en
Chris mungall
Erica Marcos
Ningxian Fan
Paul Fabry
Randi Vita
Ryan R. Brinkman
Shunzhou Deng
Alan Ruttenburg
Alexander D. Diehl
Amogh Madireddi
Anna Maria Masci
Anthony Huffman
Barry Smith
Bjoern Peters
Edison Ong
Hong Yu
Jason Hu
Jie Zheng
Kallan Roan
Khadeejah Khan
Lindsay Cowell
Melanie Courtot
Ningxian Fan
Omar Tibi
Philip Huang
Randi Vita
Rebecca Racz
Richard H. Scheuermann
Rohit Goru
Ronak Sutariya
Samantha G. Sayers (SGS)
Thomas Todd
Yongqun "Oliver" He (YH)
Yu Lin (YL)
Yuanyi (Penny) Pan
Zuoshuang "Allen" Xiang
2023-11-17
The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
OWL-DL
Vaccine Ontology
2023-11-17
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
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.
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 label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
OBO Operations committee
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
alternative label
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
IEDB alternative term
An alternative term used by the IEDB.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
A GeneID in the NCBI Gene database
Oliver He, Yue Liu
NCBI GeneID
the NCBI LocusTag name of a gene
Oliver He, Yue Liu
NCBI LocusTag
a date of content modification
Oliver He, Yue Liu
modification date
The NCBITaxon ontology ID of an organism.
Oliver He, Yue Liu
organism NCBITaxon ID
A chromosome ID where a gene is located.
Oliver He
chromosome ID of gene
an annotation property that specifies the type of a gene
Oliver He
type of gene
an annotation property that specifies a nomenclature status
Oliver He
nomenclature status
An annotation property that represents a gene's association with PubMed publication(s).
Yongqun He
has PubMed association
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
OBO Operations call
logical characteristic of object property
'part disjoint with' 'defined by construct' """
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX : <http://example.org/
CONSTRUCT {
[
a owl:Restriction ;
owl:onProperty :part_of ;
owl:someValuesFrom ?a ;
owl:disjointWith [
a owl:Restriction ;
owl:onProperty :part_of ;
owl:someValuesFrom ?b
]
]
}
WHERE {
?a :part_disjoint_with ?b .
}
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
defined by construct
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
2023-03-03
abbreviation
A synonym type for describing ambiguous synonyms
2023-03-03
ambiguous synonym
A synonym type for describing dubious synonyms
2023-03-03
dubious synonym
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
2023-03-03
layperson synonym
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
2023-03-03
plural form
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
2023-03-03
UK spelling synonym
A synonym type for common misspellings
2023-03-03
misspelling
A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
2023-03-03
misnomer
MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
A synonym type for names that have been used as primary labels in the past.
2023-07-25
previous name
The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
A synonym type for the legal entity name
2023-07-27
legal name
CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
2023-09-30
INN
International Nonproprietary Name
nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
A synonym type for describing Latin term synonyms.
2023-10-12
latin term
NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
2023-11-01
acronym
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
tooth SubClassOf 'never in taxon' value 'Aves'
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Class: ?X DisjointWith: RO_0002162 some ?Y
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
CONSTRUCT {
in_taxon: a owl:ObjectProperty .
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom ?taxon
] .
?x rdfs:subClassOf [
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom [
a owl:Class ;
owl:complementOf ?taxon
]
] .
}
WHERE {
?x never_in_taxon: ?taxon .
}
never in taxon
A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
non-overlapping with
shares no parts with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171>
CONSTRUCT {
part_of: a owl:ObjectProperty .
[
a owl:Restriction ;
owl:onProperty part_of: ;
owl:someValuesFrom ?x ;
a owl:Restriction ;
owl:onProperty part_of: ;
owl:someValuesFrom ?y
]
]
}
WHERE {
?x mutually_spatially_disjoint_with: ?y .
}
mutually spatially disjoint with
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
taxonomic class assertion
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
CONSTRUCT {
in_taxon: a owl:ObjectProperty .
?witness rdfs:label ?label .
?witness rdfs:subClassOf ?x .
?witness rdfs:subClassOf [
a owl:Restriction ;
owl:onProperty in_taxon: ;
owl:someValuesFrom ?taxon
] .
}
WHERE {
?x present_in_taxon: ?taxon .
BIND(IRI(CONCAT(
"http://purl.obolibrary.org/obo/RO_0002175#",
MD5(STR(?x)),
"-",
MD5(STR(?taxon))
)) as ?witness)
BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label)
}
The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
present in taxon
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
logical macro assertion on an object property
A shortcut relationship that holds between two entities based on their identity criteria
logical macro assertion involving identity
A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.
in approximate one to one relationship with
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
is opposite of
external_definition
axiom_lost_from_external_ontology
homology_notes
has_relational_adjective
taxon_notes
development_notes
external_ontology_notes
fma_set_term
Oliver He, Omar Tibi
An annotation property that represents a matched vaccine identifier used in the VIOLIN database.
VIOLIN vaccine ID
VIOLIN vaccine ID
An annotation property that represents the trade name of a product.
YH
trade name
trade name
An annotation property that represents the active ingredient of a vaccine.
Oliver He
has vaccine active ingredient
has vaccine active ingredient
An annotation property that represents the vaccine ingredient of a vaccine. Such an ingredient may not be active.
Oliver He
has vaccine ingredient
has vaccine ingredient
An annotation property that describes the dose information of a vaccine
Oliver He
vaccine dose annotation
vaccine dose annotation
The vaccine Prevnar (trade name) has a FDA-defined proper name: Pneumococcal 7-valent Conjugate Vaccine (Diphtheria CRM197 Protein). Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
An annotation property that represents the proper name of a vaccine, which is defined in an official way such as one defined by FDA.
Oliver He, Kallan Roan
vaccine proper name
vaccine proper name
The vaccine Prevnar has the manufacturer: Wyeth Pharmaceuticals Inc. Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
An annotation property that represents the manufacturer of a product such as vaccine
Oliver He, Kallan Roan
manufacturer
manufacturer
The vaccine Prevnar has the indications:
- Immunization of infants 2, 4, 6 and 12-15 months of age to prevent invasive pneumococcal disease.
- Immunization of infants and toddlers against otitis media caused by vaccine serotypes.
Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
An annotation property that represents the indications of a vaccine defined by the USA FDA.
Oliver He, Kallan Roan
FDA vaccine indications
FDA vaccine indications
Prevnar has the package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM137038.pdf . Recorded on 11/26/2018.
An annotation property that represents a URL of the package insert PDF document of a licensed vaccine
Oliver He, Kallan Roan
vaccine package insert PDF URL
vaccine package insert PDF URL
A number that is generated by FDA based on a request from an applicant of a product licensing.
Oliver He, Kallan Roan
vaccine submission’s tracking number
https://www.fda.gov/downloads/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/ProceduresSOPPs/UCM461225.pdf
BLA 101094
vaccine STN
RxNORM ID
RxNORM ID
has Protegen id
has Protegen id
has Protegen annotation
has Protegen annotation
As seen: http://purl.bioontology.org/ontology/RXNORM/901644, the RxNORM vaccine term "Prevnar 13 vaccine 0.5 ML Prefilled Syringe" has Preferred Name of: 0.5 ML Streptococcus pneumoniae serotype 1 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 14 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 18C capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 19A capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 19F capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 23F capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 3 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 4 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 5 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 6A capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 6B capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0088 MG/ML / Streptococcus pneumoniae serotype 7F capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 9V capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML Prefilled Syringe [Prevnar 13]". In this case, the whole preferred name is annotated under the annotation property "RxNORM Preferred Name".
RxNORM Preferred Name
RxNORM Preferred Name
An identifier assigned by the Vaccine Adjuvant Compendium (VAC: https://vac.niaid.nih.gov/)
https://vac.niaid.nih.gov/
VAC adjuvant ID
An annotation property that represents the annotated information about the antigens used for a specific vaccine.
Oliver He, Penny Pan
https://en.wikipedia.org/wiki/Antigen
vaccine antigen annotation
vaccine preparation annotation
vaccine response annotation
This is annotation property that refers to a specific CVX ID.
Penny Pan, Oliver He
https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx
CVX code
An annotation property that shows the status of vaccine developmeint including: clinical trial, research, licensed, or Emergency Use Authorization (EUA).
Oliver He, Jie Zheng, Anthony Huffman, Penny Pan
status of vaccine development
has_rank
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/18
has broad synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/18
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
has exact synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
has narrow synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
has related synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), 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.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
precedes
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
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
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
site of
[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
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
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
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
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
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
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 an organism and an organism that has vector role.
obsolete_has vector
true
A relation between an organism and an organism that has host role.
obsolete_has host
true
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
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.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a 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 journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
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
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
located in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
has boundary
has_2D_boundary
has 2D boundary
A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
x 'cell expresses' y iff:
cell(x)
AND gene(y)
AND exists some 'transcription, DNA templated (GO_0006351)'(t)
AND t occurs_in x
AND t has_input y
cell expresses
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
https://wiki.geneontology.org/Happens_during
David Osumi-Sutherland
o
overlaps
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Connects a biological entity to its taxon of origin.
in taxon
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.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
gene product of
every HOTAIR lncRNA is the gene product of some HOXC gene
every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
has gene product
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
over-expressed in
g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
under-expressed in
c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
has biological role
c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
has application role
c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
has chemical role
x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
ubiquitously expressed in
y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
expresses
inverse of ubiquiotously expressed in
ubiquitously expresses
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.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
inheres in part of
characteristic of part of
A relationship that holds via some environmental process
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
ecologically related to
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
member of
has member is a mereological relation between a collection and an item.
SIO
has member
X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
has host
has vector
depends on
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
towards
x is transcribed from y if and only if x is synthesized from template y
http://www.ncbi.nlm.nih.gov/pubmed/20226267
transcribed from
inverse of transcribed from
http://www.ncbi.nlm.nih.gov/pubmed/20226267
transcribed to
x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
http://www.ncbi.nlm.nih.gov/pubmed/20226267
ribosomal translation of
inverse of ribosomal translation of
http://www.ncbi.nlm.nih.gov/pubmed/20226267
ribosomally translates to
DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
DEPRECATED inheres in
true
DEPRECATED bearer of
true
a type of 'has vaccine component' relation that specifies a vaccine conjugate protein for a specific vaccine
has vaccine conjugate protein
YH
a type of 'has vaccine vector' relation that specifies a bacterial vaccine vector
has bacterial vaccine vector
has_vaccine_contraindication is a relation that specifies contraindication of a vaccine.
This relation may be replaced by has_vaccine_allergen. We need to determine if any vaccine contraindicator is not a vaccine allergen.
YH
has vaccine contraindication
a type of 'has vaccine vector' that is specifically for viral vaccine vector
has viral vaccine vector
a 'has vaccine component' relation that specifies the plasmid used for development of a particular DNA vaccine.
YH
has DNA vaccine plasmid
infection_of is a relation between a disorder and an infectious pathogen.
The relation 'infection_of' is introduced to represent an infection caused by an infectious pathogen. A pathogen infection is a disorder. Since the number of pathogens is large, there are numerous infections. To make the description of a specific infection simple, the shortcut term 'infection_of' is defined:
infection_of X = infection and has_part some (organism X and has_disposition some infectious disposition)
YH, XZ, MC, BP, AR
infection_of
an object property that specifies a process that is induced by vaccination of a vaccine
YH
induced by vaccination of
a 'has vaccine component' relation that specifies a gene inserted to DNA vaccine plasmid for development of a particular DNA vaccine, and this gene encodes for a protein antigen.
YH
has DNA vaccine antigen gene
an object property that defines a relation between a vaccine and its component
YL, YH
has vaccine component
an object property that specifies a vaccine antigen
YL, YH
This relation only works for those vaccine antigen that is physically part of a vaccine preparation. It does not include those antigens that are not part of vaccine. For example, a protein antigen expressed in a DNA vaccine is not a part of vaccine pe ser. In this case, the vaccine expresses the protein, but the gene is part of the vaccine, not the protein. For the case, we can use the relation 'DNA vaccine expresses protein antigen' under the relation 'expresses'.
has vaccine antigen
a type of 'has vaccine antigen' relation that is specifically for vaccine protective protein antigen used in subunit vaccine development
YL, YH
has subunit vaccine antigen
a type of 'has vaccine antigen' relation that is specifically for vaccine protective antigen component
YL, YH
has vaccine protective antigen
a type of 'has vaccine component' relation that is specifically for vaccine adjuvant component
YL, YH
has vaccine adjuvant
a type of 'has vaccine component' relation that is specifically for vaccine vector component
YL, YH
has vaccine vector
a object property that specifies a relation between a vaccine and a vaccine allergen
YH
has vaccine allergen
an object property that indicates a secretion of a material (e.g., protein) from a vaccine organism.
YH
vaccine organism secretes
YL, YH
a 'has vaccine component' relation that is specifically used for vaccine preservative
has vaccine preservative
an object property that specifies a relation between a vaccine and a vaccinate route
vaccinated in route
an object property that specifies a relation between a vaccine and its vaccinee
has vaccinee
YH
an 'expresses' relation that specifies a relation between a DNA vaccine and a protein antigen to be expressed by the DNA vaccine.
DNA vaccine expresses protein antigen
"A vaccinates B" means that the vaccine A is used for vaccinating the host B (e.g., human).
A relationship between a vaccine instance and an organism type such that if the vaccine instance is given to an instance of the organism by the process vaccination, then it changes the organism's disposition to have an immune response against a disease.
YH, AR, ZX, MC
vaccinates
has_vaccine_allegen is a relation that specifies an allegen to a vaccine.
YH
has_vaccine_allergen
an object property that represents a mutational relation between a vaccine organism and another material (e.g., gene or protein). the mutated material initially exists in the original wildtype organism.
YH
vaccine organism has mutation
YH
an object property that specifies a relation between a vaccine and a vaccine virmugen.
This is a short cut relation.
Domain: vaccine
Range: a gene
Shortcut:
is_specified_output_of some
('preparation of gene mutant vaccine' and (has_specified_input some gene))
has vaccine virmugen
YH
a 'has subunit vaccine antigen' relation that indicates the antigen is protective.
has subunit vaccine protective antigen
is_distributed_by is a relation that specifies a company that distributes a product (e.g., vaccine). The company is very likely not the manufacturer of the product.
YH, ZX
is_distributed_by
a shortcut relation that equals to:
'processed material' and (is_specified_output_of some 'vaccine preparation') and ('has function' some ('vaccine function' and ('is realized by' only ('vaccine immunization' and (realizes some ('vaccine host role' and (role_of some 'organism' and has_disposition some disease)))))))).
The domain of this relation is a vaccine.
The range of this relation is a disease.
Asiyah Yu Lin
Oliver He
immunization against disease
vaccine immunization against disease
immunizes against disease
an object property that represents an organism has a mutation of a specific gene from the organism genome.
Yongqun He
has gene mutation
a shortcut relation that equals to:
'processed material' and (is_specified_output_of some 'vaccine preparation') and ('has function' some ('vaccine function' and ('is realized by' only ('vaccine immunization' and (realizes some ('vaccine host role' and (role_of some 'organism')))))))).
The domain of this relation is a vaccine.
The range of this relation is a organism.
YL
Yongqun He
immunization for host
vaccine immunization for host
immunizes host
An object property that represents a relation between a vaccine with a prime-boost schedule and a vaccine used for priming.
Oliver He
has prime vaccine
An object property that represents a relation between a vaccine with a prime-boost schedule and a vaccine used for boost.
Oliver He
has boost vaccine
a shortcut relation that equals to:
processed material and (is_specified_output_of some vaccine preparation) and (has function some (vaccine function and (is realized by only (vaccine immunization and (realizes some ('immunization target role' and (role_of some 'MICROBE'))))))))
The domain of this relation is a vaccine.
The range of this relation is a microbe (a bacterium, a virus, a fungus, and a parasite)
Yongqun He
immunization against microbe
vaccine immunization against microbe
immunizes against microbe
a shortcut object property that represents a relation between a vaccine and a disease process where the vaccine immunizes a host against a disease process.
Oliver He
immunizes against disease process
An object property that represents a relation between a material entity and biological process
Anthony Huffman, Oliver He
up-expressed as immune signature of
An object property that represents a relation between a material entity (such as vaccine or vaccine adjuvant) and an immune profile where the material entity can induce the immune profile in a host.
Oliver He, Amogh Madireddi
induces immune profile
A vaccine adjuvant T-vant has molecular receptor of TLR4. Reference: https://vac.niaid.nih.gov/view?id=61.
An object property that represents a relation between a material entity and a molecular entitiy that serves as the molecular receptor to the material entity.
Oliver He
has molecular receptor
A relationship between relationship between a material entity and a parasite where the material entity causes some processagainst some parasite such that transmitting to additional hosts or vectors.
capable of blocking transmission (of life cycle)
A relationship between relationship between a vaccine and a parasite where the vaccine immunizes against some parasite such that transmitting to additional hosts or vectors.
