Vaccine Ontology
type: Ontology
version IRI: vo.owl
default language: en
contributor: Chris mungall
contributor: Erica Marcos
contributor: Ningxian Fan
contributor: Paul Fabry
contributor: Randi Vita
contributor: Ryan R. Brinkman
contributor: Shunzhou Deng
creator: Alan Ruttenburg
creator: Alexander D. Diehl
creator: Amogh Madireddi
creator: Anna Maria Masci
creator: Anthony Huffman
creator: Barry Smith
creator: Bjoern Peters
creator: Edison Ong
creator: Ellen Zhang
creator: Hong Yu
creator: Jason Hu
creator: Jie Zheng
creator: Josh Monickaraj
creator: Kallan Roan
creator: Khadeejah Khan
creator: Le Liu
creator: Lindsay Cowell
creator: Melanie Courtot
creator: Ningxian Fan
creator: Omar Tibi
creator: Philip Huang
creator: Randi Vita
creator: Rebecca Racz
creator: Richard H. Scheuermann
creator: Rohit Goru
creator: Ronak Sutariya
creator: Samantha G. Sayers (SGS)
creator: Taiyu Lin
creator: Thomas Todd
creator: Xingxian Li
creator: Yongqun "Oliver" He (YH)
creator: Yu Lin (YL)
creator: Yuanyi (Penny) Pan
creator: Yuping Zheng
creator: Zuoshuang "Allen" Xiang
description: 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 clinical vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
format: OWL-DL
subject: An ontology in the domain of vaccine and vaccination
license: http://creativecommons.org/licenses/by/4.0/
version info: 2026-01-23

BFO OWL specification label
type: AnnotationProperty
definition: 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.
curator note: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

example of usage
type: AnnotationProperty
editor preferred term: example of usage
has curation status: IAO_0000122
definition: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

in branch
type: AnnotationProperty
editor preferred term: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: IAO_0000122
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: IAO_0000122
definition: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: IAO_0000122
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred term: alternative label
has curation status: IAO_0000125
definition: 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.
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: 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).

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: IAO_0000122
definition: 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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred term: has obsolescence reason
definition: 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred term: curator note
has curation status: IAO_0000122
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred term: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: IAO_0000125
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
editor preferred term: ontology term requester
has curation status: IAO_0000125
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

is denotator type
type: AnnotationProperty
editor preferred term: is denotator type
definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

imported from
type: AnnotationProperty
editor preferred term: imported from
has curation status: IAO_0000125
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred term: expand expression to
example of usage: 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)"
definition: 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
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred term: expand assertion to
example of usage: 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)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred term: first order logic expression
term editor: PERSON:Alan Ruttenberg

antisymmetric property
type: AnnotationProperty
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg
sub property of: logical characteristic of object property

OBO foundry unique label
type: AnnotationProperty
editor preferred term: OBO foundry unique label
has curation status: IAO_0000125
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: 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 .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has ID digit count
type: AnnotationProperty
editor preferred term: has ID digit count
example of usage: 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"
definition: 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)
term editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
editor preferred term: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: 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
term editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
editor preferred term: has ID policy for
example of usage: 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"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
editor preferred term: has ID prefix
example of usage: 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"
definition: 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.
term editor: Person:Alan Ruttenberg

elucidation
type: AnnotationProperty
editor preferred term: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: 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

has associated axiom(nl)
type: AnnotationProperty
editor preferred term: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred term: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred term: is allocated id range
definition: 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"
term editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

has ontology root term
type: AnnotationProperty
editor preferred term: has ontology root term
definition: 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.
term editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred term: may be identical to
definition: 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.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
editor preferred term: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: 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

term replaced by
type: AnnotationProperty
editor preferred term: term replaced by
has curation status: IAO_0000125
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

ISA alternative term
type: AnnotationProperty
editor preferred term: ISA alternative term
has curation status: IAO_0000122
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
term editor: Person: Alejandra Gonzalez-Beltran
term editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
sub property of: alternative label

IEDB alternative term
type: AnnotationProperty
editor preferred term: IEDB alternative term
has curation status: IAO_0000122
definition: An alternative term used by the IEDB.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
sub property of: alternative label

NCBI GeneID
type: AnnotationProperty
definition: A GeneID in the NCBI Gene database
term editor: Oliver He, Yue Liu

NCBI LocusTag
type: AnnotationProperty
definition: the NCBI LocusTag name of a gene
term editor: Oliver He, Yue Liu

modification date
type: AnnotationProperty
definition: a date of content modification
term editor: Oliver He, Yue Liu

organism NCBITaxon ID
type: AnnotationProperty
definition: The NCBITaxon ontology ID of an organism.
term editor: Oliver He, Yue Liu

chromosome ID of gene
type: AnnotationProperty
definition: A chromosome ID where a gene is located.
term editor: Oliver He

type of gene
type: AnnotationProperty
definition: an annotation property that specifies the type of a gene
term editor: Oliver He

nomenclature status
type: AnnotationProperty
definition: an annotation property that specifies a nomenclature status
term editor: Oliver He

has PubMed association
type: AnnotationProperty
definition: An annotation property that represents a gene's association with PubMed publication(s).
term editor: Yongqun He

logical characteristic of object property
type: AnnotationProperty
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call
created by: http://orcid.org/0000-0001-5208-3432

defined by construct
type: AnnotationProperty
example of usage: '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 . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8688-6599

preferred label for community
type: AnnotationProperty
example of usage: The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing).
definition: A provenance property that denotes a synonym to be the preferred one for a specific community.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/185
contributor: https://orcid.org/0000-0002-7356-1779
created: 2025-06-02

abbreviation
type: AnnotationProperty
example of usage: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
definition: A synonym type for describing abbreviations or initalisms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

ambiguous synonym
type: AnnotationProperty
definition: A synonym type for describing ambiguous synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

dubious synonym
type: AnnotationProperty
definition: A synonym type for describing dubious synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

layperson synonym
type: AnnotationProperty
example of usage: EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
definition: A synonym type for describing layperson or colloquial synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

plural form
type: AnnotationProperty
example of usage: CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
definition: A synonym type for describing pluralization synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

UK spelling synonym
type: AnnotationProperty
example of usage: CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
definition: A synonym type for describing UK spelling variants
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

misspelling
type: AnnotationProperty
definition: A synonym type for common misspellings
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/132
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

misnomer
type: AnnotationProperty
definition: A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/133
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

previous name
type: AnnotationProperty
example of usage: 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.
definition: A synonym type for names that have been used as primary labels in the past.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/139
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-07-25
sub property of: SynonymTypeProperty

legal name
type: AnnotationProperty
example of usage: The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
definition: A synonym type for the legal entity name
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/141
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-07-27
sub property of: SynonymTypeProperty

International Nonproprietary Name
type: AnnotationProperty
example of usage: 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
definition: 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.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/149
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-09-30
has exact synonym: INN
sub property of: SynonymTypeProperty

latin term
type: AnnotationProperty
example of usage: nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
definition: A synonym type for describing Latin term synonyms.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/146
contributor: https://orcid.org/0000-0002-1773-2692
created: 2023-10-12
sub property of: SynonymTypeProperty

acronym
type: AnnotationProperty
example of usage: 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.
definition: A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/135
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-11-01
sub property of: SynonymTypeProperty

has symbol
type: AnnotationProperty
example of usage: A serial number such as "12324X"; a stop sign; a written proper name such as "OBI
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/144
contributor: https://orcid.org/0000-0002-6523-4866
created: 2024-03-25

temporal interpretation
type: AnnotationProperty
definition: 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.
sub property of: logical macro assertion on an object property

never in taxon
type: AnnotationProperty
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947
expand assertion to: Class: ?X DisjointWith: RO_0002162 some ?Y
defined by construct: 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 . }
sub property of: taxonomic class assertion

mutually spatially disjoint with
type: AnnotationProperty
definition: 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.
alternative label: non-overlapping with
alternative label: shares no parts with
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
defined by construct: 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 . }
sub property of: logical macro assertion on a class

taxonomic class assertion
type: AnnotationProperty
definition: 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.
sub property of: logical macro assertion on a class

present in taxon
type: AnnotationProperty
definition: 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
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
defined by construct: 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) }
comment: 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.
sub property of: taxonomic class assertion

logical macro assertion
type: AnnotationProperty
definition: 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 on a class
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a class
editor note: The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
sub property of: logical macro assertion

logical macro assertion on a property
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
definition: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
sub property of: logical macro assertion on a property

logical macro assertion involving identity
type: AnnotationProperty
definition: A shortcut relationship that holds between two entities based on their identity criteria
sub property of: logical macro assertion

in approximate one to one relationship with
type: AnnotationProperty
definition: 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.
sub property of: logical macro assertion involving identity

is opposite of
type: AnnotationProperty
example of usage: 'anterior end of organism' is-opposite-of 'posterior end of organism'
example of usage: 'increase in temperature' is-opposite-of 'decrease in temperature'
definition: 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).
sub property of: in approximate one to one relationship with

external_definition
type: AnnotationProperty

axiom_lost_from_external_ontology
type: AnnotationProperty

homology_notes
type: AnnotationProperty

has_relational_adjective
type: AnnotationProperty

taxon_notes
type: AnnotationProperty

development_notes
type: AnnotationProperty

external_ontology_notes
type: AnnotationProperty

fma_set_term
type: AnnotationProperty

VIOLIN vaccine ID
type: AnnotationProperty
definition: An annotation property that represents a matched vaccine identifier used in the VIOLIN database.
term editor: Oliver He
term editor: Omar Tibi

trade name
type: AnnotationProperty
definition: An annotation property that represents the trade name of a product.
term editor: Oliver He

has vaccine active ingredient
type: AnnotationProperty
definition: An annotation property that represents the active ingredient of a vaccine.
term editor: Oliver He
sub property of: has vaccine ingredient

has vaccine ingredient
type: AnnotationProperty
definition: An annotation property that represents the vaccine ingredient of a vaccine. Such an ingredient may not be active.
term editor: Oliver He

vaccine dose annotation
type: AnnotationProperty
definition: An annotation property that describes the dose information of a vaccine
term editor: Oliver He

obsolete vaccine proper name
type: AnnotationProperty
example of usage: 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
definition: An annotation property that represents the proper name of a vaccine, which is defined in an official way such as one defined by FDA.
term editor: Kallan Roan
term editor: Oliver He
has obsolescence reason: IAO_0000226
deprecated: true

obsolete vaccine manufacturer
type: AnnotationProperty
example of usage: The vaccine Prevnar has the manufacturer: Wyeth Pharmaceuticals Inc. Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
definition: An annotation property that represents the manufacturer of a vaccine
term editor: Kallan Roan
term editor: Oliver He
has obsolescence reason: IAO_0000226
deprecated: true

FDA vaccine indications
type: AnnotationProperty
example of usage: 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
definition: An annotation property that represents the indications of a vaccine defined by the USA FDA.
term editor: Kallan Roan
term editor: Oliver He

vaccine package insert PDF URL
type: AnnotationProperty
example of usage: Prevnar has the package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM137038.pdf . Recorded on 11/26/2018.
definition: An annotation property that represents a URL of the package insert PDF document of a licensed vaccine
term editor: Kallan Roan
term editor: Oliver He

vaccine STN
type: AnnotationProperty
definition: An annotation property that indicate the number that is generated by FDA based on a request from an applicant of a product licensing.
term editor: Kallan Roan
term editor: Oliver He
definition source: https://www.fda.gov/downloads/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/ProceduresSOPPs/UCM461225.pdf

RxNorm ID
type: AnnotationProperty

obsolete has Protegen id
type: AnnotationProperty
has obsolescence reason: IAO_0000226
deprecated: true

obsolete has Protegen annotation
type: AnnotationProperty
has obsolescence reason: IAO_0000226
deprecated: true

RxNorm Preferred Name
type: AnnotationProperty
example of usage: 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".
sub property of: alternative label

RxNorm Synonym
type: AnnotationProperty
sub property of: alternative label

VAC adjuvant ID
type: AnnotationProperty
definition: An identifier assigned by the Vaccine Adjuvant Compendium (VAC: https://vac.niaid.nih.gov/)
definition source: https://vac.niaid.nih.gov/

vaccine antigen annotation
type: AnnotationProperty
definition: An annotation property that represents the annotated information about the antigens used for a specific vaccine.
term editor: Oliver He
term editor: Penny Pan
definition source: https://en.wikipedia.org/wiki/Antigen

obsolete vaccine preparation annotation
type: AnnotationProperty
has obsolescence reason: IAO_0000226
deprecated: true

vaccine response annotation
type: AnnotationProperty

CVX code
type: AnnotationProperty
definition: An annotation property that refers to a specific CVX ID.
term editor: Oliver He
term editor: Penny Pan
definition source: https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp

obsolete status of vaccine development
type: AnnotationProperty
definition: An annotation property that shows the status of vaccine developmeint including: clinical trial, research, licensed, or Emergency Use Authorization (EUA).
term editor: Anthony Huffman
term editor: Jie Zheng
term editor: Oliver He
term editor: Penny Pan
has obsolescence reason: IAO_0000226
deprecated: true

OMOP concept ID
type: AnnotationProperty
definition: An annotation property that represents an identifier of RxNorm or RxNorm extension concept assigned by OMOP.

RxNorm OMOP extension ID
type: AnnotationProperty
definition: An annotation property that represents an identifier of RxNorm extension term assigned by OMOP.

CVX full vaccine name
type: AnnotationProperty
definition: An annotation property that refers to full vaccine name in CVX code set.
sub property of: alternative label

CVX short description
type: AnnotationProperty
definition: An annotation property that refers to short description in CVX code set.

has_rank
type: AnnotationProperty

has broad synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
sub property of: alternative label

has cross-reference
type: AnnotationProperty
example of usage: disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
definition: An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/123
contributor: https://orcid.org/0000-0002-7356-1779
created: 2024-03-18

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
sub property of: alternative label

has narrow synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
sub property of: alternative label

has related synonym
type: AnnotationProperty
definition: 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.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
sub property of: alternative label

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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/
editor note: 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'.
alternative label: part_of
temporal interpretation: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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/
editor note: 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'.
alternative label: has_part
temporal interpretation: RO_0001901

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
elucidation: [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])
comment: 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

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: 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])
comment: 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

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
editor preferred term: preceded by
definition: 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.
editor note: 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.
alternative label: is preceded by
alternative label: preceded_by
imported from: ro.owl
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: happens during
editor preferred term: precedes
definition: 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.
imported from: ro.owl

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred term: occurs in
definition: 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
alternative label: occurs_in
alternative label: unfolds in
alternative label: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
editor preferred term: site of
definition: [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
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

process profile of
type: ObjectProperty
domain: process profile
range: process
imported from: bfo.owl

is about
type: ObjectProperty
example of usage: This document is about information artifacts and their representations
has curation status: IAO_0000125
definition: A (currently) primitive relation that relates an information artifact to an entity.
editor note: 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.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: iao.owl

mentions
type: ObjectProperty
sub property of: is about
has curation status: IAO_0000125
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
editor note: 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)
editor note: 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
term editor: PERSON: Jonathan Rees
term editor: Person: Alan Ruttenberg
imported from: iao.owl

has_specified_input
type: ObjectProperty
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: IAO_0000122
definition: The inverse property of is_specified_input_of
editor note: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: is_specified_input_of
example of usage: 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
has curation status: IAO_0000122
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

has_specified_output
type: ObjectProperty
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
editor preferred term: has_specified_output
has curation status: IAO_0000122
definition: The inverse property of is_specified_output_of
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: obi.owl

is_manufactured_by
type: ObjectProperty
domain: material entity
range: manufacturer
editor preferred term: is_manufactured_by
example of usage: 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)
has curation status: IAO_0000123
definition: 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.
term editor: Alan Ruttenberg
term editor: Liju Fan
alternative label: has_make
alternative label: has_manufacturer
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: is_specified_output_of
has curation status: IAO_0000122
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred term: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: IAO_0000120
definition: 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.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: obi.owl

has grain
type: ObjectProperty
sub property of: has part
editor preferred term: has grain
has curation status: IAO_0000120
definition: 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.
editor note: 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
term editor: PERSON: Alan Ruttenberg
definition source: 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
imported from: obi.owl

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred term: objective_achieved_by
has curation status: IAO_0000122
definition: 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.
term editor: OBI
definition source: OBI
imported from: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred term: has value specification
has curation status: IAO_0000120
definition: A relation between an information content entity and a value specification that specifies its value.
term editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
editor preferred term: inheres in
example of usage: this fragility is a characteristic of this vase
example of usage: this red color is a characteristic of this apple
definition: 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.
alternative label: inheres_in
imported from: ro.owl
temporal interpretation: RO_0001901
comment: 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.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
editor note: 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.
alternative label: bearer_of
alternative label: is bearer of
imported from: ro.owl
temporal interpretation: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
alternative label: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: Class
  union of: process
  union of: specifically dependent continuant
example of usage: 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).
example of usage: 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).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.

concretizes
type: ObjectProperty
domain: Class
  union of: process
  union of: specifically dependent continuant
range: generically dependent continuant
example of usage: 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).
example of usage: 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).
definition: A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative label: function_of
alternative label: is function of
imported from: ro.owl
comment: 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
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative label: is quality of
alternative label: quality_of
imported from: ro.owl
comment: 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
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative label: is role of
alternative label: role_of
imported from: ro.owl
comment: 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.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative label: has_function
imported from: ro.owl

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: 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.
alternative label: has_quality
imported from: ro.owl

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative label: has_role
imported from: ro.owl

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
imported from: ro.owl

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
imported from: ro.owl
in subset: RO_0002259
comment: 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.

derives from
type: ObjectProperty
inverse of: derives into
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: IAO_0000125
definition: 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
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative label: derives_from

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: IAO_0000125
definition: 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
editor note: 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'.
alternative label: derives_into

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
editor preferred term: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: 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/
alternative label: location_of
temporal interpretation: RO_0001901

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred term: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: 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
editor note: 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/
alternative label: located_in
temporal interpretation: RO_0001901
source: http://www.obofoundry.org/ro/#OBO_REL:located_in

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: 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.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: 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.

2D boundary of
type: ObjectProperty
inverse of: has 2D boundary
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: 2D_boundary_of
alternative label: boundary of
alternative label: is 2D boundary of
alternative label: is boundary of
temporal interpretation: RO_0001901

has 2D boundary
type: ObjectProperty
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: has boundary
alternative label: has_2D_boundary
temporal interpretation: RO_0001901

cell expresses
type: ObjectProperty
sub property of: expresses
definition: 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.
term editor: https://orcid.org/0000-0002-7073-9172
imported from: ro.owl
description: 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

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: David Osumi-Sutherland
imported from: ro.owl
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

starts during
type: ObjectProperty
sub property of: temporally related to
term editor: David Osumi-Sutherland
alternative label: io
imported from: ro.owl
in subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: starts during
sub property of: ends during
type: TransitiveProperty
term editor: David Osumi-Sutherland
alternative label: d
alternative label: during
imported from: ro.owl
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
term editor: David Osumi-Sutherland
alternative label: o
alternative label: overlaps
imported from: ro.owl
in subset: ro-eco
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
has curation status: IAO_0000125
definition: 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.
term editor: 0000-0001-9227-417X
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947
imported from: ro.owl
in subset: ro-eco
comment: Connects a biological entity to its taxon of origin.

has component
type: ObjectProperty
sub property of: has part
has curation status: IAO_0000125
definition: 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.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: 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.
imported from: ro.owl
temporal interpretation: RO_0001901
in subset: ro-eco

gene product of
type: ObjectProperty
sub property of: genomically related to
has curation status: IAO_0000125
definition: 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"
editor note: 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.
term editor: https://orcid.org/0000-0002-6601-2165
imported from: ro.owl

has gene product
type: ObjectProperty
sub property of: genomically related to
example of usage: every HOTAIR lncRNA is the gene product of some HOXC gene
example of usage: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
has curation status: IAO_0000125
definition: 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
term editor: https://orcid.org/0000-0002-6601-2165
imported from: ro.owl

expressed in
type: ObjectProperty
sub property of: genomically related to
example of usage: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
has curation status: IAO_0000125
definition: 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
term editor: https://orcid.org/0000-0002-6601-2165
imported from: ro.owl

temporally related to
type: ObjectProperty
has curation status: IAO_0000125
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Allen's interval algebra
curator note: 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.
imported from: ro.owl
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

over-expressed in
type: ObjectProperty
sub property of: expressed in
definition: g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
imported from: ro.owl

under-expressed in
type: ObjectProperty
sub property of: expressed in
definition: g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
imported from: ro.owl

has biological role
type: ObjectProperty
sub property of: has role
definition: c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
imported from: ro.owl

has application role
type: ObjectProperty
sub property of: has role
definition: c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
imported from: ro.owl

has chemical role
type: ObjectProperty
sub property of: has role
definition: c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
imported from: ro.owl

ubiquitously expressed in
type: ObjectProperty
sub property of: expressed in
has curation status: IAO_0000125
definition: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
editor note: 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.
term editor: https://orcid.org/0000-0002-6601-2165
imported from: ro.owl

expresses
type: ObjectProperty
sub property of: genomically related to
has curation status: IAO_0000125
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
imported from: ro.owl

ubiquitously expresses
type: ObjectProperty
sub property of: expresses
has curation status: IAO_0000125
definition: inverse of ubiquiotously expressed in
term editor: https://orcid.org/0000-0002-6601-2165
imported from: ro.owl
in subset: RO_0002259

characteristic of part of
type: ObjectProperty
sub property of: depends on
definition: 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.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: ro.owl
temporal interpretation: RO_0001901

evolutionarily related to
type: ObjectProperty
definition: A relationship that holds via some environmental process
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
imported from: ro.owl

genomically related to
type: ObjectProperty
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
curator note: 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
imported from: ro.owl

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative label: is member of
alternative label: member part of
definition source: SIO
temporal interpretation: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
temporal interpretation: RO_0001901

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: ro.owl

depends on
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165
imported from: ro.owl

towards
type: ObjectProperty
sub property of: depends on
definition: 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
editor note: 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.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: ro.owl

transcribed from
type: ObjectProperty
sub property of: genomically related to
definition: x is transcribed from y if and only if x is synthesized from template y
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
imported from: ro.owl

transcribed to
type: ObjectProperty
sub property of: genomically related to
definition: inverse of transcribed from
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
imported from: ro.owl
in subset: RO_0002259

ribosomal translation of
type: ObjectProperty
sub property of: genomically related to
definition: 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
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
imported from: ro.owl

ribosomally translates to
type: ObjectProperty
sub property of: genomically related to
definition: inverse of ribosomal translation of
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267
imported from: ro.owl

realizable has basis in
type: ObjectProperty
sub property of: causally related to
imported from: ro.owl
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:20:01Z

disease has basis in
type: ObjectProperty
sub property of: realizable has basis in
sub property of: causal relationship with disease as subject
imported from: ro.owl
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:26:47Z

causal relationship with disease as subject
type: ObjectProperty
sub property of: causally related to
sub property of: disease relationship
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
imported from: ro.owl
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-11-05T03:50:54Z

DEPRECATED inheres in
type: ObjectProperty
comment: 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: true

DEPRECATED bearer of
type: ObjectProperty
deprecated: true

disease relationship
type: ObjectProperty
definition: This relation groups relations between diseases and any other kind of entity.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
imported from: ro.owl
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-09-26T00:00:32Z

has vaccine conjugate protein
type: ObjectProperty
sub property of: has vaccine component
definition: A type of 'has vaccine component' relation that specifies a vaccine conjugate protein for a specific vaccine

has bacterial vaccine vector
type: ObjectProperty
sub property of: has vaccine vector
range: Bacteria
definition: A type of 'has vaccine vector' relation that specifies a bacterial vaccine vector
term editor: Oliver He

has vaccine contraindication
type: ObjectProperty
definition: A relation that specifies contraindication of a vaccine.
editor note: This relation may be replaced by has_vaccine_allergen. We need to determine if any vaccine contraindicator is not a vaccine allergen.
term editor: Oliver He

has viral vaccine vector
type: ObjectProperty
sub property of: has vaccine vector
definition: A type of 'has vaccine vector' that is specifically for viral vaccine vector

has DNA vaccine plasmid
type: ObjectProperty
sub property of: has vaccine component
definition: A 'has vaccine component' relation that specifies the plasmid used for development of a particular DNA vaccine.
term editor: Oliver He

infection_of
type: ObjectProperty
definition: A relation between a disorder and an infectious pathogen.
editor note: 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)
term editor: Alan Ruttenburg
term editor: Allen Xiang
term editor: Bjoern Peters
term editor: Melanie Courtot
term editor: Oliver He

induced by vaccination of
type: ObjectProperty
definition: An object property that specifies a process that is induced by vaccination of a vaccine
term editor: Oliver He

has DNA vaccine antigen gene
type: ObjectProperty
sub property of: has vaccine component
definition: 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.
term editor: Oliver He

has vaccine component
type: ObjectProperty
sub property of: has component
domain: vaccine
definition: An object property that defines a relation between a vaccine and its component
term editor: Asiyah Yu Lin
term editor: Oliver He

has vaccine antigen
type: ObjectProperty
definition: An object property that specifies a vaccine antigen
editor note: 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'.
term editor: Asiyah Yu Lin
term editor: Oliver He

has subunit vaccine antigen
type: ObjectProperty
sub property of: has vaccine antigen
definition: A type of 'has vaccine antigen' relation that is specifically for vaccine protective protein antigen used in subunit vaccine development
term editor: Asiyah Yu Lin
term editor: Oliver He

has vaccine protective antigen
type: ObjectProperty
sub property of: has vaccine antigen
definition: A type of 'has vaccine antigen' relation that is specifically for vaccine protective antigen component
term editor: Asiyah Yu Lin
term editor: Oliver He

has vaccine adjuvant
type: ObjectProperty
sub property of: has vaccine component
definition: A type of 'has vaccine component' relation that is specifically for vaccine adjuvant component
term editor: Asiyah Yu Lin
term editor: Oliver He

has vaccine vector
type: ObjectProperty
sub property of: has vaccine component
range: recombinant vaccine vector
definition: A type of 'has vaccine component' relation that is specifically for vaccine vector component
term editor: Asiyah Yu Lin
term editor: Oliver He

has vaccine allergen
type: ObjectProperty
definition: An object property that specifies a relation between a vaccine and a vaccine allergen
term editor: Oliver He

vaccine organism secretes
type: ObjectProperty
domain: vaccine
definition: An object property that indicates a secretion of a material (e.g., protein) from a vaccine organism.
term editor: Oliver He

has vaccine preservative
type: ObjectProperty
sub property of: has vaccine component
definition: A 'has vaccine component' relation that is specifically used for vaccine preservative
term editor: Asiyah Yu Lin
term editor: Oliver He

vaccinated in route
type: ObjectProperty
domain: vaccine
range: route of administration
definition: An object property that specifies a relation between a vaccine and a vaccinate route

has vaccinee
type: ObjectProperty
domain: vaccine
definition: An object property that specifies a relation between a vaccine and its vaccinee

DNA vaccine expresses protein antigen
type: ObjectProperty
sub property of: expresses
definition: An 'expresses' relation that specifies a relation between a DNA vaccine and a protein antigen to be expressed by the DNA vaccine.
term editor: Oliver He

obsolete vaccinates
type: ObjectProperty
example of usage: "A vaccinates B" means that the vaccine A is used for vaccinating the host B (e.g., human).
definition: A relation 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.
term editor: Alan Ruttenburg
term editor: Allen Xiang
term editor: Melanie Courtot
term editor: Oliver He
deprecated: true

obsolete has_vaccine_allergen
type: ObjectProperty
definition: has_vaccine_allegen is a relation that specifies an allegen to a vaccine.
term editor: Oliver He
deprecated: true

vaccine organism has mutation
type: ObjectProperty
definition: 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.
term editor: Oliver He

has vaccine virmugen
type: ObjectProperty
definition: An object property that specifies a relation between a vaccine and a vaccine virmugen.
editor note: This is a shortcut relation. Domain: vaccine Range: a gene Shortcut: is_specified_output_of some ('preparation of gene mutant vaccine' and (has_specified_input some gene))
term editor: Oliver He

has subunit vaccine protective antigen
type: ObjectProperty
sub property of: has subunit vaccine antigen
definition: A 'has subunit vaccine antigen' relation that indicates the antigen is protective.
term editor: Oliver He

is_distributed_by
type: ObjectProperty
definition: A relation that specifies a company that distributes a product (e.g., vaccine). The company is very likely not the manufacturer of the product.
term editor: Allen Xiang
term editor: Oliver He

immunizes against disease
type: ObjectProperty
domain: vaccine
range: disease
definition: A shortcut relation that is equivalent 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.
term editor: Asiyah Yu Lin
term editor: Oliver He
alternative label: immunization against disease
alternative label: vaccine immunization against disease

has gene mutation
type: ObjectProperty
definition: An object property that represents an organism has a mutation of a specific gene from the organism genome.
term editor: Oliver He

immunizes recipient
type: ObjectProperty
domain: vaccine
range: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: VO_0001274
definition: A shortcut relation that is equivalent 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 recipient role' and (role_of some 'organism')))))))). The domain of this relation is a vaccine. The range of this relation is a organism.
term editor: Anna Maria Masci
term editor: Asiyah Yu Lin
term editor: Barry Smith
term editor: Jie Zheng
term editor: Oliver He
alternative label: immunization for host
alternative label: immunization for recipient
alternative label: immunizes host
alternative label: vaccine immunization for host
alternative label: vaccine immunization for recipient

has prime vaccine
type: ObjectProperty
definition: An object property that represents a relation between a vaccine with a prime-boost schedule and a vaccine used for priming.
term editor: Oliver He

has boost vaccine
type: ObjectProperty
domain: vaccine
range: vaccine
definition: An object property that represents a relation between a vaccine with a prime-boost schedule and a vaccine used for boost.
term editor: Oliver He

immunizes against pathogen
type: ObjectProperty
domain: vaccine
range: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: pathogen role
definition: A shortcut relation that is equivalent 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 'pathogen')))))))) The domain of this relation is a vaccine. The range of this relation is a pathogen (a bacterium, a virus, a fungus, and a parasite) Ranges: organism and 'has role' some 'pathogen role'
term editor: Oliver He
alternative label: immunization against pathogen
alternative label: immunizes against microbe
alternative label: vaccine immunization against pathogen
term tracker item: https://github.com/vaccineontology/VO/issues/675

test in lab animal model
type: ObjectProperty
domain: vaccine
range: organism
definition: A shortcut relation that is equivalent to: ('vaccine' and 'has function' some ('vaccine function' and ('is realized by' some ('vaccine immunization' and 'has participant' some ('organism' and 'has role' some 'laboratory animal model role'))))). The domain of this relation is a vaccine. The range of this relation is a organism.
term editor: Jie Zheng
term editor: Oliver He

obsolete immunizes against disease process
type: ObjectProperty
definition: 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.
term editor: Oliver He
has obsolescence reason: IAO_0000226
deprecated: true

up-expressed as immune signature of
type: ObjectProperty
domain: material entity
range: process
definition: An object property that represents a relation between a material entity and biological process
term editor: Anthony Huffman
term editor: Oliver He

induces immune profile
type: ObjectProperty
definition: 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.
term editor: Amogh Madireddi
term editor: Oliver He

target receptor
type: ObjectProperty
example of usage: The vaccine adjuvant T-vant targets the molecular receptor TLR4. Reference: https://vac.niaid.nih.gov/view?id=61.
definition: An object property that represents a relation in which a material entity specifically interacts with or targets a molecular entity acting as a receptor.
term editor: Jie Zheng
term editor: Oliver He

capable of blocking transmission (of life cycle)
type: ObjectProperty
definition: A relation between a material entity and a parasite where the material entity causes some process against some parasite such that transmitting to additional hosts or vectors.

blocks transmission of pathogen via vaccine
type: ObjectProperty
sub property of: immunizes against pathogen
sub property of: capable of blocking transmission (of life cycle)
definition: A relation between a vaccine and a parasite where the vaccine immunizes against some parasite such that the parasite is blocked transmitting to additional hosts or vectors.
term tracker item: https://github.com/vaccineontology/VO/issues/675

vaccine immunity response transferrable to organism
type: ObjectProperty
definition: A relation 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

has flu season
type: ObjectProperty
term editor: Ellen Zhang
term editor: Jie Zheng
term editor: Xingxian Li
term tracker item: flu season

has drug brand name
type: ObjectProperty
term editor: Jie Zheng
term tracker item: brand name

has drug dose form
type: ObjectProperty
term editor: Jie Zheng
term tracker item: drug form

has drug package
type: ObjectProperty
term editor: Jie Zheng
term tracker item: drug package

has drug supplier
type: ObjectProperty
term editor: Jie Zheng
term tracker item: organization

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: 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.
editor note: 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
editor note: 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
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
elucidation: 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])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (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]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: 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.
elucidation: 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])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: 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
elucidation: 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])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

spatiotemporal region
type: Class
subclass of: occurrent
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: 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])
editor note: 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)
has associated axiom(fol): (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]
comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: 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.
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (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]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
elucidation: 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])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (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]
has associated axiom(fol): (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]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (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]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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])
editor note: 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.
has associated axiom(fol): (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]
comment: 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.

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: 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.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: 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.
editor note: 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.
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object part
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: 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
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: 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])
has associated axiom(fol): (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]

Axiom
annotated source: fiat object part
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: fiat object part
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: 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])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: 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)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: 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).
definition source: 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.
elucidation: 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])
has associated axiom(fol): (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]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: 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.
editor note: 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).
editor note: 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
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: 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])

Axiom
annotated source: object
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
comment: 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.

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: 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.
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: 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])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: 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).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
elucidation: 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])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (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]
has associated axiom(fol): (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]

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: 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])
editor note: 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.
editor note: 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
editor note: 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.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (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]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: 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

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: 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])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: 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
example of usage: 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.
example of usage: 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.
definition: 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])
elucidation: 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])
has associated axiom(fol): (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]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: 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.
example of usage: a marriage bond, an instance of requited love, an obligation between one person and another.
definition: 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])
has associated axiom(fol): (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]

Axiom
annotated source: relational quality
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: 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])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: 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.
elucidation: 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])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative label: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: 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])

Axiom
annotated source: history
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

phenol
type: Class
subclass of: molecular entity
definition: An organic hydroxy compound that consists of benzene bearing a single hydroxy substituent. The parent of the class of phenols.
imported from: chebi.owl
charge: 0
formula: C6H6O
inchi: InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
inchikey: ISWSIDIOOBJBQZ-UHFFFAOYSA-N
mass: 94.11120
monoisotopicmass: 94.04186
smiles: Oc1ccccc1
has alternative id: CHEBI:14777
has alternative id: CHEBI:25966
has alternative id: CHEBI:43543
has alternative id: CHEBI:8071
has cross-reference: CAS:108-95-2
has cross-reference: DrugBank:DB03255
has cross-reference: Drug_Central:4266
has cross-reference: Gmelin:2794
has cross-reference: HMDB:HMDB0000228
has cross-reference: KEGG:C00146
has cross-reference: KEGG:C15584
has cross-reference: KEGG:D00033
has cross-reference: KEGG:D06536
has cross-reference: KNApSAcK:C00002664
has cross-reference: PDBeChem:IPH
has cross-reference: PMID:12058733
has cross-reference: PMID:16953321
has cross-reference: PMID:17852157
has cross-reference: PMID:19029204
has cross-reference: PMID:20886261
has cross-reference: PMID:21492257
has cross-reference: PMID:21689881
has cross-reference: PMID:21809019
has cross-reference: PMID:21822930
has cross-reference: Reaxys:969616
has cross-reference: UM-BBD_compID:c0128
has cross-reference: Wikipedia:Phenol
has exact synonym: PHENOL
has exact synonym: Phenol
has exact synonym: phenol
has OBO namespace: chebi_ontology
has related synonym: Benzenol
has related synonym: Carbolsaeure
has related synonym: Hydroxybenzene
has related synonym: Karbolsaeure
has related synonym: Oxybenzene
has related synonym: PhOH
has related synonym: Phenic acid
has related synonym: Phenylic acid
has related synonym: Phenylic alcohol
has related synonym: acide carbolique
has related synonym: acide phenique
has related synonym: carbolic acid
id: CHEBI:15882
in subset: 3 STAR

urea
type: Class
subclass of: molecular entity
definition: A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O).
imported from: chebi.owl
charge: 0
formula: CH4N2O
inchi: InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)
inchikey: XSQUKJJJFZCRTK-UHFFFAOYSA-N
mass: 60.05534
monoisotopicmass: 60.03236
smiles: NC(N)=O
has alternative id: CHEBI:15292
has alternative id: CHEBI:27218
has alternative id: CHEBI:46379
has alternative id: CHEBI:9888
has cross-reference: CAS:57-13-6
has cross-reference: DrugBank:DB03904
has cross-reference: Drug_Central:4264
has cross-reference: ECMDB:ECMDB04172
has cross-reference: Gmelin:1378
has cross-reference: HMDB:HMDB0000294
has cross-reference: KEGG:C00086
has cross-reference: KEGG:D00023
has cross-reference: KNApSAcK:C00007314
has cross-reference: MetaCyc:UREA
has cross-reference: PDBeChem:URE
has cross-reference: PMID:18037357
has cross-reference: PMID:22770225
has cross-reference: PPDB:1728
has cross-reference: Reaxys:635724
has cross-reference: UM-BBD_compID:c0165
has cross-reference: Wikipedia:Urea
has cross-reference: YMDB:YMDB00003
has exact synonym: UREA
has exact synonym: Urea
has exact synonym: urea
has OBO namespace: chebi_ontology
has related synonym: 1728
has related synonym: Carbamide
has related synonym: E927b
has related synonym: H2NC(O)NH2
has related synonym: Harnstoff
has related synonym: Karbamid
has related synonym: carbamide
has related synonym: carbonyldiamide
has related synonym: ur
has related synonym: uree
id: CHEBI:16199
in subset: 3 STAR

lipopolysaccharide
type: Class
subclass of: molecular entity
definition: 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).
imported from: chebi.owl
has alternative id: CHEBI:14520
has alternative id: CHEBI:25062
has alternative id: CHEBI:6494
has cross-reference: KEGG:C00338
has cross-reference: PMID:15589368
has cross-reference: PMID:24186868
has cross-reference: PMID:24506665
has cross-reference: PMID:24642373
has cross-reference: PMID:24659348
has exact synonym: Lipopolysaccharide
has OBO namespace: chebi_ontology
has related synonym: LPS
has related synonym: lipopolysaccharides
id: CHEBI:16412
in subset: 3 STAR

peptide
type: Class
subclass of: molecular entity
definition: 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.
imported from: chebi.owl
charge: 0
formula: (C2H2NOR)nC2H3NOR
has alternative id: CHEBI:14753
has alternative id: CHEBI:25906
has alternative id: CHEBI:7990
has cross-reference: KEGG:C00012
has exact synonym: Peptide
has exact synonym: peptides
has OBO namespace: chebi_ontology
has related synonym: Peptid
has related synonym: peptido
has related synonym: peptidos
id: CHEBI:16670
in subset: 3 STAR

formaldehyde
type: Class
subclass of: molecular entity
definition: An aldehyde resulting from the formal oxidation of methanol.
imported from: chebi.owl
charge: 0
formula: CH2O
inchi: InChI=1S/CH2O/c1-2/h1H2
inchikey: WSFSSNUMVMOOMR-UHFFFAOYSA-N
mass: 30.02598
monoisotopicmass: 30.01056
smiles: [H]C([H])=O
has alternative id: CHEBI:14274
has alternative id: CHEBI:24077
has alternative id: CHEBI:337763
has alternative id: CHEBI:5142
has cross-reference: CAS:50-00-0
has cross-reference: DrugBank:DB03843
has cross-reference: Drug_Central:3244
has cross-reference: Gmelin:445
has cross-reference: HMDB:HMDB0001426
has cross-reference: KEGG:C00067
has cross-reference: KEGG:D00017
has cross-reference: MetaCyc:FORMALDEHYDE
has cross-reference: PDBeChem:FOR
has cross-reference: PMID:110589
has cross-reference: PMID:12686735
has cross-reference: PMID:15091529
has cross-reference: PMID:16423181
has cross-reference: PMID:17618393
has cross-reference: PMID:18837732
has cross-reference: PMID:25042713
has cross-reference: PMID:7381846
has cross-reference: PMID:7548723
has cross-reference: PMID:7689168
has cross-reference: PMID:7896413
has cross-reference: PMID:9686972
has cross-reference: PPDB:359
has cross-reference: Reaxys:1209228
has cross-reference: UM-BBD_compID:c0122
has cross-reference: Wikipedia:Formaldehyde
has exact synonym: FORMALDEHYDE
has exact synonym: Formaldehyde
has exact synonym: formaldehyde
has OBO namespace: chebi_ontology
has related synonym: FORMALIN
has related synonym: Formaldehyd
has related synonym: Formalin
has related synonym: Methanal
has related synonym: Methylene oxide
has related synonym: Oxomethane
has related synonym: Oxomethylene
id: CHEBI:16842
in subset: 3 STAR

streptomycin
type: Class
subclass of: molecular entity
definition: A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class
imported from: chebi.owl
charge: 0
formula: C21H39N7O12
inchi: 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
inchikey: UCSJYZPVAKXKNQ-HZYVHMACSA-N
mass: 581.57434
monoisotopicmass: 581.26567
has alternative id: CHEBI:15119
has alternative id: CHEBI:26784
has alternative id: CHEBI:45745
has alternative id: CHEBI:9284
has cross-reference: CAS:57-92-1
has cross-reference: DrugBank:DB01082
has cross-reference: Drug_Central:2481
has cross-reference: HMDB:HMDB0015214
has cross-reference: KEGG:C00413
has cross-reference: KEGG:D08531
has cross-reference: MetaCyc:STREPTOMYCIN
has cross-reference: PDBeChem:SRY
has cross-reference: PMID:11228320
has cross-reference: PMID:11905029
has cross-reference: PMID:12118520
has cross-reference: PMID:13030054
has cross-reference: PMID:13116094
has cross-reference: PMID:13136149
has cross-reference: PMID:13596285
has cross-reference: PMID:13691614
has cross-reference: PMID:13985260
has cross-reference: PMID:13990247
has cross-reference: PMID:14623118
has cross-reference: PMID:14828344
has cross-reference: PMID:14852338
has cross-reference: PMID:14939639
has cross-reference: PMID:15081082
has cross-reference: PMID:15137533
has cross-reference: PMID:15207172
has cross-reference: PMID:15686853
has cross-reference: PMID:15736038
has cross-reference: PMID:16904706
has cross-reference: PMID:17105735
has cross-reference: PMID:17238915
has cross-reference: PMID:17429930
has cross-reference: PMID:18173084
has cross-reference: PMID:18916143
has cross-reference: PMID:19052412
has cross-reference: PMID:19335957
has cross-reference: PMID:21350946
has cross-reference: PMID:21362244
has cross-reference: PMID:21593257
has cross-reference: PMID:21937264
has cross-reference: PMID:22101040
has cross-reference: Pesticides:streptomycin
has cross-reference: Reaxys:74498
has cross-reference: Wikipedia:Streptomycin
has exact synonym: 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
has exact synonym: STREPTOMYCIN
has OBO namespace: chebi_ontology
has related synonym: 2,4-Diguanidino-3,5,6-trihydroxycyclohexyl 5-deoxy-2-O-(2-deoxy-2-methylamino-alpha-L-glucopyranosyl)-3-C-formyl-beta-L-lyxopentanofuranoside
has related synonym: Kantrex
has related synonym: SM
has related synonym: [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}
has related synonym: streomycin
has related synonym: streptomycin
id: CHEBI:17076
in subset: 3 STAR

lactose
type: Class
subclass of: molecular entity
definition: 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.
imported from: chebi.owl
charge: 0
formula: C12H22O11
inchi: 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
inchikey: GUBGYTABKSRVRQ-QKKXKWKRSA-N
mass: 342.297
monoisotopicmass: 342.11621
has alternative id: CHEBI:10296
has alternative id: CHEBI:10380
has alternative id: CHEBI:14497
has alternative id: CHEBI:22460
has alternative id: CHEBI:22760
has alternative id: CHEBI:25005
has alternative id: CHEBI:27755
has alternative id: CHEBI:613009
has cross-reference: CAS:63-42-3
has cross-reference: GlyGen:G74621DY
has cross-reference: GlyTouCan:G74621DY
has cross-reference: Gmelin:882872
has cross-reference: KEGG:C00243
has cross-reference: KEGG:D00046
has cross-reference: KEGG:G10504
has cross-reference: KNApSAcK:C00001136
has cross-reference: PMID:1292745
has cross-reference: PMID:17329833
has cross-reference: PMID:18300214
has cross-reference: PMID:19053747
has cross-reference: PMID:19846069
has cross-reference: PMID:19913595
has cross-reference: PMID:20094999
has cross-reference: PMID:20503067
has cross-reference: PMID:20699559
has cross-reference: PMID:20873837
has cross-reference: PMID:20961532
has cross-reference: PMID:21403918
has cross-reference: PMID:2432147
has cross-reference: PMID:2456994
has cross-reference: PMID:28690131
has cross-reference: PMID:28807538
has cross-reference: PMID:6194884
has cross-reference: PMID:7574700
has cross-reference: Reaxys:1292745
has exact synonym: beta-D-galactopyranosyl-(1->4)-D-glucopyranose
has exact synonym: lactose
has OBO namespace: chebi_ontology
has related synonym: (+)-lactose
has related synonym: (Gal)1 (Glc)1
has related synonym: 1-beta-D-Galactopyranosyl-4-D-glucopyranose
has related synonym: 4-(beta-D-galactosido)-D-glucose
has related synonym: 4-O-beta-D-galactopyranosyl-D-glucose
has related synonym: D-lactose
has related synonym: Galbeta1-4Glc
has related synonym: Lac
has related synonym: Laktobiose
has related synonym: Laktose
has related synonym: Milchzucker
has related synonym: Milk sugar
has related synonym: WURCS=2.0/2,2,1/[a2122h-1x_1-5][a2112h-1b_1-5]/1-2/a4-b1
has related synonym: beta-D-Gal-(1->4)-D-Glc
has related synonym: beta-D-Galp-(1->4)-D-Glcp
has related synonym: beta-Gal1,4-Glc
has related synonym: lactobiose
has related synonym: milk sugar
id: CHEBI:17716
in subset: 3 STAR

gentamycin
type: Class
subclass of: molecular entity
definition: Any of a group of aminoglycoside antibiotics produced by fermentation of some Micromonospora spp.
imported from: chebi.owl
has alternative id: CHEBI:14293
has alternative id: CHEBI:24206
has alternative id: CHEBI:24212
has alternative id: CHEBI:5306
has cross-reference: CAS:1403-66-3
has cross-reference: DrugBank:DB00798
has cross-reference: KEGG:C00505
has exact synonym: 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
has OBO namespace: chebi_ontology
has related synonym: Gentamicin
has related synonym: gentamycins
id: CHEBI:17833
in subset: 3 STAR

sucrose
type: Class
subclass of: molecular entity
definition: 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.
imported from: chebi.owl
charge: 0
formula: C12H22O11
inchi: 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
inchikey: CZMRCDWAGMRECN-UGDNZRGBSA-N
mass: 342.29650
monoisotopicmass: 342.11621
has alternative id: CHEBI:15128
has alternative id: CHEBI:26812
has alternative id: CHEBI:45795
has alternative id: CHEBI:9314
has cross-reference: CAS:57-50-1
has cross-reference: DrugBank:DB02772
has cross-reference: Drug_Central:4610
has cross-reference: Gmelin:97695
has cross-reference: HMDB:HMDB0000258
has cross-reference: KEGG:C00089
has cross-reference: KEGG:D00025
has cross-reference: KEGG:D06533
has cross-reference: KEGG:G00370
has cross-reference: KNApSAcK:C00001151
has cross-reference: MetaCyc:SUCROSE
has cross-reference: PDBeChem:SUC
has cross-reference: PMID:11021636
has cross-reference: PMID:11093712
has cross-reference: PMID:11111003
has cross-reference: PMID:12065720
has cross-reference: PMID:12706980
has cross-reference: PMID:13508893
has cross-reference: PMID:15291457
has cross-reference: PMID:15660210
has cross-reference: PMID:15792978
has cross-reference: PMID:15845855
has cross-reference: PMID:16228482
has cross-reference: PMID:16304615
has cross-reference: PMID:16313996
has cross-reference: PMID:16525719
has cross-reference: PMID:16660545
has cross-reference: PMID:16663947
has cross-reference: PMID:16665852
has cross-reference: PMID:17233733
has cross-reference: PMID:17439666
has cross-reference: PMID:17597061
has cross-reference: PMID:18625236
has cross-reference: PMID:19199566
has cross-reference: PMID:19726178
has cross-reference: PMID:21703290
has cross-reference: PMID:21972845
has cross-reference: PMID:22085755
has cross-reference: PMID:22311778
has cross-reference: PMID:22404833
has cross-reference: PMID:22751876
has cross-reference: Reaxys:1435311
has cross-reference: Reaxys:90825
has cross-reference: Wikipedia:Sucrose
has exact synonym: SUCROSE
has exact synonym: Sucrose
has exact synonym: beta-D-fructofuranosyl alpha-D-glucopyranoside
has exact synonym: sucrose
has OBO namespace: chebi_ontology
has related synonym: 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside
has related synonym: Cane sugar
has related synonym: Saccharose
has related synonym: Sacharose
has related synonym: White sugar
has related synonym: beta-D-Fruf-(2<->1)-alpha-D-Glcp
has related synonym: sacarosa
has related synonym: table sugar
id: CHEBI:17992
in subset: 3 STAR

molecular entity
type: Class
subclass of: chemical entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
imported from: chebi.owl
has exact synonym: molecular entity
has OBO namespace: chebi_ontology
has related synonym: entidad molecular
has related synonym: entidades moleculares
has related synonym: entite moleculaire
has related synonym: molecular entities
has related synonym: molekulare Entitaet
id: CHEBI:23367
in subset: 3 STAR

chemical entity
type: Class
subclass of: material entity
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
imported from: chebi.owl
has exact synonym: chemical entity
has OBO namespace: chebi_ontology
id: CHEBI:24431
in subset: 3 STAR

sodium chloride
type: Class
subclass of: molecular entity
definition: An inorganic chloride salt having sodium(1+) as the counterion.
imported from: chebi.owl
charge: 0
formula: ClNa
inchi: InChI=1S/ClH.Na/h1H;/q;+1/p-1
inchikey: FAPWRFPIFSIZLT-UHFFFAOYSA-M
mass: 58.44247
monoisotopicmass: 57.95862
smiles: [Na+].[Cl-]
has cross-reference: CAS:7647-14-5
has cross-reference: Gmelin:13673
has cross-reference: KEGG:C13563
has cross-reference: KEGG:D02056
has cross-reference: MetaCyc:NACL
has cross-reference: PPDB:595
has cross-reference: Reaxys:3534976
has cross-reference: Wikipedia:Sodium_Chloride
has exact synonym: sodium chloride
has OBO namespace: chebi_ontology
has related synonym: Kochsalz
has related synonym: NaCl
has related synonym: Natriumchlorid
has related synonym: chlorure de sodium
has related synonym: cloruro sodico
has related synonym: common salt
has related synonym: halite
has related synonym: natrii chloridum
has related synonym: rock salt
has related synonym: salt
has related synonym: table salt
id: CHEBI:26710
in subset: 3 STAR

aspartame
type: Class
subclass of: peptide
definition: 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.
imported from: chebi.owl
charge: 0
formula: C14H18N2O5
inchi: 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
inchikey: IAOZJIPTCAWIRG-QWRGUYRKSA-N
mass: 294.304
monoisotopicmass: 294.12157
has alternative id: CHEBI:45047
has cross-reference: CAS:22839-47-0
has cross-reference: DrugBank:DB00168
has cross-reference: HMDB:HMDB0001894
has cross-reference: KEGG:C11045
has cross-reference: KEGG:D02381
has cross-reference: PDBeChem:PME
has cross-reference: PMID:1771173
has cross-reference: PMID:2013754
has cross-reference: PMID:21150094
has cross-reference: PMID:21372000
has cross-reference: PMID:22354473
has cross-reference: PMID:24355796
has cross-reference: PMID:24925367
has cross-reference: PMID:24944748
has cross-reference: PMID:24965331
has cross-reference: PMID:25431414
has cross-reference: PMID:25543075
has cross-reference: PMID:25786106
has cross-reference: PMID:25951455
has cross-reference: PMID:25991916
has cross-reference: PMID:26015492
has cross-reference: PMID:26099025
has cross-reference: PMID:26159964
has cross-reference: PMID:26247507
has cross-reference: PMID:26308194
has cross-reference: PMID:26321723
has cross-reference: PMID:26377607
has cross-reference: PMID:26582819
has cross-reference: PMID:26593524
has cross-reference: PMID:26912665
has cross-reference: PMID:27015640
has cross-reference: PMID:27038223
has cross-reference: PMID:27088715
has cross-reference: PMID:27127997
has cross-reference: PMID:27216413
has cross-reference: PMID:27298583
has cross-reference: PMID:27492574
has cross-reference: PMID:27565676
has cross-reference: PMID:27614095
has cross-reference: PMID:27640132
has cross-reference: PMID:27699780
has cross-reference: PMID:27728881
has cross-reference: PMID:27840415
has cross-reference: PMID:27845306
has cross-reference: PMID:30000570
has cross-reference: PMID:37291632
has cross-reference: PMID:37297402
has cross-reference: PMID:37454665
has cross-reference: Patent:US3492131
has cross-reference: Reaxys:2223850
has cross-reference: Wikipedia:Aspartame
has exact synonym: Aspartame
has exact synonym: methyl L-alpha-aspartyl-L-phenylalaninate
has OBO namespace: chebi_ontology
has related synonym: 1-methyl N-L-alpha-aspartyl-L-phenylalanate
has related synonym: 3-Amino-N-(alpha-carboxyphenethyl)succinamic acid N-methyl ester
has related synonym: 3-Amino-N-(alpha-methoxycarbonylphenethyl) succinamic acid
has related synonym: AminoSweet
has related synonym: Asp-phe-ome
has related synonym: Aspartylphenylalanine methyl ester
has related synonym: E 951
has related synonym: L-Aspartyl-L-phenylalanine methyl ester
has related synonym: NutraSweet
has related synonym: Sanecta
has related synonym: aspartam
has related synonym: aspartamo
has related synonym: aspartamum
id: CHEBI:2877
in subset: 3 STAR

glucitol
type: Class
subclass of: molecular entity
imported from: chebi.owl
charge: 0
formula: C6H14O6
mass: 182.172
monoisotopicmass: 182.07904
has alternative id: CHEBI:15093
has alternative id: CHEBI:26724
has alternative id: CHEBI:26726
has alternative id: CHEBI:33795
has alternative id: CHEBI:33796
has alternative id: CHEBI:9201
has cross-reference: Beilstein:1721909
has cross-reference: Gmelin:83165
has cross-reference: Wikipedia:Sorbitol
has exact synonym: glucitol
has OBO namespace: chebi_ontology
has related synonym: Sorbitol
has related synonym: gulitol
has related synonym: rel-(2R,3R,4R,5S)-hexane-1,2,3,4,5,6-hexol
id: CHEBI:30911
in subset: 3 STAR

saccharin
type: Class
subclass of: molecular entity
definition: 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.
imported from: chebi.owl
charge: 0
formula: C7H5NO3S
inchi: InChI=1S/C7H5NO3S/c9-7-5-3-1-2-4-6(5)12(10,11)8-7/h1-4H,(H,8,9)
inchikey: CVHZOJJKTDOEJC-UHFFFAOYSA-N
mass: 183.18500
monoisotopicmass: 182.99901
smiles: O=C1NS(=O)(=O)c2ccccc12
has alternative id: CHEBI:49717
has cross-reference: CAS:81-07-2
has cross-reference: Gmelin:4203
has cross-reference: HMDB:HMDB0029723
has cross-reference: KEGG:D01085
has cross-reference: MetaCyc:CPD-5581
has cross-reference: PDBeChem:LSA
has cross-reference: PMID:24456165
has cross-reference: PMID:24549104
has cross-reference: PMID:24739358
has cross-reference: PMID:24780866
has cross-reference: Reaxys:6888
has cross-reference: Wikipedia:Saccharin
has exact synonym: 1,2-benzisothiazol-3(2H)-one 1,1-dioxide
has exact synonym: Saccharin
has OBO namespace: chebi_ontology
has related synonym: 1,1-Dioxo-1,2-benzisothiazol-3(2H)-one
has related synonym: 1,1-Dioxo-1,2-dihydro-benzo[d]isothiazol-3-one
has related synonym: 1,2-Benzisothiazol-3(2H)-one 1,1-dioxide
has related synonym: 1,2-Benzisothiazolin-3-one 1,1-dioxide
has related synonym: 1,2-Dihydro-2-ketobenzisosulfonazole
has related synonym: 1,2-Dihydro-2-ketobenzisosulphonazole
has related synonym: 2,3-Dihydro-3-oxobenzisosulfonazole
has related synonym: 2,3-Dihydro-3-oxobenzisosulphonazole
has related synonym: 3-Hydroxybenzisothiazole-S,S-dioxide
has related synonym: Anhydro-o-sulfaminebenzoic acid
has related synonym: Benzo-2-sulphimide
has related synonym: Benzoic acid sulfimide
has related synonym: Benzoic sulfimide
has related synonym: Benzoic sulphimide
has related synonym: Benzosulfimide
has related synonym: Benzosulphimide
has related synonym: Benzoylsulfonic Imide
has related synonym: Saccharimide
has related synonym: Saccharine
has related synonym: o-Benzoic sulfimide
has related synonym: o-Benzosulfimide
has related synonym: o-Sulfobenzimide
has related synonym: o-Sulfobenzoic acid imide
id: CHEBI:32111
in subset: 3 STAR

aluminium hydroxide
type: Class
subclass of: molecular entity
imported from: chebi.owl
charge: 0
formula: AlH3O3
formula: H3AlO3
inchi: InChI=1S/Al.3H2O/h;3*1H2/q+3;;;/p-3
inchikey: WNROFYMDJYEPJX-UHFFFAOYSA-K
mass: 78.00356
monoisotopicmass: 77.98976
smiles: [H]O[Al](O[H])O[H]
has alternative id: CHEBI:30193
has alternative id: CHEBI:31195
has cross-reference: CAS:21645-51-2
has cross-reference: Drug_Central:4250
has cross-reference: Gmelin:22216
has cross-reference: KEGG:C13391
has cross-reference: KEGG:D02859
has cross-reference: Wikipedia:Aluminum_Hydroxide
has exact synonym: aluminium(3+) hydroxide
has exact synonym: aluminium(III) hydroxide
has exact synonym: trihydroxidoaluminium
has OBO namespace: chebi_ontology
has related synonym: Al(OH)3
has related synonym: Aluminiumhydroxid
has related synonym: Aluminum hydroxide
id: CHEBI:33130
in subset: 3 STAR

sodium phosphate
type: Class
subclass of: molecular entity
imported from: chebi.owl
has cross-reference: CAS:7632-05-5
has cross-reference: Wikipedia:Sodium_phosphates
has exact synonym: sodium phosphate
has OBO namespace: chebi_ontology
has related synonym: phosphoric acid, sodium salt
has related synonym: sodium orthophosphate
has related synonym: sodium phosphates
has related synonym: sodium salt of phosphoric acid
id: CHEBI:37586
in subset: 3 STAR

dextran
type: Class
subclass of: molecular entity
definition: A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages.
imported from: chebi.owl
has cross-reference: CAS:9004-54-0
has cross-reference: KEGG:C00372
has cross-reference: KEGG:D00060
has cross-reference: KEGG:D06541
has cross-reference: KEGG:G10502
has cross-reference: PMID:8154046
has OBO namespace: chebi_ontology
has related synonym: (1,6-alpha-D-Glucosyl)m
has related synonym: (1,6-alpha-D-Glucosyl)m+1
has related synonym: (1,6-alpha-D-Glucosyl)n
has related synonym: (1,6-alpha-D-Glucosyl)n+1
has related synonym: 1,6-alpha-D-Glucan
has related synonym: Dextran 40
has related synonym: Dextran 70
has related synonym: Dextran 75
has related synonym: dextran
has related synonym: dextrane
has related synonym: dextrano
has related synonym: dextrans
has related synonym: dextranum
id: CHEBI:52071
in subset: 3 STAR

polysorbate 20
type: Class
subclass of: molecular entity
definition: 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.
imported from: chebi.owl
charge: 0
formula: C58H114O26
mass: 1226.75977
monoisotopicmass: 1226.760
has cross-reference: CAS:9005-64-5
has cross-reference: KEGG:C11624
has cross-reference: KEGG:D05565
has cross-reference: Reaxys:8187252
has cross-reference: Reaxys:8973037
has cross-reference: Wikipedia:Polysorbate_20
has OBO namespace: chebi_ontology
has related synonym: Polyoxyethylene (20) sorbitan monolaurate
has related synonym: Polyoxyethylene sorbitan monolaurate
has related synonym: Polysorbate
has related synonym: Polysorbate 20
has related synonym: Tween 20
has related synonym: polisorbato
has related synonym: polysorbate
has related synonym: polysorbatum
id: CHEBI:53424
in subset: 3 STAR

polysorbate 80
type: Class
subclass of: molecular entity
definition: 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.
imported from: chebi.owl
charge: 0
formula: C64H124O26
mass: 1308.83802
monoisotopicmass: 1308.838
has alternative id: CHEBI:9785
has cross-reference: CAS:9005-65-6
has cross-reference: KEGG:C11625
has cross-reference: KEGG:D01067
has cross-reference: Reaxys:8187125
has cross-reference: Reaxys:8190601
has cross-reference: Reaxys:8898414
has cross-reference: Reaxys:9040798
has cross-reference: Wikipedia:Polysorbate_80
has OBO namespace: chebi_ontology
has related synonym: Glycol (polysorbate 80)
has related synonym: Polyethylene oxide sorbitan mono-oleate
has related synonym: Polyoxyethylene (20) sorbitan monooleate
has related synonym: Polyoxyethylene sorbitan monooleate
has related synonym: Polyoxyethylene sorbitan oleate
has related synonym: Polysorbate 80
has related synonym: Tween 80
has related synonym: polisorbato
has related synonym: polysorbate
has related synonym: polysorbatum
id: CHEBI:53426
in subset: 3 STAR

monosodium glutamate
type: Class
subclass of: molecular entity
definition: An organic sodium salt that is the monosodium salt of glutamic acid.
imported from: chebi.owl
charge: 0
formula: C5H8NNaO4
inchi: 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
inchikey: LPUQAYUQRXPFSQ-UHFFFAOYSA-M
mass: 169.11110
monoisotopicmass: 169.03510
smiles: [Na+].[NH3+]C(CCC([O-])=O)C([O-])=O
has cross-reference: PMID:22293291
has cross-reference: Reaxys:17003240
has exact synonym: sodium 2-azaniumylpentanedioate
has OBO namespace: chebi_ontology
has related synonym: MSG
has related synonym: sodium 2-ammoniopentanedioate
has related synonym: sodium glutamate
id: CHEBI:64220
in subset: 3 STAR

neomycin
type: Class
subclass of: molecular entity
definition: A broad-spectrum highly toxic antibiotic or mixture of antibiotics produced by a streptomyces (Streptomyces fradiae) and used medically especially to treat local infections.
imported from: chebi.owl
has cross-reference: CAS:1404-04-2
has cross-reference: DrugBank:DB00994
has cross-reference: KEGG:C00384
has cross-reference: KEGG:D08260
has exact synonym: Neomycin
has OBO namespace: chebi_ontology
id: CHEBI:7507
in subset: 3 STAR

thimerosal
type: Class
subclass of: molecular entity
definition: An alkylmercury compound (approximately 49% mercury by weight) used as an antiseptic and antifungal agent.
imported from: chebi.owl
charge: 0
formula: C9H9HgNaO2S
formula: C9H9HgO2S.Na
inchi: 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
inchikey: RTKIYNMVFMVABJ-UHFFFAOYSA-L
mass: 404.81233
monoisotopicmass: 405.99274
smiles: [Na+].CC[Hg]Sc1ccccc1C([O-])=O
has cross-reference: CAS:54-64-8
has cross-reference: Gmelin:1677155
has cross-reference: KEGG:D00864
has cross-reference: PMID:18837732
has cross-reference: PMID:21616561
has cross-reference: PMID:21785120
has cross-reference: PMID:22015977
has cross-reference: PMID:22366633
has cross-reference: PMID:22658806
has cross-reference: PMID:22811707
has cross-reference: PMID:23145070
has cross-reference: PMID:23223227
has cross-reference: PMID:23282150
has cross-reference: PMID:23401210
has cross-reference: PMID:23554557
has cross-reference: PMID:23843785
has cross-reference: PMID:23949514
has cross-reference: PMID:23965928
has cross-reference: PMID:23992327
has cross-reference: PMID:25042713
has cross-reference: PPDB:3062
has cross-reference: Reaxys:8169555
has cross-reference: VSDB:3062
has exact synonym: Thimerosal
has exact synonym: sodium [(2-carboxylatophenyl)sulfanyl](ethyl)mercurate(1-)
has exact synonym: sodium ethyl[2-(sulfanyl-kappaS)benzoato(2-)]mercurate(1-)
has OBO namespace: chebi_ontology
has related synonym: Merthiolate
has related synonym: Thiomersal
has related synonym: [(o-carboxyphenyl)thio]ethylmercury sodium salt
has related synonym: ethyl(2-mercaptobenzoato-S)mercury sodium salt
has related synonym: ethylmercurithiosalicylate sodium
has related synonym: ethylmercurithiosalicylic acid sodium salt
has related synonym: mercurothiolate
has related synonym: o-(ethylmercurithio)benzoic acid sodium salt
has related synonym: sodium ethylmercurithiosalicylate
has related synonym: sodium merthiolate
has related synonym: thiomersal
has related synonym: thiomersalate
has related synonym: thiomersalum
has related synonym: tiomersal
id: CHEBI:9546
in subset: 3 STAR

cell
type: Class
subclass of: anatomical structure
definition: 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.
imported from: cl.owl
has cross-reference: CALOHA:TS-2035
has cross-reference: FBbt:00007002
has cross-reference: FMA:68646
has cross-reference: GO:0005623
has cross-reference: KUPO:0000002
has cross-reference: MESH:D002477
has cross-reference: VHOG:0001533
has cross-reference: WBbt:0004017
has cross-reference: XAO:0003012
has cross-reference: ZFA:0009000
in subset: cellxgene subset
in subset: upper level
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

mononuclear phagocyte
type: Class
subclass of: phagocyte (sensu Vertebrata)
subclass of: mononuclear cell
definition: A vertebrate phagocyte with a single nucleus.
imported from: cl.owl
present in taxon: Homo sapiens
description: This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in hom…
has cross-reference: BTO:0001433
has cross-reference: ZFA:0009064
has cross-reference: https://cellxgene.cziscience.com/cellguide/CL_0000113
in subset: cellxgene subset
in subset: human reference atlas

hepatocyte
type: Class
subclass of: eukaryotic cell
definition: 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.
imported from: cl.owl
present in taxon: Homo sapiens
description: This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjuga…
has cross-reference: BTO:0000575
has cross-reference: CALOHA:TS-0454
has cross-reference: FMA:14515
has cross-reference: ZFA:0009111
has cross-reference: https://cellxgene.cziscience.com/cellguide/CL_0000182
in subset: cellxgene subset
in subset: human reference atlas
comment: Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.

motile cell
type: Class
subclass of: cell
definition: A cell that moves by its own activities.
imported from: cl.owl
has cross-reference: ZFA:0009136

single nucleate cell
type: Class
subclass of: eukaryotic cell
subclass of: nucleate cell
definition: A cell with a single nucleus.
imported from: cl.owl

erythrocyte
type: Class
subclass of: myeloid cell
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
imported from: cl.owl
present in taxon: Homo sapiens
has cross-reference: BTO:0000424
has cross-reference: CALOHA:TS-0290
has cross-reference: FMA:81100
has exact synonym: RBC
has exact synonym: red blood cell
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: human reference atlas

phagocyte
type: Class
subclass of: motile cell
definition: Any cell capable of ingesting particulate matter via phagocytosis.
imported from: cl.owl
has cross-reference: BTO:0001044
has cross-reference: FMA:83806
has cross-reference: MESH:D010586
has cross-reference: ZFA:0009140
in subset: cellxgene subset

macrophage
type: Class
subclass of: mononuclear phagocyte
subclass of: myeloid leukocyte
definition: 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.
imported from: cl.owl
present in taxon: Homo sapiens
has cross-reference: BTO:0000801
has cross-reference: CALOHA:TS-0587
has cross-reference: FMA:63261
has cross-reference: FMA:83585
has cross-reference: MESH:D008264
has cross-reference: ZFA:0009141
has exact synonym: histiocyte
in subset: blood and immune upper slim
in subset: cellxgene subset
in subset: general cell types upper slim
in subset: human reference atlas
comment: Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.

eukaryotic cell
type: Class
subclass of: cell
definition: Any cell that in taxon some Eukaryota.
imported from: cl.owl
has cross-reference: MESH:D005057
in subset: cellxgene subset

phagocyte (sensu Vertebrata)
type: Class
subclass of: phagocyte
subclass of: eukaryotic cell
definition: A phagocyte in vertebrates that is able to phagocytosis.
imported from: cl.owl

leukocyte
type: Class
subclass of: motile cell
subclass of: eukaryotic cell
subclass of: hematopoietic cell
subclass of: nucleate cell
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
imported from: cl.owl
present in taxon: Homo sapiens
has cross-reference: BTO:0000751
has cross-reference: CALOHA:TS-0549
has cross-reference: FMA:62852
has cross-reference: MESH:D007962
has cross-reference: NCIT:C12529
has cross-reference: ZFA:0009309
has exact synonym: leucocyte
has exact synonym: white blood cell
has related synonym: immune cell
in subset: cellxgene subset
in subset: human reference atlas

myeloid cell
type: Class
subclass of: eukaryotic cell
subclass of: hematopoietic cell
definition: A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
imported from: cl.owl
has cross-reference: BTO:0001441
has cross-reference: CALOHA:TS-0647
has cross-reference: MESH:D022423
has cross-reference: ZFA:0009324
in subset: cellxgene subset

myeloid leukocyte
type: Class
subclass of: leukocyte
subclass of: myeloid cell
definition: A cell of the monocyte, granulocyte, or mast cell lineage.
imported from: cl.owl
has cross-reference: ZFA:0009326
in subset: cellxgene subset

mononuclear cell
type: Class
subclass of: single nucleate cell
subclass of: leukocyte
definition: A leukocyte with a single non-segmented nucleus in the mature form.
imported from: cl.owl
has cross-reference: BTO:0000878
has cross-reference: CALOHA:TS-0768
has cross-reference: FMA:86713
has cross-reference: ZFA:0009357
has exact synonym: mononuclear leukocyte
has narrow synonym: peripheral blood mononuclear cell
in subset: blood and immune upper slim
in subset: cellxgene subset

hematopoietic cell
type: Class
subclass of: cell
definition: A cell of a hematopoietic lineage.
imported from: cl.owl
has cross-reference: BTO:0000574
has cross-reference: CALOHA:TS-2017
has cross-reference: FMA:70366
has cross-reference: FMA:83598
has cross-reference: ZFA:0005830
has exact synonym: haematopoietic cell
has exact synonym: haemopoietic cell
has exact synonym: hemopoietic cell
in subset: cellxgene subset

nucleate cell
type: Class
subclass of: cell
definition: A cell containing at least one nucleus.
imported from: cl.owl
contributor: https://orcid.org/0000-0003-1980-3228
creation date: 2010-09-07T03:32:33Z
has cross-reference: FMA:67513

Streptococcus pneumonia
type: Class
subclass of: bacterial pneumonia
definition: A bacterial pneumonia has_material_basis_in Streptococcus pneumoniae.
imported from: doid.owl
has cross-reference: ICD10CM:J13
has cross-reference: ICD9CM:481
has OBO namespace: disease_ontology
id: DOID:0040084
in subset: DO IEDB slim
in subset: DO infectious disease slim

chikungunya
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in infection located_in joint, has_material_basis_in Chikungunya virus (Alphavirus chikungunya), which is transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom arthralgia, and has_symptom maculopapular rash.
imported from: doid.owl
has cross-reference: GARD:6038
has exact synonym: Chikungunya fever
has OBO namespace: disease_ontology
id: DOID:0050012
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: zoonotic infectious disease

disease by infectious agent
type: Class
subclass of: disease
definition: 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.
imported from: doid.owl
IEDB alternative term: infectious disease
has alternative id: DOID:10115
has alternative id: DOID:11078
has alternative id: DOID:1304
has alternative id: DOID:1321
has alternative id: DOID:2040
has alternative id: DOID:2288
has alternative id: DOID:3099
has alternative id: DOID:4120
has alternative id: DOID:4620
has alternative id: DOID:5256
has alternative id: DOID:945
has alternative id: DOID:95
has alternative id: DOID:9532
has alternative id: DOID:9696
has cross-reference: ICD9CM:079.0
has cross-reference: UMLS_CUI:C0001485
has exact synonym: infectious disease
has OBO namespace: disease_ontology
id: DOID:0050117
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: DO infectious disease slim
comment: DO:wk

tick-borne encephalitis
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Tick-borne encephalitis virus (Orthoflavivirus encephalitidis), which is transmitted_by Ixodes ticks. The infection has_symptom drowsiness, has_symptom confusion, has_symptom sensory disturbances, and has_symptom paralysis.
imported from: doid.owl
has alternative id: DOID:0050176
has alternative id: DOID:10251
has alternative id: DOID:10252
has cross-reference: GARD:5216
has cross-reference: ICD10CM:A84.1
has cross-reference: ICD9CM:063.2
has cross-reference: MESH:D004675
has cross-reference: SNOMEDCT_US_2023_03_01:16901001
has cross-reference: UMLS_CUI:C0014054
has exact synonym: Central European encephalitis
has exact synonym: Far Eastern TBE
has exact synonym: Russian spring-summer encephalitis
has exact synonym: Siberian tick-borne encephalitis
has exact synonym: Taiga encephalitis
has exact synonym: Western European tick-borne encephalitis
has exact synonym: west-Siberian encephalitis
has OBO namespace: disease_ontology
id: DOID:0050175
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: tick-borne infectious disease

primary bacterial infectious disease
type: Class
subclass of: bacterial infectious disease
definition: 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.
imported from: doid.owl
has OBO namespace: disease_ontology
id: DOID:0050338
in subset: DO FlyBase slim
in subset: DO infectious disease slim

respiratory system cancer
type: Class
subclass of: organ system cancer
subclass of: respiratory system disease
definition: An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract.
imported from: doid.owl
has OBO namespace: disease_ontology
id: DOID:0050615

organ system cancer
type: Class
subclass of: cancer
definition: A cancer that is classified based on the organ it starts in.
imported from: doid.owl
created by: snadendla
creation date: 2011-06-13T03:28:33Z
has cross-reference: MESH:D009371
has OBO namespace: disease_ontology
id: DOID:0050686
in subset: DO MGI slim

cell type cancer
type: Class
subclass of: cancer
definition: A cancer that is classified by the type of cell from which it is derived.
imported from: doid.owl
created by: snadendla
creation date: 2011-06-13T03:28:50Z
has OBO namespace: disease_ontology
id: DOID:0050687
in subset: DO MGI slim

mantle cell lymphoma
type: Class
subclass of: B-cell lymphoma
definition: A B-cell lymphocytic neoplasm due to CD5 positive antigen-naive pregerminal center B-cell within the mantle zone that surrounds normal germinal center follicles.
imported from: doid.owl
created by: lschriml
creation date: 2012-09-18T02:00:45Z
has cross-reference: GARD:6969
has cross-reference: ICDO:9673/3
has cross-reference: MESH:D020522
has OBO namespace: disease_ontology
id: DOID:0050746
in subset: DO cancer slim
in subset: DO rare slim

lymphoma
type: Class
subclass of: lymphatic system cancer
subclass of: hematologic cancer
definition: A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs.
imported from: doid.owl
has alternative id: DOID:1033
has alternative id: DOID:353
has cross-reference: ICD10CM:C85.9
has cross-reference: ICDO:9590/3
has cross-reference: MESH:D008223
has cross-reference: NCI:C3208
has cross-reference: NCI:C7065
has cross-reference: SNOMEDCT_US_2023_03_01:118600007
has cross-reference: SNOMEDCT_US_2023_03_01:414628006
has cross-reference: UMLS_CUI:C0024299
has cross-reference: UMLS_CUI:C0598798
has exact synonym: lymphoid cancer
has OBO namespace: disease_ontology
id: DOID:0060058
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus

lymphatic system cancer
type: Class
subclass of: immune system cancer
definition: An immune system cancer that is located_in the lymphatic system and is characterized by uncontrolled cellular proliferation of lymphoid tissue.
imported from: doid.owl
created by: lschriml
creation date: 2011-05-11T01:05:14Z
has OBO namespace: disease_ontology
id: DOID:0060073

immune system cancer
type: Class
subclass of: organ system cancer
subclass of: immune system disease
definition: An organ system cancer located_in the immune system that is characterized by uncontrolled cellular proliferation in organs of the immune system.
imported from: doid.owl
created by: lschriml
creation date: 2011-06-08T01:11:18Z
has cross-reference: ICDO:9392/3
has OBO namespace: disease_ontology
id: DOID:0060083
in subset: DO cancer slim

thoracic benign neoplasm
type: Class
subclass of: disease of cellular proliferation
subclass of: disease of anatomical entity
definition: An organ system benign neoplam that is located_in the thoracic cavity.
imported from: doid.owl
created by: lschriml
creation date: 2011-07-15T01:55:57Z
has OBO namespace: disease_ontology
id: DOID:0060097

musculoskeletal system cancer
type: Class
subclass of: organ system cancer
subclass of: musculoskeletal system disease
definition: An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs.
imported from: doid.owl
created by: lschriml
creation date: 2011-07-15T02:30:51Z
has alternative id: DOID:0060124
has exact synonym: skeletal system cancer
has OBO namespace: disease_ontology
id: DOID:0060100

pharynx cancer
type: Class
subclass of: gastrointestinal system cancer
definition: A gastrointestinal system cancer that is located_in the pharynx.
imported from: doid.owl
created by: lschriml
creation date: 2011-07-27T01:26:34Z
has cross-reference: MESH:D010610
has cross-reference: NCI:C3325
has cross-reference: SNOMEDCT_US_2023_03_01:126685009
has cross-reference: UMLS_CUI:C0031347
has exact synonym: pharyngeal neoplasm
has exact synonym: pharynx neoplasm
has OBO namespace: disease_ontology
has related synonym: pharyngeal cancer
id: DOID:0060119
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

bone disease
type: Class
subclass of: connective tissue disease
definition: A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function.
imported from: doid.owl
has alternative id: DOID:1290
has cross-reference: ICD10CM:M89.9
has cross-reference: MESH:D001847
has cross-reference: SNOMEDCT_US_2023_03_01:76069003
has cross-reference: UMLS_CUI:C0005940
has OBO namespace: disease_ontology
has related synonym: skeletal disease
id: DOID:0080001

meningococcal meningitis
type: Class
subclass of: bacterial meningitis
definition: A bacterial meningitis that has_material_basis_in Neisseria meningitidis infection.
imported from: doid.owl
has cross-reference: ICD10CM:A39.0
has cross-reference: ICD9CM:036.0
has cross-reference: MESH:D008585
has OBO namespace: disease_ontology
id: DOID:0080176
in subset: DO infectious disease slim

haemophilus meningitis
type: Class
subclass of: bacterial meningitis
definition: A bacterial meningitis that has_material_basis_in Haemophilus influenzae infection.
imported from: doid.owl
has cross-reference: ICD10CM:G00.0
has cross-reference: ICD9CM:320.0
has cross-reference: MESH:D008583
has OBO namespace: disease_ontology
id: DOID:0080179
in subset: DO infectious disease slim

hepatobiliary system cancer
type: Class
subclass of: gastrointestinal system cancer
definition: A gastrointestinal system cancer that is located_in the hepatobiliary system.
imported from: doid.owl
has OBO namespace: disease_ontology
id: DOID:0080355

COVID-19
type: Class
subclass of: viral infectious disease
definition: A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2, a subtype of Betacoronavirus pandemicum.
imported from: doid.owl
has cross-reference: ICD10CM:U07.1
has cross-reference: MESH:D000086382
has cross-reference: NCI:C171133
has cross-reference: SNOMEDCT_US_2023_03_01:840539006
has cross-reference: UMLS_CUI:C5203670
has exact synonym: 2019 Novel Coronavirus (2019-nCoV)
has exact synonym: 2019-nCoV infection
has exact synonym: COVID19
has exact synonym: SARS-CoV-2 infection
has exact synonym: Wuhan coronavirus infection
has exact synonym: Wuhan seafood market pneumonia virus infection
has OBO namespace: disease_ontology
id: DOID:0080600
in subset: DO infectious disease slim
in subset: NCIthesaurus

graft-versus-host disease
type: Class
subclass of: immune system disease
definition: An immune system disease that is characterized by recognition by mature donor T cells, that contaminate the allogeneic bone marrow, of the recipient's tissue as foreign, causing a severe inflammatory disease characterized by rashes, diarrhea, and liver disease, and that has_material_basis_in an associated with variation in the interleukin-10 gene (IL10) on chromosome 1q32.
imported from: doid.owl
has cross-reference: ICD11:4B24
has cross-reference: MESH:D006086
has cross-reference: MIM:614395
has cross-reference: ORDO:39812
has exact synonym: GvHD
has exact synonym: graft versus host disease
has OBO namespace: disease_ontology
id: DOID:0081267
in subset: DO rare slim

small intestine cancer
type: Class
subclass of: intestinal cancer
definition: An intestinal cancer that is located_in the small intestine.
imported from: doid.owl
has cross-reference: GARD:9385
has cross-reference: ICD10CM:C17
has cross-reference: ICD9CM:152.9
has cross-reference: NCI:C7523
has cross-reference: SNOMEDCT_US_2023_03_01:363509000
has cross-reference: UMLS_CUI:C0153425
has OBO namespace: disease_ontology
id: DOID:10154
in subset: DO rare slim
in subset: NCIthesaurus

intestinal cancer
type: Class
subclass of: gastrointestinal system cancer
subclass of: intestinal disease
definition: A gastrointestinal system cancer that is located_in the intestine.
imported from: doid.owl
has cross-reference: ICD10CM:C26.0
has cross-reference: ICD9CM:159.0
has cross-reference: MESH:D007414
has cross-reference: NCI:C4572
has cross-reference: SNOMEDCT_US_2023_03_01:93838000
has cross-reference: UMLS_CUI:C0346627
has exact synonym: malignant intestinal tumors
has exact synonym: malignant neoplasm of intestine
has OBO namespace: disease_ontology
id: DOID:10155
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

mumps
type: Class
subclass of: gastrointestinal system disease
subclass of: viral infectious disease
definition: A viral infectious disease that results in inflammation located in salivary gland, has_material_basis_in Mumps rubulavirus, which is transmitted by droplet spread of saliva or mucus from the mouth, nose, or throat of an infected person, or transmitted by contaminated fomites. The infection has symptom fever, has symptom headache, has symptom muscle aches, has symptom tiredness, has symptom loss of appetite, has symptom swollen and tender salivary glands under the ears or jaw on one or both sides of the face.
imported from: doid.owl
has cross-reference: GARD:7116
has cross-reference: ICD10CM:B26
has cross-reference: ICD9CM:072
has cross-reference: MESH:D009107
has cross-reference: NCI:C29888
has cross-reference: SNOMEDCT_US_2023_03_01:154352008
has cross-reference: UMLS_CUI:C0026780
has OBO namespace: disease_ontology
id: DOID:10264
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

prostate cancer
type: Class
subclass of: male reproductive organ cancer
definition: A male reproductive organ cancer that is located_in the prostate.
imported from: doid.owl
has alternative id: DOID:514
has cross-reference: ICD10CM:C61
has cross-reference: ICD9CM:185
has cross-reference: KEGG:05215
has cross-reference: MESH:D011471
has cross-reference: MIM:176807
has cross-reference: MIM:300147
has cross-reference: MIM:300704
has cross-reference: MIM:601518
has cross-reference: MIM:602759
has cross-reference: MIM:608656
has cross-reference: MIM:608658
has cross-reference: MIM:609299
has cross-reference: MIM:609558
has cross-reference: MIM:610321
has cross-reference: MIM:610997
has cross-reference: MIM:611100
has cross-reference: MIM:611868
has cross-reference: MIM:611928
has cross-reference: MIM:611955
has cross-reference: MIM:611958
has cross-reference: MIM:611959
has cross-reference: NCI:C3343
has cross-reference: NCI:C7378
has cross-reference: ORDO:1331
has cross-reference: SNOMEDCT_US_2023_03_01:126906006
has cross-reference: SNOMEDCT_US_2023_03_01:93974005
has cross-reference: UMLS_CUI:C0033578
has cross-reference: UMLS_CUI:C0376358
has exact synonym: NGP - new growth of prostate
has exact synonym: hereditary prostate cancer
has exact synonym: malignant tumor of the prostate
has exact synonym: prostate cancer, familial
has exact synonym: prostate neoplasm
has exact synonym: prostatic cancer
has exact synonym: prostatic neoplasm
has exact synonym: tumor of the prostate
has OBO namespace: disease_ontology
id: DOID:10283
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

bacterial infectious disease
type: Class
subclass of: disease by infectious agent
definition: A disease by infectious agent that results_in infection, has_material_basis_in Bacteria.
imported from: doid.owl
has cross-reference: ICD10CM:A49.9
has cross-reference: MESH:D001424
has cross-reference: NCI:C2890
has cross-reference: SNOMEDCT_US_2023_03_01:87628006
has cross-reference: UMLS_CUI:C0004623
has OBO namespace: disease_ontology
id: DOID:104
in subset: DO AGR slim
in subset: DO FlyBase slim
in subset: DO infectious disease slim
in subset: NCIthesaurus

stomach cancer
type: Class
subclass of: gastrointestinal system cancer
definition: A gastrointestinal system cancer that is located_in the stomach.
imported from: doid.owl
has alternative id: DOID:10539
has alternative id: DOID:10542
has alternative id: DOID:10543
has alternative id: DOID:4713
has cross-reference: GARD:7704
has cross-reference: ICD10CM:C16
has cross-reference: ICD10CM:C16.2
has cross-reference: ICD10CM:C16.5
has cross-reference: ICD10CM:C16.6
has cross-reference: ICD9CM:151
has cross-reference: ICD9CM:151.4
has cross-reference: ICD9CM:151.5
has cross-reference: ICD9CM:151.6
has cross-reference: MESH:D013274
has cross-reference: MIM:613659
has cross-reference: NCI:C3387
has cross-reference: NCI:C9331
has cross-reference: SNOMEDCT_US_2023_03_01:126824007
has cross-reference: SNOMEDCT_US_2023_03_01:269459004
has cross-reference: SNOMEDCT_US_2023_03_01:269460009
has cross-reference: SNOMEDCT_US_2023_03_01:93717002
has cross-reference: SNOMEDCT_US_2023_03_01:94074003
has cross-reference: UMLS_CUI:C0024623
has cross-reference: UMLS_CUI:C0038356
has cross-reference: UMLS_CUI:C0153421
has cross-reference: UMLS_CUI:C0153422
has cross-reference: UMLS_CUI:C0153423
has exact synonym: gastric cancer
has exact synonym: gastric neoplasm
has OBO namespace: disease_ontology
id: DOID:10534
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim
comment: OMIM mapping confirmed by DO. [SN].

