiratory system fluid/secretion
digestive system secreted substance
Any gland that is part of the digestive system.
digestive system gland
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
sputum
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
The external junctural region between the lower part of the abdomen and the thigh.
inguinal part of abdomen
An organism containing a developing embryo, fetus, or unborn offspring within the body.
gravid organism
The axilla is the area directly under the joint where the forelimb connects to the shoulder.
axilla
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
An organ of the digestive tract that is capable of retaining and storing food.
food storage organ
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
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
endochondral element
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
Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
umbilical cord blood
subdivision of tube
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
An 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
Any organ component layer that consists of muscle tissue.
layer of muscle tissue
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 region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
external soft tissue zone
A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning.
nasal turbinal
Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule.
anterior nasal wall
Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
left side of back
Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
right side of back
"A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]
length unit
"A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia]
mass unit
"A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia]
time unit
"A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia]
temperature unit
"A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG]
area unit
"A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG]
concentration unit
"A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG]
mass density unit
"A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia]
area density unit
"A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST]
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." [Wikipedia:Wikipedia]
parts per notation unit
"A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia]
density unit
"A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia]
dimensionless unit
"A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia]
percent
"A dimensionless unit which denotes a simple count of things." [MGED:MGED]
count unit
"A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia]
ratio
"A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia]
fraction
"A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline]
cell concentration unit
"A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG]
catalytic (activity) concentration unit
"A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST]
volume per unit volume
"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." [UO:PC]
dose unit
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
Haemophilus influenzae serotype b
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
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.
platelet count
The number of times the HEART VENTRICLES contract per unit of time, usually per minute.
heart rate
The mass or quantity of heaviness of an individual at BIRTH. It is expressed by units of pounds or kilograms.
birth weight
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
An fasting blood glucose measurement is a measurement of glucose in the blood of a patient at some defined time point after eating.
fasting blood glucose measurement
The point in time at which an individual was born.
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 condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
poisoning
A disease that involves the genitourinary system.
A disease that involves the genitourinary system. [database_cross_reference: MONDO:patterns/location]
disease of genitourinary system
the ending of pregnancy by removing a fetus or embryo before it can survive outside the uterus.
abortion
Obsolete Class
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
obsolete bottom household wealth index
true
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
obsolete middle household wealth index
true
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
obsolete top household wealth index
true
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
obsolete no airbrick
true
A information content entity indicating that the household eats in restaurants.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete record of eating in restaurants
true
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
obsolete record of no cooking at home
true
An information content entity indicates no toilet facility in the dwelling.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete record of no toilet facility
true
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
obsolete record of using neighbours' toilet
true
A time of screening occurring during the initial human subject enrollment period.
Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey
Penn Group
PRISM
obsolete time of screening during initial enrollment
true
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
obsolete time of screenng after initial enrollment
true
PRISM
obsolete unknown withdrawal reason
true
PRISM
obsolete withdrew due to death
true
PRISM
obsolete inability to comply with protocol
true
PRISM
obsolete moved out of area
true
PRISM
obsolete reached 11 years of age
true
PRISM
obsolete unable to be located for over 120 days
true
PRISM
obsolete withdrawal of all children under care
true
PRISM
obsolete withdrawal of informed consent
true
PRISM
obsolete unknown cause of death
true
PRISM
obsolete complications of HIV
true
PRISM
obsolete diarrheal illness
true
PRISM
obsolete suicide
true
PRISM
obsolete Bwindi Hospital
true
PRISM
obsolete Jinja Hospital
true
PRISM
obsolete Kauka Health Centre
true
PRISM
obsolete Kihihi Health Centre IV
true
PRISM
obsolete Nagongera Health Centre IV
true
PRISM
obsolete Tororo District Hospital
true
PRISM
obsolete record of unknown death location
true
An organization that manufactures mosquito traps and other mosquito control products.
obsolete BioGents
true
A ratio unit that denotes the mean enzymatic activity of a field-collected population of specimens compared to that of a reference population, normalized by a base two logarithmic transformation.
Person: John Judkins
VBcv:0001116
unit of log2 ratio of specimen population mean enzymatic activity to that of reference specimen population
A ratio unit that denotes the median enzymatic activity of a field-collected population of specimens compared to that of a reference population, normalized by a base two logarithmic transformation.
Person: John Judkins
VBcv:0001124
unit of log2 ratio of specimen population median enzymatic activity to that of reference specimen population
A fraction unit that denotes the fraction of a population exhibiting higher enzymatic activity than the 99th percentile of a reference population.
Person: John Judkins
VBcv:0001111
unit of population fraction with greater enzymatic activity than 99th percentile of reference population
An organization that monitors mosquito species in the Florida Keys district, performs abatement, and is located in the Florida Keys, Florida, USA.
Florida Keys Mosquito Control district organization
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
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
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
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolete_core
true
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
Alan Ruttenberg
defined class
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Alan Ruttenberg
named class expression
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
Illumina
Philippe Rocca-Serra
Illumina
BioGents
An organization that manufactures mosquito traps and other mosquito control products.
John Judkins
WEB:https://eu.biogents.com/about-biogents/
BioGents
"A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG]
microgram
"A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG]
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." [NIST:NIST]
degree Celsius
"A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia]
minute
"A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia]
hour
"A time unit which is equal to 24 hours." [Wikipedia:Wikipedia]
day
"A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia]
year
"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]." [UOC:GVG]
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]." [UOC:GVG]
parts per billion
"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." [Wikipedia:Wikipedia]
pi
"A dimensionless count unit which denotes the number of molecules." [MGED:MGED]
molecule count
"A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED]
purity percentage
"A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED]
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." [Wikipedia:Wikipedia]
degree Fahrenheit
"A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia]
pH
"A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST]
liter per kilogram
"A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST]
milliliter per kilogram
"A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST]
microliter per kilogram
"A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline]
cells per milliliter
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST]
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." [NIST:NIST]
katal per liter
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST]
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." [NIST:NIST]
milliliter per liter
"A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG]
gram per deciliter
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG]
milligram per liter
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG]
microgram per milliliter
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG]
microgram per liter
"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." [UO:PC]
milligram per square meter
"An area unit which is equivalent to 1 furlong x 1 chain. This is equal to an area of 4,046.856,4224 square meters, or 43,500 square feet." [Wikipedia:Wikipedia]
acre
"An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared." [NIST:NIST]
gram per square meter
"A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS]
micrograms per wheaton bottle