Anthony Huffman, Anna Maria Masci, Oliver He, Jie Zheng
blocks transmission of pathogen via vaccine
A relationship between a vaccine X and organism Y where the vaccine X generates an immune response in a vaccinated organism and the immune product (e.g., antibody) can be transferred to the organism Y
Anthony Huffman, Anna Maria Masci, Oliver He, Jie Zheng
vaccine immunity response transferrable to organism
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
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
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
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
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]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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]
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
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]
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
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
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
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]
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
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
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
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])
Digestive gland of crustaceans with functions approximately analogous to liver and pancreas of vertebrates - enzyme secretion, food absorption and storage.
hepatopancreas
1: The trunk of an elephant; also: any long flexible snout. 2: Any of various elongated or extensible tubular processes as the sucking organ of a butterfly of the oral region of an invertebrate.
proboscis
An organic hydroxy compound that consists of benzene bearing a single hydroxy substituent. The parent of the class of phenols.
0
C6H6O
InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
94.11120
94.04186
Oc1ccccc1
CHEBI:14777
CHEBI:25966
CHEBI:43543
CHEBI:8071
Beilstein:969616
CAS:108-95-2
DrugBank:DB03255
Drug_Central:4266
Gmelin:2794
HMDB:HMDB0000228
KEGG:C00146
KEGG:C15584
KEGG:D00033
KEGG:D06536
KNApSAcK:C00002664
PDBeChem:IPH
PMID:12058733
PMID:16953321
PMID:17852157
PMID:19029204
PMID:20886261
PMID:21492257
PMID:21689881
PMID:21809019
PMID:21822930
Reaxys:969616
UM-BBD_compID:c0128
Wikipedia:Phenol
PHENOL
Phenol
phenol
chebi_ontology
Benzenol
Carbolsaeure
Hydroxybenzene
Karbolsaeure
Oxybenzene
PhOH
Phenic acid
Phenylic acid
Phenylic alcohol
acide carbolique
acide phenique
carbolic acid
CHEBI:15882
phenol
A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O).
0
CH4N2O
InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)
XSQUKJJJFZCRTK-UHFFFAOYSA-N
60.05534
60.03236
NC(N)=O
CHEBI:15292
CHEBI:27218
CHEBI:46379
CHEBI:9888
Beilstein:635724
CAS:57-13-6
DrugBank:DB03904
Drug_Central:4264
ECMDB:ECMDB04172
Gmelin:1378
HMDB:HMDB0000294
KEGG:C00086
KEGG:D00023
KNApSAcK:C00007314
MetaCyc:UREA
PDBeChem:URE
PMID:18037357
PMID:22770225
PPDB:1728
Reaxys:635724
UM-BBD_compID:c0165
Wikipedia:Urea
YMDB:YMDB00003
UREA
Urea
urea
chebi_ontology
1728
Carbamide
E927b
H2NC(O)NH2
Harnstoff
Karbamid
carbamide
carbonyldiamide
ur
uree
CHEBI:16199
urea
Liposaccharide natural compounds consisting of a trisaccharide repeating unit (two heptose units and octulosonic acid) with oligosaccharide side chains and 3-hydroxytetradecanoic acid units (they are a major constituent of the cell walls of Gram-negative bacteria).
CHEBI:14520
CHEBI:25062
CHEBI:6494
KEGG:C00338
PMID:15589368
PMID:24186868
PMID:24506665
PMID:24642373
PMID:24659348
Lipopolysaccharide
chebi_ontology
LPS
lipopolysaccharides
CHEBI:16412
lipopolysaccharide
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.
0
(C2H2NOR)nC2H3NOR
CHEBI:14753
CHEBI:25906
CHEBI:7990
KEGG:C00012
Peptide
peptides
chebi_ontology
Peptid
peptido
peptidos
CHEBI:16670
peptide
An aldehyde resulting from the formal oxidation of methanol.
0
CH2O
InChI=1S/CH2O/c1-2/h1H2
WSFSSNUMVMOOMR-UHFFFAOYSA-N
30.02598
30.01056
[H]C([H])=O
CHEBI:14274
CHEBI:24077
CHEBI:337763
CHEBI:5142
Beilstein:1209228
CAS:50-00-0
DrugBank:DB03843
Drug_Central:3244
Gmelin:445
HMDB:HMDB0001426
KEGG:C00067
KEGG:D00017
MetaCyc:FORMALDEHYDE
PDBeChem:FOR
PMID:110589
PMID:12686735
PMID:15091529
PMID:16423181
PMID:17618393
PMID:18837732
PMID:25042713
PMID:7381846
PMID:7548723
PMID:7689168
PMID:7896413
PMID:9686972
PPDB:359
Reaxys:1209228
UM-BBD_compID:c0122
Wikipedia:Formaldehyde
FORMALDEHYDE
Formaldehyde
formaldehyde
chebi_ontology
FORMALIN
Formaldehyd
Formalin
Methanal
Methylene oxide
Oxomethane
Oxomethylene
CHEBI:16842
formaldehyde
A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class
0
C21H39N7O12
InChI=1S/C21H39N7O12/c1-5-21(36,4-30)16(40-17-9(26-2)13(34)10(31)6(3-29)38-17)18(37-5)39-15-8(28-20(24)25)11(32)7(27-19(22)23)12(33)14(15)35/h4-18,26,29,31-36H,3H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/t5-,6-,7+,8-,9-,10-,11+,12-,13-,14+,15+,16-,17-,18-,21+/m0/s1
UCSJYZPVAKXKNQ-HZYVHMACSA-N
581.57434
581.26567
CN[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O[C@H]1[C@@H](O[C@@H](C)[C@]1(O)C=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](NC(N)=N)[C@@H](O)[C@@H]1NC(N)=N
CHEBI:15119
CHEBI:26784
CHEBI:45745
CHEBI:9284
Beilstein:74498
CAS:57-92-1
DrugBank:DB01082
Drug_Central:2481
HMDB:HMDB0015214
KEGG:C00413
KEGG:D08531
MetaCyc:STREPTOMYCIN
PDBeChem:SRY
PMID:11228320
PMID:11905029
PMID:12118520
PMID:13030054
PMID:13116094
PMID:13136149
PMID:13596285
PMID:13691614
PMID:13985260
PMID:13990247
PMID:14623118
PMID:14828344
PMID:14852338
PMID:14939639
PMID:15081082
PMID:15137533
PMID:15207172
PMID:15686853
PMID:15736038
PMID:16904706
PMID:17105735
PMID:17238915
PMID:17429930
PMID:18173084
PMID:18916143
PMID:19052412
PMID:19335957
PMID:21350946
PMID:21362244
PMID:21593257
PMID:21937264
PMID:22101040
Pesticides:streptomycin
Reaxys:74498
Wikipedia:Streptomycin
N,N'''-[(1R,2R,3S,4R,5R,6S)-4-{5-deoxy-2-O-[2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl]-3-C-formyl-alpha-L-lyxofuranosyloxy}-2,5,6-trihydroxycyclohexane-1,3-diyl]diguanidine
STREPTOMYCIN
chebi_ontology
2,4-Diguanidino-3,5,6-trihydroxycyclohexyl 5-deoxy-2-O-(2-deoxy-2-methylamino-alpha-L-glucopyranosyl)-3-C-formyl-beta-L-lyxopentanofuranoside
Kantrex
SM
[2-deoxy-2-(dimethylamino)-alpha-L-glucopyranosyl]-(1->2)-[5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl]-(1->4)-{N',N'''-[(1,3,5/2,4,6)-2,4,5,6-tetrahydroxycyclohexane-1,3-diyl]diguanidine}
streomycin
streptomycin
CHEBI:17076
streptomycin
A glycosylglucose disaccharide, found most notably in milk, that consists of D-galactose and D-glucose fragments bonded through a beta-1->4 glycosidic linkage. The glucose fragment can be in either the alpha- or beta-pyranose form, whereas the galactose fragment can only have the beta-pyranose form.
0
C12H22O11
InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10-,11?,12+/m1/s1
GUBGYTABKSRVRQ-QKKXKWKRSA-N
342.297
342.11621
OC[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](O)C(O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@H]1O
CHEBI:10296
CHEBI:10380
CHEBI:14497
CHEBI:22460
CHEBI:22760
CHEBI:25005
CHEBI:27755
CHEBI:613009
Beilstein:1292745
CAS:63-42-3
GlyGen:G74621DY
GlyTouCan:G74621DY
Gmelin:882872
KEGG:C00243
KEGG:D00046
KEGG:G10504
KNApSAcK:C00001136
PMID:1292745
PMID:17329833
PMID:18300214
PMID:19053747
PMID:19846069
PMID:19913595
PMID:20094999
PMID:20503067
PMID:20699559
PMID:20873837
PMID:20961532
PMID:21403918
PMID:2432147
PMID:2456994
PMID:28690131
PMID:28807538
PMID:6194884
PMID:7574700
Reaxys:1292745
beta-D-galactopyranosyl-(1->4)-D-glucopyranose
lactose
chebi_ontology
(+)-lactose
(Gal)1 (Glc)1
1-beta-D-Galactopyranosyl-4-D-glucopyranose
4-(beta-D-galactosido)-D-glucose
4-O-beta-D-galactopyranosyl-D-glucose
D-lactose
Galbeta1-4Glc
Lac
Laktobiose
Laktose
Milchzucker
Milk sugar
WURCS=2.0/2,2,1/[a2122h-1x_1-5][a2112h-1b_1-5]/1-2/a4-b1
beta-D-Gal-(1->4)-D-Glc
beta-D-Galp-(1->4)-D-Glcp
beta-Gal1,4-Glc
lactobiose
milk sugar
CHEBI:17716
lactose
Any of a group of aminoglycoside antibiotics produced by fermentation of some Micromonospora spp.
CHEBI:14293
CHEBI:24206
CHEBI:24212
CHEBI:5306
CAS:1403-66-3
DrugBank:DB00798
KEGG:C00505
4,6-diamino-3-[3-deoxy-4-C-methyl-3-(methylamino)pentopyranosyloxy]-2-hydroxycyclohexyl 2-amino-2,3,4,6,7-pentadeoxy-6-(methylamino)heptopyranoside
chebi_ontology
Gentamicin
gentamycins
CHEBI:17833
gentamycin
A glycosyl glycoside formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose.
0
C12H22O11
InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1
CZMRCDWAGMRECN-UGDNZRGBSA-N
342.29650
342.11621
OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
CHEBI:15128
CHEBI:26812
CHEBI:45795
CHEBI:9314
Beilstein:90825
CAS:57-50-1
DrugBank:DB02772
Drug_Central:4610
Gmelin:97695
HMDB:HMDB0000258
KEGG:C00089
KEGG:D00025
KEGG:D06533
KEGG:G00370
KNApSAcK:C00001151
MetaCyc:SUCROSE
PDBeChem:SUC
PMID:11021636
PMID:11093712
PMID:11111003
PMID:12065720
PMID:12706980
PMID:13508893
PMID:15291457
PMID:15660210
PMID:15792978
PMID:15845855
PMID:16228482
PMID:16304615
PMID:16313996
PMID:16525719
PMID:16660545
PMID:16663947
PMID:16665852
PMID:17233733
PMID:17439666
PMID:17597061
PMID:18625236
PMID:19199566
PMID:19726178
PMID:21703290
PMID:21972845
PMID:22085755
PMID:22311778
PMID:22404833
PMID:22751876
Reaxys:1435311
Reaxys:90825
Wikipedia:Sucrose
SUCROSE
Sucrose
beta-D-fructofuranosyl alpha-D-glucopyranoside
sucrose
chebi_ontology
1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside
Cane sugar
Saccharose
Sacharose
White sugar
beta-D-Fruf-(2<->1)-alpha-D-Glcp
sacarosa
table sugar
CHEBI:17992
sucrose
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
chebi_ontology
entidad molecular
entidades moleculares
entite moleculaire
molecular entities
molekulare Entitaet
CHEBI:23367
molecular entity
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
chebi_ontology
CHEBI:24431
chemical entity
An inorganic chloride salt having sodium(1+) as the counterion.
0
ClNa
InChI=1S/ClH.Na/h1H;/q;+1/p-1
FAPWRFPIFSIZLT-UHFFFAOYSA-M
58.44247
57.95862
[Na+].[Cl-]
Beilstein:3534976
CAS:7647-14-5
Gmelin:13673
KEGG:C13563
KEGG:D02056
MetaCyc:NACL
PPDB:595
Reaxys:3534976
Wikipedia:Sodium_Chloride
sodium chloride
chebi_ontology
Kochsalz
NaCl
Natriumchlorid
chlorure de sodium
cloruro sodico
common salt
halite
natrii chloridum
rock salt
salt
table salt
CHEBI:26710
sodium chloride
A dipeptide obtained by formal condensation of the alpha-carboxy group of L-aspartic acid with the amino group of methyl L-phenylalaninate. Commonly used as an artificial sweetener.
0
C14H18N2O5
InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1
IAOZJIPTCAWIRG-QWRGUYRKSA-N
294.304
294.12157
C(C[C@@H](C(N[C@@H](CC1=CC=CC=C1)C(=O)OC)=O)N)(=O)O
CHEBI:45047
Beilstein:2223850
CAS:22839-47-0
DrugBank:DB00168
HMDB:HMDB0001894
KEGG:C11045
KEGG:D02381
PDBeChem:PME
PMID:1771173
PMID:2013754
PMID:21150094
PMID:21372000
PMID:22354473
PMID:24355796
PMID:24925367
PMID:24944748
PMID:24965331
PMID:25431414
PMID:25543075
PMID:25786106
PMID:25951455
PMID:25991916
PMID:26015492
PMID:26099025
PMID:26159964
PMID:26247507
PMID:26308194
PMID:26321723
PMID:26377607
PMID:26582819
PMID:26593524
PMID:26912665
PMID:27015640
PMID:27038223
PMID:27088715
PMID:27127997
PMID:27216413
PMID:27298583
PMID:27492574
PMID:27565676
PMID:27614095
PMID:27640132
PMID:27699780
PMID:27728881
PMID:27840415
PMID:27845306
PMID:30000570
PMID:37291632
PMID:37297402
PMID:37454665
Patent:US3492131
Reaxys:2223850
Wikipedia:Aspartame
Aspartame
methyl L-alpha-aspartyl-L-phenylalaninate
chebi_ontology
1-methyl N-L-alpha-aspartyl-L-phenylalanate
3-Amino-N-(alpha-carboxyphenethyl)succinamic acid N-methyl ester
3-Amino-N-(alpha-methoxycarbonylphenethyl) succinamic acid
AminoSweet
Asp-phe-ome
Aspartylphenylalanine methyl ester
E 951
L-Aspartyl-L-phenylalanine methyl ester
NutraSweet
Sanecta
aspartam
aspartamo
aspartamum
CHEBI:2877
aspartame
0
C6H14O6
182.172
182.07904
CHEBI:15093
CHEBI:26724
CHEBI:26726
CHEBI:33795
CHEBI:33796
CHEBI:9201
Beilstein:1721909
Gmelin:83165
Wikipedia:Sorbitol
glucitol
chebi_ontology
Sorbitol
gulitol
rel-(2R,3R,4R,5S)-hexane-1,2,3,4,5,6-hexol
CHEBI:30911
glucitol
A 1,2-benzisothiazole having a keto-group at the 3-position and two oxo substituents at the 1-position. It is used as an artificial sweetening agent.
0
C7H5NO3S
InChI=1S/C7H5NO3S/c9-7-5-3-1-2-4-6(5)12(10,11)8-7/h1-4H,(H,8,9)
CVHZOJJKTDOEJC-UHFFFAOYSA-N
183.18500
182.99901
O=C1NS(=O)(=O)c2ccccc12
CHEBI:49717
Beilstein:6888
CAS:81-07-2
Gmelin:4203
HMDB:HMDB0029723
KEGG:D01085
MetaCyc:CPD-5581
PDBeChem:LSA
PMID:24456165
PMID:24549104
PMID:24739358
PMID:24780866
Reaxys:6888
Wikipedia:Saccharin
1,2-benzisothiazol-3(2H)-one 1,1-dioxide
Saccharin
chebi_ontology
1,1-Dioxo-1,2-benzisothiazol-3(2H)-one
1,1-Dioxo-1,2-dihydro-benzo[d]isothiazol-3-one
1,2-Benzisothiazol-3(2H)-one 1,1-dioxide
1,2-Benzisothiazolin-3-one 1,1-dioxide
1,2-Dihydro-2-ketobenzisosulfonazole
1,2-Dihydro-2-ketobenzisosulphonazole
2,3-Dihydro-3-oxobenzisosulfonazole
2,3-Dihydro-3-oxobenzisosulphonazole
3-Hydroxybenzisothiazole-S,S-dioxide
Anhydro-o-sulfaminebenzoic acid
Benzo-2-sulphimide
Benzoic acid sulfimide
Benzoic sulfimide
Benzoic sulphimide
Benzosulfimide
Benzosulphimide
Benzoylsulfonic Imide
Saccharimide
Saccharine
o-Benzoic sulfimide
o-Benzosulfimide
o-Sulfobenzimide
o-Sulfobenzoic acid imide
CHEBI:32111
saccharin
0
AlH3O3
H3AlO3
InChI=1S/Al.3H2O/h;3*1H2/q+3;;;/p-3
WNROFYMDJYEPJX-UHFFFAOYSA-K
78.00356
77.98976
[H]O[Al](O[H])O[H]
CHEBI:30193
CHEBI:31195
CAS:21645-51-2
Drug_Central:4250
Gmelin:22216
KEGG:C13391
KEGG:D02859
Wikipedia:Aluminum_Hydroxide
aluminium(3+) hydroxide
aluminium(III) hydroxide
trihydroxidoaluminium
chebi_ontology
Al(OH)3
Aluminiumhydroxid
Aluminum hydroxide
CHEBI:33130
aluminium hydroxide
CAS:7632-05-5
Wikipedia:Sodium_phosphates
sodium phosphate
chebi_ontology
phosphoric acid, sodium salt
sodium orthophosphate
sodium phosphates
sodium salt of phosphoric acid
CHEBI:37586
sodium phosphate
A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages.