Alzheimer's disease
type: Class
subclass of: central nervous system disease
definition: A tauopathy that is characterized by memory lapses, confusion, emotional instability and progressive loss of mental ability and results in progressive memory loss, impaired thinking, disorientation, and changes in personality and mood starting and leads in advanced cases to a profound decline in cognitive and physical functioning and is marked histologically by the degeneration of brain neurons especially in the cerebral cortex and by the presence of neurofibrillary tangles and plaques containing beta-amyloid.
imported from: doid.owl
has cross-reference: GARD:10254
has cross-reference: ICD10CM:G30
has cross-reference: ICD9CM:331.0
has cross-reference: KEGG:05010
has cross-reference: MESH:D000544
has cross-reference: NCI:C2866
has cross-reference: SNOMEDCT_US_2023_03_01:73768007
has cross-reference: UMLS_CUI:C0002395
has exact synonym: Alzheimer disease
has exact synonym: Alzheimers dementia
has OBO namespace: disease_ontology
id: DOID:10652
in subset: DO RAD slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

Japanese encephalitis
type: Class
subclass of: central nervous system disease
subclass of: viral infectious disease
definition: A viral infectious disease that results_in infection located_in brain, has_material_basis_in Japanese encephalitis virus (Orthoflavivirus japonicum), which is transmitted_by Culex tritaeniorhynchus mosquito bite. The infection has_symptom headache, has_symptom high fever, has_symptom neck stiffness, has_symptom stupor, has_symptom disorientation, has_symptom coma, has_symptom tremors, has_symptom convulsions, and has_symptom spastic paralysis.
imported from: doid.owl
has cross-reference: GARD:6797
has cross-reference: ICD10CM:A83.0
has cross-reference: ICD9CM:062.0
has cross-reference: MESH:D004672
has cross-reference: NCI:C34577
has cross-reference: SNOMEDCT_US_2023_03_01:266194002
has cross-reference: UMLS_CUI:C0014057
has exact synonym: Japanese B encephalitis
has OBO namespace: disease_ontology
id: DOID:10844
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

ovarian disease
type: Class
subclass of: female reproductive system disease
subclass of: endocrine system disease
definition: A female reproductive system disease that is located_in the ovary.
imported from: doid.owl
has cross-reference: MESH:D010049
has cross-reference: NCI:C26841
has cross-reference: SNOMEDCT_US_2023_03_01:5552004
has cross-reference: UMLS_CUI:C0029928
has OBO namespace: disease_ontology
id: DOID:1100
in subset: NCIthesaurus

urinary bladder cancer
type: Class
subclass of: urinary system cancer
definition: An urinary system cancer that results_in malignant growth located_in the urinary bladder.
imported from: doid.owl
has alternative id: DOID:5428
has cross-reference: GARD:12210
has cross-reference: ICD10CM:C67
has cross-reference: ICD9CM:188
has cross-reference: KEGG:05219
has cross-reference: MESH:D001749
has cross-reference: MIM:109800
has cross-reference: NCI:C2901
has cross-reference: NCI:C9334
has cross-reference: SNOMEDCT_US_2023_03_01:126885006
has cross-reference: SNOMEDCT_US_2023_03_01:363455001
has cross-reference: UMLS_CUI:C0005684
has cross-reference: UMLS_CUI:C0005695
has exact synonym: bladder cancer
has exact synonym: tumor of the bladder
has OBO namespace: disease_ontology
id: DOID:11054
in subset: DO CFDE slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim
comment: OMIM mapping confirmed by DO. [SN].

Brucella suis brucellosis
type: Class
subclass of: brucellosis
definition: 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.
imported from: doid.owl
has OBO namespace: disease_ontology
id: DOID:11076
in subset: DO infectious disease slim
in subset: gram-negative bacterial infectious disease
in subset: zoonotic infectious disease

brucellosis
type: Class
subclass of: primary bacterial infectious disease
definition: 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.
imported from: doid.owl
has alternative id: DOID:0050060
has cross-reference: GARD:5966
has cross-reference: ICD10CM:A23
has cross-reference: ICD9CM:023
has cross-reference: MESH:D002006
has cross-reference: NCI:C84602
has cross-reference: SNOMEDCT_US_2023_03_01:154296006
has cross-reference: UMLS_CUI:C0006309
has exact synonym: Maltese fever
has exact synonym: undulant fever
has OBO namespace: disease_ontology
has related synonym: Bang's disease
has related synonym: Gibraltar fever
has related synonym: Malta fever
has related synonym: Mediterranean fever
id: DOID:11077
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: gram-negative bacterial infectious disease
in subset: zoonotic infectious disease

Q fever
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that is a zoonotic infectious disease affecting multiple organs, has_material_basis_in Coxiella burnetii, which is transmitted_by inhalation of air contaminated by barnyard dust containing dried placental material, birth fluids, or excreta of infected herd animals, transmitted_by ingestion of contaminated milk, transmitted_by tick bites and transmitted_by contact with infected person. The infection has_symptom fever, has_symptom headache, has_symptom cough, has_symptom pleuritic chest pain, has_symptom myalgia and has_symptom arthralgia.
imported from: doid.owl
has cross-reference: GARD:7515
has cross-reference: ICD10CM:A78
has cross-reference: ICD9CM:083.0
has cross-reference: MESH:D011778
has cross-reference: NCI:C34970
has cross-reference: SNOMEDCT_US_2023_03_01:266205000
has cross-reference: UMLS_CUI:C0034362
has exact synonym: Infection due to Coxiella burnetii
has OBO namespace: disease_ontology
id: DOID:11100
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: gram-negative bacterial infectious disease
in subset: zoonotic infectious disease

sarcoma
type: Class
subclass of: cell type cancer
definition: A cell type cancer that has_material_basis_in abnormally proliferating cells derives from embryonic mesoderm.
imported from: doid.owl
has alternative id: DOID:3936
has cross-reference: ICD10CM:C49
has cross-reference: ICD9CM:171.9
has cross-reference: ICDO:8800/3
has cross-reference: SNOMEDCT_US_2023_03_01:93765001
has cross-reference: UMLS_CUI:C0153519
has exact synonym: connective and soft tissue neoplasm
has exact synonym: tumor of soft tissue and skeleton
has OBO namespace: disease_ontology
id: DOID:1115
in subset: DO RAD slim
in subset: DO cancer slim
in subset: TopNodes DOcancerslim

pertussis
type: Class
subclass of: bacterial infectious disease
definition: A commensal bacterial infectious disease that results_in inflammation located_in respiratory tract, has_material_basis_in Bordetella pertussis, or has_material_basis_in Bordetella parapertussis, which produce toxins that paralyze the cilia of the respiratory epithelial cells. The infection is characterized by a prolonged, high-pitched, deeply indrawn breath (whoop).
imported from: doid.owl
has alternative id: DOID:11333
has alternative id: DOID:11751
has cross-reference: KEGG:05133
has cross-reference: MESH:D001885
has cross-reference: SNOMEDCT_US_2023_03_01:26484003
has cross-reference: UMLS_CUI:C0006015
has exact synonym: WC - Whooping cough
has exact synonym: bordetella infection
has exact synonym: whooping cough
has OBO namespace: disease_ontology
id: DOID:1116
in subset: DO infectious disease slim
in subset: gram-negative bacterial infectious disease

Human papillomavirus infectious disease
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that has_material_basis_in human papillomaviruses, which establish productive infections only in the stratified epithelium of the skin or mucous membranes. These viruses cause warts and sometimes tumors. They are transmitted_by sexual contact.
imported from: doid.owl
has cross-reference: MESH:D030361
has exact synonym: HPV
has OBO namespace: disease_ontology
id: DOID:11166
in subset: DO infectious disease slim

rabies
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results in inflammation located in brain or located in spinal cord, has_material_basis_in Rabies virus, which is transmitted by bite of an infected animal, or transmitted by contact of mucous membranes with saliva of an infected animal. The infection has symptom fever, has symptom headache, has symptom prickling or itching sensation at the site of bite, has symptom anxiety, has symptom confusion, has symptom agitation, has symptom delirium, has symptom difficulty swallowing, has symptom hydrophobia, and has symptom paralysis.
imported from: doid.owl
has cross-reference: GARD:7516
has cross-reference: ICD10CM:A82
has cross-reference: ICD9CM:071
has cross-reference: MESH:D011818
has cross-reference: NCI:C28182
has cross-reference: SNOMEDCT_US_2023_03_01:14168008
has cross-reference: UMLS_CUI:C0034494
has exact synonym: Lyssa
has OBO namespace: disease_ontology
id: DOID:11260
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: zoonotic infectious disease

tetanus
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that results in prolonged contraction of skeletal muscle fibers, has_material_basis_in Clostridium tetani, which produces tetanospasmin, a neurotoxin, which is carried to the brain and spinal cord, where it binds irreversibly to receptors inhibiting neurotransmission. Damaged upper motor neurons cannot control reflex responses to afferent sensory stimuli.
imported from: doid.owl
has cross-reference: GARD:5144
has cross-reference: ICD10CM:A35
has cross-reference: ICD9CM:037
has cross-reference: MESH:D013742
has cross-reference: NCI:C85185
has cross-reference: SNOMEDCT_US_2023_03_01:154312006
has cross-reference: UMLS_CUI:C0039614
has exact synonym: Infection due to Clostridium tetani
has exact synonym: clostridial tetanus
has OBO namespace: disease_ontology
id: DOID:11338
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: gram-positive bacterial infectious disease

diphtheria
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that is characterized by sore throat, low fever, and an adherent membrane (a pseudomembrane) on the tonsils, pharynx, and/or nasal cavity. A milder form of diphtheria can be restricted to the skin. It is caused by Corynebacterium diphtheriae, an aerobic Gram-positive bacterium. Diphtheria toxin spreads through the bloodstream and can lead to potentially life-threatening complications that affect other organs of the body, such as the heart and kidneys.
imported from: doid.owl
has alternative id: DOID:4132
has cross-reference: GARD:1875
has cross-reference: MESH:D003354
has cross-reference: SNOMEDCT_US_2023_03_01:397434007
has cross-reference: UMLS_CUI:C0010153
has exact synonym: corynebacterium infection
has OBO namespace: disease_ontology
id: DOID:11405
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: gram-positive bacterial infectious disease

Lyme disease
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that results_in infection, has_material_basis_in Borrelia burgdorferi, which is transmitted_by blacklegged tick (Ixodes scapularis) or transmitted_by western blacklegged tick (Ixodes pacificus). The infection has_symptom fever, has_symptom headache, has_symptom fatigue, and has_symptom skin rash called erythema migrans. If left untreated, infection can spread to joints, the heart, and the nervous system.
imported from: doid.owl
has alternative id: DOID:12233
has cross-reference: GARD:12073
has cross-reference: ICD10CM:A69.2
has cross-reference: ICD9CM:088.81
has cross-reference: MESH:D008193
has cross-reference: MESH:D020852
has cross-reference: NCI:C45161
has cross-reference: SNOMEDCT_US_2023_03_01:154376000
has cross-reference: SNOMEDCT_US_2023_03_01:715507005
has cross-reference: UMLS_CUI:C0024198
has cross-reference: UMLS_CUI:C0752235
has exact synonym: Bannwarth syndrome
has exact synonym: Bannworth's syndrome
has exact synonym: Lyme borreliosis
has exact synonym: Neurological Lyme disease
has exact synonym: lyme neuroboInOwlrreliosis
has exact synonym: neuroboInOwlrreliosis
has OBO namespace: disease_ontology
id: DOID:11729
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: gram-negative bacterial infectious disease
in subset: tick-borne infectious disease
in subset: zoonotic infectious disease

peripheral nervous system neoplasm
type: Class
subclass of: nervous system cancer
subclass of: peripheral nervous system disease
definition: A nervous system cancer that is located in the peripheral nervous system.
imported from: doid.owl
has alternative id: DOID:3194
has cross-reference: MESH:D010524
has cross-reference: MESH:D018317
has cross-reference: NCI:C3321
has cross-reference: NCI:C4972
has cross-reference: SNOMEDCT_US_2023_03_01:126980002
has cross-reference: SNOMEDCT_US_2023_03_01:189946005
has cross-reference: UMLS_CUI:C0031118
has cross-reference: UMLS_CUI:C0206727
has exact synonym: neoplasm of peripheral nerve
has exact synonym: nerve sheath neoplasm
has exact synonym: tumor of PNS
has OBO namespace: disease_ontology
id: DOID:1192
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

head and neck cancer
type: Class
subclass of: organ system cancer
definition: An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.
imported from: doid.owl
has cross-reference: GARD:12425
has cross-reference: MESH:D006258
has cross-reference: NCI:C3077
has cross-reference: SNOMEDCT_US_2023_03_01:255055008
has cross-reference: UMLS_CUI:C0018671
has exact synonym: head and neck neoplasm
has exact synonym: head and neck tumours
has exact synonym: head/neck neoplasm
has exact synonym: tumor of head and neck
has OBO namespace: disease_ontology
id: DOID:11934
in subset: DO CFDE slim
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

female reproductive organ cancer
type: Class
subclass of: reproductive organ cancer
subclass of: female reproductive system disease
definition: A reproductive organ cancer that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva.
imported from: doid.owl
has alternative id: DOID:1244
has alternative id: DOID:1281
has cross-reference: ICD10CM:C57
has cross-reference: ICD9CM:184
has cross-reference: MESH:D005833
has cross-reference: NCI:C3053
has cross-reference: NCI:C4913
has cross-reference: SNOMEDCT_US_2023_03_01:126907002
has cross-reference: SNOMEDCT_US_2023_03_01:188207007
has cross-reference: UMLS_CUI:C0017416
has cross-reference: UMLS_CUI:C0153585
has cross-reference: UMLS_CUI:C0699889
has exact synonym: female reproductive cancer
has exact synonym: malignant Gynecologic tumor
has exact synonym: malignant neoplasm of female genital organ
has OBO namespace: disease_ontology
id: DOID:120
in subset: DO cancer slim
in subset: NCIthesaurus

allergic disease
type: Class
subclass of: immune system disease
definition: An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods.
imported from: doid.owl
IEDB alternative term: allergic disease
has cross-reference: ICD10CM:T78.40
has cross-reference: MESH:D006967
has cross-reference: NCI:C3114
has cross-reference: SNOMEDCT_US_2023_03_01:257550005
has cross-reference: UMLS_CUI:C0020517
has exact synonym: allergic hypersensitivity disease
has exact synonym: hypersensitivity
has exact synonym: hypersensitivity reaction type I disease
has OBO namespace: disease_ontology
id: DOID:1205
in subset: NCIthesaurus

dengue disease
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results in infection, has_material_basis_in Dengue virus (Orthoflavivirus denguei), which are transmitted by Aedes mosquito bite. The infection has symptom fever, has symptom severe headache, has symptom severe pain behind the eyes, has symptom joint pain, has symptom muscle and bone pain, has symptom rash, and has symptom mild bleeding.
imported from: doid.owl
has alternative id: DOID:0050142
has cross-reference: GARD:6254
has cross-reference: ICD10CM:A90
has cross-reference: ICD9CM:061
has cross-reference: MESH:D003715
has cross-reference: NCI:C34528
has cross-reference: SNOMEDCT_US_2023_03_01:38362002
has cross-reference: UMLS_CUI:C0011311
has exact synonym: Dengue Fever
has exact synonym: breakbone fever
has exact synonym: classic dengue
has OBO namespace: disease_ontology
has related synonym: classical dengue
id: DOID:12205
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: zoonotic infectious disease

malaria
type: Class
subclass of: parasitic infectious disease
definition: 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.
imported from: doid.owl
has alternative id: DOID:12552
has cross-reference: EFO:0001068
has cross-reference: GARD:6961
has cross-reference: ICD10CM:B54
has cross-reference: ICD9CM:084
has cross-reference: MESH:D008288
has cross-reference: NCI:C34797
has cross-reference: ORDO:673
has cross-reference: SNOMEDCT_US_2023_03_01:154374002
has cross-reference: UMLS_CUI:C0024530
has exact synonym: induced malaria
has OBO namespace: disease_ontology
id: DOID:12365
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI.

leukemia
type: Class
subclass of: hematologic cancer
definition: A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells.
imported from: doid.owl
has alternative id: DOID:9145
has cross-reference: ICD10CM:C95.90
has cross-reference: ICD9CM:208
has cross-reference: ICDO:9800/3
has cross-reference: MESH:D007938
has cross-reference: NCI:C3161
has cross-reference: SNOMEDCT_US_2023_03_01:255049003
has cross-reference: UMLS_CUI:C0023418
has OBO namespace: disease_ontology
id: DOID:1240
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus

hepatitis A
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in inflammation located_in liver, has_material_basis_in Hepatitis A virus (Hepatovirus ahepa), which is transmitted_by ingestion of contaminated food or water, or transmitted_by direct contact with an infected person. The infection has_symptom fever, has_symptom fatigue, has_symptom loss of appetite, has_symptom nausea, has_symptom vomiting, has_symptom abdominal pain, has_symptom clay-colored bowel movements, has_symptom joint pain, and has_symptom jaundice.
imported from: doid.owl
has alternative id: DOID:12547
has cross-reference: MESH:D006506
has cross-reference: NCI:C3096
has cross-reference: SNOMEDCT_US_2023_03_01:40468003
has cross-reference: UMLS_CUI:C0019159
has exact synonym: Viral hepatitis, type A
has OBO namespace: disease_ontology
has related synonym: Viral hepatitis A
id: DOID:12549
in subset: DO infectious disease slim
in subset: NCIthesaurus

respiratory syncytial virus infectious disease
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in infection located_in upper respiratory tract or located_in lower respiratory tract, has_material_basis_in Human respiratory syncytial virus, which is transmitted_by droplet spread of nasal secretions from an infected person while coughing or sneezing, or transmitted_by contaminated fomites. The infection has_symptom runny nose, has_symptom fever, has_symptom cough, has_symptom wheezing, and has_symptom respiratory distress.
imported from: doid.owl
has cross-reference: MESH:D018357
has cross-reference: NCI:C3354
has cross-reference: SNOMEDCT_US_2023_03_01:186750007
has cross-reference: UMLS_CUI:C0035235
has exact synonym: RSV
has exact synonym: respiratory syncytial virus
has OBO namespace: disease_ontology
id: DOID:1273
in subset: DO infectious disease slim
in subset: NCIthesaurus

brain cancer
type: Class
subclass of: central nervous system cancer
definition: A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain.
imported from: doid.owl
has alternative id: DOID:2125
has alternative id: DOID:2126
has alternative id: DOID:3543
has alternative id: DOID:6649
has alternative id: DOID:911
has cross-reference: ICD10CM:C71
has cross-reference: ICD9CM:191
has cross-reference: ICD9CM:239.6
has cross-reference: MESH:D001932
has cross-reference: NCI:C170814
has cross-reference: NCI:C2907
has cross-reference: NCI:C3568
has cross-reference: NCI:C5115
has cross-reference: NCI:C7710
has cross-reference: SNOMEDCT_US_2023_03_01:126952004
has cross-reference: SNOMEDCT_US_2023_03_01:428061005
has cross-reference: SNOMEDCT_US_2023_03_01:93727008
has cross-reference: UMLS_CUI:C0006118
has cross-reference: UMLS_CUI:C0153633
has cross-reference: UMLS_CUI:C0220624
has cross-reference: UMLS_CUI:C0750974
has cross-reference: UMLS_CUI:C0750979
has cross-reference: UMLS_CUI:C1334557
has exact synonym: BT - Brain tumour
has exact synonym: adult brain tumor
has exact synonym: adult malignant brain neoplasm
has exact synonym: brain neoplasm
has exact synonym: brain neoplasm, adult
has exact synonym: malignant brain tumour
has exact synonym: malignant primary brain neoplasm
has exact synonym: malignant primary brain tumor
has exact synonym: malignant tumor of Brain
has exact synonym: malignant tumor of adult brain
has exact synonym: neoplasm of brain
has exact synonym: primary brain neoplasm
has exact synonym: primary brain tumor
has exact synonym: primary malignant neoplasm of brain
has exact synonym: tumor of the Brain
has OBO namespace: disease_ontology
id: DOID:1319
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

lung cancer
type: Class
subclass of: respiratory system cancer
subclass of: lung disease
definition: A respiratory system cancer that is located_in the lung.
imported from: doid.owl
has alternative id: DOID:13075
has alternative id: DOID:1322
has alternative id: DOID:9881
has cross-reference: ICD10CM:C34.1
has cross-reference: ICD10CM:C34.2
has cross-reference: ICD10CM:C34.3
has cross-reference: ICD9CM:162.3
has cross-reference: ICD9CM:162.4
has cross-reference: ICD9CM:162.5
has cross-reference: ICD9CM:162.8
has cross-reference: MIM:211980
has cross-reference: MIM:608935
has cross-reference: MIM:612571
has cross-reference: MIM:612593
has cross-reference: MIM:614210
has cross-reference: SNOMEDCT_US_2023_03_01:187860004
has cross-reference: SNOMEDCT_US_2023_03_01:187864008
has cross-reference: SNOMEDCT_US_2023_03_01:187868006
has cross-reference: SNOMEDCT_US_2023_03_01:187874006
has cross-reference: UMLS_CUI:C0024624
has cross-reference: UMLS_CUI:C0153491
has cross-reference: UMLS_CUI:C0153492
has cross-reference: UMLS_CUI:C0153493
has OBO namespace: disease_ontology
has related synonym: lung neoplasm
id: DOID:1324
in subset: DO CFDE slim
in subset: DO cancer slim
in subset: TopNodes DOcancerslim

typhoid fever
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that is a communicable systemic illness, has_material_basis_in Salmonella enterica subsp enterica serovar Typhi, which is transmitted_by ingestion of food or water contaminated with the feces of an infected person. The infection has_symptom fever, has_symptom diarrhea, has_symptom prostration, has_symptom headache, has_symptom splenomegaly, has_symptom liver enlargement, has_symptom eruption of rose-colored spots, and has_symptom leukopenia.
imported from: doid.owl
has alternative id: DOID:3054
has cross-reference: GARD:9564
has cross-reference: ICD10CM:A01.0
has cross-reference: ICD9CM:002.0
has cross-reference: MESH:D014435
has cross-reference: NCI:C35089
has cross-reference: SNOMEDCT_US_2023_03_01:186091002
has cross-reference: UMLS_CUI:C0041466
has exact synonym: Typhoid
has OBO namespace: disease_ontology
id: DOID:13258
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: gram-negative bacterial infectious disease

parasitic infectious disease
type: Class
subclass of: disease by infectious agent
definition: 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.
imported from: doid.owl
has alternative id: DOID:11681
has alternative id: DOID:13509
has alternative id: DOID:1396
has alternative id: DOID:1494
has alternative id: DOID:2114
has alternative id: DOID:2293
has alternative id: DOID:2922
has alternative id: DOID:3564
has alternative id: DOID:4191
has alternative id: DOID:886
has alternative id: DOID:948
has alternative id: DOID:9639
has alternative id: DOID:9644
has cross-reference: ICD10CM:H44.12
has cross-reference: ICD9CM:360.13
has cross-reference: NCI:C34587
has cross-reference: SNOMEDCT_US_2023_03_01:57100005
has cross-reference: UMLS_CUI:C0014238
has exact synonym: Ectoparasitic disease
has exact synonym: parasitemia
has OBO namespace: disease_ontology
id: DOID:1398
in subset: DO AGR slim
in subset: DO infectious disease slim
in subset: NCIthesaurus

Plasmodium falciparum malaria
type: Class
subclass of: malaria
definition: 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.
imported from: doid.owl
has cross-reference: ICD10CM:B50
has cross-reference: ICD9CM:084.0
has cross-reference: MESH:D016778
has cross-reference: NCI:C34798
has cross-reference: SNOMEDCT_US_2023_03_01:62676009
has cross-reference: UMLS_CUI:C0024535
has exact synonym: Malaria fever, subtertian
has exact synonym: falciparum malaria
has exact synonym: malignant tertian fever
has OBO namespace: disease_ontology
id: DOID:14067
in subset: DO infectious disease slim
in subset: NCIthesaurus

Brucella melitensis brucellosis
type: Class
subclass of: brucellosis
definition: 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.
imported from: doid.owl
has cross-reference: ICD10CM:A23.0
has cross-reference: ICD9CM:023.0
has cross-reference: SNOMEDCT_US_2023_03_01:186305007
has cross-reference: UMLS_CUI:C0302362
has OBO namespace: disease_ontology
id: DOID:14456
in subset: DO infectious disease slim
in subset: gram-negative bacterial infectious disease
in subset: zoonotic infectious disease

Brucella abortus brucellosis
type: Class
subclass of: brucellosis
definition: 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.
imported from: doid.owl
has cross-reference: ICD10CM:A23.1
has cross-reference: ICD9CM:023.1
has cross-reference: MESH:D002007
has cross-reference: SNOMEDCT_US_2023_03_01:427795000
has cross-reference: UMLS_CUI:C0302363
has OBO namespace: disease_ontology
id: DOID:14457
in subset: DO infectious disease slim
in subset: gram-negative bacterial infectious disease
in subset: zoonotic infectious disease

disease of cellular proliferation
type: Class
subclass of: disease
definition: A disease that is characterized by abnormally rapid cell division.
imported from: doid.owl
IEDB alternative term: neoplasm
has alternative id: DOID:0000818
has exact synonym: cell process disease
has exact synonym: neoplasm
has OBO namespace: disease_ontology
id: DOID:14566
in subset: DO FlyBase slim
in subset: DO RAD slim

cholera
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that is described as an acute, diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae, which is characterized by profuse watery diarrhea, vomiting, leg cramps, circulatory collapse and shock.
imported from: doid.owl
has cross-reference: GARD:6043
has cross-reference: ICD10CM:A00
has cross-reference: ICD9CM:001
has cross-reference: MESH:D002771
has cross-reference: SNOMEDCT_US_2023_03_01:186087007
has cross-reference: UMLS_CUI:C0008354
has exact synonym: Cholera - Vibrio cholerae
has exact synonym: Cholera due to Vibrio cholerae
has exact synonym: Vibrio cholerae
has OBO namespace: disease_ontology
id: DOID:1498
in subset: DO FlyBase slim
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: GOLD
in subset: gram-negative bacterial infectious disease

reproductive system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in reproductive system organs.
imported from: doid.owl
has alternative id: DOID:6309
has cross-reference: NCI:C27613
has cross-reference: UMLS_CUI:C1335037
has exact synonym: genital system disease
has OBO namespace: disease_ontology
id: DOID:15
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: NCIthesaurus

head and neck carcinoma
type: Class
subclass of: head and neck cancer
subclass of: carcinoma
definition: A head and neck cancer that has_material_basis_in epithelial cells and is located in the upper aerodigestive tract, including the lip, oral cavity (mouth), nasal cavity, paranasal sinuses, pharynx, and larynx.
imported from: doid.owl
has cross-reference: NCI:C6077
has cross-reference: UMLS_CUI:C1334927
has exact synonym: carcinoma of the neck
has OBO namespace: disease_ontology
has related synonym: carcinoma of neck
id: DOID:1542
in subset: DO cancer slim
in subset: NCIthesaurus

respiratory system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
imported from: doid.owl
has alternative id: DOID:3226
has cross-reference: ICD10CM:J98
has cross-reference: ICD9CM:519
has cross-reference: SNOMEDCT_US_2023_03_01:155603009
has cross-reference: UMLS_CUI:C0029582
has OBO namespace: disease_ontology
id: DOID:1579
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: DO RAD slim

rheumatic fever
type: Class
subclass of: bacterial infectious disease
definition: A connective tissue disease that develops from an antecedent Group A Streptococcal pharyngeal infection and has_symptom carditis, has_symptom polyarthritis, has_symptom chorea, has_symptom erythema marginatum, has_symptom subcutaneous nodules, has_symptom arthralgia, has_symptom prolonged PR interval, and/or has_symptom fever.
imported from: doid.owl
has alternative id: DOID:1006
has alternative id: DOID:1007
has cross-reference: GARD:5699
has cross-reference: ICD10CM:I00
has cross-reference: ICD10CM:I00-I02
has cross-reference: ICD9CM:390
has cross-reference: ICD9CM:390-392.99
has cross-reference: MESH:D012213
has cross-reference: NCI:C34984
has cross-reference: SNOMEDCT_US_2023_03_01:155265007
has cross-reference: SNOMEDCT_US_2023_03_01:274095001
has cross-reference: UMLS_CUI:C0035436
has cross-reference: UMLS_CUI:C0264743
has exact synonym: ACUTE RHEUMATIC FEVER
has exact synonym: RhF - Rheumatic fever
has OBO namespace: disease_ontology
id: DOID:1586
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: gram-positive bacterial infectious disease

breast cancer
type: Class
subclass of: organ system cancer
subclass of: disease of anatomical entity
definition: An organ system cancer that originates in the mammary gland.
imported from: doid.owl
has alternative id: DOID:1648
has alternative id: DOID:4241
has cross-reference: ICD10CM:C50
has cross-reference: MESH:D001943
has cross-reference: MIM:114480
has cross-reference: NCI:C9335
has cross-reference: SNOMEDCT_US_2023_03_01:254837009
has cross-reference: UMLS_CUI:C0006142
has exact synonym: breast tumor
has exact synonym: malignant neoplasm of breast
has exact synonym: malignant tumor of the breast
has exact synonym: mammary cancer
has exact synonym: mammary tumor
has exact synonym: primary breast cancer
has OBO namespace: disease_ontology
has related synonym: mammary neoplasm
id: DOID:1612
in subset: DO CFDE slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

cancer
type: Class
subclass of: disease of cellular proliferation
definition: A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
imported from: doid.owl
has cross-reference: ICD10CM:C80.1
has cross-reference: ICD9CM:199
has cross-reference: ICDO:8000/3
has cross-reference: MESH:D009369
has cross-reference: NCI:C9305
has cross-reference: SNOMEDCT_US_2023_03_01:269513004
has cross-reference: UMLS_CUI:C0006826
has exact synonym: malignant neoplasm
has exact synonym: malignant tumor
has exact synonym: primary cancer
has OBO namespace: disease_ontology
id: DOID:162
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO GXD slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
comment: Updating out dated UMLS CUI.

musculoskeletal system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that occurs in the muscular and/or skeletal system.
imported from: doid.owl
has cross-reference: MESH:D009140
has cross-reference: NCI:C107377
has cross-reference: SNOMEDCT_US_2023_03_01:268047003
has cross-reference: UMLS_CUI:C0026857
has OBO namespace: disease_ontology
id: DOID:17
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: NCIthesaurus

endocrine gland cancer
type: Class
subclass of: organ system cancer
definition: An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
imported from: doid.owl
has alternative id: DOID:10009
has cross-reference: ICD10CM:C75.9
has cross-reference: ICD9CM:194.9
has cross-reference: MESH:D004701
has cross-reference: NCI:C3010
has cross-reference: NCI:C3575
has cross-reference: SNOMEDCT_US_2023_03_01:127015005
has cross-reference: SNOMEDCT_US_2023_03_01:93780007
has cross-reference: UMLS_CUI:C0014132
has cross-reference: UMLS_CUI:C0153658
has exact synonym: Endocrine tumor
has exact synonym: endocrine neoplasm
has exact synonym: malignant Endocrine tumor
has exact synonym: malignant neoplasm of endocrine gland
has exact synonym: malignant tumour of endocrine gland
has exact synonym: neoplasm of endocrine gland
has exact synonym: neoplasm of endocrine system
has OBO namespace: disease_ontology
id: DOID:170
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

benign peritoneal mesothelioma
type: Class
subclass of: thoracic benign neoplasm
imported from: doid.owl
has cross-reference: NCI:C7633
has cross-reference: UMLS_CUI:C1377610
has exact synonym: Mesothelioma of Peritoneum
has OBO namespace: disease_ontology
id: DOID:1789
in subset: NCIthesaurus

pancreatic cancer
type: Class
subclass of: endocrine gland cancer
subclass of: endocrine system disease
definition: An endocrine gland cancer located_in the pancreas.
imported from: doid.owl
has alternative id: DOID:14356
has alternative id: DOID:1797
has alternative id: DOID:3588
has alternative id: DOID:9859
has cross-reference: GARD:9364
has cross-reference: ICD10CM:C25.0
has cross-reference: ICD10CM:C25.1
has cross-reference: ICD10CM:C25.2
has cross-reference: ICD9CM:157.0
has cross-reference: ICD9CM:157.1
has cross-reference: ICD9CM:157.2
has cross-reference: ICD9CM:157.8
has cross-reference: KEGG:05212
has cross-reference: MESH:D010190
has cross-reference: NCI:C3305
has cross-reference: ORDO:1333
has cross-reference: ORDO:217074
has cross-reference: SNOMEDCT_US_2023_03_01:126859007
has cross-reference: SNOMEDCT_US_2023_03_01:187796007
has cross-reference: SNOMEDCT_US_2023_03_01:93715005
has cross-reference: SNOMEDCT_US_2023_03_01:93823001
has cross-reference: SNOMEDCT_US_2023_03_01:94082003
has cross-reference: UMLS_CUI:C0030297
has cross-reference: UMLS_CUI:C0153458
has cross-reference: UMLS_CUI:C0153459
has cross-reference: UMLS_CUI:C0153460
has cross-reference: UMLS_CUI:C0153463
has exact synonym: Ca body of pancreas
has exact synonym: Ca head of pancreas
has exact synonym: Ca tail of pancreas
has exact synonym: malignant neoplasm of body of pancreas
has exact synonym: malignant neoplasm of head of pancreas
has exact synonym: malignant neoplasm of tail of pancreas
has exact synonym: pancreas neoplasm
has exact synonym: pancreatic neoplasm
has exact synonym: pancreatic tumor
has OBO namespace: disease_ontology
id: DOID:1793
in subset: DO CFDE slim
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim
comment: Xref MGI.

urinary system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
imported from: doid.owl
has alternative id: DOID:579
has cross-reference: NCI:C27599
has cross-reference: UMLS_CUI:C1335051
has exact synonym: Non-neoplastic urinary tract disease
has exact synonym: urinary tract disease
has OBO namespace: disease_ontology
id: DOID:18
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: NCIthesaurus

bone cancer
type: Class
subclass of: bone disease
subclass of: connective tissue cancer
definition: A connective tissue cancer that is located_in bone and is characterized by uncontrolled cellular proliferation that destroys normal bone tissue.
imported from: doid.owl
has alternative id: DOID:3348
has cross-reference: MESH:D001859
has cross-reference: NCI:C9343
has cross-reference: SNOMEDCT_US_2023_03_01:126537000
has cross-reference: UMLS_CUI:C0005967
has exact synonym: CA - bone cancer
has exact synonym: bone neoplasm
has exact synonym: bone tumour
has exact synonym: malignant bone neoplasm
has exact synonym: malignant bone tumour
has exact synonym: malignant neoplasm of bone
has exact synonym: malignant osseous tumor
has exact synonym: neoplasm of bone
has exact synonym: osseous tumor
has OBO namespace: disease_ontology
id: DOID:184
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

melanoma
type: Class
subclass of: cell type cancer
definition: 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.
imported from: doid.owl
has cross-reference: EFO:0000756
has cross-reference: ICDO:8720/3
has cross-reference: KEGG:05218
has cross-reference: MESH:D008545
has cross-reference: NCI:C3224
has cross-reference: SNOMEDCT_US_2023_03_01:2092003
has cross-reference: UMLS_CUI:C0025202
has exact synonym: Naevocarcinoma
has exact synonym: malignant melanoma
has OBO namespace: disease_ontology
id: DOID:1909
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

reproductive organ cancer
type: Class
subclass of: organ system cancer
subclass of: reproductive system disease
definition: An organ system cancer that is manifested in the reproductive organs.
imported from: doid.owl
has alternative id: DOID:1900
has cross-reference: NCI:C3674
has cross-reference: UMLS_CUI:C0178830
has exact synonym: Reproductive tumor
has exact synonym: malignant reproductive system neoplasm
has OBO namespace: disease_ontology
has related synonym: cancer of reproductive system
id: DOID:193
in subset: NCIthesaurus

atherosclerosis
type: Class
subclass of: disease of anatomical entity
imported from: doid.owl
has cross-reference: EFO:0003914
has cross-reference: ICD10CM:I70
has cross-reference: ICD9CM:440
has cross-reference: MESH:D050197
has cross-reference: NCI:C35768
has cross-reference: SNOMEDCT_US_2023_03_01:155414001
has cross-reference: UMLS_CUI:C0004153
has OBO namespace: disease_ontology
id: DOID:1936
in subset: DO RAD slim
in subset: NCIthesaurus

fallopian tube cancer
type: Class
subclass of: female reproductive organ cancer
definition: A female reproductive organ cancer that is located_in fallopian tube.
imported from: doid.owl
has alternative id: DOID:1961
has cross-reference: GARD:9162
has cross-reference: ICD10CM:C57.0
has cross-reference: ICD9CM:183.2
has cross-reference: MESH:D005185
has cross-reference: NCI:C3032
has cross-reference: NCI:C7480
has cross-reference: SNOMEDCT_US_2023_03_01:126916003
has cross-reference: SNOMEDCT_US_2023_03_01:93794008
has cross-reference: UMLS_CUI:C0015558
has cross-reference: UMLS_CUI:C0153579
has exact synonym: fallopian tube neoplasm
has exact synonym: malignant neoplasm of uterine tube
has exact synonym: malignant tumor of fallopian tube
has exact synonym: malignant tumour of fallopian tube
has exact synonym: neoplasm of fallopian tube
has exact synonym: tumor of the fallopian tube
has exact synonym: tumor, fallopian tube, malignant
has OBO namespace: disease_ontology
id: DOID:1964
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

rectum cancer
type: Class
subclass of: colorectal cancer
definition: A colorectal cancer that is located_in the rectum.
imported from: doid.owl
has alternative id: DOID:1989
has cross-reference: ICD10CM:C20
has cross-reference: ICD9CM:154.1
has cross-reference: MESH:D012004
has cross-reference: NCI:C7418
has cross-reference: NCI:C9382
has cross-reference: SNOMEDCT_US_2023_03_01:254582000
has cross-reference: SNOMEDCT_US_2023_03_01:93984006
has cross-reference: UMLS_CUI:C0007113
has cross-reference: UMLS_CUI:C0949022
has exact synonym: carcinoma of rectum
has exact synonym: carcinoma of the rectum
has exact synonym: malignant Rectal tumor
has exact synonym: malignant neoplasm of rectum
has exact synonym: malignant rectum tumor
has exact synonym: malignant tumor of rectum
has exact synonym: rectal cancer
has OBO namespace: disease_ontology
has related synonym: cancer of rectum
id: DOID:1993
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

connective tissue cancer
type: Class
subclass of: musculoskeletal system cancer
subclass of: connective tissue disease
definition: A musculoskeletal system cancer that is located_in connective tissue.
imported from: doid.owl
has cross-reference: MESH:D009372
has cross-reference: SNOMEDCT_US_2023_03_01:126598008
has cross-reference: UMLS_CUI:C0027656
has exact synonym: Tumour of connective tissue
has exact synonym: connective tissue neoplasm
has exact synonym: mesenchymal tissue malignant neoplasm
has exact synonym: neoplasm of connective tissues
has OBO namespace: disease_ontology
id: DOID:201
in subset: TopNodes DOcancerslim

hepatitis B
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in inflammation located_in liver, has_material_basis_in Hepatitis B virus (Orthohepadnavirus hominoidei), which is transmitted_by sexual contact, blood transfusions, or fomites like needles or syringes. The infection has_symptom fever, fatigue, loss of appetite, nausea, vomiting, abdominal pain, clay-colored bowel movements, joint pain, and jaundice.
imported from: doid.owl
has alternative id: DOID:12591
has alternative id: DOID:12592
has alternative id: DOID:2042
has cross-reference: EFO:0004197
has cross-reference: MESH:D006509
has cross-reference: NCI:C3097
has cross-reference: SNOMEDCT_US_2023_03_01:66071002
has cross-reference: UMLS_CUI:C0019163
has exact synonym: chronic hepatitis B
has exact synonym: hepatitis B infection
has OBO namespace: disease_ontology
has related synonym: Serum hepatitis
id: DOID:2043
in subset: DO infectious disease slim
in subset: NCIthesaurus
in subset: sexually transmitted infectious disease

tularemia
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that has_material_basis_in Francisella tularensis, which is transmitted by dog tick bite (Dermacentor variabilis), transmitted by deer flies (Chrysops sp) or transmitted by contact with infected animal tissues.
imported from: doid.owl
has cross-reference: GARD:396
has cross-reference: ICD9CM:021.8
has cross-reference: SNOMEDCT_US_2023_03_01:186298002
has cross-reference: UMLS_CUI:C0029835
has OBO namespace: disease_ontology
id: DOID:2123
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: gram-negative bacterial infectious disease
in subset: tick-borne infectious disease
in subset: zoonotic infectious disease

colon cancer
type: Class
subclass of: colorectal cancer
definition: A colorectal cancer that is located_in the colon.
imported from: doid.owl
has cross-reference: ICD10CM:C18
has cross-reference: ICD9CM:153
has cross-reference: MESH:D003110
has cross-reference: NCI:C9242
has cross-reference: SNOMEDCT_US_2023_03_01:363406005
has cross-reference: UMLS_CUI:C0007102
has OBO namespace: disease_ontology
id: DOID:219
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

female reproductive system disease
type: Class
subclass of: reproductive system disease
definition: A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
imported from: doid.owl
has cross-reference: ICD9CM:629.9
has cross-reference: MESH:D005831
has cross-reference: SNOMEDCT_US_2023_03_01:38233001
has cross-reference: UMLS_CUI:C0017411
has OBO namespace: disease_ontology
id: DOID:229

ovarian cancer
type: Class
subclass of: ovarian disease
subclass of: female reproductive organ cancer
definition: A female reproductive organ cancer that is located_in the ovary.
imported from: doid.owl
has alternative id: DOID:0060070
has alternative id: DOID:2144
has alternative id: DOID:9595
has cross-reference: GARD:7295
has cross-reference: ICD10CM:C56
has cross-reference: ICD9CM:183.0
has cross-reference: MESH:D010051
has cross-reference: MIM:167000
has cross-reference: MIM:607893
has cross-reference: NCI:C4984
has cross-reference: NCI:C7431
has cross-reference: ORDO:213500
has cross-reference: ORDO:213517
has cross-reference: SNOMEDCT_US_2023_03_01:123843001
has cross-reference: SNOMEDCT_US_2023_03_01:372117006
has cross-reference: SNOMEDCT_US_2023_03_01:93934004
has cross-reference: UMLS_CUI:C0919267
has cross-reference: UMLS_CUI:C1140680
has cross-reference: UMLS_CUI:C1299247
has exact synonym: malignant Ovarian tumor
has exact synonym: malignant tumour of ovary
has exact synonym: ovarian neoplasm
has exact synonym: ovary neoplasm
has exact synonym: primary ovarian cancer
has exact synonym: tumor of the Ovary
has OBO namespace: disease_ontology
id: DOID:2394
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

hematologic cancer
type: Class
subclass of: organ system cancer
subclass of: hematopoietic system disease
definition: An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes.
imported from: doid.owl
has alternative id: DOID:1034
has alternative id: DOID:2532
has cross-reference: MESH:D019337
has cross-reference: NCI:C27134
has cross-reference: SNOMEDCT_US_2023_03_01:414388001
has cross-reference: UMLS_CUI:C0376544
has exact synonym: Hematologic malignancy
has exact synonym: Hematologic neoplasm
has exact synonym: Hematological tumors
has exact synonym: blood cancer
has exact synonym: hematopoietic and lymphoid system tumor
has exact synonym: hematopoietic cancer
has exact synonym: hematopoietic neoplasm
has exact synonym: hematopoietic tumors
has exact synonym: malignant hematopoietic neoplasm
has OBO namespace: disease_ontology
id: DOID:2531
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

kidney cancer
type: Class
subclass of: urinary system cancer
definition: A urinary system cancer that is located_in the kidney.
imported from: doid.owl
has alternative id: DOID:11834
has alternative id: DOID:3676
has cross-reference: ICD10CM:C64
has cross-reference: ICD9CM:189.0
has cross-reference: MESH:D007680
has cross-reference: NCI:C120456
has cross-reference: NCI:C3150
has cross-reference: NCI:C7548
has cross-reference: SNOMEDCT_US_2023_03_01:126880001
has cross-reference: SNOMEDCT_US_2023_03_01:93849006
has cross-reference: UMLS_CUI:C0022665
has cross-reference: UMLS_CUI:C0494158
has cross-reference: UMLS_CUI:C0740457
has exact synonym: malignant neoplasm of kidney except pelvis
has exact synonym: malignant tumour of kidney
has exact synonym: renal cancer
has OBO namespace: disease_ontology
id: DOID:263
in subset: DO CFDE slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

endocrine system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
imported from: doid.owl
has cross-reference: ICD10CM:E34.9
has cross-reference: ICD9CM:259.9
has cross-reference: MESH:D004700
has cross-reference: NCI:C3009
has cross-reference: SNOMEDCT_US_2023_03_01:67432001
has cross-reference: UMLS_CUI:C0014130
has OBO namespace: disease_ontology
id: DOID:28
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: DO RAD slim
in subset: NCIthesaurus

immune system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the immune system.
imported from: doid.owl
has cross-reference: EFO:0000540
has cross-reference: ICD10CM:D89.9
has cross-reference: ICD9CM:279.9
has cross-reference: SNOMEDCT_US_2023_03_01:154782004
has cross-reference: UMLS_CUI:C0041806
has OBO namespace: disease_ontology
id: DOID:2914
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO GXD slim
in subset: DO MGI slim

adenocarcinoma
type: Class
subclass of: carcinoma
definition: A carcinoma that has_material_basis_in abnormally proliferating cells, derives_from epithelial cells, which originate in glandular tissue.
imported from: doid.owl
has cross-reference: ICDO:8140/3
has cross-reference: MESH:D000230
has cross-reference: NCI:C2852
has cross-reference: SNOMEDCT_US_2023_03_01:35917007
has cross-reference: UMLS_CUI:C0001418
has OBO namespace: disease_ontology
id: DOID:299
in subset: NCIthesaurus

carcinoma
type: Class
subclass of: cell type cancer
definition: A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
imported from: doid.owl
has alternative id: DOID:2428
has alternative id: DOID:6570
has cross-reference: ICDO:8010/3
has cross-reference: MESH:D002277
has cross-reference: MESH:D009375
has cross-reference: NCI:C2916
has cross-reference: NCI:C3709
has cross-reference: SNOMEDCT_US_2023_03_01:188083002
has cross-reference: SNOMEDCT_US_2023_03_01:269513004
has cross-reference: SNOMEDCT_US_2023_03_01:71298006
has cross-reference: UMLS_CUI:C0007097
has cross-reference: UMLS_CUI:C0553707
has cross-reference: UMLS_CUI:C1368683
has exact synonym: epithelial cancer
has exact synonym: epithelioma
has exact synonym: malignant Epithelioma
has OBO namespace: disease_ontology
id: DOID:305
in subset: DO FlyBase slim
in subset: DO cancer slim
in subset: NCIthesaurus

glioblastoma
type: Class
subclass of: malignant astrocytoma
definition: A malignant astrocytoma characterized by the presence of small areas of necrotizing tissue that is surrounded by anaplastic cells as well as the presence of hyperplastic blood vessels, and that has_material_basis_in abnormally proliferating cells derives_from multiple cell types including astrocytes and oligondroctyes.
imported from: doid.owl
has alternative id: DOID:3075
has alternative id: DOID:3080
has cross-reference: GARD:2491
has cross-reference: ICDO:9440/3
has cross-reference: MESH:D005909
has cross-reference: NCI:C129295
has cross-reference: NCI:C39750
has cross-reference: NCI:C9094
has cross-reference: SNOMEDCT_US_2023_03_01:63634009
has cross-reference: UMLS_CUI:C0017636
has cross-reference: UMLS_CUI:C0278878
has cross-reference: UMLS_CUI:C1514422
has exact synonym: GBM
has exact synonym: adult glioblastoma multiforme
has exact synonym: glioblastoma multiforme
has exact synonym: grade IV adult Astrocytic tumor
has exact synonym: primary glioblastoma multiforme
has exact synonym: spongioblastoma multiforme
has OBO namespace: disease_ontology
id: DOID:3068
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus

malignant astrocytoma
type: Class
subclass of: cell type cancer
subclass of: central nervous system cancer
definition: A malignant glioma that is has_material_basis_in astrocyte cells, a type of star-shaped glial cell, located in the brain and spinal cord.
imported from: doid.owl
has alternative id: DOID:4861
has cross-reference: ICDO:9400/3
has cross-reference: MESH:D001254
has cross-reference: NCI:C4951
has cross-reference: NCI:C60781
has cross-reference: SNOMEDCT_US_2023_03_01:189914005
has cross-reference: SNOMEDCT_US_2023_03_01:99131000119108
has cross-reference: UMLS_CUI:C0004114
has cross-reference: UMLS_CUI:C0750935
has exact synonym: Astrocytic tumor
has exact synonym: astrocytoma of Cerebrum
has exact synonym: astrocytoma of brain
has exact synonym: astroglioma
has exact synonym: cerebral astrocytoma
has OBO namespace: disease_ontology
id: DOID:3069
in subset: DO cancer slim
in subset: NCIthesaurus

nervous system cancer
type: Class
subclass of: organ system cancer
subclass of: nervous system disease
definition: An organ system cancer located_in the nervous system that affects the central or peripheral nervous system.
imported from: doid.owl
has alternative id: DOID:1193
has alternative id: DOID:3195
has alternative id: DOID:4695
has cross-reference: ICD9CM:192.9
has cross-reference: MESH:D009380
has cross-reference: NCI:C35562
has cross-reference: SNOMEDCT_US_2023_03_01:188306000
has cross-reference: UMLS_CUI:C0027665
has cross-reference: UMLS_CUI:C0153643
has cross-reference: UMLS_CUI:C1334956
has exact synonym: malignant neoplasm of nervous system
has exact synonym: neoplasm of nervous system
has exact synonym: nervous system neoplasm
has exact synonym: neural neoplasm
has exact synonym: neural tumor
has exact synonym: tumor of the nervous system
has OBO namespace: disease_ontology
id: DOID:3093
in subset: NCIthesaurus

hepatobiliary disease
type: Class
subclass of: gastrointestinal system disease
definition: A gastrointestinal system disease that is located_in the liver and/or biliary tract.
imported from: doid.owl
has cross-reference: MESH:D004066
has cross-reference: NCI:C3959
has cross-reference: UMLS_CUI:C0267792
has exact synonym: liver and biliary tract disease
has OBO namespace: disease_ontology
id: DOID:3118
in subset: NCIthesaurus

gastrointestinal system cancer
type: Class
subclass of: organ system cancer
subclass of: gastrointestinal system disease
definition: An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
imported from: doid.owl
has alternative id: DOID:4945
has alternative id: DOID:8377
has cross-reference: ICD10CM:C26.9
has cross-reference: ICD9CM:239.0
has cross-reference: MESH:D004067
has cross-reference: MESH:D005770
has cross-reference: NCI:C3052
has cross-reference: NCI:C4890
has cross-reference: SNOMEDCT_US_2023_03_01:128348002
has cross-reference: SNOMEDCT_US_2023_03_01:276806006
has cross-reference: SNOMEDCT_US_2023_03_01:428905002
has cross-reference: UMLS_CUI:C0012243
has cross-reference: UMLS_CUI:C0017185
has cross-reference: UMLS_CUI:C0685938
has exact synonym: GI tumor
has exact synonym: digestive system cancer
has exact synonym: gastrointestinal tract cancer
has OBO namespace: disease_ontology
id: DOID:3119
in subset: DO FlyBase slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

mpox
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus (Orthopoxvirus monkeypox), which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy.
imported from: doid.owl
has cross-reference: GARD:10722
has cross-reference: ICD10CM:B04
has cross-reference: ICD9CM:059.01
has cross-reference: MESH:D045908
has cross-reference: NCI:C128421
has cross-reference: SNOMEDCT_US_2023_03_01:240466002
has cross-reference: UMLS_CUI:C0276180
has exact synonym: monkeypox
has OBO namespace: disease_ontology
id: DOID:3292
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: zoonotic infectious disease
comment: November 2022 WHO name update.

central nervous system disease
type: Class
subclass of: nervous system disease
definition: A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
imported from: doid.owl
has cross-reference: ICD10CM:G96.9
has cross-reference: MESH:D002493
has cross-reference: NCI:C2934
has cross-reference: SNOMEDCT_US_2023_03_01:267144009
has cross-reference: UMLS_CUI:C0007682
has OBO namespace: disease_ontology
id: DOID:331
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: NCIthesaurus

osteosarcoma
type: Class
subclass of: bone cancer
definition: A bone sarcoma that is located_in bone that has_material_basis_in cells of mesenchymal origin. It usually involves bones and less frequently extraosseous sites. It often involves the long bones (particularly distal femur, proximal tibia, and proximal humerus).
imported from: doid.owl
has alternative id: DOID:183
has cross-reference: GARD:7284
has cross-reference: ICDO:9180/3
has cross-reference: MESH:D012516
has cross-reference: MESH:D018213
has cross-reference: MIM:259500
has cross-reference: NCI:C9145
has cross-reference: ORDO:668
has cross-reference: SNOMEDCT_US_2023_03_01:189878003
has cross-reference: UMLS_CUI:C0029463
has cross-reference: UMLS_CUI:C0206639
has exact synonym: Osteogenic sarcoma
has exact synonym: Skeletal sarcoma
has exact synonym: bone tissue neoplasm
has exact synonym: osteoid sarcoma
has OBO namespace: disease_ontology
id: DOID:3347
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

Ewing sarcoma
type: Class
subclass of: connective tissue cancer
definition: A connective tissue cancer that has_material_basis_in neural crest cells derives_from undeveloped, undifferentiated neuroectoderm.
imported from: doid.owl
has alternative id: DOID:0050607
has alternative id: DOID:4158
has alternative id: DOID:4390
has alternative id: DOID:4391
has alternative id: DOID:4392
has alternative id: DOID:4980
has cross-reference: GARD:6390
has cross-reference: ICDO:9364/3
has cross-reference: MESH:C563168
has cross-reference: MESH:D012512
has cross-reference: MESH:D018241
has cross-reference: MIM:612219
has cross-reference: NCI:C27901
has cross-reference: NCI:C27903
has cross-reference: NCI:C4817
has cross-reference: NCI:C7542
has cross-reference: NCI:C7806
has cross-reference: NCI:C9341
has cross-reference: SNOMEDCT_US_2023_03_01:134210007
has cross-reference: SNOMEDCT_US_2023_03_01:73676002
has cross-reference: SNOMEDCT_US_2023_03_01:76909002
has cross-reference: UMLS_CUI:C0553580
has cross-reference: UMLS_CUI:C0684337
has cross-reference: UMLS_CUI:C0796547
has cross-reference: UMLS_CUI:C0863029
has cross-reference: UMLS_CUI:C0877849
has cross-reference: UMLS_CUI:C1334408
has exact synonym: Ewing's family localized tumor
has exact synonym: Ewing's sarcoma/peripheral primitive neuroectodermal tumor
has exact synonym: Ewing's tumor
has exact synonym: Ewings sarcoma
has exact synonym: Ewings sarcoma-primitive neuroectodermal tumor
has exact synonym: PNET of Thoracopulmonary Region
has exact synonym: localized Ewing sarcoma
has exact synonym: localized Ewing's sarcoma
has exact synonym: localized Ewing's sarcoma/peripheral primitive neuroectodermal tumor
has exact synonym: localized Ewing's tumor
has exact synonym: localized peripheral primitive neuroectodermal tumor
has exact synonym: peripheral primitive neuroectodermal tumor
has OBO namespace: disease_ontology
id: DOID:3369
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

uterine disease
type: Class
subclass of: female reproductive system disease
definition: A female reproductive system disease that is located_in the uterus.
imported from: doid.owl
has cross-reference: ICD10CM:N85.9
has cross-reference: ICD9CM:621.9
has cross-reference: MESH:D014591
has cross-reference: NCI:C26907
has cross-reference: SNOMEDCT_US_2023_03_01:237068005
has cross-reference: UMLS_CUI:C0042131
has OBO namespace: disease_ontology
id: DOID:345
in subset: NCIthesaurus

liver cancer
type: Class
subclass of: hepatobiliary system cancer
subclass of: endocrine gland cancer
subclass of: hepatobiliary disease
definition: A hepatobiliary system cancer that is located_in the liver.
imported from: doid.owl
has alternative id: DOID:12300
has alternative id: DOID:269
has alternative id: DOID:7330
has alternative id: DOID:915
has alternative id: DOID:919
has cross-reference: ICD10CM:C22.0
has cross-reference: ICD10CM:C22.9
has cross-reference: ICD9CM:155.0
has cross-reference: ICD9CM:155.2
has cross-reference: MESH:D008113
has cross-reference: NCI:C34803
has cross-reference: NCI:C7692
has cross-reference: SNOMEDCT_US_2023_03_01:126851005
has cross-reference: SNOMEDCT_US_2023_03_01:187771009
has cross-reference: SNOMEDCT_US_2023_03_01:93870000
has cross-reference: UMLS_CUI:C0023903
has cross-reference: UMLS_CUI:C0024620
has cross-reference: UMLS_CUI:C0345904
has cross-reference: UMLS_CUI:C0854795
has exact synonym: Ca liver - primary
has exact synonym: Resectable malignant neoplasm of Liver
has exact synonym: hepatic cancer
has exact synonym: hepatic neoplasm
has exact synonym: malignant hepato-biliary neoplasm
has exact synonym: malignant neoplasm of liver
has exact synonym: malignant neoplasm of liver, not specified as primary or secondary
has exact synonym: malignant neoplasm of liver, primary
has exact synonym: malignant tumor of liver
has exact synonym: neoplasm of liver
has exact synonym: non-resectable primary hepatic malignant neoplasm
has exact synonym: primary liver cancer
has exact synonym: primary malignant neoplasm of liver
has exact synonym: resectable malignant neoplasm of the liver
has OBO namespace: disease_ontology
id: DOID:3571
in subset: DO CFDE slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

central nervous system cancer
type: Class
subclass of: nervous system cancer
subclass of: central nervous system disease
definition: A nervous system cancer that is located_in the central nervous system.
imported from: doid.owl
has alternative id: DOID:0060093
has alternative id: DOID:1318
has cross-reference: EFO:0000326
has cross-reference: ICD10CM:C72.9
has cross-reference: MESH:D016543
has cross-reference: NCI:C4627
has cross-reference: NCI:C9293
has cross-reference: SNOMEDCT_US_2023_03_01:126951006
has cross-reference: SNOMEDCT_US_2023_03_01:93744007
has cross-reference: UMLS_CUI:C0085136
has cross-reference: UMLS_CUI:C0348374
has exact synonym: CNS neoplasm
has exact synonym: central nervous system tumor
has exact synonym: central nervous system tumors
has exact synonym: malignant neoplasm of central nervous system
has exact synonym: malignant tumor of CNS
has exact synonym: neoplasm of central nervous system
has OBO namespace: disease_ontology
id: DOID:3620
in subset: NCIthesaurus

uterine cancer
type: Class
subclass of: female reproductive organ cancer
subclass of: uterine disease
definition: A female reproductive organ cancer that is located_in the uterus.
imported from: doid.owl
has alternative id: DOID:4363
has cross-reference: ICD10CM:C55
has cross-reference: ICD9CM:179
has cross-reference: MESH:D014594
has cross-reference: NCI:C3435
has cross-reference: NCI:C3552
has cross-reference: SNOMEDCT_US_2023_03_01:126908007
has cross-reference: SNOMEDCT_US_2023_03_01:371973000
has cross-reference: UMLS_CUI:C0042138
has cross-reference: UMLS_CUI:C0153567
has exact synonym: CA - cancer of uterus
has exact synonym: Tumour of uterus
has exact synonym: malignant neoplasm of uterus
has exact synonym: malignant uterine tumor
has exact synonym: neoplasm of uterus
has exact synonym: uterine tumor
has exact synonym: uterus neoplasm
has OBO namespace: disease_ontology
id: DOID:363
in subset: DO CFDE slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

gastric adenocarcinoma
type: Class
subclass of: adenocarcinoma
subclass of: stomach carcinoma
definition: A stomach carcinoma that derives_from epithelial cells of glandular origin.
imported from: doid.owl
has cross-reference: NCI:C4004
has cross-reference: SNOMEDCT_US_2023_03_01:408647009
has cross-reference: UMLS_CUI:C0278701
has exact synonym: adenocarcinoma of stomach
has exact synonym: stomach adenocarcinoma
has OBO namespace: disease_ontology
id: DOID:3717
in subset: DO cancer slim
in subset: NCIthesaurus

male reproductive organ cancer
type: Class
subclass of: reproductive organ cancer
subclass of: male reproductive system disease
definition: A reproductive organ cancer that is manifested in the male genital system. This includes organs such as the penis and scrotum.
imported from: doid.owl
has alternative id: DOID:10284
has cross-reference: ICD10CM:C63.9
has cross-reference: ICD9CM:187.9
has cross-reference: MESH:D005834
has cross-reference: NCI:C3054
has cross-reference: NCI:C8561
has cross-reference: SNOMEDCT_US_2023_03_01:126895004
has cross-reference: SNOMEDCT_US_2023_03_01:363515000
has cross-reference: UMLS_CUI:C0017417
has cross-reference: UMLS_CUI:C0153606
has exact synonym: male genital cancer
has exact synonym: male reproductive system neoplasm
has exact synonym: malignant neoplasm of male genital organ
has exact synonym: malignant neoplasm of male genital organ or tract
has exact synonym: malignant neoplasm of male genital organs
has exact synonym: malignant tumor of male Reproductive system
has exact synonym: malignant tumor of male genital organ
has exact synonym: neoplasm of male genital organ
has exact synonym: tumor of male Reproductive system
has OBO namespace: disease_ontology
has related synonym: male genital neoplasm
id: DOID:3856
in subset: NCIthesaurus

lung carcinoma
type: Class
subclass of: lung cancer
subclass of: carcinoma
definition: A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis.
imported from: doid.owl
has cross-reference: EFO:0001071
has cross-reference: NCI:C4878
has cross-reference: SNOMEDCT_US_2023_03_01:154485001
has cross-reference: UMLS_CUI:C0684249
has exact synonym: cancer of lung
has OBO namespace: disease_ontology
has related synonym: carcinoma of lung
id: DOID:3905
in subset: DO cancer slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

lung non-small cell carcinoma
type: Class
subclass of: lung carcinoma
definition: A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
imported from: doid.owl
has cross-reference: EFO:0003060
has cross-reference: KEGG:05223
has cross-reference: MESH:D002289
has cross-reference: NCI:C2926
has cross-reference: SNOMEDCT_US_2023_03_01:254637007
has cross-reference: UMLS_CUI:C0007131
has exact synonym: NSCLC
has exact synonym: Non-small cell lung cancer
has exact synonym: non-small cell lung carcinoma
has OBO namespace: disease_ontology
id: DOID:3908
in subset: DO cancer slim
in subset: NCIthesaurus

tuberculosis
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that is located_in lungs, located_in lymph nodes, located_in pericardium, located_in brain, located_in pleura or located_in gastrointestinal tract, has_material_basis_in Mycobacterium tuberculosis, which is transmitted_by droplets released into the air when an infected person coughs or sneezes.
imported from: doid.owl
has alternative id: DOID:10096
has alternative id: DOID:12688
has alternative id: DOID:12691
has alternative id: DOID:415
has alternative id: DOID:9901
has alternative id: DOID:9902
has cross-reference: GARD:7827
has cross-reference: MESH:D014375
has cross-reference: SNOMEDCT_US_2023_03_01:15202009
has cross-reference: UMLS_CUI:C0041295
has OBO namespace: disease_ontology
id: DOID:399
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: gram-positive bacterial infectious disease

urinary system cancer
type: Class
subclass of: organ system cancer
subclass of: urinary system disease
definition: An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra.
imported from: doid.owl
has cross-reference: ICD10CM:C68.9
has cross-reference: ICD9CM:189.9
has cross-reference: SNOMEDCT_US_2023_03_01:448233000
has cross-reference: UMLS_CUI:C0348371
has OBO namespace: disease_ontology
id: DOID:3996

disease
type: Class
subclass of: disposition
definition: 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.
imported from: doid.owl
has cross-reference: MESH:D004194
has cross-reference: NCI:C2991
has cross-reference: SNOMEDCT_US_2023_03_01:64572001
has cross-reference: UMLS_CUI:C0012634
has OBO namespace: disease_ontology
id: DOID:4
in subset: DO RAD slim
in subset: NCIthesaurus

autoimmune disease
type: Class
subclass of: immune system disease
definition: An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues.
imported from: doid.owl
IEDB alternative term: autoimmune disease
has cross-reference: ICD9CM:720
has cross-reference: MIM:109100
has cross-reference: UMLS_CUI:C0003089
has exact synonym: autoimmune hypersensitivity disease
has exact synonym: hypersensitivity reaction type II disease
has OBO namespace: disease_ontology
id: DOID:417
comment: Xref MGI.