CAS:9004-54-0
KEGG:C00372
KEGG:D00060
KEGG:D06541
KEGG:G10502
PMID:8154046
chebi_ontology
(1,6-alpha-D-Glucosyl)m
(1,6-alpha-D-Glucosyl)m+1
(1,6-alpha-D-Glucosyl)n
(1,6-alpha-D-Glucosyl)n+1
1,6-alpha-D-Glucan
Dextran 40
Dextran 70
Dextran 75
dextran
dextrane
dextrano
dextrans
dextranum
CHEBI:52071
dextran
A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a dodecanoyl group.
0
C58H114O26
1226.75977
1226.760
Beilstein:8973037
CAS:9005-64-5
KEGG:C11624
KEGG:D05565
Reaxys:8187252
Reaxys:8973037
Wikipedia:Polysorbate_20
chebi_ontology
Polyoxyethylene (20) sorbitan monolaurate
Polyoxyethylene sorbitan monolaurate
Polysorbate
Polysorbate 20
Tween 20
polisorbato
polysorbate
polysorbatum
CHEBI:53424
polysorbate 20
A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by an oleoyl group.
0
C64H124O26
1308.83802
1308.838
CHEBI:9785
Beilstein:8187125
CAS:9005-65-6
KEGG:C11625
KEGG:D01067
Reaxys:8187125
Reaxys:8190601
Reaxys:8898414
Reaxys:9040798
Wikipedia:Polysorbate_80
chebi_ontology
Glycol (polysorbate 80)
Polyethylene oxide sorbitan mono-oleate
Polyoxyethylene (20) sorbitan monooleate
Polyoxyethylene sorbitan monooleate
Polyoxyethylene sorbitan oleate
Polysorbate 80
Tween 80
polisorbato
polysorbate
polysorbatum
CHEBI:53426
polysorbate 80
An organic sodium salt that is the monosodium salt of glutamic acid.
0
C5H8NNaO4
InChI=1S/C5H9NO4.Na/c6-3(5(9)10)1-2-4(7)8;/h3H,1-2,6H2,(H,7,8)(H,9,10);/q;+1/p-1
LPUQAYUQRXPFSQ-UHFFFAOYSA-M
169.11110
169.03510
[Na+].[NH3+]C(CCC([O-])=O)C([O-])=O
PMID:22293291
Reaxys:17003240
sodium 2-azaniumylpentanedioate
chebi_ontology
MSG
sodium 2-ammoniopentanedioate
sodium glutamate
CHEBI:64220
monosodium glutamate
A broad-spectrum highly toxic antibiotic or mixture of antibiotics produced by a streptomyces (Streptomyces fradiae) and used medically especially to treat local infections.
CAS:1404-04-2
DrugBank:DB00994
KEGG:C00384
KEGG:D08260
Neomycin
chebi_ontology
CHEBI:7507
neomycin
An alkylmercury compound (approximately 49% mercury by weight) used as an antiseptic and antifungal agent.
0
C9H9HgNaO2S
C9H9HgO2S.Na
InChI=1S/C7H6O2S.C2H5.Hg.Na/c8-7(9)5-3-1-2-4-6(5)10;1-2;;/h1-4,10H,(H,8,9);1H2,2H3;;/q;;2*+1/p-2
RTKIYNMVFMVABJ-UHFFFAOYSA-L
404.81233
405.99274
[Na+].CC[Hg]Sc1ccccc1C([O-])=O
Beilstein:8169555
CAS:54-64-8
Gmelin:1677155
KEGG:D00864
PMID:18837732
PMID:21616561
PMID:21785120
PMID:22015977
PMID:22366633
PMID:22658806
PMID:22811707
PMID:23145070
PMID:23223227
PMID:23282150
PMID:23401210
PMID:23554557
PMID:23843785
PMID:23949514
PMID:23965928
PMID:23992327
PMID:25042713
PPDB:3062
Reaxys:8169555
VSDB:3062
Thimerosal
sodium [(2-carboxylatophenyl)sulfanyl](ethyl)mercurate(1-)
sodium ethyl[2-(sulfanyl-kappaS)benzoato(2-)]mercurate(1-)
chebi_ontology
Merthiolate
Thiomersal
[(o-carboxyphenyl)thio]ethylmercury sodium salt
ethyl(2-mercaptobenzoato-S)mercury sodium salt
ethylmercurithiosalicylate sodium
ethylmercurithiosalicylic acid sodium salt
mercurothiolate
o-(ethylmercurithio)benzoic acid sodium salt
sodium ethylmercurithiosalicylate
sodium merthiolate
thiomersal
thiomersalate
thiomersalum
tiomersal
CHEBI:9546
thimerosal
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
The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
hepatocyte
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
erythrocyte
A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
macrophage
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.
infectious disease
DOID:10115
DOID:11078
DOID:1304
DOID:1321
DOID:2040
DOID:2288
DOID:3099
DOID:4120
DOID:4620
DOID:5256
DOID:945
DOID:95
DOID:9532
DOID:9696
ICD9CM:079.0
UMLS_CUI:C0001485
infectious disease
disease_ontology
DOID:0050117
DO:wk
disease by infectious agent
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.
disease_ontology
DOID:0050338
primary bacterial infectious disease
A cancer that is classified by the type of cell from which it is derived.
snadendla
2011-06-13T03:28:50Z
disease_ontology
DOID:0050687
cell type cancer
A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
ICD10CM:A49.9
MESH:D001424
NCI:C2890
SNOMEDCT_US_2023_03_01:87628006
UMLS_CUI:C0004623
disease_ontology
DOID:104
bacterial infectious disease
A brucellosis that involves an infection caused by Brucella suis [NCBITaxon:29461] in swine and humans. The disease has_symptom fever, has_symptom chills, has_symptom malaise, has_symptom diaphoresis, has_symptom arthralgia, has_symptom myalgia, has_symptom headache, has_symptom anorexia, and has_symptom fatigue.
disease_ontology
DOID:11076
Brucella suis brucellosis
A primary bacterial infectious disease that is caused by the bacteria of the genus Brucella, when humans come in contact with contaminated animals or animal products or ingestion of infected food products. The disease has_symptom fever, has_symptom sweat, has_symptom headache, has_symptom back pain, has_symptom physical weakness, has_symptom joint pain and has_symptom fatigue.
DOID:0050060
GARD:5966
ICD10CM:A23
ICD9CM:023
MESH:D002006
NCI:C84602
SNOMEDCT_US_2023_03_01:154296006
UMLS_CUI:C0006309
Maltese fever
undulant fever
disease_ontology
Bang's disease
Gibraltar fever
Malta fever
Mediterranean fever
DOID:11077
brucellosis
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.
DOID:12552
EFO:0001068
GARD:6961
ICD10CM:B54
ICD9CM:084
MESH:D008288
NCI:C34797
SNOMEDCT_US_2023_03_01:154374002
UMLS_CUI:C0024530
induced malaria
disease_ontology
DOID:12365
Xref MGI.
malaria
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.
DOID:11681
DOID:13509
DOID:1396
DOID:1494
DOID:2114
DOID:2293
DOID:2922
DOID:3564
DOID:4191
DOID:886
DOID:948
DOID:9639
DOID:9644
ICD10CM:H44.12
ICD9CM:360.13
NCI:C34587
SNOMEDCT_US_2023_03_01:57100005
UMLS_CUI:C0014238
Ectoparasitic disease
parasitemia
disease_ontology
DOID:1398
parasitic infectious disease
A malaria described as a severe form of the disease caused by a parasite Plasmodium falciparum, which is marked by irrregular recurrence of paroxysms and prolonged or continuous fever.
ICD10CM:B50
ICD9CM:084.0
MESH:D016778
NCI:C34798
SNOMEDCT_US_2023_03_01:62676009
UMLS_CUI:C0024535
Malaria fever, subtertian
falciparum malaria
malignant tertian fever
disease_ontology
DOID:14067
Plasmodium falciparum malaria
A brucellosis that involves an infection caused by Brucella melitensis [NCBITaxon:29459] in cattle, goats, sheep and humans. The disease has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom limb pain and has_symptom back pain.
ICD10CM:A23.0
ICD9CM:023.0
SNOMEDCT_US_2023_03_01:186305007
UMLS_CUI:C0302362
disease_ontology
DOID:14456
Brucella melitensis brucellosis
A brucellosis that involves an infection caused by Brucella abortus [NCBITaxon:235] in cattle and humans. The disease has_symptom fever, has_symptom chills, has_symptom sweats, has_symptom weight loss, has_symptom malaise, has_symptom headaches, has_symptom myalgia, and has_symptom arthralgia.
ICD10CM:A23.1
ICD9CM:023.1
MESH:D002007
SNOMEDCT_US_2023_03_01:427795000
UMLS_CUI:C0302363
disease_ontology
DOID:14457
Brucella abortus brucellosis
A disease that is characterized by abnormally rapid cell division.
neoplasm
DOID:0000818
cell process disease
neoplasm
disease_ontology
DOID:14566
disease of cellular proliferation
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
DOID:3226
ICD10CM:J98
ICD9CM:519
SNOMEDCT_US_2023_03_01:155603009
UMLS_CUI:C0029582
disease_ontology
DOID:1579
respiratory system disease
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
ICD10CM:C80.1
ICD9CM:199
ICDO:8000/3
MESH:D009369
NCI:C9305
SNOMEDCT_US_2023_03_01:269513004
UMLS_CUI:C0006826
malignant neoplasm
malignant tumor
primary cancer
disease_ontology
DOID:162
Updating out dated UMLS CUI.
cancer
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye.
EFO:0000756
ICDO:8720/3
KEGG:05218
MESH:D008545
NCI:C3224
SNOMEDCT_US_2023_03_01:2092003
UMLS_CUI:C0025202
Naevocarcinoma
malignant melanoma
disease_ontology
DOID:1909
melanoma
MESH:D008545
A parasitic infectious disease that is caused by parasitic protozoa which are microorganisms classified as unicellular eukaryotes.
DOID:0060003
DOID:10553
DOID:3734
DOID:3804
DOID:947
ICD10CM:B64
MESH:D011528
NCI:C34953
SNOMEDCT_US_2023_03_01:95896000
UMLS_CUI:C0033740
mastigophora infectious disease
sarcomastigophora infectious disease
disease_ontology
DOID:2789
parasitic protozoa infectious disease
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
MESH:D004194
NCI:C2991
SNOMEDCT_US_2023_03_01:64572001
UMLS_CUI:C0012634
disease_ontology
DOID:4
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.
ICD10CM:B20
ICD9CM:042-042.99
MESH:D015658
NCI:C3108
SNOMEDCT_US_2023_03_01:86406008
UMLS_CUI:C0019693
HIV infection
disease_ontology
DOID:526
human immunodeficiency virus infectious disease
A disease that manifests in a defined anatomical structure.
DOID:1
DOID:2
DOID:5
DOID:71
DOID:72
DOID:8
disease_ontology
DOID:7
disease of anatomical entity
A viral infectious disease that results in infection, located in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness.
DOID:8468
ICD10CM:J11.1
ICD9CM:487
MESH:D007251
NCI:C53482
SNOMEDCT_US_2023_03_01:155559006
UMLS_CUI:C0021400
Influenza with other manifestations
flu
influenza with non-respiratory manifestation
disease_ontology
DOID:8469
influenza
A disease by infectious agent that results in infection, has_material_basis_in Viruses.
DOID:1329
ICD10CM:A94
ICD10CM:B34.9
ICD9CM:060-066.99
MESH:D001102
MESH:D014777
NCI:C3439
NCI:C34396
SNOMEDCT_US_2023_03_01:34014006
SNOMEDCT_US_2023_03_01:40610006
UMLS_CUI:C0003723
UMLS_CUI:C0042769
Viral Infection
Viral disease
virus infection
disease_ontology
DOID:934
viral infectious disease
fma
FMA:12278
Hormone
An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
Wikipedia:Adaptive_immune_system
acquired immune response
immune memory response
biological_process
GO:0002250
adaptive immune response
An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract.
GO:0002386
GO:0002422
immune response in MALT
immune response in mucosal-associated lymphoid tissue
immune response in urogenital tract
biological_process
GO:0002385
mucosal immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
biological_process
GO:0006955
immune response
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.
https://github.com/geneontology/go-ontology/issues/24968
jl
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
antibody
cellular_component
GO:0019814
Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
immunoglobulin 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.
GO:0043234
macromolecular complex
macromolecule complex
protein containing complex
protein complex
protein-protein complex
cellular_component
GO:0032991
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
protein-containing complex
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
GO:0051869
physiological response to stimulus
biological_process
GO:0050896
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to stimulus
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
cell division
A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
mah
2010-03-24T01:44:53Z
IgG1
IgG2
IgG2a
IgG2b
IgG2c
IgG3
IgG4
cellular_component
GO:0071735
Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species.
IgG immunoglobulin complex
A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
mah
2010-03-24T01:44:53Z
cellular_component
GO:0071738
Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
IgD immunoglobulin complex
A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
mah
2010-03-24T01:44:53Z
cellular_component
GO:0071742
Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
IgE immunoglobulin complex
A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
mah
2010-03-24T01:44:53Z
IgA1 antibody
IgA2 antibody
cellular_component
GO:0071745
Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
IgA immunoglobulin complex
A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
mah
2010-03-24T01:44:53Z
cellular_component
GO:0071753
Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
IgM immunoglobulin complex
conditional specification
A directive information entity that specifies what should happen if the trigger condition is fulfilled.
PlanAndPlannedProcess Branch
OBI branch derived
OBI_0000349
conditional specification
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
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
A report that is published in a journal.
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
OBI_0000159
group:OBI
journal article
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
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
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
report
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on
something that has completed." Should it be restricted to those things
that are completed? For example, a progress report is (usually) about
something that definitely has *not* been completed, or may include
(only) projections. I think the definition would not suffer if the
whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
GROUP: OBI
OBI_0000099
report
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, 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.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
Clint Dowland
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
https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131
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
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
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
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 symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen.
The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction.
parasite role
A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized.
infectious agent role
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 symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
primary host role
The role is realized in developmental and reproduction processes of the host's partner in symbiosis.
definitive host role
A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle.
intermediate host role
A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced.
parasite host role
An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role.
infectious agent vector role
An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
biological vector of infectious agent role
A disposition to initiate processes that result in a disorder.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
pathogenicity
A pathogenic disposition is realized in processes that create a disorder.
The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.
pathogenic disposition
A material entity with a pathogenic disposition.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
pathogen
A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
Albert Goldfain
Alexander Diehl
Lindsay Cowell
virulence factor
house mouse
mouse
NCBITaxon:85055
GC_ID:1
house mouse
mouse
ncbi_taxonomy
Mus musculus
GC_ID:1
rat
rats
ncbi_taxonomy
Rattus
NCBITaxon:84274
GC_ID:1
domestic guinea pig
guinea pig
ncbi_taxonomy
Cavia aperea porcellus
Cavia cobaya
Mus porcellus
Cavia porcellus
GC_ID:1
chinchillas
chinchillas and viscachas
ncbi_taxonomy
Chinchillidae
GC_ID:1
ncbi_taxonomy
Vira
Viridae
viruses
Viruses
GC_ID:1
ncbi_taxonomy
Poxviridae
GC_ID:1
ncbi_taxonomy
Chordopoxvirinae
GC_ID:1
ncbi_taxonomy
Orthopoxvirus
NCBITaxon:130669
NCBITaxon:130670
GC_ID:1
monkey pox virus
ncbi_taxonomy
Monkeypox virus
GC_ID:1
vaccinia virus VV
ncbi_taxonomy
Vaccinia virus
NCBITaxon:12871
GC_ID:1
small pox virus
smallpox
smallpox virus
variola virus VAR
ncbi_taxonomy
Variola virus
GC_ID:1
Contagious pustular dermatitis virus
ncbi_taxonomy
Orf virus
GC_ID:1
ncbi_taxonomy
Avipoxvirus
FWPV
GC_ID:1
Avipoxvirus clade A1
Fowlpoxvirus
fowl poxvirus
fowlpox virus FP
fowlpox virus FPV
ncbi_taxonomy
Fowlpox virus
GC_ID:1
Pigeon pox virus
Pigeon poxvirus
pigeonpox virus PPV
ncbi_taxonomy
Pigeonpox virus
GC_ID:1
H5N1
ncbi_taxonomy
H5N1 subtype
GC_ID:1
ncbi_taxonomy
Herpesviridae
GC_ID:1
Alphaherpesviruses
ncbi_taxonomy
Alphaherpesvirinae
GC_ID:1
ncbi_taxonomy
Simplexvirus
HSV-1
HSV1
GC_ID:1
Herpes simplex virus type 1
Human herpesvirus type 1
herpes simplex virus 1 HSV-1
herpes simplex virus HSV-1
herpes simplex virus type 1 HSV-1
herpes simplex virus type 1 HSV1
herpes simplex virus type-1 HSV-1
ncbi_taxonomy
Herpes simplex virus 1
Human herpesvirus 1
Human alphaherpesvirus 1
HSV2
GC_ID:1
Herpes simplex virus (type 2)
Herpes simplex virus II
Herpes simplex virus type 2
Herpes simplex virus type 2 (HSV-2)
Human herpesvirus 2
ncbi_taxonomy
Herpes simplex virus 2
herpes simplex virus type 2 HSV-2
Human alphaherpesvirus 2
GC_ID:1
ncbi_taxonomy
Varicellovirus
NCBITaxon:11265
NCBITaxon:12738
BoHV-1
GC_ID:1
Bovine herpesvirus 1
Bovine herpesvirus type 1
Bovine herpesvirus-1
Bovine rhinotracheitis virus
bovine herpesvirus 1 BHV 1
bovine herpesvirus 1 BHV-1
bovine herpesvirus 1 BHV1
bovine herpesvirus BHV-1
bovine herpesvirus type 1 BHV-1
bovine herpesvirus type-1 BHV-1
infectious bovine rhinotracheitis virus BHV-1
ncbi_taxonomy
Infectious bovine rhinotracheitis virus
Bovine alphaherpesvirus 1
EHV-1
GC_ID:1
Equid herpesvirus 1
Equine herpesvirus 1
Equine herpesvirus type 1
Equine herpesvirus-1
equine abortion virus
equine herpesvirus 1 EHV-1
equine herpesvirus type-1
ncbi_taxonomy
equine herpesvirus type 1 EHV-1
Equid alphaherpesvirus 1
GC_ID:1
Felid herpesvirus 1
Feline alphaherpesvirus 1
Feline herpesvirus 1
Feline herpesvirus type 1
feline herpesvirus
feline herpesvirus type 1 FHV-1
feline herpesvirus-1
feline herpesvirus-1 FHV-1
ncbi_taxonomy
Felid alphaherpesvirus 1
HHV-3
VZV
GC_ID:1
Human herpes virus 3
Human herpesvirus 3
Varicella Zoster Virus
Varicella-zoster virus
varicella zoster virus VZV
varicella-zoster virus VZV
ncbi_taxonomy
Human alphaherpesvirus 3
NCBITaxon:44156
PRV
GC_ID:1
Alphaherpesvirus pseudorabies virus PRV
Aujeszky's disease virus
Pseudorabies Virus PRV
Pseudorabies virus
Suid herpesvirus 1
Suid herpesvirus type 1
ncbi_taxonomy
Suid alphaherpesvirus 1
GC_ID:1
Betaherpesviruses
ncbi_taxonomy
Betaherpesvirinae
HHV-5
GC_ID:1
Human cytomegalovirus
Human herpesvirus 5
human herpesvirus type 5
ncbi_taxonomy
Human betaherpesvirus 5
GC_ID:1
Mouse cytomegalovirus 1
Murid herpesvirus 1
Murine cytomegalovirus
murine cytomegalovirus (MCMV)
murine cytomegalovirus MCMV
murine herpesvirus 1
ncbi_taxonomy
Murid betaherpesvirus 1
NCBITaxon:10342
NCBITaxon:12743
NCBITaxon:46620
GaHV-1
ILTV
GC_ID:1
Avian infectious laryngotracheitis virus
Gallid herpesvirus 1
Gallid herpesvirus type 1
Laryngotracheitis virus
infectious laryngotracheitis virus ILTV
ncbi_taxonomy
Infectious laryngotracheitis virus
Gallid alphaherpesvirus 1
NCBITaxon:38013
NCBITaxon:39111
NCBITaxon:43684
GaHV-2
MDV1
GC_ID:1
Gallid herpesvirus 2
Gallid herpesvirus type 2
Marek disease virus
Marek disease virus type 1
Marek's disease herpesvirus
Marek's disease herpesvirus 1
Marek's disease virus
Marek's disease virus (MDV)
Marek's disease virus MDV
Marek's disease virus MDV1
Marek's disease virus serotype 1 MDV-1
Marek's disease virus type 1 MDV1
Mareks disease virus
ncbi_taxonomy
Marek's disease virus type 1
Gallid alphaherpesvirus 2
GC_ID:1
mammalian hepatitis B-type viruses
ncbi_taxonomy
Orthohepadnavirus
HBV
GC_ID:1
Human hepatitis B virus
hepatitis B virus (HBV)
hepatitis B virus HBV
hepatitis B virus, HBV
human hepatitis B virus HBV
ncbi_taxonomy
Hepatitis B virus
NCBITaxon:72150
GC_ID:1
Anatid Herpes virus-1
Anatid herpesvirus 1
Duck enteritis virus
Duck plague virus
ncbi_taxonomy
Anatid alphaherpesvirus 1
GC_ID:1
Baculovirus
Baculovirus sp.
ncbi_taxonomy
unidentified baculovirus
ASFV
GC_ID:1
African swine fever virus ASF
African swine fever virus ASFV
African swine fever virus, ASFV
ncbi_taxonomy
African swine fever virus
GC_ID:1
ncbi_taxonomy
Adenoviridae
GC_ID:1
ncbi_taxonomy
Mastadenovirus
NCBITaxon:12607
GC_ID:1
Canine adenovirus type 1
Canine adenovirus type 1 Cav-1
Mastadenovirus c1
Mastadenovirus can1
canine adenovirus type 1 Can1
dog adenovirus 1
ncbi_taxonomy
Canine adenovirus 1
GC_ID:1
Canine adenovirus type 2
Canine adenovirus type 2 Cav-1
Mastadenovirus c2
Mastadenovirus can2
dog adenovirus 2
ncbi_taxonomy
Canine adenovirus 2
GC_ID:1
Adenovirus
ncbi_taxonomy
unidentified adenovirus
GC_ID:1
Canine adenovirus
Canine adenovirus A
ncbi_taxonomy
Canine mastadenovirus A
GC_ID:1
Human Papilloma Virus
human papillomavirus HPV
ncbi_taxonomy
Human papillomavirus
GC_ID:1
ncbi_taxonomy
Bovine papillomavirus
GC_ID:11
ncbi_taxonomy
Clostridium perfringens (type D)
Clostridium perfringens D
FPLV
GC_ID:1
Feline panleucopenia virus
Feline panleukopaenia virus
ncbi_taxonomy
Feline panleukopenia virus
GC_ID:1
ncbi_taxonomy
Feline panleukopenia virus (strain 193)
CPV
GC_ID:1
ncbi_taxonomy
Canine parvovirus
MEV
GC_ID:1
ncbi_taxonomy
Mink enteritis virus
PPV
GC_ID:1
porcine parvovirus PPV
ncbi_taxonomy
Porcine parvovirus
GC_ID:1
Orbiviridae
Orbiviruses
ncbi_taxonomy
Orbivirus
GC_ID:1
Rotaviruses
ncbi_taxonomy
Rotavirus
GC_ID:1
ncbi_taxonomy
Porcine rotavirus
GC_ID:1
bovine rotavirus BRV
ncbi_taxonomy
Bovine rotavirus
GC_ID:1
ncbi_taxonomy
Equine rotavirus
GC_ID:1
ncbi_taxonomy
Birnaviridae
NCBITaxon:12740
IBDV
GC_ID:1
Avian infectious bursal disease virus
Gumboro virus
Infectious bursal disease virus of chickens
infectious bursal disease virus IBDV
ncbi_taxonomy
Infectious bursal disease virus
NCBITaxon:12744
IPNV
GC_ID:1
infectious pancreatic necrosis virus IPNV
ncbi_taxonomy
Infectious pancreatic necrosis virus
GC_ID:1
Alphaviridae
arboviruses group A
ncbi_taxonomy
Alphavirus
GC_ID:1
Eastern equine encephalomyelitis virus
eastern equine encephalomyelitis EEE
eastern equine encephalomyelitis virus EEEV
ncbi_taxonomy
Eastern equine encephalitis virus
GC_ID:1
ncbi_taxonomy
Sindbis virus
VEE
VEEV
GC_ID:1
Venezuelan equine encephalitis VEE
Venezuelan equine encephalitis virus VEE
Venezuelan equine encephalomyelitis virus
ncbi_taxonomy
Venezuelan equine encephalitis virus
GC_ID:1
ncbi_taxonomy
Western equine encephalomyelitis virus
Western equine encephalitis virus
GC_ID:1
ncbi_taxonomy
Rubivirus
GC_ID:1
ncbi_taxonomy
Rubella virus
EAV
GC_ID:1
ncbi_taxonomy
Equine arteritis virus
GC_ID:1
Flavivirus (arbovirus group B)
ncbi_taxonomy
Flaviviridae
GC_ID:1
arboviruses group B
ncbi_taxonomy
Flavivirus
GC_ID:1
Japanese encephalitis (JE) virus
Japanese encephalitis virus JE
Japanese encephalitis virus JEV
ncbi_taxonomy
Japanese encephalitis virus
WNV
GC_ID:1
ncbi_taxonomy
West Nile virus
TBEV
GC_ID:1
FSME virus
Tick born encephalitis virus
tick-borne encephalitis virus TBE virus
tick-borne encephalitis virus TBEV
ncbi_taxonomy
Tick-borne encephalitis virus
YFV
GC_ID:1
Flavivirus febricis
yellow fever virus YFV
ncbi_taxonomy
Yellow fever virus
GC_ID:1
PMID:12832207
PMID:7747470
ncbi_taxonomy
Pestivirus
NCBITaxon:12625
NCBITaxon:54314
GC_ID:1
PMID:7747470
Hog cholera virus
Pestivirus type 2
classical swine fever virus CSFV
swine fever virus
ncbi_taxonomy
Classical swine fever virus
NCBITaxon:121864
BVDV
BVDV-1
GC_ID:1
PMID:7747470
Bovine viral diarrhea virus
Bovine viral diarrhea virus type 1
Bovine viral diarrhea virus-1
Mucosal disease virus
Pestivirus type 1
bovine viral diarrhea virus BVDV
bovine viral diarrhea virus type I
ncbi_taxonomy
Bovine viral diarrhea virus 1
GC_ID:11
PMID:11411686
PMID:28066339
ncbi_taxonomy
Porphyromonas gulae
GC_ID:1
ncbi_taxonomy
Coronaviridae
IBV
GC_ID:1
Avian infectious bronchitis virus
avian infectious bronchitis coronavirus IBV
avian infectious bronchitis virus IBV
avian infectious bronchitis virus, IBV
infectious bronchitis virus IBV
ncbi_taxonomy
Infectious bronchitis virus
BCV
BECV
GC_ID:1
Bovine enteritic coronavirus
Bovine enteritic coronavirus BECV
bovine coronavirus BCV
bovine enteric coronavirus
calf diarrheal coronavirus
neonatal calf diarrhea virus
ncbi_taxonomy
Bovine coronavirus
FIPV
GC_ID:1
ncbi_taxonomy
Feline infectious peritonitis virus
NCBITaxon:12859
TGEV
GC_ID:1
Porcine transmissable gastroenteritis coronavirus
Porcine transmissible gastroenteritis coronavirus
porcine transmissible gastroenteritis virus
transmissible gastroenteritis coronavirus
transmissible gastroenteritis virus TGEV
ncbi_taxonomy
Transmissible gastroenteritis virus
GC_ID:1
Canine enteric coronavirus
canine coronavirus CCV
ncbi_taxonomy
Canine coronavirus
GC_ID:1
negative-sense genome single-stranded RNA viruses
ncbi_taxonomy
Mononegavirales
GC_ID:1
ncbi_taxonomy
Paramyxoviridae
GC_ID:1
Morbilliviruses
ncbi_taxonomy
Morbillivirus
NCBITaxon:11230
GC_ID:1
Cell-associated subacute sclerosing panencephalitis
Measles virus
Subacute sclerosing panencephalitis virus
measles virus MV
rougeole virus
rubeola virus
subacute sclerose panencephalitis virus
subacute sclerosing panencephalitis virus, SSPEV
ncbi_taxonomy
Measles morbillivirus
RDV
GC_ID:1
Rinderpest virus
rinderpest virus RPV
rinderpest virus RV
ncbi_taxonomy
Rinderpest morbillivirus
GC_ID:1
Pneumovirinae
ncbi_taxonomy
Pneumoviridae
NCBITaxon:12604
BRS
BRSV
GC_ID:1
Bovine respiratory syncytial virus
bovine RSV
bovine respiratory syncytial virus BRSV
ncbi_taxonomy
Bovine orthopneumovirus
HRSV
GC_ID:1
Human respiratory syncytial virus
human RSV
ncbi_taxonomy
Human orthopneumovirus
NCBITaxon:11267
GC_ID:1
Filovirus
ncbi_taxonomy
Filoviridae
GC_ID:1
PMID:16186241
ncbi_taxonomy
Rhabdoviridae
GC_ID:1
ncbi_taxonomy
Lyssavirus
NCBITaxon:12873
NCBITaxon:12874
VHSV
GC_ID:1
Haemorrhagic septicemia virus
Hemorrhagic septicemia virus
Viral haemorrhagic septicaemia virus
hemorragic septicemy virus of fish
viral haemorrhagic scepticaemia virus VHS
viral haemorrhagic septicaemia virus VHSV
viral hemorrhagic septicemia virus VHSV
ncbi_taxonomy
Viral hemorrhagic septicemia virus
IHNV
GC_ID:1
ncbi_taxonomy
Infectious hematopoietic necrosis virus
GC_ID:1
Rabies lyssavirus
Rabies virus
ncbi_taxonomy
Lyssavirus rabies
GC_ID:1
ncbi_taxonomy
Orthomyxoviridae
GC_ID:1
Influenza virus
Influenza virus sp.