Ebola virus disease
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that is a hemorrhagic fever, has_material_basis_in Bundibugyo virus (Orthoebolavirus bundibugyoense), Sudan ebolavirus (Orthoebolavirus sudanense), Tai Forest ebolavirus (Orthoebolavirus taiense), or Zaire ebolavirus (Orthoebolavirus zairense), which are transmitted_by contact with the body fluids of an infected animal or person, transmitted by contaminated fomites, or transmitted by infected medical equipment. The infection has_symptom fever, has_symptom headache, has_symptom joint pain, has_symptom muscle aches, has_symptom sore throat, has_symptom weakness, has_symptom diarrhea, has_symptom vomiting, has_symptom stomach pain, has_symptom rash, has_symptom red eyes, has_symptom hiccups, and has_symptom internal and external bleeding.
imported from: doid.owl
has cross-reference: GARD:2035
has cross-reference: ICD10CM:A98.4
has cross-reference: MESH:D019142
has cross-reference: NCI:C36171
has cross-reference: SNOMEDCT_US_2023_03_01:123323003
has cross-reference: UMLS_CUI:C0282687
has exact synonym: Ebola
has exact synonym: Ebola disease
has exact synonym: Ebola hemorrhagic fever
has OBO namespace: disease_ontology
id: DOID:4325
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: zoonotic infectious disease

cervical cancer
type: Class
subclass of: uterine cancer
definition: A female reproductive organ cancer that is located_in the cervix.
imported from: doid.owl
has alternative id: DOID:4361
has cross-reference: ICD10CM:C53
has cross-reference: ICD9CM:180
has cross-reference: MESH:D002583
has cross-reference: MIM:603956
has cross-reference: NCI:C2940
has cross-reference: NCI:C9311
has cross-reference: SNOMEDCT_US_2023_03_01:123841004
has cross-reference: SNOMEDCT_US_2023_03_01:254885005
has cross-reference: UMLS_CUI:C0007847
has cross-reference: UMLS_CUI:C0007873
has exact synonym: cervical neoplasm
has exact synonym: cervix cancer
has exact synonym: cervix uteri cancer
has exact synonym: neoplasm of uterine cervix
has exact synonym: tumor of the Cervix Uteri
has exact synonym: uterine cervical neoplasm
has OBO namespace: disease_ontology
id: DOID:4362
in subset: DO CFDE slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

bile duct cancer
type: Class
subclass of: hepatobiliary system cancer
subclass of: hepatobiliary disease
definition: A biliary tract cancer that is located_in the bile duct.
imported from: doid.owl
has alternative id: DOID:10019
has cross-reference: ICD10CM:C24.0
has cross-reference: ICD9CM:156.1
has cross-reference: MESH:D001650
has cross-reference: NCI:C2898
has cross-reference: NCI:C7483
has cross-reference: SNOMEDCT_US_2023_03_01:93790004
has cross-reference: UMLS_CUI:C0005396
has cross-reference: UMLS_CUI:C0153453
has exact synonym: Ca extrahepatic bile ducts
has exact synonym: bile duct tumor
has exact synonym: malignant neoplasm of the extrahepatic bile duct
has OBO namespace: disease_ontology
id: DOID:4606
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

male reproductive system disease
type: Class
subclass of: reproductive system disease
definition: A reproductive system disease that affects male reproductive organs.
imported from: doid.owl
has cross-reference: ICD10CM:N50.9
has cross-reference: ICD9CM:608.9
has cross-reference: MESH:D005832
has cross-reference: SNOMEDCT_US_2023_03_01:64557000
has cross-reference: UMLS_CUI:C0017412
has OBO namespace: disease_ontology
id: DOID:48

bile duct adenocarcinoma
type: Class
subclass of: adenocarcinoma
subclass of: bile duct carcinoma
definition: A bile duct carcinoma that derives_from epithelial cells of glandular origin.
imported from: doid.owl
has cross-reference: NCI:C27813
has cross-reference: SNOMEDCT_US_2023_03_01:70179006
has cross-reference: UMLS_CUI:C1370800
has OBO namespace: disease_ontology
id: DOID:4896
in subset: DO cancer slim
in subset: NCIthesaurus

bile duct carcinoma
type: Class
subclass of: carcinoma
subclass of: bile duct cancer
definition: A bile duct cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
imported from: doid.owl
has cross-reference: MESH:D001650
has cross-reference: NCI:C27814
has cross-reference: SNOMEDCT_US_2023_03_01:70179006
has cross-reference: UMLS_CUI:C0740277
has OBO namespace: disease_ontology
id: DOID:4897
in subset: NCIthesaurus

cholangiocarcinoma
type: Class
subclass of: bile duct adenocarcinoma
definition: A bile duct adenocarcinoma that has_material_basis_in bile duct epithelial cells.
imported from: doid.owl
has alternative id: DOID:5249
has cross-reference: ICD10CM:C22.1
has cross-reference: ICDO:8160/3
has cross-reference: MESH:D018281
has cross-reference: NCI:C4436
has cross-reference: NCI:C8265
has cross-reference: SNOMEDCT_US_2023_03_01:70179006
has cross-reference: UMLS_CUI:C0206698
has cross-reference: UMLS_CUI:C0280725
has exact synonym: adult primary Cholangiocarcinoma
has exact synonym: adult primary cholangiocellular carcinoma
has exact synonym: cholangiosarcoma
has OBO namespace: disease_ontology
id: DOID:4947
in subset: DO cancer slim
in subset: NCIthesaurus

poliomyelitis
type: Class
subclass of: peripheral nervous system disease
subclass of: viral infectious disease
definition: A viral infectious disease that results in destruction located in motor neurons, has_material_basis_in Human poliovirus 1, has_material_basis_in Human poliovirus 2, or has_material_basis_in Human poliovirus 3, which are transmitted by ingestion of food or water contaminated with feces, or transmitted by direct contact with the oral secretions. The infection has symptom fever, has symptom sore throat, has symptom headache, has symptom vomiting, has symptom fatigue, has symptom neck stiffness, has symptom muscle spasms, and has symptom acute flaccid paralysis.
imported from: doid.owl
has cross-reference: GARD:7413
has cross-reference: ICD10CM:A80
has cross-reference: ICD9CM:045
has cross-reference: MESH:D011051
has cross-reference: NCI:C35550
has cross-reference: SNOMEDCT_US_2023_03_01:54839009
has cross-reference: UMLS_CUI:C0032371
has OBO namespace: disease_ontology
id: DOID:4953
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

bone marrow cancer
type: Class
subclass of: hematologic cancer
definition: A hematopoietic cancer that derives_from the blood-forming stem cells of the bone marrow.
imported from: doid.owl
has alternative id: DOID:2356
has alternative id: DOID:2761
has cross-reference: EFO:0004251
has cross-reference: ICD10CM:D47.1
has cross-reference: MESH:D009196
has cross-reference: SNOMEDCT_US_2023_03_01:128925001
has cross-reference: UMLS_CUI:C0027022
has exact synonym: bone Marrow tumor
has exact synonym: bone marrow neoplasm
has exact synonym: malignant bone Marrow tumor
has exact synonym: malignant neoplasm of bone marrow
has OBO namespace: disease_ontology
id: DOID:4960
in subset: DO cancer slim

esophageal cancer
type: Class
subclass of: gastrointestinal system cancer
definition: A gastrointestinal system cancer that is located_in the esophagus.
imported from: doid.owl
has alternative id: DOID:10291
has alternative id: DOID:10292
has alternative id: DOID:10448
has alternative id: DOID:1102
has alternative id: DOID:1104
has cross-reference: GARD:6383
has cross-reference: ICD10CM:C15.3
has cross-reference: ICD10CM:C15.4
has cross-reference: ICD10CM:C15.5
has cross-reference: ICD9CM:150.2
has cross-reference: ICD9CM:150.3
has cross-reference: ICD9CM:150.4
has cross-reference: ICD9CM:150.5
has cross-reference: ICD9CM:150.8
has cross-reference: MESH:D004938
has cross-reference: MIM:133239
has cross-reference: NCI:C3028
has cross-reference: NCI:C3533
has cross-reference: NCI:C3534
has cross-reference: NCI:C3535
has cross-reference: NCI:C4764
has cross-reference: SNOMEDCT_US_2023_03_01:126817006
has cross-reference: SNOMEDCT_US_2023_03_01:187729008
has cross-reference: SNOMEDCT_US_2023_03_01:93656003
has cross-reference: SNOMEDCT_US_2023_03_01:93877002
has cross-reference: SNOMEDCT_US_2023_03_01:93895004
has cross-reference: SNOMEDCT_US_2023_03_01:94119000
has cross-reference: UMLS_CUI:C0014859
has cross-reference: UMLS_CUI:C0153413
has cross-reference: UMLS_CUI:C0153414
has cross-reference: UMLS_CUI:C0153415
has cross-reference: UMLS_CUI:C0153416
has cross-reference: UMLS_CUI:C0496775
has exact synonym: Ca lower third oesophagus
has exact synonym: Ca middle third oesophagus
has exact synonym: esophagus cancer
has exact synonym: malignant neoplasm of distal third of esophagus
has exact synonym: malignant neoplasm of lower third of oesophagus
has exact synonym: malignant neoplasm of middle third of oesophagus
has exact synonym: malignant neoplasm of proximal third of esophagus
has exact synonym: malignant neoplasm of upper third esophagus
has exact synonym: malignant tumor of Distal Third of esophagus
has exact synonym: malignant tumor of Proximal Third of esophagus
has exact synonym: malignant tumor of abdominal esophagus
has exact synonym: malignant tumor of the middle Third of the esophagus
has OBO namespace: disease_ontology
id: DOID:5041
in subset: DO CFDE slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim

human immunodeficiency virus infectious disease
type: Class
subclass of: viral infectious disease
definition: 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.
imported from: doid.owl
has cross-reference: ICD10CM:B20
has cross-reference: ICD9CM:042-042.99
has cross-reference: MESH:D015658
has cross-reference: NCI:C3108
has cross-reference: SNOMEDCT_US_2023_03_01:86406008
has cross-reference: UMLS_CUI:C0019693
has exact synonym: HIV infection
has OBO namespace: disease_ontology
id: DOID:526
in subset: DO infectious disease slim
in subset: NCIthesaurus
in subset: zoonotic infectious disease

intestinal disease
type: Class
subclass of: gastrointestinal system disease
definition: A gastrointestinal system disease that is located_in the intestine.
imported from: doid.owl
has alternative id: DOID:10759
has alternative id: DOID:11222
has alternative id: DOID:11789
has alternative id: DOID:8531
has alternative id: DOID:8558
has alternative id: DOID:8591
has cross-reference: ICD10CM:K63.9
has cross-reference: ICD9CM:569.9
has cross-reference: MESH:D007410
has cross-reference: NCI:C26801
has cross-reference: SNOMEDCT_US_2023_03_01:266483008
has cross-reference: UMLS_CUI:C0021831
has OBO namespace: disease_ontology
id: DOID:5295
in subset: NCIthesaurus

lung small cell carcinoma
type: Class
subclass of: lung carcinoma
definition: A lung carcinoma that has_material_basis_in primitive-appearing cells that are smaller than normal cells and is located_in the lung.
imported from: doid.owl
has alternative id: DOID:0050875
has cross-reference: KEGG:05222
has cross-reference: MESH:D055752
has cross-reference: MIM:182280
has cross-reference: NCI:C4917
has cross-reference: SNOMEDCT_US_2023_03_01:254632001
has cross-reference: UMLS_CUI:C0149925
has OBO namespace: disease_ontology
id: DOID:5409
in subset: DO cancer slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

stomach carcinoma
type: Class
subclass of: stomach cancer
subclass of: carcinoma
definition: A stomach cancer that is located_in the stomach.
imported from: doid.owl
has cross-reference: EFO:0000178
has cross-reference: NCI:C4911
has cross-reference: SNOMEDCT_US_2023_03_01:154446008
has cross-reference: UMLS_CUI:C0699791
has exact synonym: cancer of the stomach
has exact synonym: carcinoma of stomach
has exact synonym: gastric carcinoma
has OBO namespace: disease_ontology
id: DOID:5517
in subset: DO cancer slim
in subset: NCIthesaurus

head and neck squamous cell carcinoma
type: Class
subclass of: head and neck carcinoma
definition: A head and neck carcinoma that has_material_basis_in squamous cells that line the moist, mucosal surfaces inside the head and neck.
imported from: doid.owl
has cross-reference: GARD:8503
has cross-reference: MESH:D000077195
has cross-reference: MIM:275355
has cross-reference: NCI:C34447
has cross-reference: SNOMEDCT_US_2023_03_01:716659002
has cross-reference: UMLS_CUI:C1168401
has exact synonym: carcinoma of the head and neck
has exact synonym: squamous cell carcinoma of the head and neck
has exact synonym: squamous cell carcinomas of head and neck
has OBO namespace: disease_ontology
id: DOID:5520
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

peripheral nervous system disease
type: Class
subclass of: nervous system disease
definition: A nervous system disease that affects the peripheral nervous system.
imported from: doid.owl
has alternative id: DOID:13069
has cross-reference: NCI:C119734
has cross-reference: NCI:C27587
has cross-reference: UMLS_CUI:C0031117
has cross-reference: UMLS_CUI:C1335029
has OBO namespace: disease_ontology
has related synonym: peripheral nerve disease
has related synonym: peripheral neuropathy
id: DOID:574
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: NCIthesaurus

acquired immunodeficiency syndrome
type: Class
subclass of: human immunodeficiency virus infectious disease
definition: A Human immunodeficiency virus infectious disease that results_in reduction in the numbers of CD4-bearing helper T cells below 200 per microliter of blood or 14% of all lymphocytes thereby rendering the subject highly vulnerable to life-threatening infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted_by sexual contact, transmitted_by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted_by congenital method, and transmitted_by contaminated needles. Opportunistic infections are common in people with AIDS.
imported from: doid.owl
has cross-reference: EFO:0000765
has cross-reference: ICD10CM:B20
has cross-reference: MESH:D000163
has cross-reference: NCI:C2851
has cross-reference: SNOMEDCT_US_2023_03_01:62479008
has cross-reference: UMLS_CUI:C0001175
has exact synonym: AIDS
has exact synonym: acquired Immune deficiency
has OBO namespace: disease_ontology
has related synonym: acquired immune deficiency syndrome
id: DOID:635
in subset: DO infectious disease slim
in subset: NCIthesaurus
in subset: zoonotic infectious disease

connective tissue disease
type: Class
subclass of: musculoskeletal system disease
definition: A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
imported from: doid.owl
has cross-reference: MESH:D003240
has cross-reference: NCI:C26729
has cross-reference: SNOMEDCT_US_2023_03_01:201432001
has cross-reference: UMLS_CUI:C0009782
has exact synonym: connective tissue disorder
has exact synonym: disorder of connective tissue
has OBO namespace: disease_ontology
id: DOID:65
in subset: NCIthesaurus

plasma cell neoplasm
type: Class
subclass of: B-cell lymphoma
definition: A mature B-cell neoplasm that is composed of plasma cells.
imported from: doid.owl
has cross-reference: EFO:0000200
has cross-reference: MESH:D010265
has cross-reference: SNOMEDCT_US_2023_03_01:71390001
has cross-reference: UMLS_CUI:C1136084
has exact synonym: Plasma cell dyscrasia
has exact synonym: Plasma cell tumour
has exact synonym: Plasmacytic tumor
has OBO namespace: disease_ontology
id: DOID:6536

hepatocellular carcinoma
type: Class
subclass of: liver carcinoma
definition: A liver carcinoma that has_material_basis_in undifferentiated hepatocytes and located_in the liver.
imported from: doid.owl
has alternative id: DOID:5005
has cross-reference: EFO:0000182
has cross-reference: ICD10CM:C22.0
has cross-reference: ICDO:8170/3
has cross-reference: MESH:D006528
has cross-reference: MIM:114550
has cross-reference: NCI:C3099
has cross-reference: ORDO:88673
has cross-reference: SNOMEDCT_US_2023_03_01:154469006
has cross-reference: UMLS_CUI:C2239176
has exact synonym: Hepatoma
has OBO namespace: disease_ontology
id: DOID:684
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

liver carcinoma
type: Class
subclass of: carcinoma
subclass of: liver cancer
definition: A liver cancer that has_material_basis_in epithelial cells.
imported from: doid.owl
has cross-reference: NCI:C7927
has cross-reference: UMLS_CUI:C0279000
has exact synonym: Liver and Intrahepatic bile duct carcinoma
has OBO namespace: disease_ontology
id: DOID:686
in subset: NCIthesaurus

disease of anatomical entity
type: Class
subclass of: disease
definition: A disease that manifests in a defined anatomical structure.
imported from: doid.owl
has alternative id: DOID:1
has alternative id: DOID:2
has alternative id: DOID:5
has alternative id: DOID:71
has alternative id: DOID:72
has alternative id: DOID:8
has OBO namespace: disease_ontology
id: DOID:7
in subset: DO RAD slim

B-cell lymphoma
type: Class
subclass of: lymphoma
definition: A non-Hodgkin lymphoma that has_material_basis_in B cells.
imported from: doid.owl
has cross-reference: GARD:5877
has cross-reference: MESH:D016393
has cross-reference: NCI:C3457
has cross-reference: SNOMEDCT_US_2023_03_01:109979007
has cross-reference: UMLS_CUI:C0079731
has exact synonym: B-cell lymphocytic neoplasm
has OBO namespace: disease_ontology
id: DOID:707
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus

hematopoietic system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that has_material_basis_in hematopoietic cells.
imported from: doid.owl
has cross-reference: ICD10CM:D75.9
has cross-reference: ICD9CM:289.9
has cross-reference: MESH:D006402
has cross-reference: NCI:C26323
has cross-reference: SNOMEDCT_US_2023_03_01:154785002
has cross-reference: UMLS_CUI:C0018939
has exact synonym: Blood disease
has exact synonym: Blood dyscrasia
has exact synonym: DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS
has exact synonym: Hematological disease
has exact synonym: blood disorder
has exact synonym: disease of haematopoietic system
has exact synonym: disease of hematopoietic system
has exact synonym: haematopoietic system disease
has OBO namespace: disease_ontology
id: DOID:74
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: NCIthesaurus

anthrax disease
type: Class
subclass of: primary bacterial infectious disease
definition: A primary bacterial infectious disease that results_in infection located_in skin, located_in lung lymph nodes or located_in gastrointestinal tract, has_material_basis_in Bacillus anthracis, transmitted_by contact with infected animals or animal products, transmitted_by airborne spores or transmitted_by ingestion of undercooked meat from infected animals and has_symptom skin ulcer, has_symptom nausea, has_symptom poor appetite, has_symptom bloody diarrhea, has_symptom fever or has_symptom shortness of breath.
imported from: doid.owl
has cross-reference: GARD:8157
has cross-reference: ICD10CM:A22
has cross-reference: ICD9CM:022
has cross-reference: MESH:D000881
has cross-reference: NCI:C84565
has cross-reference: SNOMEDCT_US_2023_03_01:154295005
has cross-reference: UMLS_CUI:C0003175
has OBO namespace: disease_ontology
id: DOID:7427
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: gram-positive bacterial infectious disease
in subset: zoonotic infectious disease

neuroblastoma
type: Class
subclass of: peripheral nervous system neoplasm
definition: An autonomic nervous system neoplasm that derives_from immature nerve cells.
imported from: doid.owl
has cross-reference: EFO:0000621
has cross-reference: GARD:7185
has cross-reference: ICDO:9500/3
has cross-reference: MESH:D009447
has cross-reference: NCI:C3270
has cross-reference: ORDO:635
has cross-reference: SNOMEDCT_US_2023_03_01:432328008
has cross-reference: UMLS_CUI:C0027819
has OBO namespace: disease_ontology
id: DOID:769
in subset: DO cancer slim
in subset: DO childhood cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

gastrointestinal system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the gastrointestinal tract.
imported from: doid.owl
has alternative id: DOID:27
has alternative id: DOID:944
has cross-reference: ICD10CM:K92.9
has cross-reference: ICD9CM:520-579.99
has cross-reference: MESH:D004066
has cross-reference: SNOMEDCT_US_2023_03_01:53619000
has cross-reference: UMLS_CUI:C0012242
has exact synonym: GIT disease
has exact synonym: Gastroenteropathy
has exact synonym: alimentary system disease
has exact synonym: digestive system disorder
has exact synonym: gastrointestinal disease
has exact synonym: gastrointestinal disorder
has OBO namespace: disease_ontology
id: DOID:77
in subset: DO AGR slim
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim

influenza
type: Class
subclass of: respiratory system disease
subclass of: viral infectious disease
definition: A viral infectious disease that results in infection, located in respiratory tract, has_material_basis_in Influenzavirus A (Alphainfluenzavirus), has_material_basis_in Influenzavirus B (Betainfluenzavirus), or has_material_basis_in Influenzavirus C (Gammainfluenzavirus), 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.
imported from: doid.owl
has alternative id: DOID:8468
has cross-reference: ICD10CM:J11.1
has cross-reference: ICD9CM:487
has cross-reference: MESH:D007251
has cross-reference: NCI:C53482
has cross-reference: SNOMEDCT_US_2023_03_01:155559006
has cross-reference: UMLS_CUI:C0021400
has exact synonym: Influenza with other manifestations
has exact synonym: flu
has exact synonym: influenza with non-respiratory manifestation
has OBO namespace: disease_ontology
id: DOID:8469
in subset: DO infectious disease slim
in subset: NCIthesaurus

arthritis
type: Class
subclass of: bone disease
definition: A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in joint.
imported from: doid.owl
has cross-reference: ICD10CM:M19.90
has cross-reference: MESH:D001168
has cross-reference: NCI:C2883
has cross-reference: SNOMEDCT_US_2023_03_01:372091005
has cross-reference: UMLS_CUI:C0003864
has exact synonym: Inflammatory disorder of joint
has OBO namespace: disease_ontology
id: DOID:848
in subset: NCIthesaurus

lung disease
type: Class
subclass of: respiratory system disease
definition: A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
imported from: doid.owl
has alternative id: DOID:11894
has alternative id: DOID:11895
has alternative id: DOID:29
has alternative id: DOID:766
has cross-reference: ICD10CM:J98.4
has cross-reference: MESH:D008171
has cross-reference: NCI:C3198
has cross-reference: SNOMEDCT_US_2023_03_01:266374002
has cross-reference: UMLS_CUI:C0024115
has OBO namespace: disease_ontology
id: DOID:850
in subset: DO RAD slim
in subset: NCIthesaurus
comment: Updating out dated CUI and removing lung abscess as a synonym.

herpes zoster
type: Class
subclass of: nervous system disease
subclass of: viral infectious disease
definition: A viral infectious disease that results_in infection located_in nerve fiber, has_material_basis_in Human herpesvirus 3, which reactivates after appearing as chickenpox in childhood. The virus is transmitted_by direct contact with the rash, which can develop into chickenpox in newly-infected individuals. The infection has_symptom rash which is followed by blisters, has_symptom headache, has_symptom fever, has_symptom malaise, has_symptom itching, has_symptom burning pain, and has_symptom paresthesia.
imported from: doid.owl
has alternative id: DOID:8554
has alternative id: DOID:8555
has alternative id: DOID:8772
has alternative id: DOID:8801
has alternative id: DOID:9085
has cross-reference: ICD10CM:B02
has cross-reference: ICD9CM:053
has cross-reference: MESH:D006562
has cross-reference: NCI:C71079
has cross-reference: SNOMEDCT_US_2023_03_01:186514003
has cross-reference: UMLS_CUI:C0019360
has exact synonym: Shingles
has exact synonym: herpes zona
has OBO namespace: disease_ontology
id: DOID:8536
in subset: DO infectious disease slim
in subset: NCIthesaurus

oropharynx cancer
type: Class
subclass of: pharynx cancer
definition: A pharynx cancer that is located_in the oropharynx.
imported from: doid.owl
has alternative id: DOID:8684
has alternative id: DOID:8851
has alternative id: DOID:8949
has alternative id: DOID:9168
has cross-reference: ICD10CM:C10
has cross-reference: ICD10CM:C10.2
has cross-reference: ICD10CM:C10.3
has cross-reference: ICD10CM:C10.8
has cross-reference: ICD9CM:146
has cross-reference: ICD9CM:146.5
has cross-reference: ICD9CM:146.6
has cross-reference: ICD9CM:146.7
has cross-reference: NCI:C7398
has cross-reference: SNOMEDCT_US_2023_03_01:187686007
has cross-reference: SNOMEDCT_US_2023_03_01:93933005
has cross-reference: SNOMEDCT_US_2023_03_01:93971002
has cross-reference: UMLS_CUI:C0153382
has cross-reference: UMLS_CUI:C0153388
has cross-reference: UMLS_CUI:C0153389
has cross-reference: UMLS_CUI:C0153390
has exact synonym: Oropharyngeal carcinoma
has exact synonym: malignant Oropharyngeal tumor
has exact synonym: malignant tumor of oropharynx
has exact synonym: malignant tumour of mesopharynx
has exact synonym: oropharyngeal cancer
has OBO namespace: disease_ontology
id: DOID:8557
in subset: DO cancer slim
in subset: NCIthesaurus

measles
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in infection located_in skin, has_material_basis_in Measles virus, which is transmitted_by contact with oronasal secretions, or semen of an infected person. The infection has_symptom fever, has_symptom cough, has_symptom coryza, has_symptom conjunctivitis, and has_symptom maculopapular, erythematous rash.
imported from: doid.owl
has alternative id: DOID:8621
has alternative id: DOID:8963
has alternative id: DOID:9112
has cross-reference: GARD:3434
has cross-reference: ICD10CM:B05
has cross-reference: ICD9CM:055
has cross-reference: MESH:D008457
has cross-reference: NCI:C96406
has cross-reference: SNOMEDCT_US_2023_03_01:154338006
has cross-reference: UMLS_CUI:C0025007
has exact synonym: morbilli
has OBO namespace: disease_ontology
id: DOID:8622
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

nervous system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
imported from: doid.owl
has cross-reference: ICD10CM:G98
has cross-reference: ICD9CM:349.9
has cross-reference: MESH:D009422
has cross-reference: NCI:C26835
has cross-reference: SNOMEDCT_US_2023_03_01:155262005
has cross-reference: UMLS_CUI:C0027765
has OBO namespace: disease_ontology
id: DOID:863
in subset: DO CFDE slim
in subset: DO GXD slim
in subset: DO MGI slim
in subset: NCIthesaurus

chickenpox
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in infection located_in skin, has_material_basis_in Human herpesvirus 3, which is transmitted_by direct contact with secretions from the rash, or transmitted_by droplet spread of respiratory secretions. The infection has_symptom anorexia, has_symptom myalgia, has_symptom nausea, has_symptom fever, has_symptom headache, has_symptom sore throat, and has_symptom blisters.
imported from: doid.owl
has alternative id: DOID:8658
has alternative id: DOID:8693
has alternative id: DOID:9243
has cross-reference: ICD10CM:B01.9
has cross-reference: ICD9CM:052
has cross-reference: MESH:D002644
has cross-reference: NCI:C97132
has cross-reference: SNOMEDCT_US_2023_03_01:186508005
has cross-reference: UMLS_CUI:C0008049
has exact synonym: varicella
has OBO namespace: disease_ontology
id: DOID:8659
in subset: DO infectious disease slim
in subset: NCIthesaurus

smallpox
type: Class
subclass of: disease of anatomical entity
subclass of: viral infectious disease
definition: A viral infectious disease that results in infection located in skin, has_material_basis_in Variola virus (Orthopoxvirus variola), which is transmitted by droplets from oral, nasal or pharyngeal mucosa, transmitted by contact with the body fluids, or transmitted by fomites. The infection results in formation of lesions, first on the face, hands and forearms and later on the trunk.
imported from: doid.owl
has cross-reference: GARD:7444
has cross-reference: ICD10CM:B03
has cross-reference: ICD9CM:050
has cross-reference: MESH:D012899
has cross-reference: NCI:C35027
has cross-reference: SNOMEDCT_US_2023_03_01:266193008
has cross-reference: UMLS_CUI:C0037354
has exact synonym: Ordinary smallpox
has OBO namespace: disease_ontology
id: DOID:8736
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

bacterial pneumonia
type: Class
subclass of: bacterial infectious disease
subclass of: lung disease
definition: A pneumonia involving inflammation of the lungs caused by bacteria.
imported from: doid.owl
has alternative id: DOID:13815
has cross-reference: ICD10CM:J15.9
has cross-reference: ICD9CM:482.9
has cross-reference: MESH:D018410
has cross-reference: NCI:C26704
has cross-reference: SNOMEDCT_US_2023_03_01:53084003
has cross-reference: UMLS_CUI:C0004626
has exact synonym: Pneumonia due to other gram-negative bacteria
has exact synonym: gram-negative pneumonia
has OBO namespace: disease_ontology
id: DOID:874
in subset: DO infectious disease slim
in subset: GOLD
in subset: NCIthesaurus

rubella
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results_in infection located_in skin, has_material_basis_in Rubella virus (Rubivirus rubellae), which is transmitted_by droplet spread of oronasal secretions from the infected person through coughing and sneezing, and transmitted_by congenital method. The infection has_symptom rash on the face which spreads to the trunk and limbs, has_symptom fever, has_symptom lymphadenopathy, has_symptom joint pains, has_symptom headache, and has_symptom conjunctivitis.
imported from: doid.owl
has alternative id: DOID:11765
has alternative id: DOID:1463
has alternative id: DOID:1464
has alternative id: DOID:8780
has alternative id: DOID:8816
has alternative id: DOID:8909
has alternative id: DOID:9106
has alternative id: DOID:9116
has alternative id: DOID:9162
has alternative id: DOID:9179
has cross-reference: GARD:4742
has cross-reference: ICD10CM:B06.9
has cross-reference: ICD9CM:056
has cross-reference: MESH:D012409
has cross-reference: NCI:C85051
has cross-reference: SNOMEDCT_US_2023_03_01:266192003
has cross-reference: UMLS_CUI:C0035920
has exact synonym: german measles
has OBO namespace: disease_ontology
id: DOID:8781
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

herpes zoster oticus
type: Class
subclass of: poliomyelitis
definition: A viral infectious disease that results_in inflammation located_in facial nerve, which leads to paralysis of one side of the face, has_material_basis_in Human herpesvirus 3, which reactivates after appearing as chickenpox in childhood. The infection has_symptom vesicular rash of the ear or mouth, has_symptom tinnitus, has_symptom vertigo, has_symptom otalgia, and has_symptom headache.
imported from: doid.owl
has cross-reference: GARD:7525
has cross-reference: ICD10CM:B02.21
has cross-reference: ICD9CM:053.11
has cross-reference: MESH:D016697
has cross-reference: NCI:C84763
has cross-reference: SNOMEDCT_US_2023_03_01:21954000
has cross-reference: UMLS_CUI:C0017409
has exact synonym: Geniculate herpes zoster
has exact synonym: Herpes zoster auricularis
has exact synonym: Herpetic geniculate ganglionitis
has exact synonym: Ramsay Hunt syndrome type 2
has exact synonym: Ramsay Hunt syndrome type II
has exact synonym: Ramsey Hunt syndrome
has exact synonym: geniculate neuralgia
has exact synonym: nervus intermedius neuralgia
has OBO namespace: disease_ontology
id: DOID:9210
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

colorectal cancer
type: Class
subclass of: intestinal cancer
definition: A large intestine cancer that is located_in the colon and/or located_in the rectum.
imported from: doid.owl
has cross-reference: ICD10CM:C18.9
has cross-reference: KEGG:05210
has cross-reference: MESH:D015179
has cross-reference: MIM:114500
has cross-reference: NCI:C2956
has cross-reference: NCI:C4978
has cross-reference: SNOMEDCT_US_2023_03_01:126837005
has cross-reference: SNOMEDCT_US_2023_03_01:93854002
has cross-reference: UMLS_CUI:C0009404
has cross-reference: UMLS_CUI:C0346629
has OBO namespace: disease_ontology
id: DOID:9256
in subset: DO CFDE slim
in subset: DO FlyBase slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

nasopharynx carcinoma
type: Class
subclass of: respiratory system cancer
subclass of: pharynx cancer
subclass of: carcinoma
definition: A pharynx cancer that is located in the nasopharynx, the uppermost region of the pharynx or throat, where the nasal passages and auditory tubes join the remainder of the upper respiratory tract.
imported from: doid.owl
has alternative id: DOID:8813
has alternative id: DOID:8814
has alternative id: DOID:9057
has alternative id: DOID:9144
has alternative id: DOID:9197
has alternative id: DOID:9229
has cross-reference: GARD:7163
has cross-reference: ICD10CM:C11
has cross-reference: ICD10CM:C11.0
has cross-reference: ICD10CM:C11.1
has cross-reference: ICD10CM:C11.2
has cross-reference: ICD10CM:C11.3
has cross-reference: ICD9CM:147
has cross-reference: ICD9CM:147.0
has cross-reference: ICD9CM:147.1
has cross-reference: ICD9CM:147.2
has cross-reference: ICD9CM:147.3
has cross-reference: MESH:D009303
has cross-reference: MIM:161550
has cross-reference: MIM:607107
has cross-reference: NCI:C9321
has cross-reference: ORDO:150
has cross-reference: SNOMEDCT_US_2023_03_01:187692001
has cross-reference: SNOMEDCT_US_2023_03_01:187693006
has cross-reference: SNOMEDCT_US_2023_03_01:187700006
has cross-reference: SNOMEDCT_US_2023_03_01:363398003
has cross-reference: SNOMEDCT_US_2023_03_01:93919005
has cross-reference: SNOMEDCT_US_2023_03_01:94078000
has cross-reference: UMLS_CUI:C0153392
has cross-reference: UMLS_CUI:C0153393
has cross-reference: UMLS_CUI:C0153394
has cross-reference: UMLS_CUI:C0153395
has cross-reference: UMLS_CUI:C0153396
has cross-reference: UMLS_CUI:C0238301
has exact synonym: Nasopharyngeal carcinoma
has exact synonym: malignant Nasopharyngeal tumor
has exact synonym: malignant neoplasm of nasopharynx
has exact synonym: nasopharynx cancer
has OBO namespace: disease_ontology
has related synonym: carcinoma of nasopharynx
id: DOID:9261
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

viral infectious disease
type: Class
subclass of: disease by infectious agent
definition: A disease by infectious agent that results in infection, has_material_basis_in Viruses.
imported from: doid.owl
has alternative id: DOID:1329
has cross-reference: ICD10CM:A94
has cross-reference: ICD10CM:B34.9
has cross-reference: ICD9CM:060-066.99
has cross-reference: MESH:D001102
has cross-reference: MESH:D014777
has cross-reference: NCI:C3439
has cross-reference: NCI:C34396
has cross-reference: SNOMEDCT_US_2023_03_01:34014006
has cross-reference: SNOMEDCT_US_2023_03_01:40610006
has cross-reference: UMLS_CUI:C0003723
has cross-reference: UMLS_CUI:C0042769
has exact synonym: Viral Infection
has exact synonym: Viral disease
has exact synonym: virus infection
has OBO namespace: disease_ontology
id: DOID:934
in subset: DO AGR slim
in subset: DO FlyBase slim
in subset: DO infectious disease slim
in subset: NCIthesaurus

diabetes mellitus
type: Class
subclass of: disease
definition: A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.
imported from: doid.owl
has alternative id: DOID:0081062
has cross-reference: ICD10CM:E08-E13
has cross-reference: ICD9CM:250
has cross-reference: MESH:D003920
has cross-reference: NCI:C2985
has cross-reference: SNOMEDCT_US_2023_03_01:267467004
has cross-reference: UMLS_CUI:C0011849
has exact synonym: diabetes
has OBO namespace: disease_ontology
id: DOID:9351
in subset: NCIthesaurus

bacterial meningitis
type: Class
subclass of: bacterial infectious disease
subclass of: central nervous system disease
definition: A meningitis that has_material_basis_in a bacterial infection.
imported from: doid.owl
has cross-reference: GARD:5881
has cross-reference: ICD10CM:G00
has cross-reference: ICD9CM:320
has cross-reference: MESH:D016920
has cross-reference: NCI:C118297
has cross-reference: SNOMEDCT_US_2023_03_01:267680008
has cross-reference: UMLS_CUI:C0085437
has OBO namespace: disease_ontology
id: DOID:9470
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus

multiple myeloma
type: Class
subclass of: bone marrow cancer
definition: A myeloid neoplasm that is located_in the plasma cells in bone marrow.
imported from: doid.owl
has cross-reference: EFO:0001378
has cross-reference: GARD:7108
has cross-reference: ICD10CM:C90.0
has cross-reference: ICD9CM:203.0
has cross-reference: MESH:D009101
has cross-reference: MIM:254500
has cross-reference: NCI:C3242
has cross-reference: ORDO:29073
has cross-reference: SNOMEDCT_US_2023_03_01:94705007
has cross-reference: UMLS_CUI:C0026764
has exact synonym: myeloma
has OBO namespace: disease_ontology
id: DOID:9538
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

yellow fever
type: Class
subclass of: viral infectious disease
definition: A viral infectious disease that results in infection, has_material_basis_in Yellow fever virus (Orthoflavivirus flavi), which is transmitted by Aedes, transmitted by Haemagogus, or transmitted by Sabethes species of mosquitoes. The infection has symptom fever, has symptom muscle pain, has symptom backache, has symptom headache, has symptom shivers, has symptom loss of appetite, has symptom jaundice, and has symptom bleeding from the mouth, nose, eyes or stomach leading to vomitus containing blood.
imported from: doid.owl
has alternative id: DOID:9683
has alternative id: DOID:9684
has cross-reference: GARD:7914
has cross-reference: ICD10CM:A95
has cross-reference: ICD9CM:060
has cross-reference: MESH:D015004
has cross-reference: NCI:C35547
has cross-reference: SNOMEDCT_US_2023_03_01:154345006
has cross-reference: UMLS_CUI:C0043395
has exact synonym: Sylvatic yellow fever
has exact synonym: Yellow fever, sylvan
has exact synonym: jungle yellow fever
has exact synonym: urban yellow fever
has OBO namespace: disease_ontology
id: DOID:9682
in subset: DO infectious disease slim
in subset: DO rare slim
in subset: NCIthesaurus
in subset: zoonotic infectious disease

Hormone
type: Class
subclass of: molecular entity
imported from: fma.owl
has OBO namespace: fma
id: FMA:12278

adaptive immune response
type: Class
subclass of: immune response
definition: 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).
imported from: go.owl
has cross-reference: Wikipedia:Adaptive_immune_system
has exact synonym: acquired immune response
has exact synonym: immune memory response
has OBO namespace: biological_process
id: GO:0002250

mucosal immune response
type: Class
subclass of: immune response
definition: An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract.
imported from: go.owl
has alternative id: GO:0002386
has alternative id: GO:0002422
has narrow synonym: immune response in MALT
has narrow synonym: immune response in mucosal-associated lymphoid tissue
has narrow synonym: immune response in urogenital tract
has OBO namespace: biological_process
id: GO:0002385

immune response
type: Class
subclass of: response to stimulus
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl
has OBO namespace: biological_process
id: GO:0006955
in subset: goslim drosophila

biological_process
type: Class
subclass of: process
definition: 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.
term tracker item: https://github.com/geneontology/go-ontology/issues/24968
imported from: go.owl
created by: jl
creation date: 2012-09-19T15:05:24Z
has alternative id: GO:0000004
has alternative id: GO:0007582
has alternative id: GO:0044699
has cross-reference: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has OBO namespace: biological_process
has related synonym: single organism process
has related synonym: single-organism process
id: GO:0008150
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim pombe
in subset: goslim yeast
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended 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.

immunoglobulin complex
type: Class
subclass of: protein-containing complex
definition: 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.
imported from: go.owl
has narrow synonym: antibody
has OBO namespace: cellular_component
id: GO:0019814
in subset: goslim pir
comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.

protein-containing complex
type: Class
subclass of: material entity
definition: 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.
imported from: go.owl
has alternative id: GO:0043234
has exact synonym: macromolecular complex
has exact synonym: macromolecule complex
has exact synonym: protein containing complex
has narrow synonym: protein complex
has narrow synonym: protein-protein complex
has OBO namespace: cellular_component
id: GO:0032991
in subset: goslim agr
in subset: goslim chembl
in subset: goslim euk cellular processes ribbon
in subset: goslim flybase ribbon
in subset: goslim mouse
in subset: goslim pir
comment: 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.

response to stimulus
type: Class
subclass of: biological_process
definition: 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.
imported from: go.owl
has alternative id: GO:0051869
has exact synonym: physiological response to stimulus
has OBO namespace: biological_process
id: GO:0050896
in subset: gocheck do not annotate
in subset: goslim agr
in subset: goslim flybase ribbon
in subset: goslim mouse
in subset: goslim pir
in subset: goslim prokaryote
in subset: goslim prokaryote ribbon
comment: 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.

IgG immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
definition: 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.
imported from: go.owl
created by: mah
creation date: 2010-03-24T01:44:53Z
has narrow synonym: IgG1
has narrow synonym: IgG2
has narrow synonym: IgG2a
has narrow synonym: IgG2b
has narrow synonym: IgG2c
has narrow synonym: IgG3
has narrow synonym: IgG4
has OBO namespace: cellular_component
id: GO:0071735
comment: Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species.

IgD immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
definition: 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.
imported from: go.owl
created by: mah
creation date: 2010-03-24T01:44:53Z
has OBO namespace: cellular_component
id: GO:0071738
comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available.

IgE immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
definition: 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.
imported from: go.owl
created by: mah
creation date: 2010-03-24T01:44:53Z
has OBO namespace: cellular_component
id: GO:0071742
comment: Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available.

IgA immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
definition: 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.
imported from: go.owl
created by: mah
creation date: 2010-03-24T01:44:53Z
has narrow synonym: IgA1 antibody
has narrow synonym: IgA2 antibody
has OBO namespace: cellular_component
id: GO:0071745
comment: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available.

IgM immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
definition: 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.
imported from: go.owl
created by: mah
creation date: 2010-03-24T01:44:53Z
has OBO namespace: cellular_component
id: GO:0071753
comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available.

conditional specification
type: Class
subclass of: directive information entity
editor preferred term: conditional specification
has curation status: IAO_0000120
definition: A directive information entity that specifies what should happen if the trigger condition is fulfilled.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000349
imported from: iao.owl

measurement unit label
type: Class
subclass of: datum label
editor preferred term: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: IAO_0000125
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 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.
editor note: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
imported from: iao.owl

objective specification
type: Class
subclass of: directive information entity
editor preferred term: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: IAO_0000122
definition: 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.
editor note: 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."
editor note: 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.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative label: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: iao.owl

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: IAO_0000122
definition: A directive information entity that describes an action the bearer will take.
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: iao.owl

datum label
type: Class
subclass of: information content entity
editor preferred term: datum label
has curation status: IAO_0000123
definition: 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
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: GROUP: IAO
curator note: 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.
imported from: iao.owl

journal article
type: Class
subclass of: report
subclass of: publication
editor preferred term: journal article
example of usage: 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.
has curation status: IAO_0000120
definition: A report that is published in a journal.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000159
definition source: group:OBI
imported from: iao.owl

data item
type: Class
subclass of: information content entity
editor preferred term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000125
definition: 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.
editor note: 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.
editor note: 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.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative label: data
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred term: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
definition: A generically dependent continuant that is about some thing.
editor note: 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).
editor note: 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.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: iao.owl

scalar measurement datum
type: Class
subclass of: measurement datum
example of usage: 10 feet. 3 ml.
has curation status: IAO_0000120
definition: A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
imported from: iao.owl

directive information entity
type: Class
subclass of: information content entity
has curation status: IAO_0000122
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 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.
editor note: 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.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
imported from: iao.owl

algorithm
type: Class
subclass of: plan specification
editor preferred term: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: IAO_0000120
definition: 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.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
imported from: iao.owl

curation status specification
type: Class
equivalent class: Class
  one of: IAO_0000002
  one of: IAO_0000120
  one of: IAO_0000121
  one of: IAO_0000122
  one of: IAO_0000123
  one of: IAO_0000124
  one of: IAO_0000125
  one of: IAO_0000423
  one of: IAO_0000428
subclass of: data about an ontology part
editor preferred term: curation status specification
has curation status: IAO_0000125
definition: 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.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

report
type: Class
subclass of: document
editor preferred term: report
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
has curation status: IAO_0000125
definition: 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).
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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
editor note: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition source: GROUP: OBI
definition source: OBI_0000099
imported from: iao.owl

data set
type: Class
subclass of: data item
editor preferred term: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: IAO_0000125
definition: 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.
editor note: 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
editor note: 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.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI
imported from: iao.owl

data about an ontology part
type: Class
subclass of: data item
editor preferred term: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

plan specification
type: Class
subclass of: directive information entity
editor preferred term: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000122
definition: 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.
editor note: 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.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
term editor: Clint Dowland
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: iao.owl
comment: 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

measurement datum
type: Class
subclass of: data item
editor preferred term: measurement datum
example of usage: 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,}.
has curation status: IAO_0000125
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: iao.owl

obsolescence reason specification
type: Class
equivalent class: Class
  one of: IAO_0000103
  one of: IAO_0000226
  one of: IAO_0000227
  one of: IAO_0000228
  one of: IAO_0000229
  one of: OMO_0001000
subclass of: data about an ontology part
editor preferred term: obsolescence reason specification
has curation status: IAO_0000125
definition: 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.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

document
type: Class
subclass of: information content entity
editor preferred term: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: IAO_0000120
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter
imported from: iao.owl

publication
type: Class
subclass of: document
editor preferred term: publication
example of usage: journal article, newspaper story, book, etc.
has curation status: IAO_0000120
definition: A document that is the output of a publishing process.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
term editor: PERSON: Lawrence Hunter
alternative label: published document
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
imported from: iao.owl
comment: Revisit the term in Octorber 2020. Improve the defintion.

denotator type
type: Class
equivalent class: Class
  one of: IAO_0000410
  one of: IAO_0000420
  one of: IAO_0000421
subclass of: data about an ontology part
editor preferred term: denotator type
example of usage: 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.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

identifier
type: Class
subclass of: information content entity
editor preferred term: identifier
definition: An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
term editor: Justin Whorton
term editor: Mathias Brochhausen
alternative label: proper name
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
imported from: iao.owl
creator: Mathias Brochhausen
comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)

ontology module
type: Class
subclass of: data about an ontology part
editor preferred term: ontology module
editor note: 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.
alternative label: ontology file
curator note: 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.

base ontology module
type: Class
subclass of: ontology module
editor preferred term: base ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

editors ontology module
type: Class
subclass of: ontology module
editor preferred term: editors ontology module
definition: 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.
alternative label: source ontology module

main release ontology module
type: Class
subclass of: ontology module
editor preferred term: main release ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

bridge ontology module
type: Class
subclass of: ontology module
editor preferred term: bridge ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

import ontology module
type: Class
subclass of: subset ontology module
editor preferred term: import ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative label: import file

subset ontology module
type: Class
subclass of: ontology module
editor preferred term: subset ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative label: ontology slim
alternative label: subset ontology

curation subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: curation subset ontology module
definition: 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.

analysis subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: analysis ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.

single layer subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: single layer ontology module
definition: 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.
alternative label: ribbon subset

exclusion subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: exclusion subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative label: antislim

external import ontology module
type: Class
subclass of: import ontology module
editor preferred term: external import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative label: external import

species subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: species subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative label: taxon subset

reasoned ontology module
type: Class
subclass of: ontology module
editor preferred term: reasoned ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

generated ontology module
type: Class
subclass of: ontology module
editor preferred term: generated ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

template generated ontology module
type: Class
subclass of: generated ontology module
editor preferred term: template generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
editor preferred term: taxonomic bridge ontology module

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
editor preferred term: ontology module subsetted by expressivity

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: obo basic subset ontology module
definition: 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

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: ontology module subsetted by OWL profile

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
editor preferred term: EL++ ontology module

parasite role
type: Class
subclass of: role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl
comment: In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen.
comment: 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.

definitive host role
type: Class
subclass of: host role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative label: primary host role
imported from: ido.owl
comment: The role is realized in developmental and reproduction processes of the host's partner in symbiosis.

infectious agent vector role
type: Class
subclass of: role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl
comment: The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role.

biological vector of infectious agent role
type: Class
subclass of: infectious agent vector role
definition: An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

pathogenic disposition
type: Class
subclass of: disposition
definition: A disposition to initiate processes that result in a disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative label: pathogenicity
imported from: ido.owl
comment: A pathogenic disposition is realized in processes that create a disorder.
comment: 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.

pathogen
type: Class
subclass of: material entity
definition: A material entity with a pathogenic disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

virulence factor
type: Class
subclass of: molecular entity
definition: A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

infection
type: Class
subclass of: material entity
definition: A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl
comment: The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection.

mesothelioma
type: Class
subclass of: disease of cellular proliferation
definition: A usually malignant and aggressive neoplasm of the mesothelium which is often associated with exposure to asbestos.
imported from: mondo.owl

Rotavirus infection
type: Class
subclass of: disease by infectious agent
definition: Infection with any of the rotaviruses. Specific infections include human infantile diarrhea, neonatal calf diarrhea, and epidemic diarrhea of infant mice.
imported from: mondo.owl

lip and oral cavity carcinoma
type: Class
subclass of: head and neck carcinoma
definition: A carcinoma arising in the lip or oral cavity. Most oral cavity carcinomas are squamous cell carcinomas of the tongue, buccal mucosa, or gums. Less frequent morphologic variants include mucoepidermoid carcinoma and adenocarcinoma. Lip carcinomas are usually basal cell or squamous cell carcinomas.
imported from: mondo.owl

Mus musculus
type: Class
subclass of: Murinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:85055
has cross-reference: GC_ID:1
has exact synonym: house mouse
has exact synonym: mouse
has OBO namespace: ncbi_taxonomy

Rattus
type: Class
subclass of: Murinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: rat
has exact synonym: rats
has OBO namespace: ncbi_taxonomy

Cavia porcellus
type: Class
subclass of: Hystricomorpha
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:84274
has cross-reference: GC_ID:1
has exact synonym: domestic guinea pig
has exact synonym: guinea pig
has OBO namespace: ncbi_taxonomy
has related synonym: Cavia aperea porcellus
has related synonym: Cavia cobaya
has related synonym: Mus porcellus

Chinchillidae
type: Class
subclass of: Hystricomorpha
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has exact synonym: chinchillas
has exact synonym: chinchillas and viscachas
has OBO namespace: ncbi_taxonomy

Viruses
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Vira
has related synonym: Viridae
has related synonym: viruses

Poxviridae
type: Class
subclass of: Pokkesviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Chordopoxvirinae
type: Class
subclass of: Poxviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Orthopoxvirus
type: Class
subclass of: Chordopoxvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Monkeypox virus
type: Class
subclass of: Orthopoxvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:130669
has alternative id: NCBITaxon:130670
has broad synonym: MPXV
has cross-reference: GC_ID:1
has exact synonym: monkey pox virus
has exact synonym: mpox
has exact synonym: mpox virus
has OBO namespace: ncbi_taxonomy

Vaccinia virus
type: Class
subclass of: Orthopoxvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: vaccinia virus VV
has OBO namespace: ncbi_taxonomy

Variola virus
type: Class
subclass of: Orthopoxvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:12871
has cross-reference: GC_ID:1
has exact synonym: small pox virus
has exact synonym: smallpox
has exact synonym: smallpox virus
has exact synonym: variola virus VAR
has OBO namespace: ncbi_taxonomy

Orf virus
type: Class
subclass of: Chordopoxvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Contagious pustular dermatitis virus
has OBO namespace: ncbi_taxonomy

Avipoxvirus
type: Class
subclass of: Chordopoxvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Fowlpox virus
type: Class
subclass of: Avipoxvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: FWPV
has cross-reference: GC_ID:1
has exact synonym: Avipoxvirus clade A1
has exact synonym: Fowlpoxvirus
has exact synonym: fowl poxvirus
has exact synonym: fowlpox virus FP
has exact synonym: fowlpox virus FPV
has OBO namespace: ncbi_taxonomy

Pigeonpox virus
type: Class
subclass of: Avipoxvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Pigeon pox virus
has exact synonym: Pigeon poxvirus
has exact synonym: pigeonpox virus PPV
has OBO namespace: ncbi_taxonomy

H5N1 subtype
type: Class
subclass of: Influenza A virus
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has cross-reference: GC_ID:1
has exact synonym: Avian influenza virus H5N1
has exact synonym: H5N1
has OBO namespace: ncbi_taxonomy

Herpesviridae
type: Class
subclass of: Herpesvirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Alphaherpesvirinae
type: Class
subclass of: Orthoherpesviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has exact synonym: Alphaherpesviruses
has OBO namespace: ncbi_taxonomy

Simplexvirus
type: Class
subclass of: Alphaherpesvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Human alphaherpesvirus 1
type: Class
subclass of: Simplexvirus
imported from: ncbitaxon.owl
has broad synonym: HSV-1
has broad synonym: HSV1
has cross-reference: GC_ID:1
has exact synonym: Herpes simplex virus type 1
has exact synonym: Human herpesvirus type 1
has exact synonym: herpes simplex virus 1 HSV-1
has exact synonym: herpes simplex virus HSV-1
has exact synonym: herpes simplex virus type 1 HSV-1
has exact synonym: herpes simplex virus type 1 HSV1
has exact synonym: herpes simplex virus type-1 HSV-1
has OBO namespace: ncbi_taxonomy
has related synonym: Herpes simplex virus 1
has related synonym: Human herpesvirus 1

Human alphaherpesvirus 2
type: Class
subclass of: Simplexvirus
imported from: ncbitaxon.owl
has broad synonym: HSV2
has cross-reference: GC_ID:1
has exact synonym: Herpes simplex virus (type 2)
has exact synonym: Herpes simplex virus II
has exact synonym: Herpes simplex virus type 2
has exact synonym: Herpes simplex virus type 2 (HSV-2)
has exact synonym: Human herpesvirus 2
has OBO namespace: ncbi_taxonomy
has related synonym: Herpes simplex virus 2
has related synonym: herpes simplex virus type 2 HSV-2

Varicellovirus
type: Class
subclass of: Alphaherpesvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

bovine alphaherpesvirus 1
type: Class
subclass of: Varicellovirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:11265
has alternative id: NCBITaxon:12738
has broad synonym: BoHV-1
has cross-reference: GC_ID:1
has exact synonym: Bovine herpesvirus 1
has exact synonym: Bovine herpesvirus type 1
has exact synonym: Bovine herpesvirus-1
has exact synonym: Bovine rhinotracheitis virus
has exact synonym: bovine herpesvirus 1 BHV 1
has exact synonym: bovine herpesvirus 1 BHV-1
has exact synonym: bovine herpesvirus 1 BHV1
has exact synonym: bovine herpesvirus BHV-1
has exact synonym: bovine herpesvirus type 1 BHV-1
has exact synonym: bovine herpesvirus type-1 BHV-1
has exact synonym: infectious bovine rhinotracheitis virus BHV-1
has OBO namespace: ncbi_taxonomy
has related synonym: Infectious bovine rhinotracheitis virus

Equid alphaherpesvirus 1
type: Class
subclass of: Varicellovirus
imported from: ncbitaxon.owl
has broad synonym: EHV-1
has cross-reference: GC_ID:1
has exact synonym: Equid herpesvirus 1
has exact synonym: Equine herpesvirus 1
has exact synonym: Equine herpesvirus type 1
has exact synonym: Equine herpesvirus-1
has exact synonym: equine abortion virus
has exact synonym: equine herpesvirus 1 EHV-1
has exact synonym: equine herpesvirus type-1
has OBO namespace: ncbi_taxonomy
has related synonym: equine herpesvirus type 1 EHV-1

Felid alphaherpesvirus 1
type: Class
subclass of: Varicellovirus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has exact synonym: Felid herpesvirus 1
has exact synonym: Feline alphaherpesvirus 1
has exact synonym: Feline herpesvirus 1
has exact synonym: Feline herpesvirus type 1
has exact synonym: feline herpesvirus
has exact synonym: feline herpesvirus type 1 FHV-1
has exact synonym: feline herpesvirus-1
has exact synonym: feline herpesvirus-1 FHV-1
has OBO namespace: ncbi_taxonomy

Human alphaherpesvirus 3
type: Class
subclass of: Varicellovirus
imported from: ncbitaxon.owl
has broad synonym: HHV-3
has broad synonym: VZV
has cross-reference: GC_ID:1
has exact synonym: Human herpes virus 3
has exact synonym: Human herpesvirus 3
has exact synonym: Varicella Zoster Virus
has exact synonym: Varicella-zoster virus
has exact synonym: varicella zoster virus VZV
has exact synonym: varicella-zoster virus VZV
has OBO namespace: ncbi_taxonomy

Suid alphaherpesvirus 1
type: Class
subclass of: Varicellovirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:44156
has broad synonym: PRV
has cross-reference: GC_ID:1
has exact synonym: Alphaherpesvirus pseudorabies virus PRV
has exact synonym: Aujeszky's disease virus
has exact synonym: Pseudorabies Virus PRV
has exact synonym: Pseudorabies virus
has exact synonym: Suid herpesvirus 1
has exact synonym: Suid herpesvirus type 1
has OBO namespace: ncbi_taxonomy

Betaherpesvirinae
type: Class
subclass of: Orthoherpesviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has exact synonym: Betaherpesviruses
has OBO namespace: ncbi_taxonomy

Cytomegalovirus
type: Class
subclass of: Betaherpesvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Human betaherpesvirus 5
type: Class
subclass of: Cytomegalovirus
imported from: ncbitaxon.owl
has broad synonym: HHV-5
has cross-reference: GC_ID:1
has exact synonym: Human cytomegalovirus
has exact synonym: Human herpesvirus 5
has exact synonym: human herpesvirus type 5
has OBO namespace: ncbi_taxonomy

Murid betaherpesvirus 1
type: Class
subclass of: Betaherpesvirinae
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has exact synonym: Mouse cytomegalovirus 1
has exact synonym: Murid herpesvirus 1
has exact synonym: Murine cytomegalovirus
has exact synonym: murine cytomegalovirus (MCMV)
has exact synonym: murine cytomegalovirus MCMV
has exact synonym: murine herpesvirus 1
has OBO namespace: ncbi_taxonomy

Gallid alphaherpesvirus 1
type: Class
subclass of: Iltovirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:10342
has alternative id: NCBITaxon:12743
has alternative id: NCBITaxon:46620
has broad synonym: GaHV-1
has broad synonym: ILTV
has cross-reference: GC_ID:1
has exact synonym: Avian infectious laryngotracheitis virus
has exact synonym: Gallid herpesvirus 1
has exact synonym: Gallid herpesvirus type 1
has exact synonym: Laryngotracheitis virus
has exact synonym: infectious laryngotracheitis virus ILTV
has OBO namespace: ncbi_taxonomy
has related synonym: Infectious laryngotracheitis virus

Gallid alphaherpesvirus 2
type: Class
subclass of: Mardivirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:38013
has alternative id: NCBITaxon:39111
has alternative id: NCBITaxon:43684
has broad synonym: GaHV-2
has broad synonym: MDV1
has cross-reference: GC_ID:1
has exact synonym: Gallid herpesvirus 2
has exact synonym: Gallid herpesvirus type 2
has exact synonym: Marek disease virus
has exact synonym: Marek disease virus type 1
has exact synonym: Marek's disease herpesvirus
has exact synonym: Marek's disease herpesvirus 1
has exact synonym: Marek's disease virus
has exact synonym: Marek's disease virus (MDV)
has exact synonym: Marek's disease virus MDV
has exact synonym: Marek's disease virus MDV1
has exact synonym: Marek's disease virus serotype 1 MDV-1
has exact synonym: Marek's disease virus type 1 MDV1
has exact synonym: Mareks disease virus
has OBO namespace: ncbi_taxonomy
has related synonym: Marek's disease virus type 1

Orthohepadnavirus
type: Class
subclass of: Revtraviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: mammalian hepatitis B-type viruses
has OBO namespace: ncbi_taxonomy

Hepatitis B virus
type: Class
subclass of: Orthohepadnavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: HBV
has cross-reference: GC_ID:1
has exact synonym: Human hepatitis B virus
has exact synonym: hepatitis B virus (HBV)
has exact synonym: hepatitis B virus HBV
has exact synonym: hepatitis B virus, HBV
has exact synonym: human hepatitis B virus HBV
has OBO namespace: ncbi_taxonomy

anatid alphaherpesvirus 1
type: Class
subclass of: Mardivirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:72150
has cross-reference: GC_ID:1
has exact synonym: Anatid Herpes virus-1
has exact synonym: Anatid herpesvirus 1
has exact synonym: Duck enteritis virus
has exact synonym: Duck plague virus
has OBO namespace: ncbi_taxonomy

unidentified baculovirus
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Baculovirus
has exact synonym: Baculovirus sp.
has OBO namespace: ncbi_taxonomy

African swine fever virus
type: Class
subclass of: Pokkesviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: ASFV
has cross-reference: GC_ID:1
has exact synonym: African swine fever virus ASF
has exact synonym: African swine fever virus ASFV
has exact synonym: African swine fever virus, ASFV
has OBO namespace: ncbi_taxonomy

Adenoviridae
type: Class
subclass of: Bamfordvirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Mastadenovirus
type: Class
subclass of: Adenoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Canine adenovirus 1
type: Class
subclass of: Canine mastadenovirus A
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has alternative id: NCBITaxon:12607
has cross-reference: GC_ID:1
has exact synonym: Canine adenovirus type 1
has exact synonym: Canine adenovirus type 1 Cav-1
has exact synonym: Mastadenovirus c1
has exact synonym: Mastadenovirus can1
has exact synonym: canine adenovirus type 1 Can1
has exact synonym: dog adenovirus 1
has OBO namespace: ncbi_taxonomy

Canine adenovirus 2
type: Class
subclass of: Canine mastadenovirus A
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has cross-reference: GC_ID:1
has exact synonym: Canine adenovirus type 2
has exact synonym: Canine adenovirus type 2 Cav-1
has exact synonym: Mastadenovirus c2
has exact synonym: Mastadenovirus can2
has exact synonym: dog adenovirus 2
has OBO namespace: ncbi_taxonomy

unidentified adenovirus
type: Class
subclass of: Mastadenovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Adenovirus
has OBO namespace: ncbi_taxonomy

Canine mastadenovirus A
type: Class
subclass of: Mastadenovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Canine adenovirus
has exact synonym: Canine adenovirus A
has OBO namespace: ncbi_taxonomy

Human papillomavirus
type: Class
subclass of: unclassified Papillomaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Human Papilloma Virus
has exact synonym: human papillomavirus HPV
has OBO namespace: ncbi_taxonomy

Bovine papillomavirus
type: Class
subclass of: unclassified Papillomaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Clostridium perfringens D
type: Class
subclass of: Clostridium perfringens
imported from: ncbitaxon.owl
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Clostridium perfringens (type D)

Feline panleukopenia virus
type: Class
subclass of: Protoparvovirus carnivoran1
imported from: ncbitaxon.owl
has broad synonym: FPLV
has cross-reference: GC_ID:1
has exact synonym: Feline panleucopenia virus
has exact synonym: Feline panleukopaenia virus
has OBO namespace: ncbi_taxonomy

Feline panleukopenia virus (strain 193)
type: Class
subclass of: Feline panleukopenia virus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Canine parvovirus
type: Class
subclass of: Protoparvovirus carnivoran1
imported from: ncbitaxon.owl
has broad synonym: CPV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Mink enteritis virus
type: Class
subclass of: Feline panleukopenia virus
imported from: ncbitaxon.owl
has broad synonym: MEV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Porcine parvovirus
type: Class
subclass of: Protoparvovirus
imported from: ncbitaxon.owl
has broad synonym: PPV
has cross-reference: GC_ID:1
has exact synonym: porcine parvovirus PPV
has OBO namespace: ncbi_taxonomy

Orbivirus
type: Class
subclass of: Sedoreoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Orbiviridae
has exact synonym: Orbiviruses
has OBO namespace: ncbi_taxonomy

Rotavirus
type: Class
subclass of: Sedoreoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Rotaviruses
has OBO namespace: ncbi_taxonomy

Porcine rotavirus
type: Class
subclass of: Rotavirus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Bovine rotavirus
type: Class
subclass of: Rotavirus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has exact synonym: bovine rotavirus BRV
has OBO namespace: ncbi_taxonomy

Equine rotavirus
type: Class
subclass of: Rotavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Birnaviridae
type: Class
subclass of: Orthornavirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Infectious bursal disease virus
type: Class
subclass of: Birnaviridae
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:12740
has broad synonym: IBDV
has cross-reference: GC_ID:1
has exact synonym: Avian infectious bursal disease virus
has exact synonym: Gumboro virus
has exact synonym: Infectious bursal disease virus of chickens
has exact synonym: infectious bursal disease virus IBDV
has OBO namespace: ncbi_taxonomy

Infectious pancreatic necrosis virus
type: Class
subclass of: Birnaviridae
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:12744
has broad synonym: IPNV
has cross-reference: GC_ID:1
has exact synonym: infectious pancreatic necrosis virus IPNV
has OBO namespace: ncbi_taxonomy

Alphavirus
type: Class
subclass of: Alsuviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Alphaviridae
has exact synonym: arboviruses group A
has OBO namespace: ncbi_taxonomy

Eastern equine encephalitis virus
type: Class
subclass of: Alphavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Eastern equine encephalomyelitis virus
has exact synonym: eastern equine encephalomyelitis EEE
has exact synonym: eastern equine encephalomyelitis virus EEEV
has OBO namespace: ncbi_taxonomy

Sindbis virus
type: Class
subclass of: Alphavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Venezuelan equine encephalitis virus
type: Class
subclass of: Alphavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: VEE
has broad synonym: VEEV
has cross-reference: GC_ID:1
has exact synonym: Venezuelan equine encephalitis VEE
has exact synonym: Venezuelan equine encephalitis virus VEE
has exact synonym: Venezuelan equine encephalomyelitis virus
has OBO namespace: ncbi_taxonomy

Western equine encephalitis virus
type: Class
subclass of: Alphavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Western equine encephalomyelitis virus

Rubivirus
type: Class
subclass of: Hepelivirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Rubella virus
type: Class
subclass of: Rubivirus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Equine arteritis virus
type: Class
subclass of: Arteriviridae
imported from: ncbitaxon.owl
has broad synonym: EAV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Flaviviridae
type: Class
subclass of: Kitrinoviricota
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has exact synonym: Flavivirus (arbovirus group B)
has OBO namespace: ncbi_taxonomy

Flavivirus
type: Class
subclass of: Flaviviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: arboviruses group B
has OBO namespace: ncbi_taxonomy

Japanese encephalitis virus
type: Class
subclass of: Orthoflavivirus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has exact synonym: Japanese encephalitis (JE) virus
has exact synonym: Japanese encephalitis virus JE
has exact synonym: Japanese encephalitis virus JEV
has OBO namespace: ncbi_taxonomy

West Nile virus
type: Class
subclass of: Orthoflavivirus
imported from: ncbitaxon.owl
has broad synonym: WNV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Tick-borne encephalitis virus
type: Class
subclass of: Orthoflavivirus
imported from: ncbitaxon.owl
has broad synonym: TBEV
has cross-reference: GC_ID:1
has exact synonym: FSME virus
has exact synonym: Tick born encephalitis virus
has exact synonym: tick-borne encephalitis virus TBE virus
has exact synonym: tick-borne encephalitis virus TBEV
has OBO namespace: ncbi_taxonomy

Yellow fever virus
type: Class
subclass of: Orthoflavivirus
imported from: ncbitaxon.owl
has broad synonym: YFV
has cross-reference: GC_ID:1
has exact synonym: Flavivirus febricis
has exact synonym: yellow fever virus YFV
has OBO namespace: ncbi_taxonomy

Pestivirus
type: Class
subclass of: Flaviviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has cross-reference: PMID:12832207
has cross-reference: PMID:7747470
has OBO namespace: ncbi_taxonomy

Classical swine fever virus
type: Class
subclass of: Pestivirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:12625
has alternative id: NCBITaxon:54314
has cross-reference: GC_ID:1
has cross-reference: PMID:7747470
has exact synonym: Hog cholera virus
has exact synonym: Pestivirus type 2
has exact synonym: classical swine fever virus CSFV
has exact synonym: swine fever virus
has OBO namespace: ncbi_taxonomy

Bovine viral diarrhea virus 1
type: Class
subclass of: Pestivirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:121864
has broad synonym: BVDV
has broad synonym: BVDV-1
has cross-reference: GC_ID:1
has cross-reference: PMID:7747470
has exact synonym: Bovine viral diarrhea virus
has exact synonym: Bovine viral diarrhea virus type 1
has exact synonym: Bovine viral diarrhea virus-1
has exact synonym: Mucosal disease virus
has exact synonym: Pestivirus type 1
has exact synonym: bovine viral diarrhea virus BVDV
has exact synonym: bovine viral diarrhea virus type I
has OBO namespace: ncbi_taxonomy

Porphyromonas gulae
type: Class
subclass of: Porphyromonas
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:11411686
has cross-reference: PMID:28066339
has OBO namespace: ncbi_taxonomy

Coronaviridae
type: Class
subclass of: Nidovirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Infectious bronchitis virus
type: Class
subclass of: Orthocoronavirinae
imported from: ncbitaxon.owl
has broad synonym: IBV
has cross-reference: GC_ID:1
has exact synonym: Avian infectious bronchitis virus
has exact synonym: avian infectious bronchitis coronavirus IBV
has exact synonym: avian infectious bronchitis virus IBV
has exact synonym: avian infectious bronchitis virus, IBV
has exact synonym: infectious bronchitis virus IBV
has OBO namespace: ncbi_taxonomy

Bovine coronavirus
type: Class
subclass of: Betacoronavirus
imported from: ncbitaxon.owl
has broad synonym: BCV
has broad synonym: BECV
has cross-reference: GC_ID:1
has exact synonym: Bovine enteritic coronavirus
has exact synonym: Bovine enteritic coronavirus BECV
has exact synonym: bovine coronavirus BCV
has exact synonym: bovine enteric coronavirus
has exact synonym: calf diarrheal coronavirus
has exact synonym: neonatal calf diarrhea virus
has OBO namespace: ncbi_taxonomy

Feline infectious peritonitis virus
type: Class
subclass of: Alphacoronavirus 1
imported from: ncbitaxon.owl
has broad synonym: FIPV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Transmissible gastroenteritis virus
type: Class
subclass of: Alphacoronavirus 1
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:12859
has broad synonym: TGEV
has cross-reference: GC_ID:1
has exact synonym: Porcine transmissable gastroenteritis coronavirus
has exact synonym: Porcine transmissible gastroenteritis coronavirus
has exact synonym: porcine transmissible gastroenteritis virus
has exact synonym: transmissible gastroenteritis coronavirus
has exact synonym: transmissible gastroenteritis virus TGEV
has OBO namespace: ncbi_taxonomy

Canine coronavirus
type: Class
subclass of: Alphacoronavirus 1
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has exact synonym: Canine enteric coronavirus
has exact synonym: canine coronavirus CCV
has OBO namespace: ncbi_taxonomy

Mononegavirales
type: Class
subclass of: Negarnaviricota
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has exact synonym: negative-sense genome single-stranded RNA viruses
has OBO namespace: ncbi_taxonomy

Paramyxoviridae
type: Class
subclass of: Mononegavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Human respirovirus 3
type: Class
subclass of: Respirovirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:11202
has broad synonym: HPIV-3
has broad synonym: HPIV3
has cross-reference: GC_ID:1
has exact synonym: Human parainfluenza 3 virus
has exact synonym: Human parainfluenza virus 3
has exact synonym: Human parainfluenza virus type 3
has exact synonym: Parainfluenza virus type 3
has exact synonym: human parainfluenza virus 3 HPIV3
has exact synonym: human parainfluenza virus type 3 PIV3
has exact synonym: parainfluenza virus type 3 PIV-3
has OBO namespace: ncbi_taxonomy
has related synonym: human parainfluenza virus

Morbillivirus
type: Class
subclass of: Orthoparamyxovirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Morbilliviruses
has OBO namespace: ncbi_taxonomy

Measles morbillivirus
type: Class
subclass of: Morbillivirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:11230
has cross-reference: GC_ID:1
has exact synonym: Cell-associated subacute sclerosing panencephalitis
has exact synonym: Measles virus
has exact synonym: Subacute sclerosing panencephalitis virus
has exact synonym: measles virus MV
has exact synonym: rougeole virus
has exact synonym: rubeola virus
has exact synonym: subacute sclerose panencephalitis virus
has exact synonym: subacute sclerosing panencephalitis virus, SSPEV
has OBO namespace: ncbi_taxonomy

Rinderpest morbillivirus
type: Class
subclass of: Morbillivirus
imported from: ncbitaxon.owl
has broad synonym: RDV
has cross-reference: GC_ID:1
has exact synonym: Rinderpest virus
has exact synonym: rinderpest virus RPV
has exact synonym: rinderpest virus RV
has OBO namespace: ncbi_taxonomy

Pneumoviridae
type: Class
subclass of: Mononegavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has exact synonym: Pneumovirinae
has OBO namespace: ncbi_taxonomy

Bovine orthopneumovirus
type: Class
subclass of: Orthopneumovirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:12604
has broad synonym: BRS
has broad synonym: BRSV
has cross-reference: GC_ID:1
has exact synonym: bovine RSV
has exact synonym: bovine respiratory syncytial virus BRSV
has OBO namespace: ncbi_taxonomy

human respiratory syncytial virus
type: Class
subclass of: Orthopneumovirus
imported from: ncbitaxon.owl
has broad synonym: HRSV
has cross-reference: GC_ID:1
has exact synonym: Human orthopneumovirus
has exact synonym: human RSV
has OBO namespace: ncbi_taxonomy

Filoviridae
type: Class
subclass of: Mononegavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has alternative id: NCBITaxon:11267
has cross-reference: GC_ID:1
has exact synonym: Filovirus
has OBO namespace: ncbi_taxonomy

Rhabdoviridae
type: Class
subclass of: Mononegavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has cross-reference: PMID:16186241
has OBO namespace: ncbi_taxonomy

Lyssavirus
type: Class
subclass of: Rhabdoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Viral hemorrhagic septicemia virus
type: Class
subclass of: Novirhabdovirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:12873
has alternative id: NCBITaxon:12874
has broad synonym: VHSV
has cross-reference: GC_ID:1
has exact synonym: Haemorrhagic septicemia virus
has exact synonym: Hemorrhagic septicemia virus
has exact synonym: Viral haemorrhagic septicaemia virus
has exact synonym: hemorragic septicemy virus of fish
has exact synonym: viral haemorrhagic scepticaemia virus VHS
has exact synonym: viral haemorrhagic septicaemia virus VHSV
has exact synonym: viral hemorrhagic septicemia virus VHSV
has OBO namespace: ncbi_taxonomy

Infectious hematopoietic necrosis virus
type: Class
subclass of: Novirhabdovirus
imported from: ncbitaxon.owl
has broad synonym: IHNV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Lyssavirus rabies
type: Class
subclass of: Lyssavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Rabies lyssavirus
has exact synonym: Rabies virus
has OBO namespace: ncbi_taxonomy

Orthomyxoviridae
type: Class
subclass of: Polyploviricotina
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

unidentified influenza virus
type: Class
subclass of: unclassified Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Influenza virus
has exact synonym: Influenza virus sp.
has exact synonym: Influenzavirus
has exact synonym: avian influenza virus
has OBO namespace: ncbi_taxonomy

Thogotovirus dhoriense
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Dhori thogotovirus
has exact synonym: Dhori virus
has exact synonym: Tick-borne virus
has OBO namespace: ncbi_taxonomy

Influenza A virus
type: Class
subclass of: Alphainfluenzavirus
imported from: ncbitaxon.owl
has broad synonym: FLUAV
has cross-reference: GC_ID:1
has exact synonym: Human Influenza A Virus
has exact synonym: Influenza virus type A
has exact synonym: influenza A virus
has OBO namespace: ncbi_taxonomy

H1N1 subtype
type: Class
subclass of: Influenza A virus
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has cross-reference: GC_ID:1
has exact synonym: H1N1
has OBO namespace: ncbi_taxonomy

Influenza B virus
type: Class
subclass of: Betainfluenzavirus
imported from: ncbitaxon.owl
has broad synonym: FLUBV
has cross-reference: GC_ID:1
has exact synonym: Influenza virus type B
has OBO namespace: ncbi_taxonomy

Rift Valley fever virus
type: Class
subclass of: Bunyavirales
imported from: ncbitaxon.owl
has broad synonym: RVFV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Reticuloendotheliosis virus
type: Class
subclass of: Gammaretrovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11835
has alternative id: NCBITaxon:11872
has alternative id: NCBITaxon:36380
has cross-reference: GC_ID:1
has exact synonym: Avian reticuloendotheliosis virus
has exact synonym: reticuloendotheliosis virus A REV-A
has exact synonym: reticuloendotheliosis virus REV-A
has OBO namespace: ncbi_taxonomy

Lentivirus
type: Class
subclass of: Orthoretrovirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Lentivirinae
has OBO namespace: ncbi_taxonomy

Feline immunodeficiency virus
type: Class
subclass of: Lentivirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: FIV
has cross-reference: GC_ID:1
has exact synonym: feline immunodeficiency virus FIV
has OBO namespace: ncbi_taxonomy

Simian immunodeficiency virus
type: Class
subclass of: Lentivirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11677
has alternative id: NCBITaxon:11739
has alternative id: NCBITaxon:11740
has broad synonym: CIV
has broad synonym: SIV
has cross-reference: GC_ID:1
has exact synonym: Chimpanzee immunodeficiency virus
has exact synonym: Chimpanzee immunodeficiency virus (SIV(CPZ))
has exact synonym: Simian immunodeficiency virus SIVcpz
has exact synonym: simian immunodeficiency virus SIV
has exact synonym: simian immunodeficiency virus, SIV
has exact synonym: simian immunodeficiency viruses SIV
has OBO namespace: ncbi_taxonomy

Myxini
type: Class
subclass of: Vertebrata <vertebrates>
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has exact synonym: fish
has exact synonym: fishes
has OBO namespace: ncbi_taxonomy
has related synonym: Agnatha
has related synonym: Hyperotreti

Euteleostomi
type: Class
subclass of: Vertebrata <vertebrates>
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has alternative id: NCBITaxon:40673
has cross-reference: GC_ID:1
has exact synonym: bony vertebrates
has OBO namespace: ncbi_taxonomy

Feline leukemia virus
type: Class
subclass of: Gammaretrovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11920
has cross-reference: GC_ID:1
has exact synonym: Feline leukemia provirus
has exact synonym: feline leukemia virus FeLV
has OBO namespace: ncbi_taxonomy

Bovine leukemia virus
type: Class
subclass of: Orthoretrovirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: BLV
has cross-reference: GC_ID:1
has exact synonym: bovine leukemia virus BLV
has exact synonym: bovine leukemia virus, BLV
has OBO namespace: ncbi_taxonomy

Enoplea
type: Class
subclass of: Ecdysozoa
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

H3N2 subtype
type: Class
subclass of: Influenza A virus
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has cross-reference: GC_ID:1
has exact synonym: H3N2
has OBO namespace: ncbi_taxonomy

Caliciviridae
type: Class
subclass of: Picornavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Rabbit hemorrhagic disease virus
type: Class
subclass of: Caliciviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:12806
has alternative id: NCBITaxon:31701
has broad synonym: RHDV
has cross-reference: GC_ID:1
has exact synonym: Rabbit haemorrhagic disease virus
has exact synonym: rabbit hemorrhagic disease virus RHDV
has OBO namespace: ncbi_taxonomy

Feline calicivirus
type: Class
subclass of: Caliciviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: FCV
has cross-reference: GC_ID:1
has exact synonym: Feline vesivirus
has exact synonym: feline calicivirus FCV
has OBO namespace: ncbi_taxonomy

Picornaviridae
type: Class
subclass of: Picornavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Picornavirus

Enterovirus
type: Class
subclass of: Picornaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:12128
has cross-reference: GC_ID:1
has exact synonym: Enteroviruses
has OBO namespace: ncbi_taxonomy

Coxsackievirus
type: Class
subclass of: Enterovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Ecdysozoa
type: Class
subclass of: Protostomia
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Poliovirus 1
type: Class
subclass of: Enterovirus C
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has broad synonym: HPV-1
has broad synonym: PV1
has cross-reference: GC_ID:1
has exact synonym: Human poliovirus 1
has exact synonym: Human poliovirus type 1
has exact synonym: Polio virus 1
has exact synonym: Poliovirus type 1
has exact synonym: poliovirus type 1 PV1
has OBO namespace: ncbi_taxonomy

Poliovirus 2
type: Class
subclass of: Enterovirus C
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has broad synonym: HPV-2
has cross-reference: GC_ID:1
has exact synonym: Human Poliovirus type 2
has exact synonym: Human poliovirus 2
has exact synonym: Poliovirus type 2
has OBO namespace: ncbi_taxonomy

Poliovirus 3
type: Class
subclass of: Enterovirus C
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has broad synonym: HPV-3
has cross-reference: GC_ID:1
has exact synonym: Human poliovirus 3
has exact synonym: Human poliovirus type 3
has exact synonym: Polio virus 3
has OBO namespace: ncbi_taxonomy
has related synonym: Poliovirus serotype 3
has related synonym: Poliovirus type 3

Hepatovirus
type: Class
subclass of: Heptrevirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Hepatovirus A
type: Class
subclass of: Hepatovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: HAV
has cross-reference: GC_ID:1
has exact synonym: Hepatitis A virus
has OBO namespace: ncbi_taxonomy

Foot-and-mouth disease virus
type: Class
subclass of: Picornaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: FMDV
has cross-reference: GC_ID:1
has exact synonym: Foot and mouth disease virus
has exact synonym: foot and mouth disease virus FMDV
has exact synonym: foot-and-mouth disease virus FMDV
has OBO namespace: ncbi_taxonomy

Pseudomonadota
type: Class
subclass of: Pseudomonadati
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has cross-reference: GC_ID:11
has cross-reference: PMID:11321122
has cross-reference: PMID:11837318
has exact synonym: purple photosynthetic bacteria and relatives
has OBO namespace: ncbi_taxonomy
has related synonym: "Alphaproteobacteriota" Whitman et al. 2018
has related synonym: Alphaproteobacteriota
has related synonym: Proteobacteria
has related synonym: Proteobacteriota
has related synonym: proteobacteria

Cowpea mosaic virus
type: Class
subclass of: Picornavirales
imported from: ncbitaxon.owl
has broad synonym: CPMV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Gammaproteobacteria
type: Class
subclass of: Pseudomonadota
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:11
has cross-reference: PMID:23334881
has OBO namespace: ncbi_taxonomy
has related synonym: Proteobacteria gamma subdivision
has related synonym: Pseudomonadia
has related synonym: Purple bacteria, gamma subdivision
has related synonym: g-proteobacteria
has related synonym: gamma proteobacteria
has related synonym: gamma subdivision
has related synonym: gamma subgroup

Piscirickettsia salmonis
type: Class
subclass of: Thiotrichales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:1371057
has OBO namespace: ncbi_taxonomy

Bacillota
type: Class
subclass of: Bacillati
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has cross-reference: GC_ID:11
has cross-reference: PMID:10555317
has cross-reference: PMID:11034484
has cross-reference: PMID:11542017
has cross-reference: PMID:15143038
has cross-reference: PMID:25403554
has cross-reference: PMID:37409558
has cross-reference: PMID:38376502
has exact synonym: low G+C Gram-positive bacteria
has exact synonym: low GC Gram+
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillaeota
has related synonym: Bacillota corrig. Gibbons and Murray 2021
has related synonym: Bacillus/Clostridium group
has related synonym: Clostridium group firmicutes
has related synonym: Low G+C firmicutes
has related synonym: clostridial firmicutes
has related synonym: firmicutes

Borna disease virus
type: Class
subclass of: Mononegavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: BDV
has cross-reference: GC_ID:1
has cross-reference: PMID:25449305
has exact synonym: Borna disease virus BDV
has OBO namespace: ncbi_taxonomy

Hepatitis delta virus
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:12682
has broad synonym: HDV
has cross-reference: GC_ID:1
has exact synonym: Hepatitis D virus
has exact synonym: hepatitis delta virus HDV
has OBO namespace: ncbi_taxonomy

Chicken anemia virus
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has broad synonym: CAV
has cross-reference: GC_ID:1
has exact synonym: Chicken infectious anemia virus
has exact synonym: chicken anaemia agent CAA
has exact synonym: chicken anemia virus CAV
has exact synonym: chicken anemia virus, CAV
has OBO namespace: ncbi_taxonomy
has related synonym: chicken anaemia agent virus CAA

Dengue virus
type: Class
subclass of: Orthoflavivirus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Human immunodeficiency virus
type: Class
subclass of: Lentivirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: HIV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: AIDS virus

Staphylococcus
type: Class
subclass of: Bacillales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:10319469
has cross-reference: PMID:10319495
has cross-reference: PMID:10425778
has cross-reference: PMID:10758876
has cross-reference: PMID:12656157
has cross-reference: PMID:17220435
has cross-reference: PMID:9734063
has OBO namespace: ncbi_taxonomy
has related synonym: Aurococcus

Staphylococcus aureus
type: Class
subclass of: Staphylococcus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:325213
has alternative id: NCBITaxon:46170
has alternative id: NCBITaxon:72759
has cross-reference: GC_ID:11
has cross-reference: PMID:31023808
has cross-reference: PMID:8573498
has OBO namespace: ncbi_taxonomy
has related synonym: Micrococcus aureus
has related synonym: Micrococcus pyogenes
has related synonym: Staphlococcus pyogenes citreus
has related synonym: Staphylococcus aureus subsp. anaerobius
has related synonym: Staphylococcus pyogenes aureus

Respiratory syncytial virus
type: Class
subclass of: Bovine orthopneumovirus
imported from: ncbitaxon.owl
has broad synonym: RSV
has cross-reference: GC_ID:1
has exact synonym: respiratory syncytial virus RS
has exact synonym: respiratory syncytial virus RS virus
has exact synonym: respiratory syncytial virus RSV
has OBO namespace: ncbi_taxonomy

Swine influenza virus
type: Class
subclass of: unclassified Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Streptococcus
type: Class
subclass of: Bacilli
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:10555340
has cross-reference: PMID:14657115
has cross-reference: PMID:1720654
has cross-reference: PMID:19620365
has cross-reference: PMID:19880633
has cross-reference: PMID:7537076
has cross-reference: PMID:8995803
has OBO namespace: ncbi_taxonomy

Streptococcus suis
type: Class
subclass of: Streptococcus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:23245487
has cross-reference: PMID:5220563
has cross-reference: PMID:9731300
has cross-reference: PMID:9734065
has OBO namespace: ncbi_taxonomy

Streptococcus agalactiae
type: Class
subclass of: Streptococcus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:76757
has cross-reference: GC_ID:11
has cross-reference: PMID:15774692
has cross-reference: PMID:8995807
has OBO namespace: ncbi_taxonomy
has related synonym: Streptoccocus de la mammite
has related synonym: Streptococcus agalactiae contagiosae
has related synonym: Streptococcus difficile
has related synonym: Streptococcus difficilis
has related synonym: Streptococcus mastitidis

Streptococcus pneumoniae
type: Class
subclass of: Streptococcus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Diplococcus pneumoniae
has related synonym: Micrococcus pneumoniae

Streptococcus pyogenes
type: Class
subclass of: Streptococcus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Micrococcus scarlatinae
has related synonym: Streptococcus erysipelatos
has related synonym: Streptococcus hemolyticus
has related synonym: Streptococcus scarlatinae

Middle East respiratory syndrome-related coronavirus
type: Class
subclass of: Betacoronavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: MERS
has broad synonym: MERS-CoV
has cross-reference: GC_ID:1
has exact synonym: MERS coronavirus
has exact synonym: MERS virus
has exact synonym: Middle East Respiratory Syndrome Coronavirus (MERS-CoV)
has exact synonym: Middle East respiratory syndrome coronavirus
has OBO namespace: ncbi_taxonomy

Streptococcus equi
type: Class
subclass of: Streptococcus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Dicentrarchus
type: Class
subclass of: Euteleosteomorpha
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Dicentrarchus labrax
type: Class
subclass of: Dicentrarchus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: European sea bass
has exact synonym: European seabass
has OBO namespace: ncbi_taxonomy
has related synonym: Labrax labrax
has related synonym: Morone labrax
has related synonym: Perca labrax
has related synonym: Roccus labrax
has related synonym: Sciaena labrax

Spirochaetales
type: Class
subclass of: Spirochaetia
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has cross-reference: PMID:11075904
has cross-reference: PMID:11542017
has cross-reference: PMID:16558735
has cross-reference: PMID:1917844
has cross-reference: PMID:23908650
has OBO namespace: ncbi_taxonomy
has related synonym: spirochetes

Bacillales
type: Class
subclass of: Bacilli
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has alternative id: NCBITaxon:2954866
has cross-reference: GC_ID:11
has cross-reference: PMID:30896383
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus/Staphylococcus group
has related synonym: Caryophanales

Bacillus <firmicutes>
type: Class
subclass of: Bacillales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:10843090
has cross-reference: PMID:11491334
has cross-reference: PMID:1742196
has cross-reference: PMID:2223602
has cross-reference: PMID:23475340
has cross-reference: PMID:7727277
has cross-reference: PMID:8138135
has cross-reference: PMID:8863420
has exact synonym: Bacillus
has exact synonym: Bacillus rRNA group 1
has OBO namespace: ncbi_taxonomy

Enterovirus C
type: Class
subclass of: Enterovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:138953
has cross-reference: GC_ID:1
has exact synonym: Enterovirus EV-C
has exact synonym: Human enterovirus C
has exact synonym: Poliovirus
has OBO namespace: ncbi_taxonomy

Borreliella burgdorferi
type: Class
subclass of: Borreliella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:1380285
has cross-reference: PMID:1503971
has cross-reference: PMID:24744012
has cross-reference: PMID:7699027
has cross-reference: PMID:7981102
has cross-reference: PMID:8995796
has cross-reference: PMID:9336916
has exact synonym: Lyme disease spirochete
has OBO namespace: ncbi_taxonomy
has related synonym: Borrelia burgdorferi

Bacillus anthracis
type: Class
subclass of: Bacillus <firmicutes>
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1494525
has alternative id: NCBITaxon:1494531
has alternative id: NCBITaxon:1494577
has cross-reference: GC_ID:11
has cross-reference: PMID:8123566
has exact synonym: anthrax
has exact synonym: anthrax bacterium
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus cereus var. anthracis
has related synonym: Bacteridium anthracis

Boreoeutheria
type: Class
subclass of: Mammalia
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has cross-reference: PMID:11743200
has cross-reference: PMID:11791233
has OBO namespace: ncbi_taxonomy
has related synonym: Boreotheria

Clostridium
type: Class
subclass of: Bacillota
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:69207
has cross-reference: GC_ID:11
has cross-reference: PMID:26643615
has cross-reference: PMID:27488356
has OBO namespace: ncbi_taxonomy
has related synonym: Anaerobacter
has related synonym: Anaerobacter Duda et al. 1996