Influenzavirus
avian influenza virus
ncbi_taxonomy
unidentified influenza virus
GC_ID:1
Dhori thogotovirus
Dhori virus
Tick-borne virus
ncbi_taxonomy
Thogotovirus dhoriense
FLUAV
GC_ID:1
Human Influenza A Virus
Influenza virus type A
influenza A virus
ncbi_taxonomy
Influenza A virus
GC_ID:1
H1N1
ncbi_taxonomy
H1N1 subtype
RVFV
GC_ID:1
ncbi_taxonomy
Rift Valley fever virus
NCBITaxon:11835
NCBITaxon:11872
NCBITaxon:36380
GC_ID:1
Avian reticuloendotheliosis virus
reticuloendotheliosis virus A REV-A
reticuloendotheliosis virus REV-A
ncbi_taxonomy
Reticuloendotheliosis virus
GC_ID:1
Lentivirinae
ncbi_taxonomy
Lentivirus
FIV
GC_ID:1
feline immunodeficiency virus FIV
ncbi_taxonomy
Feline immunodeficiency virus
NCBITaxon:11677
NCBITaxon:11739
NCBITaxon:11740
CIV
SIV
GC_ID:1
Chimpanzee immunodeficiency virus
Chimpanzee immunodeficiency virus (SIV(CPZ))
Simian immunodeficiency virus SIVcpz
simian immunodeficiency virus SIV
simian immunodeficiency virus, SIV
simian immunodeficiency viruses SIV
ncbi_taxonomy
Simian immunodeficiency virus
GC_ID:1
fish
fishes
ncbi_taxonomy
Agnatha
Hyperotreti
Myxini
NCBITaxon:40673
GC_ID:1
bony vertebrates
ncbi_taxonomy
Euteleostomi
NCBITaxon:11920
GC_ID:1
Feline leukemia provirus
feline leukemia virus FeLV
ncbi_taxonomy
Feline leukemia virus
BLV
GC_ID:1
bovine leukemia virus BLV
bovine leukemia virus, BLV
ncbi_taxonomy
Bovine leukemia virus
GC_ID:1
ncbi_taxonomy
Enoplea
GC_ID:1
ncbi_taxonomy
Caliciviridae
NCBITaxon:12806
NCBITaxon:31701
RHDV
GC_ID:1
Rabbit haemorrhagic disease virus
rabbit hemorrhagic disease virus RHDV
ncbi_taxonomy
Rabbit hemorrhagic disease virus
FCV
GC_ID:1
Feline vesivirus
feline calicivirus FCV
ncbi_taxonomy
Feline calicivirus
GC_ID:1
ncbi_taxonomy
Picornavirus
Picornaviridae
NCBITaxon:12128
GC_ID:1
Enteroviruses
ncbi_taxonomy
Enterovirus
GC_ID:1
ncbi_taxonomy
Coxsackievirus
GC_ID:1
ncbi_taxonomy
Ecdysozoa
HPV-1
PV1
GC_ID:1
Human poliovirus 1
Human poliovirus type 1
Polio virus 1
Poliovirus type 1
poliovirus type 1 PV1
ncbi_taxonomy
Poliovirus 1
HPV-2
GC_ID:1
Human Poliovirus type 2
Human poliovirus 2
Poliovirus type 2
ncbi_taxonomy
Poliovirus 2
HPV-3
GC_ID:1
Human poliovirus 3
Human poliovirus type 3
Polio virus 3
ncbi_taxonomy
Poliovirus serotype 3
Poliovirus type 3
Poliovirus 3
GC_ID:1
ncbi_taxonomy
Hepatovirus
HAV
GC_ID:1
Hepatitis A virus
ncbi_taxonomy
Hepatovirus A
FMDV
GC_ID:1
Foot and mouth disease virus
foot and mouth disease virus FMDV
foot-and-mouth disease virus FMDV
ncbi_taxonomy
Foot-and-mouth disease virus
GC_ID:11
PMID:11321122
PMID:11837318
purple photosynthetic bacteria and relatives
ncbi_taxonomy
"Alphaproteobacteriota" Whitman et al. 2018
Alphaproteobacteriota
Proteobacteria
Proteobacteriota
proteobacteria
Pseudomonadota
GC_ID:11
PMID:23334881
ncbi_taxonomy
Proteobacteria gamma subdivision
Pseudomonadia
Purple bacteria, gamma subdivision
g-proteobacteria
gamma proteobacteria
gamma subdivision
gamma subgroup
Gammaproteobacteria
GC_ID:11
PMID:1371057
ncbi_taxonomy
Piscirickettsia salmonis
NCBITaxon:31968
GC_ID:11
PMID:10555317
PMID:11034484
PMID:11542017
PMID:15143038
PMID:25403554
PMID:37409558
Firmicutes
low G+C Gram-positive bacteria
low GC Gram+
ncbi_taxonomy
"Firmicutes" corrig. Gibbons and Murray 1978 (Approved Lists 1980)
Bacillaeota
Bacillota corrig. Gibbons and Murray 2021
Bacillus/Clostridium group
Clostridium group firmicutes
Firmicuteota
Low G+C firmicutes
clostridial firmicutes
firmicutes
Bacillota
BDV
GC_ID:1
PMID:25449305
Borna disease virus BDV
ncbi_taxonomy
Borna disease virus
NCBITaxon:12682
HDV
GC_ID:1
Hepatitis D virus
hepatitis delta virus HDV
ncbi_taxonomy
Hepatitis delta virus
CAV
GC_ID:1
Chicken infectious anemia virus
chicken anaemia agent CAA
chicken anemia virus CAV
chicken anemia virus, CAV
ncbi_taxonomy
chicken anaemia agent virus CAA
Chicken anemia virus
GC_ID:1
ncbi_taxonomy
Dengue virus
HIV
GC_ID:1
ncbi_taxonomy
AIDS virus
Human immunodeficiency virus
GC_ID:11
PMID:10319469
PMID:10319495
PMID:10425778
PMID:10758876
PMID:12656157
PMID:17220435
PMID:9734063
ncbi_taxonomy
Aurococcus
Staphylococcus
NCBITaxon:325213
NCBITaxon:46170
NCBITaxon:72759
GC_ID:11
PMID:31023808
PMID:8573498
ncbi_taxonomy
Micrococcus aureus
Micrococcus pyogenes
Staphlococcus pyogenes citreus
Staphylococcus aureus subsp. anaerobius
Staphylococcus pyogenes aureus
Staphylococcus aureus
RSV
GC_ID:1
respiratory syncytial virus RS
respiratory syncytial virus RS virus
respiratory syncytial virus RSV
ncbi_taxonomy
Respiratory syncytial virus
GC_ID:1
ncbi_taxonomy
Swine influenza virus
GC_ID:11
PMID:10555340
PMID:14657115
PMID:1720654
PMID:19620365
PMID:19880633
PMID:7537076
PMID:8995803
ncbi_taxonomy
Streptococcus
GC_ID:11
PMID:23245487
PMID:5220563
PMID:9731300
PMID:9734065
ncbi_taxonomy
Streptococcus suis
NCBITaxon:76757
GC_ID:11
PMID:15774692
PMID:8995807
ncbi_taxonomy
Streptoccocus de la mammite
Streptococcus agalactiae contagiosae
Streptococcus difficile
Streptococcus difficilis
Streptococcus mastitidis
Streptococcus agalactiae
GC_ID:11
ncbi_taxonomy
Diplococcus pneumoniae
Micrococcus pneumoniae
Streptococcus pneumoniae
GC_ID:11
ncbi_taxonomy
Micrococcus scarlatinae
Streptococcus erysipelatos
Streptococcus hemolyticus
Streptococcus scarlatinae
Streptococcus pyogenes
MERS
MERS-CoV
GC_ID:1
MERS coronavirus
MERS virus
Middle East Respiratory Syndrome Coronavirus (MERS-CoV)
Middle East respiratory syndrome coronavirus
ncbi_taxonomy
Middle East respiratory syndrome-related coronavirus
GC_ID:11
ncbi_taxonomy
Streptococcus equi
GC_ID:1
ncbi_taxonomy
Dicentrarchus
GC_ID:1
European sea bass
European seabass
ncbi_taxonomy
Labrax labrax
Morone labrax
Perca labrax
Roccus labrax
Sciaena labrax
Dicentrarchus labrax
GC_ID:11
PMID:11075904
PMID:11542017
PMID:16558735
PMID:1917844
PMID:23908650
ncbi_taxonomy
spirochetes
Spirochaetales
NCBITaxon:2954866
GC_ID:11
ncbi_taxonomy
Bacillus/Staphylococcus group
Caryophanales
Bacillales
GC_ID:11
PMID:10843090
PMID:11491334
PMID:1742196
PMID:2223602
PMID:23475340
PMID:7727277
PMID:8138135
PMID:8863420
Bacillus
Bacillus rRNA group 1
ncbi_taxonomy
Bacillus <firmicutes>
NCBITaxon:138953
GC_ID:1
Enterovirus EV-C
Human enterovirus C
Poliovirus
ncbi_taxonomy
Enterovirus C
GC_ID:11
PMID:1380285
PMID:1503971
PMID:24744012
PMID:7699027
PMID:7981102
PMID:8995796
PMID:9336916
Lyme disease spirochete
ncbi_taxonomy
Borrelia burgdorferi
Borreliella burgdorferi
NCBITaxon:1494525
NCBITaxon:1494531
NCBITaxon:1494577
GC_ID:11
PMID:8123566
anthrax
anthrax bacterium
ncbi_taxonomy
Bacillus cereus var. anthracis
Bacteridium anthracis
Bacillus anthracis
GC_ID:1
PMID:11743200
PMID:11791233
ncbi_taxonomy
Boreotheria
Boreoeutheria
NCBITaxon:69207
GC_ID:11
PMID:26643615
PMID:27488356
ncbi_taxonomy
Anaerobacter
Clostridium
GC_ID:1
ncbi_taxonomy
Euteleosteomorpha
NCBITaxon:29368
GC_ID:11
PMID:10028279
PMID:15244052
ncbi_taxonomy
Bacillus botulinus
Bacillus putrificus
Botulobacillus botulinus
Clostridium putrificum
Ermengemillus botulinus
Pacinia putrifica
Clostridium botulinum
NCBITaxon:2588446
NCBITaxon:2588447
NCBITaxon:41533
NCBITaxon:592
GC_ID:11
PMID:10758910
Salmonella enterica serovar Enteritidis
ncbi_taxonomy
Bacillus enteritidis
Salmonella enteritidis
Salmonella enterica subsp. enterica serovar Enteritidis
GC_ID:1
ncbi_taxonomy
Canine parainfluenza virus
GC_ID:11
PMID:11043982
ncbi_taxonomy
Yersinia enterocolitica subsp. enterocolitica
NCBITaxon:1683536
GC_ID:11
PMID:1374625
PMID:184898
ncbi_taxonomy
'Clostridium plagarum'
Bacillus perfringens
Bacterium welchii
Clostridium plagarum
Clostridium perfringens
NCBITaxon:10781
GC_ID:1
Parvovirus
Parvoviruses
ncbi_taxonomy
Protoparvovirus
GC_ID:11
ncbi_taxonomy
Bacillus tetani
Clostridium tetani
GC_ID:1
PMID:20206957
Papillomavirus
ncbi_taxonomy
Papillomaviridae
GC_ID:1
ncbi_taxonomy
Polyomaviridae
NCBITaxon:11762
GC_ID:1
MLV-related viruses
Mammalian type C retrovirus group
Mammalian type C retroviruses
mammalian type C oncoviruses
type C oncoviruses
ncbi_taxonomy
Gammaretrovirus
GC_ID:1
ncbi_taxonomy
Galloanseri
ducks, geese, chickens, fowl, quail, currasows and allies
Galloanserae
Bulinus
GC_ID:11
ncbi_taxonomy
Microspironema pallidum
Spirillum pallidum
Spirochaeta pallida
Spironema pallidum
Treponema pallidum
HMPV
GC_ID:1
ncbi_taxonomy
Human metapneumovirus
GC_ID:1
ncbi_taxonomy
Metapneumovirus
NCBITaxon:1634566
NCBITaxon:2293539
NCBITaxon:2293540
NCBITaxon:2293541
NCBITaxon:2293542
NCBITaxon:2293543
NCBITaxon:2293544
NCBITaxon:2293545
NCBITaxon:2293546
NCBITaxon:2293547
NCBITaxon:2364651
NCBITaxon:2364652
NCBITaxon:2364653
NCBITaxon:2364654
NCBITaxon:2364655
NCBITaxon:2364656
NCBITaxon:2364657
NCBITaxon:2364658
NCBITaxon:2364659
NCBITaxon:2364660
NCBITaxon:2482733
NCBITaxon:2482734
NCBITaxon:2482735
NCBITaxon:2482736
NCBITaxon:2482737
NCBITaxon:2482738
NCBITaxon:2482739
NCBITaxon:2482740
NCBITaxon:2482741
NCBITaxon:2482742
NCBITaxon:2482743
NCBITaxon:2482744
NCBITaxon:2482745
NCBITaxon:2482746
NCBITaxon:2482747
NCBITaxon:2482748
NCBITaxon:2482749
NCBITaxon:2484857
NCBITaxon:2484858
NCBITaxon:2485082
NCBITaxon:2485083
NCBITaxon:2485084
NCBITaxon:2485085
NCBITaxon:2485086
NCBITaxon:2485087
NCBITaxon:2485088
NCBITaxon:2485089
NCBITaxon:2485090
NCBITaxon:2485091
NCBITaxon:2485092
NCBITaxon:2485093
NCBITaxon:2485094
NCBITaxon:2485095
NCBITaxon:2485096
NCBITaxon:2486732
NCBITaxon:2486733
NCBITaxon:2486734
NCBITaxon:2486735
NCBITaxon:2486736
NCBITaxon:2486737
NCBITaxon:2486738
NCBITaxon:2486739
NCBITaxon:2486740
NCBITaxon:2486741
GC_ID:11
PMID:17773427
PMID:1906732
PMID:8782698
ncbi_taxonomy
Bacterium monocytogenes
Bacterium monocytogenes hominis
Corynebacterium infantisepticum
Corynebacterium parvulum
Erysipelothrix monocytogenes
Listerella hepatolytica
Listeria monocytogenes
GC_ID:11
PMID:1503975
PMID:8427802
ncbi_taxonomy
Bacillus insidiosus
Bacillus rhusiopathiae suis
Bacterium rhusiopathiae
Erysipelothrix erysipeloides
Erysipelothrix insidiosa
Erysipelothrix murisepticus
Erysipelothrix porci
Erysipelothrix rhusiopathiae
GC_ID:11
ncbi_taxonomy
Yersinia pseudotuberculosis complex
GC_ID:1
ncbi_taxonomy
Mammarenavirus
NCBITaxon:12461
NCBITaxon:2953663
GC_ID:1
ncbi_taxonomy
Orthohepevirus A
Paslahepevirus balayani
NCBITaxon:29512
NCBITaxon:29514
NCBITaxon:29516
GC_ID:11
PMID:10425768
PMID:1581182
PMID:19868121
PMID:9103653
ncbi_taxonomy
Leptospira
NCBITaxon:144193
GC_ID:11
PMID:10425754
PMID:19661509
PMID:29760685
PMID:30186281
PMID:7547284
PMID:7547291
PMID:7547293
PMID:8186090
ncbi_taxonomy
Turicella
Corynebacterium
GC_ID:11
PMID:7729671
ncbi_taxonomy
Bacillus diphtheriae
Bacterium diphtheriae
Microsporon diphthericum
Microsporon diphtheriticum
Mycobacterium diphtheriae
Pacinia loeffleri
Corynebacterium diphtheriae
GC_ID:11
ncbi_taxonomy
Bacillus pseudotuberculosis
Bacillus pseudotuberculosis-ovis
Corynebacterium ovis
Corynebacterium preisz-nocardi
Corynebacterium pseudotuberculosis-ovis
Mycobacterium tuberculosis-ovis
Corynebacterium pseudotuberculosis
NCBITaxon:2843297
NCBITaxon:2843299
GC_ID:11
PMID:15545494
PMID:19867994
PMID:19868337
PMID:19972157
PMID:25288661
PMID:9542090
ncbi_taxonomy
Leptospira icteroides
Spirochaeta biflexa
Spirochaeta icterogenes
Spirochaeta icterohaemorrhagiae
Spirochaeta interrogans
Spirochaeta nodosa
Leptospira interrogans
GC_ID:1
ncbi_taxonomy
Passeroidea
GC_ID:11
ncbi_taxonomy
Leptospira hardjo
Leptospira interrogans serovar Hardjo
GC_ID:11
PMID:1380284
PMID:1581193
PMID:16014496
PMID:1883713
PMID:2275850
PMID:31296783
PMID:31649146
PMID:31649147
PMID:34554081
PMID:7547284
PMID:7547304
PMID:7907223
PMID:8863452
ncbi_taxonomy
Mycobacterium Lehmann and Neumann 1896 (Approved Lists 1980)
Mycobacterium
GC_ID:11
PMID:2397193
PMID:8347508
ncbi_taxonomy
Bacillus tuberculosis gallinarum
Mycobacterium tuberculosis avium
Mycobacterium tuberculosis typus gallinaceus
Tuberculose des oiseaux
Mycobacterium avium
NCBITaxon:115863
GC_ID:11
PMID:10618079
PMID:11931153
PMID:14657105
PMID:29205127
ncbi_taxonomy
Mycobacterium bovis
Mycobacterium tuberculosis typus bovinus
Mycobacterium tuberculosis var. bovis
Mycobacterium tuberculosis variant bovis
GC_ID:11
ncbi_taxonomy
Bacillus leprae
Mycobacterium leprae
NCBITaxon:2528440
GC_ID:11
PMID:29205127
ncbi_taxonomy
Bacillus tuberculosis
Bacterium tuberculosis
Mycobacterium tuberculosis typus humanus
Mycobacterium tuberculosis var. hominis
Mycobacterium tuberculosis variant tuberculosis
Mycobacterium tuberculosis
GC_ID:11
PMID:12089250
PMID:20668542
ncbi_taxonomy
Mycobacterium balnei
Mycobacterium platypoecilus
Mycobacterium marinum
GC_ID:11
PMID:18988685
PMID:23851394
ncbi_taxonomy
Terrabacteria group
GC_ID:1
Marek's disease-like viruses
ncbi_taxonomy
Mardivirus
GC_ID:1
Infectious laryngo-tracheitis-like viruses
Infectious laryngotracheitis-like viruses
ncbi_taxonomy
Iltovirus
GC_ID:1
Marburg-like viruses
ncbi_taxonomy
Marburgvirus
GC_ID:1
ncbi_taxonomy
Clupeocephala
GC_ID:1
ncbi_taxonomy
Novirhabdovirus
GC_ID:1
ncbi_taxonomy
Orthopneumovirus
NCBITaxon:10625
BFPyV
GC_ID:1
Aves polyomavirus 1
BFDV
Budgerigar fledgling disease polyomavirus
Budgerigar fledgling disease virus
Budgerigar fledgling polyomavirus
ncbi_taxonomy
Gammapolyomavirus avis
GC_ID:11
PMID:27620848
ncbi_taxonomy
Yersiniaceae
GC_ID:11
PMID:11542086
PMID:12361288
PMID:16627635
PMID:1704793
PMID:19801389
PMID:29034857
ncbi_taxonomy
Campylobacter
GC_ID:11
PMID:11321120
PMID:1354478
ncbi_taxonomy
Spirillum fetus
Vibrio fetus
Campylobacter fetus
NCBITaxon:2172531
NCBITaxon:2182326
NCBITaxon:2201165
NCBITaxon:2211407
NCBITaxon:2211408
NCBITaxon:2211409
NCBITaxon:2293848
NCBITaxon:2293849
NCBITaxon:2293850
NCBITaxon:2303571
NCBITaxon:2305452
NCBITaxon:2305453
NCBITaxon:2305454
NCBITaxon:2305455
NCBITaxon:2305456
NCBITaxon:2305457
NCBITaxon:2305458
NCBITaxon:2305459
NCBITaxon:2340789
NCBITaxon:2478524
NCBITaxon:2572055
NCBITaxon:2572062
NCBITaxon:2572070
NCBITaxon:2572072
NCBITaxon:2572075
NCBITaxon:2572080
NCBITaxon:2572086
NCBITaxon:3042472
NCBITaxon:3042475
NCBITaxon:3042476
NCBITaxon:3042477
NCBITaxon:3042478
NCBITaxon:3042479
NCBITaxon:3042480
NCBITaxon:3042481
NCBITaxon:3042482
NCBITaxon:3042483
NCBITaxon:3042484
NCBITaxon:3042485
NCBITaxon:3042486
NCBITaxon:3042488
GC_ID:11
PMID:11321120
ncbi_taxonomy
Campylobacter fetus subsp. jejuni
Vibrio hepaticus
Vibrio jejuni
Campylobacter jejuni
GC_ID:1
Influenzavirus A
ncbi_taxonomy
Alphainfluenzavirus
GC_ID:1
Influenzavirus B
ncbi_taxonomy
Betainfluenzavirus
GC_ID:1
Influenzavirus C
ncbi_taxonomy
Gammainfluenzavirus
GC_ID:1
ncbi_taxonomy
Bunyavirales
NCBITaxon:11598
GC_ID:1
ncbi_taxonomy
Hantavirus
Orthohantavirus
NCBITaxon:38142
HIRRV
GC_ID:1
Hirame novirhabdovirus
Hirame rhabdovirus
ncbi_taxonomy
Novirhabdovirus hirame
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11542017
PMID:11542087
PMID:11760965
PMID:12054223
PMID:2112744
PMID:270744
PMID:32628106
PMID:36748408
PMID:7520741
PMID:8123559
PMID:8186100
PMID:8590690
PMID:9103655
PMID:9336922
eubacteria
ncbi_taxonomy
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
prokaryote
prokaryotes
Bacteria
GC_ID:11
ncbi_taxonomy
Flavobacteriales
GC_ID:11
PMID:11837318
PMID:25288668
PMID:26654112
ncbi_taxonomy
"Leptospiria" Cavalier-Smith 2020
Spirochaetes
Spirochaetia
GC_ID:11
PMID:12271122
Brucella suis str. 1330
ncbi_taxonomy
Brucella melitensis biovar Suis str. 1330
Brucella suis ATCC 23444
Brucella suis NCTC 10316
Brucella suis 1330
NCBITaxon:11268
GC_ID:1
Ebola virus EBO
unidentified Ebola virus
ncbi_taxonomy
Ebola virus sp.
GC_ID:11
PMID:23575986
ncbi_taxonomy
Neisseriales
GC_ID:4
PMID:13403276
PMID:16350067
ncbi_taxonomy
Borrelomycetaceae
Parasitaceae
Pleuropneumoniaceae
Mycoplasmataceae
NCBITaxon:29500
NCBITaxon:57371
GC_ID:4
PMID:10826816
PMID:11321109
PMID:11411711
PMID:11931184
PMID:13403276
PMID:15176735
PMID:16350067
PMID:16403858
PMID:25288662
PMID:8863441
PMID:8995799
ncbi_taxonomy
Asterococcus
Asteromyces
Borrelomyces
Bovimyces
Eperythrozoon
Haemobartonella
Pleuropneumonia
Mycoplasma
GC_ID:4
ncbi_taxonomy
Mycoplasma gallisepticum
Mycoplasmoides gallisepticum
GC_ID:4
PMID:11491338
PMID:1316139
PMID:1374621
PMID:8573513
ncbi_taxonomy
Mycoplasma suipneumoniae
Mesomycoplasma hyopneumoniae
NCBITaxon:219
GC_ID:11
PMID:11931154
PMID:1995031
PMID:8186097
PMID:8494747
ncbi_taxonomy
Campylobacter pylori
Campylobacter pylori subsp. pylori
Campylobacter pyloridis
Helicobacter nemestrinae
Helicobacter pylori
GC_ID:4
ncbi_taxonomy
Mycoplasma synoviae
Mycoplasmopsis synoviae
GC_ID:11
ncbi_taxonomy
Leptospira canicola
Leptospira interrogans serovar Canicola
GC_ID:11
PMID:16403855
ncbi_taxonomy
Campylobacterales
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11541975
PMID:11542064
PMID:11542149
PMID:11760965
PMID:12054223
PMID:2112744
PMID:25527841
PMID:270744
PMID:32628106
PMID:36748408
PMID:8123559
PMID:8590690
PMID:9103655
PMID:9336922
ncbi_taxonomy
Archaebacteria
Mendosicutes
Metabacteria
Monera
Procaryotae
Prokaryota
Prokaryotae
archaea
prokaryote
prokaryotes
Archaea
NCBITaxon:11619
GC_ID:1
Argentinian mammarenavirus
Junin arenavirus
Junin mammarenavirus
Junin virus
Junn mammarenavirus
ncbi_taxonomy
Mammarenavirus juninense
GC_ID:11
PMID:11756688
ncbi_taxonomy
Brucella melitensis ATCC 23456
Brucella melitensis bv. 1 str. 16M
GC_ID:11
PMID:28066370
PMID:32373076
PMID:35335701
PMID:37395662
PMID:8573514
ncbi_taxonomy
Brucella
GC_ID:11
Brucella melitensis bv. Abortus
ncbi_taxonomy
"Bacillus of abortion" Bang 1897
Bacterium abortus
Brucella melitensis biovar Abortus
Brucella abortus
GC_ID:11
Brucella melitensis bv. Ovis
ncbi_taxonomy
Brucella melitensis biovar Ovis
Brucella ovis
GC_ID:1
Negative-strand RNA viruses
ncbi_taxonomy
Negarnaviricota
GC_ID:1
ncbi_taxonomy
Polyploviricotina
GC_ID:1
ncbi_taxonomy
Orthocoronavirinae
GC_ID:1
RNA viruses
RNA viruses and viroids
ncbi_taxonomy
Riboviria
GC_ID:1
ncbi_taxonomy
Avulavirinae
GC_ID:1
ncbi_taxonomy
Orthoparamyxovirinae
GC_ID:1
ncbi_taxonomy
Rubulavirinae
NCBITaxon:11176
NDV
GC_ID:1
Avian Paramyxovirus Serotype I
Avian paramyxovirus type 1
Avian paramyxovirus type-1
Newcastle disease virus
Newcastle disease virus NDV
avian paramyxovirus 1
ncbi_taxonomy
Avian avulavirus 1
Avian orthoavulavirus 1
NCBITaxon:11161
NCBITaxon:1979165
GC_ID:1
Mumps virus
ncbi_taxonomy
Mumps rubulavirus
Mumps orthorubulavirus
GC_ID:1
ncbi_taxonomy
Avulavirus
GC_ID:1
ncbi_taxonomy
Henipavirus
GC_ID:1
PMID:30257078
ncbi_taxonomy
Metamonada
GC_ID:1
ncbi_taxonomy
Discoba
GC_ID:11
PMID:15805518
Brucella abortus biovar 1 str. 9-941
Brucella abortus bv. 1 strain 9-941
ncbi_taxonomy
Brucella abortus bv. 1 str. 9-941
GC_ID:11
ncbi_taxonomy
Bacterium tularense
Brucella tularensis
Francisella tularense
Pasteurella tularensis
Francisella tularensis
SARS-CoV-2
GC_ID:1
2019-nCoV
COVID-19 virus
HCoV-19
Human coronavirus 2019
SARS-2
SARS-CoV2
SARS2
ncbi_taxonomy
Severe acute respiratory syndrome coronavirus 2
GC_ID:1
ncbi_taxonomy
Bamfordvirae
GC_ID:1
ncbi_taxonomy
Shotokuvirae
GC_ID:1
ncbi_taxonomy
Orthornavirae
GC_ID:1
ncbi_taxonomy
Kitrinoviricota
GC_ID:1
ncbi_taxonomy
Cossaviricota
GC_ID:1
ncbi_taxonomy
Papovaviricetes
GC_ID:1
ncbi_taxonomy
Alsuviricetes
GC_ID:1
ncbi_taxonomy
Pisoniviricetes
GC_ID:1
ncbi_taxonomy
Revtraviricetes
GC_ID:1
ncbi_taxonomy
Pokkesviricetes
NCBITaxon:10880
GC_ID:1
ncbi_taxonomy
Reoviridae
Reovirales
GC_ID:1
ncbi_taxonomy
Hepelivirales
GC_ID:1
PMID:23020233
PMID:30257078
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
Eukaryota
GC_ID:1
ncbi_taxonomy
Bovinae
NCBITaxon:29525
GC_ID:11
PMID:1503973
ncbi_taxonomy
Bacteroides macacae
Bacteroides melaninogenicus subsp. macacae
Bacteroides salivosus
Porphyromonas salivosa
Porphyromonas macacae
NCBITaxon:707
GC_ID:11
ncbi_taxonomy
Listonella ordalii
Vibrio ordalii
GC_ID:11
PMID:11541974
PMID:11837318
PMID:16166687
PMID:16403855
PMID:19060069
ncbi_taxonomy
Alphabacteria
Proteobacteria alpha subdivision
Purple bacteria, alpha subdivision
a-proteobacteria
alpha proteobacteria
alpha subdivision
alpha subgroup
Alphaproteobacteria
GC_ID:11
PMID:16403855
PMID:28581923
ncbi_taxonomy
Proteobacteria beta subdivision
Purple bacteria, beta subdivision
b-proteobacteria
beta proteobacteria
beta subdivision
beta subgroup
Betaproteobacteria
NCBITaxon:12796
NCBITaxon:70172
PRRSV
GC_ID:1
Porcine reproductive and respiratory syndrome virus (PRRSV)
Porcine respiratory and reproductive syndrome virus
porcine reproductive and respiratory syndrome virus PRRSV
porcine reproductive and respiratory syndrome virus, PRRSV
ncbi_taxonomy
Porcine reproductive and respiratory syndrome virus
NCBITaxon:1435366
NCBITaxon:1435368
NCBITaxon:1435988
NCBITaxon:1439853
NCBITaxon:1487954
NCBITaxon:1487955
GC_ID:11
PMID:12734250
PMID:1283774
ncbi_taxonomy
Bacillus pseudomallei
Bacterium whitmori
Loefflerella pseudomallei
Malleomyces pseudomallei
Pseudomonas pseudomallei
Burkholderia pseudomallei
NCBITaxon:212745
GC_ID:11
PMID:10758879
PMID:10939664
PMID:15950132
PMID:18048745
PMID:23918787
PMID:7727274
PMID:9103607
ncbi_taxonomy
"Chlorobacterium" Guillebeau 1890, nom. rejic. Opin. 6 (not "Chlorobacterium" Lauterborn 1916)
Liquidomonas
Loefflerella
RNA similarity group I
Pseudomonas
NCBITaxon:1224290
NCBITaxon:1437768
NCBITaxon:1437769
NCBITaxon:1437770
NCBITaxon:1508364
NCBITaxon:1607811
NCBITaxon:1607813
NCBITaxon:1683559
NCBITaxon:1683561
NCBITaxon:1851858
NCBITaxon:1851865
NCBITaxon:1860124
NCBITaxon:665948
NCBITaxon:912077
NCBITaxon:931955
NCBITaxon:931956
NCBITaxon:931957
NCBITaxon:931958
NCBITaxon:932477
GC_ID:11
ncbi_taxonomy
Bacillus aeruginosus
Bacillus pyocyaneus
Bacterium aeruginosum
Bacterium pyocyaneum
Micrococcus pyocyaneus
Pseudomonas polycolor
Pseudomonas pyocyanea
probable synonym or variety: "Pseudomonas polycolor" Clara 1930
Pseudomonas aeruginosa
GC_ID:1
ncbi_taxonomy
Neospora caninum
GC_ID:11
PMID:8573514
ncbi_taxonomy
Micrococcus melitensis
Streptococcus Miletensis
Brucella melitensis
GC_ID:11
Brucella melitensis bv. Suis
ncbi_taxonomy
Brucella melitensis biovar Suis
Brucella suis
NCBITaxon:689832
GC_ID:1
ncbi_taxonomy
Sedoreovirinae
Sedoreoviridae
GC_ID:1
ncbi_taxonomy
Heptrevirinae
GC_ID:11
ncbi_taxonomy
Yersinia ruckeri
GC_ID:11
PMID:7547305
PMID:7857801
PMID:7981108
PMID:8123559
PMID:8347512
PMID:9226893
ncbi_taxonomy
Candidatus intracellularis
Ileal symbiont intracellularis
Lawsonia intracellularis
GC_ID:1
ncbi_taxonomy
Orthoherpesviridae
GC_ID:1
ncbi_taxonomy
Orthoflavivirus
NCBITaxon:45337
NCBITaxon:63330
GC_ID:1
PMID:7701348
Equine morbillivirus
Hendra henipavirus
Hendra virus
ncbi_taxonomy
Henipavirus hendraense
NCBITaxon:121791
GC_ID:1
Nipah henipavirus
Nipah virus
Nipah-virus
ncbi_taxonomy
Henipavirus nipahense
NCBITaxon:11103
HCV
GC_ID:1
Hepacivirus C
Hepatitis C virus
hepatitis C virus HCV
human hepatitis C virus
human hepatitis C virus HCV
human hepatitis virus C HCV
post-transfusion hepatitis non A non B virus
ncbi_taxonomy
Hepacivirus hominis
NCBITaxon:11623
NCBITaxon:12748
LCMV
GC_ID:1
Lymphocytic choriomeningitis mammarenavirus
Lymphocytic choriomeningitis virus
lymphocytic choriomeningitis virus LCMV
ncbi_taxonomy
Mammarenavirus choriomeningitidis
NCBITaxon:11620
GC_ID:1
Lassa mammarenavirus
Lassa virus
ncbi_taxonomy
Mammarenavirus lassaense
NCBITaxon:11232
CDV
GC_ID:1
Canine distemper virus
Canine morbillivirus
canine distemper virus CDV
ncbi_taxonomy
Morbillivirus canis
NCBITaxon:11593
NCBITaxon:1980519
CCHFV
GC_ID:1
Crimean-Congo haemorrhagic fever virus
Crimean-Congo hemorrhagic fever nairovirus
Crimean-Congo hemorrhagic fever orthonairovirus
Crimean-Congo hemorrhagic virus
ncbi_taxonomy
Crimean-Congo hemorrhagic fever virus
Orthonairovirus haemorrhagiae
NCBITaxon:1511906
GC_ID:1
Carnivore protoparvovirus 1
ncbi_taxonomy
Protoparvovirus carnivoran1
NCBITaxon:11215
GC_ID:1
Bovine parainfluenza 3 virus
Bovine parainfluenza virus 3
Bovine parainfluenza virus type 3
Bovine respirovirus 3
ncbi_taxonomy
Respirovirus bovis
GC_ID:1
ncbi_taxonomy
Musteloidea
GC_ID:1
PMID:11214318
PMID:11214319
PMID:12878460
ncbi_taxonomy
Laurasiatheria
GC_ID:1
PMID:11214319
PMID:12082125
PMID:12878460
PMID:15522813
ncbi_taxonomy
Euarchontoglires
GC_ID:1
PMID:11214319
PMID:12082125
PMID:15522813
Rodents and rabbits
ncbi_taxonomy
Glires
GC_ID:1
ncbi_taxonomy
Anthropoidea
Simiiformes
GC_ID:1
amniotes
ncbi_taxonomy
Amniota
GC_ID:1
diapsids
ncbi_taxonomy
Diapsida
Sauria
GC_ID:1
ncbi_taxonomy
Orthoretrovirinae
NCBITaxon:186155
GC_ID:1
Canine parvovirus-1
Minute virus of canines
ncbi_taxonomy
Canine minute virus
GC_ID:1
ncbi_taxonomy
Fungi/Metazoa group
opisthokonts
Opisthokonta
GC_ID:1
ncbi_taxonomy
Bilateria
GC_ID:1
ncbi_taxonomy
Protostomia
GC_ID:1
ncbi_taxonomy
unclassified Papillomaviridae
GC_ID:1
guinea pigs and others
ncbi_taxonomy
Hystricognathi
Hystricomorpha
GC_ID:1
carnivores
ncbi_taxonomy
carnivores
Carnivora
GC_ID:11
PMID:13200095
PMID:22427448
PMID:8240957
PMID:9103649
ncbi_taxonomy
Moraxella anatipestifer
Pasteurella anapestifer
Pasteurella anatipestifer
Pfeifferella anatipestifer
Riemerella anatipestifer
GC_ID:1
ncbi_taxonomy
Replication competent viruses
GC_ID:1
ncbi_taxonomy
unclassified Orthomyxoviridae
GC_ID:1
ncbi_taxonomy
Pecora
GC_ID:11
PMID:16299333
PMID:20462421
ncbi_taxonomy
Brucella melitensis biovar Abortus 2308
Brucella abortus 2308
NCBITaxon:10624
GC_ID:1
Polyomavirus
Polyomaviruses
ncbi_taxonomy
Polyomavirus sp.