Euteleosteomorpha
type: Class
subclass of: Clupeocephala
imported from: ncbitaxon.owl
has_rank: NCBITaxon cohort
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Clostridium botulinum
type: Class
subclass of: Clostridium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:29368
has cross-reference: GC_ID:11
has cross-reference: PMID:10028279
has cross-reference: PMID:15244052
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus botulinus
has related synonym: Bacillus putrificus
has related synonym: Botulobacillus botulinus
has related synonym: Clostridium putrificum
has related synonym: Ermengemillus botulinus
has related synonym: Pacinia putrifica

Salmonella enterica subsp. enterica serovar Enteritidis
type: Class
subclass of: Salmonella enterica subsp. enterica
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:1245786
has alternative id: NCBITaxon:2588446
has alternative id: NCBITaxon:2588447
has alternative id: NCBITaxon:41533
has alternative id: NCBITaxon:592
has cross-reference: GC_ID:11
has cross-reference: PMID:10758910
has exact synonym: Salmonella enterica serovar Enteritidis
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus enteritidis
has related synonym: Salmonella enteritidis

Canine parainfluenza virus
type: Class
subclass of: Paramyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Yersinia enterocolitica subsp. enterocolitica
type: Class
subclass of: Yersinia <enterobacteria>
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
has cross-reference: GC_ID:11
has cross-reference: PMID:11043982
has OBO namespace: ncbi_taxonomy

Clostridium perfringens
type: Class
subclass of: Clostridium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1683536
has alternative id: NCBITaxon:3298488
has cross-reference: GC_ID:11
has cross-reference: PMID:1374625
has cross-reference: PMID:184898
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium welchii
has related synonym: Clostridium perfringens (Veillon and Zuber 1898) Hauduroy et al. 1937 (Approved Lists 1980)
has related synonym: Clostridium plagarum

Protoparvovirus
type: Class
subclass of: Parvovirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:10781
has cross-reference: GC_ID:1
has exact synonym: Parvovirus
has exact synonym: Parvoviruses
has OBO namespace: ncbi_taxonomy

Clostridium tetani
type: Class
subclass of: Clostridium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus tetani

Papillomaviridae
type: Class
subclass of: Papovaviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has cross-reference: PMID:20206957
has exact synonym: Papillomavirus
has OBO namespace: ncbi_taxonomy

Polyomaviridae
type: Class
subclass of: Papovaviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Gammaretrovirus
type: Class
subclass of: Orthoretrovirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:11762
has cross-reference: GC_ID:1
has exact synonym: MLV-related viruses
has exact synonym: Mammalian type C retrovirus group
has exact synonym: Mammalian type C retroviruses
has exact synonym: mammalian type C oncoviruses
has exact synonym: type C oncoviruses
has OBO namespace: ncbi_taxonomy

Galloanserae
type: Class
subclass of: Neognathae
imported from: ncbitaxon.owl
has_rank: NCBITaxon superorder
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Galloanseri

Treponema pallidum
type: Class
subclass of: Spirochaetales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Microspironema pallidum
has related synonym: Spirillum pallidum
has related synonym: Spirochaeta pallida
has related synonym: Spironema pallidum

human metapneumovirus
type: Class
subclass of: Metapneumovirus
imported from: ncbitaxon.owl
has broad synonym: HMPV
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Metapneumovirus
type: Class
subclass of: Pneumoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Listeria monocytogenes
type: Class
subclass of: Bacillales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1634566
has alternative id: NCBITaxon:2293539
has alternative id: NCBITaxon:2293540
has alternative id: NCBITaxon:2293541
has alternative id: NCBITaxon:2293542
has alternative id: NCBITaxon:2293543
has alternative id: NCBITaxon:2293544
has alternative id: NCBITaxon:2293545
has alternative id: NCBITaxon:2293546
has alternative id: NCBITaxon:2293547
has alternative id: NCBITaxon:2364651
has alternative id: NCBITaxon:2364652
has alternative id: NCBITaxon:2364653
has alternative id: NCBITaxon:2364654
has alternative id: NCBITaxon:2364655
has alternative id: NCBITaxon:2364656
has alternative id: NCBITaxon:2364657
has alternative id: NCBITaxon:2364658
has alternative id: NCBITaxon:2364659
has alternative id: NCBITaxon:2364660
has alternative id: NCBITaxon:2482733
has alternative id: NCBITaxon:2482734
has alternative id: NCBITaxon:2482735
has alternative id: NCBITaxon:2482736
has alternative id: NCBITaxon:2482737
has alternative id: NCBITaxon:2482738
has alternative id: NCBITaxon:2482739
has alternative id: NCBITaxon:2482740
has alternative id: NCBITaxon:2482741
has alternative id: NCBITaxon:2482742
has alternative id: NCBITaxon:2482743
has alternative id: NCBITaxon:2482744
has alternative id: NCBITaxon:2482745
has alternative id: NCBITaxon:2482746
has alternative id: NCBITaxon:2482747
has alternative id: NCBITaxon:2482748
has alternative id: NCBITaxon:2482749
has alternative id: NCBITaxon:2484857
has alternative id: NCBITaxon:2484858
has alternative id: NCBITaxon:2485082
has alternative id: NCBITaxon:2485083
has alternative id: NCBITaxon:2485084
has alternative id: NCBITaxon:2485085
has alternative id: NCBITaxon:2485086
has alternative id: NCBITaxon:2485087
has alternative id: NCBITaxon:2485088
has alternative id: NCBITaxon:2485089
has alternative id: NCBITaxon:2485090
has alternative id: NCBITaxon:2485091
has alternative id: NCBITaxon:2485092
has alternative id: NCBITaxon:2485093
has alternative id: NCBITaxon:2485094
has alternative id: NCBITaxon:2485095
has alternative id: NCBITaxon:2485096
has alternative id: NCBITaxon:2486732
has alternative id: NCBITaxon:2486733
has alternative id: NCBITaxon:2486734
has alternative id: NCBITaxon:2486735
has alternative id: NCBITaxon:2486736
has alternative id: NCBITaxon:2486737
has alternative id: NCBITaxon:2486738
has alternative id: NCBITaxon:2486739
has alternative id: NCBITaxon:2486740
has alternative id: NCBITaxon:2486741
has cross-reference: GC_ID:11
has cross-reference: PMID:17773427
has cross-reference: PMID:1906732
has cross-reference: PMID:8782698
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium monocytogenes
has related synonym: Bacterium monocytogenes hominis
has related synonym: Corynebacterium infantisepticum
has related synonym: Corynebacterium parvulum
has related synonym: Erysipelothrix monocytogenes
has related synonym: Listerella hepatolytica

Erysipelothrix rhusiopathiae
type: Class
subclass of: Bacillota
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:1503975
has cross-reference: PMID:8427802
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus insidiosus
has related synonym: Bacillus rhusiopathiae suis
has related synonym: Bacterium rhusiopathiae
has related synonym: Erysipelothrix erysipeloides
has related synonym: Erysipelothrix insidiosa
has related synonym: Erysipelothrix murisepticus
has related synonym: Erysipelothrix porci

Yersinia pseudotuberculosis complex
type: Class
subclass of: Yersinia <enterobacteria>
imported from: ncbitaxon.owl
has_rank: species group
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Mammarenavirus
type: Class
subclass of: Bunyavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Paslahepevirus balayani
type: Class
subclass of: Hepelivirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:12461
has alternative id: NCBITaxon:2953663
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Orthohepevirus A

Mustelinae
type: Class
subclass of: Musteloidea
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Leptospira
type: Class
subclass of: Spirochaetia
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:29512
has alternative id: NCBITaxon:29514
has alternative id: NCBITaxon:29516
has cross-reference: GC_ID:11
has cross-reference: PMID:10425768
has cross-reference: PMID:1581182
has cross-reference: PMID:19868121
has cross-reference: PMID:9103653
has OBO namespace: ncbi_taxonomy

Corynebacterium
type: Class
subclass of: Mycobacteriales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:144193
has cross-reference: GC_ID:11
has cross-reference: PMID:10425754
has cross-reference: PMID:19661509
has cross-reference: PMID:29760685
has cross-reference: PMID:30186281
has cross-reference: PMID:7547284
has cross-reference: PMID:7547291
has cross-reference: PMID:7547293
has cross-reference: PMID:8186090
has OBO namespace: ncbi_taxonomy
has related synonym: Turicella

Corynebacterium diphtheriae
type: Class
subclass of: Corynebacterium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:7729671
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus diphtheriae
has related synonym: Bacterium diphtheriae
has related synonym: Microsporon diphthericum
has related synonym: Microsporon diphtheriticum
has related synonym: Mycobacterium diphtheriae
has related synonym: Pacinia loeffleri

Corynebacterium pseudotuberculosis
type: Class
subclass of: Corynebacterium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus pseudotuberculosis
has related synonym: Bacillus pseudotuberculosis-ovis
has related synonym: Corynebacterium ovis
has related synonym: Corynebacterium preisz-nocardi
has related synonym: Corynebacterium pseudotuberculosis-ovis
has related synonym: Mycobacterium tuberculosis-ovis

Leptospira interrogans
type: Class
subclass of: Leptospira
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:2843297
has alternative id: NCBITaxon:2843299
has cross-reference: GC_ID:11
has cross-reference: PMID:15545494
has cross-reference: PMID:19867994
has cross-reference: PMID:19868337
has cross-reference: PMID:19972157
has cross-reference: PMID:25288661
has cross-reference: PMID:9542090
has OBO namespace: ncbi_taxonomy
has related synonym: Leptospira icteroides
has related synonym: Spirochaeta biflexa
has related synonym: Spirochaeta icterogenes
has related synonym: Spirochaeta icterohaemorrhagiae
has related synonym: Spirochaeta interrogans
has related synonym: Spirochaeta nodosa

Passeroidea
type: Class
subclass of: Australaves
imported from: ncbitaxon.owl
has_rank: NCBITaxon superfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Leptospira interrogans serovar Hardjo
type: Class
subclass of: Leptospira interrogans
imported from: ncbitaxon.owl
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Leptospira hardjo

Mycobacterium
type: Class
subclass of: Mycobacteriales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:1380284
has cross-reference: PMID:1581193
has cross-reference: PMID:16014496
has cross-reference: PMID:1883713
has cross-reference: PMID:2275850
has cross-reference: PMID:31296783
has cross-reference: PMID:31649146
has cross-reference: PMID:31649147
has cross-reference: PMID:34554081
has cross-reference: PMID:7547284
has cross-reference: PMID:7547304
has cross-reference: PMID:7907223
has cross-reference: PMID:8863452
has OBO namespace: ncbi_taxonomy
has related synonym: Mycobacterium Lehmann and Neumann 1896 (Approved Lists 1980)

Mycobacterium avium
type: Class
subclass of: Mycobacterium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:2397193
has cross-reference: PMID:8347508
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus tuberculosis gallinarum
has related synonym: Mycobacterium tuberculosis avium
has related synonym: Mycobacterium tuberculosis typus gallinaceus
has related synonym: Tuberculose des oiseaux

Mycobacterium tuberculosis variant bovis
type: Class
subclass of: Mycobacterium tuberculosis
imported from: ncbitaxon.owl
has_rank: NCBITaxon biotype
has alternative id: NCBITaxon:115863
has cross-reference: GC_ID:11
has cross-reference: PMID:10618079
has cross-reference: PMID:11931153
has cross-reference: PMID:14657105
has cross-reference: PMID:29205127
has OBO namespace: ncbi_taxonomy
has related synonym: Mycobacterium bovis
has related synonym: Mycobacterium tuberculosis typus bovinus
has related synonym: Mycobacterium tuberculosis var. bovis

Mycobacterium leprae
type: Class
subclass of: Mycobacterium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus leprae

Mycobacterium tuberculosis
type: Class
subclass of: Mycobacterium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:2528440
has cross-reference: GC_ID:11
has cross-reference: PMID:29205127
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus tuberculosis
has related synonym: Bacterium tuberculosis
has related synonym: Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980)
has related synonym: Mycobacterium tuberculosis typus humanus
has related synonym: Mycobacterium tuberculosis var. hominis

Mycobacterium marinum
type: Class
subclass of: Mycobacterium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:12089250
has cross-reference: PMID:20668542
has cross-reference: PMID:38415640
has OBO namespace: ncbi_taxonomy
has related synonym: Mycobacterium balnei
has related synonym: Mycobacterium platypoecilus

Bacillati
type: Class
subclass of: Bacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon kingdom
has alternative id: NCBITaxon:31968
has alternative id: NCBITaxon:3376104
has cross-reference: GC_ID:11
has cross-reference: PMID:18988685
has exact synonym: Terrabacteria group
has OBO namespace: ncbi_taxonomy
has related synonym: Firmacutes
has related synonym: Firmicuteota
has related synonym: Firmicutes
has related synonym: Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980)
has related synonym: Terrabacteria
has related synonym: Terrabacterida

Mardivirus
type: Class
subclass of: Alphaherpesvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Marek's disease-like viruses
has OBO namespace: ncbi_taxonomy

Iltovirus
type: Class
subclass of: Alphaherpesvirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Infectious laryngo-tracheitis-like viruses
has exact synonym: Infectious laryngotracheitis-like viruses
has OBO namespace: ncbi_taxonomy

Marburgvirus
type: Class
subclass of: Filoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Marburg-like viruses
has OBO namespace: ncbi_taxonomy

Clupeocephala
type: Class
subclass of: Actinopterygii
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Novirhabdovirus
type: Class
subclass of: Rhabdoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Orthopneumovirus
type: Class
subclass of: Pneumoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Respirovirus
type: Class
subclass of: Paramyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Gammapolyomavirus avis
type: Class
subclass of: Polyomaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:10625
has broad synonym: BFPyV
has cross-reference: GC_ID:1
has exact synonym: Aves polyomavirus 1
has exact synonym: BFDV
has exact synonym: Budgerigar fledgling disease polyomavirus
has exact synonym: Budgerigar fledgling disease virus
has exact synonym: Budgerigar fledgling polyomavirus
has OBO namespace: ncbi_taxonomy

Yersiniaceae
type: Class
subclass of: Enterobacterales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:11
has cross-reference: PMID:27620848
has OBO namespace: ncbi_taxonomy

Campylobacter
type: Class
subclass of: Campylobacterales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:11542086
has cross-reference: PMID:12361288
has cross-reference: PMID:16627635
has cross-reference: PMID:1704793
has cross-reference: PMID:19801389
has cross-reference: PMID:29034857
has cross-reference: PMID:38530055
has OBO namespace: ncbi_taxonomy

Campylobacter fetus
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:11321120
has cross-reference: PMID:1354478
has OBO namespace: ncbi_taxonomy
has related synonym: Spirillum fetus
has related synonym: Vibrio fetus

Campylobacter jejuni
type: Class
subclass of: Campylobacter
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:2172531
has alternative id: NCBITaxon:2182326
has alternative id: NCBITaxon:2201165
has alternative id: NCBITaxon:2211407
has alternative id: NCBITaxon:2211408
has alternative id: NCBITaxon:2211409
has alternative id: NCBITaxon:2293848
has alternative id: NCBITaxon:2293849
has alternative id: NCBITaxon:2293850
has alternative id: NCBITaxon:2303571
has alternative id: NCBITaxon:2305452
has alternative id: NCBITaxon:2305453
has alternative id: NCBITaxon:2305454
has alternative id: NCBITaxon:2305455
has alternative id: NCBITaxon:2305456
has alternative id: NCBITaxon:2305457
has alternative id: NCBITaxon:2305458
has alternative id: NCBITaxon:2305459
has alternative id: NCBITaxon:2340789
has alternative id: NCBITaxon:2478524
has alternative id: NCBITaxon:2572055
has alternative id: NCBITaxon:2572062
has alternative id: NCBITaxon:2572070
has alternative id: NCBITaxon:2572072
has alternative id: NCBITaxon:2572075
has alternative id: NCBITaxon:2572080
has alternative id: NCBITaxon:2572086
has alternative id: NCBITaxon:2870880
has alternative id: NCBITaxon:2870881
has alternative id: NCBITaxon:2893406
has alternative id: NCBITaxon:2916035
has alternative id: NCBITaxon:2916036
has alternative id: NCBITaxon:2939732
has alternative id: NCBITaxon:2950109
has alternative id: NCBITaxon:3042472
has alternative id: NCBITaxon:3042475
has alternative id: NCBITaxon:3042476
has alternative id: NCBITaxon:3042477
has alternative id: NCBITaxon:3042478
has alternative id: NCBITaxon:3042479
has alternative id: NCBITaxon:3042480
has alternative id: NCBITaxon:3042481
has alternative id: NCBITaxon:3042482
has alternative id: NCBITaxon:3042483
has alternative id: NCBITaxon:3042484
has alternative id: NCBITaxon:3042485
has alternative id: NCBITaxon:3042486
has alternative id: NCBITaxon:3042488
has alternative id: NCBITaxon:3109033
has alternative id: NCBITaxon:3109035
has alternative id: NCBITaxon:3109036
has alternative id: NCBITaxon:3109054
has alternative id: NCBITaxon:3109055
has alternative id: NCBITaxon:3231045
has cross-reference: GC_ID:11
has cross-reference: PMID:11321120
has OBO namespace: ncbi_taxonomy
has related synonym: Campylobacter fetus subsp. jejuni
has related synonym: Vibrio hepaticus
has related synonym: Vibrio jejuni

Alphainfluenzavirus
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Influenzavirus A
has OBO namespace: ncbi_taxonomy

Betainfluenzavirus
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Influenzavirus B
has OBO namespace: ncbi_taxonomy

Gammainfluenzavirus
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Influenzavirus C
has OBO namespace: ncbi_taxonomy

Bunyavirales
type: Class
subclass of: Polyploviricotina
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Orthohantavirus
type: Class
subclass of: Bunyavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:11598
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Hantavirus

Novirhabdovirus hirame
type: Class
subclass of: Novirhabdovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:38142
has broad synonym: HIRRV
has cross-reference: GC_ID:1
has exact synonym: Hirame novirhabdovirus
has exact synonym: Hirame rhabdovirus
has OBO namespace: ncbi_taxonomy

Bacteria
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
has cross-reference: GC_ID:11
has cross-reference: PMID:10425795
has cross-reference: PMID:10425796
has cross-reference: PMID:10425797
has cross-reference: PMID:10490293
has cross-reference: PMID:10843050
has cross-reference: PMID:10939651
has cross-reference: PMID:10939673
has cross-reference: PMID:10939677
has cross-reference: PMID:11211268
has cross-reference: PMID:11321083
has cross-reference: PMID:11321113
has cross-reference: PMID:11411719
has cross-reference: PMID:11540071
has cross-reference: PMID:11542017
has cross-reference: PMID:11542087
has cross-reference: PMID:11760965
has cross-reference: PMID:12054223
has cross-reference: PMID:270744
has cross-reference: PMID:32628106
has cross-reference: PMID:36748408
has cross-reference: PMID:7520741
has cross-reference: PMID:8123559
has cross-reference: PMID:8186100
has cross-reference: PMID:8590690
has cross-reference: PMID:9103655
has cross-reference: PMID:9336922
has exact synonym: eubacteria
has OBO namespace: ncbi_taxonomy
has related synonym: Bacteria (ex Cavalier-Smith 1987)
has related synonym: Bacteria Woese et al. 2024
has related synonym: Bacteriobiota
has related synonym: Monera
has related synonym: Procaryotae
has related synonym: Prokaryota
has related synonym: Prokaryotae
has related synonym: bacteria
has related synonym: prokaryote
has related synonym: prokaryotes

Flavobacteriales
type: Class
subclass of: Bacteroidota
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Spirochaetia
type: Class
subclass of: Pseudomonadati
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:11
has cross-reference: PMID:11837318
has cross-reference: PMID:25288668
has cross-reference: PMID:26654112
has OBO namespace: ncbi_taxonomy
has related synonym: Spirochaetes

Brucella suis 1330
type: Class
subclass of: Brucella suis
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has cross-reference: PMID:12271122
has exact synonym: Brucella suis str. 1330
has OBO namespace: ncbi_taxonomy
has related synonym: Brucella melitensis biovar Suis str. 1330
has related synonym: Brucella suis ATCC 23444
has related synonym: Brucella suis NCTC 10316

Ebola virus sp.
type: Class
subclass of: Filoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11268
has cross-reference: GC_ID:1
has exact synonym: Ebola virus EBO
has exact synonym: unidentified Ebola virus
has OBO namespace: ncbi_taxonomy

Neisseriales
type: Class
subclass of: Betaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has cross-reference: PMID:23575986
has OBO namespace: ncbi_taxonomy

Mycoplasma
type: Class
subclass of: Mycoplasmatota
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:29500
has alternative id: NCBITaxon:57371
has cross-reference: GC_ID:4
has cross-reference: PMID:10826816
has cross-reference: PMID:11321109
has cross-reference: PMID:11411711
has cross-reference: PMID:11931184
has cross-reference: PMID:13403276
has cross-reference: PMID:15176735
has cross-reference: PMID:16350067
has cross-reference: PMID:16403858
has cross-reference: PMID:25288662
has cross-reference: PMID:8863441
has cross-reference: PMID:8995799
has OBO namespace: ncbi_taxonomy
has related synonym: Asterococcus
has related synonym: Asteromyces
has related synonym: Borrelomyces
has related synonym: Bovimyces
has related synonym: Eperythrozoon
has related synonym: Haemobartonella
has related synonym: Pleuropneumonia

Mycoplasmoides gallisepticum
type: Class
subclass of: Mycoplasmoidales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:4
has OBO namespace: ncbi_taxonomy
has related synonym: Mycoplasma gallisepticum

Mesomycoplasma hyopneumoniae
type: Class
subclass of: Metamycoplasmataceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:4
has cross-reference: PMID:11491338
has cross-reference: PMID:1316139
has cross-reference: PMID:1374621
has cross-reference: PMID:8573513
has OBO namespace: ncbi_taxonomy
has related synonym: Mycoplasma hyopneumoniae
has related synonym: Mycoplasma suipneumoniae

Helicobacter pylori
type: Class
subclass of: Campylobacterales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:219
has cross-reference: GC_ID:11
has cross-reference: PMID:11931154
has cross-reference: PMID:1995031
has cross-reference: PMID:8186097
has cross-reference: PMID:8494747
has OBO namespace: ncbi_taxonomy
has related synonym: Campylobacter pylori
has related synonym: Campylobacter pylori subsp. pylori
has related synonym: Campylobacter pyloridis
has related synonym: Helicobacter nemestrinae

Mycoplasmopsis synoviae
type: Class
subclass of: Metamycoplasmataceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:4
has OBO namespace: ncbi_taxonomy
has related synonym: Mycoplasma synoviae

Leptospira interrogans serovar Canicola
type: Class
subclass of: Leptospira interrogans
imported from: ncbitaxon.owl
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Leptospira canicola

Campylobacterales
type: Class
subclass of: Pseudomonadati
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has cross-reference: PMID:16403855
has OBO namespace: ncbi_taxonomy

Archaea
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
has cross-reference: GC_ID:11
has cross-reference: PMID:10425795
has cross-reference: PMID:10425796
has cross-reference: PMID:10425797
has cross-reference: PMID:10490293
has cross-reference: PMID:10843050
has cross-reference: PMID:10939651
has cross-reference: PMID:10939673
has cross-reference: PMID:10939677
has cross-reference: PMID:11211268
has cross-reference: PMID:11321083
has cross-reference: PMID:11321113
has cross-reference: PMID:11411719
has cross-reference: PMID:11540071
has cross-reference: PMID:11541975
has cross-reference: PMID:11542064
has cross-reference: PMID:11542149
has cross-reference: PMID:11760965
has cross-reference: PMID:12054223
has cross-reference: PMID:25527841
has cross-reference: PMID:270744
has cross-reference: PMID:32628106
has cross-reference: PMID:36748408
has cross-reference: PMID:8123559
has cross-reference: PMID:8590690
has cross-reference: PMID:9103655
has cross-reference: PMID:9336922
has OBO namespace: ncbi_taxonomy
has related synonym: Archaebacteria
has related synonym: Archaebiota
has related synonym: Mendosicutes
has related synonym: Metabacteria
has related synonym: Monera
has related synonym: Procaryotae
has related synonym: Prokaryota
has related synonym: Prokaryotae
has related synonym: archaea
has related synonym: prokaryote
has related synonym: prokaryotes

Mammarenavirus juninense
type: Class
subclass of: Mammarenavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11619
has cross-reference: GC_ID:1
has exact synonym: Argentinian mammarenavirus
has exact synonym: Junin arenavirus
has exact synonym: Junin mammarenavirus
has exact synonym: Junin virus
has exact synonym: Junn mammarenavirus
has OBO namespace: ncbi_taxonomy

Brucella melitensis bv. 1 str. 16M
type: Class
subclass of: Brucella melitensis
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has cross-reference: PMID:11756688
has OBO namespace: ncbi_taxonomy
has related synonym: Brucella melitensis ATCC 23456

Brucella
type: Class
subclass of: Alphaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:28066370
has cross-reference: PMID:32373076
has cross-reference: PMID:35335701
has cross-reference: PMID:37395662
has cross-reference: PMID:8573514
has OBO namespace: ncbi_taxonomy

Brucella abortus
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has exact synonym: Brucella melitensis bv. Abortus
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium abortus
has related synonym: Brucella melitensis biovar Abortus

Brucella ovis
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has exact synonym: Brucella melitensis bv. Ovis
has OBO namespace: ncbi_taxonomy
has related synonym: Brucella melitensis biovar Ovis

Negarnaviricota
type: Class
subclass of: Orthornavirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has cross-reference: GC_ID:1
has exact synonym: Negative-strand RNA viruses
has OBO namespace: ncbi_taxonomy

Polyploviricotina
type: Class
subclass of: Negarnaviricota
imported from: ncbitaxon.owl
has_rank: NCBITaxon subphylum
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Orthocoronavirinae
type: Class
subclass of: Coronaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Riboviria
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has exact synonym: RNA viruses
has exact synonym: RNA viruses and viroids
has OBO namespace: ncbi_taxonomy

Avulavirinae
type: Class
subclass of: Paramyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Orthoparamyxovirinae
type: Class
subclass of: Paramyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Rubulavirinae
type: Class
subclass of: Paramyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

avian paramyxovirus 1
type: Class
subclass of: Avulavirinae
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:11176
has broad synonym: NDV
has cross-reference: GC_ID:1
has exact synonym: Avian Paramyxovirus Serotype I
has exact synonym: Avian avulavirus 1
has exact synonym: Avian orthoavulavirus 1
has exact synonym: Avian paramyxovirus type 1
has exact synonym: Avian paramyxovirus type-1
has exact synonym: Newcastle disease virus
has exact synonym: Newcastle disease virus NDV
has OBO namespace: ncbi_taxonomy

Mumps orthorubulavirus
type: Class
subclass of: Rubulavirinae
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:11161
has alternative id: NCBITaxon:1979165
has cross-reference: GC_ID:1
has exact synonym: Mumps virus
has OBO namespace: ncbi_taxonomy
has related synonym: Mumps rubulavirus

Avulavirus
type: Class
subclass of: Avulavirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Henipavirus
type: Class
subclass of: Orthoparamyxovirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Metamonada
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has cross-reference: PMID:30257078
has OBO namespace: ncbi_taxonomy

Discoba
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Brucella abortus bv. 1 str. 9-941
type: Class
subclass of: Brucella abortus
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has cross-reference: PMID:15805518
has exact synonym: Brucella abortus biovar 1 str. 9-941
has exact synonym: Brucella abortus bv. 1 strain 9-941
has OBO namespace: ncbi_taxonomy

Francisella tularensis
type: Class
subclass of: Thiotrichales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium tularense
has related synonym: Brucella tularensis
has related synonym: Francisella tularense
has related synonym: Pasteurella tularensis

Severe acute respiratory syndrome coronavirus 2
type: Class
subclass of: Severe acute respiratory syndrome-related coronavirus
imported from: ncbitaxon.owl
has broad synonym: SARS-CoV-2
has cross-reference: GC_ID:1
has exact synonym: 2019-nCoV
has exact synonym: COVID-19 virus
has exact synonym: HCoV-19
has exact synonym: Human coronavirus 2019
has exact synonym: SARS-2
has exact synonym: SARS-CoV2
has exact synonym: SARS2
has OBO namespace: ncbi_taxonomy

Bamfordvirae
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon kingdom
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Shotokuvirae
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon kingdom
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Orthornavirae
type: Class
subclass of: Riboviria
imported from: ncbitaxon.owl
has_rank: NCBITaxon kingdom
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Kitrinoviricota
type: Class
subclass of: Orthornavirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has cross-reference: GC_ID:1
has exact synonym: Tombus-Noda-like virus sp.
has OBO namespace: ncbi_taxonomy

Cossaviricota
type: Class
subclass of: Shotokuvirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Papovaviricetes
type: Class
subclass of: Cossaviricota
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Alsuviricetes
type: Class
subclass of: Kitrinoviricota
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Pisoniviricetes
type: Class
subclass of: Orthornavirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Revtraviricetes
type: Class
subclass of: Riboviria
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Pokkesviricetes
type: Class
subclass of: Bamfordvirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Reovirales
type: Class
subclass of: Orthornavirae
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has alternative id: NCBITaxon:10880
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Reoviridae

Hepelivirales
type: Class
subclass of: Alsuviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Eukaryota
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
has cross-reference: GC_ID:1
has cross-reference: PMID:23020233
has cross-reference: PMID:30257078
has exact synonym: eucaryotes
has exact synonym: eukaryotes
has OBO namespace: ncbi_taxonomy
has related synonym: Eucarya
has related synonym: Eucaryotae
has related synonym: Eukarya
has related synonym: Eukaryotae
has related synonym: eukaryotes

Bovinae
type: Class
subclass of: Bovidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Mycoplasmoidales
type: Class
subclass of: Mycoplasmatota
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:4
has cross-reference: PMID:31385780
has cross-reference: PMID:31971499
has cross-reference: PMID:35947640
has OBO namespace: ncbi_taxonomy

Porphyromonas macacae
type: Class
subclass of: Porphyromonas
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:29525
has cross-reference: GC_ID:11
has cross-reference: PMID:1503973
has OBO namespace: ncbi_taxonomy
has related synonym: Bacteroides macacae
has related synonym: Bacteroides melaninogenicus subsp. macacae
has related synonym: Bacteroides salivosus
has related synonym: Porphyromonas salivosa

Vibrio ordalii
type: Class
subclass of: Vibrionaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:707
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Listonella ordalii

Alphaproteobacteria
type: Class
subclass of: Pseudomonadota
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:11
has cross-reference: PMID:11541974
has cross-reference: PMID:11837318
has cross-reference: PMID:16166687
has cross-reference: PMID:16403855
has cross-reference: PMID:19060069
has OBO namespace: ncbi_taxonomy
has related synonym: Alphabacteria
has related synonym: Proteobacteria alpha subdivision
has related synonym: Purple bacteria, alpha subdivision
has related synonym: a-proteobacteria
has related synonym: alpha proteobacteria
has related synonym: alpha subdivision
has related synonym: alpha subgroup

Betaproteobacteria
type: Class
subclass of: Pseudomonadota
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:11
has cross-reference: PMID:16403855
has cross-reference: PMID:28581923
has OBO namespace: ncbi_taxonomy
has related synonym: Proteobacteria beta subdivision
has related synonym: Purple bacteria, beta subdivision
has related synonym: b-proteobacteria
has related synonym: beta proteobacteria
has related synonym: beta subdivision
has related synonym: beta subgroup

Porcine reproductive and respiratory syndrome virus
type: Class
subclass of: Arteriviridae
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:12796
has alternative id: NCBITaxon:70172
has broad synonym: PRRSV
has cross-reference: GC_ID:1
has exact synonym: Porcine reproductive and respiratory syndrome virus (PRRSV)
has exact synonym: Porcine respiratory and reproductive syndrome virus
has exact synonym: porcine reproductive and respiratory syndrome virus PRRSV
has exact synonym: porcine reproductive and respiratory syndrome virus, PRRSV
has OBO namespace: ncbi_taxonomy

Burkholderia pseudomallei
type: Class
subclass of: Burkholderiales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1435366
has alternative id: NCBITaxon:1435368
has alternative id: NCBITaxon:1435988
has alternative id: NCBITaxon:1439853
has alternative id: NCBITaxon:1487954
has alternative id: NCBITaxon:1487955
has cross-reference: GC_ID:11
has cross-reference: PMID:12734250
has cross-reference: PMID:1283774
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus pseudomallei
has related synonym: Bacterium whitmori
has related synonym: Loefflerella pseudomallei
has related synonym: Malleomyces pseudomallei
has related synonym: Pseudomonas pseudomallei

Pseudomonas
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:212745
has cross-reference: GC_ID:11
has cross-reference: PMID:10758879
has cross-reference: PMID:10939664
has cross-reference: PMID:15950132
has cross-reference: PMID:18048745
has cross-reference: PMID:7727274
has cross-reference: PMID:9103607
has exact synonym: RNA similarity group I
has OBO namespace: ncbi_taxonomy
has related synonym: "Chlorobacterium" Guillebeau 1890, nom. rejic. Opin. 6 (not "Chlorobacterium" Lauterborn 1916)
has related synonym: Chryseomonas
has related synonym: Flavimonas
has related synonym: Liquidomonas
has related synonym: Loefflerella
has related synonym: Pseudomonas Migula 1894 (Approved Lists 1980)
has related synonym: Serpens
has related synonym: Serpens Hespell 1977 (Approved Lists 1980)

Pseudomonas aeruginosa
type: Class
subclass of: Pseudomonas
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1224290
has alternative id: NCBITaxon:1437768
has alternative id: NCBITaxon:1437769
has alternative id: NCBITaxon:1437770
has alternative id: NCBITaxon:1508364
has alternative id: NCBITaxon:1607811
has alternative id: NCBITaxon:1607813
has alternative id: NCBITaxon:1683559
has alternative id: NCBITaxon:1683561
has alternative id: NCBITaxon:1851858
has alternative id: NCBITaxon:1851865
has alternative id: NCBITaxon:1860124
has alternative id: NCBITaxon:2952935
has alternative id: NCBITaxon:665948
has alternative id: NCBITaxon:912077
has alternative id: NCBITaxon:931955
has alternative id: NCBITaxon:931956
has alternative id: NCBITaxon:931957
has alternative id: NCBITaxon:931958
has alternative id: NCBITaxon:932477
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus aeruginosus
has related synonym: Bacillus pyocyaneus
has related synonym: Bacterium aeruginosum
has related synonym: Bacterium pyocyaneum
has related synonym: Micrococcus pyocyaneus
has related synonym: Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (Approved Lists 1980)
has related synonym: Pseudomonas polycolor
has related synonym: Pseudomonas pyocyanea
has related synonym: probable synonym or variety: "Pseudomonas polycolor" Clara 1930

tremovirus A1
type: Class
subclass of: Tremovirus A
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has exact synonym: avian encephalomyelitis virus
has OBO namespace: ncbi_taxonomy

Metamycoplasmataceae
type: Class
subclass of: Mycoplasmoidales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:4
has cross-reference: PMID:31385780
has cross-reference: PMID:31971499
has cross-reference: PMID:35947640
has OBO namespace: ncbi_taxonomy

Severe acute respiratory syndrome coronavirus
type: Class
subclass of: Severe acute respiratory syndrome-related coronavirus
imported from: ncbitaxon.owl
has broad synonym: SARS-CoV
has cross-reference: GC_ID:1
has exact synonym: SARS coronavirus
has exact synonym: SARS virus
has OBO namespace: ncbi_taxonomy

Neospora caninum
type: Class
subclass of: Sarcocystidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Brucella melitensis
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:8573514
has OBO namespace: ncbi_taxonomy
has related synonym: Micrococcus melitensis
has related synonym: Streptococcus Miletensis

Brucella suis
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has exact synonym: Brucella melitensis bv. Suis
has OBO namespace: ncbi_taxonomy
has related synonym: Brucella melitensis biovar Suis

Sedoreoviridae
type: Class
subclass of: Reovirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has alternative id: NCBITaxon:689832
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Sedoreovirinae

Heptrevirinae
type: Class
subclass of: Picornaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Yersinia ruckeri
type: Class
subclass of: Yersinia <enterobacteria>
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Lawsonia intracellularis
type: Class
subclass of: Pseudomonadati
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:7547305
has cross-reference: PMID:7857801
has cross-reference: PMID:7981108
has cross-reference: PMID:8123559
has cross-reference: PMID:8347512
has cross-reference: PMID:9226893
has OBO namespace: ncbi_taxonomy
has related synonym: Candidatus intracellularis
has related synonym: Ileal symbiont intracellularis

Orthoherpesviridae
type: Class
subclass of: Herpesvirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Orthoflavivirus
type: Class
subclass of: Flaviviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Henipavirus hendraense
type: Class
subclass of: Henipavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:45337
has alternative id: NCBITaxon:63330
has cross-reference: GC_ID:1
has cross-reference: PMID:7701348
has exact synonym: Equine morbillivirus
has exact synonym: Hendra henipavirus
has exact synonym: Hendra virus
has OBO namespace: ncbi_taxonomy

Henipavirus nipahense
type: Class
subclass of: Henipavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:121791
has cross-reference: GC_ID:1
has exact synonym: Nipah henipavirus
has exact synonym: Nipah virus
has exact synonym: Nipah-virus
has OBO namespace: ncbi_taxonomy

Hepacivirus hominis
type: Class
subclass of: Flaviviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11103
has broad synonym: HCV
has cross-reference: GC_ID:1
has exact synonym: Hepacivirus C
has exact synonym: Hepatitis C virus
has exact synonym: hepatitis C virus HCV
has exact synonym: human hepatitis C virus
has exact synonym: human hepatitis C virus HCV
has exact synonym: human hepatitis virus C HCV
has exact synonym: post-transfusion hepatitis non A non B virus
has OBO namespace: ncbi_taxonomy

Mammarenavirus choriomeningitidis
type: Class
subclass of: Mammarenavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11623
has alternative id: NCBITaxon:12748
has broad synonym: LCMV
has cross-reference: GC_ID:1
has exact synonym: Lymphocytic choriomeningitis mammarenavirus
has exact synonym: Lymphocytic choriomeningitis virus
has exact synonym: lymphocytic choriomeningitis virus LCMV
has OBO namespace: ncbi_taxonomy

Mammarenavirus lassaense
type: Class
subclass of: Mammarenavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11620
has cross-reference: GC_ID:1
has exact synonym: Lassa mammarenavirus
has exact synonym: Lassa virus
has OBO namespace: ncbi_taxonomy

Morbillivirus canis
type: Class
subclass of: Morbillivirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11232
has cross-reference: GC_ID:1
has exact synonym: Canine morbillivirus
has OBO namespace: ncbi_taxonomy

Orthonairovirus haemorrhagiae
type: Class
subclass of: Bunyavirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11593
has alternative id: NCBITaxon:1980519
has broad synonym: CCHFV
has cross-reference: GC_ID:1
has exact synonym: Crimean-Congo haemorrhagic fever virus
has exact synonym: Crimean-Congo hemorrhagic fever nairovirus
has exact synonym: Crimean-Congo hemorrhagic fever orthonairovirus
has exact synonym: Crimean-Congo hemorrhagic virus
has OBO namespace: ncbi_taxonomy
has related synonym: Crimean-Congo hemorrhagic fever virus

Protoparvovirus carnivoran1
type: Class
subclass of: Protoparvovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1511906
has cross-reference: GC_ID:1
has exact synonym: Carnivore protoparvovirus 1
has exact synonym: Protoparvovirus carnivoran 1
has OBO namespace: ncbi_taxonomy

Respirovirus bovis
type: Class
subclass of: Respirovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:11215
has cross-reference: GC_ID:1
has exact synonym: Bovine parainfluenza 3 virus
has exact synonym: Bovine parainfluenza virus 3
has exact synonym: Bovine parainfluenza virus type 3
has exact synonym: Bovine respirovirus 3
has OBO namespace: ncbi_taxonomy

Musteloidea
type: Class
subclass of: Caniformia
imported from: ncbitaxon.owl
has_rank: NCBITaxon superfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Australaves
type: Class
subclass of: Neognathae
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Laurasiatheria
type: Class
subclass of: Boreoeutheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon superorder
has cross-reference: GC_ID:1
has cross-reference: PMID:11214318
has cross-reference: PMID:11214319
has cross-reference: PMID:12878460
has OBO namespace: ncbi_taxonomy

Euarchontoglires
type: Class
subclass of: Boreoeutheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon superorder
has cross-reference: GC_ID:1
has cross-reference: PMID:11214319
has cross-reference: PMID:12082125
has cross-reference: PMID:12878460
has cross-reference: PMID:15522813
has OBO namespace: ncbi_taxonomy

Glires
type: Class
subclass of: Euarchontoglires
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has cross-reference: PMID:11214319
has cross-reference: PMID:12082125
has cross-reference: PMID:15522813
has exact synonym: Rodents and rabbits
has OBO namespace: ncbi_taxonomy

Simiiformes
type: Class
subclass of: Primates
imported from: ncbitaxon.owl
has_rank: NCBITaxon infraorder
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Anthropoidea

Amniota
type: Class
subclass of: Euteleostomi
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has exact synonym: amniotes
has OBO namespace: ncbi_taxonomy

Sauria
type: Class
subclass of: Amniota
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has exact synonym: diapsids
has OBO namespace: ncbi_taxonomy
has related synonym: Diapsida

Orthoretrovirinae
type: Class
subclass of: Revtraviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Canine minute virus
type: Class
subclass of: Parvovirinae
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:186155
has cross-reference: GC_ID:1
has exact synonym: Canine parvovirus-1
has exact synonym: Minute virus of canines
has OBO namespace: ncbi_taxonomy

Opisthokonta
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Fungi/Metazoa group
has related synonym: opisthokonts

Bilateria
type: Class
subclass of: Opisthokonta
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Protostomia
type: Class
subclass of: Bilateria
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Neoptera
type: Class
subclass of: Ecdysozoa
imported from: ncbitaxon.owl
has_rank: NCBITaxon infraclass
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

unclassified Papillomaviridae
type: Class
subclass of: Papillomaviridae
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Herpes Simplexvirus
type: Class
subclass of: Simplexvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Hystricomorpha
type: Class
subclass of: Rodentia
imported from: ncbitaxon.owl
has_rank: NCBITaxon suborder
has cross-reference: GC_ID:1
has exact synonym: guinea pigs and others
has OBO namespace: ncbi_taxonomy
has related synonym: Hystricognathi

Carnivora
type: Class
subclass of: Laurasiatheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has exact synonym: carnivores
has OBO namespace: ncbi_taxonomy
has related synonym: carnivores

Pseudomonadati
type: Class
subclass of: Bacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon kingdom
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Mycobacterium tuberculosis variant bovis BCG
type: Class
subclass of: Mycobacterium tuberculosis variant bovis
imported from: ncbitaxon.owl
has broad synonym: BCG
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Mycobacterium bovis BCG
has related synonym: bacillus Calmette-Guerin
has related synonym: bacillus Calmette-Guerin BCG

Riemerella anatipestifer
type: Class
subclass of: Flavobacteriales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:13200095
has cross-reference: PMID:22427448
has cross-reference: PMID:8240957
has cross-reference: PMID:9103649
has OBO namespace: ncbi_taxonomy
has related synonym: Moraxella anatipestifer
has related synonym: Pasteurella anapestifer
has related synonym: Pasteurella anatipestifer
has related synonym: Pfeifferella anatipestifer

Replication competent viruses
type: Class
subclass of: Gammaretrovirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

unclassified Orthomyxoviridae
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Pecora
type: Class
subclass of: Artiodactyla
imported from: ncbitaxon.owl
has_rank: NCBITaxon infraorder
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Brucella abortus 2308
type: Class
subclass of: Brucella abortus
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has cross-reference: PMID:16299333
has cross-reference: PMID:20462421
has OBO namespace: ncbi_taxonomy
has related synonym: Brucella melitensis biovar Abortus 2308

Polyomavirus sp.
type: Class
subclass of: Polyomaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:10624
has cross-reference: GC_ID:1
has exact synonym: Polyomavirus
has exact synonym: Polyomaviruses
has OBO namespace: ncbi_taxonomy

H1N1 swine influenza virus
type: Class
subclass of: H1N1 subtype
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Streptococcus sp. 'group A'
type: Class
subclass of: Streptococcus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Streptococcus sp. (group A)
has related synonym: group A streptococci
has related synonym: group A streptococcus

Brucella canis
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has exact synonym: Brucella melitensis bv. Canis
has OBO namespace: ncbi_taxonomy
has related synonym: Brucella melitensis biovar Canis

Chikungunya virus
type: Class
subclass of: Alphavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Caniformia
type: Class
subclass of: Carnivora
imported from: ncbitaxon.owl
has_rank: NCBITaxon suborder
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Avian orthoreovirus
type: Class
subclass of: Reovirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Avian reovirus
has OBO namespace: ncbi_taxonomy

Leptospira kirschneri serovar Grippotyphosa
type: Class
subclass of: Leptospira
imported from: ncbitaxon.owl
has cross-reference: GC_ID:11
has cross-reference: PMID:1581182
has OBO namespace: ncbi_taxonomy
has related synonym: Leptospira grippotyphosa

avian metapneumovirus
type: Class
subclass of: Metapneumovirus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has exact synonym: Avian pneumovirus
has OBO namespace: ncbi_taxonomy

Leishmania <subgenus>
type: Class
subclass of: Leishmania <genus>
imported from: ncbitaxon.owl
has_rank: NCBITaxon subgenus
has cross-reference: GC_ID:1
has exact synonym: Leishmania
has OBO namespace: ncbi_taxonomy

Leishmania donovani species complex
type: Class
subclass of: Leishmania <subgenus>
imported from: ncbitaxon.owl
has_rank: species group
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Murinae
type: Class
subclass of: Rodentia
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has alternative id: NCBITaxon:109679
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Bubalus bubalis bubalis
type: Class
subclass of: Bovinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Bos bubalis bubalis

Yersinia enterocolitica subsp. enterocolitica 8081
type: Class
subclass of: Yersinia enterocolitica subsp. enterocolitica
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has exact synonym: Yersinia enterocolitica subsp. enterocolitica str. 8081
has exact synonym: Yersinia enterocolitica subsp. enterocolitica strain 8081
has OBO namespace: ncbi_taxonomy

Rubulavirus
type: Class
subclass of: Rubulavirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Caprine alphaherpesvirus 1
type: Class
subclass of: Varicellovirus
imported from: ncbitaxon.owl
has broad synonym: CpHV-1
has cross-reference: GC_ID:1
has exact synonym: Caprine herpesvirus 1
has exact synonym: Caprine herpesvirus type 1
has exact synonym: goat herpesvirus
has OBO namespace: ncbi_taxonomy

Orbivirus alphaequi
type: Class
subclass of: Orbivirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:10896
has broad synonym: AHSV
has cross-reference: GC_ID:1
has exact synonym: African horse sickness group
has exact synonym: African horse sickness virus
has exact synonym: African horse sickness virus (AHSV)
has exact synonym: African horsesickness virus
has OBO namespace: ncbi_taxonomy
has related synonym: African horse sickness virus AHSV

Bluetongue virus
type: Class
subclass of: Orbivirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:12591
has cross-reference: GC_ID:1
has exact synonym: Bluetongue virus group
has exact synonym: bluetongue virus BTV
has OBO namespace: ncbi_taxonomy

Quailpox virus
type: Class
subclass of: Avipoxvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Parvovirinae
type: Class
subclass of: Cossaviricota
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Aliivibrio salmonicida
type: Class
subclass of: Vibrionaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:18048732
has OBO namespace: ncbi_taxonomy
has related synonym: Vibrio salmonicida

Mammalia
type: Class
subclass of: Amniota
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has exact synonym: mammals
has OBO namespace: ncbi_taxonomy
has related synonym: mammals

Turkey adenovirus 3
type: Class
subclass of: Adenoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has broad synonym: TAdV-3
has cross-reference: GC_ID:1
has exact synonym: Marble spleen disease virus
has exact synonym: Turkey adenovirus serotype 3
has exact synonym: Turkey haemorrhagic enteritis virus
has exact synonym: Turkey hemorrhagic enteritis virus
has exact synonym: hemorrhagic enteritis virus
has OBO namespace: ncbi_taxonomy

Plasmodium (Vinckeia)
type: Class
subclass of: Plasmodium
imported from: ncbitaxon.owl
has_rank: NCBITaxon subgenus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Vinckeia

Plasmodium (Plasmodium)
type: Class
subclass of: Plasmodium
imported from: ncbitaxon.owl
has_rank: NCBITaxon subgenus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Plasmodium

Aconoidasida
type: Class
subclass of: Apicomplexa
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Hematozoa Vivier 1982

Eimeriorina
type: Class
subclass of: Apicomplexa
imported from: ncbitaxon.owl
has_rank: NCBITaxon suborder
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Sarcocystis neurona
type: Class
subclass of: Sarcocystidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Brucella abortus S19
type: Class
subclass of: Brucella abortus
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has exact synonym: Brucella abortus str. S19
has exact synonym: Brucella abortus strain S19
has OBO namespace: ncbi_taxonomy

Canarypox virus
type: Class
subclass of: Avipoxvirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has broad synonym: CNPV
has cross-reference: GC_ID:1
has exact synonym: Avipoxvirus clade B1
has exact synonym: Canary poxvirus
has OBO namespace: ncbi_taxonomy

Brucella microti
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:399128
has cross-reference: GC_ID:11
has cross-reference: PMID:18218934
has OBO namespace: ncbi_taxonomy

Brucella ovis ATCC 25840
type: Class
subclass of: Brucella ovis
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has exact synonym: Brucella ovis str. ATCC 25840
has exact synonym: Brucella ovis strain ATCC 25840
has OBO namespace: ncbi_taxonomy

Neogale vison
type: Class
subclass of: Mustelinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:9667
has cross-reference: GC_ID:1
has exact synonym: American mink
has exact synonym: mink
has OBO namespace: ncbi_taxonomy
has related synonym: Mustela vison
has related synonym: Neovison vison

Picornavirales
type: Class
subclass of: Pisoniviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Brucella suis ATCC 23445
type: Class
subclass of: Brucella suis
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has cross-reference: PMID:19346311
has exact synonym: Brucella suis str. ATCC 23445
has exact synonym: Brucella suis strain ATCC 23445
has OBO namespace: ncbi_taxonomy

Fungi
type: Class
subclass of: Opisthokonta
imported from: ncbitaxon.owl
has_rank: NCBITaxon kingdom
has cross-reference: GC_ID:1
has cross-reference: PMID:11062127
has cross-reference: PMID:12684019
has OBO namespace: ncbi_taxonomy
has related synonym: Mycota
has related synonym: fungi

Moraxella bovis
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Haemophilus bovis
has related synonym: Moraxella (subgen. Moraxella Lwoff 1939) bovis
has related synonym: Moraxella duplex des bovids

Brucella canis ATCC 23365
type: Class
subclass of: Brucella canis
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has cross-reference: PMID:19346311
has exact synonym: Brucella canis str. ATCC 23365
has exact synonym: Brucella canis strain ATCC 23365
has OBO namespace: ncbi_taxonomy

Neisseria meningitidis
type: Class
subclass of: Neisseriales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Diplokokkus intracellularis meningitidis
has related synonym: Micrococcus intracellularis
has related synonym: Micrococcus meningitidis
has related synonym: Micrococcus meningitidis cerebrospinalis
has related synonym: Neisseria weichselbaumii

Psittacid alphaherpesvirus 1
type: Class
subclass of: Iltovirus
imported from: ncbitaxon.owl
has broad synonym: PsHV-1
has cross-reference: GC_ID:1
has exact synonym: Pacheco's disease virus
has exact synonym: Psittacid herpesvirus 1
has OBO namespace: ncbi_taxonomy

Salmoninae
type: Class
subclass of: Salmonidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has exact synonym: trouts, salmons & chars
has OBO namespace: ncbi_taxonomy

Bordetella
type: Class
subclass of: Burkholderiales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:11491321
has OBO namespace: ncbi_taxonomy

Bordetella bronchiseptica
type: Class
subclass of: Bordetella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:514
has cross-reference: GC_ID:11
has cross-reference: PMID:8240949
has cross-reference: PMID:8782670
has cross-reference: PMID:9226899
has OBO namespace: ncbi_taxonomy
has related synonym: Alcaligenes bronchicanis
has related synonym: Alcaligenes bronchisepticus
has related synonym: Bacillus bronchicanis
has related synonym: Bacillus bronchisepticus
has related synonym: Bacterium bronchisepticus
has related synonym: Brucella bronchiseptica
has related synonym: Haemophilus bronchisepticus

Bordetella pertussis
type: Class
subclass of: Bordetella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:8240949
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium tussis-convulsivae
has related synonym: Haemophilus pertussis
has related synonym: Hemophilus pertussis
has related synonym: Microbe de la coqueluche

Bordetella avium
type: Class
subclass of: Bordetella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:4074238
has OBO namespace: ncbi_taxonomy

Enterobacteriaceae
type: Class
subclass of: Enterobacterales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:11
has cross-reference: PMID:10555323
has cross-reference: PMID:10555334
has cross-reference: PMID:16166704
has cross-reference: PMID:27620848
has OBO namespace: ncbi_taxonomy
has related synonym: Enterobacteraceae
has related synonym: enterobacteria
has related synonym: gamma-3 proteobacteria

Bovine viral diarrhea virus 2
type: Class
subclass of: Pestivirus
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:136447
has alternative id: NCBITaxon:64986
has alternative id: NCBITaxon:96055
has broad synonym: BVDV type II
has broad synonym: BVDV-2
has cross-reference: GC_ID:1
has cross-reference: PMID:7747470
has exact synonym: Bovine viral diarrhea virus genotype 2
has exact synonym: Bovine viral diarrhea virus type 2
has exact synonym: Bovine viral diarrhea virus-2
has exact synonym: bovine viral diarrhea virus type II
has exact synonym: pestivirus type 4
has OBO namespace: ncbi_taxonomy

Mycoplasmatota
type: Class
subclass of: Bacillati
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has cross-reference: GC_ID:11
has exact synonym: Tenericutes
has OBO namespace: ncbi_taxonomy
has related synonym: "Mollicutaeota" Oren et al. 2015
has related synonym: "Tenericutes" Murray 1984
has related synonym: Mollicutota

Brucella melitensis ATCC 23457
type: Class
subclass of: Brucella melitensis
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has cross-reference: GC_ID:11
has cross-reference: PMID:19346311
has exact synonym: Brucella melitensis str. ATCC 23457
has exact synonym: Brucella melitensis strain ATCC 23457
has OBO namespace: ncbi_taxonomy

Herpesvirales
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Coccidioides
type: Class
subclass of: Fungi
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Vibrio anguillarum
type: Class
subclass of: Vibrio
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:28167
has alternative id: NCBITaxon:665
has cross-reference: GC_ID:11
has cross-reference: PMID:21296930
has OBO namespace: ncbi_taxonomy
has related synonym: Achromobacter ichthyodermis
has related synonym: Listonella anguillara
has related synonym: Listonella anguillarum
has related synonym: Pseudomonas ichthyodermis
has related synonym: Vibrio ichthyodermis
has related synonym: Vibrio piscium
has related synonym: Vibrio piscium var. japonicus

Isavirus salaris
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:155284
has alternative id: NCBITaxon:86501
has cross-reference: GC_ID:1
has exact synonym: Salmon isavirus
has OBO namespace: ncbi_taxonomy

Dintheria
type: Class
subclass of: Enoplea
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Escherichia coli
type: Class
subclass of: Enterobacteriaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1637691
has alternative id: NCBITaxon:1806490
has alternative id: NCBITaxon:469598
has alternative id: NCBITaxon:662101
has alternative id: NCBITaxon:662104
has cross-reference: GC_ID:11
has cross-reference: PMID:10319482
has exact synonym: E. coli
has exact synonym: Escherichia/Shigella coli
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus coli
has related synonym: Bacterium coli
has related synonym: Bacterium coli commune
has related synonym: Enterococcus coli

Trypanosomatidae
type: Class
subclass of: Discoba
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Leishmania <genus>
type: Class
subclass of: Trypanosomatidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Leishmania
has OBO namespace: ncbi_taxonomy

Leishmania amazonensis
type: Class
subclass of: Leishmania <subgenus>
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:31284
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Leishmania (Leishmania) amazonensis
has related synonym: Leishmania mexicana amazonensis

Leishmania donovani
type: Class
subclass of: Leishmania donovani species complex
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Leishmania (Leishmania) donovani

Leishmania major
type: Class
subclass of: Leishmania <subgenus>
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Leishmania (Leishmania) major
has related synonym: Leishmania tropica major

Tritrichomonas suis
type: Class
subclass of: Metamonada
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:33701
has alternative id: NCBITaxon:5724
has cross-reference: GC_ID:1
has cross-reference: PMID:12046599
has cross-reference: PMID:15734659
has cross-reference: PMID:22000167
has OBO namespace: ncbi_taxonomy

Leishmania infantum
type: Class
subclass of: Leishmania donovani species complex
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:5662
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Leishmania (Leishmania) infantum
has related synonym: Leishmania donovani infantum

Brucella microti CCM 4915
type: Class
subclass of: Brucella microti
imported from: ncbitaxon.owl
has_rank: NCBITaxon strain
has alternative id: NCBITaxon:399127
has cross-reference: GC_ID:11
has cross-reference: PMID:19653890
has exact synonym: Brucella microti str. CCM 4915
has exact synonym: Brucella microti strain CCM 4915
has OBO namespace: ncbi_taxonomy
has related synonym: Brucella sp. CCM 4915

Trypanosoma
type: Class
subclass of: Trypanosomatidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Trypanosoma brucei
type: Class
subclass of: Trypanosoma
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Trypanosoma (Trypanozoon) brucei
has related synonym: Trypanosoma brucei subgroup

Trypanosoma cruzi
type: Class
subclass of: Trypanosoma
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Giardia intestinalis
type: Class
subclass of: Metamonada
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has cross-reference: PMID:11432808
has cross-reference: PMID:19135417
has OBO namespace: ncbi_taxonomy
has related synonym: Giardia duodenalis
has related synonym: Giardia lamblia
has related synonym: Lamblia intestinalis

Entamoeba histolytica
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Naegleria
type: Class
subclass of: Discoba
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Naegleria gruberi
type: Class
subclass of: Naegleria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Naegleria fowleri
type: Class
subclass of: Naegleria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: brain-eating amoeba
has OBO namespace: ncbi_taxonomy

Apicomplexa
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has cross-reference: GC_ID:1
has exact synonym: apicomplexans
has OBO namespace: ncbi_taxonomy
has related synonym: apicomplexans

Eimeria
type: Class
subclass of: Eimeriorina
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Eimeria tenella
type: Class
subclass of: Eimeria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Eimeria maxima
type: Class
subclass of: Eimeria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Cryptosporidium parvum
type: Class
subclass of: Eimeriorina
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:2200815
has alternative id: NCBITaxon:2200816
has alternative id: NCBITaxon:2200817
has alternative id: NCBITaxon:2200818
has alternative id: NCBITaxon:2200819
has alternative id: NCBITaxon:2200820
has alternative id: NCBITaxon:2200821
has alternative id: NCBITaxon:2200822
has alternative id: NCBITaxon:2200823
has alternative id: NCBITaxon:2200824
has alternative id: NCBITaxon:2200825
has alternative id: NCBITaxon:2200826
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Sarcocystidae
type: Class
subclass of: Eimeriorina
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Sarcocystids

Toxoplasma gondii
type: Class
subclass of: Sarcocystidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Plasmodium
type: Class
subclass of: Aconoidasida
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Plasmodium berghei
type: Class
subclass of: Plasmodium (Vinckeia)
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Plasmodium chabaudi
type: Class
subclass of: Plasmodium (Vinckeia)
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Plasmodium falciparum
type: Class
subclass of: Plasmodium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: malaria parasite P. falciparum
has OBO namespace: ncbi_taxonomy
has related synonym: Plasmodium (Laverania) falciparum

Plasmodium knowlesi
type: Class
subclass of: Plasmodium (Plasmodium)
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Plasmodium vivax
type: Class
subclass of: Plasmodium (Plasmodium)
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: malaria parasite P. vivax
has OBO namespace: ncbi_taxonomy
has related synonym: Haemamoeba vivax
has related synonym: Haemamoeba vivax Grassi and Feletti, 1890

Plasmodium yoelii
type: Class
subclass of: Plasmodium (Vinckeia)
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Plasmodium yoelli

Piroplasmida
type: Class
subclass of: Aconoidasida
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has exact synonym: Piroplasmids
has OBO namespace: ncbi_taxonomy

Babesia
type: Class
subclass of: Piroplasmida
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Babesia bovis
type: Class
subclass of: Babesia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Babesia bigemina
type: Class
subclass of: Babesia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Babesia canis
type: Class
subclass of: Babesia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Theileria
type: Class
subclass of: Piroplasmida
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Theileria annulata
type: Class
subclass of: Theileria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Theileria parva
type: Class
subclass of: Theileria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Salmonella
type: Class
subclass of: Enterobacteriaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:10319519
has cross-reference: PMID:10939679
has cross-reference: PMID:12072558
has cross-reference: PMID:15653929
has cross-reference: PMID:15653930
has cross-reference: PMID:3231714
has cross-reference: PMID:37486130
has cross-reference: PMID:9731304
has OBO namespace: ncbi_taxonomy

Salmonella enterica subsp. enterica
type: Class
subclass of: Salmonella
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
has alternative id: NCBITaxon:149049
has cross-reference: GC_ID:11
has cross-reference: PMID:15653929
has cross-reference: PMID:15653930
has cross-reference: PMID:7149525
has OBO namespace: ncbi_taxonomy
has related synonym: Salmonella cholerae-suis subsp. cholerae-suis
has related synonym: Salmonella choleraesuis subsp. choleraesuis
has related synonym: Salmonella enterica I
has related synonym: Salmonella enterica subsp. I
has related synonym: Salmonella enterica subsp. Subsp. I
has related synonym: Salmonella enterica subsp. Subsp. Ixxx

Salmonella enterica subsp. enterica serovar Gallinarum
type: Class
subclass of: Salmonella enterica subsp. enterica
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:41510
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Salmonella enterica serovar Gallinarum
has related synonym: Salmonella gallinarum

Schistosoma
type: Class
subclass of: Protostomia
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Schistosoma japonicum
type: Class
subclass of: Schistosoma
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Schistosoma mansoni
type: Class
subclass of: Schistosoma
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Monkeypox virus Zaire-96-I-16
type: Class
subclass of: Monkeypox virus
imported from: ncbitaxon.owl
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Shigella
type: Class
subclass of: Enterobacteriaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:26834722
has OBO namespace: ncbi_taxonomy

Shigella dysenteriae
type: Class
subclass of: Shigella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:12054222
has exact synonym: Escherichia/Shigella dysenteriae
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus dysenteriae
has related synonym: Bacillus dysentericus
has related synonym: Bacillus shigae
has related synonym: Eberthella dysenteriae
has related synonym: Shigella shigae

Shigella flexneri
type: Class
subclass of: Shigella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has exact synonym: Escherichia flexneri
has exact synonym: Escherichia/Shigella flexneri
has OBO namespace: ncbi_taxonomy
has related synonym: Shigella paradysenteriae

Shigella sonnei
type: Class
subclass of: Shigella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium sonnei

Yersinia <enterobacteria>
type: Class
subclass of: Yersiniaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has exact synonym: Yersinia
has OBO namespace: ncbi_taxonomy

Yersinia pestis
type: Class
subclass of: Yersinia pseudotuberculosis complex
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:15084509
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus pestis
has related synonym: Bacterium pestis
has related synonym: Pasteurella pestis
has related synonym: Pestisella pestis
has related synonym: Yersinia pseudotuberculosis subsp. pestis

Yersinia pseudotuberculosis
type: Class
subclass of: Yersinia pseudotuberculosis complex
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1161941
has cross-reference: GC_ID:11
has cross-reference: PMID:2223608
has cross-reference: PMID:23919959
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus pseudotuberkulosis
has related synonym: Bacterium pseudotuberculosis
has related synonym: Pasteurella lymphangitidis
has related synonym: Pasteurella pseudotuberculosis
has related synonym: Shigella pseudotuberculosis

Trichinella spiralis
type: Class
subclass of: Enoplea
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Trichina spiralis

Edwardsiella <enterobacteria>
type: Class
subclass of: Enterobacterales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has exact synonym: Edwardsiella
has OBO namespace: ncbi_taxonomy
has related synonym: Asakusa group
has related synonym: Bartholomew group

Edwardsiella tarda
type: Class
subclass of: Edwardsiella <enterobacteria>
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1471792
has alternative id: NCBITaxon:1471793
has cross-reference: GC_ID:11
has cross-reference: PMID:27539016
has OBO namespace: ncbi_taxonomy
has related synonym: Edwardsiella anguillimortifera
has related synonym: Paracolobactrum anguillimortiferum

Vibrionaceae
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:11
has cross-reference: PMID:15143042
has cross-reference: PMID:4954820
has cross-reference: PMID:8427811
has OBO namespace: ncbi_taxonomy
has related synonym: gamma-3 proteobacteria

Aeromonas
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:11155981
has cross-reference: PMID:12067377
has cross-reference: PMID:12807216
has cross-reference: PMID:1380286
has cross-reference: PMID:1380289
has cross-reference: PMID:15388703
has cross-reference: PMID:16560691
has cross-reference: PMID:17012583
has cross-reference: PMID:17158971
has cross-reference: PMID:19567585
has cross-reference: PMID:7520733
has cross-reference: PMID:8347521
has cross-reference: PMID:8934910
has OBO namespace: ncbi_taxonomy

Aeromonas hydrophila
type: Class
subclass of: Aeromonas
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1426505
has alternative id: NCBITaxon:1426713
has alternative id: NCBITaxon:1471787
has alternative id: NCBITaxon:1471788
has alternative id: NCBITaxon:1538469
has alternative id: NCBITaxon:329135
has alternative id: NCBITaxon:329140
has alternative id: NCBITaxon:346633
has alternative id: NCBITaxon:346634
has alternative id: NCBITaxon:582196
has alternative id: NCBITaxon:582198
has alternative id: NCBITaxon:582214
has alternative id: NCBITaxon:582215
has alternative id: NCBITaxon:582216
has alternative id: NCBITaxon:582217
has alternative id: NCBITaxon:582218
has alternative id: NCBITaxon:582219
has alternative id: NCBITaxon:582220
has alternative id: NCBITaxon:582221
has alternative id: NCBITaxon:582222
has alternative id: NCBITaxon:582223
has alternative id: NCBITaxon:582224
has alternative id: NCBITaxon:582225
has alternative id: NCBITaxon:582226
has alternative id: NCBITaxon:582228
has alternative id: NCBITaxon:582229
has alternative id: NCBITaxon:582231
has alternative id: NCBITaxon:582236
has alternative id: NCBITaxon:582237
has alternative id: NCBITaxon:582240
has alternative id: NCBITaxon:582250
has alternative id: NCBITaxon:582251
has alternative id: NCBITaxon:582253
has alternative id: NCBITaxon:582254
has alternative id: NCBITaxon:582265
has alternative id: NCBITaxon:582266
has alternative id: NCBITaxon:582267
has alternative id: NCBITaxon:582279
has alternative id: NCBITaxon:582282
has alternative id: NCBITaxon:582284
has alternative id: NCBITaxon:582286
has alternative id: NCBITaxon:582287
has alternative id: NCBITaxon:582289
has alternative id: NCBITaxon:582290
has alternative id: NCBITaxon:582291
has alternative id: NCBITaxon:582292
has alternative id: NCBITaxon:582295
has alternative id: NCBITaxon:582297
has alternative id: NCBITaxon:582299
has alternative id: NCBITaxon:582300
has alternative id: NCBITaxon:582302
has alternative id: NCBITaxon:582303
has alternative id: NCBITaxon:582304
has alternative id: NCBITaxon:582305
has alternative id: NCBITaxon:582306
has alternative id: NCBITaxon:582307
has alternative id: NCBITaxon:582308
has alternative id: NCBITaxon:582309
has alternative id: NCBITaxon:582310
has alternative id: NCBITaxon:582311
has alternative id: NCBITaxon:582312
has alternative id: NCBITaxon:582313
has alternative id: NCBITaxon:582314
has alternative id: NCBITaxon:582315
has alternative id: NCBITaxon:582316
has alternative id: NCBITaxon:582317
has alternative id: NCBITaxon:582318
has alternative id: NCBITaxon:582319
has alternative id: NCBITaxon:582320
has alternative id: NCBITaxon:582321
has alternative id: NCBITaxon:582322
has alternative id: NCBITaxon:582323
has alternative id: NCBITaxon:582324
has alternative id: NCBITaxon:98358
has cross-reference: GC_ID:11
has cross-reference: PMID:16560691

Aeromonas salmonicida
type: Class
subclass of: Aeromonas
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1055664
has alternative id: NCBITaxon:697046
has cross-reference: GC_ID:11
has cross-reference: PMID:19965992
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus salmonicida
has related synonym: Bacterium salmonicida
has related synonym: Proteus salmonicida

Borreliella
type: Class
subclass of: Spirochaetales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:1618316
has cross-reference: GC_ID:11
has cross-reference: PMID:10515907
has cross-reference: PMID:10758897
has cross-reference: PMID:16585709
has cross-reference: PMID:24744012
has cross-reference: PMID:27930271
has cross-reference: PMID:28141502
has cross-reference: PMID:30154058
has cross-reference: PMID:30586413
has cross-reference: PMID:31454394
has cross-reference: PMID:31722850
has cross-reference: PMID:31836459
has cross-reference: PMID:32320380
has cross-reference: PMID:35816828
has cross-reference: PMID:36748499
has cross-reference: PMID:7981102
has cross-reference: PMID:8573491
has cross-reference: PMID:8934900
has cross-reference: PMID:8995795
has cross-reference: PMID:9336916
has exact synonym: Lyme Disease Borrelia
has OBO namespace: ncbi_taxonomy
has related synonym: Borrelia burgdorferi group
has related synonym: Borrelia burgdorferi sensu lato

Vibrio
type: Class
subclass of: Vibrionaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:705
has cross-reference: GC_ID:11
has cross-reference: PMID:1371064
has cross-reference: PMID:17978204
has cross-reference: PMID:21057054
has cross-reference: PMID:21296930
has cross-reference: PMID:24409173
has cross-reference: PMID:4935323
has cross-reference: PMID:7520733
has cross-reference: PMID:8590667
has OBO namespace: ncbi_taxonomy
has related synonym: Beneckea
has related synonym: Listonella
has related synonym: Microspira
has related synonym: Pacinia

Vibrio cholerae
type: Class
subclass of: Vibrio
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:140100
has alternative id: NCBITaxon:376726
has cross-reference: GC_ID:11
has cross-reference: PMID:1015934
has cross-reference: PMID:9272984
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillo virgola del Koch
has related synonym: Bacillus cholerae
has related synonym: Bacillus cholerae-asiaticae
has related synonym: Kommabacillus
has related synonym: Liquidivibrio cholerae
has related synonym: Microspira comma
has related synonym: Pacinia cholerae-asiaticae
has related synonym: Spirillum cholerae
has related synonym: Spirillum cholerae-asiaticae
has related synonym: Vibrio albensis
has related synonym: Vibrio cholera
has related synonym: Vibrio cholerae biovar albensis
has related synonym: Vibrio cholerae bv. albensis
has related synonym: Vibrio cholerae-asiaticae
has related synonym: Vibrio comma

Edwardsiella ictaluri
type: Class
subclass of: Edwardsiella <enterobacteria>
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Avihepatovirus A
type: Class
subclass of: Picornaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:352473
has broad synonym: DHV-1
has cross-reference: GC_ID:1
has exact synonym: Duck hepatitis A virus
has exact synonym: Duck hepatitis virus 1
has exact synonym: Duck hepatitis virus type 1
has OBO namespace: ncbi_taxonomy

Coronavirinae
type: Class
subclass of: Coronaviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Alphacoronavirus 1
type: Class
subclass of: Orthocoronavirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Alphacoronavirus-1
has OBO namespace: ncbi_taxonomy

Betacoronavirus
type: Class
subclass of: Orthocoronavirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:156439
has cross-reference: GC_ID:1
has exact synonym: Coronavirus group 2
has exact synonym: Group 2 species
has OBO namespace: ncbi_taxonomy
has related synonym: Coronavirus

Severe acute respiratory syndrome-related coronavirus
type: Class
subclass of: Betacoronavirus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:227859
has alternative id: NCBITaxon:311178
has broad synonym: HCoV-SARS
has broad synonym: SARS
has broad synonym: SARSr-CoV
has broad synonym: SARSrCoV
has cross-reference: GC_ID:1
has exact synonym: Human coronavirus (strain SARS)
has exact synonym: SARS-like coronavirus
has exact synonym: SARS-related coronavirus
has OBO namespace: ncbi_taxonomy

Tremovirus A
type: Class
subclass of: Heptrevirinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Triatominae
type: Class
subclass of: Neoptera
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has exact synonym: kissing bugs
has OBO namespace: ncbi_taxonomy

Pasteurellaceae
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:11
has cross-reference: PMID:10843050
has cross-reference: PMID:15280320
has cross-reference: PMID:15388716
has cross-reference: PMID:17220461
has cross-reference: PMID:2223605
has cross-reference: PMID:29923825
has OBO namespace: ncbi_taxonomy

Actinobacillus pleuropneumoniae
type: Class
subclass of: Pasteurellaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:1847295
has OBO namespace: ncbi_taxonomy
has related synonym: Haemophilus pleuropneumoniae

Anopheles <genus>
type: Class
subclass of: Neoptera
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: Anopheles
has OBO namespace: ncbi_taxonomy

Thiotrichales
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Thiomicrospira group
has related synonym: Thiothrix/Francisella group

Haemophilus
type: Class
subclass of: Pasteurellaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:1736960
has OBO namespace: ncbi_taxonomy

Haemophilus influenzae
type: Class
subclass of: Haemophilus
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium influenzae
has related synonym: Coccobacillus pfeifferi
has related synonym: Haemophilus meningitidis
has related synonym: Influenza-bacillus
has related synonym: Mycobacterium influenzae

Histophilus somni
type: Class
subclass of: Pasteurellaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:163489
has alternative id: NCBITaxon:214923
has cross-reference: GC_ID:11
has cross-reference: PMID:13130032
has cross-reference: PMID:4333932
has OBO namespace: ncbi_taxonomy
has related synonym: Haemophilus agni
has related synonym: Haemophilus ovis
has related synonym: Haemophilus somnifer
has related synonym: Haemophilus somnus
has related synonym: Hemophilus agni
has related synonym: Histophilus ovis

Glaesserella parasuis
type: Class
subclass of: Pasteurellaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:5821848
has OBO namespace: ncbi_taxonomy
has related synonym: Haemophilus parasuis

Pasteurella multocida
type: Class
subclass of: Pasteurellaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:15184562
has OBO namespace: ncbi_taxonomy
has related synonym: Bacterium multocidum
has related synonym: Micrococcus gallicidus
has related synonym: Pasteurella cholerae-gallinarum
has related synonym: Pasteurella gallicida

Mannheimia haemolytica
type: Class
subclass of: Pasteurellaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:746
has cross-reference: GC_ID:11
has cross-reference: PMID:10028248
has cross-reference: PMID:8782683
has OBO namespace: ncbi_taxonomy
has related synonym: Pasteurella haemolytica Newsom and Cross 1932 (Approved Lists 1980)

Rickettsiales
type: Class
subclass of: Alphaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has cross-reference: PMID:11760958
has cross-reference: PMID:8240958
has exact synonym: rickettsias
has OBO namespace: ncbi_taxonomy
has related synonym: alpha-1 proteobacteria

Arteriviridae
type: Class
subclass of: Nidovirales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Nidovirales
type: Class
subclass of: Pisoniviricetes
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Theileria lestoquardi
type: Class
subclass of: Theileria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:61430
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Theileria hirci

Vertebrata <vertebrates>
type: Class
subclass of: Bilateria
imported from: ncbitaxon.owl
has_rank: NCBITaxon clade
has cross-reference: GC_ID:1
has exact synonym: Vertebrata
has exact synonym: vertebrates
has OBO namespace: ncbi_taxonomy
has related synonym: vertebrates

Coxiella burnetii
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:9226923
has OBO namespace: ncbi_taxonomy
has related synonym: Rickettsia burneti
has related synonym: Rickettsia diaporica

Rickettsia
type: Class
subclass of: Rickettsiales
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:10939649
has cross-reference: PMID:11491333
has cross-reference: PMID:14662925
has cross-reference: PMID:9103608
has OBO namespace: ncbi_taxonomy

Actinopterygii
type: Class
subclass of: Euteleostomi
imported from: ncbitaxon.owl
has_rank: NCBITaxon superclass
has cross-reference: GC_ID:1
has exact synonym: fish
has exact synonym: fishes
has exact synonym: ray-finned fishes
has OBO namespace: ncbi_taxonomy
has related synonym: Actinopterygi
has related synonym: Osteichthyes
has related synonym: bony fishes

Clostridium perfringens C
type: Class
subclass of: Clostridium perfringens
imported from: ncbitaxon.owl
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Siluriformes
type: Class
subclass of: Clupeocephala
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has exact synonym: catfishes
has OBO namespace: ncbi_taxonomy

Salmonidae
type: Class
subclass of: Euteleosteomorpha
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has cross-reference: PMID:15062801
has exact synonym: salmonids
has OBO namespace: ncbi_taxonomy

Oncorhynchus mykiss
type: Class
subclass of: Salmoninae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:1311475
has cross-reference: GC_ID:1
has exact synonym: rainbow trout
has OBO namespace: ncbi_taxonomy
has related synonym: Oncorhynchus nerka mykiss
has related synonym: Parasalmo mykiss
has related synonym: Salmo mykiss

Burkholderiales
type: Class
subclass of: Betaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has cross-reference: PMID:16403855
has OBO namespace: ncbi_taxonomy
has related synonym: Burkholderia/Oxalobacter/Ralstonia group

Chlamydia
type: Class
subclass of: Pseudomonadati
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:83553
has cross-reference: GC_ID:11
has cross-reference: PMID:10319462
has cross-reference: PMID:11211265
has cross-reference: PMID:21048221
has cross-reference: PMID:21048222
has cross-reference: PMID:23620152
has cross-reference: PMID:25618261
has cross-reference: PMID:9103632
has cross-reference: PMID:9103637
has OBO namespace: ncbi_taxonomy
has related synonym: "Prowazekia" Coles 1953
has related synonym: Bedsonia
has related synonym: Chlamydophila
has related synonym: Miyagawanella
has related synonym: Rakeia
has related synonym: Rickettsiaformis

Chlamydia trachomatis
type: Class
subclass of: Chlamydia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:10192388
has cross-reference: PMID:10319462
has cross-reference: PMID:8102247
has cross-reference: PMID:8347519
has OBO namespace: ncbi_taxonomy
has related synonym: Chlamydozoon trachomatis
has related synonym: Rickettsia trachomae
has related synonym: Rickettsia trachomatis

Escherichia coli O157:H7
type: Class
subclass of: Escherichia coli
imported from: ncbitaxon.owl
has_rank: NCBITaxon serotype
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Chlamydia psittaci
type: Class
subclass of: Chlamydia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:812
has cross-reference: GC_ID:11
has cross-reference: PMID:10319462
has cross-reference: PMID:12807198
has cross-reference: PMID:8102247
has cross-reference: PMID:8347519
has OBO namespace: ncbi_taxonomy
has related synonym: Chlamydophila psittaci
has related synonym: Chlamydozoon psittaci
has related synonym: Ehrlichia psittaci
has related synonym: Rickettsia psittaci
has related synonym: Rickettsiaformis psittacosis

Chlamydia abortus
type: Class
subclass of: Chlamydia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:10319462
has cross-reference: PMID:12807198
has cross-reference: PMID:25618261
has OBO namespace: ncbi_taxonomy
has related synonym: Chlamydia psittaci (Lillie 1930) Page 1968
has related synonym: Chlamydia psittaci serotype 1
has related synonym: Chlamydophila abortus

Chlamydia pneumoniae
type: Class
subclass of: Chlamydia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:811
has cross-reference: GC_ID:11
has cross-reference: PMID:10319462
has cross-reference: PMID:8102247
has cross-reference: PMID:8347519
has OBO namespace: ncbi_taxonomy
has related synonym: Chlamydophila pneumoniae

Chlamydia muridarum
type: Class
subclass of: Chlamydia
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:10319462
has exact synonym: agent of mouse pneumonitis
has OBO namespace: ncbi_taxonomy
has related synonym: Chlamydia trachomatis MoPn

Porphyromonas
type: Class
subclass of: Bacteroidota
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:11
has cross-reference: PMID:15774632
has cross-reference: PMID:24158948
has cross-reference: PMID:25481042
has cross-reference: PMID:8186083
has cross-reference: PMID:8590687
has OBO namespace: ncbi_taxonomy

Mycobacteriales
type: Class
subclass of: Bacillati
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has alternative id: NCBITaxon:1761
has cross-reference: GC_ID:11
has cross-reference: PMID:11837321
has cross-reference: PMID:1736962
has cross-reference: PMID:19244447
has cross-reference: PMID:31157615
has OBO namespace: ncbi_taxonomy
has related synonym: Corynebacteriales
has related synonym: Corynebacteriales Goodfellow and Jones 2015
has related synonym: Corynebacteriineae
has related synonym: Corynebacteriineae corrig. Stackebrandt et al. 1997
has related synonym: Corynebacterineae
has related synonym: Mycobacteriales Janke 1924 (Approved Lists 1980)
has related synonym: Mycobacteriineae

Porcine circovirus 2
type: Class
subclass of: Shotokuvirae
imported from: ncbitaxon.owl
has broad synonym: PCV2
has cross-reference: GC_ID:1
has exact synonym: Porcine circovirus Type II
has exact synonym: Porcine circovirus type 2
has exact synonym: Porcine circovirus-2
has OBO namespace: ncbi_taxonomy

Aves
type: Class
subclass of: Sauria
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:1
has exact synonym: birds
has OBO namespace: ncbi_taxonomy
has related synonym: avian
has related synonym: birds

Neognathae
type: Class
subclass of: Aves
imported from: ncbitaxon.owl
has_rank: NCBITaxon infraclass
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Anas
type: Class
subclass of: Galloanserae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has exact synonym: ducks
has OBO namespace: ncbi_taxonomy

Phasianidae
type: Class
subclass of: Galloanserae
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has alternative id: NCBITaxon:9099
has cross-reference: GC_ID:1
has exact synonym: turkeys
has OBO namespace: ncbi_taxonomy

Leptospira interrogans serovar Icterohaemorrhagiae
type: Class
subclass of: Leptospira interrogans
imported from: ncbitaxon.owl
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Gallus gallus
type: Class
subclass of: Phasianidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: Gallus domesticus
has exact synonym: bantam
has exact synonym: chicken
has exact synonym: chickens
has OBO namespace: ncbi_taxonomy
has related synonym: Gallus gallus domesticus
has related synonym: Phasianus gallus

Salmonella enterica subsp. enterica serovar Typhi
type: Class
subclass of: Salmonella enterica subsp. enterica
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:41530
has alternative id: NCBITaxon:601
has alternative id: NCBITaxon:72667
has cross-reference: GC_ID:11
has cross-reference: PMID:10319519
has cross-reference: PMID:10758910
has cross-reference: PMID:15653930
has cross-reference: PMID:16558776
has cross-reference: PMID:9336938
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus typhi
has related synonym: Bacterium (subgen. Eberthella) typhi
has related synonym: Salmonella choleraesuis serovar Typhi
has related synonym: Salmonella choleraesuis typhi
has related synonym: Salmonella enterica ser. typhi
has related synonym: Salmonella enterica serotype Typhi
has related synonym: Salmonella enterica serovar Typhi
has related synonym: Salmonella typhi

Salmonella enterica subsp. enterica serovar Typhimurium
type: Class
subclass of: Salmonella enterica subsp. enterica
imported from: ncbitaxon.owl
has alternative id: NCBITaxon:41532
has alternative id: NCBITaxon:59210
has alternative id: NCBITaxon:602
has cross-reference: GC_ID:11
has cross-reference: PMID:10758910
has cross-reference: PMID:15653930
has cross-reference: PMID:9336938
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus typhimurium
has related synonym: Salmonella choleraesuis serotype typhimurium
has related synonym: Salmonella enterica 1,4,[5],12,:i:1,2
has related synonym: Salmonella enterica ser. typhimurium
has related synonym: Salmonella enterica serotype Typhimurium
has related synonym: Salmonella enterica serovar Typhimurium
has related synonym: Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:1,2
has related synonym: Salmonella typhi-murium
has related synonym: Salmonella typhimurium

Meleagris gallopavo
type: Class
subclass of: Phasianidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: common turkey
has exact synonym: turkey
has exact synonym: wild turkey
has OBO namespace: ncbi_taxonomy

Bacilli
type: Class
subclass of: Bacillota
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy
has related synonym: Bacillus/Lactobacillus/Streptococcus group
has related synonym: Firmibacteria

Enterobacterales
type: Class
subclass of: Gammaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:11
has cross-reference: PMID:27620848
has OBO namespace: ncbi_taxonomy
has related synonym: Enterobacteriaceae and related endosymbionts
has related synonym: Enterobacteriaceae group
has related synonym: Enterobacteriales
has related synonym: gamma-3 proteobacteria

Artiodactyla
type: Class
subclass of: Laurasiatheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has exact synonym: even-toed ungulates & whales
has OBO namespace: ncbi_taxonomy
has related synonym: Cetartiodactyla
has related synonym: even-toed ungulates & whales

Psittacidae
type: Class
subclass of: Australaves
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has exact synonym: parrot
has exact synonym: parrots
has OBO namespace: ncbi_taxonomy

Leptospira sp. Pomona
type: Class
subclass of: Leptospira
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has OBO namespace: ncbi_taxonomy

Primates
type: Class
subclass of: Euarchontoglires
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has exact synonym: primate
has OBO namespace: ncbi_taxonomy
has related synonym: Primata
has related synonym: primates

Platyrrhini
type: Class
subclass of: Simiiformes
imported from: ncbitaxon.owl
has_rank: NCBITaxon parvorder
has cross-reference: GC_ID:1
has exact synonym: New World monkeys
has exact synonym: monkey
has exact synonym: monkeys
has OBO namespace: ncbi_taxonomy

Neorickettsia risticii
type: Class
subclass of: Rickettsiales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:11
has cross-reference: PMID:11760958
has cross-reference: PMID:1736961
has cross-reference: PMID:7537065
has exact synonym: Potomac horse fever agent
has exact synonym: equine monocytic ehrlichiosis agent
has OBO namespace: ncbi_taxonomy
has related synonym: Ehrlichia risticii

Catarrhini
type: Class
subclass of: Simiiformes
imported from: ncbitaxon.owl
has_rank: NCBITaxon parvorder
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Chlorocebus aethiops
type: Class
subclass of: Catarrhini
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: African green monkey
has exact synonym: African green monkeys
has exact synonym: grivet
has exact synonym: savanah monkey
has OBO namespace: ncbi_taxonomy
has related synonym: Cercopithecus aethiops
has related synonym: Ceropithecus aethiops
has related synonym: Simia aethiops

Homo sapiens
type: Class
subclass of: Catarrhini
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: human
has OBO namespace: ncbi_taxonomy

Canidae
type: Class
subclass of: Caniformia
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has exact synonym: dog, coyote, wolf, fox
has OBO namespace: ncbi_taxonomy

Canis
type: Class
subclass of: Canidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Canis lupus
type: Class
subclass of: Canis
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: gray wolf
has exact synonym: grey wolf
has OBO namespace: ncbi_taxonomy

Canis lupus familiaris
type: Class
subclass of: Canis lupus
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
has cross-reference: GC_ID:1
has exact synonym: dog
has exact synonym: dogs
has OBO namespace: ncbi_taxonomy
has related synonym: Canis borealis
has related synonym: Canis canis
has related synonym: Canis domesticus
has related synonym: Canis familiaris
has related synonym: Canis lupus borealis

Vulpes
type: Class
subclass of: Canidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has alternative id: NCBITaxon:68731
has alternative id: NCBITaxon:9609
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy
has related synonym: Fennecus

Procyon lotor
type: Class
subclass of: Musteloidea
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: northern raccoon
has exact synonym: raccoon
has OBO namespace: ncbi_taxonomy
has related synonym: Ursus lotor

Mustela putorius furo
type: Class
subclass of: Mustelinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
has alternative id: NCBITaxon:77150
has cross-reference: GC_ID:1
has exact synonym: black ferret
has exact synonym: domestic ferret
has exact synonym: ferret
has OBO namespace: ncbi_taxonomy
has related synonym: Mustela furo

Felis
type: Class
subclass of: Carnivora
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Felis catus
type: Class
subclass of: Felis
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:36475
has cross-reference: GC_ID:1
has cross-reference: PMID:17600185
has cross-reference: PMID:8581300
has cross-reference: PMID:8603894
has exact synonym: cat
has exact synonym: cats
has exact synonym: domestic cat
has OBO namespace: ncbi_taxonomy
has related synonym: Felis domesticus
has related synonym: Felis silvestris catus

Bacteroidota
type: Class
subclass of: Pseudomonadati
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
has alternative id: NCBITaxon:171554
has cross-reference: GC_ID:11
has cross-reference: PMID:11541229
has cross-reference: PMID:11542017
has cross-reference: PMID:28066339
has exact synonym: BCF group
has exact synonym: Bacteroides-Cytophaga-Flexibacter group
has exact synonym: CFB group
has exact synonym: Cytophaga-Flexibacter-Bacteroides phylum
has OBO namespace: ncbi_taxonomy
has related synonym: "Bacteroidota" Whitman et al. 2018
has related synonym: Bacteroidetes
has related synonym: CFB group bacteria
has related synonym: Sphingobacteria

Balaenoptera borealis
type: Class
subclass of: Artiodactyla
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: sei whale
has OBO namespace: ncbi_taxonomy

Equidae
type: Class
subclass of: Laurasiatheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has exact synonym: horses
has OBO namespace: ncbi_taxonomy

Equus caballus
type: Class
subclass of: Equidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: domestic horse
has exact synonym: equine
has exact synonym: horse
has OBO namespace: ncbi_taxonomy
has related synonym: Equus przewalskii f. caballus
has related synonym: Equus przewalskii forma caballus

Sus scrofa
type: Class
subclass of: Artiodactyla
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: pig
has exact synonym: pigs
has exact synonym: swine
has exact synonym: wild boar
has OBO namespace: ncbi_taxonomy

Cervidae
type: Class
subclass of: Pecora
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has exact synonym: deer
has OBO namespace: ncbi_taxonomy

Bovidae
type: Class
subclass of: Pecora
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Bison
type: Class
subclass of: Bovinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Bison bison
type: Class
subclass of: Bison
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has cross-reference: GC_ID:1
has exact synonym: American bison
has exact synonym: Bison
has OBO namespace: ncbi_taxonomy
has related synonym: Bos (Bison) bison
has related synonym: Bos bison

Bos taurus
type: Class
subclass of: Bovinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:272461
has cross-reference: GC_ID:1
has exact synonym: bovine
has exact synonym: cow
has exact synonym: dairy cow
has exact synonym: domestic cattle
has exact synonym: domestic cow
has exact synonym: ox
has OBO namespace: ncbi_taxonomy
has related synonym: Bos bovis
has related synonym: Bos primigenius taurus

Capra hircus
type: Class
subclass of: Caprinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:57076
has cross-reference: GC_ID:1
has exact synonym: domestic goat
has exact synonym: goat
has exact synonym: goats
has OBO namespace: ncbi_taxonomy
has related synonym: Capra aegagrus hircus

Ovis
type: Class
subclass of: Caprinae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Ovis aries
type: Class
subclass of: Ovis
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:9936
has cross-reference: GC_ID:1
has exact synonym: domestic sheep
has exact synonym: lambs
has exact synonym: sheep
has exact synonym: wild sheep
has OBO namespace: ncbi_taxonomy
has related synonym: Ovis ammon aries
has related synonym: Ovis orientalis aries
has related synonym: Ovis ovis

Flavobacterium columnare
type: Class
subclass of: Flavobacteriales
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:29531
has cross-reference: GC_ID:11
has cross-reference: PMID:11594628
has cross-reference: PMID:16560903
has cross-reference: PMID:29593693
has OBO namespace: ncbi_taxonomy
has related synonym: Chondrococcus columnaris
has related synonym: Cytophaga columnaris
has related synonym: Flavobacterium columnare (Bernardet and Grimont 1989) Bernardet et al. 1996
has related synonym: Flexibacter columnaris
has related synonym: Flexibacter columnaris (ex Davis 1922) Bernardet and Grimont 1989

Caprinae
type: Class
subclass of: Bovidae
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has cross-reference: GC_ID:1
has OBO namespace: ncbi_taxonomy

Oryctolagus cuniculus
type: Class
subclass of: Glires
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has alternative id: NCBITaxon:34833
has alternative id: NCBITaxon:9985
has cross-reference: GC_ID:1
has exact synonym: European rabbit
has exact synonym: Japanese white rabbit
has exact synonym: domestic rabbit
has exact synonym: rabbit
has exact synonym: rabbits
has OBO namespace: ncbi_taxonomy
has related synonym: Lepus cuniculus

Rodentia
type: Class
subclass of: Glires
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has cross-reference: GC_ID:1
has exact synonym: rodent
has OBO namespace: ncbi_taxonomy
has related synonym: rodents

Tuberculin Skin Test
type: Class
subclass of: assay
definition: A test to determine if a subject has ever had a tuberculosis infection. A small amount of purified tuberculosis protein is placed under the skin of the forearm and a positive skin reaction indicates previous exposure to Mycobacterium tuberculosis.
imported from: ncit.owl

adverse event
type: Class
subclass of: pathological bodily process
definition: 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.
editor note: 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'.
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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'.
term editor: Yongqun He
alternative label: AE
alternative label: adverse reaction
definition source: WEB: http://en.wikipedia.org/wiki/Adverse_event
definition source: WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
imported from: oae.owl
comment: The OAE official website is: http://www.oae-ontology.org/.

vaccine adverse event
type: Class
subclass of: adverse event
definition: an adverse event that occurs after a vaccination.
term editor: YH
imported from: oae.owl

contraindication
type: Class
subclass of: disposition
definition: 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.
term editor: Yongqun He, Sirarat Sarntivijai, Mathias Brochhausen, William Hogan, ‎Philip E. Empey
definition source: http://en.wikipedia.org/wiki/Contraindication
imported from: oae.owl

vaccine-induced adverse event
type: Class
subclass of: vaccine adverse event
definition: an adverse event that is induced by a vaccination.
term editor: YH
imported from: oae.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: '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.)
editor note: 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.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: 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)
imported from: obi.owl

regulator role
type: Class
subclass of: regulatory role
editor preferred term: regulator role
example of usage: 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
has curation status: IAO_0000120
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
term editor: Person:Jennifer Fostel
alternative label: regulator
definition source: OBI
imported from: obi.owl

regulation-assigned role
type: Class
subclass of: regulatory role
editor preferred term: regulation-assigned role
example of usage: Approval letter
has curation status: IAO_0000123
definition: Regulation-assigned role is a regulatory role defined by legislation or governmental orders
term editor: Person: Jennifer Fostel
imported from: obi.owl

regulatory role
type: Class
subclass of: role
editor preferred term: regulatory role
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
has curation status: IAO_0000120
definition: 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.
term editor: GROUP: Role branch
definition source: OBI, CDISC
curator note: 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
imported from: obi.owl

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
editor preferred term: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: IAO_0000122
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
imported from: obi.owl

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred term: evaluant role
example of usage: 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.
has curation status: IAO_0000122
definition: 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
editor note: 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)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred term: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: IAO_0000122
definition: A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
editor note: Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
term editor: PlanAndPlannedProcess Branch
alternative label: measuring
alternative label: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method

reagent role
type: Class
subclass of: reactant role
editor preferred term: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: IAO_0000120
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
term editor: PERSON:Matthew Brush
alternative label: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
imported from: obi.owl
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred term: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: IAO_0000122
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative label: material transformation
definition source: OBI branch derived
imported from: obi.owl

population
type: Class
subclass of: material entity
editor preferred term: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: IAO_0000125
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
term editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process
imported from: obi.owl

antigen role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: immune response
editor preferred term: antigen role
has curation status: IAO_0000123
definition: A role of a material entity that is being recognized in whole or in part by receptors of the immune system such as antibodies or T cell receptors.
editor note: An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens
term editor: Role Branch
definition source: OBI
curator note: 9Mar09 waiting for discussion with immunology terms
imported from: obi.owl

organization
type: Class
subclass of: material entity
editor preferred term: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: IAO_0000122
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: obi.owl

protocol
type: Class
subclass of: plan specification
editor preferred term: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: IAO_0000122
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: obi.owl
ISA alternative term: study protocol

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: material combination
subclass of: Restriction
  on property: realizes
  some values from: material to be added role
subclass of: Restriction
  on property: realizes
  some values from: target of material addition role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred term: adding a material entity into a target
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
has curation status: IAO_0000122
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
term editor: BP
definition source: branch derived
imported from: obi.owl

intraperitoneal injection
type: Class
equivalent class: Class
  intersection of: intraperitoneal administration
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
subclass of: injection
subclass of: intraperitoneal administration
editor preferred term: intraperitoneal injection
has curation status: IAO_0000123
definition: is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
term editor: BP
imported from: obi.owl

material to be added role
type: Class
subclass of: role
editor preferred term: material to be added role
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
has curation status: IAO_0000120
definition: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
term editor: Role Branch
definition source: OBI
curator note: 9 March 09 from discussion with PA branch
imported from: obi.owl

transfer function
type: Class
subclass of: function
editor preferred term: transfer function
has curation status: IAO_0000122
definition: A transfer function is a function to displace a material from one location to another.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

syringe
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: syringe
example of usage: Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
has curation status: IAO_0000122
definition: A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
term editor: Philippe Rocca-Serra
definition source: OBI Instrument adapted from Wikipedia
imported from: obi.owl

injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
editor preferred term: injection
example of usage: Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
has curation status: IAO_0000120
definition: injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
term editor: Philippe Rocca-Serra
definition source: OBI Biomaterial
imported from: obi.owl

intraperitoneal administration
type: Class
equivalent class: Class
  intersection of: administering substance in vivo
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: role of
        some values from: peritoneum
subclass of: administering substance in vivo
editor preferred term: intraperitoneal administration
example of usage: Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
has curation status: IAO_0000123
definition: The administration of a substance into the peritoneum of an organism
term editor: Person:Bjoern Peters
imported from: obi.owl

adding material objective
type: Class
subclass of: material combination objective
editor preferred term: adding material objective
example of usage: creating a mouse infected with LCM virus
has curation status: IAO_0000122
definition: is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
term editor: BP
imported from: obi.owl

assay objective
type: Class
subclass of: objective specification
editor preferred term: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: IAO_0000122
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
term editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

target of material addition role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
editor preferred term: target of material addition role
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
has curation status: IAO_0000120
definition: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
editor note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
term editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: regulator role
subclass of: organization
editor preferred term: regulatory agency
example of usage: The US Environmental Protection Agency
has curation status: IAO_0000122
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator
imported from: obi.owl

material transformation objective
type: Class
subclass of: objective specification
editor preferred term: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: IAO_0000122
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative label: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
editor preferred term: manufacturing
has curation status: IAO_0000122
definition: A planned process with the objective to produce a processed material which will have a function for future use.
editor note: A person or organization (having manufacturer role) is a participant in this process
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred term: manufacturing objective
has curation status: IAO_0000122
definition: is the objective to manufacture a material of a certain function (device)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred term: manufacturer role
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
has curation status: IAO_0000123
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
term editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

scattered molecular aggregate
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has grain
  some values from: molecular entity
subclass of: Restriction
  on property: has grain
  all values from: molecular entity
editor preferred term: scattered molecular aggregate
example of usage: the sodium and chloride ions in a glass of salt water
has curation status: IAO_0000123
definition: a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
term editor: PERSON: Alan Ruttenberg
alternative label: Collective
definition source: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: obi.owl

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred term: material combination
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
has curation status: IAO_0000122
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
term editor: bp
definition source: bp
imported from: obi.owl

statistical hypothesis test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: data transformation
editor preferred term: statistical hypothesis test
has curation status: IAO_0000120
definition: A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

statistical hypothesis test objective
type: Class
subclass of: data transformation objective
editor preferred term: statistical hypothesis test objective
has curation status: IAO_0000123
definition: is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation.
term editor: James Malone
term editor: Person:Helen Parkinson
alternative label: hypothesis test objective
definition source: WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
imported from: obi.owl

creating a mixture of molecules in solution
type: Class
subclass of: material combination
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: chemical solution
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
editor preferred term: creating a mixture of molecules in solution
example of usage: The production of PBS
has curation status: IAO_0000120
definition: is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
term editor: Bjoern Peters
definition source: PERSON: Helen Parkinson
imported from: obi.owl

material combination objective
type: Class
subclass of: material transformation objective
editor preferred term: material combination objective
has curation status: IAO_0000122
definition: is an objective to obtain an output material that contains several input materials.
term editor: PPPB branch
definition source: bp
imported from: obi.owl

pathogen challenge
type: Class
subclass of: in vivo challenge
subclass of: Restriction
  on property: realizes
  some values from: host role
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: role of
      some values from: Class
        intersection of: organism
        intersection of: Restriction
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: role of
      some values from: Class
        intersection of: organism
        intersection of: Restriction
editor preferred term: pathogen challenge
has curation status: IAO_0000123
definition: The administration of a live pathogenic organism to a host.
imported from: obi.owl

pathogen role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: organism
subclass of: Restriction
  on property: realized in
  all values from: disease course
editor preferred term: pathogen role
example of usage: Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383
has curation status: IAO_0000120
definition: pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role
term editor: GROUP: Role Branch
definition source: OBI
curator note: 6 April 2009: from the Vaccine Community
imported from: obi.owl

host role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: organism
editor preferred term: host role
example of usage: In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
has curation status: IAO_0000120
definition: host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
editor note: 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
term editor: GROUP: Role Branch
definition source: 30 Mar09 submitted by vaccine community
definition source: OBI
definition source: http://en.wikipedia.org/wiki/Host_(biology)
imported from: obi.owl

study design independent variable
type: Class
subclass of: VO_0010288
subclass of: Restriction
  on property: part of
  some values from: study design
editor preferred term: independent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
has curation status: IAO_0000122
definition: a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
editor note: 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative label: experimental factor
alternative label: independent variable
definition source: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
imported from: obi.owl
ISA alternative term: study factor

study design dependent variable
type: Class
subclass of: VO_0010288
subclass of: Restriction
  on property: part of
  some values from: study design
editor preferred term: dependent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
has curation status: IAO_0000122
definition: dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
editor note: 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative label: dependent variable
definition source: WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
imported from: obi.owl

material maintenance objective
type: Class
subclass of: objective specification
editor preferred term: material maintenance objective
has curation status: IAO_0000122
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters
imported from: obi.owl

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: manufacturer role
subclass of: material entity
editor preferred term: manufacturer
has curation status: IAO_0000123
definition: A person or organization that has a manufacturer role.
imported from: obi.owl

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred term: material maintenance
has curation status: IAO_0000123
definition: A planned process with the objective to maintain some or all of the characteristics of an input material over time.
imported from: obi.owl

record of missing knowledge
type: Class
subclass of: information content entity
editor preferred term: record of missing knowledge
example of usage: A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
has curation status: IAO_0000120
definition: An information content entity created to indicate that information about something is not available to the person recording it.
editor note: This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
term editor: Bjoern Peters
imported from: obi.owl

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: categorical value specification
editor preferred term: categorical measurement datum
has curation status: IAO_0000120
definition: A measurement datum that is reported on a categorical scale.
term editor: Bjoern Peters
alternative label: nominal mesurement datum
definition source: Bjoern Peters
imported from: obi.owl

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred term: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: IAO_0000122
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
term editor: PERSON: Helen Parkinson
alternative label: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

dose specification
type: Class
subclass of: directive information entity
editor preferred term: dose specification
example of usage: a protocol specifying to administer 1 ml of vaccine to a mouse
has curation status: IAO_0000123
definition: a directive information entity that describes the dose that will be administered to a target
imported from: obi.owl

dose
type: Class
subclass of: measurement datum
editor preferred term: dose
example of usage: An organism has been injected 1ml of vaccine
has curation status: IAO_0000123
definition: A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
imported from: obi.owl

categorical value specification
type: Class
subclass of: value specification
editor preferred term: categorical value specification
has curation status: IAO_0000123
definition: A value specification that is specifies one category out of a fixed number of nominal categories
term editor: PERSON:Bjoern Peters
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred term: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: IAO_0000122
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
term editor: PERSON:Bjoern Peters
imported from: obi.owl

in vivo challenge
type: Class
subclass of: administering substance in vivo
editor preferred term: in vivo challenge
has curation status: IAO_0000120
definition: The administration of a challenge to a live host.
term editor: Hector Guzman-Orozco
definition source: IEDB
imported from: obi.owl

reactant role
type: Class
subclass of: role
editor preferred term: reactant role
has curation status: IAO_0000123
definition: A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction.
term editor: Sebastian Duesing
imported from: obi.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred term: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: IAO_0000122
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: obi.owl

phosphate buffered saline solution
type: Class
subclass of: chemical solution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: scattered molecular aggregate
    intersection of: Restriction
      on property: has grain
      all values from: sodium chloride
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: scattered molecular aggregate
    intersection of: Restriction
      on property: has grain
      all values from: sodium phosphate
subclass of: Restriction
  on property: has role
  some values from: buffer role
editor preferred term: phosphate buffered saline solution
example of usage: PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes.
has curation status: IAO_0000122
definition: Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic).
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Tina Boussard
alternative label: PBS buffer
definition source: WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline
imported from: obi.owl

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
editor preferred term: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: IAO_0000122
definition: A planned process that produces output data from input data.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative label: data analysis
alternative label: data processing
definition source: Branch editors
imported from: obi.owl

data transformation objective
type: Class
subclass of: objective specification
editor preferred term: data transformation objective
example of usage: normalize objective
has curation status: IAO_0000122
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

ANOVA
type: Class
subclass of: statistical hypothesis test
editor preferred term: ANOVA
has curation status: IAO_0000123
definition: A statistical hypothesis test in which the means of several groups are all equal.
term editor: James Malone
imported from: obi.owl

chemical solution
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: scattered molecular aggregate
      intersection of: Restriction
        on property: has role
        some values from: solvent role
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: scattered molecular aggregate
      intersection of: Restriction
        on property: has role
        some values from: solute role
subclass of: material entity
editor preferred term: chemical solution
example of usage: PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
has curation status: IAO_0000122
definition: A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
alternative label: liquid chemical solution
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

buffer role
type: Class
subclass of: role
editor preferred term: buffer role
example of usage: A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
has curation status: IAO_0000125
definition: a role which inheres in some molecular entity realized during the process of buffering
term editor: Person:Helen Parkinson
term editor: Person:Philippe Rocca-Serra
alternative label: buffer
definition source: OBI
imported from: obi.owl

solvent role
type: Class
subclass of: reactant role
subclass of: Restriction
  on property: characteristic of
  some values from: molecular entity
subclass of: Restriction
  on property: realized in
  all values from: creating a mixture of molecules in solution
editor preferred term: solvent role
example of usage: PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
has curation status: IAO_0000125
definition: solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
editor note: The class CHEBI:solvent is logically equivalent to this class, iff it is properly subsumed under the BFO:role branch. The label and textual definition of this CHEBI class are however misleadingly denoting the material entity that bears this role and not the role itself. The OBI modeling was needed as what is considered a solvent in a mixture can depend on the intent of the person creating the mixture. It would be great if this could be dealt with in CHEBI itself. See also https://github.com/obi-ontology/obi/issues/1771.
term editor: Philippe Rocca-Serra
definition source: adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
imported from: obi.owl

solute role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: molecular entity
subclass of: Restriction
  on property: realized in
  all values from: creating a mixture of molecules in solution
editor preferred term: solute role
example of usage: PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
has curation status: IAO_0000125
definition: solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
imported from: obi.owl

storage
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: storage
example of usage: PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
has curation status: IAO_0000120
definition: A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.
term editor: Philippe Rocca-Serra
definition source: OBI-Branch
imported from: obi.owl

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred term: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: IAO_0000122
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
term editor: PERSON: Chris Stoeckert
alternative label: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

administering substance in vivo
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: Class
subclass of: planned process
editor preferred term: administering substance in vivo
example of usage: Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
example of usage: injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
has curation status: IAO_0000125
definition: A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
editor note: Different routes and means of administration should go as children underneath this
editor note: Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
editor note: needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
term editor: Bjoern Peters
term editor: Person:Bjoern Peters
definition source: IEDB
imported from: obi.owl

antigen
type: Class
equivalent class: Restriction
  on property: has role
  some values from: antigen role
subclass of: material entity
editor preferred term: antigen
has curation status: IAO_0000123
definition: A material entity that has the antigen role.
term editor: IEDB
definition source: IEDB
imported from: obi.owl

gene
type: Class
subclass of: material entity
definition: A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
term editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
imported from: ogg.owl

gene of Bacteria
type: Class
subclass of: gene
definition: A gene of an organism of Bacteria
term editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 2

gene of Proteobacteria
type: Class
subclass of: gene of Bacteria
definition: A gene of an organism of Proteobacteria
term editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 1224

gene of Mycobacterium tuberculosis H37Rv
type: Class
subclass of: gene of Bacteria
definition: A gene of an organism of Mycobacterium tuberculosis H37Rv
term editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 83332

gene of Brucella melitensis bv. 1 str. 16M
type: Class
subclass of: gene of Proteobacteria
definition: A gene of an organism of Brucella melitensis bv. 1 str. 16M
term editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 224914

protein-coding gene of Mycobacterium tuberculosis H37Rv
type: Class
subclass of: gene of Mycobacterium tuberculosis H37Rv
definition: A gene of Mycobacterium tuberculosis H37Rv that has a protein-coding gene disposition
term editor: Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 83332

protein-coding gene of Brucella melitensis bv. 1 str. 16M
type: Class
subclass of: gene of Brucella melitensis bv. 1 str. 16M
definition: A gene of Brucella melitensis bv. 1 str. 16M that has a protein-coding gene disposition
term editor: Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 224914

panC
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 885459
NCBI LocusTag: Rv3602c
modification date: 20140405
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 20980199
description: Pantoate--beta-alanine ligase PanC (pantothenate synthetase) (pantoate activating enzyme)

secA2
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 885594
NCBI LocusTag: Rv1821
modification date: 20140329
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 17030572; 18487341; 19240020; 20980199; 24297168
description: Possible preprotein translocase ATPase SecA2

panD
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 885596
NCBI LocusTag: Rv3601c
modification date: 20140405
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 20980199
description: Probable aspartate 1-decarboxylase precursor PanD (aspartate alpha-decarboxylase)

lysA
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 886960
NCBI LocusTag: Rv1293
modification date: 20140405
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 16511157; 19543810; 20980199
description: Diaminopimelate decarboxylase LysA (DAP decarboxylase)

fadD26
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 887603
NCBI LocusTag: Rv2930
modification date: 20140322
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 15749014; 20553505; 20980199
description: Fatty-acid-AMP ligase FadD26 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)

trpD
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 887681
NCBI LocusTag: Rv2192c
modification date: 20140405
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 16337227; 20980199; 23363292
description: Probable anthranilate phosphoribosyltransferase TrpD

leuD
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 888225
NCBI LocusTag: Rv2987c
modification date: 20140405
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 19194004; 20980199
description: Probable 3-isopropylmalate dehydratase (small subunit) LeuD (isopropylmalate isomerase) (alpha-IPM isomerase) (IPMI)

drrC
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 888491
NCBI LocusTag: Rv2938
modification date: 20140322
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 20980199
description: Probable daunorubicin-dim-transport integral membrane protein ABC transporter DrrC

sigE
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 888751
NCBI LocusTag: Rv1221
modification date: 20140406
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 16513743; 18192397; 18606740; 18657035; 20980199
description: Alternative RNA polymerase sigma factor SigE

phoP
type: Class
subclass of: protein-coding gene of Mycobacterium tuberculosis H37Rv
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 888772
NCBI LocusTag: Rv0757
modification date: 20140322
organism NCBITaxon ID: 83332
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 9634230; 12368430; 16573683; 18052041; 18065542; 18065544; 18282096; 18757548; 18946503; 19820095; 20363229; 20814030; 20980199; 21634789; 22072719; 22880126
description: Possible two component system response transcriptional positive regulator PhoP

BMEI1364
type: Class
subclass of: protein-coding gene of Brucella melitensis bv. 1 str. 16M
term editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
NCBI GeneID: 1197075
NCBI LocusTag: BMEI1364
modification date: 20140222
organism NCBITaxon ID: 224914
chromosome ID of gene: I
type of gene: protein-coding
nomenclature status: NCBI-supplied
has PubMed association: PMID: 11756688; 12271122; 23161025
description: transcriptional regulatory protein MUCR

bodily process
type: Class
subclass of: process
term editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:53:49Z
imported from: ogms.owl

pathological bodily process
type: Class
subclass of: bodily process
definition: A bodily process that is clinically abnormal.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:54:29Z
imported from: ogms.owl

disease course
type: Class
subclass of: process
definition: The totality of all processes through which a given disease instance is realized.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:55:44Z
imported from: ogms.owl

Triatominae hindgut
type: Class
equivalent class: Class
  intersection of: hindgut
  intersection of: Restriction
    on property: part of
    some values from: Triatominae
subclass of: hindgut
definition: A hindgut that is a part of or originated from a Triatominae bug.
term editor: Priti Parikh
imported from: opl.owl

Plasmodium falciparum exflagellated microgametocyte stage
type: Class
equivalent class: Class
  intersection of: exflagellated microgametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum microgametocyte stage
subclass of: exflagellated microgametocyte stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: An exflagellated microgametocyte stage in the lifecycle of Plasmodium falciparum that occurs in the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum exflagellated microgametocyte stage
imported from: opl.owl

Plasmodium falciparum microgametocyte stage
type: Class
equivalent class: Class
  intersection of: microgametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum gametocyte stage
subclass of: Plasmodium microgametocyte stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: A microgametocyte stage in the Plasmodium falciparum lifecycle that occurs either in the bloodstream of a human host or the midgut of a mosquito vector.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: P. Parkh
term editor: S. Khan.
alternative label: P. falciparum microgametocyte stage
imported from: opl.owl

microgamete stage
type: Class
subclass of: parasite lifecycle stage
subclass of: gamete stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A gamete stage in apicomplexan parasites when exflagellated microgametocyte divides into microgamete.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Matt Berriman
imported from: opl.owl

macrogametocyte stage
type: Class
subclass of: gametocyte stage
definition: A gametocyte stage where a cell differentiates into a female sexual form called macrogametocyte.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
imported from: opl.owl

Anopheles midgut
type: Class
equivalent class: Class
  intersection of: midgut
  intersection of: Restriction
    on property: part of
    some values from: Anopheles <genus>
subclass of: midgut
definition: A midgut that is a part of or originated from an Anopheles mosquito.
term editor: Jie Zheng
imported from: opl.owl

trypomastigote stage
type: Class
subclass of: parasite lifecycle stage
subclass of: Restriction
  on property: in taxon
  some values from: Trypanosoma
definition: A parasite lifecycle stage of trypanosomes. In trypomastigote stage, the kinetoplast is near the posterior end of the body, and the flagellum lies attached to the cell body for most of its length by an undulating membrane.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: Wikipedia: Trypanosomatid
imported from: opl.owl

Plasmodium falciparum erythrocytic schizont stage
type: Class
equivalent class: Class
  intersection of: erythrocytic schizont stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum schizont stage
subclass of: Plasmodium erythrocytic schizont stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: An erythrocytic schizont stage in the Plasmodium falciparum lifecycle that occurs in the infected erythrocytes of a human host.
editor note: updated according to OPL terms Plasmodium final excel file from C. Janse, S. Khan
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum erythorcytic schizont stage
imported from: opl.owl

merozoite stage
type: Class
subclass of: parasite lifecycle stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A parasite lifecycle stage of apicomplexan species where a daughter cell, called merozoite is produced from schizont through schizogony.
editor note: adjusted to be more general
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarM.htm
imported from: opl.owl

Homo sapiens hepatocyte
type: Class
equivalent class: Class
  intersection of: hepatocyte
  intersection of: Restriction
    on property: part of
    some values from: Homo sapiens
subclass of: Vertebrate hepatocyte
definition: A hepatocyte that is a part of or originated from a human (Homo sapiens).
term editor: Priti Parikh
alternative label: human hepatocyte
imported from: opl.owl
has cross-reference: FMA:14515

Plasmodium falciparum erythrocytic ring trophozoite stage
type: Class
equivalent class: Class
  intersection of: erythrocytic ring trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum erythrocytic trophozoite stage
subclass of: Plasmodium erythrocytic ring trophozoite stage
definition: An erythrocytic ring trophozoite stage in the Plasmodium falciparum life cycle that occurs in erythrocytes of a human host. During this stage some Plasmodium falciparum merozoites undergo asexual reproduction cycle in erythrocytes and form young trophozoites that are referred to as "ring form" due to their morphology.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum erythrocytic ring trophozoite stage
definition source: Wikipedia: Plasmodium falciparum biology
imported from: opl.owl

Trypanosoma brucei lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Trypanosoma brucei
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Trypanosoma brucei.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: T. brucei lifecycle stage
imported from: opl.owl

Plasmodium falciparum microgametocyte
type: Class
subclass of: Plasmodium falciparum gametocyte
subclass of: Plasmodium microgametocyte
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum microgametocyte stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum gametocyte that is a male gametocyte and found in either bloodstream of a human host or midgut of a mosquito vector. The microgametocyte is a precursor cell of the microgamete.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum microgametocyte
imported from: opl.owl

trophozoite stage
type: Class
subclass of: parasite lifecycle stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A parasite lifecycle stage of some protozoan parasites that is a non-reproductive, feeding and growing stage.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarT.htm
imported from: opl.owl

hepatic schizont stage
type: Class
subclass of: schizont stage
definition: A schizont stage that occurs in hepatocyte where sporozoites mature into a schizont.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Matt Berriman
term editor: Priti Parikh
definition source: PMID:11006474
imported from: opl.owl

Plasmodium falciparum schizont
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium schizont
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum schizont stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum divides through schizogony. Depending on its location, it is either called hepatic or erythrocytic schizont. The schizont is a dividing stage with 2 or more nuclei.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum schizont
imported from: opl.owl

Plasmodium falciparum macrogametocyte stage
type: Class
equivalent class: Class
  intersection of: macrogametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum gametocyte stage
subclass of: Plasmodium macrogametocyte stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: A macrogametocyte stage in the Plasmodium falciparum lifecycle that occurs either in the bloodstream of a human host or the midgut of a mosquito vector.
editor note: gametocytes are mainly found in the blood
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
term editor: S. Khan
alternative label: P. falciparum macrogametocyte stage
imported from: opl.owl

oocyst stage
type: Class
subclass of: parasite lifecycle stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A parasite lifecycle stage of sporozoa consisting of a zygote enclosed by cyst wall.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: Mosby's Medical Dictionary, 8th edition. � 2009, Elsevier. (http://medical-dictionary.thefreedictionary.com/oocyst)
imported from: opl.owl

Plasmodium falciparum macrogamete stage
type: Class
equivalent class: Class
  intersection of: macrogamete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum gamete stage
subclass of: Plasmodium macrogamete stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: A macrogamete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum macrogamete stage
imported from: opl.owl

erythrocytic schizont stage
type: Class
subclass of: schizont stage
definition: A schizont stage that occurs in erythrocytes where trophozoites mature into a schizont and schizont produces daughter trophozoites or merozoites.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Matt Berriman
term editor: Priti Parikh
definition source: PMID: 11006474
imported from: opl.owl

schizont stage
type: Class
subclass of: parasite lifecycle stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A parasite lifecycle stage that is the multinucleate stage in the development of some members of the Sarcodina and some sporozoans during schizogony.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: http://medical-dictionary.thefreedictionary.com/schizont
imported from: opl.owl

macrogamete stage
type: Class
subclass of: parasite lifecycle stage
subclass of: gamete stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A gamete stage in parasites when macrogametocytes produce macrogametes through the process known as gametogenesis.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: http://www.tulane.edu/~wiser/malaria/mal_lc.PDF
imported from: opl.owl

Plasmodium falciparum ookinete
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium ookinete
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum ookinete stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium falciparum that is a 'banana-shaped' form and originates from the round zygote. The ookinete is found in the midgut of a mosquito vector and traverses the midgut wall of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum ookinete
definition source: Wikipedia: Plasmodium falciparum biology
imported from: opl.owl

Plasmodium falciparum hepatic schizont stage
type: Class
equivalent class: Class
  intersection of: hepatic schizont stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum schizont stage
subclass of: Plasmodium hepatic schizont stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens hepatocyte
definition: A hepatic schizont stage in the lifecycle of Plasmodium falciparum that occurs in the infected hepatocytes of a human host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum hepatic schizont stage
imported from: opl.owl

Homo sapiens erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: part of
    some values from: Homo sapiens
subclass of: Primates erythrocyte
definition: An erythrocyte that is a part of or originated from a human (Homo sapiens).
term editor: Priti Parikh
alternative label: human RBC
alternative label: human erythrocyte
alternative label: human red blood cell
imported from: opl.owl
has cross-reference: FMA:62845

Plasmodium falciparum merozoite stage
type: Class
equivalent class: Class
  intersection of: merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium merozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: A merozoite stage in the Plasmodium falciparum lifecycle that occurs in the bloodstream or hepatocytes of a human host.
term editor: Chris Stoeckert
term editor: Priti Parikh
alternative label: P. falciparum merozoite stage
imported from: opl.owl

Plasmodium falciparum erythrocytic schizont
type: Class
subclass of: Plasmodium falciparum schizont
subclass of: Plasmodium erythrocytic schizont
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum erythrocytic schizont stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum schizont that is found in infected erythrocytes of a human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum erythrocytic schizont
imported from: opl.owl

Plasmodium falciparum oocyst stage
type: Class
equivalent class: Class
  intersection of: oocyst stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium oocyst stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: An oocyst stage in the Plasmodium falciparum lifecycle that occurs on the hemocoel side of the midgut of a mosquito vector. During this stage Plasmodium falciparum ookinete invades and escapes midgut wall of mosquito and embed itself onto the exterior of the gut membrane and develop encysted zygote, called oocyst.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum oocyst stage
imported from: opl.owl

Plasmodium falciparum sporozoite stage
type: Class
equivalent class: Class
  intersection of: sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium sporozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens blood
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles salivary gland
definition: A sporozoite stage in the Plasmodium falciparum lifecycle that occurs in the salivary glands of the mosquito and invades hepatocytes in the human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Matt Berrimen
term editor: Priti Parikh
term editor: S. Khan
alternative label: P. falciparum sporozoite stage
imported from: opl.owl

Homo sapiens blood
type: Class
equivalent class: Class
  intersection of: blood
  intersection of: Restriction
    on property: part of
    some values from: Homo sapiens
subclass of: Mammalia blood
definition: Blood that is part of or originated from a human (Homo sapiens).
editor note: previous def was: blood of human
term editor: Chris Stoeckert
alternative label: human blood
definition source: OPL
imported from: opl.owl

exflagellated microgametocyte stage
type: Class
subclass of: microgametocyte stage
definition: A microgametocyte stage in some apicomplexan parasites where microgametocyte gets matured and form microgamete through the process known as exflagellation.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
imported from: opl.owl

Anopheles salivary gland
type: Class
equivalent class: Class
  intersection of: saliva-secreting gland
  intersection of: Restriction
    on property: part of
    some values from: Anopheles <genus>
subclass of: saliva-secreting gland
definition: A salivary gland that is a part of or originated from an Anopheles mosquito.
term editor: Priti Parikh
imported from: opl.owl

Plasmodium falciparum merozoite
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium merozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum merozoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum that is produced in a schizont, found in the bloodstream of a human host and invades erythrocytes.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
alternative label: P. falciparum merozoite
imported from: opl.owl

Plasmodium falciparum sporozoite
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum sporozoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens blood
subclass of: Restriction
  on property: located in
  some values from: Anopheles salivary gland
definition: A Plasmodium falciparum is formed in the oocyst. It migrates to and resides in the salivary glands of the mosquito vector. A distinction is made between oocyst-derived and salivary gland-derived sporozoites. Sporozoites invade hepatocytes in the vertebrate host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum sporozoite
definition source: Wikipedia: Plasmodium falciparum biology
imported from: opl.owl

Plasmodium falciparum oocyst
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium oocyst
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum oocyst stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium falciparum that oocyst is formed, after traversal of the midgut wall by the ookinete stage, on the hemocoel side of the midgut wall of the mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum oocyst
imported from: opl.owl

erythrocytic ring trophozoite stage
type: Class
subclass of: erythrocytic trophozoite stage
definition: An early trophozoite stage of Plasmodium sp. where a large central vacuole and peripheral nucleus give an appearance of a signet ring.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarR.htm
imported from: opl.owl

microgametocyte stage
type: Class
subclass of: gametocyte stage
definition: A gametocyte stage where a cell differentiates into a male sexual form called microgametocyte.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
imported from: opl.owl

Plasmodium falciparum trophozoite
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium trophozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum trophozoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum is a feeding form. The trophozoite stage has only 1 nucleus. Depending on its location, it is either called hepatic or erythrocytic trophozoite.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum trophozoite
imported from: opl.owl

gametocyte stage
type: Class
subclass of: life cycle stage
definition: A life cycle stage where a cell differentiates into male or female sexual forms.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
imported from: opl.owl

sporozoite stage
type: Class
subclass of: parasite lifecycle stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A parasite lifecycle stage of some sporozoans where cells divide through sporogony producing daughter cells called sporozoites that infect new hosts.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarS.htm
imported from: opl.owl

ookinete stage
type: Class
subclass of: parasite lifecycle stage
subclass of: Restriction
  on property: in taxon
  some values from: parasite organism
definition: A parasite lifecycle stage of some sporozoans where motile and elongated zygote is formed by the fertilization of the macrogamete during the sexual reproductive phase of the sporozoan life cycle, specifically the malarial parasite Plasmodium.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
definition source: Mosby's Medical Dictionary, 8th edition. � 2009, Elsevier. (http://medical-dictionary.thefreedictionary.com/ookinete)
imported from: opl.owl

Plasmodium falciparum schizont stage
type: Class
equivalent class: Class
  intersection of: schizont stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium schizont stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: A schizont stage in the Plasmodium falciparum lifecycle that occurs in erythrocytes or in hepatocytes.
editor note: updated according to OPL terms Plasmodium final excel file from C. Janse, S. Khan
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum schizont stage
imported from: opl.owl

Plasmodium falciparum zygote
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium zygote
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum zygote stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium falciparum zygote is formed after fertilisation of the macrogamete by a microgamete in the midgut of the mosquito vector. This round form is the only diploid stage in the Plasmodium falciparum life cycle.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: P. Parkh
term editor: S. Khan
alternative label: P. falciparum zygote
definition source: Wikipedia: Plasmodium falciparum biology
imported from: opl.owl

Plasmodium falciparum exflagellated microgametocyte
type: Class
subclass of: Plasmodium falciparum microgametocyte
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum exflagellated microgametocyte stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium falciparum microgametocyte that is matured with flagellated motile microgametes still attached to its central body. Exflagellated microgametocyte of Plasmodium falciparum is found in the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Matt Berriman
term editor: Priti Parikh
alternative label: P. falciparum exflagellated microgametocyte
imported from: opl.owl

Trypanosoma cruzi trypomastigote
type: Class
subclass of: Trypanosoma cruzi
subclass of: Restriction
  on property: participates in
  some values from: Trypanosoma cruzi trypomastigote stage
subclass of: Restriction
  on property: located in
  some values from: Triatominae hindgut
subclass of: Restriction
  on property: located in
  some values from: Mammalia blood
subclass of: Restriction
  on property: located in
  some values from: Mammalia macrophage
definition: A Trypanosoma cruzi that is found in the bloodstream of infected mammals. It is a non-dividing form that is infectious for its insect vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: T. cruzi trypomastigote
definition source: http://dna.kdna.ucla.edu/parasite_course-old/cruzi_files/intro.htm
imported from: opl.owl

Plasmodium falciparum lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Plasmodium falciparum.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum lifecycle stage
imported from: opl.owl

Plasmodium falciparum macrogamete
type: Class
subclass of: Plasmodium falciparum gamete
subclass of: Plasmodium macrogamete
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum macrogamete stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium falciparum gamete that is a matured form of the macrogametocyte and is found in the midgut of a mosquito vector. The macrogamete is fertilized by the microgamete, forming the zygote
term editor: Chris Stoeckert
term editor: Jie Zheng
alternative label: P. falciparum macrogamete
imported from: opl.owl

Trypanosoma cruzi trypomastigote stage
type: Class
equivalent class: Class
  intersection of: trypomastigote stage
  intersection of: Restriction
    on property: in taxon
    some values from: Trypanosoma cruzi
subclass of: trypomastigote stage
subclass of: Trypanosoma cruzi lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Triatominae hindgut
subclass of: Restriction
  on property: occurs in
  some values from: Mammalia blood
subclass of: Restriction
  on property: occurs in
  some values from: Mammalia macrophage
definition: A trypomastigote stage in the Trypanosoma cruzi lifecycle that occurs either in the vertebrate host or an insect vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: T. cruzi trypomastigote stage
imported from: opl.owl

Plasmodium falciparum microgamete stage
type: Class
equivalent class: Class
  intersection of: microgamete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum gamete stage
subclass of: Plasmodium microgamete stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: A microgamete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum microgamete stage
imported from: opl.owl

human parasite role
type: Class
subclass of: parasite role
definition: A parasite role which is realized only during parasitic infection of a human.
editor note: previous def was not about a role.
term editor: Chris Stoeckert
term editor: Priti Parikh
imported from: opl.owl

Plasmodium falciparum microgamete
type: Class
subclass of: Plasmodium falciparum gamete
subclass of: Plasmodium microgamete
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum microgamete stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium falciparum gamete that is a matured form of exflagellated microgametocyte and found in the midgut of a mosquito vector. The microgamete fertilizes the macrogamete, forming the zygote.
term editor: Chris Stoeckert
term editor: Jie Zheng
alternative label: P. falciparum microgamete
imported from: opl.owl

Trypanosoma brucei trypomastigote stage
type: Class
equivalent class: Class
  intersection of: trypomastigote stage
  intersection of: Restriction
    on property: in taxon
    some values from: Trypanosoma brucei
subclass of: trypomastigote stage
subclass of: Trypanosoma brucei lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Mammalia cerebrospinal fluid
subclass of: Restriction
  on property: occurs in
  some values from: Mammalia blood
definition: A trypomastigote stage in the Trypanosoma brucei lifecycle that occurs in the vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: T. brucei trypomastigote stage
imported from: opl.owl

parasite lifecycle stage
type: Class
equivalent class: Class
  intersection of: life cycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: parasite organism
subclass of: life cycle stage
definition: A life cycle stage of a parasite.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
imported from: opl.owl

Trypanosoma brucei trypomastigote
type: Class
subclass of: Trypanosoma brucei
subclass of: Restriction
  on property: participates in
  some values from: Trypanosoma brucei trypomastigote stage
subclass of: Restriction
  on property: located in
  some values from: Mammalia cerebrospinal fluid
subclass of: Restriction
  on property: located in
  some values from: Mammalia blood
definition: A Trypanosoma brucei that is a Trypomastigote form of Trypanosoma brucei. In this form the large kinetoplast is postnuclear and is at the most posterior part of the body and the flagellum emerges from the flagellar pocket, and runs along the entire length of the body as an undulating membrane.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: T. brucei trypomastigote
definition source: http://dna.kdna.ucla.edu/parasite_course-old/african%20tryps%20new_files/contents1.htm
imported from: opl.owl

Trypanosoma cruzi lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Trypanosoma cruzi
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Trypanosoma cruzi.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: T. cruzi lifecycle stage
imported from: opl.owl

Plasmodium falciparum ookinete stage
type: Class
equivalent class: Class
  intersection of: ookinete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium ookinete stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: An ookinete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector and on the outside of the midgut.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum ookinete stage
imported from: opl.owl

Plasmodium falciparum hepatic schizont
type: Class
subclass of: Plasmodium falciparum schizont
subclass of: Plasmodium hepatic schizont
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum hepatic schizont stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens hepatocyte
definition: A Plasmodium falciparum schizont that is found in infected hepatocytes (i.e., liver cells) of a human host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum hepatic schizont
imported from: opl.owl

Plasmodium falciparum gametocyte stage
type: Class
equivalent class: Class
  intersection of: gametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium gametocyte stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: A gametocyte stage in the lifecycle of Plasmodium falciparum.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum gametocyte stage
imported from: opl.owl

Plasmodium falciparum zygote stage
type: Class
equivalent class: Class
  intersection of: zygote stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium zygote stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: A zygote stage in the Plasmodium falciparum lifecycle that occurs in the midgut of the mosquito vector where a microgamete and a macrogamete fertilizes each other to produce a diploid cell.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parikh
alternative label: P. falciparum zygote stage
definition source: Wikipedia: Plasmodium falciparum biology
imported from: opl.owl

Plasmodium falciparum macrogametocyte
type: Class
subclass of: Plasmodium falciparum gametocyte
subclass of: Plasmodium macrogametocyte
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum macrogametocyte stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum gametocyte that is a female gametocyte and found either in bloodstream of a human host or midgut of mosquito vector. The macrogametocyte is a precursor of the macrogamete.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum macrogametocyte
imported from: opl.owl

Plasmodium falciparum erythrocytic trophozoite stage
type: Class
equivalent class: Class
  intersection of: erythrocytic trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum trophozoite stage
subclass of: Plasmodium erythrocytic trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: An erythrocytic trophozoite stage in the Plasmodium falciparum life cycle that occurs in erythrocytes of a human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum erythrocytic trophozoite stage
imported from: opl.owl

Plasmodium falciparum erythrocytic ring trophozoite
type: Class
subclass of: Plasmodium falciparum erythrocytic trophozoite
subclass of: Plasmodium erythrocytic ring trophozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum erythrocytic ring trophozoite stage
definition: A Plasmodium falciparum erythrocytic trophozoite that is found in erythrocytes. It is a young trophozoite stage that has a typical 'ring-like' appearance. Ring-form trophozoites of Plasmodium falciparum are often thin and delicate, measuring on average 1/5 the diameter of the red blood cell.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Priti Parkh
term editor: S. Khan
alternative label: P. falciparum erythrocytic ring trophozoite
definition source: http://www.dpd.cdc.gov/dpdx/html/frames/m-r/malaria/falciparum/body_malariadffalcring.htm
imported from: opl.owl

parasite organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: parasite role
subclass of: organism
definition: An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class.
term editor: Jie Zheng
term editor: Priti Parikh
definition source: http://www.merriam-webster.com/dictionary/parasite
imported from: opl.owl

Plasmodium falciparum hepatic merozoite
type: Class
subclass of: Plasmodium falciparum merozoite
subclass of: Plasmodium hepatic merozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum hepatic merozoite stage
definition: A Plasmodium falciparum merozoite that is produced in a hepatic schizont and released into the bloodstream of a human host. These forms invade erythrocytes.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum hepatic merozoite
imported from: opl.owl

Plasmodium falciparum erythrocytic merozoite
type: Class
subclass of: Plasmodium falciparum merozoite
subclass of: Plasmodium erythrocytic merozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum erythrocytic merozoite stage
definition: A Plasmodium falciparum merozoite that is produced in an erythrocytic schizont and released into the bloodstream of a human host. These forms invade erythrocytes.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum erythrocytic merozoite
imported from: opl.owl

erythrocytic trophozoite stage
type: Class
subclass of: trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: erythrocyte
definition: A trophozoite stage in some protozoan parasite life cycle that occurs in erythrocytes.
editor note: definition adapted from that for P. falciparum erythrocytic trophozoite stage and parent trophozoite stage
term editor: Chris Stoeckert
imported from: opl.owl

Plasmodium falciparum erythrocytic trophozoite
type: Class
subclass of: Plasmodium falciparum trophozoite
subclass of: Plasmodium erythrocytic trophozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum erythrocytic trophozoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum trophozoite that is found in erythrocytes. It is a feeding stage with a single nucleus.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum erythrocytic trophozoite
imported from: opl.owl

Plasmodium falciparum erythrocytic merozoite stage
type: Class
equivalent class: Class
  intersection of: erythrocytic merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum merozoite stage
subclass of: Plasmodium erythrocytic merozoite stage
definition: An erythrocytic merozoite stage in the Plasmodium falciparum lifecycle that occurs in the bloodstream of a human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum erythrocytic merozoite stage
imported from: opl.owl

Plasmodium falciparum hepatic merozoite stage
type: Class
equivalent class: Class
  intersection of: hepatic merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum merozoite stage
subclass of: Plasmodium hepatic merozoite stage
definition: A hepatic merozoite stage in the Plasmodium falciparum lifecycle that occurs in the hepatocyte of a human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum hepatic merozoite stage
imported from: opl.owl

hepatic merozoite stage
type: Class
subclass of: merozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: hepatocyte
definition: A merozoite stage in the Plasmodium lifecycle that occurs in the hepatocyte of a vertebrate host.
editor note: definition adapted from that for P. falciparum hepatic merozoite stage
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

erythrocytic merozoite stage
type: Class
subclass of: merozoite stage
definition: A merozoite stage in the apicomplexan lifecycle that occurrs in the bloodstream of a vertebrate host.
editor note: definition adapted from that for P. falciparum salivary erythrocytic merozoite stage and from the general merozoite definition
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium falciparum gametocyte
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium gametocyte
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum gametocyte stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium falciparum that is located either in the bloodstream of the human host or midgut of mosquito vector. Gametocytes are the precursor cells of the macro- or micro-gametes.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: K. Louis
term editor: S Khan
imported from: opl.owl

Plasmodium falciparum hepatic trophozoite stage
type: Class
equivalent class: Class
  intersection of: hepatic trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum trophozoite stage
subclass of: Plasmodium hepatic trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens hepatocyte
definition: A hepatic trophozoite stage in the Plasmodium falciparum life cycle that occurs in hepatocytes of a human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum hepatic trophozoite stage
imported from: opl.owl

Plasmodium falciparum trophozoite stage
type: Class
equivalent class: Class
  intersection of: trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: A trophozoite stage in the Plasmodium falciparum lifecycle that occurs in a human host.
term editor: Chris Stoeckert
term editor: Jie Zheng
alternative label: P. falciparum trophozoite stage
imported from: opl.owl

Plasmodium falciparum oocyst-derived sporozoite stage
type: Class
equivalent class: Class
  intersection of: oocyst-derived sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum sporozoite stage
subclass of: Plasmodium oocyst-derived sporozoite stage
definition: A sporozoite stage in the Plasmodium falciparum lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
imported from: opl.owl

salivary gland-derived sporozoite stage
type: Class
subclass of: sporozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: saliva-secreting gland
definition: A sporozoite stage in the Plasmodium lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the vertebrate host.
editor note: definition adapted from that for P. falciparum salivary gland derived sporozoite stage
term editor: Chris Stoeckert
imported from: opl.owl

Plasmodium falciparum salivary gland-derived sporozoite stage
type: Class
equivalent class: Class
  intersection of: salivary gland-derived sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum sporozoite stage
subclass of: Plasmodium salivary gland-derived sporozoite stage
definition: A salivary gland-derived sporozoite stage in the Plasmodium falciparum lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
imported from: opl.owl

Plasmodium falciparum salivary gland-derived sporozoite
type: Class
subclass of: Plasmodium falciparum sporozoite
subclass of: Plasmodium salivary gland-derived sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum salivary gland-derived sporozoite stage
definition: A Plasmodium falciparum sporozoite that is formed in the oocyst. It migrates to and resides in the salivary glands of the mosquito vector. Sporozoites invade hepatocytes in a human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum salivary gland-derived sporozoite
imported from: opl.owl

oocyst-derived sporozoite stage
type: Class
subclass of: sporozoite stage
definition: A sporozoite stage in some parasite lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the vertebrate host.
editor note: definition adapted from that for P. falciparum oocyte derived sporozoite stage
term editor: Chris Stoeckert
imported from: opl.owl

Plasmodium falciparum hepatic trophozoite
type: Class
subclass of: Plasmodium falciparum trophozoite
subclass of: Plasmodium hepatic trophozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum hepatic trophozoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens hepatocyte
definition: A Plasmodium falciparum trophozoite that is found in hepatocytes of a human host. It is a feeding stage with a single nucleus
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum hepatic trophozoite
imported from: opl.owl

Plasmodium falciparum gamete
type: Class
subclass of: Plasmodium falciparum
subclass of: Plasmodium gamete
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum gamete stage
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium falciparum that is found in midgut of mosquito vector. There are two forms of gametes: micro- and macrogametocytes.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum gamete
imported from: opl.owl

Plasmodium falciparum oocyst-derived sporozoite
type: Class
subclass of: Plasmodium falciparum sporozoite
subclass of: Plasmodium oocyst-derived sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium falciparum oocyst-derived sporozoite stage
definition: A Plasmodium falciparum sporozoite that is found in the infected hepatocytes of a human host.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum oocyst-derived sporozoite
imported from: opl.owl

gamete stage
type: Class
subclass of: life cycle stage
definition: A life cycle stage of some parasites that develop into mature sexual cells.
term editor: Jie Zheng
imported from: opl.owl

hepatic trophozoite stage
type: Class
subclass of: trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: hepatocyte
definition: A trophozoite stage in some protozoan parasite life cycle that occurs in hepatocytes.
editor note: definition adapted from that for P. falciparum hepatic trophozoite stage and from parent trophozoite stage
term editor: Chris Stoeckert
imported from: opl.owl

Plasmodium falciparum gamete stage
type: Class
equivalent class: Class
  intersection of: gamete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium falciparum
subclass of: Plasmodium falciparum lifecycle stage
subclass of: Plasmodium gamete stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: A gamete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector.
term editor: C. Janse
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: S. Khan
alternative label: P. falciparum gamete stage
imported from: opl.owl

Plasmodium gamete
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: gamete stage
subclass of: Plasmodium
definition: A Plasmodium that is found in the midgut of a mosquito vector during gamete lifecycle stage. There are two forms of gametes: micro- and macrogametocytes.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium macrogamete
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: macrogamete stage
subclass of: Plasmodium gamete
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium gamete that is in a matured form of the macrogametocyte and found in the midgut of a mosquito vector. The macrogamete is fertilized by the microgamete, forming the zygote.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium microgamete
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: microgamete stage
subclass of: Plasmodium gamete
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium gamete that is in a matured form of exflagellated microgametocyte and found in the midgut of a mosquito vector. The microgamete fertilises the macrogamete, forming the zygote.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium gametocyte
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: gametocyte stage
subclass of: Plasmodium
definition: A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium macrogametocyte
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: macrogametocyte stage
subclass of: Plasmodium gametocyte
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: located in
  some values from: Vertebrate erythrocyte
definition: A Plasmodium gametocyte that is a female gametocyte of Plasmodium and found either in the bloodstream of the vertebrate host or midgut of mosquito vector. The macrogametocyte is a precursor of the macrogamete.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium microgametocyte
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: microgametocyte stage
subclass of: Plasmodium gametocyte
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: located in
  some values from: Vertebrate erythrocyte
definition: A Plasmodium gametocyte that is a male gametocyte of Plasmodium and found either in the bloodstream of a vertebrate host or midgut of a mosquito vector. The microgametocyte is a precursor cell of the microgamete
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium merozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: merozoite stage
subclass of: Plasmodium
definition: A Plasmodium that is during merozoite lifecycle stage, occurs in the bloodstream of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium erythrocytic merozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: erythrocytic merozoite stage
subclass of: Plasmodium merozoite
definition: A Plasmodium merozoite that is produced in an erythrocytic schizont and released into the bloodstream of a vertebrate host. These forms invade erythrocytes.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium hepatic merozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: hepatic merozoite stage
subclass of: Plasmodium merozoite
definition: A Plasmodium merozoite that is produced in a hepatic schizont and released into the bloodstream of a vertebrate host. These forms invade erythrocytes.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium oocyst
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: oocyst stage
subclass of: Plasmodium
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium that is formed after traversal of the midgut wall by the ookinete stage, on the hemocoel side of the midgut wall of the mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium ookinete
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: ookinete stage
subclass of: Plasmodium
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium that is a 'banana-shaped' form originates from the round zygote. The ookinete is found in the midgut of a mosquito vector and traverses the midgut wall of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium schizont
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: schizont stage
subclass of: Plasmodium
definition: A Plasmodium that is a form divides through schizogony. Depending on its location, it is either called hepatic or erythrocytic schizont. The schizont is a dividing stage with 2 or more nuclei.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium erythrocytic schizont
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: erythrocytic schizont stage
subclass of: Plasmodium schizont
subclass of: Restriction
  on property: located in
  some values from: Vertebrate erythrocyte
definition: A Plasmodium schizont that is found in infected erythrocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium hepatic schizont
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: hepatic schizont stage
subclass of: Plasmodium schizont
subclass of: Restriction
  on property: located in
  some values from: Vertebrate hepatocyte
definition: A Plasmodium schizont that is found in infected hepatocytes (i.e. liver cells) of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium sporozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: sporozoite stage
subclass of: Plasmodium
subclass of: Restriction
  on property: located in
  some values from: Anopheles salivary gland
subclass of: Restriction
  on property: located in
  some values from: Vertebrate blood
subclass of: Restriction
  on property: located in
  some values from: Vertebrate hepatocyte
definition: A Plasmodium that is formed in the oocyst and migrates to and reside in the salivary glands of the mosquito vector. A distinction is made between oocyst-derived and salivary gland-derived sporozoites. Sporozoites invade hepatocytes in the vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium oocyst-derived sporozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: oocyst-derived sporozoite stage
subclass of: Plasmodium sporozoite
definition: A Plasmodium sporozoite that is found in the infected hepatocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium salivary gland-derived sporozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: salivary gland-derived sporozoite stage
subclass of: Plasmodium sporozoite
definition: A Plasmodium sporozoite that is found in the salivary glands of the mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium trophozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: trophozoite stage
subclass of: Plasmodium
subclass of: Restriction
  on property: located in
  some values from: Vertebrate erythrocyte
subclass of: Restriction
  on property: located in
  some values from: Vertebrate hepatocyte
definition: A Plasmodium that is a feeding form which has a single nucleus during the trophozoite stage. Depending on its location, it is either called hepatic or erythrocytic trophozoite.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium erythrocytic trophozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: erythrocytic trophozoite stage
subclass of: Plasmodium trophozoite
subclass of: Restriction
  on property: located in
  some values from: Vertebrate erythrocyte
definition: A Plasmodium trophozoite that is found in erythrocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium erythrocytic ring trophozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: erythrocytic ring trophozoite stage
subclass of: Plasmodium erythrocytic trophozoite
definition: A Plasmodium erythrocytic trophozoite that has a typical 'ring-like' appearance. Ring-form trophozoites of Plasmodium are often thin and delicate, measuring on average 1/5 the diameter of the red blood cell.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium hepatic trophozoite
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: hepatic trophozoite stage
subclass of: Plasmodium trophozoite
subclass of: Restriction
  on property: located in
  some values from: Vertebrate hepatocyte
definition: A Plasmodium trophozoite that is found in hepatocytes.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium zygote
type: Class
equivalent class: Class
  intersection of: Plasmodium
  intersection of: Restriction
    on property: participates in
    some values from: zygote stage
subclass of: Plasmodium
subclass of: Restriction
  on property: located in
  some values from: Anopheles midgut
definition: A Plasmodium that is formed after fertilization of the macrogamete by a microgamete in the midgut of the mosquito vector. This round form is the only diploid stage in the Plasmodium life cycle.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Ulrike Boehme
term tracker item: https://github.com/OPL-ontology/OPL/issues/2
ontology term requester: GeneDB
imported from: opl.owl

Plasmodium gamete stage
type: Class
equivalent class: Class
  intersection of: gamete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: parasite lifecycle stage
subclass of: gamete stage
definition: A gamete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium macrogamete stage
type: Class
equivalent class: Class
  intersection of: macrogamete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: macrogamete stage
subclass of: Plasmodium gamete stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: A macrogamete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium microgamete stage
type: Class
equivalent class: Class
  intersection of: microgamete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: microgamete stage
subclass of: Plasmodium gamete stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: A microgamete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium gametocyte stage
type: Class
equivalent class: Class
  intersection of: gametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: gametocyte stage
subclass of: parasite lifecycle stage
definition: A gametocyte stage in the lifecycle of Plasmodium.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium macrogametocyte stage
type: Class
equivalent class: Class
  intersection of: macrogametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: macrogametocyte stage
subclass of: Plasmodium gametocyte stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate erythrocyte
definition: A macrogametocyte stage in the Plasmodium lifecycle that occurs either in the bloodstream of a vertebrate host or the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium microgametocyte stage
type: Class
equivalent class: Class
  intersection of: microgametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: microgametocyte stage
subclass of: Plasmodium gametocyte stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate erythrocyte
definition: A microgametocyte stage in the Plasmodium lifecycle that occurs either in the bloodstream of a vertebrate host or the midgut of a mosquito vector.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium merozoite stage
type: Class
equivalent class: Class
  intersection of: merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: merozoite stage
definition: A merozoite stage in the Plasmodium lifecycle that occurs in the bloodstream or hepatocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium erythrocytic merozoite stage
type: Class
equivalent class: Class
  intersection of: erythrocytic merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: erythrocytic merozoite stage
subclass of: Plasmodium merozoite stage
definition: An erythrocytic merozoite stage in the Plasmodium lifecycle that occurs in the bloodstream of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium hepatic merozoite stage
type: Class
equivalent class: Class
  intersection of: hepatic merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: hepatic merozoite stage
subclass of: Plasmodium merozoite stage
definition: A hepatic merozoite stage in the Plasmodium lifecycle that occurs in the hepatocyte of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium oocyst stage
type: Class
equivalent class: Class
  intersection of: oocyst stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: oocyst stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: An oocyst stage in the Plasmodium lifecycle that occurs on the hemocoel side of the midgut of a mosquito vector. During this stage Plasmodium ookinete invades and escapes midgut wall of mosquito and embed itself onto the exterior of the gut membrane and develop encysted zygote, called oocyst.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium ookinete stage
type: Class
equivalent class: Class
  intersection of: ookinete stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: ookinete stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: An ookinete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector and on the outside of the midgut.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium schizont stage
type: Class
equivalent class: Class
  intersection of: schizont stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: schizont stage
definition: A schizont stage in the Plasmodium lifecycle that occurs in erythrocytes or in hepatocytes.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium erythrocytic schizont stage
type: Class
equivalent class: Class
  intersection of: erythrocytic schizont stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: erythrocytic schizont stage
subclass of: Plasmodium schizont stage
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate erythrocyte
definition: An erythrocytic schizont stage in the Plasmodium lifecycle that occurs in the infected erythrocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium hepatic schizont stage
type: Class
equivalent class: Class
  intersection of: hepatic schizont stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: hepatic schizont stage
subclass of: Plasmodium schizont stage
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate hepatocyte
definition: A hepatic schizont stage in the Plasmodium lifecycle that occurs in the infected hepatocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium sporozoite stage
type: Class
equivalent class: Class
  intersection of: sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: sporozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles salivary gland
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate blood
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate hepatocyte
definition: A sporozoite stage in the Plasmodium lifecycle that occurs in the salivary glands of the mosquito and invades hepatocytes in the vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium oocyst-derived sporozoite stage
type: Class
equivalent class: Class
  intersection of: oocyst-derived sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: oocyst-derived sporozoite stage
subclass of: Plasmodium sporozoite stage
definition: A sporozoite stage in the Plasmodium lifecycle that develops in oocyst of the mosquito midgut.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Omar harb
imported from: opl.owl

Plasmodium salivary gland-derived sporozoite stage
type: Class
equivalent class: Class
  intersection of: salivary gland-derived sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: salivary gland-derived sporozoite stage
subclass of: Plasmodium sporozoite stage
definition: A salivary gland-derived sporozoite stage in the Plasmodium lifecycle that occurs in the salivary glands of the mosquito and invades hepatocytes in the vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
term editor: Omar harb
imported from: opl.owl

Plasmodium trophozoite stage
type: Class
equivalent class: Class
  intersection of: trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate erythrocyte
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate hepatocyte
definition: A trophozoite stage in the Plasmodium lifecycle that occurs in a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium erythrocytic trophozoite stage
type: Class
equivalent class: Class
  intersection of: erythrocytic trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: erythrocytic trophozoite stage
subclass of: Plasmodium trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate erythrocyte
definition: An erythrocytic trophozoite stage in the Plasmodium life cycle that occurs in erythrocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium erythrocytic ring trophozoite stage
type: Class
equivalent class: Class
  intersection of: erythrocytic ring trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: erythrocytic ring trophozoite stage
subclass of: Plasmodium erythrocytic trophozoite stage
definition: An erythrocytic ring trophozoite stage in the Plasmodium life cycle that occurs in erythrocytes of a vertebrate host. During this stage some Plasmodium merozoites undergo asexual reproduction cycle in erythrocytes and form young trophozoites that are referred to as "ring form" due to their morphology.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium hepatic trophozoite stage
type: Class
equivalent class: Class
  intersection of: hepatic trophozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: hepatic trophozoite stage
subclass of: Plasmodium trophozoite stage
subclass of: Restriction
  on property: occurs in
  some values from: Vertebrate hepatocyte
definition: A hepatic trophozoite stage in the Plasmodium life cycle that occurs in hepatocytes of a vertebrate host.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Plasmodium zygote stage
type: Class
equivalent class: Class
  intersection of: zygote stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium
subclass of: parasite lifecycle stage
subclass of: zygote stage
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles midgut
definition: A zygote stage in the Plasmodium lifecycle that occurs in the midgut of the mosquito vector where a microgamete and a macrogamete fertilizes each other to produce a diploid cell.
term editor: Chris Stoeckert
term editor: Jie Zheng
imported from: opl.owl

Vertebrate blood
type: Class
equivalent class: Class
  intersection of: blood
  intersection of: Restriction
    on property: part of
    some values from: Vertebrata <vertebrates>
subclass of: blood
definition: Blood that is part of or originated from a vertebrate.
term editor: Jie Zheng
definition source: OPL
imported from: opl.owl

Vertebrate erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: part of
    some values from: Vertebrata <vertebrates>
subclass of: erythrocyte
definition: An erythrocyte that is a part of or originated from a vertebrate.
term editor: Jie Zheng
definition source: OPL
imported from: opl.owl

Vertebrate hepatocyte
type: Class
equivalent class: Class
  intersection of: hepatocyte
  intersection of: Restriction
    on property: part of
    some values from: Vertebrata <vertebrates>
subclass of: hepatocyte
definition: A hepatocyte that is a part of or originated from a vertebrate.
term editor: Jie Zheng
definition source: OPL
imported from: opl.owl

Mammalia cerebrospinal fluid
type: Class
equivalent class: Class
  intersection of: cerebrospinal fluid
  intersection of: Restriction
    on property: part of
    some values from: Mammalia
subclass of: cerebrospinal fluid
definition: Cerebrospinal fluid that is a part of or originated from a mammal.
term editor: Jie Zheng
imported from: opl.owl

Mammalia blood
type: Class
equivalent class: Class
  intersection of: blood
  intersection of: Restriction
    on property: part of
    some values from: Mammalia
subclass of: Vertebrate blood
definition: Blood that is part of or originated from a mammalia.
term editor: Jie Zheng
imported from: opl.owl

Mammalia macrophage
type: Class
equivalent class: Class
  intersection of: macrophage
  intersection of: Restriction
    on property: part of
    some values from: Mammalia
subclass of: macrophage
definition: A macrophage that is a part of or originated from a mammalia.
term editor: Jie Zheng
imported from: opl.owl

tachyzoite stage
type: Class
subclass of: parasite lifecycle stage
definition: A parasite lifecycle stage that parasite replicates rapidly within the host cell.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7744739/
imported from: opl.owl

Plasmodium vivax sporozoite
type: Class
subclass of: Plasmodium vivax
subclass of: Plasmodium sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium vivax sporozoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens blood
subclass of: Restriction
  on property: located in
  some values from: Anopheles salivary gland
definition: A Plasmodium vivax is formed in the oocyst. It migrates to and resides in the gut of the mosquito vector.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Plasmodium vivax merozoite
type: Class
subclass of: Plasmodium vivax
subclass of: Plasmodium merozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium vivax merozoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens erythrocyte
definition: A Plasmodium vivax that is found in the bloodstream of the human host and invades erythrocytes.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Plasmodium berghei sporazoite
type: Class
subclass of: Plasmodium berghei
subclass of: Plasmodium sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium berghei sporazoite stage
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens blood
subclass of: Restriction
  on property: located in
  some values from: Anopheles salivary gland
definition: A Plasmodium berghei is formed in the oocyst. It migrates to and resides in the gut of the mosquito vector.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Neospora caninum tachyzoite
type: Class
subclass of: Neospora caninum
subclass of: Restriction
  on property: participates in
  some values from: Neospora caninum tachyzoite stage
subclass of: Restriction
  on property: located in
  some values from: Canis
definition: A Neospora caninum that is found intracellular in the intermediate hosts in which asexual replication takes place.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890850/
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Sarcocystis neurona merozoite
type: Class
subclass of: Sarcocystis neurona
subclass of: Restriction
  on property: participates in
  some values from: Sarcocystis neurona merozoite stage
subclass of: Restriction
  on property: located in
  some values from: Canis lupus familiaris erythrocyte
definition: A Sarcocystis neurona that is found in the bloodstream of the human host and invades erythrocytes.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.ncbi.nlm.nih.gov/books/NBK574577/
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Toxoplasma gondii tachyzoite
type: Class
subclass of: Toxoplasma gondii
subclass of: Restriction
  on property: participates in
  some values from: Toxoplasma gondii tachyzoite stage
subclass of: Restriction
  on property: located in
  some values from: Mammalia
definition: A Toxoplasma gondii that is formed in tissue in a host and replicates quickly. This replaces the previous term as .
term editor: Anthony Huffman
term editor: Jie Zheng
alternative label: Toxoplasma gondii trophozoite
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106833/
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Plasmodium vivax sporozoite stage
type: Class
equivalent class: Class
  intersection of: sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium vivax
subclass of: Plasmodium sporozoite stage
subclass of: Plasmodium vivax lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens blood
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles salivary gland
definition: A sporozoite stage in Plasmodium vivax life cycle.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Plasmodium vivax merozoite stage
type: Class
equivalent class: Class
  intersection of: merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium vivax
subclass of: Plasmodium merozoite stage
subclass of: Plasmodium vivax lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens erythrocyte
definition: A merozoite stage in the Plasmodium vivax life cycle.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Plasmodium berghei sporazoite stage
type: Class
equivalent class: Class
  intersection of: sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium berghei
subclass of: Plasmodium sporozoite stage
subclass of: Plasmodium berghei lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens hepatocyte
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens blood
subclass of: Restriction
  on property: occurs in
  some values from: Anopheles salivary gland
definition: A sporozoite stage in the Plasmodium berghei life cycle.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Neospora caninum tachyzoite stage
type: Class
equivalent class: Class
  intersection of: tachyzoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Neospora caninum
subclass of: tachyzoite stage
subclass of: Neospora caninum lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Canis
definition: A tachyzoite stage in the Neospora caninum life cycle.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890850/
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Sarcocystis neurona merozoite stage
type: Class
equivalent class: Class
  intersection of: merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Sarcocystis neurona
subclass of: merozoite stage
subclass of: Sarcocystis neurona lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Canis lupus familiaris erythrocyte
definition: A merozoite stage in the Sarcocystis neurona life cycle.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://wcvm.usask.ca/learnaboutparasites/parasites/sarcocystis-neurona.php
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Toxoplasma gondii tachyzoite stage
type: Class
equivalent class: Class
  intersection of: tachyzoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Toxoplasma gondii
subclass of: tachyzoite stage
subclass of: Toxoplasma gondii lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Mammalia
definition: A tachyzoite stage in the Toxoplasma gondii life cycle.
editor note: Tachyzoites can be found in various organs and tissues during the acute phase of Toxoplasma gondii infection, including lymph nodes, spleen, liver, lungs, and the central nervous system.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106833/
term tracker item: https://github.com/OPL-ontology/OPL/issues/21
ontology term requester: He Group
imported from: opl.owl

Canis lupus familiaris erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: part of
    some values from: Canis lupus familiaris
subclass of: Vertebrate erythrocyte
definition: An erythrocyte that is a part of or originated from a Canis lupus familiaris.
term editor: Jie Zheng
definition source: He Group
imported from: opl.owl

Plasmodium vivax lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium vivax
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Plasmodium vivax.
term editor: Jie Zheng
definition source: He Group
imported from: opl.owl

Plasmodium berghei lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium berghei
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Plasmodium berghei.
term editor: Jie Zheng
definition source: He Group
imported from: opl.owl

Neospora caninum lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Neospora caninum
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Neospora caninum.
term editor: Jie Zheng
definition source: He Group
imported from: opl.owl

Sarcocystis neurona lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Sarcocystis neurona
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Sarcocystis neurona.
term editor: Jie Zheng
definition source: He Group
imported from: opl.owl

Toxoplasma gondii lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Toxoplasma gondii
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Toxoplasma gondii.
term editor: Jie Zheng
definition source: He Group
imported from: opl.owl

Plasmodium yoelii sporozoite
type: Class
subclass of: Plasmodium yoelii
subclass of: Plasmodium sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium yoelii sporozoite stage
definition: A Plasmodium yoelii in sporozoite stage.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium yoelii merozoite
type: Class
subclass of: Plasmodium yoelii
subclass of: Plasmodium merozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium yoelii merozoite stage
subclass of: Restriction
  on property: located in
  some values from: Primates erythrocyte
definition: A Plasmodium yoelii in merozoite stage.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium yoelii gametocyte
type: Class
subclass of: Plasmodium yoelii
subclass of: Plasmodium gametocyte
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium yoelii gametocyte stage
subclass of: Restriction
  on property: located in
  some values from: Primates erythrocyte
definition: A Plasmodium yoelii in gametocyte stage.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium chabaudi sporozoite
type: Class
subclass of: Plasmodium chabaudi
subclass of: Plasmodium sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium chabaudi sporozoite stage
definition: A Plasmodium chabaudi in sporozoite stage.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium knowlesi sporozoite
type: Class
subclass of: Plasmodium knowlesi
subclass of: Plasmodium sporozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium knowlesi sporozoite stage
definition: A Plasmodium knowlesi in sporozoite stage.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium knowlesi merozoite
type: Class
subclass of: Plasmodium knowlesi
subclass of: Plasmodium merozoite
subclass of: Restriction
  on property: participates in
  some values from: Plasmodium knowlesi merozoite stage
subclass of: Restriction
  on property: located in
  some values from: Primates erythrocyte
definition: A Plasmodium knowlesi in merozoite stage.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium yoelii sporozoite stage
type: Class
equivalent class: Class
  intersection of: sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium yoelii
subclass of: Plasmodium sporozoite stage
subclass of: Plasmodium yoelii lifecycle stage
definition: A sporozoite stage in the Plasmodium yoelii.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium yoelii merozoite stage
type: Class
equivalent class: Class
  intersection of: merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium yoelii
subclass of: Plasmodium merozoite stage
subclass of: Plasmodium yoelii lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Primates erythrocyte
definition: A merozoite stage in the Plasmodium yoelii.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium yoelii gametocyte stage
type: Class
equivalent class: Class
  intersection of: gametocyte stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium yoelii
subclass of: Plasmodium gametocyte stage
subclass of: Plasmodium yoelii lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Primates erythrocyte
definition: A gametocyte stage in the Plasmodium yoelii.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium chabaudi sporozoite stage
type: Class
equivalent class: Class
  intersection of: sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium chabaudi
subclass of: Plasmodium sporozoite stage
subclass of: Plasmodium chabaudi lifecycle stage
definition: A sporozoite stage in the Plasmodium chabaudi.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium knowlesi sporozoite stage
type: Class
equivalent class: Class
  intersection of: sporozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium knowlesi
subclass of: Plasmodium sporozoite stage
subclass of: Plasmodium knowlesi lifecycle stage
definition: A sporozoite stage in the Plasmodium knowlesi.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Plasmodium knowlesi merozoite stage
type: Class
equivalent class: Class
  intersection of: merozoite stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium knowlesi
subclass of: Plasmodium merozoite stage
subclass of: Plasmodium knowlesi lifecycle stage
subclass of: Restriction
  on property: occurs in
  some values from: Primates erythrocyte
definition: A merozoite stage in the Plasmodium knowlesi.
term editor: Anthony Huffman
term editor: Jie Zheng
definition source: https://www.cdc.gov/dpdx/malaria/index.html
term tracker item: https://github.com/OPL-ontology/OPL/issues/24
ontology term requester: He Group
imported from: opl.owl

Primates erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: part of
    some values from: Primates
subclass of: Vertebrate erythrocyte
definition: An erythrocyte that is a part of or originated from a primate.
term editor: Jie Zheng
alternative label: primate erythrocyte
definition source: He Group
ontology term requester: He Group
imported from: opl.owl

Plasmodium yoelii lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium yoelii
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Plasmodium yoelii.
term editor: Jie Zheng
definition source: He Group
ontology term requester: He Group
imported from: opl.owl

Plasmodium chabaudi lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium chabaudi
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Plasmodium chabaudi.
term editor: Jie Zheng
definition source: He Group
ontology term requester: He Group
imported from: opl.owl

Plasmodium knowlesi lifecycle stage
type: Class
equivalent class: Class
  intersection of: parasite lifecycle stage
  intersection of: Restriction
    on property: in taxon
    some values from: Plasmodium knowlesi
subclass of: parasite lifecycle stage
definition: A lifecycle stage of Plasmodium knowlesi.
term editor: Jie Zheng
definition source: He Group
ontology term requester: He Group
imported from: opl.owl

biomarker role
type: Class
subclass of: role
term editor: Yingtong Liu, Anthony Huffman, Oliver He
imported from: opmi.owl

biomarker
type: Class
equivalent class: Restriction
  on property: has role
  some values from: biomarker role
subclass of: material entity
definition: Material entity that has a measurable quality, or that participates in a measurement process profile, which can be used as an indicator of an underlying biological state or identity.
editor note: The NIH Biomarkers and Surrogate Endpoint Working Group defined a biomarker as “A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention” (https://pubmed.ncbi.nlm.nih.gov/11240971/). However, the definition of 'characteriistc' is unclear, so we do not use the exact definintion in the ontology.
term editor: Yingtong Liu, Anthony Huffman, Oliver He
definition source: https://en.wikipedia.org/wiki/Biomarker
definition source: https://en.wikipedia.org/wiki/Biomarker_(cell)
definition source: https://en.wikipedia.org/wiki/Biomarker_(medicine)
imported from: opmi.owl

immune biomarker
type: Class
subclass of: biomarker
definition: Biomarker that has a measurable quality or process profile(s), that can be used as an indicator of an underlying immune state or identity.
term editor: Anthony Huffman, Oliver He
definition source: A biomarker that is indicative of an immune response
definition source: https://pubmed.ncbi.nlm.nih.gov/22072636/
definition source: https://pubmed.ncbi.nlm.nih.gov/32286245/
imported from: opmi.owl

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
imported from: pato.owl
has alternative id: PATO:0000072
has OBO namespace: quality
id: PATO:0000001

age
type: Class
subclass of: time
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0000011
in subset: attribute slim
in subset: scalar slim

frequency
type: Class
subclass of: quality
definition: A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0000044
in subset: attribute slim
in subset: scalar slim

biological sex
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0000047
in subset: attribute slim

time
type: Class
subclass of: physical quality
definition: A quality in which events occur in sequence.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0000165
in subset: attribute slim
in subset: scalar slim

viability
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0000169
in subset: attribute slim
in subset: disposition slim

viable
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0000719
in subset: disposition slim
in subset: value slim

volume
type: Class
subclass of: physical object quality
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0000918
in subset: attribute slim
in subset: mpath slim
in subset: scalar slim

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
imported from: pato.owl
has alternative id: PATO:0002079
has cross-reference: Wikipedia:Physical_property
has exact synonym: relational physical quality
has OBO namespace: quality
id: PATO:0001018
in subset: attribute slim

efficiency
type: Class
subclass of: physical quality
definition: A physical quality inhering in a bearer by virtue of ratio of the bearer's output to the bearer's input.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0001029
in subset: attribute slim

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
imported from: pato.owl
has alternative id: PATO:0001237
has alternative id: PATO:0001238
has cross-reference: snap:Quality
has exact synonym: monadic quality of a continuant
has exact synonym: multiply inhering quality of a physical entity
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has OBO namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

dead
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0001422
in subset: value slim

inefficient
type: Class
subclass of: efficiency
definition: An efficiency quality inhering in a bearer by virtue of the bearer's lacking efficiency.
imported from: pato.owl
is opposite of: efficient
has OBO namespace: quality
id: PATO:0001677
in subset: value slim

efficient
type: Class
subclass of: efficiency
definition: An efficiency quality inhering in a bearer by virtue of the bearer's having efficiency.
imported from: pato.owl
is opposite of: inefficient
has OBO namespace: quality
id: PATO:0001678
in subset: value slim

organismal quality
type: Class
subclass of: physical object quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: pato.owl
has OBO namespace: quality
id: PATO:0001995

virulence
type: Class
subclass of: organismal quality
definition: A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism.
imported from: pato.owl
contributor: 0000-0002-2061-091X
creation date: 2009-10-30T05:04:06Z
has OBO namespace: quality
id: PATO:0002146
in subset: attribute slim
in subset: scalar slim

reduced virulence
type: Class
subclass of: virulence
subclass of: decreased object quality
definition: A virulence that is relatively low.
imported from: pato.owl
is opposite of: PATO_0002148
contributor: 0000-0002-2061-091X
creation date: 2009-10-30T05:05:02Z
has exact synonym: attenuated
has OBO namespace: quality
id: PATO:0002147
in subset: value slim

decreased object quality
type: Class
subclass of: quality
subclass of: physical object quality
definition: A quality of an object that has a value that is decreased compared to normal or average.
imported from: pato.owl
is opposite of: PATO_0002305
contributor: 0000-0002-2061-091X
creation date: 2011-06-16T06:51:54Z
has OBO namespace: quality
id: PATO:0002303

protein
type: Class
subclass of: molecular entity
definition: An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
imported from: pr.owl
has exact synonym: natural protein
has narrow synonym: native protein
has OBO namespace: protein
id: PR:000000001
comment: Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Note also that the definition excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to PR:000064867 ("protein-containing molecular entity"). Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB).