GC_ID:1
ncbi_taxonomy
H1N1 swine influenza virus
GC_ID:11
ncbi_taxonomy
Streptococcus sp. (group A)
group A streptococci
group A streptococcus
Streptococcus sp. 'group A'
GC_ID:11
Brucella melitensis bv. Canis
ncbi_taxonomy
Brucella melitensis biovar Canis
Brucella canis
GC_ID:1
ncbi_taxonomy
Chikungunya virus
GC_ID:1
ncbi_taxonomy
Caniformia
GC_ID:1
Avian reovirus
ncbi_taxonomy
Avian orthoreovirus
GC_ID:11
PMID:1581182
ncbi_taxonomy
Leptospira grippotyphosa
Leptospira kirschneri serovar Grippotyphosa
GC_ID:1
Avian pneumovirus
ncbi_taxonomy
Avian metapneumovirus
GC_ID:1
Leishmania
ncbi_taxonomy
Leishmania <subgenus>
GC_ID:1
ncbi_taxonomy
Leishmania donovani species complex
NCBITaxon:109679
GC_ID:1
ncbi_taxonomy
Murinae
GC_ID:1
ncbi_taxonomy
Bos bubalis bubalis
Bubalus bubalis bubalis
GC_ID:11
Yersinia enterocolitica subsp. enterocolitica str. 8081
Yersinia enterocolitica subsp. enterocolitica strain 8081
ncbi_taxonomy
Yersinia enterocolitica subsp. enterocolitica 8081
GC_ID:1
ncbi_taxonomy
Rubulavirus
CpHV-1
GC_ID:1
Caprine herpesvirus 1
Caprine herpesvirus type 1
goat herpesvirus
ncbi_taxonomy
Caprine alphaherpesvirus 1
NCBITaxon:10896
AHSV
GC_ID:1
African horse sickness group
African horse sickness virus (AHSV)
African horsesickness virus
ncbi_taxonomy
African horse sickness virus AHSV
African horse sickness virus
NCBITaxon:12591
GC_ID:1
Bluetongue virus group
bluetongue virus BTV
ncbi_taxonomy
Bluetongue virus
GC_ID:1
ncbi_taxonomy
Quailpox virus
GC_ID:1
ncbi_taxonomy
Parvovirinae
GC_ID:11
PMID:18048732
ncbi_taxonomy
Vibrio salmonicida
Aliivibrio salmonicida
mammals
GC_ID:1
mammals
ncbi_taxonomy
mammals
Mammalia
TAdV-3
GC_ID:1
Marble spleen disease virus
Turkey adenovirus serotype 3
Turkey haemorrhagic enteritis virus
Turkey hemorrhagic enteritis virus
hemorrhagic enteritis virus
ncbi_taxonomy
Turkey adenovirus 3
GC_ID:1
ncbi_taxonomy
Vinckeia
Plasmodium (Vinckeia)
GC_ID:1
ncbi_taxonomy
Hematozoa Vivier 1982
Aconoidasida
GC_ID:1
ncbi_taxonomy
Eimeriorina
GC_ID:1
ncbi_taxonomy
Sarcocystis neurona
GC_ID:11
Brucella abortus str. S19
Brucella abortus strain S19
ncbi_taxonomy
Brucella abortus S19
CNPV
GC_ID:1
Avipoxvirus clade B1
Canary poxvirus
ncbi_taxonomy
Canarypox virus
NCBITaxon:399128
GC_ID:11
PMID:18218934
ncbi_taxonomy
Brucella microti
GC_ID:11
Brucella ovis str. ATCC 25840
Brucella ovis strain ATCC 25840
ncbi_taxonomy
Brucella ovis ATCC 25840
GC_ID:1
ncbi_taxonomy
Picornavirales
GC_ID:11
PMID:19346311
Brucella suis str. ATCC 23445
Brucella suis strain ATCC 23445
ncbi_taxonomy
Brucella suis ATCC 23445
GC_ID:1
PMID:11062127
PMID:12684019
ncbi_taxonomy
Mycota
fungi
Fungi
GC_ID:11
PMID:19346311
Brucella canis str. ATCC 23365
Brucella canis strain ATCC 23365
ncbi_taxonomy
Brucella canis ATCC 23365
GC_ID:11
ncbi_taxonomy
Diplokokkus intracellularis meningitidis
Micrococcus intracellularis
Micrococcus meningitidis
Micrococcus meningitidis cerebrospinalis
Neisseria weichselbaumii
Neisseria meningitidis
PsHV-1
GC_ID:1
Pacheco's disease virus
Psittacid herpesvirus 1
ncbi_taxonomy
Psittacid alphaherpesvirus 1
GC_ID:1
trouts, salmons & chars
ncbi_taxonomy
Salmoninae
true insects
Insecta
GC_ID:11
PMID:11491321
ncbi_taxonomy
Bordetella
NCBITaxon:514
GC_ID:11
PMID:8240949
PMID:8782670
PMID:9226899
ncbi_taxonomy
Alcaligenes bronchicanis
Alcaligenes bronchisepticus
Bacillus bronchicanis
Bacillus bronchisepticus
Bacterium bronchisepticus
Brucella bronchiseptica
Haemophilus bronchisepticus
Bordetella bronchiseptica
GC_ID:11
PMID:8240949
ncbi_taxonomy
Bacterium tussis-convulsivae
Haemophilus pertussis
Hemophilus pertussis
Microbe de la coqueluche
Bordetella pertussis
GC_ID:11
PMID:4074238
ncbi_taxonomy
Bordetella avium
GC_ID:11
PMID:10555323
PMID:10555334
PMID:16166704
PMID:27620848
ncbi_taxonomy
Enterobacteraceae
enterobacteria
gamma-3 proteobacteria
Enterobacteriaceae
NCBITaxon:136447
NCBITaxon:64986
NCBITaxon:96055
BVDV type II
BVDV-2
GC_ID:1
PMID:7747470
Bovine viral diarrhea virus genotype 2
Bovine viral diarrhea virus type 2
Bovine viral diarrhea virus-2
bovine viral diarrhea virus type II
pestivirus type 4
ncbi_taxonomy
Bovine viral diarrhea virus 2
GC_ID:11
Tenericutes
ncbi_taxonomy
"Mollicutaeota" Oren et al. 2015
"Tenericutes" Murray 1984
Mollicutota
Mycoplasmatota
GC_ID:11
PMID:19346311
Brucella melitensis str. ATCC 23457
Brucella melitensis strain ATCC 23457
ncbi_taxonomy
Brucella melitensis ATCC 23457
GC_ID:1
ncbi_taxonomy
Herpesvirales
GC_ID:1
ncbi_taxonomy
Coccidioides
NCBITaxon:28167
NCBITaxon:665
GC_ID:11
PMID:21296930
ncbi_taxonomy
Achromobacter ichthyodermis
Listonella anguillara
Listonella anguillarum
Pseudomonas ichthyodermis
Vibrio ichthyodermis
Vibrio piscium
Vibrio piscium var. japonicus
Vibrio anguillarum
NCBITaxon:155284
NCBITaxon:86501
GC_ID:1
Salmon isavirus
ncbi_taxonomy
Isavirus salaris
GC_ID:1
ncbi_taxonomy
Dintheria
Oncomelania
NCBITaxon:1637691
NCBITaxon:1806490
NCBITaxon:469598
NCBITaxon:662101
NCBITaxon:662104
GC_ID:11
PMID:10319482
E. coli
Escherichia/Shigella coli
ncbi_taxonomy
Bacillus coli
Bacterium coli
Bacterium coli commune
Enterococcus coli
Escherichia coli
GC_ID:1
ncbi_taxonomy
Trypanosomatidae
Leishmania
GC_ID:1
Leishmania
ncbi_taxonomy
Leishmania <genus>
NCBITaxon:31284
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) amazonensis
Leishmania mexicana amazonensis
Leishmania amazonensis
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) donovani
Leishmania donovani
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) major
Leishmania tropica major
Leishmania major
NCBITaxon:33701
NCBITaxon:5724
GC_ID:1
PMID:12046599
PMID:15734659
PMID:22000167
ncbi_taxonomy
Tritrichomonas suis
NCBITaxon:5662
GC_ID:1
ncbi_taxonomy
Leishmania (Leishmania) infantum
Leishmania donovani infantum
Leishmania infantum
NCBITaxon:399127
GC_ID:11
PMID:19653890
Brucella microti str. CCM 4915
Brucella microti strain CCM 4915
ncbi_taxonomy
Brucella sp. CCM 4915
Brucella microti CCM 4915
GC_ID:1
ncbi_taxonomy
Trypanosoma
GC_ID:1
ncbi_taxonomy
Trypanosoma (Trypanozoon) brucei
Trypanosoma brucei subgroup
Trypanosoma brucei
GC_ID:1
ncbi_taxonomy
Trypanosoma cruzi
GC_ID:1
PMID:11432808
PMID:19135417
ncbi_taxonomy
Giardia duodenalis
Giardia lamblia
Lamblia intestinalis
Giardia intestinalis
GC_ID:1
ncbi_taxonomy
Entamoeba histolytica
GC_ID:1
ncbi_taxonomy
Naegleria
GC_ID:1
ncbi_taxonomy
Naegleria gruberi
GC_ID:1
brain-eating amoeba
ncbi_taxonomy
Naegleria fowleri
GC_ID:1
apicomplexans
ncbi_taxonomy
apicomplexans
Apicomplexa
GC_ID:1
ncbi_taxonomy
Eimeria
Eimeria acervulina
GC_ID:1
ncbi_taxonomy
Eimeria tenella
GC_ID:1
ncbi_taxonomy
Eimeria maxima
Cryptosporidium
NCBITaxon:2200815
NCBITaxon:2200816
NCBITaxon:2200817
NCBITaxon:2200818
NCBITaxon:2200819
NCBITaxon:2200820
NCBITaxon:2200821
NCBITaxon:2200822
NCBITaxon:2200823
NCBITaxon:2200824
NCBITaxon:2200825
NCBITaxon:2200826
GC_ID:1
ncbi_taxonomy
Cryptosporidium parvum
GC_ID:1
ncbi_taxonomy
Sarcocystids
Sarcocystidae
GC_ID:1
ncbi_taxonomy
Toxoplasma gondii
GC_ID:1
ncbi_taxonomy
Plasmodium
GC_ID:1
ncbi_taxonomy
Plasmodium berghei
Plasmodium chabaudi
malaria parasite P. falciparum
GC_ID:1
malaria parasite P. falciparum
ncbi_taxonomy
Plasmodium (Laverania) falciparum
Plasmodium falciparum
Plasmodium knowlesi
malaria parasite P. vivax
GC_ID:1
malaria parasite P. vivax
ncbi_taxonomy
Haemamoeba vivax
Haemamoeba vivax Grassi and Feletti, 1890
Plasmodium vivax
GC_ID:1
ncbi_taxonomy
Plasmodium yoelli
Plasmodium yoelii
GC_ID:1
Piroplasmids
ncbi_taxonomy
Piroplasmida
GC_ID:1
ncbi_taxonomy
Babesia
GC_ID:1
ncbi_taxonomy
Babesia bovis
GC_ID:1
ncbi_taxonomy
Babesia bigemina
GC_ID:1
ncbi_taxonomy
Babesia canis
GC_ID:1
ncbi_taxonomy
Theileria
GC_ID:1
ncbi_taxonomy
Theileria annulata
GC_ID:1
ncbi_taxonomy
Theileria parva
GC_ID:11
PMID:10319519
PMID:10939679
PMID:12072558
PMID:15653929
PMID:15653930
PMID:3231714
PMID:37486130
PMID:9731304
ncbi_taxonomy
Salmonella
NCBITaxon:149049
GC_ID:11
PMID:15653929
PMID:15653930
PMID:7149525
ncbi_taxonomy
Salmonella cholerae-suis subsp. cholerae-suis
Salmonella choleraesuis subsp. choleraesuis
Salmonella enterica I
Salmonella enterica subsp. I
Salmonella enterica subsp. Subsp. I
Salmonella enterica subsp. Subsp. Ixxx
Salmonella enterica subsp. enterica
NCBITaxon:41510
GC_ID:11
ncbi_taxonomy
Salmonella enterica serovar Gallinarum
Salmonella gallinarum
Salmonella enterica subsp. enterica serovar Gallinarum
GC_ID:1
ncbi_taxonomy
Schistosoma
GC_ID:1
ncbi_taxonomy
Schistosoma japonicum
GC_ID:1
ncbi_taxonomy
Schistosoma mansoni
Schistosoma haematobium
GC_ID:1
ncbi_taxonomy
Monkeypox virus Zaire-96-I-16
GC_ID:11
PMID:26834722
ncbi_taxonomy
Shigella
GC_ID:11
PMID:12054222
Escherichia/Shigella dysenteriae
ncbi_taxonomy
Bacillus dysenteriae
Bacillus dysentericus
Bacillus shigae
Eberthella dysenteriae
Shigella shigae
Shigella dysenteriae
GC_ID:11
Escherichia flexneri
Escherichia/Shigella flexneri
ncbi_taxonomy
Shigella paradysenteriae
Shigella flexneri
GC_ID:11
ncbi_taxonomy
Bacterium sonnei
Shigella sonnei
GC_ID:11
Yersinia
ncbi_taxonomy
Yersinia <enterobacteria>
GC_ID:11
PMID:15084509
ncbi_taxonomy
Bacillus pestis
Bacterium pestis
Pasteurella pestis
Pestisella pestis
Yersinia pseudotuberculosis subsp. pestis
Yersinia pestis
NCBITaxon:1161941
GC_ID:11
PMID:2223608
PMID:23919959
ncbi_taxonomy
Bacillus pseudotuberkulosis
Bacterium pseudotuberculosis
Pasteurella lymphangitidis
Pasteurella pseudotuberculosis
Shigella pseudotuberculosis
Yersinia pseudotuberculosis
GC_ID:1
ncbi_taxonomy
Trichinella spiralis
GC_ID:11
Edwardsiella
ncbi_taxonomy
Asakusa group
Bartholomew group
Edwardsiella <enterobacteria>
NCBITaxon:1471792
NCBITaxon:1471793
GC_ID:11
PMID:27539016
ncbi_taxonomy
Edwardsiella anguillimortifera
Paracolobactrum anguillimortiferum
Edwardsiella tarda
GC_ID:11
PMID:15143042
PMID:4954820
PMID:8427811
ncbi_taxonomy
gamma-3 proteobacteria
Vibrionaceae
GC_ID:11
PMID:11155981
PMID:12067377
PMID:12807216
PMID:1380286
PMID:1380289
PMID:15388703
PMID:16560691
PMID:17012583
PMID:17158971
PMID:19567585
PMID:7520733
PMID:8347521
PMID:8934910
ncbi_taxonomy
Aeromonas
NCBITaxon:1471787
NCBITaxon:1471788
NCBITaxon:329135
NCBITaxon:329140
NCBITaxon:346633
NCBITaxon:346634
NCBITaxon:582196
NCBITaxon:582198
NCBITaxon:582214
NCBITaxon:582215
NCBITaxon:582216
NCBITaxon:582217
NCBITaxon:582218
NCBITaxon:582219
NCBITaxon:582220
NCBITaxon:582221
NCBITaxon:582222
NCBITaxon:582223
NCBITaxon:582224
NCBITaxon:582225
NCBITaxon:582226
NCBITaxon:582228
NCBITaxon:582229
NCBITaxon:582231
NCBITaxon:582236
NCBITaxon:582237
NCBITaxon:582240
NCBITaxon:582250
NCBITaxon:582251
NCBITaxon:582253
NCBITaxon:582254
NCBITaxon:582265
NCBITaxon:582266
NCBITaxon:582267
NCBITaxon:582279
NCBITaxon:582282
NCBITaxon:582284
NCBITaxon:582286
NCBITaxon:582287
NCBITaxon:582289
NCBITaxon:582290
NCBITaxon:582291
NCBITaxon:582292
NCBITaxon:582295
NCBITaxon:582297
NCBITaxon:582299
NCBITaxon:582300
NCBITaxon:582302
NCBITaxon:582303
NCBITaxon:582304
NCBITaxon:582305
NCBITaxon:582306
NCBITaxon:582307
NCBITaxon:582308
NCBITaxon:582309
NCBITaxon:582310
NCBITaxon:582311
NCBITaxon:582312
NCBITaxon:582313
NCBITaxon:582314
NCBITaxon:582315
NCBITaxon:582316
NCBITaxon:582317
NCBITaxon:582318
NCBITaxon:582319
NCBITaxon:582320
NCBITaxon:582321
NCBITaxon:582322
NCBITaxon:582323
NCBITaxon:582324
NCBITaxon:98358
GC_ID:11
PMID:16560691
PMID:19965992
PMID:23485124
PMID:932684
ncbi_taxonomy
Aeromonas dourgesi
Aeromonas hydrophila (Chester 1901) Stanier 1943 (Approved Lists 1980)
Aeromonas liquefaciens
Bacillus hydrophilus fuscus
Bacterium hydrophilum
Proteus hydrophilus
Proteus ichthyosmius
Pseudomonas hydrophila
Aeromonas hydrophila
molluscs
mollusks
Mollusca
NCBITaxon:1055664
NCBITaxon:697046
GC_ID:11
PMID:19965992
ncbi_taxonomy
Bacillus salmonicida
Bacterium salmonicida
Proteus salmonicida
Aeromonas salmonicida
NCBITaxon:1618316
GC_ID:11