Toll-like receptor
type: Class
subclass of: protein
definition: A protein that has a core domain composition consisting of a signal peptide, an extracellular domain with multiple Leucine rich repeat (Pfam:PF13855) domain (LRR), a cysteine-rich region, a single-pass transmembrane domain and a C-terminal cytoplasmic tail containing a TIR domain (Pfam:PF01582).
imported from: pr.owl
has cross-reference: PIRSF:PIRSF800008
has exact synonym: fam:TLR
has OBO namespace: protein
id: PR:000001096
comment: Category=family.

Toll-like receptor 1
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR1 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1751
has exact synonym: CD281
has exact synonym: TIL
has exact synonym: TLR1
has exact synonym: Toll/interleukin-1 receptor-like protein
has OBO namespace: protein
has related synonym: KIAA0012
id: PR:000001151
comment: Category=gene.

Toll-like receptor 2
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR2 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1752
has exact synonym: CD282
has exact synonym: TLR2
has exact synonym: Toll/interleukin-1 receptor-like protein 4
has OBO namespace: protein
has related synonym: TIL4
id: PR:000001153
comment: Category=gene.

Toll-like receptor 3
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR3 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1753
has exact synonym: CD283
has exact synonym: TLR3
has OBO namespace: protein
id: PR:000001154
comment: Category=gene.

Toll-like receptor 4
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR4 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has broad synonym: Toll
has cross-reference: IUPHARobj:1754
has exact synonym: CD284
has exact synonym: TLR4
has OBO namespace: protein
has related synonym: Lps
id: PR:000001155
comment: Category=gene.

Toll-like receptor 5
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR5 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1755
has exact synonym: TLR5
has exact synonym: Toll/interleukin-1 receptor-like protein 3
has OBO namespace: protein
has related synonym: TIL3
id: PR:000001156
comment: Category=gene.

Toll-like receptor 6
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR6 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1756
has exact synonym: CD286
has exact synonym: TLR6
has OBO namespace: protein
id: PR:000001157
comment: Category=gene.

Toll-like receptor 7
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR7 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1757
has exact synonym: TLR7
has OBO namespace: protein
has related synonym: UNQ248/PRO285
id: PR:000001158
comment: Category=gene.

Toll-like receptor 8
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR8 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1758
has exact synonym: CD288
has exact synonym: TLR8
has OBO namespace: protein
has related synonym: UNQ249/PRO286
id: PR:000001159
comment: Category=gene.

Toll-like receptor 9
type: Class
subclass of: Toll-like receptor
definition: A Toll-like receptor that is a translation product of the human TLR9 gene or a 1:1 ortholog thereof. Non-methylated CpG motifs, present in viral and bacterial DNA, are one of many pathogen-associated molecular patterns (PAMP) recognized by the mammalian innate immune system. Recognition of this PAMP occurs through a specific interaction with Toll-like receptor 9 and this interaction can induce cytokine responses that influence both innate and adaptive immune responses.
imported from: pr.owl
has cross-reference: IUPHARobj:1759
has exact synonym: CD289
has exact synonym: TLR9
has OBO namespace: protein
has related synonym: UNQ5798/PRO19605
id: PR:000001160
comment: Category=gene.

C-type lectin domain family 6 member A
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CLEC6A gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:2928
has exact synonym: C-type lectin superfamily member 10
has exact synonym: CLEC6A
has exact synonym: DC-associated C-type lectin 2
has exact synonym: dectin-2
has exact synonym: dendritic cell-associated C-type lectin 2
has OBO namespace: protein
has related synonym: CLECSF10
has related synonym: Clec4n
has related synonym: DECTIN2
id: PR:000001806
comment: Category=gene. Requested by=CL.

C-type lectin domain family 7 member A
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CLEC7A gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:2927
has exact synonym: C-type lectin superfamily member 12
has exact synonym: CD369
has exact synonym: CLEC7A
has exact synonym: DC-associated C-type lectin 1
has exact synonym: beta-glucan receptor
has exact synonym: dectin-1
has exact synonym: dendritic cell-associated C-type lectin 1
has OBO namespace: protein
has related synonym: BGR
has related synonym: CLECSF12
has related synonym: DECTIN1
has related synonym: UNQ539/PRO1082
id: PR:000001807
comment: Category=gene. Requested by=CL.

interferon-inducible protein AIM2
type: Class
subclass of: protein
definition: A protein that is a translation product of the human AIM2 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:2923
has exact synonym: AIM2
has exact synonym: Ifi-210
has exact synonym: absent in melanoma 2
has exact synonym: interferon-inducible protein 210
has exact synonym: interferon-inducible protein p210
has OBO namespace: protein
has related synonym: Gm1313
has related synonym: Ifi210
id: PR:000003874
comment: Category=gene.

C-type lectin domain family 4 member E
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CLEC4E gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:2929
has exact synonym: C-type lectin superfamily member 9
has exact synonym: CLEC4E
has exact synonym: macrophage-inducible C-type lectin
has OBO namespace: protein
has related synonym: CLECSF9
has related synonym: MINCLE
has related synonym: UNQ218/PRO244
id: PR:000005570
comment: Category=gene.

interferon-induced helicase C domain-containing protein 1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human IFIH1 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:2921
has exact synonym: IFIH1
has exact synonym: MDA-5
has exact synonym: RIG-I-like receptor 2
has exact synonym: RLR-2
has exact synonym: RNA helicase-DEAD box protein 116
has exact synonym: helicard
has exact synonym: helicase with 2 CARD domains
has exact synonym: interferon induced with helicase C domain protein 1
has exact synonym: interferon-induced with helicase C domain protein 1
has exact synonym: melanoma differentiation-associated protein 5
has exact synonym: murabutide down-regulated protein
has OBO namespace: protein
has related synonym: MDA5
has related synonym: RH116
id: PR:000008910
comment: Category=gene.

NACHT, LRR and PYD domains-containing protein 3
type: Class
subclass of: protein
definition: A protein that is a translation product of the human NLRP3 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1770
has exact synonym: CLR1.1
has exact synonym: NLRP3
has exact synonym: PYRIN-containing APAF1-like protein 1
has exact synonym: angiotensin/vasopressin receptor AII/AVP-like
has exact synonym: caterpiller protein 1.1
has exact synonym: cold autoinflammatory syndrome 1 protein
has exact synonym: cold autoinflammatory syndrome 1 protein homolog
has exact synonym: cryopyrin
has exact synonym: mast cell maturation-associated-inducible protein 1
has OBO namespace: protein
has related synonym: C1orf7
has related synonym: CIAS1
has related synonym: Mmig1
has related synonym: NALP3
has related synonym: PYPAF1
id: PR:000011271
comment: Category=gene.

nucleotide-binding oligomerization domain-containing protein 1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human NOD1 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1762
has exact synonym: NOD1
has exact synonym: caspase recruitment domain-containing protein 4
has OBO namespace: protein
has related synonym: CARD4
id: PR:000011305
comment: Category=gene.

nucleotide-binding oligomerization domain-containing protein 2
type: Class
subclass of: protein
definition: A protein that is a translation product of the human NOD2 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:1763
has exact synonym: NOD2
has exact synonym: caspase recruitment domain-containing protein 15
has exact synonym: inflammatory bowel disease protein 1
has OBO namespace: protein
has related synonym: CARD15
has related synonym: IBD1
id: PR:000011306
comment: Category=gene.

superoxide dismutase [Cu-Zn]
type: Class
subclass of: protein
definition: A SODC domain protein that is a translation product of the human SOD1 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: SOD1
has OBO namespace: protein
id: PR:000015399
comment: Category=gene.

C-type lectin domain family 9 member A
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CLEC9A gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: CD370
has exact synonym: CLEC9A
has OBO namespace: protein
has related synonym: UNQ9341/PRO34046
id: PR:000026296
comment: Category=gene.

antiviral innate immune response receptor RIG-I
type: Class
subclass of: protein
definition: A protein that is a translation product of the human RIGI gene or a 1:1 ortholog thereof.
imported from: pr.owl
has cross-reference: IUPHARobj:2920
has exact synonym: ATP-dependent RNA helicase DDX58
has exact synonym: DEAD box protein 58
has exact synonym: RIG-1
has exact synonym: RIG-I
has exact synonym: RIG-I-like receptor 1
has exact synonym: RIGI
has exact synonym: RLR-1
has exact synonym: RNA sensor RIG-I
has exact synonym: probable ATP-dependent RNA helicase DDX58
has exact synonym: retinoic acid-inducible gene 1 protein
has exact synonym: retinoic acid-inducible gene I protein
has OBO namespace: protein
has related synonym: DDX58
id: PR:000029394
comment: Category=gene.

protein MB21D1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CGAS gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: 2'3'-cGAMP synthase
has exact synonym: CGAS
has exact synonym: Mab-21 domain-containing protein 1
has exact synonym: cGAMP synthase
has OBO namespace: protein
has related synonym: C6orf150
has related synonym: MB21D1
id: PR:000030833
comment: Category=gene.

obsolete protein-containing material entity
type: Class
subclass of: Thing
definition: OBSOLETE. A material entity that minimally consists of a protein.
imported from: pr.owl
consider: PR:000064867
has OBO namespace: protein
id: PR:000050567
comment: Note: Made obsolete since the term definition was much broader than intended. Originally meant to include only single proteins (and derivatives thereof; PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566), it instead also included cells defined as having certain protein attachments.
deprecated: true

spike glycoprotein (SARS-CoV-2)
type: Class
subclass of: protein
definition: A protein that is a translation product of the S gene in SARS-CoV-2.
imported from: pr.owl
has cross-reference: GenPept:YP_009724390
has cross-reference: UniProtKB:P0DTC2
has exact synonym: E2 (SARS-CoV-2)
has exact synonym: S (SARS2)
has exact synonym: S glycoprotein (SARS-CoV-2)
has exact synonym: peplomer protein (SARS-CoV-2)
has exact synonym: surface glycoprotein (SARS-CoV-2)
has OBO namespace: protein
has related synonym: 2
has related synonym: GU280_gp02
has related synonym: S
id: PR:P0DTC2
comment: Category=organism-gene. Note: 1273 aa protein. Undergoes additional processing by proteolytic cleavage.

envelope small membrane protein (SARS-CoV-2)
type: Class
subclass of: VO_0004990
definition: Category=organism-gene. Note: 75 aa protein. A protein that is a translation product of the E gene in SARS-CoV-2.
alternative label: E (SARS2)
alternative label: envelope protein (SARS-CoV-2)
alternative label: sM protein (SARS-CoV-2)
imported from: pr.owl
has cross-reference: UniProtKB:P0DTC4

nose
type: Class
subclass of: organ
subclass of: ectoderm-derived structure
definition: The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
imported from: uberon.owl
external_definition: Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
external_definition: a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
external_definition: the organ that is specialized for smell and is part of the respiratory system
taxon_notes: the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
has cross-reference: BTO:0000840
has cross-reference: CALOHA:TS-2037
has cross-reference: EHDAA2:0001274
has cross-reference: EHDAA:1502
has cross-reference: EMAPA:16542
has cross-reference: EV:0100037
has cross-reference: EV:0100370
has cross-reference: FMA:46472
has cross-reference: GAID:77
has cross-reference: MA:0000281
has cross-reference: MAT:0000139
has cross-reference: MESH:D009666
has cross-reference: MIAA:0000139
has cross-reference: NCIT:C12756
has cross-reference: SCTID:181195007
has cross-reference: TAO:0000047
has cross-reference: UMLS:C0028429
has cross-reference: Wikipedia:Nose
has cross-reference: ZFA:0000047
has cross-reference: galen:Nose
has exact synonym: nasal sac
has exact synonym: nose
has exact synonym: peripheral olfactory organ
has OBO namespace: uberon
has related synonym: nasus
has related synonym: olfactory apparatus
has related synonym: proboInOwlscis
id: UBERON:0000004
in subset: efo slim
in subset: major organ
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

serous membrane
type: Class
subclass of: mesoderm-derived structure
subclass of: multicellular anatomical structure
definition: Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
imported from: uberon.owl
external_definition: A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
external_definition: a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
external_ontology_notes: in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
contributor: cmungall
has cross-reference: FMA:9581
has cross-reference: GAID:19
has cross-reference: MESH:D012704
has cross-reference: NCIT:C13169
has cross-reference: SCTID:362878009
has cross-reference: TAO:0005425
has cross-reference: UMLS:C0036760
has cross-reference: Wikipedia:Serous_membrane
has cross-reference: ZFA:0005425
has exact synonym: tunica serosa
has exact synonym: wall of serous sac
has OBO namespace: uberon
has related synonym: serosa
id: UBERON:0000042
in subset: uberon slim
in subset: vertebrate core

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: uberon.owl
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: Fungi
has cross-reference: AAO:0010825
has cross-reference: AEO:0000003
has cross-reference: BILA:0000003
has cross-reference: CARO:0000003
has cross-reference: EHDAA2:0003003
has cross-reference: EMAPA:0
has cross-reference: FBbt:00007001
has cross-reference: FMA:305751
has cross-reference: FMA:67135
has cross-reference: GAID:781
has cross-reference: HAO:0000003
has cross-reference: MA:0003000
has cross-reference: MESH:D000825
has cross-reference: SCTID:362889002
has cross-reference: TAO:0000037
has cross-reference: TGMA:0001823
has cross-reference: VHOG:0001759
has cross-reference: XAO:0003000
has cross-reference: ZFA:0000037
has cross-reference: http://dbpedia.org/ontology/AnatomicalStructure
has exact synonym: biological structure
has exact synonym: connected biological structure
has OBO namespace: uberon
id: UBERON:0000061
in subset: common anatomy
in subset: upper level

organ
type: Class
subclass of: multicellular anatomical structure
definition: Anatomical structure that performs a specific function or group of functions [WP].
imported from: uberon.owl
never in taxon: NCBITaxon_110815
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: Fungi
external_definition: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
external_ontology_notes: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
has cross-reference: BIRNLEX:4
has cross-reference: CARO:0020004
has cross-reference: EFO:0000634
has cross-reference: EMAPA:35949
has cross-reference: ENVO:01000162
has cross-reference: FMA:67498
has cross-reference: MA:0003001
has cross-reference: NCIT:C13018
has cross-reference: SCTID:272625005
has cross-reference: UMLS:C0178784
has cross-reference: WBbt:0003760
has cross-reference: Wikipedia:Organ_(anatomy)
has OBO namespace: uberon
has related synonym: anatomical unit
has related synonym: body organ
has related synonym: element
id: UBERON:0000062
in subset: common anatomy
in subset: upper level

organ part
type: Class
subclass of: multicellular anatomical structure
definition: A multicellular structure that is a part of an organ.
curator note: currently defined in a very broad sense, may be replaced by more specific classes in the future
imported from: uberon.owl
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: Fungi
has cross-reference: AAO:0011124
has cross-reference: BIRNLEX:16
has cross-reference: EFO:0000635
has cross-reference: FMA:82472
has cross-reference: SCTID:113343008
has cross-reference: SCTID:91717005
has exact synonym: cardinal organ part
has OBO namespace: uberon
has related synonym: regional part of organ
id: UBERON:0000064
in subset: common anatomy
in subset: efo slim
in subset: non informative
in subset: upper level

life cycle stage
type: Class
subclass of: occurrent
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
editor note: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
imported from: uberon.owl
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: Fungi
external_ontology_notes: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
external_ontology_notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
has cross-reference: BILS:0000105
has cross-reference: EFO:0000399
has cross-reference: FBdv:00007012
has cross-reference: FMA:24120
has cross-reference: HsapDv:0000000
has cross-reference: MESH:D008018
has cross-reference: MmusDv:0000000
has cross-reference: OlatDv:0000010
has cross-reference: PdumDv:0000090
has cross-reference: WBls:0000002
has cross-reference: XAO:1000000
has cross-reference: ZFS:0000000
has cross-reference: ZFS:0100000
has cross-reference: ncithesaurus:Developmental_Stage
has narrow synonym: developmental stage
has narrow synonym: stage
has OBO namespace: uberon
id: UBERON:0000105
in subset: common anatomy
in subset: efo slim
in subset: upper level

zygote stage
type: Class
subclass of: life cycle stage
definition: A stage at which the organism is a single cell produced by means of sexual reproduction.
imported from: uberon.owl
homology_notes: As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
has cross-reference: BILS:0000106
has cross-reference: BilaDO:0000005
has cross-reference: EFO:0001322
has cross-reference: EHDAA:27
has cross-reference: FBdv:00005288
has cross-reference: IDOMAL:0000302
has cross-reference: NCIT:C12601
has cross-reference: PdumDv:0000100
has cross-reference: VHOG:0000745
has cross-reference: Wikipedia:Zygote
has cross-reference: XAO:1000001
has cross-reference: ZFS:0000001
has exact synonym: 1-cell stage
has exact synonym: fertilized egg stage
has exact synonym: one cell stage
has OBO namespace: uberon
has related synonym: fertilized egg stage
has related synonym: one-cell stage
has related synonym: zygote
has related synonym: zygotum
id: UBERON:0000106
in subset: efo slim

mouth
type: Class
subclass of: subdivision of digestive tract
definition: The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
imported from: uberon.owl
external_definition: Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
homology_notes: Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
has_relational_adjective: oral
development_notes: some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
external_ontology_notes: in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
has cross-reference: AAO:0010355
has cross-reference: BTO:0001090
has cross-reference: BTO:0004698
has cross-reference: CALOHA:TS-1315
has cross-reference: EFO:0000825
has cross-reference: EHDAA2:0001326
has cross-reference: EHDAA:542
has cross-reference: EMAPA:16262
has cross-reference: FBbt:00003126
has cross-reference: FMA:49184
has cross-reference: GAID:75
has cross-reference: MA:0000341
has cross-reference: MA:0002474
has cross-reference: MAT:0000038
has cross-reference: MESH:D009055
has cross-reference: MIAA:0000038
has cross-reference: SCTID:21082005
has cross-reference: TADS:0000040
has cross-reference: TAO:0000547
has cross-reference: TAO:0000590
has cross-reference: TGMA:0000131
has cross-reference: VHOG:0000280
has cross-reference: VHOG:0000812
has cross-reference: Wikipedia:Mouth
has cross-reference: XAO:0003029
has cross-reference: ZFA:0000547
has cross-reference: ZFA:0000590
has cross-reference: galen:Mouth
has exact synonym: regio oralis
has narrow synonym: adult mouth
has OBO namespace: uberon
has related synonym: cavital oralis
has related synonym: cavitas oris
has related synonym: cavum oris
has related synonym: mouth cavity
has related synonym: oral region
has related synonym: oral vestibule
has related synonym: rima oris
has related synonym: stoma
has related synonym: stomatodaeum
has related synonym: trophic apparatus
has related synonym: vestibule of mouth
has related synonym: vestibulum oris
id: UBERON:0000165
in subset: efo slim
in subset: major organ
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

blood
type: Class
subclass of: bodily fluid
definition: A fluid that is composed of blood plasma and erythrocytes.
curator note: This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
imported from: uberon.owl
present in taxon: Homo sapiens
external_definition: A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
external_definition: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
axiom_lost_from_external_ontology: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
homology_notes: Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
contributor: cmungall
contributor: tmeehan
has cross-reference: AAO:0000046
has cross-reference: BTO:0000089
has cross-reference: CALOHA:TS-0079
has cross-reference: EFO:0000296
has cross-reference: EHDAA2:0000176
has cross-reference: EHDAA:418
has cross-reference: EMAPA:16332
has cross-reference: ENVO:02000027
has cross-reference: EV:0100047
has cross-reference: FMA:9670
has cross-reference: GAID:965
has cross-reference: MA:0000059
has cross-reference: MESH:D001769
has cross-reference: MIAA:0000315
has cross-reference: NCIT:C12434
has cross-reference: TAO:0000007
has cross-reference: UMLS:C0005767
has cross-reference: VHOG:0000224
has cross-reference: Wikipedia:Blood
has cross-reference: XAO:0000124
has cross-reference: ZFA:0000007
has cross-reference: galen:Blood
has exact synonym: portion of blood
has exact synonym: vertebrate blood
has OBO namespace: uberon
has related synonym: whole blood
id: UBERON:0000178
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.
imported from: uberon.owl
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: Fungi
has cross-reference: AAO:0010264
has cross-reference: AEO:0000006
has cross-reference: BILA:0000006
has cross-reference: CARO:0000006
has cross-reference: EHDAA2:0003006
has cross-reference: FBbt:00007016
has cross-reference: FMA:67165
has cross-reference: HAO:0000006
has cross-reference: TAO:0001836
has cross-reference: TGMA:0001826
has cross-reference: VHOG:0001721
has OBO namespace: uberon
id: UBERON:0000465
in subset: common anatomy
in subset: upper level

stomach
type: Class
subclass of: subdivision of digestive tract
subclass of: digestive system element
definition: An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
imported from: uberon.owl
never in taxon: NCBITaxon 7864
never in taxon: NCBITaxon 7878
never in taxon: NCBITaxon 7955
never in taxon: NCBITaxon 9259
present in taxon: Homo sapiens
external_definition: Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
homology_notes: It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
taxon_notes: We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
has cross-reference: AAO:0000579
has cross-reference: ANISEED:1235297
has cross-reference: BTO:0001307
has cross-reference: CALOHA:TS-0980
has cross-reference: EFO:0000837
has cross-reference: EHDAA2:0001915
has cross-reference: EHDAA:2993
has cross-reference: EMAPA:17021
has cross-reference: EV:0100070
has cross-reference: FMA:7148
has cross-reference: GAID:293
has cross-reference: MA:0000353
has cross-reference: MAT:0000051
has cross-reference: MESH:D013270
has cross-reference: MIAA:0000051
has cross-reference: NCIT:C12391
has cross-reference: SCTID:181246003
has cross-reference: TAO:0002121
has cross-reference: UMLS:C0038351
has cross-reference: VHOG:0000408
has cross-reference: Wikipedia:Stomach
has cross-reference: XAO:0000128
has cross-reference: galen:Stomach
has narrow synonym: stomach chamber
has OBO namespace: uberon
has related synonym: anterior intestine
has related synonym: gaster
has related synonym: mesenteron
has related synonym: ventriculus
id: UBERON:0000945
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

saliva-secreting gland
type: Class
subclass of: oral gland
definition: Saliva-secreting exocrine glands of the oral cavity[GO].
curator note: currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.
imported from: uberon.owl
external_definition: A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
homology_notes: In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]
taxon_notes: The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands
has cross-reference: BTO:0001203
has cross-reference: CALOHA:TS-0892
has cross-reference: EFO:0000859
has cross-reference: EHDAA2:0001775
has cross-reference: EHDAA:7987
has cross-reference: EMAPA:17751
has cross-reference: EV:0100059
has cross-reference: FBbt:00005382
has cross-reference: FMA:9597
has cross-reference: GAID:937
has cross-reference: MA:0000346
has cross-reference: MAT:0000079
has cross-reference: MESH:D012469
has cross-reference: MIAA:0000079
has cross-reference: NCIT:C12426
has cross-reference: SCTID:181236000
has cross-reference: UMLS:C0036098
has cross-reference: VHOG:0000376
has cross-reference: Wikipedia:Salivary_gland
has cross-reference: galen:SalivaryGland
has exact synonym: salivary gland
has OBO namespace: uberon
has related synonym: glandulae salivariae
id: UBERON:0001044
in subset: efo slim
in subset: functional classification
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

midgut
type: Class
subclass of: subdivision of digestive tract
definition: Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
editor note: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
imported from: uberon.owl
homology_notes: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
taxon_notes: In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
external_ontology_notes: in FMA this represents an embryonic region.
has cross-reference: BILA:0000086
has cross-reference: BTO:0000863
has cross-reference: EFO:0001950
has cross-reference: EHDAA2:0001185
has cross-reference: EHDAA:983
has cross-reference: EMAPA:16255
has cross-reference: FBbt:00005383
has cross-reference: FMA:45617
has cross-reference: MA:0001564
has cross-reference: NCIT:C34210
has cross-reference: SCTID:361410004
has cross-reference: TGMA:0001036
has cross-reference: UMLS:C0231052
has cross-reference: VHOG:0000290
has cross-reference: Wikipedia:Midgut
has cross-reference: XAO:0000103
has OBO namespace: uberon
has related synonym: mesenteron
id: UBERON:0001045
in subset: developmental classification
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

hindgut
type: Class
subclass of: subdivision of digestive tract
definition: The caudalmost subdivision of a digestive tract.
editor note: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class
imported from: uberon.owl
external_definition: the caudal portion of the primitive digestive tube of the embryo
homology_notes: The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
external_ontology_notes: in FMA this class has no children. In MA it has a single child hindgut epithelium
has cross-reference: AAO:0011052
has cross-reference: BILA:0000087
has cross-reference: BTO:0000510
has cross-reference: EHDAA2:0000779
has cross-reference: EHDAA:975
has cross-reference: EMAPA:16715
has cross-reference: FBbt:00005384
has cross-reference: FMA:45618
has cross-reference: MA:0001527
has cross-reference: NCIT:C34188
has cross-reference: SCTID:362856002
has cross-reference: TGMA:0001020
has cross-reference: UMLS:C0231053
has cross-reference: VHOG:0000459
has cross-reference: Wikipedia:Hindgut
has cross-reference: XAO:0000104
has OBO namespace: uberon
has related synonym: metenteron
id: UBERON:0001046
in subset: developmental classification
in subset: pheno slim
in subset: uberon slim

anatomical entity
type: Class
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
imported from: uberon.owl
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: Fungi
has cross-reference: AAO:0010841
has cross-reference: AEO:0000000
has cross-reference: BFO:0000004
has cross-reference: BILA:0000000
has cross-reference: BIRNLEX:6
has cross-reference: CARO:0000000
has cross-reference: EHDAA2:0002229
has cross-reference: FBbt:10000000
has cross-reference: FMA:62955
has cross-reference: HAO:0000000
has cross-reference: MA:0000001
has cross-reference: NCIT:C12219
has cross-reference: TAO:0100000
has cross-reference: TGMA:0001822
has cross-reference: UMLS:C1515976
has cross-reference: WBbt:0000100
has cross-reference: XAO:0000000
has cross-reference: ZFA:0100000
has OBO namespace: uberon
id: UBERON:0001062
in subset: common anatomy
in subset: upper level

skeletal muscle tissue
type: Class
subclass of: muscle tissue
definition: Muscle tissue that consists primarily of skeletal muscle fibers.
editor note: TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
imported from: uberon.owl
external_definition: Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
external_definition: Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
homology_notes: This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
contributor: RDruzinsky
contributor: cmungall
contributor: dosumis
contributor: mellybelly
has broad synonym: skeletal muscle
has cross-reference: EMAPA:32716
has cross-reference: FMA:14069
has cross-reference: MA:0002439
has cross-reference: NCIT:C13050
has cross-reference: SCTID:426215008
has cross-reference: UMLS:C0242692
has cross-reference: Wikipedia:Skeletal_striated_muscle
has OBO namespace: uberon
has related synonym: skeletal muscle system
has related synonym: somatic muscle
id: UBERON:0001134
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

urinary bladder
type: Class
subclass of: mesoderm-derived structure
subclass of: bladder organ
definition: Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
imported from: uberon.owl
never in taxon: Aves
present in taxon: Homo sapiens
external_definition: A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
external_definition: Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
homology_notes: In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
has_relational_adjective: vesical
taxon_notes: The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
has broad synonym: bladder
has cross-reference: AAO:0000623
has cross-reference: BTO:0001418
has cross-reference: CALOHA:TS-1090
has cross-reference: EFO:0000290
has cross-reference: EHDAA2:0000174
has cross-reference: EHDAA:9328
has cross-reference: EMAPA:18321
has cross-reference: EV:0100098
has cross-reference: FMA:15900
has cross-reference: GAID:0000004
has cross-reference: MA:0000380
has cross-reference: MAT:0000122
has cross-reference: MESH:D001743
has cross-reference: MIAA:0000122
has cross-reference: NCIT:C12414
has cross-reference: SCTID:302512001
has cross-reference: UMLS:C0005682
has cross-reference: VHOG:0000740
has cross-reference: Wikipedia:Urinary_bladder
has cross-reference: XAO:0000154
has cross-reference: galen:UrinaryBladder
has exact synonym: vesica urinaria
has OBO namespace: uberon
has related synonym: urocyst
has related synonym: vesica
id: UBERON:0001255
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim

cerebrospinal fluid
type: Class
subclass of: bodily fluid
definition: A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
editor note: many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]
imported from: uberon.owl
external_definition: Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
homology_notes: In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]
external_ontology_notes: EHDAA2 models this as developing from CP, which is wrong
external_ontology_notes: the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
has cross-reference: BIRNLEX:1798
has cross-reference: BTO:0000237
has cross-reference: CALOHA:TS-0130
has cross-reference: EFO:0000329
has cross-reference: EHDAA2:0004441
has cross-reference: ENVO:02000029
has cross-reference: EV:0100311
has cross-reference: FMA:20935
has cross-reference: GAID:1181
has cross-reference: MA:0002503
has cross-reference: MAT:0000499
has cross-reference: MESH:D002555
has cross-reference: NCIT:C12692
has cross-reference: TAO:0002184
has cross-reference: UMLS:C0007806
has cross-reference: VHOG:0001278
has cross-reference: Wikipedia:Cerebrospinal_fluid
has cross-reference: ZFA:0001626
has exact synonym: CSF
has exact synonym: cerebral spinal fluid
has OBO namespace: uberon
has related synonym: liquor cerebrospinalis
has related synonym: spinal fluid
id: UBERON:0001359
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

vein
type: Class
subclass of: blood vessel
definition: Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
editor note: TODO - check with MA - vein vs venous blood vessel
imported from: uberon.owl
external_definition: Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
homology_notes: The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
has_relational_adjective: venous
fma_set_term: FMA_63814
has broad synonym: venous subtree
has broad synonym: venous vessel
has cross-reference: AAO:0010212
has cross-reference: AEO:0000209
has cross-reference: BTO:0000234
has cross-reference: CALOHA:TS-1108
has cross-reference: EFO:0000816
has cross-reference: EHDAA2:0003254
has cross-reference: EMAPA:35906
has cross-reference: EV:0100031
has cross-reference: FMA:50723
has cross-reference: GAID:492
has cross-reference: MA:0000067
has cross-reference: MAT:0000037
has cross-reference: MESH:D014680
has cross-reference: MIAA:0000037
has cross-reference: NCIT:C12814
has cross-reference: SCTID:181367001
has cross-reference: TAO:0000082
has cross-reference: UMLS:C0042449
has cross-reference: VHOG:0001743
has cross-reference: Wikipedia:Vein
has cross-reference: XAO:0000115
has cross-reference: ZFA:0000082
has cross-reference: galen:Vein
has exact synonym: venous tree organ part
has OBO namespace: uberon
has related synonym: vascular element
has related synonym: vena
has related synonym: venae
id: UBERON:0001638
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

blood vessel
type: Class
subclass of: mesoderm-derived structure
subclass of: multicellular anatomical structure
definition: A vessel through which blood circulates in the body.
editor note: consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
imported from: uberon.owl
present in taxon: Homo sapiens
external_definition: Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
external_definition: Any of the vessels through which blood circulates in the body.[AAO]
homology_notes: The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
taxon_notes: annelids have blood vessels, but this class is not applicable to annelids.
external_ontology_notes: FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
has broad synonym: vascular element
has cross-reference: AAO:0011004
has cross-reference: AEO:0000207
has cross-reference: BTO:0001102
has cross-reference: CALOHA:TS-0080
has cross-reference: EFO:0000817
has cross-reference: EHDAA2:0003252
has cross-reference: EHDAA:240
has cross-reference: EMAPA:32743
has cross-reference: EMAPA:35993
has cross-reference: FMA:50722
has cross-reference: FMA:63183
has cross-reference: GAID:169
has cross-reference: MA:0000060
has cross-reference: MAT:0000393
has cross-reference: MESH:D001808
has cross-reference: NCIT:C12679
has cross-reference: NLXANAT:090901
has cross-reference: SCTID:361097006
has cross-reference: TAO:0002137
has cross-reference: UMLS:C0005847
has cross-reference: VHOG:0001250
has cross-reference: Wikipedia:Blood_vessel
has cross-reference: XAO:0001011
has cross-reference: ZFA:0005314
has exact synonym: region of vascular tree organ
has exact synonym: vascular tree organ region
has OBO namespace: uberon
has related synonym: vas sanguineum
id: UBERON:0001981
in subset: efo slim
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

hypodermis
type: Class
subclass of: organ part
subclass of: mesoderm-derived structure
definition: Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
imported from: uberon.owl
present in taxon: Homo sapiens
external_definition: A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
external_definition: A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
has_relational_adjective: hypodermal
has_relational_adjective: subcutaneous
has_relational_adjective: subcutaneus
external_ontology_notes: BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
has cross-reference: BTO:0001314
has cross-reference: CALOHA:TS-2366
has cross-reference: EMAPA:37505
has cross-reference: FMA:70544
has cross-reference: MESH:D040521
has cross-reference: NCIT:C33645
has cross-reference: TAO:0001136
has cross-reference: UMLS:C0278403
has cross-reference: Wikipedia:Hypodermis
has cross-reference: ZFA:0001136
has exact synonym: hypoderm
has exact synonym: vertebrate hypodermis
has OBO namespace: uberon
has related synonym: sub-tegumental tissue
has related synonym: subcutaneous tissue
has related synonym: subcutis
has related synonym: subtegumental tissue
has related synonym: superficial fascia
has related synonym: tela subcutanea
id: UBERON:0002072
in subset: human reference atlas
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

skin of body
type: Class
subclass of: organ
subclass of: ectoderm-derived structure
definition: The organ covering the body that consists of the dermis and epidermis.
curator note: consider 'integumentary system' for invertebrates
imported from: uberon.owl
present in taxon: Homo sapiens
external_ontology_notes: MA uses the term skin to refer to what is called here: zone of skin
has cross-reference: BTO:0001253
has cross-reference: CALOHA:TS-0934
has cross-reference: EFO:0000962
has cross-reference: EHDAA2:0001844
has cross-reference: EMAPA:17525
has cross-reference: FMA:7163
has cross-reference: MESH:D012867
has cross-reference: MFMO:0000099
has cross-reference: NCIT:C12470
has cross-reference: SCTID:181469002
has cross-reference: UMLS:C1123023
has cross-reference: Wikipedia:Skin
has cross-reference: XAO:0000023
has cross-reference: galen:Skin
has exact synonym: entire skin
has exact synonym: skin organ
has OBO namespace: uberon
has related synonym: entire integument
has related synonym: integument
has related synonym: integumental organ
has related synonym: pelt
has related synonym: skin
id: UBERON:0002097
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: pheno slim
in subset: uberon slim

peritoneum
type: Class
subclass of: serous membrane
definition: A serous membrane that lines the peritoneal cavity[VHOG,modified].
editor note: TODO - in ZFA is_a epithelium
imported from: uberon.owl
external_definition: An epithelium that lines the peritoneal cavity.[TAO]
external_definition: Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
has_relational_adjective: peritoneal
external_ontology_notes: todo: check MA/EMAPA.
has cross-reference: AAO:0010814
has cross-reference: BTO:0001472
has cross-reference: CALOHA:TS-2072
has cross-reference: EV:0100087
has cross-reference: FMA:9584
has cross-reference: GAID:18
has cross-reference: MA:0000449
has cross-reference: MESH:D010537
has cross-reference: NCIT:C12770
has cross-reference: TAO:0005120
has cross-reference: UMLS:C0031153
has cross-reference: VHOG:0001257
has cross-reference: Wikipedia:Peritoneum
has cross-reference: XAO:0000139
has cross-reference: ZFA:0005120
has cross-reference: galen:Peritoneum
has OBO namespace: uberon
has related synonym: peritonaeum
id: UBERON:0002358
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

muscle tissue
type: Class
subclass of: mesoderm-derived structure
subclass of: multicellular anatomical structure
definition: Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
imported from: uberon.owl
mutually spatially disjoint with: UBERON_0003714
external_definition: One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
has cross-reference: AAO:0000306
has cross-reference: AEO:0000122
has cross-reference: CALOHA:TS-0642
has cross-reference: EHDAA2:0003122
has cross-reference: EMAPA:32715
has cross-reference: FMA:9641
has cross-reference: MA:0002437
has cross-reference: MESH:D009132
has cross-reference: NCIT:C12435
has cross-reference: SCTID:91727004
has cross-reference: UMLS:C2328219
has cross-reference: Wikipedia:Muscle_tissue
has cross-reference: galen:MuscleTissue
has exact synonym: muscular tissue
has exact synonym: portion of muscle tissue
has exact synonym: textus muscularis
has OBO namespace: uberon
id: UBERON:0002385
in subset: uberon slim
comment: Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.

gland
type: Class
subclass of: organ
definition: An organ that functions as a secretory or excretory organ.
imported from: uberon.owl
mutually spatially disjoint with: UBERON_0001434
has_relational_adjective: glandular
has cross-reference: AAO:0000212
has cross-reference: AEO:0000096
has cross-reference: BTO:0000522
has cross-reference: EFO:0000797
has cross-reference: EHDAA2:0003096
has cross-reference: EHDAA:2161
has cross-reference: EMAPA:18425
has cross-reference: FBbt:00100317
has cross-reference: FMA:7146
has cross-reference: FMA:86294
has cross-reference: HAO:0000375
has cross-reference: MA:0003038
has cross-reference: MAT:0000021
has cross-reference: MIAA:0000021
has cross-reference: NCIT:C13319
has cross-reference: SCTID:134358001
has cross-reference: UMLS:C1285092
has cross-reference: Wikipedia:Gland
has cross-reference: WikipediaCategory:Glands
has cross-reference: galen:Gland
has exact synonym: glandular organ
has OBO namespace: uberon
has related synonym: Druese
has related synonym: glandula
id: UBERON:0002530
in subset: efo slim
in subset: pheno slim
in subset: uberon slim

gland of digestive tract
type: Class
subclass of: gland
subclass of: digestive system element
definition: A gland that is part of a digestive tract [Automatically generated definition].
imported from: uberon.owl
has cross-reference: EMAPA:18815
has cross-reference: MA:0003202
has exact synonym: digestive tract gland
has exact synonym: gland of digestive tract
has exact synonym: gland of lower gastrointestinal tract
has exact synonym: gut gland
has exact synonym: lower gastrointestinal tract gland
has OBO namespace: uberon
id: UBERON:0003408

mesoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the mesoderm.
curator note: Grouping term for query purposes
imported from: uberon.owl
has exact synonym: mesodermal derivative
has OBO namespace: uberon
id: UBERON:0004120
in subset: grouping class

ectoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the ectoderm.
curator note: Grouping term for query purposes
imported from: uberon.owl
has exact synonym: ectodermal deriviative
has OBO namespace: uberon
id: UBERON:0004121
in subset: grouping class

subdivision of digestive tract
type: Class
subclass of: organ part
definition: A proximal-distal subdivision of the digestive tract.
curator note: intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
imported from: uberon.owl
present in taxon: Homo sapiens
has cross-reference: FBbt:00100315
has cross-reference: FMA:71131
has OBO namespace: uberon
has related synonym: alimentary system subdivision
has related synonym: gut section
has related synonym: intestinal tract
has related synonym: segment of intestinal tract
has related synonym: subdivision of alimentary system
id: UBERON:0004921
in subset: human reference atlas
in subset: non informative

bodily fluid
type: Class
subclass of: material anatomical entity
definition: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
imported from: uberon.owl
has broad synonym: fluid
has cross-reference: BIRNLEX:20
has cross-reference: EMAPA:37441
has cross-reference: FMA:280556
has cross-reference: GAID:266
has cross-reference: MESH:D001826
has cross-reference: Wikipedia:Body_fluid
has cross-reference: galen:BodyFluid
has exact synonym: body fluid
has OBO namespace: uberon
id: UBERON:0006314
in subset: pheno slim

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
imported from: uberon.owl
present in taxon: NCBITaxon_33090
present in taxon: NCBITaxon_33208
present in taxon: Fungi
has cross-reference: CARO:0010000
has cross-reference: FBbt:00100313
has exact synonym: multicellular structure
has OBO namespace: uberon
id: UBERON:0010000
in subset: common anatomy
in subset: upper level

oral gland
type: Class
subclass of: gland of digestive tract
definition: Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
imported from: uberon.owl
external_ontology_notes: Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
has alternative id: UBERON:0003293
has cross-reference: EHDAA2:0001327
has cross-reference: EHDAA:2181
has cross-reference: EMAPA:16572
has cross-reference: EMAPA:16723
has cross-reference: VHOG:0000652
has narrow synonym: buccal gland
has OBO namespace: uberon
has related synonym: gland of oral opening
has related synonym: gland of oral region
has related synonym: mouth gland
has related synonym: oral cavity gland
has related synonym: oral region gland
id: UBERON:0010047

digestive system element
type: Class
subclass of: organ
definition: Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
imported from: uberon.owl
has cross-reference: EMAPA:37843
has cross-reference: SCTID:272627002
has exact synonym: digestive organ
has exact synonym: digestive system organ
has OBO namespace: uberon
id: UBERON:0013765
in subset: grouping class
in subset: pheno slim

bladder organ
type: Class
subclass of: organ
definition: A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
imported from: uberon.owl
has cross-reference: BTO:0000123
has narrow synonym: bladder
has OBO namespace: uberon
id: UBERON:0018707

part of pathogen organism in vaccine
type: Class
equivalent class: Class
  intersection of: pathogen organism component in vaccine
  intersection of: Restriction
    on property: part of
    some values from: organism
subclass of: pathogen organism component in vaccine
subclass of: Restriction
  on property: part of
  some values from: organism
definition: A pathogen component in vaccine that contains only a part of the pathogen organism instead of the whole organism.
term editor: Oliver He
in subset: vaccine component

vaccine
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: has function
    some values from: vaccine function
subclass of: processed material
subclass of: Restriction
  on property: is_specified_input_of
  some values from: vaccine preparation
subclass of: Restriction
  on property: has function
  some values from: Class
    intersection of: vaccine function
    intersection of: Restriction
      on property: realized in
      some values from: vaccine immunization
definition: Material entity that is manufactured to realize the vaccine function.
editor note: Many vaccines are developed to protect against infectious pathogens that causes infectious diseases. Many vaccines are also being developed against other diseases such as cancer, allergy, and autoimmune diseases.
term editor: Allen Xiang
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Bjoern Peters
term editor: Jie Zheng
term editor: Lindsay Cowell
term editor: Melanie Courtot
term editor: Oliver He
term editor: Ronak Sutariya
has cross-reference: MeSH: D014612
in subset: vaccine

vaccination
type: Class
equivalent class: Class
  intersection of: administering substance in vivo
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: role of
        some values from: vaccine
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: organism
subclass of: administering substance in vivo
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: role of
      some values from: vaccine
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: role of
      some values from: organism
subclass of: Restriction
  on property: has participant
  some values from: vaccine
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: has role
      some values from: VO_0001274
definition: Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response.
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Bjoern Peters
term editor: Jie Zheng
term editor: Oliver He
alternative label: vaccine administration
in subset: process

ACAM2000 vaccine
type: Class
equivalent class: Class
  intersection of: vaccinia virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0018930
subclass of: USA licensed human vaccine
subclass of: vaccinia virus vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001220
subclass of: VO_0010452
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0004854
subclass of: Restriction
  on property: vaccinated in route
  some values from: VO_0003051
subclass of: Restriction
  on property: immunizes against disease
  some values from: smallpox
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Variola virus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000686
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0005568
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0018930
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=96
definition source: http://purl.bioontology.org/ontology/RXNORM/833083
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm180810.htm
VIOLIN vaccine ID: 96
trade name: ACAM2000
FDA vaccine indications: Active immunization against smallpox disease for persons determined to be at high risk for smallpox infection.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142572.pdf
vaccine STN: BL 125158
in subset: vaccine

ActHIB vaccine
type: Class
equivalent class: Class
  intersection of: Haemophilus influenzae serotype b vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015362
subclass of: conjugate vaccine
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010437
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0001254
subclass of: Restriction
  on property: has component
  some values from: VO_0003049
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000703
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015362
editor note: Preparation: The vaccine consists of the Haemophilus b capsular polysaccharide (polyribosyl-ribitol-phosphate, PRP), a high molecular weight polymer prepared from the Haemophilus influenzae type b (HiB) strain 1482 grown in a semi-synthetic medium, covalently bound to tetanus toxoid. The tetanus toxoid is prepared by extraction, ammonium sulfate purification, and formalin inactivation of the toxin from cultures of Clostridium tetani (Harvard strain) grown in a modified Mueller and Miller medium. The toxoid is filter sterilized prior to the conjugation process. When ActHIB vaccine is reconstituted with saline diluent, each single dose of 0.5 mL is formulated to contain 10 mu g of purified capsular polysaccharide conjugated to 24 mu g of inactivated tetanus toxoid, and 8.5% of sucrose (ActHIB 2005). Reference: http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=157&keywords=
term editor: Kallan Roan
term editor: Oliver He
definition source: PMID:1517908
definition source: PMID:1735812
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=157
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm174743.htm
VIOLIN vaccine ID: 157
trade name: ActHIB
FDA vaccine indications: ActHIB vaccine is indicated for the active immunization of infants and children 2 months through 5 years of age for the prevention of invasive disease caused by H influenzae type b.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM109841.pdf
vaccine STN: 103935
in subset: vaccine

Adacel vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015364
subclass of: USA licensed human vaccine
subclass of: toxoid vaccine
subclass of: combination vaccine
subclass of: Canada licensed human vaccine
subclass of: Diphtheria-Tetanus-Pertussis vaccine
subclass of: VO_0001214
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003199
subclass of: Restriction
  on property: has component
  some values from: VO_0003200
subclass of: Restriction
  on property: has component
  some values from: VO_0003201
subclass of: Restriction
  on property: has component
  some values from: VO_0003202
subclass of: Restriction
  on property: has component
  some values from: VO_0003384
subclass of: Restriction
  on property: has component
  some values from: VO_0003455
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015364
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=371
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=383
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=774
definition source: http://purl.bioontology.org/ontology/RXNORM/605718
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm172481.htm
VIOLIN vaccine ID: 371
VIOLIN vaccine ID: 383
VIOLIN vaccine ID: 774
trade name: Adacel
FDA vaccine indications: Booster immunization against tetanus, diphtheria and pertussis as a single dose in individuals 10 through 64 years of age.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142764.pdf
vaccine STN: BL 125111
in subset: vaccine

Afluria vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001236
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0020650
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: VO_0001176
subclass of: VO_0001236
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has vaccine allergen
  some values from: neomycin
subclass of: Restriction
  on property: has vaccine allergen
  some values from: VO_0000912
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Influenza A virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Influenza B virus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000689
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0005570
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0020650
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=325
definition source: WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094043.htm
VIOLIN vaccine ID: 325
trade name: AFLURIA
FDA vaccine indications: For active immunization of persons ages 6 months of age and older against influenza disease caused by influenza virus subtypes A and type B present in the vaccine.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM263239.pdf
vaccine STN: BL 125254
in subset: vaccine

Attenuvax vaccine
type: Class
equivalent class: Class
  intersection of: Measles virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015370
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001220
subclass of: VO_0010441
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015370
term editor: Oliver He
trade name: Attenuvax
in subset: vaccine
comment: Product Name: Measles Virus Vaccine, Live

vaccine-induced lymphocyte activation
type: Class
subclass of: vaccine-induced leukocyte activation
term editor: Oliver He
in subset: vaccine-induced response

vaccine-induced B cell antigen processing and presentation
type: Class
subclass of: vaccine-induced B cell mediated immunity
term editor: Oliver He
in subset: vaccine-induced response

vaccine-induced B cell cytokine production
type: Class
subclass of: vaccine-induced B cell mediated immunity
term editor: Oliver He
in subset: vaccine-induced response

vaccine B cell epitope
type: Class
subclass of: VO_0000811
term editor: Oliver He
alternative label: B cell epitope in vaccine
in subset: material entity

vaccine-induced B cell mediated immunity
type: Class
subclass of: VO_0010462
term editor: Oliver He
in subset: vaccine-induced response

Bacillus anthracis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Bacillus anthracis
subclass of: VO_0003536
subclass of: Restriction
  on property: immunizes against disease
  some values from: anthrax disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacillus anthracis
definition: A vaccine that protects against Bacillus anthrax that causes anthrax.
term editor: Oliver He
alternative label: anthrax vaccine
has cross-reference: MeSH: D022122
in subset: vaccine

Biothrax vaccine
type: Class
equivalent class: Class
  intersection of: Bacillus anthracis vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015374
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0010291
subclass of: VO_0010434
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: protein of pathogen organism as vaccine component
subclass of: Restriction
  on property: has component
  some values from: VO_0004208
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: anthrax disease
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacillus anthracis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000688
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0005567
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015374
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=15
definition source: http://purl.bioontology.org/ontology/RXNORM/404894
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm133822.htm
VIOLIN vaccine ID: 15
trade name: Biothrax
FDA vaccine indications: For the active immunization for the prevention of disease caused by Bacillus anthracis in persons between 18 and 65 years of age at high risk of exposure.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/BloodBloodProducts/ApprovedProducts/LicensedProductsBLAs/UCM074923.pdf
vaccine STN: BL 103821
in subset: vaccine

Boostrix vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015375
subclass of: USA licensed human vaccine
subclass of: toxoid vaccine
subclass of: combination vaccine
subclass of: Canada licensed human vaccine
subclass of: Diphtheria-Tetanus-Pertussis vaccine
subclass of: VO_0001214
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003199
subclass of: Restriction
  on property: has component
  some values from: VO_0003200
subclass of: Restriction
  on property: has component
  some values from: VO_0003201
subclass of: Restriction
  on property: has component
  some values from: VO_0003384
subclass of: Restriction
  on property: has component
  some values from: VO_0003455
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015375
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=372
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=385
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=772
definition source: http://purl.bioontology.org/ontology/RXNORM/583411
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm172925.htm
VIOLIN vaccine ID: 372
VIOLIN vaccine ID: 385
VIOLIN vaccine ID: 772
trade name: Boostrix
FDA vaccine indications: Booster immunization against tetanus, diphtheria and pertussis as a single dose in individuals 10 years of age and older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/UCM152842.pdf
vaccine STN: BL 125106
in subset: vaccine

killed vaccine
type: Class
subclass of: inactivated vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
definition: whole organism vaccine that uses killed pathogen organism as its component.
term editor: Asiyah Yu Lin
in subset: vaccine

Brucella abortus DNA vaccine pcDNA-SOD
type: Class
subclass of: VO_0001225
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: expresses
  some values from: sodC from B. abortus strain 2308
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A Brucella abortus vaccine that expresses Cu/Zn SOD with DNA plasmid pcDNA.
term editor: Oliver He
definition source: PMID:15039330
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=138
VIOLIN vaccine ID: 138
in subset: vaccine

pVAX DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella abortus strain RB51 vaccine vector
type: Class
subclass of: bacterial vaccine vector
definition: A bacterial vaccine vector that uses B. abortus vaccine strain RB51 as the vector.
term editor: Oliver He
in subset: vaccine component

Brucella abortus vaccine RB51
type: Class
subclass of: prophylactic vaccine
subclass of: licensed cattle vaccine
subclass of: VO_0001134
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: has gene mutation
  some values from: VO_0000794
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Bison bison
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000890
definition: Brucella abortus vaccine RB51 is a Brucella abortus vaccine that is licensed in the USA since 1992.
term editor: Oliver He
alternative label: B. abortus RB51
alternative label: Brucella RB-51
alternative label: Brucella RB51
alternative label: SRB51
definition source: PMID:10534009
definition source: PMID:11193615
definition source: PMID:11500423
definition source: PMID:11504226
definition source: PMID:11504238
definition source: PMID:11553603
definition source: PMID:11768128
definition source: PMID:12119140
definition source: PMID:12438380
definition source: PMID:12704101
definition source: PMID:1439207
definition source: PMID:16713034
definition source: PMID:17653832
definition source: PMID:17894637
definition source: PMID:18836016
definition source: PMID:1908158
definition source: PMID:19362381
definition source: PMID:19439382
definition source: PMID:7622248
definition source: PMID:7806364
definition source: PMID:7927779
definition source: PMID:8039890
definition source: PMID:8740701
definition source: PMID:8890203
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=10
definition source: WEB: http://rb51.com
VIOLIN vaccine ID: 10
in subset: vaccine

Brucella abortus vaccine strain 19
type: Class
subclass of: prophylactic vaccine
subclass of: licensed cattle vaccine
subclass of: VO_0001134
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A live attenuated Brucella abortus vaccine that is licensed and used in many countries.
term editor: Oliver He
alternative label: Brucella S19
alternative label: Brucella strain-19
definition source: PMID:11058778
definition source: PMID:8039890
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=109
VIOLIN vaccine ID: 109
in subset: vaccine

pVAX1 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Brucella
subclass of: VO_0003550
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella
definition: A vaccine that protects against Brucella that causes brucellosis in animals and humans.
term editor: Oliver He
alternative label: brucellosis vaccine
has cross-reference: MeSH: D002004
in subset: vaccine

pCMV4 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
has alternative id: VO:0000217
in subset: vaccine component

pAp031 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Comvax vaccine
type: Class
equivalent class: Class
  intersection of: Haemophilus b and Hepatitis B vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0018953
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Haemophilus b and Hepatitis B vaccine
subclass of: VO_0010437
subclass of: VO_0010439
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0003150
subclass of: Restriction
  on property: has component
  some values from: VO_0003408
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis B
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatitis B virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0018953
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=3180
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=368
definition source: http://purl.bioontology.org/ontology/RXNORM/139056
VIOLIN vaccine ID: 3180
VIOLIN vaccine ID: 368
trade name: Comvax
in subset: vaccine
comment: Product Name: Haemophilus b Conjugate Vaccine (Meningococcal Protein Conjugate) & Hepatitis B Vaccine (Recombinant)

Daptacel vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0018954
subclass of: USA licensed human vaccine
subclass of: toxoid vaccine
subclass of: combination vaccine
subclass of: Diphtheria-Tetanus-Pertussis vaccine
subclass of: VO_0001214
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003199
subclass of: Restriction
  on property: has component
  some values from: VO_0003200
subclass of: Restriction
  on property: has component
  some values from: VO_0003201
subclass of: Restriction
  on property: has component
  some values from: VO_0003202
subclass of: Restriction
  on property: has component
  some values from: VO_0003384
subclass of: Restriction
  on property: has component
  some values from: VO_0003455
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0018954
editor note: Vaccine components see http://www.vaccinesafety.edu/components-DTaP.htm
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=356
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=363
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=775
definition source: http://purl.bioontology.org/ontology/RXNORM/352572
definition source: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM241874.pdf
VIOLIN vaccine ID: 356
VIOLIN vaccine ID: 363
VIOLIN vaccine ID: 775
trade name: DAPTACEL
FDA vaccine indications: Indicated for active immunization against diphtheria, tetanus and pertussis as a five dose series in infants and children 6 weeks through 6 years of age (prior to 7th birthday).
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM103037.pdf
vaccine STN: 103666
in subset: vaccine

Decavac vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0018955
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Diphtheria-Tetanus vaccine
subclass of: VO_0010436
subclass of: VO_0010445
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0018955
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=369
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=386
VIOLIN vaccine ID: 369
VIOLIN vaccine ID: 386
trade name: DECAVAC
in subset: vaccine
comment: Product Name: Tetanus & Diphtheria Toxoids Adsorbed for Adult Use

MenHibrix vaccine
type: Class
equivalent class: Class
  intersection of: Haemophilus influenzae serotype b vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019074
subclass of: conjugate vaccine
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: combination vaccine
subclass of: VO_0001214
subclass of: VO_0010290
subclass of: VO_0010437
subclass of: VO_0010444
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has component
  some values from: VO_0004859
subclass of: Restriction
  on property: has component
  some values from: VO_0004860
subclass of: Restriction
  on property: has component
  some values from: VO_0015013
subclass of: Restriction
  on property: immunizes against disease
  some values from: meningococcal meningitis
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Neisseria meningitidis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019074
definition: A vaccine for active immunization to prevent invasive disease caused by Neisseria meningitidis serogroups C and Y and Haemophilus influenzae type b. MENHIBRIX is approved for use in children 6 weeks of age through 18 months of age.
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=3832
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=3833
definition source: http://purl.bioontology.org/ontology/RXNORM/1437912
definition source: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm308566.htm
VIOLIN vaccine ID: 3832
VIOLIN vaccine ID: 3833
trade name: MenHibrix
FDA vaccine indications: Indicated for active immunization to prevent invasive disease caused by Neisseria meningitidis serogroups C and Y and Haemophilus influenzae type b for children 6 weeks of age through 18 months of age.
vaccine STN: BL 125363/0
in subset: vaccine

DNA vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: DNA vaccine role
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
definition: A vaccine that is composed of a plasmid vaccine vector (a circular double stranded DNA molecule) containing the whole of parts of genes encoding one or more vaccine antigen proteins.
term editor: Oliver He
alternative label: genetic vaccine
alternative label: naked DNA vaccine
alternative label: nucleic acid vaccine
in subset: vaccine

Diphtheria and Tetanus Toxoids Adsorbed USP vaccine by Sanofi Pasteur Inc
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Diphtheria-Tetanus vaccine
subclass of: VO_0010436
subclass of: VO_0010445
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
term editor: Oliver He
alternative label: Diphtheria and Tetanus Toxoids Adsorbed USP by Sanofi Pasteur Inc
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=313
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=353
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=362
VIOLIN vaccine ID: 313
VIOLIN vaccine ID: 353
VIOLIN vaccine ID: 362
in subset: vaccine
comment: Product Name: Diphtheria & Tetanus Toxoids Adsorbed

obsolete Diphtheria and Tetanus Toxoids Adsorbed by Sanofi Pasteur Ltd
type: Class
subclass of: Thing
term editor: Oliver He
has obsolescence reason: IAO_0000227
term replaced by: Diphtheria and Tetanus Toxoids Adsorbed USP vaccine by Sanofi Pasteur Inc
comment: Product Name: Diphtheria & Tetanus Toxoids Adsorbed
comment: This term is obsolete since there is another term with the same meaning.
deprecated: true

Dryvax vaccine
type: Class
equivalent class: Class
  intersection of: vaccinia virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0018956
subclass of: USA licensed human vaccine
subclass of: vaccinia virus vaccine
subclass of: prophylactic vaccine
subclass of: VO_0010452
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: smallpox
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Variola virus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000701
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0018956
definition: A vaccinia virus vaccine that is a freeze-dried calf lymph smallpox vaccine, specifically, Dryvax is a live-virus preparation of vaccinia prepared from calf lymph.
editor note: Dryvax is a freeze-dried calf lymph smallpox vaccine. It is the world's oldest smallpox vaccine, created in the late 19th century by American Home Products, a predecessor of Wyeth. By the 1940s, Wyeth was the leading US manufacturer of the vaccine and the only manufacturer by the 1960s. After world health authorities declared smallpox had been eradicated from nature in 1980, Wyeth stopped making the vaccine.
term editor: Oliver He
definition source: http://en.wikipedia.org/wiki/Dryvax
trade name: Dryvax
in subset: vaccine
comment: Product Name: Smallpox Vaccine, Dried, Calf Lymph Type

ETEC vaccine ACAM2010
type: Class
subclass of: E. coli live attenuated vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
definition: A CFA/I‐expressing vaccine.
term editor: Oliver He
definition source: PMID:17566016
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=116
VIOLIN vaccine ID: 116
in subset: vaccine

adenovirus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Adenoviridae
subclass of: viral vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: respiratory system disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Adenoviridae
definition: A viral vaccine that protects against infection of an adenovirus.
term editor: Oliver He
term editor: Samantha G. Sayers
in subset: vaccine

vaccine persistence assay
type: Class
subclass of: assay
definition: An assay that measures the persistent survival of live vaccine in a host in vivo.
term editor: Oliver He
in subset: assay

pBacPAK9 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pBC12/CMV DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Escherichia coli vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Escherichia coli
subclass of: VO_0003552
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
definition: A bacterial vaccine that prevents against Escherichia coli infection.
term editor: Oliver He
alternative label: E. coli vaccine
has cross-reference: MeSH: D022361
in subset: vaccine

pBHT DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

FluLaval
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: VO_0001176
subclass of: VO_0001236
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has vaccine allergen
  some values from: VO_0000912
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Alphainfluenzavirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Betainfluenzavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0002498
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=327
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112845.htm
VIOLIN vaccine ID: 327
trade name: FluLaval
FDA vaccine indications: Active immunization for the prevention of disease caused by influenza A subtype viruses and type B virus contained in the vaccine. FLULAVAL is approved for use in persons 6 months of age and older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM112904.pdf
vaccine STN: BL 125163
in subset: vaccine
comment: Product Name: Influenza Virus Vaccine, Trivalent, Types A and B

FluMist
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0001178
subclass of: VO_0001236
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has vaccine allergen
  some values from: neomycin
subclass of: Restriction
  on property: has vaccine allergen
  some values from: VO_0000912
subclass of: Restriction
  on property: vaccinated in route
  some values from: intranasal route by spray
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Alphainfluenzavirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Betainfluenzavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000694
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=328
definition source: WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094047.htm
VIOLIN vaccine ID: 328
trade name: FluMist
FDA vaccine indications: For the active immunization of individuals 2-49 years of age against influenza disease caused by influenza virus subtypes A and type B contained in the vaccine.
vaccine STN: BL 125020
in subset: vaccine

Fluarix vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001236
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0021053
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: VO_0001176
subclass of: VO_0001236
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Alphainfluenzavirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Betainfluenzavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0021053
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=326
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112850.htm
VIOLIN vaccine ID: 326
trade name: Fluarix
FDA vaccine indications: For active immunization of persons 3 years of age and older for the prevention of disease caused by influenza virus subtypes A and type B contained in the vaccine.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM335392.pdf
vaccine STN: BL 125127
in subset: vaccine

Fluvirin
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: VO_0001176
subclass of: VO_0001236
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has vaccine allergen
  some values from: VO_0000912
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Alphainfluenzavirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Betainfluenzavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000696
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0005571
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=329
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112852.htm
VIOLIN vaccine ID: 329
trade name: Fluvirin
FDA vaccine indications: For active immunization of persons 4 years of age and older against influenza disease caused by influenza virus subtypes A and type B contained in the vaccine.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123694.pdf
vaccine STN: BL 103837
in subset: vaccine
comment: Product Name: Influenza Virus Vaccine, Trivalent, Types A and B

Fluzone
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: VO_0001176
subclass of: VO_0001236
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has vaccine allergen
  some values from: VO_0000912
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Alphainfluenzavirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Betainfluenzavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=330
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112854.htm
VIOLIN vaccine ID: 330
trade name: Fluzone
FDA vaccine indications: Fluzone is indicated for active immunization of persons 6 months of age and older against influenza disease caused by influenza virus subtypes A and type B contained in the vaccine.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM619664.pdf
vaccine STN: BL 103914
in subset: vaccine
comment: Product Name: Influenza Virus Vaccine, Trivalent, Types A and B

virmugen
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has role
    some values from: VO_0001361
subclass of: gene
subclass of: Restriction
  on property: has role
  some values from: VO_0001361
definition: A gene that once deleted, would make an attenuated microbe that can be used as a live attenuated vaccine against virulent pathogen.
term editor: Allen Xiang
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: gene

Gardasil vaccine
type: Class
equivalent class: Class
  intersection of: human papillomavirus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015398
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: recombinant vector vaccine
subclass of: multivalent vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010446
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has component
  some values from: protein of pathogen organism as vaccine component
subclass of: Restriction
  on property: has component
  some values from: VO_0003300
subclass of: Restriction
  on property: has component
  some values from: VO_0003301
subclass of: Restriction
  on property: has component
  some values from: VO_0003302
subclass of: Restriction
  on property: has component
  some values from: VO_0003303
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: Human papillomavirus infectious disease
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human papillomavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015398
definition: Quadrivalent vaccine meaning it protects against 4 strains of virus (types 6, 11, 16, and 18). The vaccine was made using genetic engineering techniques. The genes that encode a specific protein from each of these strains are expressed in yeast in large-scale fermentation cultures. Protein purification methods are then used to isolate the proteins and make the vaccine. Cited from: http://biotech.about.com/b/2008/09/03/gardasil-safety-of-genetically-engineered-hpv-vaccine-still-in-question.htm
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=337
definition source: http://purl.bioontology.org/ontology/RXNORM/659877
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094042.htm
VIOLIN vaccine ID: 337
trade name: Gardasil
FDA vaccine indications: - Prevention of vulvar and vaginal cancer - Vaccination in females 9 through 26 years of age for prevention of the following diseases caused by Human Papillomavirus (HPV) Types 6, 11, 16, and 18: - Cervical Cancer - Genital warts (condyloma acuminata) and the following precancerous or dysplastic lesions: - Cervical adenocarcinoma in situ (AIS)cancer - Cervical intraepithelial neoplasia (CIN) grade 2 and grade 3 - Vulvar intraepithelial neoplasia (VIN) grade 2 and grade 3 - Vaginal intraepithelial neoplasia (VaIN) grade 2 and grade 3 - Cervical intraepithelial neoplasia (CIN) grade 1 - Vaccination in boys and men 9 through 26 years of age for the prevention of genital warts caused by HPV types 6 and 11 - Vaccination in people ages 9 through 26 years for the prevention of anal cancer and associated precancerous lesions due to human papillomavirus (HPV) types 6, 11, 16, and 18
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM111263.pdf
vaccine STN: 125126
in subset: vaccine

HIV based lentivirus vaccine vector
type: Class
subclass of: lentivirus vaccine vector
definition: a lentivirus vaccine vector that uses a HIV strain as the vector
term editor: Oliver He
in subset: vaccine component

Balb/c mouse
type: Class
subclass of: Mus musculus
term editor: Oliver He
in subset: organism

Havrix vaccine
type: Class
equivalent class: Class
  intersection of: Hepatitis A virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015344
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010438
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis A
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatovirus A
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015344
term editor: OHDSI Vaccine WG
alternative label: Havrix
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=320
VIOLIN vaccine ID: 320
trade name: HAVRIX
FDA vaccine indications: HAVRIX is indicated for active immunization against disease caused by hepatitis A virus (HAV). HAVRIX is approved for use in persons 12 months of age and older. Primary immunization should be administered at least 2 weeks prior to expected exposure to HAV.
vaccine package insert PDF URL: https://www.fda.gov/media/119388/download
vaccine STN: BL 103475
in subset: vaccine

Neisseria meningitidis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Neisseria meningitidis
subclass of: VO_0003484
subclass of: Restriction
  on property: immunizes against disease
  some values from: meningococcal meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Neisseria meningitidis
definition: Vaccine that protects against Neisseria meningitidis infection.
term editor: Oliver He
alternative label: Meningococcal vaccine
has cross-reference: MeSH: D022401
in subset: vaccine

IPOL vaccine
type: Class
equivalent class: Class
  intersection of: Poliovirus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015420
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: inactivated viral vaccine
subclass of: VO_0010447
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003835
subclass of: Restriction
  on property: has component
  some values from: VO_0003836
subclass of: Restriction
  on property: has component
  some values from: VO_0003837
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: vaccinated in route
  some values from: subcutaneous route
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000703
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015420
definition: IPOL, Poliovirus Vaccine Inactivated is a sterile suspension of three types of poliovirus: Type 1 (Mahoney), Type 2 (MEF-1), and Type 3 (Saukett). IPOL vaccine is a highly purified, inactivated poliovirus vaccine with enhanced potency.
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=338
definition source: http://purl.bioontology.org/ontology/RXNORM/287617
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm180053.htm
VIOLIN vaccine ID: 338
trade name: IPOL
FDA vaccine indications: IPOL vaccine is indicated for active immunization of infants (as young as 6 weeks of age), children and adults for the prevention of poliomyelitis caused by poliovirus Types 1, 2, and 3.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM133479.pdf
vaccine STN: 103930
in subset: vaccine

vaccine related journal article
type: Class
subclass of: journal article
subclass of: Restriction
  on property: mentions
  some values from: vaccine
definition: A jourmal article that mentions a vaccine, which was retrieved from PubMed and annotated using VO-SciMinner.
term editor: Asiyah Yu Lin
definition source: PMID:21871085
in subset: information content entity

Imovax Rabies (USA)
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: inactivated viral vaccine
subclass of: VO_0010448
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003857
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: rabies
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Lyssavirus rabies
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000703
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015414
definition: The Imovax(R) 9 Rabies Vaccine is a sterile, stable, freeze-dried 10 suspension of rabies virus prepared from strain PM-1503-3M.
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=341
definition source: http://purl.bioontology.org/ontology/RXNORM/1659730
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm180097.htm
VIOLIN vaccine ID: 341
trade name: IMOVAX
FDA vaccine indications: Vaccine for use in all age groups for pre-exposure and post-exposure prophylaxis against rabies.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM133484.pdf
vaccine STN: 103931
in subset: vaccine

Infanrix vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015416
subclass of: USA licensed human vaccine
subclass of: toxoid vaccine
subclass of: combination vaccine
subclass of: Canada licensed human vaccine
subclass of: Diphtheria-Tetanus-Pertussis vaccine
subclass of: VO_0001214
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: protein of pathogen organism as vaccine component
subclass of: Restriction
  on property: has component
  some values from: VO_0003199
subclass of: Restriction
  on property: has component
  some values from: VO_0003200
subclass of: Restriction
  on property: has component
  some values from: VO_0003201
subclass of: Restriction
  on property: has component
  some values from: VO_0003384
subclass of: Restriction
  on property: has component
  some values from: VO_0003455
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015416
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=355
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=361
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=776
definition source: http://purl.bioontology.org/ontology/RXNORM/224903
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm101568.htm
VIOLIN vaccine ID: 355
VIOLIN vaccine ID: 361
VIOLIN vaccine ID: 776
trade name: INFANRIX
FDA vaccine indications: For active immunization against diphtheria, tetanus, and pertussis as a 5-dose series in infants and children 6 weeks to 7 years of age.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM124514.pdf
vaccine STN: BL 103647
in subset: vaccine

influenza virus vaccine H5N1 (Sanofi Pasteur Inc)
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001176
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H5N1 subtype
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=324
definition source: WEB: http://atomicnewsreview.org/2009/10/22/approval-for-the-arepanrix%E2%84%A2-gsk-vaccine-in-canada/
VIOLIN vaccine ID: 324
in subset: vaccine
comment: Product Name: Influenza Virus Vaccine, H5N1 (for National Stockpile)

JE-Vax vaccine
type: Class
equivalent class: Class
  intersection of: Japanese encephalitis virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015423
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: inactivated viral vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010440
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: subcutaneous route
subclass of: Restriction
  on property: immunizes against disease
  some values from: Japanese encephalitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Japanese encephalitis virus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000698
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015423
definition: JE-VAX is a sterile, lyophilized vaccine for subcutaneous use, prepared by inoculating mice intracerebrally with Japanese encephalitis (JE) virus, "Nakayama-NIH" strain.
term editor: Kallan Roan
term editor: Oliver He
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm179149.htm
trade name: JE-Vax
FDA vaccine indications: Indicated for Active Immunization against JE for persons one year age and older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123761.pdf
vaccine STN: BL 125280
in subset: vaccine

Kinrix vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019072
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: toxoid vaccine
subclass of: inactivated viral vaccine
subclass of: Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
subclass of: VO_0001214
subclass of: VO_0010435
subclass of: VO_0010436
subclass of: VO_0010445
subclass of: VO_0010447
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: protein of pathogen organism as vaccine component
subclass of: Restriction
  on property: has component
  some values from: VO_0003196
subclass of: Restriction
  on property: has component
  some values from: VO_0003199
subclass of: Restriction
  on property: has component
  some values from: VO_0003200
subclass of: Restriction
  on property: has component
  some values from: VO_0003201
subclass of: Restriction
  on property: has component
  some values from: VO_0003384
subclass of: Restriction
  on property: has component
  some values from: VO_0003455
subclass of: Restriction
  on property: has component
  some values from: VO_0003835
subclass of: Restriction
  on property: has component
  some values from: VO_0003836
subclass of: Restriction
  on property: has component
  some values from: VO_0003837
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019072
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=358
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=365
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=5551
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=5581
definition source: http://purl.bioontology.org/ontology/RXNORM/801721
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm172495.htm
VIOLIN vaccine ID: 358
VIOLIN vaccine ID: 365
VIOLIN vaccine ID: 5551
VIOLIN vaccine ID: 5581
trade name: KINRIX
FDA vaccine indications: Active immunization against diphtheria, tetanus, pertussis, and poliomyelitis as the fifth dose in the diphtheria, tetanus, and acellular pertussis (DTaP) vaccine series and the fourth dose in the inactivated poliovirus vaccine (IPV) series in children 4 through 6 years of age whose previous DTaP vaccine doses have been with INFANRIX(R) and/or PEDIARIX(R) for the first three doses and INFANRIX(R) for the fourth dose.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM241453.pdf
vaccine STN: BL 125260
in subset: vaccine
comment: Product Name: Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed and Inactivated Poliovirus Vaccine
comment: Trade Name: KINRIX

Listeria monocytogenes vaccine vector
type: Class
subclass of: bacterial vaccine vector
definition: a bacterial vaccine vector that uses L. moncytogenes as the vector.
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 1639

M-M-R II vaccine
type: Class
equivalent class: Class
  intersection of: Measles-Mumps-Rubella vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015426
subclass of: USA licensed human vaccine
subclass of: combination vaccine
subclass of: Canada licensed human vaccine
subclass of: Measles-Mumps-Rubella vaccine
subclass of: VO_0001220
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0015054
subclass of: Restriction
  on property: has component
  some values from: VO_0015056
subclass of: Restriction
  on property: vaccinated in route
  some values from: subcutaneous route
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes against disease
  some values from: rubella
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rubella virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015426
definition: A Measles-Mumps-Rubella vaccine that is live attenuated and manufactured by Merck & Co, Inc.
term editor: Kallan Roan
term editor: Oliver He
alternative label: MMR II
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=374
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=375
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=601
definition source: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm094050.htm
VIOLIN vaccine ID: 374
VIOLIN vaccine ID: 375
VIOLIN vaccine ID: 601
trade name: M-M-R II
FDA vaccine indications: M-M-R II is indicated for simultaneous vaccination against measles, mumps, and rubella in individuals 12 months of age or older.For active immunization against invasive meningococcal disease caused by Neisseria meningiditis serogroups A, C, Y, and W-135. Menomune – A/C/Y/W-135 vaccine is approved for use in persons 2 years of age and older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123789.pdf
vaccine STN: BL 101069
in subset: vaccine

M-M-Vax vaccine
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Measles-Mumps vaccine
subclass of: VO_0001220
subclass of: VO_0010441
subclass of: VO_0010442
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
definition: A Measles-Mumps vaccine that is manufactured by Merck and used for human.
term editor: Oliver He
alternative label: M-M-Vax
alternative label: MEASLES + MUMPS (MM-VAX)
alternative label: MM-VAX
definition source: http://novaccine.com/wp-content/uploads/2014/02/mmvax_package_insert.pdf
trade name: M-M-Vax
in subset: vaccine
comment: Product Name: Measles and Mumps Virus Vaccine, Live

Menactra vaccine
type: Class
equivalent class: Class
  intersection of: VO_0003441
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015429
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0003441
subclass of: VO_0010444
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has component
  some values from: VO_0001256
subclass of: Restriction
  on property: has component
  some values from: VO_0003049
subclass of: Restriction
  on property: has component
  some values from: VO_0015063
subclass of: Restriction
  on property: has component
  some values from: VO_0015067
subclass of: Restriction
  on property: has component
  some values from: VO_0015069
subclass of: Restriction
  on property: has component
  some values from: VO_0015070
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: meningococcal meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Neisseria meningitidis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015429
definition: Menactra, Meningococcal (Groups A, C, Y and W-135) Polysaccharide Diphtheria Toxoid Conjugate Vaccine, is indicated for active immunization to prevent invasive meningococcal disease caused by Neisseria meningitidis serogroups A, C, Y and W-135.
term editor: Kallan Roan
term editor: Oliver He
alternative label: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=381
definition source: WEB: http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm176044.htm
VIOLIN vaccine ID: 381
trade name: Menactra
FDA vaccine indications: Active immunization of individuals 9 months through 55 years of age for the prevention of invasive meningococcal disease caused by Neisseria meningitidis serogroups A, C, Y and W-135.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM131170.pdf
vaccine STN: 125089
in subset: vaccine
comment: Product Name: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine
comment: Trade Name: Menactra

Menomune A/C/Y/W-135 vaccine
type: Class
equivalent class: Class
  intersection of: Neisseria meningitidis vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019076
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010289
subclass of: VO_0010290
subclass of: VO_0010444
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has component
  some values from: VO_0001256
subclass of: Restriction
  on property: has component
  some values from: VO_0004859
subclass of: Restriction
  on property: has component
  some values from: VO_0004860
subclass of: Restriction
  on property: has component
  some values from: VO_0004886
subclass of: Restriction
  on property: has component
  some values from: VO_0004888
subclass of: Restriction
  on property: has vaccine allergen
  some values from: VO_0000913
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: meningococcal meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Neisseria meningitidis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
term editor: Kallan Roan
term editor: Oliver He
alternative label: Menomune A C Y W135
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=316
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm179991.htm
VIOLIN vaccine ID: 316
trade name: Menomune-A/C/Y/W-135
FDA vaccine indications: For active immunization against invasive meningococcal disease caused by Neisseria meningiditis serogroups A, C, Y, and W-135. Menomune - A/C/Y/W-135 vaccine is approved for use in persons 2 years of age and older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM308370.pdf
vaccine STN: BL 103926
in subset: vaccine

Meruvax II vaccine
type: Class
equivalent class: Class
  intersection of: VO_0010637
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019077
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001220
subclass of: VO_0010450
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: vaccinated in route
  some values from: subcutaneous route
subclass of: Restriction
  on property: immunizes against disease
  some values from: rubella
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rubella virus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019077
term editor: Oliver He
trade name: Meruvax II
in subset: vaccine
comment: Product Name: Rubella Virus Vaccine Live

Mumpsvax vaccine
type: Class
equivalent class: Class
  intersection of: Mumps virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015441
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0010442
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015441
term editor: Oliver He
trade name: Mumpsvax
in subset: vaccine
comment: Product Name: Mumps Virus Vaccine Live

pBI/tTA DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pBISIA DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Mycobacterium tuberculosis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Mycobacterium tuberculosis
subclass of: Mycobacterium vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
definition: A Mycobacterium vaccine that protects against Mycobacterium tuberculosis.
term editor: Oliver He
alternative label: tuberculosis vaccine
in subset: vaccine

Mycobax vaccine
type: Class
subclass of: VO_0000771
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
definition: Mycobax is a BCG vaccine that is made by Sanofi Pasteur, Ltd. Ref: http://www.biopharma.com/cgi/full6.lasso?Key=412.65916
term editor: Oliver He
alternative label: Mycobax
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=315
VIOLIN vaccine ID: 315
trade name: Mycobax
in subset: vaccine
comment: Product Name: BCG Vaccine

Fluzone High-dose
type: Class
subclass of: Fluzone
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Influenza A virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Betainfluenzavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
definition: an influenza vaccine that is similar to Fluzone but has high dose.
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=754
definition source: WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305079.pdf
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112854.htm
VIOLIN vaccine ID: 754
FDA vaccine indications: Fluzone High-Dose is indicated for active immunization of persons 65 years of age and older against influenza disease caused by influenza virus subtypes A and type B contained in the vaccine.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM619541.pdf
vaccine STN: BL 103914
in subset: vaccine
comment: Product Name: Influenza Virus Vaccine, Trivalent, Types A and B

pBK-SFV DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

influenza A (H1N1) 2009 Monovalent Vaccine (Novartis)
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001176
subclass of: VO_0003211
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H1N1 subtype
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000696
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=453
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm181973.htm
VIOLIN vaccine ID: 453
FDA vaccine indications: Active immunization of persons 4 years of age and older against influenza disease caused by pandemic (H1N1) 2009 virus.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM182242.pdf
vaccine STN: 103837
in subset: vaccine

Pediarix vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019079
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: recombinant vector vaccine
subclass of: Canada licensed human vaccine
subclass of: Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: protein of pathogen organism as vaccine component
subclass of: Restriction
  on property: has component
  some values from: VO_0003150
subclass of: Restriction
  on property: has component
  some values from: VO_0003196
subclass of: Restriction
  on property: has component
  some values from: VO_0003384
subclass of: Restriction
  on property: has component
  some values from: VO_0003455
subclass of: Restriction
  on property: has component
  some values from: VO_0003835
subclass of: Restriction
  on property: has component
  some values from: VO_0003836
subclass of: Restriction
  on property: has component
  some values from: VO_0003837
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis B
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatitis B virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019079
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=357
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=364
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=610
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=611
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=760
definition source: http://purl.bioontology.org/ontology/RXNORM/352877
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm146759.htm
VIOLIN vaccine ID: 357
VIOLIN vaccine ID: 364
VIOLIN vaccine ID: 610
VIOLIN vaccine ID: 611
VIOLIN vaccine ID: 760
trade name: Pediarix
FDA vaccine indications: For active immunization against diphtheria, tetanus, pertussis, infection caused by all known subtypes of hepatitis B virus, and poliomyelitis. PEDIARIX is approved for use as a three-dose series in infants born of hepatitis B surface antigen (HBsAg)-negative mothers. PEDIARIX may be given as early as 6 weeks of age through 6 years of age (prior to the 7th birthday).
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM241874.pdf
vaccine STN: BL 103907
in subset: vaccine

PedvaxHIB vaccine
type: Class
equivalent class: Class
  intersection of: Haemophilus influenzae serotype b vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015447
subclass of: conjugate vaccine
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0010437
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003049
subclass of: Restriction
  on property: has component
  some values from: VO_0003408
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015447
definition: PedvaxHIB is a highly purified capsular polysaccharide (polyribosylribitol phosphate or PRP) of Haemophilus influenzae type b (Haemophilus b, Ross strain) that is covalently bound to an outer membrane protein complex (OMPC) of the B11 strain of Neisseria meningitidis serogroup B.
term editor: Kallan Roan
term editor: Oliver He
definition source: PMID:2791073
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=161
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm253644.htm
VIOLIN vaccine ID: 161
trade name: Liquid PedvaxHIB
FDA vaccine indications: Liquid PedvaxHIB is indicated for routine vaccination against invasive disease caused by Haemophilus influenzae type b in infants and children 2 to 71 months of age.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM253652.pdf
vaccine STN: BL 103237/5285
in subset: vaccine

Pentacel vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019080
subclass of: USA licensed human vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010163
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: protein of pathogen organism as vaccine component
subclass of: Restriction
  on property: has component
  some values from: VO_0003196
subclass of: Restriction
  on property: has component
  some values from: VO_0003384
subclass of: Restriction
  on property: has component
  some values from: VO_0003455
subclass of: Restriction
  on property: has component
  some values from: VO_0003835
subclass of: Restriction
  on property: has component
  some values from: VO_0003836
subclass of: Restriction
  on property: has component
  some values from: VO_0003837
subclass of: Restriction
  on property: has component
  some values from: VO_0015014
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019080
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=359
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=367
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=613
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=614
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=765
definition source: http://purl.bioontology.org/ontology/RXNORM/674453
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm172502.htm
VIOLIN vaccine ID: 359
VIOLIN vaccine ID: 367
VIOLIN vaccine ID: 613
VIOLIN vaccine ID: 614
VIOLIN vaccine ID: 765
trade name: Pentacel
FDA vaccine indications: For active immunization against diphtheria, tetanus, pertussis, poliomyelitis and invasive disease caused by Haemophilus influenzae type b when administered to infants and children 6 weeks through 4 years of age (prior to fifth birthday).
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM109810.pdf
vaccine STN: 125145
in subset: vaccine

Plague vaccine by Greer Laboratories Inc
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0010482
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Yersinia pestis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000691
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=319
VIOLIN vaccine ID: 319
in subset: vaccine
comment: Product Name: Plague Vaccine

pBudCE4.1 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Plasmodium falciparum vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Plasmodium falciparum
subclass of: malaria vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: malaria
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Plasmodium falciparum
definition: a malaria vaccine that protects against malaria caused by Plasmodium falciparum.
term editor: Oliver He
in subset: vaccine

Pneumovax 23 vaccine
type: Class
equivalent class: Class
  intersection of: polyvalent pneumococcal vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015451
subclass of: USA licensed human vaccine
subclass of: polyvalent pneumococcal vaccine
subclass of: multivalent vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has component
  some values from: VO_0000888
subclass of: Restriction
  on property: has component
  some values from: VO_0003212
subclass of: Restriction
  on property: has component
  some values from: VO_0003217
subclass of: Restriction
  on property: has component
  some values from: VO_0003218
subclass of: Restriction
  on property: has component
  some values from: VO_0003219
subclass of: Restriction
  on property: has component
  some values from: VO_0003220
subclass of: Restriction
  on property: has component
  some values from: VO_0003221
subclass of: Restriction
  on property: has component
  some values from: VO_0003222
subclass of: Restriction
  on property: has component
  some values from: VO_0003223
subclass of: Restriction
  on property: has component
  some values from: VO_0003224
subclass of: Restriction
  on property: has component
  some values from: VO_0003225
subclass of: Restriction
  on property: has component
  some values from: VO_0003226
subclass of: Restriction
  on property: has component
  some values from: VO_0003227
subclass of: Restriction
  on property: has component
  some values from: VO_0003232
subclass of: Restriction
  on property: has component
  some values from: VO_0003246
subclass of: Restriction
  on property: has component
  some values from: VO_0003248
subclass of: Restriction
  on property: has component
  some values from: VO_0003249
subclass of: Restriction
  on property: has component
  some values from: VO_0003250
subclass of: Restriction
  on property: has component
  some values from: VO_0003252
subclass of: Restriction
  on property: has component
  some values from: VO_0003253
subclass of: Restriction
  on property: has component
  some values from: VO_0003254
subclass of: Restriction
  on property: has component
  some values from: VO_0003255
subclass of: Restriction
  on property: has component
  some values from: VO_0003561
subclass of: Restriction
  on property: has component
  some values from: VO_0003959
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: Streptococcus pneumonia
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Streptococcus pneumoniae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015451
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=317
definition source: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm179996.htm
VIOLIN vaccine ID: 317
trade name: Pneumovax 23
FDA vaccine indications: PNEUMOVAX 23 is indicated for active immunization against pneumococcal disease caused by those pneumococcal types included in the vaccine in persons 50 years of age or older and persons greater than or equal to 2 years of age who are at increased risk for pneumococcal disease.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM257088.pdf
vaccine STN: BLA 101094
in subset: vaccine
comment: Product Name: Pneumococcal Vaccine, Polyvalent

Poliovax vaccine
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0010447
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
term editor: Oliver He
alternative label: Poliovax
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=339
VIOLIN vaccine ID: 339
trade name: Poliovax
in subset: vaccine
comment: Product Name: Poliovirus Vaccine Inactivated (Human Diploid Cell)

Prevnar vaccine
type: Class
equivalent class: Class
  intersection of: polyvalent pneumococcal vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015457
subclass of: conjugate vaccine
subclass of: USA licensed human vaccine
subclass of: polyvalent pneumococcal vaccine
subclass of: multivalent vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has component
  some values from: VO_0003049
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: Streptococcus pneumonia
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Streptococcus pneumoniae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000701
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015457
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=318
definition source: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
definition source: https://www.prevnar13.com/
VIOLIN vaccine ID: 318
trade name: Prevnar
FDA vaccine 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.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM137038.pdf
vaccine STN: 103905
in subset: vaccine
comment: Product Name: Pneumococcal 7-valent Conjugate Vaccine (Diphtheria CRM197 Protein)
comment: STN: BLA 101094

ProQuad vaccine
type: Class
equivalent class: Class
  intersection of: Measles-Mumps-Rubella-Varicella vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015461
subclass of: USA licensed human vaccine
subclass of: combination vaccine
subclass of: Measles-Mumps-Rubella-Varicella vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003273
subclass of: Restriction
  on property: has component
  some values from: VO_0015054
subclass of: Restriction
  on property: has component
  some values from: VO_0015056
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes against disease
  some values from: chickenpox
subclass of: Restriction
  on property: immunizes against disease
  some values from: rubella
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human alphaherpesvirus 3
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rubella virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015461
definition: A Measles-Mumps-Rubella-Vericella vaccine that is live and manufactured by Merck & Co, Inc.
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=376
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=377
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=378
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=379
definition source: WEB: http://www.merck.com/product/usa/pi_circulars/p/proquad/proquad_pi.pdf
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm188806.htm
VIOLIN vaccine ID: 376
VIOLIN vaccine ID: 377
VIOLIN vaccine ID: 378
VIOLIN vaccine ID: 379
trade name: PROQUAD
FDA vaccine indications: For vaccination against measles, mumps, rubella, and varicella in children 12 months to 12 years of age.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123793.pdf
vaccine STN: 125108
in subset: vaccine

Fluzone Intradermal Quadrivalent
type: Class
subclass of: USA licensed human vaccine
subclass of: multivalent vaccine
subclass of: VO_0001176
subclass of: VO_0004673
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: vaccinated in route
  some values from: VO_0000887
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Alphainfluenzavirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Betainfluenzavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=5567
definition source: WEB: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112854.htm
VIOLIN vaccine ID: 5567
trade name: Fluzone Intradermal
FDA vaccine indications: Fluzone Intradermal Quadrivalent indicated for active immunization for use in adults 18 through 64 years of age against influenza disease caused by influenza virus subtypes A and type B contained in the vaccine.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM566500.pdf
vaccine STN: BL 103914
in subset: vaccine

mineral salt vaccine adjuvant
type: Class
subclass of: vaccine adjuvant
definition: A vaccine adjuvant that is formed as a mineral salt.
term editor: Oliver He
term editor: Samantha G. Sayers
in subset: vaccine adjuvant

RabAvert vaccine
type: Class
equivalent class: Class
  intersection of: Rabies virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015464
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010448
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003862
subclass of: Restriction
  on property: has vaccine allergen
  some values from: chicken ovalbumin egg protein allergen
subclass of: Restriction
  on property: immunizes against disease
  some values from: rabies
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Lyssavirus rabies
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000696
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015464
definition: RabAvert Rabies Vaccine is a sterile, freeze-dried vaccine obtained by growing the fixed-virus strain Flury Low Egg Passage (LEP) in primary cultures of chicken fibroblasts.
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=6181
definition source: WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf
definition source: http://purl.bioontology.org/ontology/RXNORM/219579
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm133517.htm
VIOLIN vaccine ID: 6181
trade name: RabAvert
FDA vaccine indications: Pre-exposure and post-exposure immunization of children and adults
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM312931.pdf
vaccine STN: BL 103334
in subset: vaccine

Rabies vaccine Adsorbed by BioPort Corp
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0010448
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: rabies
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Lyssavirus rabies
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000688
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=340
VIOLIN vaccine ID: 340
in subset: vaccine
comment: Product Name: Rabies Vaccine Adsorbed

Adenovirus Type 4 and Type 7 Vaccine, Live, Oral
type: Class
subclass of: adenovirus vaccine
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001220
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: VO_0000886
subclass of: Restriction
  on property: immunizes against disease
  some values from: respiratory system disease
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Adenoviridae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0003164
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0005564
term editor: Kallan Roan
term editor: Oliver He
term editor: Samantha G. Sayers
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=3116
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm247508.htm
VIOLIN vaccine ID: 3116
FDA vaccine indications: Indicated for active immunization for the prevention of febrile acute respiratory disease caused by Adenovirus Type 4 and Type 7.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM247515.pdf
vaccine STN: BL 125296/0
CVX code: 143
OMOP concept ID: 40213264
CVX full vaccine name: Adenovirus, type 4 and type 7, live, oral
CVX short description: Adenovirus types 4 and 7
has cross-reference: SNOMEDCT: 442561000
has cross-reference: UMLS_CUI: C0695130
in subset: vaccine

RotaTeq vaccine
type: Class
equivalent class: Class
  intersection of: Rotavirus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019084
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: multivalent vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0001220
subclass of: VO_0010449
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
subclass of: Restriction
  on property: has component
  some values from: VO_0004820
subclass of: Restriction
  on property: has component
  some values from: VO_0004822
subclass of: Restriction
  on property: has component
  some values from: VO_0004823
subclass of: Restriction
  on property: has component
  some values from: VO_0004824
subclass of: Restriction
  on property: has component
  some values from: VO_0004825
subclass of: Restriction
  on property: vaccinated in route
  some values from: VO_0000886
subclass of: Restriction
  on property: immunizes against disease
  some values from: Rotavirus infection
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rotavirus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019084
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=344
definition source: http://purl.bioontology.org/ontology/RXNORM/496892
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094063.htm
VIOLIN vaccine ID: 344
trade name: RotaTeq
FDA vaccine indications: For prevention of rotavirus gastroenteritis in infants 6 weeks to 32 weeks of age caused by types G1, G2, G3, G4, and G9.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142288.pdf
vaccine STN: BL 125122
in subset: vaccine

SIV based lentivirus vaccine vector
type: Class
subclass of: lentivirus vaccine vector
definition: a lentivirus vaccine vector that uses a SIV strain as the vector
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 11723

Pcaggs DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine-induced T-helper 1 type immune response
type: Class
subclass of: vaccine-induced T cell mediated immunity
term editor: Oliver He
definition source: https://academic.oup.com/cid/article/32/1/76/311106
in subset: vaccine-induced response
comment: T helper type 1 (Th1) lymphocytes secrete secrete interleukin (IL)-2, interferon-γ, and lymphotoxin-α and stimulate type 1 immunity, which is characterized by intense phagocytic activity. https://academic.oup.com/cid/article/32/1/76/311106

vaccine-induced T-helper 2 type immune response
type: Class
subclass of: vaccine-induced T cell mediated immunity
term editor: Oliver He
definition source: https://academic.oup.com/cid/article/32/1/76/311106
in subset: vaccine-induced response
comment: Th2 cells secrete IL-4, IL-5, IL-9, IL-10, and IL-13 and stimulate type 2 immunity, which is characterized by high antibody titers. https://academic.oup.com/cid/article/32/1/76/311106

TENIVAC vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019089
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: toxoid vaccine
subclass of: combination vaccine
subclass of: Diphtheria-Tetanus vaccine
subclass of: VO_0001214
subclass of: VO_0010436
subclass of: VO_0010445
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019089
term editor: Kallan Roan
term editor: Oliver He
alternative label: Tenivac
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=370
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=384
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm152800.htm
VIOLIN vaccine ID: 370
VIOLIN vaccine ID: 384
trade name: TENIVAC
FDA vaccine indications: Indicated for active immunization for the prevention of tetanus and diphtheria in persons 7 years of age and older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM152826.pdf
vaccine STN: 103171
in subset: vaccine

TICE BCG
type: Class
subclass of: USA licensed human vaccine
subclass of: live attenuated vaccine
subclass of: VO_0007656
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: VO_0003053
subclass of: Restriction
  on property: immunizes against disease
  some values from: cancer
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0010377
term editor: Kallan Roan
term editor: Oliver He
alternative label: BCG Live
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=351
VIOLIN vaccine ID: 351
trade name: TICE BCG
FDA vaccine indications: For the treatment and prophylaxis of carcinoma in situ (CIS) of the urinary bladder. For the prophylaxis of primary or recurrent state Ta and/or T1 papillary tumors following transurethral resection (TUR).
vaccine package insert PDF URL: https://www.fda.gov/media/76396/download
vaccine STN: 102821
in subset: cancer vaccine

TYPHIM VI vaccine
type: Class
equivalent class: Class
  intersection of: VO_0003443
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0018838
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0003443
subclass of: VO_0010451
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003849
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: typhoid fever
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Salmonella enterica subsp. enterica serovar Typhi
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000703
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0018838
definition: Typhim Vi, Typhoid Vi Polysaccharide Vaccine, for intramuscular use, is a sterile solution containing the cell surface Vi polysaccharide extracted from Salmonella enterica serovar Typhi, S typhi Ty2 strain.
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=352
definition source: http://purl.bioontology.org/ontology/RXNORM/114883
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094072.htm
VIOLIN vaccine ID: 352
trade name: Typhim Vi
FDA vaccine indications: For active immunization against typhoid fever for persons two years of age or older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142811.pdf
vaccine STN: 103936
in subset: vaccine

vaccine T cell epitope
type: Class
subclass of: VO_0000811
term editor: Oliver He
alternative label: T cell epitope in vaccine
in subset: material entity

vaccine-induced T cell mediated immunity
type: Class
subclass of: VO_0010462
term editor: Oliver He
in subset: vaccine-induced response

T cell vaccine antigen processing and presentation
type: Class
subclass of: vaccine-induced T cell mediated immunity
term editor: Oliver He
in subset: vaccine-induced response

Brucella abortus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Brucella abortus
subclass of: Brucella vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
term editor: Oliver He
in subset: vaccine

Tetanus Toxoid Adsorbed by Aventis Pasteur Inc vaccine
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: toxoid vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010436
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has component
  some values from: thimerosal vaccine preservative
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
term editor: Oliver He
alternative label: Tetanus Toxoid Adsorbed by Aventis Pasteur Inc
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=631
VIOLIN vaccine ID: 631
in subset: vaccine
comment: Product Name: Tetanus Toxoid Adsorbed

E. coli O157:H7 intimin vaccine
type: Class
subclass of: E. coli subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
editor note: E. coli Int280a has been found to be a protective antigen. This subunit vaccine uses E. coli Int280a combined with adjuvant. This antigen can be used for development of type-specific EPEC or EHEC vaccine.
term editor: Oliver He
definition source: PMID:11500434
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=277
VIOLIN vaccine ID: 277
in subset: vaccine

Tetanus and Diphtheria Toxoids Adsorbed vaccine by MA Biologic Lab
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: toxoid vaccine
subclass of: Diphtheria-Tetanus vaccine
subclass of: VO_0010436
subclass of: VO_0010445
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000693
term editor: Oliver He
alternative label: Tetanus and Diphtheria Toxoids Adsorbed by MA Biologic Lab
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=5574
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=5582
VIOLIN vaccine ID: 5574
VIOLIN vaccine ID: 5582
in subset: vaccine
comment: Product Name: Tetanus & Diphtheria Toxoids Adsorbed for Adult Use

Tripedia vaccine
type: Class
equivalent class: Class
  intersection of: Diphtheria-Tetanus-Pertussis vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019090
subclass of: USA licensed human vaccine
subclass of: Diphtheria-Tetanus-Pertussis vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019090
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=354
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=366
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=777
VIOLIN vaccine ID: 354
VIOLIN vaccine ID: 366
VIOLIN vaccine ID: 777
trade name: Tripedia
in subset: vaccine
comment: Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed

Twinrix vaccine
type: Class
equivalent class: Class
  intersection of: licensed human Hepatitis A & B vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0018834
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: recombinant vector vaccine
subclass of: inactivated viral vaccine
subclass of: Canada licensed human vaccine
subclass of: licensed human Hepatitis A & B vaccine
subclass of: VO_0001214
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis A
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis B
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatitis B virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatovirus A
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0018834
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=349
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=350
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094035.htm
VIOLIN vaccine ID: 349
VIOLIN vaccine ID: 350
trade name: Twinrix
FDA vaccine indications: Active immunization of persons 18 years of age or older against disease caused by hepatitis A virus and infection by all known subtypes of hepatitis B virus.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM110079.pdf
vaccine STN: BL 103850
in subset: vaccine

pCAGGST7 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine-induced T cell activation
type: Class
subclass of: vaccine-induced lymphocyte activation
in subset: vaccine-induced response

pCBINT DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCdm7 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

microbial derivative vaccine adjuvant
type: Class
subclass of: vaccine adjuvant
definition: A vaccine adjuvant that contains microbial derived material.
term editor: Oliver He
term editor: Samantha G. Sayers
in subset: vaccine adjuvant

Varivax vaccine
type: Class
equivalent class: Class
  intersection of: Varicella-zoster virus live vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019091
subclass of: USA licensed human vaccine
subclass of: Varicella-zoster virus live vaccine
subclass of: prophylactic vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: subcutaneous route
subclass of: Restriction
  on property: immunizes against disease
  some values from: chickenpox
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human alphaherpesvirus 3
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019091
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=347
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094073.htm
VIOLIN vaccine ID: 347
FDA vaccine indications: Indicated for active immunization for the prevention of varicella in individuals 12 months of age and older
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142812.pdf
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142813.pdf
vaccine STN: BL 103552
in subset: vaccine

Vivotif (USA)
type: Class
subclass of: VO_0003353
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: immunizes against disease
  some values from: typhoid fever
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Salmonella enterica subsp. enterica serovar Typhi
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000687
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=248
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm094070.htm
VIOLIN vaccine ID: 248
trade name: Vivotif
FDA vaccine indications: For immunization of adults and children greater than 6 years of age against disease caused by Salmonella typhi.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142807.pdf
vaccine STN: 103123
in subset: vaccine

YF-Vax vaccine
type: Class
equivalent class: Class
  intersection of: VO_0003134
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019095
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0003134
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: has component
  some values from: VO_0003371
subclass of: Restriction
  on property: has vaccine allergen
  some values from: VO_0000912
subclass of: Restriction
  on property: vaccinated in route
  some values from: subcutaneous route
subclass of: Restriction
  on property: immunizes against disease
  some values from: yellow fever
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Yellow fever virus
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019095
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=346
definition source: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm180913.htm
VIOLIN vaccine ID: 346
trade name: YF-Vax
FDA vaccine indications: For active immunization of persons 9 months of age and older who: - Are living in or traveling to endemic areas; - Travelling internationally to countries that require evidence of vaccination from entering travelers or; - Laboratory Personnel who might be expose to virulent yellow fever virus or to concentrated preparations of the yellow fever vaccine strain by direct or indirect contact or by aerosols should by vaccinated.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142831.pdf
vaccine STN: BL 103915
in subset: vaccine

Yellow fever 17D vaccine vector
type: Class
subclass of: viral vaccine vector
definition: a viral vaccine vector that uses Yellow fever vaccine strain 17D as the vector.
term editor: Oliver He
definition source: PMID: 16755933
in subset: vaccine component
see also: NCBI Taxonomy ID: 11090

yellow fever virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Yellow fever virus
subclass of: VO_0003546
subclass of: Restriction
  on property: immunizes against disease
  some values from: yellow fever
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Yellow fever virus
definition: A viral vaccine that protects against infection with Yellow fever virus.
term editor: Oliver He
alternative label: yellow fever vaccine
in subset: vaccine

Zostavax vaccine
type: Class
equivalent class: Class
  intersection of: Varicella-zoster virus live vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019096
subclass of: USA licensed human vaccine
subclass of: Varicella-zoster virus live vaccine
subclass of: prophylactic vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: subcutaneous route
subclass of: Restriction
  on property: immunizes against disease
  some values from: herpes zoster
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human alphaherpesvirus 3
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000695
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019096
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=348
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm136941.htm
VIOLIN vaccine ID: 348
trade name: Zostavax
FDA vaccine indications: For prevention of herpes zoster (shingles) in individuals 50 years of age and older.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM132831.pdf
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM285015.pdf
vaccine STN: 125123
in subset: vaccine

licensed turkey vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001478
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed bird vaccine
subclass of: VO_0001478
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Meleagris gallopavo
term editor: Oliver He
in subset: vaccine

live attenuated vaccine organism
type: Class
equivalent class: Class
  intersection of: vaccine organism
  intersection of: Restriction
    on property: has quality
    some values from: vaccine organism live attenuated
subclass of: vaccine organism
subclass of: Restriction
  on property: has quality
  some values from: vaccine organism live attenuated
definition: a vaccine organism that is live and attenuated
term editor: Oliver He
in subset: organism

aluminum hydroxide vaccine adjuvant
type: Class
subclass of: VO_0000884
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005310
definition: An aluminum vaccine adjuvant that contains aluminum hydroxide.
term editor: Oliver He
alternative label: alum
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

aluminum phosphate vaccine adjuvant
type: Class
subclass of: VO_0000884
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005310
definition: An aluminum vaccine adjuvant that is aluminum phosphate.
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: Adju-Phos®
alternative label: Al(PO)4
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

vaccination frequency
type: Class
subclass of: frequency
definition: Vaccination frequency is a qualitative term that represents how many times vaccination has occurred.
term editor: Oliver He
in subset: quality

pcDNA I/Amp DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

calcium phosphate vaccine adjuvant
type: Class
subclass of: mineral salt vaccine adjuvant
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005310
definition: A mineral salt vaccine adjuvant composed of calcium phosphate.
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: CaHPO4
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

pcDNA3 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Freund's emulsified oil adjuvant
type: Class
subclass of: VO_0001355
definition: An emulsion vaccine adjuvant that consists of a water-in-oil emulsion of aqueous antigen in paraffin (mineral) oil of low specific gravity and low viscosity. It is named after Jules T. Freund (1890-1960), Hungarian-born American immunologist. It is a water in oil emulsion.
term editor: Oliver He
term editor: Samantha G. Sayers
in subset: vaccine adjuvant

vaccine-induced T cell proliferation
type: Class
subclass of: vaccine-induced T cell activation
in subset: vaccine-induced response

vaccine-induced adaptive immune response
type: Class
subclass of: vaccine-induced immune response
term editor: Oliver He
in subset: vaccine-induced response

adenovirus vaccine vector
type: Class
subclass of: viral vaccine vector
definition: a viral vaccine vector that uses an adenovirus as the vector.
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 10508

combination vaccine role
type: Class
subclass of: vaccine role
definition: A vaccine role that indicates the vaccine being a combination vaccine.
term editor: Oliver He
in subset: role

complete Freund's adjuvant
type: Class
subclass of: Freund's emulsified oil adjuvant
subclass of: VO_0005626
subclass of: VO_0005740
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005309
subclass of: Restriction
  on property: target receptor
  some values from: Toll-like receptor 2
subclass of: Restriction
  on property: target receptor
  some values from: Toll-like receptor 4
definition: A Freund's emulsified oil adjuvant that contains inactivated and dried mycobacteria, usually Mycobacterium tuberculosis (the pathogenic agent of tuberculosis).
term editor: Oliver He
alternative label: Freund's Complete Adjuvant
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

agglutinating antibody role
type: Class
subclass of: antibody role
term editor: Oliver He
in subset: role

obsolete virulence factor
type: Class
subclass of: Thing
term editor: Oliver He
deprecated: true

incomplete Freund's adjuvant
type: Class
subclass of: Freund's emulsified oil adjuvant
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005310
definition: A Freund's emulsified oil adjuvant that does not contain the mycobacterial components.
term editor: Oliver He
alternative label: Freund's Incomplete Adjuvant
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

cholera toxin vaccine adjuvant
type: Class
subclass of: microbial derivative vaccine adjuvant
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005376
definition: A microbial derivative vaccine adjuvant consisting of cholera toxin (CT) from Vibrio cholerae.
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: CT
alternative label: cholera toxin
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

alphavirus vaccine vector
type: Class
subclass of: viral vaccine vector
definition: a viral vaccine vector that uses an alphavirus as the vector.
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 11019

recombinant vaccine vector role
type: Class
subclass of: VO_0003439
definition: A vaccine vector role that inheres in a recombinant vaccine vector as a vaccine component. The combination of a recombinant vaccine vector and a heterogenous protective antigen(s) inserted inside the vector for a recombinant vector vaccine.
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: role

Corynebacterium-derived P40 vaccine adjuvant
type: Class
subclass of: microbial derivative vaccine adjuvant
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005309
definition: A microbial derivative vaccine adjuvant that is the P40 particulate fraction isolated from Corynebacterium.
term editor: Oliver He
term editor: Samantha G. Sayers
definition source: PMID:8447157
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

vaccine adjuvant role
type: Class
subclass of: vaccine additive role
definition: an adjuvant role that inheres in a vaccine component which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen.
term editor: Oliver He
in subset: role
comment: The Latin "adjuvans" means to help, particularly to reach a goal. Adjuvant therapy for cancer is surgery followed by chemotherapy or radiation to help decrease the risk of the cancer recurring (coming back). An adjuvant is a substance that helps and enhances the pharmacological effect of a drug or increases the ability of an antigen to stimulate the immune system.

antibody role
type: Class
subclass of: role
term editor: Oliver He
in subset: role

antibody titer
type: Class
subclass of: titer
definition: A titer of antibody that shows how much antibody an organism has produced that recognizes a particular epitope, expressed as the greatest dilution ratio (or its reciprocal) that still gives a positive result. ELISA is a common means of determining antibody titers.
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Antibody_titer
in subset: data item

immunized
type: Class
subclass of: organismal quality
definition: an organismal quality that indicates an organism (e.g., human) is immunized against a disease.
editor note: To assign the state of 'immunized', we will need to do some assay to measure indicators of immunity, e.g., antibody titers in serum samples.
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: quality

Francisella tularensis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Francisella tularensis
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against disease
  some values from: tularemia
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Francisella tularensis
definition: a bacterial vaccine against an infection with F. tularensis.
term editor: Oliver He
in subset: vaccine

toxoid vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: toxoid vaccine
definition: A vaccine preparation that results in the generation of a toxoid vaccine
term editor: Oliver He
in subset: vaccine preparation

sodC from B. abortus strain 2308
type: Class
subclass of: virmugen
subclass of: VO_0000793
subclass of: VO_0001232
subclass of: Restriction
  on property: has role
  some values from: protective antigen role
subclass of: Restriction
  on property: has role
  some values from: VO_0001361
subclass of: Restriction
  on property: in taxon
  some values from: Brucella abortus 2308
definition: A Brucella abortus gene that has the name sodC and comes from strain 2308.
term editor: Oliver He
in subset: gene
comment: IMMUNOGENICITY: The SodC protein induces antigen-specific Th1 immune response, as indicated by the specific induction of serum IgG2a, but not IgG1, antibodies and by the secretion of IFN-alpha but not IL-4, by the Cu/Zn SOD-stimulated splenocytes. This gene has been used for vaccine development [PubMed: 10816475][PubMed: 11953393][PubMed: 12933826]. MUTATION: An isogenic sodC mutant constructed from B abortus 2308 by gene replacement exhibited much greater susceptibility to killing by exogenous O(2)(-) than the parental 2308 strain, supporting a role for SodC in protecting this bacterium from O(2)(-) stress. The B abortus sodC mutant was much more sensitive to killing by cultured resident peritoneal macrophages from C57BL6J mice than 2308, and its attenuation in cultured murine macrophages was enhanced when these phagocytes were treated with gamma interferon. The attenuation of the B abortus sodC mutant in both resting and IFN-gamma-activated macrophages was alleviated in the presence of the NADPH oxidase inhibitor apocynin. Consistently, the B abortus sodC mutant also displayed significant attenuation in infected C57BL6J mice compared to the parental strain. These findings suggest that SodC protects B abortus 2308 from the respiratory burst of host macrophages [PubMed: 15845493].
see also: NCBI Gene GI: 3827840; NCBITaxon: 234

obsolete bacterial gene
type: Class
subclass of: Thing
term editor: Oliver He
deprecated: true

viral gene
type: Class
subclass of: gene
term editor: Oliver He
in subset: gene

HIV gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

pcDNA3.1 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

live attenuated vaccine preparation by serial passages in vitro
type: Class
subclass of: live attenuated vaccine preparation
example of usage: Brucella abortus cattle vaccine RB51 was developed by serial passages of virulent B. abortus strain 2308 in vitro in rifampin agar plates (Reference: PMID: 1908158).
definition: A live attenuated vaccine prepraration process that is performed by serial passages in vitro for pathogen attenuation.
term editor: Oliver He
in subset: vaccine preparation

influenza A (H1N1) 2009 Monovalent Vaccine (Sanofi Pasteur)
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001176
subclass of: VO_0003211
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H1N1 subtype
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=454
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm181971.htm
VIOLIN vaccine ID: 454
FDA vaccine indications: Active immunization of persons 6 months of age and older against influenza disease caused by pandemic (H1N1) 2009 virus.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM182404.pdf
vaccine STN: 103914
in subset: vaccine

Escherichia coli gene
type: Class
subclass of: gene of Bacteria
term editor: Oliver He
alternative label: E. coli gene
in subset: gene

vaccine organism avirulent
type: Class
subclass of: virulence
definition: a virulence of vaccine organism that shows an avirulent pheontype of the organism as the major component of a vaccine. The avirulence means that an vaccine organism is not virulent and does not cause pathogenic phenotype in a host organism.
term editor: Oliver He
in subset: quality

vaccine-induced gene up-regulation controlling intracellular bacterial replication
type: Class
subclass of: vaccine-induced up-regulated gene expression
in subset: vaccine-induced response

Mycobacterium tuberculosis gene
type: Class
subclass of: gene of Bacteria
subclass of: Restriction
  on property: in taxon
  some values from: Mycobacterium tuberculosis
term editor: Oliver He
in subset: gene

bacterial vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Bacteria
subclass of: VO_0005504
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacteria
definition: A vaccine that targets against a bacterial disease.
term editor: Oliver He
has cross-reference: MeSH: D001428
in subset: vaccine

bacterial vaccine vector
type: Class
subclass of: recombinant vaccine vector
definition: a vaccine vector that uses a live bacterium as the vector
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 2

pcDNA3.1V5HisTOPO/TA DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Salmonella gene
type: Class
subclass of: gene of Bacteria
subclass of: Restriction
  on property: in taxon
  some values from: Salmonella
term editor: Oliver He
in subset: gene

Shigella gene
type: Class
subclass of: gene of Bacteria
subclass of: Restriction
  on property: in taxon
  some values from: Shigella
term editor: Oliver He
in subset: gene

protozoan gene
type: Class
subclass of: gene
term editor: Oliver He
in subset: gene

Plasmodium gene
type: Class
subclass of: protozoan gene
term editor: Oliver He
in subset: gene

Plasmodium falciparum gene
type: Class
subclass of: Plasmodium gene
term editor: Oliver He
in subset: gene

vaccine organism live attenuated
type: Class
subclass of: virulence
definition: a virulence of vaccine organism that shows an attenuated pheontype of the organism as the major component of a vaccine.
term editor: Oliver He
in subset: quality

Leishmania gene
type: Class
subclass of: protozoan gene
term editor: Oliver He
in subset: gene

pCEP4 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine-induced T cell differentiation
type: Class
subclass of: vaccine-induced T cell activation
in subset: vaccine-induced response

cancer vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against disease
    some values from: cancer
subclass of: VO_0005503
subclass of: Restriction
  on property: immunizes against disease
  some values from: cancer
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
definition: Vaccine that prevents or treats cancer.
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Jie Zheng
term editor: Oliver He
alternative label: neoplasm vaccine
alternative label: tumor vaccine
has cross-reference: MeSH:D019496
in subset: cancer vaccine

inactivated vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has part
  some values from: VO_0001103
subclass of: Restriction
  on property: has_specified_output
  some values from: inactivated vaccine
definition: A vaccine preparation that results in the generation of a inactivated vaccine
term editor: Oliver He
in subset: vaccine preparation

vaccine component
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: part of
    some values from: vaccine
subclass of: material entity
subclass of: Restriction
  on property: part of
  some values from: vaccine
definition: a processed material that is output of the vaccine preparation and part of a vaccine.
term editor: Oliver He
alternative label: cardinal part of vaccine
alternative label: vaccine ingredient
in subset: vaccine component

vaccine-induced cell activation
type: Class
subclass of: vaccine-induced immune response
term editor: Oliver He
in subset: vaccine-induced response

lipopolysaccharide vaccine adjuvant
type: Class
subclass of: microbial derivative vaccine adjuvant
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005309
definition: A microbial derivative vaccine adjuvant made from bacterial lipopolysaccharide (LPS) of gram-negative bacteria.
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: LPS
alternative label: LPS vaccine adjuvant
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

vaccine-induced antibacterial agglutination antibody response
type: Class
subclass of: vaccine-induced humoral immune response
term editor: Oliver He
in subset: vaccine-induced response

Japanese encephalitis virus gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

Ebola virus gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

Influenza virus gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

RNA vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: RNA vaccine role
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: RNA vaccine role
definition: A vaccine that uses RNA(s) derived from a pathogen organism.
editor note: Using RNA may eliminate the problem of having to tailor a vaccine for each individual patient with their specific immunity. The advantage of RNA is that it can be used for all immunity types and can be taken from a single cell. DNA vaccines need to produce RNA which then prompts the manufacture of proteins. However, RNA vaccine eliminates the step from DNA to RNA.
term editor: Oliver He
alternative label: mRNA vaccine
definition source: https://en.wikipedia.org/wiki/RNA_vaccine
in subset: vaccine

muramyl dipeptide vaccine adjuvant
type: Class
subclass of: VO_0001357
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005309
subclass of: Restriction
  on property: target receptor
  some values from: nucleotide-binding oligomerization domain-containing protein 2
definition: A synthetic vaccine adjuvant formulated to correspond to a component found in a water-soluble extract of cell walls of mycobacteria used in complete Freund's adjuvant (CFA).
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: MDP
alternative label: Muramyl Dipeptide Adjuvant
alternative label: muramyl dipeptide
definition source: PMID:344799
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

Dengue virus gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

colony forming unit
type: Class
subclass of: titer
definition: A titer measurement of viable bacterial or fungal numbers. Unlike in direct microscopic counts where all cells, dead and living, are counted, CFU measures viable cells. By convenience the results are given as CFU/mL (colony-forming units per milliliter) for water, and CFU/g (colony-forming units per gram) for soil or other porous material.
term editor: Oliver He
alternative label: CFU
definition source: WEB: http://en.wikipedia.org/wiki/Colony-forming_unit
in subset: data item

squalene vacccine adjuvant
type: Class
subclass of: VO_0001355
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005311
definition: An emulsion vaccine adjuvant that contains an organic polymer with some antigenic epitopes which might be shared with other organic polymers acting as immunostimulators.
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: Squalene-based Adjuvants
alternative label: squalene
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

arlacel A vaccine adjuvant
type: Class
subclass of: VO_0001357
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005311
definition: A synthetic vaccine adjuvant that is an emulsifier called Arlacel A.
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: arlacel A
definition source: PMID:2042393
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

Montanide 103 vaccine adjuvant
type: Class
subclass of: VO_0001271
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005311
definition: A Montanide vaccine adjuvant that is Montanide 103.
term editor: Oliver He
alternative label: Montanide 103
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

Bordetella pertussis component vaccine adjuvant
type: Class
subclass of: microbial derivative vaccine adjuvant
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0010500
definition: A microbial derivitive vaccine adjuvant that contains components from killed Bordetella pertussis. The killed B. pertussis has a strong adjuvant effect on the diphtheria and tetanus toxoids in the DPT vaccines.
term editor: Oliver He
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

FDA licensed vaccine role
type: Class
subclass of: VO_0000812
definition: a USA licensed vaccine role that inheres ina vaccine approven to be by the US FDA to be used for humans in the USA.
term editor: Oliver He
in subset: role

conjugate vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: conjugate vaccine role
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
definition: Conjugate vaccine is vaccine that conjugates/links antigens to the molecules that form the outer coat of disease-causing bacteria to promote an immune response.
term editor: Oliver He
in subset: vaccine
comment: A conjugate vaccine is created by covalently attaching a poor (polysaccharide organism) antigen to a carrier protein (preferably from the same microorganism), thereby conferring the immunological attributes of the carrier on the attached antigen. --from wikipedia.

recombinant vector vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: recombinant vector vaccine
definition: A vaccine preparation that results in the generation of a recombinant vector vaccine
term editor: Oliver He
in subset: vaccine preparation

obsolete West Nile virus gene
type: Class
subclass of: Thing
term editor: Oliver He
has obsolescence reason: IAO_0000227
term tracker item: https://github.com/vaccineontology/VO/issues/643
term replaced by: VO_0001448
deprecated: true

chickenpox virus gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

Rubella virus gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

influenza A virus A/California/7/2009 (H1N1) antigen
type: Class
subclass of: VO_0015084
term editor: Khadeejah Khan
term editor: Oliver He
definition source: http://purl.bioontology.org/ontology/RXNORM/1657331
in subset: vaccine component

Porcilis-PCV2 vaccine
type: Class
subclass of: licensed pig vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001524
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Sus scrofa
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Porcine circovirus 2
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000204
editor note: Characteristics: Inactivated baculovirus expressed PCV2 ORF2 protein; adjuvanted
term editor: Oliver He
alternative label: Porcilis-PCV2
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=387
VIOLIN vaccine ID: 387
in subset: vaccine

Hepatitis A virus gene
type: Class
subclass of: viral gene
term editor: Oliver He
in subset: gene

Suvaxyn PCV2 vaccine
type: Class
subclass of: licensed pig vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001524
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Sus scrofa
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Porcine circovirus 2
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000205
editor note: Characteristics: Inactivated PCD1-2 chimera; adjuvanted
term editor: Oliver He
alternative label: Suvaxyn PCV2
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=388
VIOLIN vaccine ID: 388
in subset: vaccine

licensed pig vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001474
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001474
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Sus scrofa
term editor: Oliver He
in subset: vaccine

vaccine contraindication
type: Class
subclass of: contraindication
definition: A vaccine contraindication is a contraindication that increases the risks of a vaccination.
term editor: Oliver He
alternative label: contraindication for vaccination
in subset: disposition

vaccine in research role
type: Class
subclass of: vaccine role
definition: A vaccine role that is not licensed or in clinical trial; instead, it has been experimently approved to induce protection or treatment effect in vivo in at least an experimental animal model.
term editor: Oliver He
in subset: role

pHIS64 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

hemagglutination-inhibition assay
type: Class
subclass of: immune response detection assay
definition: an immune response detection assay that detects specific antiviral antibodies in a test serum. The serum, usually a twofold dilution series, is mixed with a standard number, usually 4 to 8 HA units, of virus and incubated prior to the addition of a standard suspension of erythrocytes. The highest dilution of serum that inhibits hemagglutination is the HI titer of the serum. For example, influenza (AI) viruses agglutinate erythrocytes through the interaction of the virus surface glycoprotein, the hemagglutinin (HA), with receptors on the surface of the erythrocyte. Inhibition of the agglutination reaction by HA subtype-specific antisera is the basis of the hemagglutination-inhibition (HI) assay.
term editor: Oliver He
alternative label: HI assay
in subset: assay

vaccine organism inactivated
type: Class
subclass of: VO_0001139
definition: an organismal quality of a whole organism vaccine where the whole organism is inactivated/killed and lacks the capability of replication.
term editor: Oliver He
alternative label: vaccine organism killed
in subset: quality

pCI DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0001010
definition: a DNA vaccine plasmid that uses the plasmid labeled pCI.
term editor: Allen Xiang
term editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/nuccore/5870896
in subset: vaccine component

hypersensitivity to chicken product
type: Class
subclass of: vaccine contraindication
term editor: Oliver He
in subset: disposition

pCI-neo DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCMV DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCMV-1 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

obsolete pCMV4 DNA vaccine plasmid
type: Class
subclass of: Thing
term editor: Allen Xiang
term editor: Oliver He
has obsolescence reason: IAO_0000227
term tracker item: https://github.com/vaccineontology/VO/issues/643
term replaced by: pCMV4 DNA vaccine plasmid
deprecated: true

hypersensitivity to chicken egg
type: Class
subclass of: hypersensitivity to chicken product
term editor: Oliver He
in subset: disposition

vaccine solvent
type: Class
subclass of: vaccine component
definition: a vaccine component that is used to dissolve vaccine powder into liquid. The vaccine in a powder form has to be reconstituted by mixing vaccine powder with vaccine solvent before administered.
term editor: Oliver He
alternative label: vaccine diluent
alternative label: vaccine liquid diluent
in subset: vaccine component

pCMVI.UBF3/2 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCMV-3FUB DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCMV-int DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCMV-LacZ DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

hypersensitivity to antibiotic
type: Class
subclass of: vaccine contraindication
term editor: Oliver He
in subset: disposition

hypersensitivity to neomycin
type: Class
subclass of: hypersensitivity to antibiotic
term editor: Oliver He
in subset: disposition

hypersensitivity to polymyxin
type: Class
subclass of: hypersensitivity to antibiotic
term editor: Oliver He
in subset: disposition

reaction to previous vaccination
type: Class
subclass of: vaccine contraindication
term editor: Oliver He
in subset: disposition

vaccine powder
type: Class
subclass of: vaccine component
definition: a vaccine component that contains the solid form of all vaccine components. A vaccine can be reconstituted by mixing vaccine powder with vaccine solvent.
term editor: Oliver He
in subset: vaccine component

bacterial vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: bacterial vaccine
definition: A vaccine preparation that results in the generation of a bacterial vaccine
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine preparation

pCMV-LIC DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCMVLuc DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pCR3 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

life-threatening reaction to previous vaccination
type: Class
subclass of: reaction to previous vaccination
term editor: Oliver He
in subset: disposition

pCR3.1 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

life-threatening reaction to previous influenza vaccination
type: Class
subclass of: life-threatening reaction to previous vaccination
term editor: Oliver He
in subset: disposition

pCR4-TOPO DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

hypersensitivity to gentamicin
type: Class
subclass of: hypersensitivity to antibiotic
term editor: Oliver He
in subset: disposition

vaccine dominant epitope
type: Class
subclass of: VO_0000811
term editor: Oliver He
alternative label: dominant epitope in vaccine
in subset: material entity

vaccine-induced down-regulated gene expression
type: Class
subclass of: vaccine-induced gene response
term editor: Oliver He
in subset: vaccine-induced response

hypersensitity to gelatin
type: Class
subclass of: vaccine contraindication
term editor: Oliver He
in subset: disposition

inactivated vaccine preparation using heat inactivation
type: Class
subclass of: inactivated vaccine preparation
definition: A vaccine prepraration process that is performed by heat inactivation of virulent pathogen.
term editor: Oliver He
in subset: vaccine preparation

CFU reduction assay
type: Class
subclass of: assay
definition: CFU reduction assay is an assay that measures the reduction of the colony forming units of infected pathogens in vaccine-vaccinated animals compared to nonvaccinated animals.
term editor: Oliver He
in subset: assay

assay of CFU reduction in spleen
type: Class
subclass of: CFU reduction assay
definition: assay of CFU reduction in spleen is a CFU reduction assay that is measured using the extracted spleen as the tissue for isolation of infected pathogens.
term editor: Oliver He
in subset: assay

hypersensitity to arginine
type: Class
subclass of: vaccine contraindication
editor note: Arginine is a conditionally essential amino acid, meaning most of the time it can be manufactured by the human body, and does not need to be obtained directly through the diet. The biosynthetic pathway however does not produce sufficient arginine, and some must still be consumed through diet. Individuals who have poor nutrition or certain physical conditions may be advised to increase their intake of foods containing arginine. Infants are unable to meet their requirements and thus arginine is nutritionally essential for infants.
term editor: Oliver He
in subset: disposition

edibility
type: Class
subclass of: physical object quality
definition: A physical quality inhering in a bearer by virtue of the bearer being fit to be eaten.
editor note: Melanie has submitted this term and its two subclasses to obo: http://sourceforge.net/tracker/?func=detail&aid=2873643&group_id=76834&atid=595654
term editor: Melanie Courtot
term editor: Oliver He
in subset: quality

edible
type: Class
subclass of: edibility
definition: A quality of edibility that inheres in a bearer by virtue of the bearer being suitable for oral ingestion as food, drug, or vaccine.
term editor: Oliver He
in subset: quality
comment: This term may be submitted to PATO.

vaccine efficacy
type: Class
subclass of: efficiency
definition: Vaccine efficacy is an efficacy of a vaccine in induction of protective immune response in vivo or protection against infection of a virulent pathogen. Specifically, vaccine efficacy (VE) is the percentage reduction in disease incidence attributable to vaccination, calculated by means of the following equation: VE(%) = (U - V)/U x 100 where U = the incidence in unvaccinated people and V = the incidence in vaccinated people. Ref: Hadler TC, et al. Immunization in developing countries. In: Vaccines. Editors: Plotkin S, et al. 2008. p1542-71.
term editor: Oliver He
in subset: quality

history of asthma
type: Class
subclass of: vaccine contraindication
term editor: Oliver He
in subset: disposition

vaccine-induced antiviral neutralizing antibody response
type: Class
subclass of: vaccine-induced humoral immune response
term editor: Oliver He
in subset: vaccine-induced response

pcREV DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pgp.LAMP-1 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
definition: A DNA vaccine plasmid vector that has the plasmid label pgp.LAMP-1. This plasmid has a CMV promoter and contains the human lysosomal-associated membrane protein-1 signal sequence.
term editor: Oliver He
term editor: Rebecca Racz
in subset: vaccine component
see also: PMID: 19356616

pDRVISV1.0 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pECK DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pES DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
definition: A DNA vaccine plasmid vector that has the plasmid label pES. This plasmid has a CMV promoter and contains a kanamycin resistance gene.
term editor: Oliver He
term editor: Rebecca Racz
in subset: vaccine component
see also: PMID: 19406186

usage of bronchodilator
type: Class
subclass of: vaccine contraindication
term editor: Oliver He
in subset: disposition

pET21a DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pET-28a DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pGA DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pGEX-3X DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine-induced follicular dendritic cell activation
type: Class
subclass of: vaccine-induced cell activation
term editor: Oliver He
in subset: vaccine-induced response

usage of steroid
type: Class
subclass of: vaccine contraindication
term editor: Oliver He
in subset: disposition

pIRES DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

sodB(Ft) vaccine
type: Class
subclass of: Francisella tularensis vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: tularemia
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Francisella tularensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: sodBFt is a live vaccine strain mutant of Francisella tularensis with reduced Fe-superoxide dismutase gene expression. Ref: PMID:18692537.
term editor: Oliver He
alternative label: sodB(Ft)
definition source: PMID:16923916
definition source: PMID:18692537
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=55
VIOLIN vaccine ID: 55
in subset: vaccine
comment: C57BL/6 mice were vaccinated intranasally (i.n.) with the sodB(Ft) mutant and challenged i.n. with lethal doses of F. tularensis SchuS4. SodB(Ft) vaccinated mice following SchuS4 challenge exhibited significantly reduced bacterial burden in lungs, liver and spleen, regulated production of pro-inflammatory cytokines and less severe histopathological lesions compared to the LVS vaccinated mice. The sodB(Ft) vaccination induced a potent humoral immune response and protection against SchuS4 required both CD4 and CD8 T cells in the vaccinated mice

fungal disease
type: Class
subclass of: disease
term editor: Oliver He
in subset: disposition

fungal vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Fungi
subclass of: VO_0005563
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Fungi
definition: A vaccine that targets against a fungus infection.
term editor: Oliver He
has cross-reference: MeSH: D005657
in subset: vaccine

Francisella tularensis vaccine LVS
type: Class
subclass of: Francisella tularensis vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: tularemia
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Francisella tularensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A live attenuated Francisella tularensis vaccine. It is available in American Type Culture Collection with ATCC ID: 29684.
term editor: Oliver He
alternative label: F. tularensis vaccine LVS
definition source: PMID:16912944
definition source: PMID:8757866
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=52
VIOLIN vaccine ID: 52
in subset: vaccine

pIRES2 DsRed2 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine-induced T cell interferon-gamma production
type: Class
subclass of: vaccine specific T cell cytokine production
in subset: vaccine-induced response

pING DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pJW24 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pJW4303 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pK0 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine function
type: Class
equivalent class: Class
  union of: preventive vaccine function
  union of: therapeutic vaccine function
subclass of: function
definition: To induce or modify protective or therapeutic immune response against a disease.
editor note: PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term.
term editor: Alan Ruttenburg
term editor: Allen Xiang
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Jie Zheng
term editor: Melanie Courtot
term editor: Oliver He
in subset: disposition

pK3 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pMV60 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pMAMneoBlue DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

herpesvirus vaccine vector
type: Class
subclass of: viral vaccine vector
definition: a viral vaccine vector that uses a herpesvirus as the vector.
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 10292

pMASIA DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pND DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine-induced gene response
type: Class
subclass of: vaccine-induced response
term editor: Oliver He
alternative label: vaccine-induced host gene response
in subset: vaccine-induced response

vaccine-induced immune response
type: Class
subclass of: vaccine-induced response
definition: An immune system process that is realized in the calibrated response of the recipient to a vaccine.
editor note: The definition of this term is based on the definition of 'immune response (GO:0006955)' . It is a child term of this GO term.
term editor: Asiyah Yu Lin
term editor: Oliver He
alternative label: vaccine-induced host immune response
in subset: vaccine-induced response

vaccine-induced response
type: Class
subclass of: process
subclass of: Restriction
  on property: has participant
  some values from: organism
subclass of: Restriction
  on property: has participant
  some values from: vaccine
definition: Process that specifies the organism's response to an administered vaccine.
term editor: Asiyah Yu Lin
term editor: Jie Zheng
term editor: Oliver He
alternative label: vaccine-induced host response
term tracker item: https://github.com/vaccineontology/VO/issues/781
in subset: process

host response to vaccine adjuvant
type: Class
subclass of: host response to vaccine component
definition: a process that specifies host response to a vaccine adjuvant.
term editor: Oliver He
in subset: process

host response to vaccine component
type: Class
subclass of: process
definition: Process that specifies host response to a vaccine component.
term editor: Oliver He
in subset: process

host response to vaccine antigen
type: Class
subclass of: host response to vaccine component
definition: a process that specifies host response to a vaccine antigen.
term editor: Oliver He
in subset: process

host response to vaccine vaccine vector
type: Class
subclass of: host response to vaccine component
definition: a process that specifies host response to a vaccine vector.
term editor: Oliver He
in subset: process

pND2 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pNGVL DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

human immunodeficiency virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Human immunodeficiency virus
subclass of: viral vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: acquired immunodeficiency syndrome
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human immunodeficiency virus
definition: A viral vaccine that protects against infection with human immunodeficiency virus that causes AIDS.
term editor: Oliver He
alternative label: AIDS vaccine
alternative label: HIV vaccine
in subset: vaccine

pNL3-gal DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pN4a-gal DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

company
type: Class
subclass of: organization
definition: A legal organization that represents an association of people with a specific objective.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Company
in subset: material entity

Brucella melitensis strain VTRM1 vaccine
type: Class
subclass of: VO_0001135
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. melitensis strain VTRM1
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=135
VIOLIN vaccine ID: 135
in subset: vaccine

pRc/CMV DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pRc/CMV2 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella suis strain VTRS1 vaccine
type: Class
subclass of: VO_0001136
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella suis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. suis VTRS1
alternative label: Brucella suis strain VTRS1
definition source: PMID:17428946
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=136
VIOLIN vaccine ID: 136
in subset: vaccine

pRK DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pRSV DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pRSV0 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

KKF24 vaccine
type: Class
subclass of: Francisella tularensis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tularemia
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Francisella tularensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: KKF24 is a recombinant strain of Francisella novicida U112 with iglC mutation (F. novicida delta-iglC::ermC). PMID:14680699.
term editor: Oliver He
term editor: Rebecca Racz
alternative label: KKF24
definition source: PMID:16552035
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=60
VIOLIN vaccine ID: 60
in subset: vaccine
comment: An iglC mutant is highly attenuated in mice. Inoculated mice were challenged 30 days later with wild type F. tularensis and were highly protected

Francisella tularensis vaccine LVS LPS
type: Class
subclass of: Francisella tularensis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tularemia
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Francisella tularensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: F. tularensis vaccine LVS LPS
alternative label: F. tularensis vaccine LVS lipopolysaccharide
definition source: PMID:10722593
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=58
VIOLIN vaccine ID: 58
in subset: vaccine

obsolete vaccine-induced antibody mediated immune response
type: Class
subclass of: Thing
term editor: Oliver He
has obsolescence reason: IAO_0000227
term replaced by: vaccine-induced humoral immune response
deprecated: true

vaccine emulsifier
type: Class
equivalent class: Class
  intersection of: vaccine component
  intersection of: Restriction
    on property: has role
    some values from: VO_0003025
subclass of: VO_0000850
subclass of: Restriction
  on property: has role
  some values from: VO_0003025
definition: a vaccine additive that stabilizes the vaccine emulsification manufacturing process and makes emulsion of the vaccine easier.
term editor: Asiyah Yu Lin
term editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/16337664
in subset: vaccine component
comment: Emulsifiers help bind ingredients together and keep them from separating, most commonly with oil and water. An emulsifier is also a surfactant that reduces the surface tension of a liquid and results in an easier, smoother spread. Reference: http://www.wisegeek.org/what-is-polysorbate-80.htm

Brucella melitensis lipopolysaccharide vaccine
type: Class
subclass of: VO_0001223
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has component
  some values from: lipopolysaccharide
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. melitensis lipopolysaccharide vaccine
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=137
VIOLIN vaccine ID: 137
in subset: vaccine

Brucella melitensis LPS-GBOMP noncovalent complex vaccine
type: Class
subclass of: VO_0001223
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. melitensis LPS-GBOMP noncovalent complex vaccine
alternative label: B. melitensis LPS-GBOMP subunit vaccine
definition source: PMID:8723881
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=307
VIOLIN vaccine ID: 307
in subset: vaccine

pSC65 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pSG2 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

inactivated vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: VO_0010008
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
definition: A whole organism vaccine that uses an inativated pathogen organism as its component.
term editor: Oliver He
alternative label: inactivated organism vaccine
alternative label: killed vaccine
in subset: vaccine

pSG5 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Psin DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pTARGET DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pTH DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pTHamp DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella abortus DNA vaccine encoding BCSP31, SOD and L7/L12
type: Class
subclass of: VO_0001225
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: expresses
  some values from: sodC from B. abortus strain 2308
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. abortus DNA vaccine expressing BCSP31, SOD and L7/L12
definition source: PMID:17570767
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=211
VIOLIN vaccine ID: 211
in subset: vaccine

pTR600 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella abortus conjugate vaccine using L7/L12
type: Class
subclass of: VO_0000956
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010928
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
term editor: Oliver He
alternative label: recombinant B. abortus L7/L12 vaccine
definition source: PMID:8873388
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=111
VIOLIN vaccine ID: 111
in subset: vaccine

pTVG4 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella melitensis DNA vaccine encoding Omp31
type: Class
subclass of: VO_0001226
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: expresses
  some values from: VO_0010939
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. melitensis DNA vaccine encoding Omp31
definition source: PMID:17428946
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=293
VIOLIN vaccine ID: 293
in subset: vaccine

pUC18 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pUC19 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pV1J DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Mycoplasma hyopneumoniae vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Mesomycoplasma hyopneumoniae
subclass of: Mycoplasma vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mesomycoplasma hyopneumoniae
definition: bacterial vaccine that protect against Mycoplasma hyopneumoniae infection
term editor: Asiyah Yu Lin
in subset: vaccine

inedible
type: Class
subclass of: edibility
definition: A quality of edibility that inheres in a bearer by virtue of the bearer being not suitable for oral ingestion.
term editor: Melanie Courtot
term editor: Oliver He
in subset: quality

pVCL(pCXN2-mVIN) DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

tertiary vaccination
type: Class
subclass of: boost vaccination
subclass of: Restriction
  on property: preceded by
  some values from: VO_0000903
definition: tertiary vaccination is a vaccination that is performed at the third time in a row.
term editor: Oliver He
term editor: Thom Todd
in subset: vaccination

Protozoa
type: Class
subclass of: Eukaryota
definition: Protozoa are a diverse group of unicellular eukaryotic organisms,[1] many of which are motile. Originally, protozoa had been defined as unicellular protists with animal-like behavior, e.g., movement. Protozoa were regarded as the partner group of protists to protophyta, which have plant-like behaviour, e.g., photosynthesis.(http://en.wikipedia.org/wiki/Protozoa)
term editor: Asiyah Yu Lin
in subset: organism

pVR1012 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine injection site
type: Class
subclass of: VO_0003247
definition: A vaccination site that is used for injection of a vaccine.
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: site

pVR1012x/s DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pWRG1644 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella melitensis bp26 deletion vaccine
type: Class
subclass of: VO_0001135
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: has gene mutation
  some values from: VO_0002561
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Ovis aries
definition: A B. melitensis vaccine that is recombinant B. melitensis Rev. 1 vaccine with the bp26 deletion. It has similar vaccine efficacy to Rev. 1. Its advantage compared to Rev. 1 is that this feature of bp26 deletion promotes diagnosis. PMID:17070627.
term editor: Oliver He
alternative label: B. melitensis bp26 deletion vaccine
alternative label: Brucella CGV26
alternative label: CGV26
definition source: PMID:16519974
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=295
VIOLIN vaccine ID: 295
in subset: vaccine

Francisella tularensis vaccine FSC043
type: Class
subclass of: Francisella tularensis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tularemia
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Francisella tularensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A spontaneous mutant of the SCHU S4 strain that protects against virulent F. tularensis infection.
term editor: Oliver He
alternative label: F. tularensis vaccine FSC043
definition source: PMID:16299332
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=57
VIOLIN vaccine ID: 57
in subset: vaccine

intramuscular route
type: Class
subclass of: route of administration
definition: A route of administration that inject the material(such as vaccines, allergens) directly into a muscle.
term editor: Asiyah Yu Lin
term editor: Oliver He
alternative label: intramuscular injection route
in subset: site

intranasal route
type: Class
subclass of: route of administration
definition: A rounte of administration that located in nose.
term editor: Oliver He
in subset: site

intranasal route by drop
type: Class
subclass of: intranasal route
term editor: Oliver He
in subset: site

intranasal route by spray
type: Class
subclass of: intranasal route
term editor: Oliver He
in subset: site

intraperitoneal route
type: Class
subclass of: route of administration
definition: A route of administration that located in the peritoneum.
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: site

Brucella melitensis WR201 vaccine
type: Class
subclass of: VO_0001135
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. melitensis WR201
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=308
VIOLIN vaccine ID: 308
in subset: vaccine

pWRG7077 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella abortus bacA mutant vaccine
type: Class
subclass of: VO_0001134
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. abortus bacA mutant
alternative label: Brucella abortus bacA mutant
definition source: PMID:17196866
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=301
VIOLIN vaccine ID: 301
in subset: vaccine

influenza A (H1N1) 2009 Monovalent vaccine (CSL Limited)
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001176
subclass of: VO_0003211
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H1N1 subtype
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000689
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=452
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm181975.htm
VIOLIN vaccine ID: 452
FDA vaccine indications: Active immunization of persons ages 6 months and older against influenza disease caused by pandemic (H1N1) 2009 virus.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM182401.pdf
vaccine STN: 125254
in subset: vaccine

influenza A (H1N1) 2009 Monovalent vaccine (MedImmune LLC)
type: Class
subclass of: USA licensed human vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001178
subclass of: VO_0003211
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has role
  some values from: VO_0010393
subclass of: Restriction
  on property: vaccinated in route
  some values from: intranasal route
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H1N1 subtype
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000694
term editor: Kallan Roan
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=456
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm181970.htm
VIOLIN vaccine ID: 456
FDA vaccine indications: Active immunization of individuals 2-49 years of age against influenza disease caused by pandemic (H1N1) 2009 virus.
vaccine package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM182406.pdf
vaccine STN: 125020
in subset: vaccine

live virulent vaccine role
type: Class
subclass of: vaccine role
definition: Vaccine role that is characteristic of a live virulent vaccine.
term editor: Jie Zheng
in subset: role

Adjumer vaccine adjuvant
type: Class
subclass of: VO_0001357
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005311
definition: A synthetic vaccine adjuvant that is PCPP salt.
term editor: Samantha G. Sayers
alternative label: Adjumer
alternative label: PCPP salt
alternative label: polyidi (carboxylatophenoxy) lphosphazene
alternative label: polyphosphazene
definition source: PMID:75551218
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

Megan Egg vaccine
type: Class
subclass of: licensed chicken vaccine
subclass of: prophylactic vaccine
subclass of: Salmonella vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Gallus gallus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Salmonella
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0001027
definition: Megan Egg is a Salmonella vaccine that that consists of a double gene-deleted S. enterica serovar Typhimurium strain and is formulated fro immunization of pullets. Megan Egg contains the same Megan Vac1 organism but Megan Vac1 is used for younger birds (broilers).
term editor: Oliver He
alternative label: Megan Egg
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=752
definition source: WEB: http://www.fda.gov/ohrms/dockets/dockets/00n0504/00N-0504_emc-001650-02.pdf
VIOLIN vaccine ID: 752
in subset: vaccine

pWRM DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

obsolete B. ovis microparticle subunit vaccine
type: Class
subclass of: Thing
term editor: Oliver He
definition source: PMID:16481077
has obsolescence reason: IAO_0000227
term tracker item: https://github.com/vaccineontology/VO/issues/697
term replaced by: VO_0004146
deprecated: true

pzz DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pME18100 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

pVIVO2 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

Brucella recombinant SurA protein vaccine
type: Class
subclass of: recombinant vector vaccine
subclass of: VO_0001221
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: Brucella rSurA protein vaccine
alternative label: Brucella recombinant SurA protein
definition source: PMID:17686554
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=445
VIOLIN vaccine ID: 445
in subset: vaccine

lentivirus vaccine vector
type: Class
subclass of: viral vaccine vector
definition: a viral vaccine vector that uses a lentivirus as the vector.
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 11646

pcDNA1.1/Amp DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

vaccine-induced leukocyte activation
type: Class
subclass of: vaccine-induced cell activation
term editor: Oliver He
in subset: vaccine-induced response

USA licensed human vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: FDA licensed vaccine role
subclass of: licensed human vaccine
subclass of: VO_0001485
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
definition: a licensed human vaccine that is licensed in the USA.
term editor: Oliver He
alternative label: FDA licensed vaccine
definition source: https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm093833.htm
in subset: vaccine

licensed vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: vaccine
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
definition: A vaccine that is licensed for commercial use.
term editor: Oliver He
in subset: vaccine

pRK7 DNA vaccine plasmid
type: Class
subclass of: DNA vaccine plasmid vector
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000023
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine component

lipopolysaccharide of pathogen organism as vaccine component
type: Class
subclass of: part of pathogen organism in vaccine
term editor: Oliver He
in subset: vaccine component

liposome-based vaccine adjuvant
type: Class
subclass of: VO_0001356
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005311
definition: A particulate antigen delivery system vaccine adjuvant that contains particles made up of concentric lipid membranes containing phospholipids and other lipids in a bilayer configuration separated by aqueous compartments. It is a relatively stable but non-covalently-bound complex of saponin adjuvant Quil-A, cholesterol and amphipathic antigen in a molar ratio of approximately 1:1:1. The spectrum of viral capsid antigens and non-viral amphipathic antigens of relevance for human vaccination, incorporated into ISCOMs, comprises influenza, measles, rabies, gp340 from EB-virus, gp120 from HIV, Plasmodium falciparum and Trypanosoma cruzi.
term editor: Oliver He
alternative label: Liposomes
definition source: http://www.vaccination.inoz.com/adjuvants.html
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

live attenuated vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: VO_0010038
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
definition: A vaccine that is made from microbes that have been attenuated (weakened) in the laboratory so that they can't cause disease.
term editor: Oliver He
alternative label: attenuated vaccine
in subset: vaccine

live vaccine organism
type: Class
equivalent class: Class
  intersection of: vaccine organism
  intersection of: Restriction
    on property: has quality
    some values from: VO_0001145
subclass of: vaccine organism
subclass of: Restriction
  on property: has quality
  some values from: VO_0001145
definition: a vaccine organism that is live
term editor: Oliver He
in subset: organism

live virulent vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: live virulent vaccine role
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: live virulent vaccine role
definition: Vaccine that uses a live, pathogenic (disease-causing) microorganism to stimulate the immune system.
term editor: Oliver He
in subset: vaccine

quaternary vaccination
type: Class
subclass of: boost vaccination
subclass of: Restriction
  on property: preceded by
  some values from: tertiary vaccination
definition: quaternary vaccination is a vaccination that is performed at the fourth time in a row.
term editor: Oliver He
term editor: Thom Todd
in subset: vaccination

profertility vaccine
type: Class
subclass of: vaccine
definition: A vaccine that is used to improve conception.
term editor: Oliver He
in subset: vaccine

Brucella recombinant DnaK protein vaccine
type: Class
subclass of: recombinant vector vaccine
subclass of: VO_0001221
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:17686554
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=292
VIOLIN vaccine ID: 292
in subset: vaccine

divalent DNA Brucella abortus vaccine using L7/L12 and Omp16
type: Class
subclass of: VO_0001225
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: divalent DNA B. abortus vaccine using L7/L12 and Omp16
definition source: PMID:16622210
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=302
VIOLIN vaccine ID: 302
in subset: vaccine

live attenuated vaccine preparation by gene mutant
type: Class
subclass of: live attenuated vaccine preparation
example of usage: 'Mycobacterium avium relA mutant vaccine' includes a gene mutation of relA from virulent Mycobacterium avium.
definition: A live attenuated vaccine prepraration process that is performed by mutation of a gene(s) from a virulent pathogen.
term editor: Allen Xiang
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: vaccine preparation

subtenon route
type: Class
subclass of: route of administration
definition: A route of administration that is through the membrane covering the muscles and nerves at the back of the eyeball
term editor: Asiyah Yu Lin
in subset: site

sublingual route
type: Class
subclass of: VO_0000886
definition: An oral route of administration that is underneath the tongue.
in subset: site

intravaginal route
type: Class
subclass of: route of administration
term editor: Asiyah Yu Lin
in subset: site

intravaginal vaccination
type: Class
subclass of: vaccination
subclass of: Restriction
  on property: occurs in
  some values from: intravaginal route
in subset: vaccination

subtenon vaccination
type: Class
subclass of: vaccination
subclass of: Restriction
  on property: occurs in
  some values from: subtenon route
in subset: vaccination
comment: YH

sublingual vaccination
type: Class
subclass of: VO_0003021
subclass of: Restriction
  on property: occurs in
  some values from: sublingual route
in subset: vaccination

pharyngeal mucosal vaccination
type: Class
subclass of: VO_0003021
subclass of: Restriction
  on property: occurs in
  some values from: VO_0000953
in subset: vaccination

vaccine-induced, adjuvant boosted T cell interferon-gramm production
type: Class
subclass of: vaccine-induced T cell interferon-gamma production
definition: a vaccine-induced T cell interferon-gramm production that results from the addition of a vaccine adjuvant
term editor: Oliver He
in subset: vaccine-induced response

IL-15 plasmid vaccine adjuvant
type: Class
subclass of: VO_0001342
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005309
term editor: Oliver He
definition source: PMID:18472194
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

Brucella abortus DNA vaccine encoding L7/L12 and P39
type: Class
subclass of: VO_0001225
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. abortus DNA vaccine encoding L7/L12 and P39
definition source: PMID:16537031
in subset: vaccine

attenuated Brucella abortus with deletion of znuA vaccine
type: Class
subclass of: VO_0001134
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: attenuated Brucella abortus with deletion of znuA
definition source: PMID:16790759
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=288
VIOLIN vaccine ID: 288
in subset: vaccine

mucosal immune response to vaccine
type: Class
subclass of: organ or tissue specific immune response to vaccine
term editor: Oliver He
in subset: vaccine-induced response

E. coli LT toxin derived vaccine adjuvant
type: Class
subclass of: microbial derivative vaccine adjuvant
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005311
definition: A microbial derivative vaccine adjuvant that is derived from E. coli heat labile toxin LT.
term editor: Josh Monickaraj
term editor: Oliver He
term editor: Samantha G. Sayers
definition source: PMID:12763689
definition source: PMID:21135101
definition source: PMID:29146379
in subset: vaccine adjuvant

Feline panleukopenia virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Feline panleukopenia virus
subclass of: viral vaccine
subclass of: VO_0001465
subclass of: Restriction
  on property: immunizes recipient
  some values from: Felis catus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Feline panleukopenia virus
definition: viral vaccine that is used to protect against Feline panleukopenia virus infection
term editor: Asiyah Yu Lin
in subset: vaccine

obsolete birds vaccine
type: Class
subclass of: Thing
definition: Vaccine that used for immunizing birds.
term editor: Asiyah Yu Lin
has obsolescence reason: IAO_0000227
term replaced by: VO_0001461
deprecated: true

Leptospira spp. vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Leptospira
subclass of: VO_0003553
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Leptospira
definition: Vaccine that protects against Leptospira spp. infection.
term editor: Asiyah Yu Lin
in subset: vaccine

Campylobacter fetus vaccine
type: Class
subclass of: Campylobacter vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Campylobacter fetus
definition: a Campylobacter bacterial vaccine that is used to protect against Campylobacter fetus infection
term editor: Asiyah Yu Lin
in subset: vaccine

Pseudomonas aeruginosa vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Pseudomonas aeruginosa
subclass of: Pseudomonas vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Pseudomonas aeruginosa
definition: bacterial vaccine that is used to protect against Pseudomonas aeruginosa infection
term editor: Asiyah Yu Lin
in subset: vaccine

Bordetella bronchiseptica vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Bordetella bronchiseptica
subclass of: Bordetella vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella bronchiseptica
definition: Bordetella bacterial vaccine that is used to protect against Bordetella bronchiseptica infection
term editor: Asiyah Yu Lin
in subset: vaccine

inactivated vaccine organism
type: Class
equivalent class: Class
  intersection of: vaccine organism
  intersection of: Restriction
    on property: has quality
    some values from: vaccine organism inactivated
subclass of: vaccine organism
subclass of: Restriction
  on property: has quality
  some values from: vaccine organism inactivated
term editor: Allen Xiang
term editor: Asiyah Yu Lin
term editor: Oliver He
alternative label: a vaccine organism that is inactived/killed
alternative label: killed vaccine organism
in subset: organism

licensed rabbit vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Oryctolagus cuniculus
subclass of: licensed vaccine
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Oryctolagus cuniculus
in subset: vaccine

neutralizing antibody role
type: Class
subclass of: antibody role
term editor: Oliver He
in subset: role

microencapsulated Brucella melitensis mutant vaccine
type: Class
subclass of: VO_0001135
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A live attenuated Brucella melitensis vaccine that is composed of live Brucella melitensis attenuated mutant vjbR::Tn5 (BMEII1116) delivered using a microsphere delivery system.
term editor: Oliver He
alternative label: microencapsulated B. melitensis mutant vaccine
definition source: PMID:18362129
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=304
VIOLIN vaccine ID: 304
in subset: vaccine
comment: The deletion of vjbR gene in Brucella melitensis strain 16M made a live attenuated vaccine and provided significance protection against mice

vaccine-induced T cell interferon-gramm production boosted by IL-15 vaccine adjuvant
type: Class
subclass of: vaccine-induced, adjuvant boosted T cell interferon-gramm production
definition: A vaccine-induced adjuvant boosted T cell interferon-gramm production that results from the addition of a IL-15 vaccine adjuvant
term editor: Oliver He
definition source: PMID: 18472194
in subset: vaccine-induced response

prime-boost vaccine
type: Class
subclass of: vaccine
definition: A vaccine that contains one vaccine for priming and at least one other vaccine for boosting.
term editor: Oliver He
term editor: Rebecca Racz
in subset: vaccine

prime-boost vaccine with DNA vaccine priming
type: Class
subclass of: DNA vaccine
subclass of: prime-boost vaccine
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
definition: A prime-boost vaccine that contains one DNA vaccine for priming and at least one other vaccine for boosting.
term editor: Oliver He
term editor: Rebecca Racz
in subset: vaccine

AIDSVAX vaccine
type: Class
subclass of: human immunodeficiency virus vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: acquired immunodeficiency syndrome
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human immunodeficiency virus
alternative label: AIDSVAX
definition source: PMID:12848591
definition source: http://en.wikipedia.org/wiki/AIDSVAX
in subset: vaccine

porin-S-LPS from Brucella abortus strain 2308 vaccine
type: Class
subclass of: VO_0001221
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: complex of porin and S-LPS from B. abortus strain 2308
alternative label: porin-S-LPS from B. abortus strain 2308
definition source: PMID:2844673
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=291
VIOLIN vaccine ID: 291
in subset: vaccine

Brucella abortus RB51WboA vaccine
type: Class
subclass of: VO_0001134
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. abortus RB51WboA
alternative label: Brucella abortus RB51WboA
definition source: PMID:15327798
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=13
VIOLIN vaccine ID: 13
in subset: vaccine

AIDSVAX B/B vaccine
type: Class
subclass of: AIDSVAX vaccine
subclass of: prophylactic vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: immunizes against disease
  some values from: acquired immunodeficiency syndrome
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human immunodeficiency virus
definition: The AIDSVAX that is bicovalent vaccine including two kinds of gp120 protein: MN rgp120/HIV-1 and GNE8 rgp120/HIV-1 (MN and GNE8 are strain names).
editor note: link to another well-known study: VAX004
editor note: linkto the clinical trail database by : ClinicalTrials.gov Identifier: NCT00002441
alternative label: AIDSVAX B/B
in subset: vaccine

AIDSVAX B/E vaccine
type: Class
subclass of: AIDSVAX vaccine
subclass of: prophylactic vaccine
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: immunizes against disease
  some values from: acquired immunodeficiency syndrome
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human immunodeficiency virus
alternative label: AIDSVAX B/E
in subset: vaccine

recombinant O. anthropi 49237SOD vaccine
type: Class
subclass of: VO_0000957
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has component
  some values from: bacterial vaccine vector
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: recombinant O. anthropi 49237SOD
definition source: PMID:11953393
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=113
VIOLIN vaccine ID: 113
in subset: vaccine

organ or tissue specific immune response to vaccine
type: Class
subclass of: vaccine-induced immune response
term editor: Oliver He
in subset: vaccine-induced response

licensed horse vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001472
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001472
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Equidae
term editor: Oliver He
in subset: vaccine

Pandemrix vaccine
type: Class
equivalent class: Class
  intersection of: influenza virus vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0021072
subclass of: prophylactic vaccine
subclass of: H1N1 influenza vaccine
subclass of: VO_0010415
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0001346
subclass of: Restriction
  on property: has component
  some values from: VO_0003036
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H1N1 subtype
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000690
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0021072
definition: Pandemrix is an influenza vaccine for influenza pandemics, such as the H1N1 2009 flu pandemic colloquially called the swine flu. The vaccine was developed by GlaxoSmithKline and patented in September 2006.
term editor: Asiyah Yu Lin
alternative label: Pandemrix H1N1
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=3957
definition source: http://en.wikipedia.org/wiki/Pandemrix
VIOLIN vaccine ID: 3957
in subset: vaccine
comment: ATC code:J07BB02
comment: As well as the active antigen derived from A/California/7/2009 (H1N1), the vaccine contains an immunologic adjuvant AS03 which consists of DL-alpha-tocopherol (vitamin E), squalene and polysorbate 80. Thiomersal (thimerosal) is added as a preservative. Being manufactured in chicken eggs, it contains trace amounts of egg proteins. Additional important non-medicinal ingredients are formaldehyde, sodium deoxycholate, and sucrose. (http://en.wikipedia.org/wiki/Pandemrix)

Brucella melitensis Bp26 and Tf protein vaccine
type: Class
subclass of: VO_0001223
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. melitensis Bp26 and Tf protein vaccine
alternative label: B. melitensis Bp26 and trigger factor
definition source: PMID:17239499
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=300
VIOLIN vaccine ID: 300
in subset: vaccine

Brucella melitensis P39 recombinant protein vaccine
type: Class
subclass of: recombinant vector vaccine
subclass of: VO_0001223
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010948
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A Brucella subunit vaccine that uses recombinant Brucella melitensis 16M P39, a putative periplasmic binding protein.
term editor: Oliver He
alternative label: B. melitensis P39 recombinant protein vaccine
definition source: PMID:11447155
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=198
VIOLIN vaccine ID: 198
in subset: vaccine

recombinant chimera BLSOmp31 vaccine
type: Class
subclass of: recombinant vector vaccine
subclass of: Brucella melitensis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: rBLSOmp31
alternative label: recombinant chimera BLSOmp31
definition source: PMID:17442465
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=212
VIOLIN vaccine ID: 212
in subset: vaccine

Panvax vaccine
type: Class
subclass of: H1N1 influenza vaccine
subclass of: VO_0003495
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H1N1 subtype
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000689
definition: Panvax is an H1N1 unadjuvanted monovalent vaccine.
term editor: Melanie Courtot
term editor: Oliver He
alternative label: Panvax
definition source: WEB: http://www.infowars.com/h1n1-panvax-training-powerpoint-received-by-health-care-workers-in-australia/
in subset: vaccine

vaccine additive role
type: Class
subclass of: vaccine component role
definition: A role inheres in a material entity, that has been added into a vaccine's formulation by the manufacture for a specific purpose. For example: adjuvant to enhance the effect of immunogen, perservatives, stablizers and those materials added for affecting PH and isotonicity.
term editor: Asiyah Yu Lin
term editor: Oliver He
definition source: Page 73, Chapter 6, Vaccine, 5th Edition. EXPERT CONSULT by Plotkin SA., et. al. 2008
in subset: role

intravenous route
type: Class
subclass of: route of administration
definition: A route of administration that is located in the vein
term editor: Oliver He
term editor: Thom Todd
in subset: site

protozoan vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Protozoa
subclass of: VO_0005563
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Protozoa
definition: A vaccine that protects against some protozoan disease.
term editor: Oliver He
alternative label: parasite vaccine
alternative label: parasitic vaccine
has cross-reference: MeSH: D016052
in subset: vaccine

Menactra injection 0.5mL vial
type: Class
subclass of: Menactra vaccine
subclass of: Restriction
  on property: has part
  some values from: VO_0015064
subclass of: Restriction
  on property: has part
  some values from: VO_0015066
subclass of: Restriction
  on property: has part
  some values from: VO_0015068
subclass of: Restriction
  on property: has part
  some values from: VO_0015071
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: FDA licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has component
  some values from: VO_0001256
subclass of: Restriction
  on property: has component
  some values from: VO_0003049
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: meningococcal meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Neisseria meningitidis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000700
term editor: Oliver He
alternative label: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine injection 0.5mL vial
definition source: WEB: http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm176044.htm
has cross-reference: SNOMEDCT: 416532007
has cross-reference: UMLS_CUI:C1563043
in subset: vaccine
comment: Product Name: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine injection 0.5mL vial
comment: Trade Name: Menactra

Varicella-zoster virus live vaccine
type: Class
subclass of: Varicella-zoster virus vaccine
subclass of: VO_0001220
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: chickenpox
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human alphaherpesvirus 3
definition: a Varicella-zoster virus vaccine that is live attenuated.
term editor: Oliver He
in subset: vaccine

pathogen organism component in vaccine
type: Class
equivalent class: Class
  intersection of: vaccine component
  intersection of: Class
    union of: organism
    union of: Restriction
      on property: part of
      some values from: organism
subclass of: vaccine component
definition: a vaccine component that originates from an organism such as a pathogen or a modified organism.
term editor: Oliver He
in subset: vaccine component

Brucella abortus pcDNA-BLS
type: Class
subclass of: VO_0001225
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: expresses
  some values from: VO_0010927
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. abortus pcDNA-BLS
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=199
VIOLIN vaccine ID: 199
in subset: vaccine

melanoma vaccine
type: Class
equivalent class: Class
  intersection of: cancer vaccine
  intersection of: Restriction
    on property: immunizes against disease
    some values from: melanoma
subclass of: cancer vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: melanoma
definition: A cancer vaccine that is used against melanoma, a malignant tumor of melanocytes.
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Melanoma
has cross-reference: SNOMEDCT:373869007
has cross-reference: UMLS_CUI:C0796561
in subset: cancer vaccine

escheriosome-mediated delivery of Brucella abortus L7/L12 vaccine
type: Class
subclass of: VO_0001221
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: escheriosome-encapsulated B. abortus L7/L12
alternative label: escheriosome-mediated delivery of B. abortus L7/L12
definition source: PMID:17931756
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=298
VIOLIN vaccine ID: 298
in subset: vaccine

polyvalent pneumococcal vaccine
type: Class
subclass of: prophylactic vaccine
subclass of: Canada licensed human vaccine
subclass of: VO_0010453
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: has component
  some values from: VO_0000888
subclass of: Restriction
  on property: has component
  some values from: VO_0001254
subclass of: Restriction
  on property: immunizes against disease
  some values from: Streptococcus pneumonia
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Streptococcus pneumoniae
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000699
definition: a pneumococcal vaccine that is formed using polyvalent polysaccharides
term editor: Oliver He
definition source: WEB: http://www.who.int/vaccines/en/pneumococcus.shtml
in subset: vaccine
comment: The most common form of the polyvalent pneumococcal vaccine is called the protein-polysaccharide combinations which is known as conjugate vaccines and contain 7-11 selected polysaccharides bound to a protein carrier. The protein-polysaccharide combinations are able to induce a T-cell dependent immune response. These vaccines are likely to be protective even in children under two years of age, and may reduce pneumococcal transmission through a herd effect.