PMID:10515907
PMID:10758897
PMID:16585709
PMID:24744012
PMID:27930271
PMID:28141502
PMID:30154058
PMID:30586413
PMID:31454394
PMID:31722850
PMID:31836459
PMID:32320380
PMID:35816828
PMID:36748499
PMID:7981102
PMID:8573491
PMID:8934900
PMID:8995795
PMID:9336916
Lyme Disease Borrelia
ncbi_taxonomy
Borrelia burgdorferi group
Borrelia burgdorferi sensu lato
Borreliella
Biomphalaria
NCBITaxon:705
GC_ID:11
PMID:1371064
PMID:17978204
PMID:21057054
PMID:21296930
PMID:24409173
PMID:4935323
PMID:7520733
PMID:8590667
ncbi_taxonomy
Beneckea
Listonella
Microspira
Pacinia
Vibrio
NCBITaxon:140100
NCBITaxon:376726
GC_ID:11
PMID:1015934
PMID:9272984
ncbi_taxonomy
Bacillo virgola del Koch
Bacillus cholerae
Bacillus cholerae-asiaticae
Kommabacillus
Liquidivibrio cholerae
Microspira comma
Pacinia cholerae-asiaticae
Spirillum cholerae
Spirillum cholerae-asiaticae
Vibrio albensis
Vibrio cholera
Vibrio cholerae biovar albensis
Vibrio cholerae bv. albensis
Vibrio cholerae-asiaticae
Vibrio comma
Vibrio cholerae
GC_ID:11
ncbi_taxonomy
Edwardsiella ictaluri
NCBITaxon:352473
DHV-1
GC_ID:1
Duck hepatitis A virus
Duck hepatitis virus 1
Duck hepatitis virus type 1
ncbi_taxonomy
Avihepatovirus A
GC_ID:1
ncbi_taxonomy
Coronavirinae
GC_ID:1
Alphacoronavirus-1
ncbi_taxonomy
Alphacoronavirus 1
NCBITaxon:156439
GC_ID:1
Coronavirus group 2
Group 2 species
ncbi_taxonomy
Coronavirus
Betacoronavirus
NCBITaxon:227859
NCBITaxon:311178
HCoV-SARS
SARS
SARSr-CoV
SARSrCoV
GC_ID:1
Human coronavirus (strain SARS)
SARS-like coronavirus
SARS-related coronavirus
ncbi_taxonomy
Severe acute respiratory syndrome-related coronavirus
GC_ID:1
ncbi_taxonomy
Tremovirus A
kissing bugs
Triatominae
GC_ID:11
PMID:10843050
PMID:15280320
PMID:15388716
PMID:17220461
PMID:2223605
PMID:29923825
ncbi_taxonomy
Pasteurellaceae
GC_ID:11
PMID:1847295
ncbi_taxonomy
Haemophilus pleuropneumoniae
Actinobacillus pleuropneumoniae
Anopheles
GC_ID:1
Anopheles
ncbi_taxonomy
Anopheles <genus>
sand flies
sandflies
Phlebotominae
GC_ID:11
ncbi_taxonomy
Thiomicrospira group
Thiothrix/Francisella group
Thiotrichales
GC_ID:11
PMID:1736960
ncbi_taxonomy
Haemophilus
GC_ID:11
ncbi_taxonomy
Bacterium influenzae
Coccobacillus pfeifferi
Haemophilus meningitidis
Influenza-bacillus
Mycobacterium influenzae
Haemophilus influenzae
NCBITaxon:163489
NCBITaxon:214923
GC_ID:11
PMID:13130032
PMID:4333932
ncbi_taxonomy
Haemophilus agni
Haemophilus ovis
Haemophilus somnifer
Haemophilus somnus
Hemophilus agni
Histophilus ovis
Histophilus somni
GC_ID:11
PMID:5821848
ncbi_taxonomy
Haemophilus parasuis
Glaesserella parasuis
Glossina
tsetse flies
tsetse fly
Glossina <genus>
GC_ID:11
PMID:15184562
ncbi_taxonomy
Bacterium multocidum
Micrococcus gallicidus
Pasteurella cholerae-gallinarum
Pasteurella gallicida
Pasteurella multocida
NCBITaxon:746
GC_ID:11
PMID:10028248
PMID:8782683
ncbi_taxonomy
Pasteurella haemolytica Newsom and Cross 1932 (Approved Lists 1980)
Mannheimia haemolytica
GC_ID:11
PMID:11760958
PMID:8240958
rickettsias
ncbi_taxonomy
alpha-1 proteobacteria
Rickettsiales
GC_ID:1
ncbi_taxonomy
Arteriviridae
GC_ID:1
ncbi_taxonomy
Nidovirales
NCBITaxon:61430
GC_ID:1
ncbi_taxonomy
Theileria hirci
Theileria lestoquardi
Vertebrata
vertebrates
GC_ID:1
Vertebrata
vertebrates
ncbi_taxonomy
vertebrates
Vertebrata <vertebrates>
GC_ID:11
PMID:9226923
ncbi_taxonomy
Rickettsia burneti
Rickettsia diaporica
Coxiella burnetii
GC_ID:11
PMID:10939649
PMID:11491333
PMID:14662925
PMID:9103608
ncbi_taxonomy
Rickettsia
GC_ID:1
fish
fishes
ray-finned fishes
ncbi_taxonomy
Actinopterygi
Osteichthyes
bony fishes
Actinopterygii
GC_ID:11
ncbi_taxonomy
Clostridium perfringens C
GC_ID:1
catfishes
ncbi_taxonomy
Siluriformes
GC_ID:1
PMID:15062801
salmonids
ncbi_taxonomy
Salmonidae
NCBITaxon:1311475
GC_ID:1
rainbow trout
ncbi_taxonomy
Oncorhynchus nerka mykiss
Parasalmo mykiss
Salmo mykiss
Oncorhynchus mykiss
GC_ID:11
PMID:16403855
ncbi_taxonomy
Burkholderia/Oxalobacter/Ralstonia group
Burkholderiales
NCBITaxon:83553
GC_ID:11
PMID:10319462
PMID:11211265
PMID:21048221
PMID:21048222
PMID:23620152
PMID:25618261
PMID:9103632
PMID:9103637
ncbi_taxonomy
"Prowazekia" Coles 1953
Bedsonia
Chlamydophila
Miyagawanella
Rakeia
Rickettsiaformis
Chlamydia
GC_ID:11
PMID:10192388
PMID:10319462
PMID:8102247
PMID:8347519
ncbi_taxonomy
Chlamydozoon trachomatis
Rickettsia trachomae
Rickettsia trachomatis
Chlamydia trachomatis
GC_ID:11
ncbi_taxonomy
Escherichia coli O157:H7
NCBITaxon:812
GC_ID:11
PMID:10319462
PMID:12807198
PMID:8102247
PMID:8347519
ncbi_taxonomy
Chlamydophila psittaci
Chlamydozoon psittaci
Ehrlichia psittaci
Rickettsia psittaci
Rickettsiaformis psittacosis
Chlamydia psittaci
GC_ID:11
PMID:10319462
PMID:12807198
PMID:25618261
ncbi_taxonomy
Chlamydia psittaci (Lillie 1930) Page 1968
Chlamydia psittaci serotype 1
Chlamydophila abortus
Chlamydia abortus
NCBITaxon:811
GC_ID:11
PMID:10319462
PMID:8102247
PMID:8347519
ncbi_taxonomy
Chlamydophila pneumoniae
Chlamydia pneumoniae
GC_ID:11
PMID:10319462
agent of mouse pneumonitis
ncbi_taxonomy
Chlamydia trachomatis MoPn
Chlamydia muridarum
GC_ID:11
PMID:15774632
PMID:24158948
PMID:25481042
PMID:8186083
PMID:8590687
ncbi_taxonomy
Porphyromonas
NCBITaxon:1761
GC_ID:11
PMID:11837321
PMID:1736962
PMID:19244447
PMID:31157615
ncbi_taxonomy
Corynebacteriales
Corynebacteriales Goodfellow and Jones 2015
Corynebacterineae
Mycobacteriales Janke 1924 (Approved Lists 1980)
Mycobacteriales
PCV2
GC_ID:1
Porcine circovirus Type II
Porcine circovirus type 2
Porcine circovirus-2
ncbi_taxonomy
Porcine circovirus 2
GC_ID:1
birds
ncbi_taxonomy
avian
birds
Aves
GC_ID:1
ncbi_taxonomy
Neognathae
GC_ID:1
ducks
ncbi_taxonomy
Anas
NCBITaxon:9099
GC_ID:1
turkeys
ncbi_taxonomy
Phasianidae
GC_ID:11
ncbi_taxonomy
Leptospira interrogans serovar Icterohaemorrhagiae
Gallus domesticus
bantam
chicken
chickens
GC_ID:1
Gallus domesticus
bantam
chicken
chickens
ncbi_taxonomy
Gallus gallus domesticus
Phasianus gallus
Gallus gallus
NCBITaxon:41530
NCBITaxon:601
NCBITaxon:72667
GC_ID:11
PMID:10319519
PMID:10758910
PMID:15653930
PMID:16558776
PMID:9336938
ncbi_taxonomy
Bacillus typhi
Bacterium (subgen. Eberthella) typhi
Salmonella choleraesuis serovar Typhi
Salmonella choleraesuis typhi
Salmonella enterica ser. typhi
Salmonella enterica serotype Typhi
Salmonella enterica serovar Typhi
Salmonella typhi
Salmonella enterica subsp. enterica serovar Typhi
NCBITaxon:41532
NCBITaxon:59210
NCBITaxon:602
GC_ID:11
PMID:10758910
PMID:15653930
PMID:9336938
ncbi_taxonomy
Bacillus typhimurium
Salmonella choleraesuis serotype typhimurium
Salmonella enterica 1,4,[5],12,:i:1,2
Salmonella enterica ser. typhimurium
Salmonella enterica serotype Typhimurium
Salmonella enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:1,2
Salmonella typhi-murium
Salmonella typhimurium
Salmonella enterica subsp. enterica serovar Typhimurium
GC_ID:1
common turkey
turkey
wild turkey
ncbi_taxonomy
Meleagris gallopavo
GC_ID:11
ncbi_taxonomy
Bacillus/Lactobacillus/Streptococcus group
Firmibacteria
Bacilli
GC_ID:11
PMID:27620848
ncbi_taxonomy
Enterobacteriaceae and related endosymbionts
Enterobacteriaceae group
Enterobacteriales
gamma-3 proteobacteria
Enterobacterales
GC_ID:1
whales, hippos, ruminants, pigs, camels etc.
ncbi_taxonomy
Cetartiodactyla
even-toed ungulates
Artiodactyla
GC_ID:1
parrot
parrots
ncbi_taxonomy
Psittacidae
GC_ID:11
ncbi_taxonomy
Leptospira sp. Pomona
primate
Primates
GC_ID:1
New World monkeys
monkey
monkeys
ncbi_taxonomy
Platyrrhini
GC_ID:11
PMID:11760958
PMID:1736961
PMID:7537065
Potomac horse fever agent
equine monocytic ehrlichiosis agent
ncbi_taxonomy
Ehrlichia risticii
Neorickettsia risticii
GC_ID:1
ncbi_taxonomy
Catarrhini
GC_ID:1
African green monkey
African green monkeys
grivet
savanah monkey
ncbi_taxonomy
Cercopithecus aethiops
Ceropithecus aethiops
Simia aethiops
Chlorocebus aethiops
human
GC_ID:1
human
ncbi_taxonomy
Homo sapiens
GC_ID:1
dog, coyote, wolf, fox
ncbi_taxonomy
Canidae
GC_ID:1
ncbi_taxonomy
Canis
GC_ID:1
gray wolf
grey wolf
ncbi_taxonomy
Canis lupus
dog
dogs
GC_ID:1
dog
dogs
ncbi_taxonomy
Canis canis
Canis domesticus
Canis familiaris
Canis lupus familiaris
NCBITaxon:68731
NCBITaxon:9609
GC_ID:1
ncbi_taxonomy
Fennecus
Vulpes
GC_ID:1
northern raccoon
raccoon
ncbi_taxonomy
Ursus lotor
Procyon lotor
NCBITaxon:77150
GC_ID:1
black ferret
domestic ferret
ferret
ncbi_taxonomy
Mustela furo
Mustela putorius furo
GC_ID:1
ncbi_taxonomy
Felis
NCBITaxon:36475
GC_ID:1
PMID:17600185
PMID:8581300
PMID:8603894
cat
cats
domestic cat
ncbi_taxonomy
Felis domesticus
Felis silvestris catus
Felis catus
NCBITaxon:171554
GC_ID:11
PMID:11541229
PMID:11542017
PMID:28066339
BCF group
Bacteroides-Cytophaga-Flexibacter group
CFB group
Cytophaga-Flexibacter-Bacteroides phylum
ncbi_taxonomy
"Bacteroidota" Whitman et al. 2018
Bacteroidetes
CFB group bacteria
Sphingobacteria
Bacteroidota
GC_ID:1
sei whale
ncbi_taxonomy
Balaenoptera borealis
GC_ID:1
horses
ncbi_taxonomy
Equidae
GC_ID:1
domestic horse
equine
horse
ncbi_taxonomy
Equus przewalskii f. caballus
Equus przewalskii forma caballus
Equus caballus
GC_ID:1
pig
pigs
swine
wild boar
ncbi_taxonomy
Sus scrofa
GC_ID:1
deer
ncbi_taxonomy
Cervidae
white-tailed deer
Odocoileus virginianus
GC_ID:1
ncbi_taxonomy
Bovidae
GC_ID:1
ncbi_taxonomy
Bison
GC_ID:1
American bison
Bison
ncbi_taxonomy
Bos (Bison) bison
Bos bison
Bison bison
bovine
cattle
cow
dairy cow
domestic cattle
domestic cow
ox
oxen
NCBITaxon:272461
GC_ID:1
bovine
cattle
cow
dairy cow
domestic cattle
domestic cow
ox
oxen
ncbi_taxonomy
Bos bovis
Bos primigenius taurus
Bos taurus
NCBITaxon:57076
GC_ID:1
domestic goat
goat
goats
ncbi_taxonomy
Capra aegagrus hircus
Capra hircus
GC_ID:1
ncbi_taxonomy
Ovis
NCBITaxon:9936
GC_ID:1
domestic sheep
lambs
sheep
wild sheep
ncbi_taxonomy
Ovis ammon aries
Ovis orientalis aries
Ovis ovis
Ovis aries
NCBITaxon:29531
GC_ID:11
PMID:11594628
PMID:16560903
PMID:29593693
ncbi_taxonomy
Chondrococcus columnaris
Cytophaga columnaris
Flavobacterium columnare (Bernardet and Grimont 1989) Bernardet et al. 1996
Flexibacter columnaris
Flexibacter columnaris (ex Davis 1922) Bernardet and Grimont 1989
Flavobacterium columnare
GC_ID:1
ncbi_taxonomy
Caprinae
NCBITaxon:34833
NCBITaxon:9985
GC_ID:1
European rabbit
Japanese white rabbit
domestic rabbit
rabbit
rabbits
ncbi_taxonomy
Lepus cuniculus
Oryctolagus cuniculus
GC_ID:1
rodent
ncbi_taxonomy
rodents
Rodentia
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.
Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action).
Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper.
We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process.
The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
Yongqun He
AE
adverse reaction
WEB: http://en.wikipedia.org/wiki/Adverse_event
WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
The OAE official website is: http://www.oae-ontology.org/.
adverse event
an adverse event that occurs after a vaccination.
YH
vaccine adverse event
A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment.
Yongqun He, Sirarat Sarntivijai, Mathias Brochhausen, William Hogan, Philip E. Empey
http://en.wikipedia.org/wiki/Contraindication
contraindication
an adverse event that is induced by a vaccination.
YH
vaccine-induced adverse event
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
regulator role
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
regulator
OBI
regulator role
regulation-assigned role
Approval letter
Regulation-assigned role is a regulatory role defined by legislation or governmental orders
Person: Jennifer Fostel
regulation-assigned role
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
OBI, CDISC
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
regulatory role
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
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