Staphylococcus toxoid vaccine
type: Class
subclass of: toxoid vaccine
subclass of: VO_0000770
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Staphylococcus
term editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/10700309
in subset: vaccine
comment: a Staphyloccoccus vaccine that is made using engineered toxoid.

period of persistence of vaccine induced immune response
type: Class
subclass of: one-dimensional temporal region
definition: period of persistence of vaccine induced immune response is a temporal interval during which a vaccine-induced immune response continuously exists. This term is related to the process 'persistence of vaccine induced immune response'.
term editor: Melanie Courtot
term editor: Oliver He
in subset: temporal region

phase 1 vaccine trial
type: Class
subclass of: vaccine clinical trial
definition: A vaccine clinical trial that investigates the safety profile of a vaccine in a small group (10-50) of healthy volunteers.
term editor: Oliver He
in subset: process

phase 2 vaccine trial
type: Class
subclass of: vaccine clinical trial
definition: A vaccine clinical trial that studies vaccine efficacy with a target population (numbering 50-100). Different dosage levels will also be explored at this stage to determine the optimum dose.
term editor: Oliver He
in subset: process

phase 3 vaccine trial
type: Class
subclass of: vaccine clinical trial
definition: A vaccine clinical trial that takes the trial to a large-scale safety and efficacy study in a relevant patient population, usually in excess of 3,000.
term editor: Oliver He
in subset: process

phase 4 vaccine trial
type: Class
subclass of: vaccine clinical trial
definition: The final stage of vaccine clinical evaluation. Phase IV occurs after a vaccine or therapy is licensed and is being used by large numbers of people. These studies are not always required or completed.
term editor: Oliver He
in subset: process

Francisella tularensis DNA vaccine rLm/iglC
type: Class
subclass of: DNA vaccine
subclass of: Francisella tularensis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: expresses
  some values from: VO_0011072
subclass of: Restriction
  on property: immunizes against disease
  some values from: tularemia
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Francisella tularensis
definition: Seven F. tularensis proteins including IglC (rLm/iglC) were expressed in recombinant L. monocytogenes (rLm) vaccines. These 7 F. tularensis proteins are: AcpA, Bfr, DnaK, GroEL, IglC, Pld and KatG from SchuS4 strain.
term editor: Allen Xiang
term editor: Oliver He
alternative label: F. tularensis DNA vaccine rLm/iglC
alternative label: rLm/iglC
alternative label: rLm/iglC vaccine
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=929
VIOLIN vaccine ID: 929
in subset: vaccine

Nontypeable Haemophilus influenzae Hap protein vaccine
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has component
  some values from: VO_0010916
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A subunit nontypeable H. influenzae vaccine that uses Hap protein.
term editor: Oliver He
alternative label: nontypeable H. influenzae Hap protein vaccine
definition source: PMID:15557618
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=170
VIOLIN vaccine ID: 170
in subset: vaccine

vaccinia virus vaccine
type: Class
subclass of: Smallpox virus vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: smallpox
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Variola virus
definition: Smallpox virus vaccine that uses vaccinia virus. The vaccine is made from a laboratory strain of the live vaccinia virus that has been attenuated, or weakened, so that it stimulates an immune response without causing the severe disease associated with smallpox.
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Vaccinia
in subset: vaccine
comment: Vaccinia virus is well known for its role as a vaccine that helped eradicate the smallpox disease, making it the first human disease to be successfully eradicated by science.

Mixed Bacterial Vaccine
type: Class
subclass of: VO_0007657
subclass of: Restriction
  on property: has function
  some values from: therapeutic vaccine function
subclass of: Restriction
  on property: has role
  some values from: vaccine in clinical trial role
subclass of: Restriction
  on property: immunizes against disease
  some values from: cancer
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
definition: Mixed Bacterial Vaccine (MBV, Coley's Toxins) is a historical, vaguely defined preparation of heat-inactivated Streptococcus pyogenes and Serratia marcescens used as non-specific immunotherapy in the treatment of cancer.
term editor: Oliver He
definition source: PMID:22847809
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=6314
VIOLIN vaccine ID: 6314
in subset: cancer vaccine

DNA vaccine plasmid vector
type: Class
subclass of: VO_0003674
definition: Vaccine vector that is a DNA plasmid used to deliver the genetic code into the cells within the body.
term editor: Oliver He
in subset: vaccine component

Brucella melitensis DNA vaccine encoding Omp31 boosted with Omp31
type: Class
subclass of: VO_0001226
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. melitensis DNA vaccine encoding Omp31 boosted with Omp31
alternative label: pCIBLSOmp31
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=446
VIOLIN vaccine ID: 446
in subset: vaccine

Moraxella bovis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Moraxella bovis
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Moraxella bovis
definition: Vaccine that protects against Moraxella bovis infection. Moraxella bovis is a Gram-negative, aerobic, oxidase-positive diplococcus that is implicated in infectious bovine keratoconjunctivitis, an eye disease of cattle, also colloquially known as Pink Eye.
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Moraxella_bovis
in subset: vaccine

Moraxella bovis bacterin vaccine
type: Class
subclass of: Moraxella bovis vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Moraxella bovis
definition: a Moraxella bovis vaccine that is prepared using a bacterial bacterin.
term editor: Oliver He
in subset: vaccine

USDA licensed vaccine role
type: Class
subclass of: VO_0000812
definition: a USA licensed vaccine role that indicates the vaccine is for veterinary uses.
term editor: Oliver He
in subset: role

vaccine approval process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: licensed vaccine
example of usage: WEB: http://news.prnewswire.com/ViewContent.aspx?ACCT=109&STORY=/www/story/09-15-2009/0005094621&EDATE @2009/10/06
example of usage: WEB: http://www.examiner.com/x-7707-Infectious-Disease-Examiner~y2009m9d15-News-Release-H1N1-vaccines-get-FDA-approval-expected-to-be-available-in-4-weeks @2009/10/06. H1N1 vaccines get FDA approval. Food and Drug Administration announced today that it has approved four vaccines against the 2009 H1N1 influenza virus. Obtaining FDA licensure of this vaccine for A (H1N1) pandemic response is a key milestone that will enable Sanofi Pasteur to provide a licensed vaccine to the U.S. government to support pandemic immunization efforts
definition: vaccine approval process is a processual entity that involves approval of a vaccine.
term editor: Alan Ruttenburg
term editor: Allen Xiang
term editor: Melanie Courtot
term editor: Oliver He
alternative label: vaccine product approval process
definition source: WEB: http://energycommerce.house.gov/images/stories/Documents/PDF/publications/109_health.pdf @2009/10/06. This is the US Health Law which includes a section about vaccine.
definition source: WEB: http://www.hhs.gov/nvpo/factsheets/fs_tableII_doc2.htm @2009/10/06 #Following the FDA's review of a license application, the sponsor and the FDA may present their findings to the FDA's Vaccines and Related Biological Products Advisory Committee (VRBPAC). This non-FDA expert committee (scientists, physicians, biostatisticians, and a consumer representative) provides advice to the Agency regarding the safety and efficacy of the vaccine for the proposed indication.
in subset: process

vaccine candidate role
type: Class
subclass of: role
definition: Role of a material entity in an investigation, which has not been experimentally or clinically verified to induce a protection or treatment in vivo in a recipient organism.
editor note: This role should be a subclass of 'test substance role', which will be mireoted from OBI by OntoFox.
term editor: Bjoern Peters
term editor: Oliver He
in subset: role

CFU measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: colony forming unit
definition: CFU measurement assay is an assay that measures the colony forming unit (CFU) of a bacterium in a specific location (e.g., spleen of a mouse).
term editor: Melanie Courtot
term editor: Oliver He
in subset: assay

vaccine effectiveness rate
type: Class
subclass of: measurement datum
definition: A measurement datum that measues the vaccine effectiveness. It is assessed with respect to prevention of the disease against which the vaccine is given. One simple method to estimate vaccine effectiveness is to use routine data on notifications of disease cases in vaccinated and unvaccinatted children and to compare the porportion of cases vaccinated with the vaccine covervage among the same age group in the general population. If p is the proportion vaccinated in the population and c is the proportion of cases reported to be vaccinated, then VE = (p-c)/p(1-c) x 100%.
term editor: Melanie Courtot
term editor: Oliver He
definition source: Hadler TC, et al. Immunization in developing countries. In: Vaccines. Editors: Plotkin S, et al. 2008. p1542-71.
definition source: WEB: http://en.wikipedia.org/wiki/Influenza_vaccine
in subset: data item

vaccine licensing
type: Class
subclass of: vaccine approval process
definition: vaccine licensing is a vaccine approval process that involves in licensing a vaccine.
term editor: Allen Xiang
term editor: Oliver He
in subset: process

licensed chicken vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001468
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed bird vaccine
subclass of: VO_0001468
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Gallus gallus
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine

poxvirus vaccine vector
type: Class
subclass of: viral vaccine vector
definition: a viral vaccine vector that uses an poxvirus as the vector.
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 10240

Salmonella paratyphi vaccine
type: Class
subclass of: Salmonella vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Salmonella
definition: a Salmonella vaccine against infection with S. paratyphi, which causes paratyphoid fevers. Paratyphoid fevers are a group of enteric illnesses caused by serotypic strains of the Salmonella genus of bacteria, S. Paratyphi.
alternative label: paratyphoid vaccine
definition source: WED: http://en.wikipedia.org/wiki/Paratyphoid_fever
in subset: vaccine

Moraxella Bovis Bacterin Piliguard Pinkeye-1 trivalent vaccine
type: Class
subclass of: Moraxella bovis bacterin vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Moraxella bovis
subclass of: Restriction
  on property: is_manufactured_by
  has value: VO_0000893
term editor: Oliver He
alternative label: Moraxella Bovis Bacterin Piliguard Pinkeye-1 Trivalent
definition source: WEB: http://www.jefferspet.com/%252332moraxella-bovis-bacterin-piliguard-pinkeye-1-trivalent/camid/liv/cp/16435/
in subset: vaccine

NPAP Brucella vaccine
type: Class
subclass of: Brucella abortus vaccine
subclass of: VO_0001214
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: Brucella vaccine using nonpathogenic alphaproteobacteria
definition source: PMID:17715332
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=275
VIOLIN vaccine ID: 275
in subset: vaccine

Parainfluenza 3 virus vaccine
type: Class
subclass of: Parainfluenza virus vaccine
definition: A viral vaccine that protects against infection with Parainfluenza 3 virus.
term editor: Oliver He
in subset: vaccine

preventive vaccine function
type: Class
subclass of: vaccine function
subclass of: Restriction
  on property: realized in
  some values from: vaccination
subclass of: Restriction
  on property: realized in
  some values from: induction of adaptive immune response to antigen
subclass of: Restriction
  on property: realized in
  some values from: disorder prevention
definition: A vaccine function realized by the process of vaccination and leading to induction of an adaptive immune response to prevent a specific disorder.
term editor: Jie Zheng
term editor: Oliver He
alternative label: prophylactic vaccine function
in subset: disposition

prime boost regimen
type: Class
subclass of: vaccination protocol
term editor: Oliver He
in subset: information content entity

APEC vaccine using GST-Iss fusion protein
type: Class
subclass of: VO_0001156
editor note: Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is a major problem for the poultry industry in the world.
term editor: Oliver He
definition source: PMID:16863080
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=134
VIOLIN vaccine ID: 134
in subset: vaccine

prophylactic vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has function
    some values from: preventive vaccine function
subclass of: vaccine
definition: a vaccine that is used for prevention against a disease.
term editor: Oliver He
in subset: vaccine

protection efficacy
type: Class
subclass of: efficiency
definition: Protection efficacy is an efficiency that is associated with protection by a biological product (e.g., vaccine) against a disease.
term editor: Oliver He
in subset: quality

protective antigen role
type: Class
subclass of: antigen role
definition: An antigen that stimulates protective immunity when used in vivo.
term editor: Oliver He
in subset: role

E. coli LB-T vaccine
type: Class
subclass of: Escherichia coli vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: E. coli heat-labile enterotoxin B-subunit (LB-T) vaccine
definition source: PMID:11500434
in subset: vaccine

E. coli O157:H7 subunit vaccine expressing Esps and Tir
type: Class
subclass of: E. coli subunit vaccine
subclass of: VO_0001466
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010940
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
term editor: Oliver He
definition source: PMID:14670317
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=274
VIOLIN vaccine ID: 274
in subset: vaccine

equine influenza vaccine
type: Class
equivalent class: Class
  intersection of: influenza virus vaccine
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Equus caballus
subclass of: influenza virus vaccine
subclass of: VO_0001472
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Equus caballus
definition: an influenza virus vaccine against equine influenza viral infection
term editor: Oliver He
in subset: vaccine

avian influenza vaccine
type: Class
equivalent class: Class
  intersection of: influenza virus vaccine
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Aves
subclass of: influenza virus vaccine
subclass of: VO_0001461
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes recipient
  some values from: Aves
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: unidentified influenza virus
definition: An influenza vaccine for avian use
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: vaccine

Coxiella burnetii vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Coxiella burnetii
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against disease
  some values from: Q fever
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Coxiella burnetii
definition: Bacterial vaccine against infection with Coxiella burnetii which causes Q fever
term editor: Oliver He
alternative label: Q fever vaccine
definition source: WEB: http://en.wikipedia.org/wiki/Q_fever
in subset: vaccine

protein of pathogen organism as vaccine component
type: Class
subclass of: part of pathogen organism in vaccine
term editor: Oliver He
in subset: vaccine component

Staphylococcus aureus bacterin vaccine
type: Class
subclass of: VO_0002502
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Staphylococcus aureus
definition: a S. aureus vaccine that uses bacterin as the protective antigen.
term editor: Oliver He
has cross-reference: SNOMEDCT: 52974007
has cross-reference: UMLS_CUI: C0310856
in subset: vaccine

soybean-expressed E. coli LTB vaccine
type: Class
subclass of: E. coli subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010943
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:17188785
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=125
VIOLIN vaccine ID: 125
in subset: vaccine

Staphylococcus aureus phage lysate vaccine
type: Class
subclass of: VO_0002502
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Staphylococcus aureus
definition: a S. aureus vaccine that uses the bacterial phage lysate as the protective antigen.
term editor: Oliver He
has cross-reference: SNOMEDCT: 34679007
has cross-reference: UMLS_CUI: C0311044
in subset: vaccine

Mycoplasma gallisepticum bacterin vaccine
type: Class
subclass of: VO_0000949
subclass of: VO_0001077
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycoplasmoides gallisepticum
definition: a Mycoplasma gallisepticum vaccine that uses bacterin as the protective antigen
term editor: Oliver He
in subset: vaccine

autogenous bacterin vaccine
type: Class
subclass of: bacterial vaccine
definition: a bacterial vaccine that uses bacterin from a bacterial strain isolated from a herd with a purpose to generate hard-specific vaccine.
term editor: Oliver He
definition source: WEB: http://addisonlabs.com/products/autogenous-bacterins.php
in subset: vaccine

autogenous poulty bacterin vaccine
type: Class
subclass of: autogenous bacterin vaccine
definition: an autogenous bacterin vaccine that is prepared for poultry use.
definition source: WEB: http://www.hygieialabs.com/autopoultry.html
in subset: vaccine

Nontypeable Haemophilus influenzae vaccine
type: Class
subclass of: VO_0012185
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: nontypeable Haemophilus influenzae
term editor: Oliver He
alternative label: nontypeable H. influenzae vaccine
in subset: vaccine

nontypeable Haemophilus influenzae
type: Class
subclass of: Haemophilus influenzae
definition: Nontypeable Haemophilus influenzae (NTHi) is a nonencapsulated Haemophilus influenzae (a gram-negative bacterium). It is the cause of a number of human respiratory tract diseases, such as otitis media, sinusitis, bronchitis, and pneumonia.
term editor: Oliver He
alternative label: NTHi
in subset: organism

Nontypeable Haemophilus influenzae rLP4/rLP6 and Moraxella catarrhalis UspA2 protein vaccine
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: has component
  some values from: VO_0010914
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
term editor: Oliver He
alternative label: non-typeable H. influenzae rLP4/rLP6 and Moraxella catarrhalis UspA2 protein vaccine
alternative label: rLP4/rLP6/UspA2
definition source: PMID:15308371
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=169
VIOLIN vaccine ID: 169
in subset: vaccine

killed nontypeable Haemophilus influenzae whole-cell vaccine
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
term editor: Oliver He
alternative label: killed nontypeable H. influenzae whole-cell vaccine
definition source: PMID:1859055
definition source: PMID:1953532
definition source: PMID:2184330
definition source: PMID:2867396
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=163
VIOLIN vaccine ID: 163
in subset: vaccine

animal Rabies vaccine
type: Class
subclass of: Rabies virus vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: rabies
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Lyssavirus rabies
definition: a Rabies virus vaccine against Rabies in animal
term editor: Oliver He
in subset: vaccine

human Rabies vaccine
type: Class
subclass of: Rabies virus vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: rabies
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Lyssavirus rabies
definition: a Rabies virus vaccine against Rabies in human
term editor: Oliver He
in subset: vaccine

E. coli vaccine using intimin polypeptide
type: Class
subclass of: E. coli subunit vaccine
subclass of: VO_0001466
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010944
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:14688094
definition source: PMID:17258324
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=122
VIOLIN vaccine ID: 122
in subset: vaccine

Nontypeable Haemophilus influenzae cell membrane vaccine (CM-Hi)
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: nontypeable H. influenzae cell membrane vaccine (CM-Hi)
definition source: PMID:10353870
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=194
VIOLIN vaccine ID: 194
in subset: vaccine

Nontypeable Haemophilus influenzae LOS-TT conjugate vaccine
type: Class
subclass of: conjugate vaccine
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Chinchillidae
term editor: Oliver He
alternative label: Nontypeable H. influenzae lipooligosaccharide-tetanus toxoid conjugate vaccine
alternative label: nontypeable H. influenzae LOS-TT conjugate vaccine
definition source: PMID:12706701
definition source: PMID:9353024
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=164
VIOLIN vaccine ID: 164
in subset: vaccine

E. coli subunit vaccine using IroN
type: Class
subclass of: E. coli subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:17145948
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=127
VIOLIN vaccine ID: 127
in subset: vaccine

recombinant protein vaccine preparation
type: Class
subclass of: subunit vaccine preparation
definition: A vaccine preparation process that uses recombinant molecular technology to prepare recombinant protein.
term editor: Oliver He
in subset: vaccine preparation

protein subunit vaccine
type: Class
subclass of: subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
definition: A subunit vaccine that is made using a part of whole organism as subunit for vaccine development.
term editor: Oliver He
in subset: vaccine

recombinant vector vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: recombinant vector vaccine role
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has component
  some values from: recombinant vaccine vector
definition: A vaccine that uses a modified virus or bacterium as the vector to deliver vaccine antigen(s) to the cells of the host body.
term editor: Oliver He
in subset: vaccine

E. coli subunit vaccine using CO393
type: Class
subclass of: E. coli subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010965
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:17145948
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=128
VIOLIN vaccine ID: 128
in subset: vaccine

chicken ovalbumin egg protein allergen
type: Class
subclass of: VO_0000912
definition: A chicken egg protein allergen where the protein allergen is ovalbumin, the main protein found in egg write, making up 60-65% of the total protein.
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Ovalbumin
in subset: material entity

typhoid live oral vaccine
type: Class
subclass of: prophylactic vaccine
subclass of: VO_0001217
subclass of: VO_0010451
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: typhoid fever
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Salmonella enterica subsp. enterica serovar Typhi
definition: a S. typhi vaccine that is live and orally administerred
term editor: Oliver He
CVX code: 25
OMOP concept ID: 40213242
CVX full vaccine name: typhoid vaccine, live, oral
in subset: vaccine

E. coli subunit vaccine using FyuA
type: Class
subclass of: E. coli subunit vaccine
subclass of: VO_0001466
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:14688094
definition source: PMID:17258324
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=126
VIOLIN vaccine ID: 126
in subset: vaccine

obsolete licensed human vaccine role
type: Class
subclass of: Thing
definition: A licensed vaccine role that is bears in a licensed human vaccine.
editor note: Discussed among Barry Smith, Anna Maria Masci, Jie Zheng and Oliver He. The vaccine recipient will be associate with vaccine directly rather than using the role.
term editor: Oliver He
has obsolescence reason: IAO_0000103
deprecated: true

immunization
type: Class
subclass of: process
definition: Process that results in an adaptive immune response to one or more antigens.
term editor: Allen Xiang
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Bjoern Peters
term editor: Jie Zheng
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
in subset: process

active immunization
type: Class
subclass of: immunization
definition: An immunization that involves the introduction of foreign molecules into a recipient body, in a way which causes the recipient to actively induce adaptive immunity against the immunization target.
term editor: Allen Xiang
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Jie Zheng
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
in subset: process

passive immunization
type: Class
subclass of: planned process
subclass of: immunization
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: immunization objective
definition: An immunization where pre-synthesized elements of the immune system are transferred to an organism so that the body does not need to produce these elements itself.
editor note: Currently, antibodies can be used for passive immunization. This method of immunization works very quickly. However, it is short lasting. The antibodies are naturally broken down. If there are no B cells to produce more antibodies, they will disappear.
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Jie Zheng
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
in subset: process

natural active immunization
type: Class
subclass of: active immunization
definition: natural active immunization is an active immunization that occur naturally when a person or animal comes in contact with antigens includeing microbes.
term editor: Allen Xiang
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
in subset: process

vaccine immunization
type: Class
subclass of: planned process
subclass of: immunization
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: VO_0001274
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
subclass of: Restriction
  on property: has_specified_input
  some values from: vaccine
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: immunization objective
definition: Immunization that is induced by a vaccine via vaccination process.
term editor: Allen Xiang
term editor: Anna Maria Masci
term editor: Barry Smith
term editor: Jie Zheng
term editor: Oliver He
alternative label: artificial active immunization
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
in subset: process

induction of adaptive immune response to antigen
type: Class
subclass of: active immunization
definition: induction of adaptive immune response to antigen is an active immunization process that results in induction of adaptive immune response to some antigens, for example, in a vaccine.
term editor: Allen Xiang
term editor: Oliver He
in subset: process

disorder prevention
type: Class
subclass of: process
definition: Process that prevents a disorder that is the physical basis of a disease.
term editor: Allen Xiang
term editor: Oliver He
in subset: process

disorder treatment
type: Class
subclass of: process
definition: Process that leads to treat a disorder that is the physical basis of a disease.
term editor: Allen Xiang
term editor: Oliver He
in subset: process

modification of adaptive immune response to antigen
type: Class
subclass of: active immunization
definition: modification of adaptive immune response to antigen is an active immunization process that results in modification of an adaptive immune response to some antigens, for example, in a therapeutic vaccine.
term editor: Allen Xiang
term editor: Oliver He
in subset: process

obsolete preventive infectious disease vaccine function
type: Class
subclass of: Thing
term editor: Allen Xiang
term editor: Oliver He
has obsolescence reason: IAO_0000226
deprecated: true

infection disorder prevention
type: Class
subclass of: disorder prevention
definition: infection disorder prevention is a process that prevents a disorder that is the physical basis of an infectious disease.
term editor: Allen Xiang
term editor: Oliver He
in subset: process

E. coli vaccine using verocytotoxin toxoid
type: Class
subclass of: VO_0000963
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:17145948
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=281
VIOLIN vaccine ID: 281
in subset: vaccine

Inactivated ETEC expressing CFA/I and CFA/II vaccine
type: Class
subclass of: VO_0000974
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
term editor: Oliver He
alternative label: Inactivated ETEC expressing CFA/I and CFA/II
definition source: PMID:1612730
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=286
VIOLIN vaccine ID: 286
in subset: vaccine

licensed sheep vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001476
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001476
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Ovis aries
term editor: Oliver He
in subset: vaccine

whole organism vaccine role
type: Class
subclass of: vaccine role
definition: a vaccine role that indicates the vaccine being a whole organism vaccine.
term editor: Oliver He
in subset: role

EHEC O157 subunit vaccine using his-tagged N-terminal intimin
type: Class
subclass of: E. coli subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
term editor: Oliver He
definition source: PMID:1612730
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=278
VIOLIN vaccine ID: 278
in subset: vaccine

vaccine organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: vaccine component role
subclass of: organism
subclass of: Restriction
  on property: has role
  some values from: vaccine component role
definition: an organism that is used as part of a vaccine
term editor: Oliver He
in subset: organism

obsolete Canada licensed veterinary vaccine role
type: Class
subclass of: Thing
definition: A Canada licensed vaccine role that indicates the vaccine is for veterinary uses.
editor note: Discussed among Barry Smith, Anna Maria Masci, Jie Zheng and Oliver He. The vaccine recipient will be associate with vaccine directly rather than using the role.
term editor: Oliver He
has obsolescence reason: IAO_0000103
deprecated: true

Diphtheria toxoid vaccine
type: Class
subclass of: toxoid vaccine
subclass of: Corynebacterium diphtheriae vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
definition: a diphtheria vaccine that uses diphtheria toxoid
term editor: Oliver He
in subset: vaccine

Nontypeable Haemophilus influenzae P5 peptide MVF/H3 vaccine
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Rattus
term editor: Oliver He
alternative label: nontypeable H. influenzae P5 peptide MVF/H3 vaccine
definition source: PMID:10603411
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=193
VIOLIN vaccine ID: 193
in subset: vaccine

Nontypeable Haemophilus influenzae rTbpB vaccine
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Rattus
term editor: Oliver He
alternative label: nontypeable H. influenzae rTbpB vaccine
definition source: PMID:10225866
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=195
VIOLIN vaccine ID: 195
in subset: vaccine

ETEC vaccine ACAM2007
type: Class
subclass of: E. coli live attenuated vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
definition: ACAM2007 is a vaccine candidate expressing CFA/II.
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=115
definition source: WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2095642/
VIOLIN vaccine ID: 115
in subset: vaccine

Pox vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Poxviridae
subclass of: viral vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Poxviridae
definition: a viral vaccine against a disease caused by a virus belong to Poxviridae.
in subset: vaccine

Quail pox vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Quailpox virus
subclass of: Pox vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Quailpox virus
definition: a Pox vaccine for Quail pox
term editor: Oliver He
in subset: vaccine

typhoid-paratyphoid vaccine
type: Class
subclass of: Salmonella vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Salmonella
definition: a Salmonella vaccine against both typhoid caused by S. typhi and paratyphoid caused by S. paratyphi.
term editor: Oliver He
in subset: vaccine

rough phenotype
type: Class
subclass of: bacterial phenotype
term editor: Oliver He
in subset: quality

human protein
type: Class
subclass of: protein
definition: a protein from human
term editor: Oliver He
in subset: protein

ETEC vaccine ACAM2017
type: Class
subclass of: E. coli live attenuated vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: has gene mutation
  some values from: VO_0010941
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
definition: ACAM2017 was derived from ACAM2007. Genes aroC, ompC, and ompF were deleted, while CS1 and pStrep were added.
term editor: Oliver He
definition source: PMID:17566016
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=117
definition source: WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2095642/
VIOLIN vaccine ID: 117
in subset: vaccine

Bacillus anthracis DNA vaccine encoding PA63
type: Class
subclass of: Bacillus anthracis vaccine
subclass of: DNA vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: expresses
  some values from: VO_0010872
subclass of: Restriction
  on property: immunizes against disease
  some values from: anthrax disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacillus anthracis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: DNA vaccine contains the gene fragment encoding AAs 173-764 of PA.
term editor: Oliver He
alternative label: B. anthracis DNA vaccine encoding PA63
definition source: PMID:9987172
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=23
VIOLIN vaccine ID: 23
in subset: vaccine

human ACPP
type: Class
subclass of: human protein
subclass of: VO_0001232
subclass of: Restriction
  on property: has role
  some values from: protective antigen role
term editor: Oliver He
in subset: protein
see also: GenBank: AC020633; Protein RefSeq: NP_001090

Bacillus anthracis DNA vaccine encoding PA83 and LF
type: Class
subclass of: Bacillus anthracis vaccine
subclass of: DNA vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: expresses
  some values from: VO_0010857
subclass of: Restriction
  on property: immunizes against disease
  some values from: anthrax disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacillus anthracis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Oryctolagus cuniculus
term editor: Oliver He
alternative label: B. anthracis DNA vaccine encoding PA83 and LF
definition source: PMID:15342913
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=30
VIOLIN vaccine ID: 30
in subset: vaccine

DAAV using PA and PGA vaccine
type: Class
subclass of: Bacillus anthracis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has component
  some values from: VO_0010872
subclass of: Restriction
  on property: immunizes against disease
  some values from: anthrax disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacillus anthracis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: DAAV using PA and PGA
definition source: PMID:12960361
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=24
VIOLIN vaccine ID: 24
in subset: vaccine

smooth phenotype
type: Class
subclass of: bacterial phenotype
term editor: Oliver He
in subset: quality

rPA with adjuvant nanoemulsion vaccine
type: Class
subclass of: Bacillus anthracis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: anthrax disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacillus anthracis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: rPA with adjuvant Nanoemulsion
definition source: PMID:17502384
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=309
VIOLIN vaccine ID: 309
in subset: vaccine

Mycobacterium tuberculosis arabinomannan-protein conjugate vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: conjugate vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: conjugate vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Oryctolagus cuniculus
term editor: Oliver He
alternative label: M. tuberculosis arabinomannan-protein conjugate
definition source: PMID:12922145
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=223
VIOLIN vaccine ID: 223
in subset: vaccine

subcutaneous route
type: Class
subclass of: route of administration
definition: A route of administration that is loacted in the hypodermis (subcutaneous tissue) region.
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: site

vaccine subdominant epitope
type: Class
subclass of: VO_0000811
term editor: Oliver He
alternative label: subdominant epitope in vaccine
in subset: material entity

subunit vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: subunit vaccine role
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
definition: A vaccine that is composed of a purified protein(s) or other antigenic determinant(s) from a disease-causing organism. A subunit vaccine does not include the whole organism of a pathogen, so the subunits have less risk of causing adverse reactions.
term editor: Oliver He
in subset: vaccine

recombinant Salmonella typhimurium secreting Mycobacterium tuberculosis ESAT-6 vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: recombinant vector vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010919
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: recombinant S. typhimurium secreting M. tuberculosis ESAT-6
definition source: PMID:11427279
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=176
VIOLIN vaccine ID: 176
in subset: vaccine

Ag85B and ESAT-6 fusion protein vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has component
  some values from: VO_0010919
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: Ag85B and ESAT-6 fusion protein
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=171
VIOLIN vaccine ID: 171
in subset: vaccine

equine EEV, VEV and WEV encephalomyelitis-influenza vaccine-tetanus toxoid
type: Class
subclass of: equine EEV, VEE & WEV encephalomyelitis-tetanus toxoid
subclass of: VO_0002422
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Venezuelan equine encephalitis virus
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: vaccine

time of survival of live vaccine inside host
type: Class
subclass of: one-dimensional temporal region
definition: time of survival of live vaccine inside host is a temporal interval during which a live vaccine survives inside a host organism. This entity is related to the process survival of live vaccine inside host.
term editor: Melanie Courtot
term editor: Oliver He
in subset: temporal region

equine EEV, VEE & WEV encephalomyelitis-tetanus toxoid
type: Class
equivalent class: Class
  intersection of: VO_0002420
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Venezuelan equine encephalitis virus
subclass of: VO_0001499
subclass of: VO_0002420
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Venezuelan equine encephalitis virus
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: vaccine

equine EEV, VEV and WEV encephalomyelitis-rhinopneumonitis-influenza vaccine-tetanus toxoid
type: Class
subclass of: equine EEV, VEE & WEV encephalomyelitis-tetanus toxoid
subclass of: VO_0002428
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Venezuelan equine encephalitis virus
term editor: Asiyah Yu Lin
in subset: vaccine

attenuated Mycobacterium bovis strain WAg539 vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: expresses
  some values from: VO_0010951
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: attenuated M. bovis strain WAg539
definition source: PMID:15784584
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=177
VIOLIN vaccine ID: 177
in subset: vaccine

human vaccinee
type: Class
subclass of: VO_0001374
subclass of: Restriction
  on property: part of
  some values from: human vaccinee
definition: a vaccinee that is a human being
in subset: organism

human vaccinee population
type: Class
subclass of: vaccinee population
subclass of: Restriction
  on property: has member
  some values from: human vaccinee
definition: a population of human beings who are vaccinated.
term tracker item: https://github.com/vaccineontology/VO/issues/630
in subset: material entity

vaccinee population
type: Class
subclass of: population
subclass of: Restriction
  on property: has member
  some values from: VO_0001374
definition: a population group that are vaccinated with a specific vaccine
term editor: Oliver He
alternative label: vaccinee group
term tracker item: https://github.com/vaccineontology/VO/issues/630
in subset: material entity

human vaccinee population at age 2-17 years old
type: Class
subclass of: human vaccinee population
subclass of: Restriction
  on property: has member
  some values from: human vaccinee at age 2-17 years old
in subset: material entity

bacterial phenotype
type: Class
subclass of: physical quality
term editor: Oliver He
in subset: quality

therapeutic vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has function
    some values from: therapeutic vaccine function
subclass of: vaccine
definition: A vaccine that is used for treatment for a disease.
term editor: Oliver He
in subset: vaccine

obsolete licensed veterinary vaccine role
type: Class
subclass of: Thing
definition: A licensed vaccine role that is bears in a licensed veterinary vaccine.
editor note: Discussed among Barry Smith, Anna Maria Masci, Jie Zheng and Oliver He. The vaccine recipient will be associate with vaccine directly rather than using the role.
term editor: Oliver He
has obsolescence reason: IAO_0000103
deprecated: true

attenuated Mycobacterium bovis strain WAg520 vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: attenuated M. bovis strain WAg520
definition source: PMID:10225931
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=179
VIOLIN vaccine ID: 179
in subset: vaccine

human vaccinee at age 2-17 years old
type: Class
subclass of: human vaccinee
subclass of: Restriction
  on property: part of
  some values from: human vaccinee at age 2-17 years old
in subset: material entity

titer
type: Class
subclass of: measurement datum
definition: A titer (or titre) is a measure of concentration. Titer testing employs serial dilution to obtain approximate quantitative information from an analytical procedure that inherently only evaluates as positive or negative. The titer corresponds to the highest dilution factor that still yields a positive reading; for example, positive readings in the first 8 serial twofold dilutions translate into a titer of 1:256.
term editor: Oliver He
definition source: WEB:http://en.wikipedia.org/wiki/Titer
in subset: data item

multivalent vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: VO_0010394
subclass of: vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0010394
definition: a vaccine that is designed to immunize against two or more strains of the same microorganism, or against two or more microorganisms.
term editor: Ningxian Fan
term editor: Oliver He
definition source: WEB: http://coastalcarolinaresearch.com/?p=679
in subset: vaccine

attenuated Mycobacterium bovis strain WAg522 vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: attenuated M. bovis strain WAg522
definition source: PMID:10225931
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=180
VIOLIN vaccine ID: 180
in subset: vaccine

recombinant nontypeable Haemophilus influenzae protein P6 vaccine with AdDP adjuvant
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: recombinant vector vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010915
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: recombinant nontypeable H. influenzae protein P6 with AdDP
definition source: PMID:15031801
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=189
VIOLIN vaccine ID: 189
in subset: vaccine

adamantylamide dipeptide vaccine adjuvant
type: Class
subclass of: VO_0001357
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005309
subclass of: Restriction
  on property: target receptor
  some values from: nucleotide-binding oligomerization domain-containing protein 2
definition: A synthetic vaccine adjuvant, adamantylamide dipeptide (AdDP) is the desmuramyl analog of MDP.
term editor: Oliver He
term editor: Samantha G. Sayers
alternative label: AdDP
definition source: PMID:8375945
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

toxin
type: Class
subclass of: molecular entity
definition: A toxin is a poisonous substance produced within living cells or organisms; man-made substances created by artificial processes are thus excluded.
term editor: Oliver He
in subset: material entity
comment: The term was first used by organic chemist Ludwig Brieger (1849-1919).[3] For a toxic substance not produced within living organisms, "toxicant" and "toxics" are also sometimes used.[citation needed]. Toxins can be small molecules, peptides, or proteins that are capable of causing disease on contact with or absorption by body tissues interacting with biological macromolecules such as enzymes or cellular receptors. Toxins vary greatly in their severity, ranging from usually minor and acute (as in a bee sting) to almost immediately deadly (as in botulinum toxin).-- from Wikipedia.

toxoid vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: VO_0000807
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
definition: A vaccine containing a toxoid, used to protect against toxins produced by certain bacteria. A toxoid (also called inactivated toxin) is a processed toxin that has been treated by chemical means, heat, or irradiation and is no longer capable of causing disease.
term editor: Oliver He
in subset: vaccine

therapeutic vaccine function
type: Class
subclass of: vaccine function
subclass of: Restriction
  on property: realized in
  some values from: vaccination
subclass of: Restriction
  on property: realized in
  some values from: disorder treatment
definition: A vaccine function realized the process of vaccination and leading to induction of an adaptive immune response to treat an existing specific disorder.
term editor: Jie Zheng
term editor: Oliver He
in subset: disposition

bacterial and viral combination vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Viruses
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Bacteria
subclass of: bacterial vaccine
subclass of: viral vaccine
subclass of: combination vaccine
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Viruses
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacteria
definition: a combination vaccine that is used against both bacterial and viral infections.
term editor: Oliver He
in subset: vaccine

Mycobacterium tuberculosis secA2 mutant vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: has gene mutation
  some values from: VO_0010950
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
term editor: Rebecca Racz
alternative label: M. tuberculosis secA2 mutant
definition source: PMID:17671656
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=222
VIOLIN vaccine ID: 222
in subset: vaccine
comment: Vaccination of mice and guinea pigs with a secA2 mutant significantly increased resistance to M. tuberculosis challenge compared with standard M. bovis bacille Calmette-Guerin vaccination

rBCG-Ag85A[Tokyo] vaccine
type: Class
subclass of: VO_0003130
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: expresses
  some values from: VO_0010936
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: rBCG-Ag85A[Tokyo]
definition source: PMID:17720625
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=236
VIOLIN vaccine ID: 236
in subset: vaccine

Vibrio vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Vibrio
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Vibrio
definition: Vaccine that protects against Vibrio infection.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Vibrio
in subset: vaccine

DNA vaccine Rv1806-1807
type: Class
subclass of: DNA vaccine
subclass of: Mycobacterium tuberculosis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
definition source: PMID:16520093
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=166
VIOLIN vaccine ID: 166
in subset: vaccine

Campylobacter vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Campylobacter
subclass of: bacterial vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Campylobacter
definition: A vaccine that protects against Campylobacter bacterial infectioni.
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine

vaccine-induced up-regulated gene expression
type: Class
subclass of: vaccine-induced gene response
term editor: Oliver He
in subset: vaccine-induced response

AAV vaccine vector
type: Class
subclass of: viral vaccine vector
definition: a viral vaccine vector that uses an AAV virus as the vector.
term editor: Oliver He
term editor: Shunzhou Deng
alternative label: Adeno-associated virus vector
definition source: PMID: 24702846; PMID: 24568220; PMID: 24660751; PMID: 24849042; PMID: 24742767; PMID: 24827459
in subset: vaccine component
see also: NCBI Taxonomy ID: 272636

vaccination protocol
type: Class
subclass of: protocol
subclass of: Restriction
  on property: is about
  some values from: vaccination
definition: vaccination protocol is the protocol of a vaccination procedure.
term editor: Oliver He
alternative label: vaccination schedule
in subset: information content entity

Chlamydia vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Chlamydia
subclass of: bacterial vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Chlamydia
definition: A vaccine that protects against Chlamydia bacterial infection.
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine

route of administration
type: Class
subclass of: site
definition: A path that is located in gross anatomical part of an organism (e.g., human) and is used for administering a vaccine, a drug, fluid, poison, or other substance into the body.
editor note: CDISC has a codelist: Rout of Administration. Desription from CDISC: The course by which a substance was administered in order to reach the site of action in the body. CDISC_SDTM_Route_of_Administration_Terminology
term editor: Asiyah Yu Lin
term editor: Oliver He
definition source: http://en.wikipedia.org/wiki/Route_of_administration
in subset: site

vaccine candidate
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has role
  some values from: vaccine candidate role
definition: vaccine candidate is a processed material that is designed to prevent or ameliorate a disorder in a target organism by modulating adaptive immune responses in that organism by administrating the vaccine.
editor note: During our call, we decided not to say vaccine candidate is an output of vaccine preparation, which may be reserved for vaccine alone. -- Aug 4, 2009.
term editor: Alan Ruttenburg
term editor: Allen Xiang
term editor: Bjoern Peters
term editor: Lindsay Cowell
term editor: Melanie Courtot
term editor: Oliver He
in subset: material entity

thimerosal vaccine preservative
type: Class
subclass of: VO_0000851
subclass of: Restriction
  on property: has part
  some values from: thimerosal
definition: vaccine preservative that has thimerosal as part.
term editor: Oliver He
in subset: vaccine component

peptide vaccine
type: Class
equivalent class: Class
  intersection of: subunit vaccine
  intersection of: Restriction
    on property: has role
    some values from: peptide vaccine role
subclass of: subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: peptide vaccine role
definition: A subunit vaccine that uses small peptide(s) as immunoepitopes.
term editor: Jie Zheng
term editor: Oliver He
alternative label: epitope vaccine
alternative label: peptide-based synthetic vaccine
definition source: https://en.wikipedia.org/wiki/Peptide_vaccine
in subset: vaccine

H1N1 influenza vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: H1N1 subtype
subclass of: influenza virus vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: influenza
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: H1N1 subtype
definition: H1N1 Influenza vaccine is an Influenza virus vaccine that is used to vaccinate against H1N1 Influenza subtype vaccine.
term editor: Oliver He
in subset: vaccine

Haemophilus somnus vaccine
type: Class
subclass of: Haemophilus vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Histophilus somni
definition: bacterial vaccine that is used to protect against Haemophilus somnus infection
term editor: Asiyah Yu Lin
in subset: vaccine

vaccine adjuvant
type: Class
equivalent class: Class
  intersection of: vaccine component
  intersection of: Restriction
    on property: has role
    some values from: vaccine adjuvant role
subclass of: VO_0000850
definition: A vaccine component is a chemical substance added to a vaccine to enhance and direct the immune response to a protective antigen. Vaccine adjuvants may cause a range of serious side-effects.
term editor: Oliver He
term editor: Paola Roncaglia
term tracker item: https://github.com/vaccineontology/VO/issues/809
in subset: vaccine adjuvant

H. influenzae gene
type: Class
subclass of: gene of Bacteria
term editor: Oliver He
in subset: gene

vaccine license application
type: Class
subclass of: vaccine regulation
definition: A vaccine regulatory process that is for vaccine producer to apply for vaccine license.
term editor: Oliver He
in subset: process

nontypeable H. influenzae gene hel (encoding P4)
type: Class
subclass of: H. influenzae gene
subclass of: VO_0001232
subclass of: Restriction
  on property: has role
  some values from: protective antigen role
editor note: Encodes for protein P4
term editor: Oliver He
in subset: gene

immune response detection assay
type: Class
subclass of: assay
definition: An assay that is used to detect the immune response of a host to vaccination of a vaccine.
term editor: Oliver He
in subset: assay

immunization objective
type: Class
subclass of: objective specification
definition: immunization objective is the specification of an objective to achieve immunization.
term editor: Allen Xiang
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
in subset: information content entity

multivalent vaccine against bacterial and viral diseases
type: Class
equivalent class: Class
  intersection of: multivalent vaccine
  intersection of: Class
    intersection of: Restriction
      on property: immunizes against pathogen
      some values from: Viruses
    intersection of: Restriction
      on property: immunizes against pathogen
      some values from: Bacteria
subclass of: multivalent vaccine
subclass of: bacterial and viral combination vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Viruses
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacteria
definition: a multivalent vaccine that is designed to immunize against at least one bacterial disease and one viral disease.
term editor: Ningxian Fan
term editor: Oliver He
in subset: vaccine

Bordetella vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Bordetella
subclass of: VO_0003532
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella
definition: a bacterial vaccine against infection of Bordetella bacterial infection
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Bordetella
in subset: vaccine

Mycobacterium tuberculosis phoP mutant SO2 vaccine
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
term editor: Rebecca Racz
alternative label: M. tuberculosis phoP mutant SO2
definition source: PMID:16564606
definition source: PMID:17084814
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=178
VIOLIN vaccine ID: 178
in subset: vaccine
comment: Study evaluated immunogenicity and protection against Mycobacterium tuberculosis in rhesus monkeys with an attenuated M. tuberculosis with a disrupted phoP gene (SO2) as a single-dose vaccine. SO2 treatment showed reduced average lung bacterial counts (1.0 and 1.2 log respectively, compared with 0.4 log for BCG) and significant protective effect by reduction in C-reactive protein levels, body weight loss, and decrease of erythrocyte-associated hematologic parameters (MCV, MCH, Hb, Ht) as markers of inflammatory infection, all relative to non-vaccinated controls

Aeromonas vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Aeromonas
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Aeromonas
definition: A bacterial vaccine that is used to protect against Aeromonas bacterial infection
term editor: Oliver He
in subset: vaccine

vaccine preparation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: VO_0001479
subclass of: Restriction
  on property: has_specified_output
  some values from: vaccine
definition: vaccine preparation is a manufacturing process to produce a vaccine.
term editor: Bjoern Peters
term editor: Oliver He
alternative label: vaccine generation
alternative label: vaccine production
in subset: process

vaccine protection assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: pathogen challenge
subclass of: Restriction
  on property: has part
  some values from: vaccination
subclass of: Restriction
  on property: has part
  some values from: VO_0001209
definition: An assay that is used to detect if a vaccine protects a host against infection of virulent pathogen after vaccine immunization.
term editor: Oliver He
alternative label: vaccine challenge experiment
in subset: assay

Mycobacterium vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Mycobacterium
subclass of: bacterial vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium
definition: Vaccine that protects against Mycobacterium bacterial infection.
term editor: Oliver He
term editor: Rebecca Racz
definition source: https://en.wikipedia.org/wiki/Mycobacterium
in subset: vaccine

vaccine specific T cell cytokine production
type: Class
subclass of: vaccine-induced T cell mediated immunity
term editor: Oliver He
in subset: vaccine-induced response

vaccine specific T cell mediated cytotoxicity
type: Class
subclass of: vaccine-induced T cell mediated immunity
term editor: Oliver He
in subset: vaccine-induced response

vaccine dose
type: Class
subclass of: dose
definition: A dose of vaccine specified by the vaccine manufacturer, distributor, or a regulatory agent.
term editor: Melanie Courtot
term editor: Oliver He
in subset: data item

vaccine clinical trial
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_input
  some values from: vaccine
definition: Planned process by which a vaccine is tested clinically for safety and effectiveness. Clinical trials are conducted in phases. Classically, clinical trials unfold in three phases in order to gather data and information about a vaccine and its performance. This will form the basis of a dossier submitted to regulatory authorities by way of an application for licensure. After a vaccine is licensed and is being used by large numbers of people, a Phase IV study may or may not be taken for vaccine clinical evaluation.
editor note: Most vaccines against a pathogen (e.g., HIV) are not tested by vaccinating people and then deliberately exposing them to virulent pathogen (e.g., HIV). This strategy is never for a vaccine against a disease as serious as HIV. The best way to determine if a vaccine is effective is to test it in a randomized, controlled, double-blind clinical trial. This type of trial is often referred to as the gold standard in medical research and provides the strongest evidence for the efficacy of a vaccine.
term editor: Oliver He
in subset: process

obsolete class
type: Class
subclass of: Thing
has obsolescence reason: IAO_0000226
deprecated: true

whole organism vaccine
type: Class
subclass of: VO_0005505
subclass of: Restriction
  on property: has role
  some values from: whole organism vaccine role
definition: A vaccine that uses whole organism as its component
term editor: Oliver He
definition source: WEB: http://onlinelibrary.wiley.com/doi/10.1038/npg.els.0000491/full
in subset: vaccine

recombinant vaccine vector
type: Class
equivalent class: Class
  intersection of: vaccine component
  intersection of: Restriction
    on property: has role
    some values from: recombinant vaccine vector role
subclass of: VO_0003674
subclass of: Restriction
  on property: has role
  some values from: recombinant vaccine vector role
definition: Vaccine vector that is a genetically engineered virus or bacterium used to deliver genetic code into the cells within the body.
editor note: a vaccine component that uses a microbe (e.g., bacterium, virus, and parasitic organism) as a vector that is inserted with the DNA(s) of a heterologous protective antigen(s) to generate a "recombinant vector vaccine". The microorganism used as a vector generally has a stable non or low pathogenic phenotype for the species the vaccine is intended for.
term editor: Jie Zheng
term editor: Oliver He
alternative label: recombinant vector
definition source: WEB: http://en.wikipedia.org/wiki/Vaccine
definition source: WEB: http://www.biosafety.be/GT/Regulatory/Veterinary_vaccines/EMEA_000404en.pdf
definition source: WEB: http://www.ema.europa.eu/docs/en_GB/document_library/Scientific_guideline/2009/09/WC500003856.pdf
in subset: vaccine component

vaccinia virus vector
type: Class
subclass of: VO_0001146
definition: an orthopoxvirus vaccine vector that uses vaccinia virus as the vector
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 10245

Yersinia vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Yersinia <enterobacteria>
subclass of: VO_0003533
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Yersinia <enterobacteria>
definition: Vaccine that protects against Yersinia bacterial infection.
term editor: Allen Xiang
term editor: Oliver He
in subset: vaccine

Edwardsiella vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Edwardsiella <enterobacteria>
subclass of: VO_0003551
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Edwardsiella <enterobacteria>
definition: A bacterial vaccine that is used to protect against Edwardsiella bacterial infection
term editor: Asiyah Yu Lin
in subset: vaccine

BCG mutant secreting listeriolysin
type: Class
subclass of: Mycobacterium tuberculosis vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: tuberculosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycobacterium tuberculosis
term editor: Oliver He
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=173
VIOLIN vaccine ID: 173
in subset: vaccine

Mycoplasma vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Mycoplasma
subclass of: bacterial vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mycoplasma
definition: Vaccine that protects against Mycoplasma bacterial infection.
term editor: Oliver He
in subset: vaccine

obsolete Canada licensed human vaccine role
type: Class
subclass of: Thing
definition: A Canada licensed vaccine role that indicates the vaccine is used for human
editor note: Discussed among Barry Smith, Anna Maria Masci, Jie Zheng and Oliver He. The vaccine recipient will be associate with vaccine directly rather than using the role.
term editor: Oliver He
has obsolescence reason: IAO_0000103
deprecated: true

delta ureC hly+ rBCG vaccine
type: Class
subclass of: VO_0001466
subclass of: VO_0003130
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
term editor: Oliver He
alternative label: delta ureC hly+ rBCG
definition source: PMID:16110326
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=437
VIOLIN vaccine ID: 437
in subset: vaccine

viral vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Viruses
subclass of: VO_0005504
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Viruses
definition: A vaccine that targets against a viral disease.
term editor: Oliver He
has cross-reference: MeSH: D014765
in subset: vaccine

viral vaccine vector
type: Class
subclass of: recombinant vaccine vector
definition: a vaccine vector that uses a virus as the vector.
term editor: Oliver He
in subset: vaccine component
see also: NCBI Taxonomy ID: 10239

Haemophilus parasuis vaccine
type: Class
subclass of: Haemophilus vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Glaesserella parasuis
definition: bacterial vaccine that is used to protect against Haemophilus parasuis infection
term editor: Asiyah Yu Lin
in subset: vaccine

vaccine organism virulent
type: Class
subclass of: virulence
definition: a virulence of vaccine that shows a virulent pheontype of the organism as the major component of a vaccine. The virulent phenotype means that an vaccine organism is virulent and is able to cause a pathogenic phenotype in a host organism.
term editor: Oliver He
in subset: quality

male biological sex datum
type: Class
subclass of: VO_0001194
example of usage: M' (intended to refer to a male biological sex), 'Male', 'Man', '1' (intended to refer to a male biological sex)
definition: A biological sex datum that represents the biological sex of an animal (including human) as being male.
term editor: Oliver He
term editor: Paul Fabry
in subset: data item

Nontypeable Haemophilus influenzae protein P6 with cholera toxin vaccine
type: Class
subclass of: Nontypeable Haemophilus influenzae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Rattus
term editor: Oliver He
alternative label: Nontypeable H. influenzae protein P6 with cholera toxin
definition source: PMID:15297063
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=188
VIOLIN vaccine ID: 188
in subset: vaccine

vaccine role
type: Class
subclass of: role
definition: Role that inheres in a prepared material entity that is designed to induce protection or treatment for a disease or infection.
term editor: Oliver He
in subset: role

animal model of vaccine research
type: Class
subclass of: role
definition: Animal model of vaccine research is a role played by some organism (e.g., mouse) that is used for vaccine research.
term editor: Oliver He
in subset: role

vaccine component role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Restriction
    on property: part of
    some values from: vaccine
definition: A role that inheres in a material entity that becomes an ingredient of a vaccine.
term editor: Oliver He
in subset: role

vaccine antigen role
type: Class
subclass of: vaccine component role
term editor: Oliver He
in subset: role

E. coli live attenuated vaccine
type: Class
equivalent class: Class
  intersection of: Escherichia coli vaccine
  intersection of: Restriction
    on property: has role
    some values from: VO_0010038
subclass of: Escherichia coli vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
in subset: vaccine

Pasteurella multocida vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Pasteurella multocida
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Pasteurella multocida
definition: Vaccine that protects against Pasteurella multocida infection.
term editor: Asiyah Yu Lin
in subset: vaccine

laboratory animal model of vaccine research
type: Class
subclass of: animal model of vaccine research
definition: Animal model of vaccine research is a role played by some organism (e.g., mouse) that is used for vaccine research in the laboratory.
term editor: Oliver He
in subset: role

vaccine protective antigen role
type: Class
subclass of: vaccine antigen role
definition: a vaccine antigen role that inheres in a vaccine antigen which is capable of inducing protective immunity.
term editor: Oliver He
in subset: role

DNA vaccine role
type: Class
subclass of: vaccine role
definition: A vaccine role that indicates the vaccine being a DNA vaccine.
term editor: Oliver He
in subset: role

subunit vaccine role
type: Class
subclass of: vaccine role
definition: A vaccine role that indicates the vaccine being a subunit vaccine.
term editor: Oliver He
in subset: role

conjugate vaccine role
type: Class
subclass of: vaccine role
definition: A vaccine role that indicates the vaccine being a conjugate vaccine.
term editor: Oliver He
in subset: role

survival assessment
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: organism
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition: Survival assessment is an assay that measures the occurence of death events in one or more organisms that are monitored over time.
editor note: Need to point out more specifically that survival/death is measured.
term editor: Oliver He
in subset: process

Haemophilus influenzae type b capsular polysaccharide vaccine
type: Class
subclass of: prophylactic vaccine
subclass of: VO_0001255
subclass of: VO_0010437
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: vaccinated in route
  some values from: intramuscular route
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
definition: A vaccine used to prevent infection by Haemophilus influenzae type b (Hib) bacteria. The vaccine works by causing your body to produce its own protection (antibodies) against the disease.
term editor: Oliver He
alternative label: H. influenzae Type b capsular polysaccharide vaccine
alternative label: Hib polysaccharide vaccine
definition source: PMID:335348
definition source: PMID:6387614
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=165
definition source: https://www.mayoclinic.org/drugs-supplements/haemophilus-b-polysaccharide-vaccine-intramuscular-route-injection-route/description/drg-20064142
VIOLIN vaccine ID: 165
in subset: vaccine

E. coli subunit vaccine
type: Class
equivalent class: Class
  intersection of: Escherichia coli vaccine
  intersection of: Restriction
    on property: has role
    some values from: subunit vaccine role
subclass of: Escherichia coli vaccine
subclass of: subunit vaccine
subclass of: Restriction
  on property: has role
  some values from: subunit vaccine role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Escherichia coli
definition: An E. coli vaccine that uses subunit antigen type.
in subset: vaccine

Bacillus anthracis recombinant vaccine using PA domain 4
type: Class
subclass of: Bacillus anthracis vaccine
subclass of: recombinant vector vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010872
subclass of: Restriction
  on property: immunizes against disease
  some values from: anthrax disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bacillus anthracis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. anthracis recombinant vaccine using PA domain 4
definition source: PMID:11854261
definition source: PMID:15935874
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=20
VIOLIN vaccine ID: 20
in subset: vaccine

licensed vaccine role
type: Class
subclass of: vaccine role
definition: A licensed vaccine role is a regulation-assigned role that indicates that a vaccine obtains official approval for commercial production and selling on the market.
term editor: Oliver He
in subset: role

vaccine in clinical trial role
type: Class
subclass of: vaccine role
definition: A vaccine in clinical trial role is a regulation-assigned role that inheres in a vaccine that is currently in clinical trial.
editor note: In medical research, clinical trials are conducted to allow safety and efficacy data to be collected for new drugs or devices.
term editor: Oliver He
in subset: role

vaccine-induced humoral immune response
type: Class
subclass of: vaccine-induced adaptive immune response
definition: Vaccine induced immue response mediated hrough a body fluid
term editor: Asiyah Yu Lin
alternative label: vaccine-induced antibody mediated immune response
in subset: vaccine-induced response

Brucella melitensis Rev. 1 with P39 deletion vaccine
type: Class
subclass of: VO_0001135
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
definition: A B. melitensis vaccine that is recombinant B. melitensis Rev. 1 vaccine with the p39 gene deletion.
term editor: Oliver He
alternative label: B. melitensis Rev. 1 P39 deletion mutant
alternative label: B. melitensis Rev. 1 with P39 deletion
definition source: PMID:9784574
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=448
VIOLIN vaccine ID: 448
in subset: vaccine

intravenous vaccination
type: Class
subclass of: vaccination
subclass of: Restriction
  on property: occurs in
  some values from: intravenous route
term editor: Asiyah Yu Lin
in subset: vaccination

licensed human vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Homo sapiens
subclass of: licensed vaccine
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
definition: a licensed vaccine with license for human use.
term editor: Oliver He
in subset: vaccine

recombinant vector vaccine role
type: Class
subclass of: vaccine role
definition: A vaccine role that indicates the vaccine being a recombinant vector vaccine.
term editor: Oliver He
in subset: role

Flavobacterium columnare vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Flavobacterium columnare
subclass of: bacterial vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Flavobacterium columnare
definition: bacterial vaccine that is used to protect against Flavobacterium columnare infection
term editor: Asiyah Yu Lin
in subset: vaccine

Clostridium vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Clostridium
subclass of: VO_0003554
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium
definition: A bacterial vaccine that protects against infection with Clostridium spp.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Clostridium
in subset: vaccine

Clostridium tetani vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Clostridium tetani
subclass of: Clostridium vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
definition: a Clostridium vaccine that protects against infection with Clostridium tetani that causes tenanus.
term editor: Kallan Roan
term editor: Oliver He
alternative label: Tetanus toxoid vaccine
alternative label: tetanus vaccine
definition source: https://vaccine-safety-training.org/tetanus-vaccine-example.html
in subset: vaccine

combination vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: combination vaccine role
subclass of: vaccine
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: immunizes against pathogen
  min qualified cardinality: 2
  on class: organism
definition: Combination vaccine is a vaccine that induces protection against multiple infectious diseases or several different serotypes of the same organism. The anitgens contained in combination vaccines are either formulated together by the manufacturer or physically mixed by a health care provider just prior to administration. Both approaches require licensure. Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1624.
term editor: Oliver He
alternative label: combo vaccine
term tracker item: https://github.com/vaccineontology/VO/issues/621
has cross-reference: MeSH: D017778
in subset: vaccine

influenza virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against disease
    some values from: influenza
subclass of: viral vaccine
definition: A viral vaccine that protects against infection with influenza virus.
term editor: Oliver He
alternative label: Influenza vaccine
in subset: vaccine
comment: There is no single 'influenza virus' in NCBI_Taxon. We usually use: ('unidentified influenza virus' or 'Influenzavirus A' or 'Influenzavirus B' or 'Influenzavirus C') However, even this may not be comprehensive.

licensed cattle vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001466
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001466
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
definition: a vaccine with license that is used for cattle.
term editor: Oliver He
in subset: vaccine

Hepatitis B virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Hepatitis B virus
subclass of: VO_0003540
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis B
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatitis B virus
definition: A viral vaccine that protects against infection with Hepatitis B virus.
term editor: Oliver He
alternative label: hepatitis B vaccine
definition source: https://en.wikipedia.org/wiki/Hepatitis_B_vaccine
in subset: vaccine

licensed fish vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001462
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001462
subclass of: Restriction
  on property: immunizes recipient
  some values from: Myxini
subclass of: Restriction
  on property: immunizes recipient
  some values from: Actinopterygii
term editor: Oliver He
in subset: vaccine

Hepatitis A virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Hepatovirus A
subclass of: VO_0003548
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis A
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatovirus A
definition: A viral vaccine that protects against infection with Hepatitis A virus.
term editor: Oliver He
alternative label: hepatitis A vaccine
in subset: vaccine

licensed goat vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Capra hircus
subclass of: licensed vaccine
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Capra hircus
term editor: Oliver He
in subset: vaccine

Yersinia pestis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Yersinia pestis
subclass of: Yersinia vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Yersinia pestis
definition: A bacteria vaccine that prevents against Yersinia pestis infection that causes plague.
term editor: Oliver He
alternative label: Plague vaccine
in subset: vaccine

licensed dog vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001467
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001467
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Canis lupus familiaris
term editor: Oliver He
in subset: vaccine

Rabies virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Lyssavirus rabies
subclass of: VO_0003545
subclass of: Restriction
  on property: immunizes against disease
  some values from: rabies
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Lyssavirus rabies
definition: A viral vaccine that protects against infection with Rabies virus.
term editor: Oliver He
alternative label: rabies vaccine
in subset: vaccine

Smallpox virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Variola virus
subclass of: VO_0003539
subclass of: Restriction
  on property: immunizes against disease
  some values from: smallpox
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Variola virus
definition: A viral vaccine that protects against infection with Smallpox virus.
term editor: Oliver He
alternative label: smallpox vaccine
in subset: vaccine

licensed cat vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001465
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001465
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Felis catus
term editor: Oliver He
in subset: vaccine

licensed ferret vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Mustela putorius furo
subclass of: licensed vaccine
subclass of: VO_0001464
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Mustela putorius furo
term editor: Oliver He
in subset: vaccine

Measles virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Measles morbillivirus
subclass of: VO_0003543
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
definition: A viral vaccine that protects against infection with Measles virus.
term editor: Oliver He
alternative label: measles vaccine
in subset: vaccine

licensed deer vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Cervidae
subclass of: licensed vaccine
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Cervidae
term editor: Oliver He
in subset: vaccine

Mumps virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Mumps orthorubulavirus
subclass of: viral vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
definition: A viral vaccine that protects against infection with Mumps virus.
term editor: Oliver He
alternative label: mumps vaccine
in subset: vaccine

licensed bird vaccine
type: Class
equivalent class: Class
  intersection of: VO_0001461
  intersection of: Restriction
    on property: has role
    some values from: licensed vaccine role
subclass of: licensed vaccine
subclass of: VO_0001461
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Aves
term editor: Oliver He
in subset: vaccine

Rotavirus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Rotavirus
subclass of: VO_0003542
subclass of: Restriction
  on property: immunizes against disease
  some values from: Rotavirus infection
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rotavirus
definition: A viral vaccine that protects against infection with Rotavirus.
term editor: Oliver He
in subset: vaccine

HIBTITER vaccine
type: Class
equivalent class: Class
  intersection of: Haemophilus influenzae serotype b vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0015412
subclass of: Haemophilus influenzae serotype b vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0015412
editor note: In most cases HibTITER was administered concomitantly with other vaccines including DTP, DTaP, hepatitis B vaccine, IPV, OPV, pneumococcal 7-valent conjugate vaccine, MMR, and/or meningococcal group C conjugate vaccine (not licensed in the US).
term editor: Oliver He
definition source: PMID:2057256
definition source: PMID:9353019
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=160
VIOLIN vaccine ID: 160
in subset: vaccine

ProHIBiT vaccine
type: Class
equivalent class: Class
  intersection of: Haemophilus influenzae serotype b vaccine
  intersection of: Restriction
    on property: has drug brand name
    has value: VO_0019083
subclass of: Haemophilus influenzae serotype b vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
subclass of: Restriction
  on property: has drug brand name
  has value: VO_0019083
editor note: Ref: http://www.rxlist.com/prohibit-drug.htm
term editor: Oliver He
definition source: PMID:2057256
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=162
VIOLIN vaccine ID: 162
in subset: vaccine

Haemophilus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Haemophilus
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus
definition: Vaccine that protects against Haemophilus infection.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Haemophilus
has cross-reference: MeSH: D018073
in subset: vaccine

Haemophilus influenzae serotype b vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Haemophilus influenzae serotype b
subclass of: VO_0012185
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
definition: A vaccine that protects against Haemophilus influenzae type b infection.
term editor: Hector Guzman-Orozco
term editor: Oliver He
alternative label: Haemophilus b vaccine
alternative label: Hib vaccine
in subset: vaccine

SC602 vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
definition: A live attenuated Shigella flexneri 2a vaccine that carries deletions of the plasmid-borne virulence gene icsA (mediating intra- and intercellular spread) and the chromosomal locus iuc (encoding aerobactin).
term editor: Oliver He
alternative label: SC602
definition source: PMID:10377124
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=259
VIOLIN vaccine ID: 259
in subset: vaccine

Poliovirus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Enterovirus C
subclass of: VO_0003547
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
definition: A viral vaccine that protects against infection with Poliovirus.
term editor: Oliver He
alternative label: polio vaccine
in subset: vaccine

Japanese encephalitis virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Japanese encephalitis virus
subclass of: VO_0003546
subclass of: Restriction
  on property: immunizes against disease
  some values from: Japanese encephalitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Japanese encephalitis virus
definition: A viral vaccine that protects against infection with Japanese encephalitis virus.
term editor: Oliver He
alternative label: Japanese encephalitis vaccine
in subset: vaccine

CVD 1208 vaccine
type: Class
subclass of: prophylactic vaccine
subclass of: Shigella flexneri vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: vaccine in clinical trial role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
definition: CVD 1208 is derived from wild type Shigella flexneri 2a strain 2457T and has defined deletions in four genes: (1) the guaBA chromosomal operon that encodes two enzymes (inositol 5'-monophosphate dehydrogenase and guanosine 5'synthase) essential for de novo purine biosynthesis; (2) set, a locus in a chromosomal pathogenicity island that encodes Shigella enterotoxin (ShET); (3) Pic, an autotransporter mucinase encoded on the opposite strand from set; and (4) sen, an invasiveness plasmid gene encoding ShET.
term editor: Oliver He
alternative label: CVD 1208
definition source: PMID:15499528
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=441
VIOLIN vaccine ID: 441
in subset: vaccine

human papillomavirus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Human papillomavirus
subclass of: VO_0003538
subclass of: Restriction
  on property: immunizes against disease
  some values from: Human papillomavirus infectious disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human papillomavirus
definition: a vaccine against human papillomavirus infection
term editor: Oliver He
has cross-reference: SNOMEDCT: 424519000
has cross-reference: UMLS_CUI: C1512511
in subset: vaccine

CVD 1208S vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
definition: CVD 1208S is the same thing as CVD 1208, but CVD 1208S was prepared using animal-free media.
term editor: Oliver He
alternative label: CVD 1208S
definition source: PMID:17938573
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=272
VIOLIN vaccine ID: 272
in subset: vaccine

Varicella-zoster virus vaccine
type: Class
subclass of: VO_0003537
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human alphaherpesvirus 3
definition: a Herpesvirus vaccine that is used against Varicella-zoster virus infection.
term editor: Kallan Roan
term editor: Oliver He
alternative label: Varicella vaccine
alternative label: chickenpox and shingles virus vaccine
in subset: vaccine

EcSf2a-2 vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
definition: A Shigella flexneri vaccine that is an aro-D mutant derivative of EcSf2a-1.
term editor: Oliver He
alternative label: EcSf2a-2
definition source: PMID:1587589
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=267
VIOLIN vaccine ID: 267
in subset: vaccine

Salmonella typhi vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Salmonella enterica subsp. enterica serovar Typhi
subclass of: Salmonella vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: typhoid fever
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Salmonella enterica subsp. enterica serovar Typhi
definition: A Salmonella vaccine against typhoid fever (or called typoid), caused by Salmonella enterica enterica, serovar Typhi.
term editor: Oliver He
alternative label: typhoid vaccine
in subset: vaccine

heat-killed virulent Shigella flexneri 2a vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: VO_0001214
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
subclass of: Restriction
  on property: test in lab animal model
  some values from: Oryctolagus cuniculus
term editor: Oliver He
alternative label: heat-killed virulent Shigella flexneri 2a
definition source: PMID:10102148
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=268
VIOLIN vaccine ID: 268
in subset: vaccine

Shigella Sfl 124 vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
definition source: PMID:1937767
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=269
VIOLIN vaccine ID: 269
in subset: vaccine

recombinant SFL124-27 expressing Shigella dysenteriae type 1 O antigen vaccine
type: Class
subclass of: recombinant vector vaccine
subclass of: Shigella dysenteriae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: has role
  some values from: recombinant vector vaccine role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella dysenteriae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: Recombinant SFL124-27 expressing S. dysenteriae type 1 O antigen
definition source: PMID:9169740
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=258
VIOLIN vaccine ID: 258
in subset: vaccine

Streptococcus pneumoniae vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Streptococcus pneumoniae
subclass of: VO_0000772
subclass of: Restriction
  on property: immunizes against disease
  some values from: Streptococcus pneumonia
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Streptococcus pneumoniae
definition: a Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases.
term editor: Oliver He
alternative label: pneumococcal vaccine
definition source: WEB: http://www.who.int/vaccines/en/pneumococcus.shtml
in subset: vaccine

Shigella dysenteriae 1 strain WRSd1 vaccine
type: Class
subclass of: Shigella dysenteriae vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella dysenteriae
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Platyrrhini
term editor: Oliver He
term editor: Rebecca Racz
alternative label: S. dysenteriae 1 strain WRSd1
definition source: PMID:12010984
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=263
VIOLIN vaccine ID: 263
in subset: vaccine
comment: An aroA and virG mutant (CVD 1203) is attenuated in guinea pigs, as shown by the Sereny test. Guinea pigs inoculated with CVD 1203 were also protected from challenge with wild type S. flexneri

Shigella flexneri 2a strain CVD 1207 vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: VO_0001217
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
definition: A live attenuated Shigella flexneri 2a vaccine with specific deletion mutations in virG, sen, set, and guaBA.
term editor: Oliver He
alternative label: S. flexneri 2a strain CVD 1207
definition source: PMID:10678904
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=260
VIOLIN vaccine ID: 260
in subset: vaccine

Shigella sonnei virG mutant vaccine
type: Class
subclass of: Shigella sonnei vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella sonnei
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
definition: A stable attenuated Shigella sonnei strain with virG mutation. PMID:9712824.
term editor: Oliver He
term editor: Rebecca Racz
definition source: PMID:11895966
definition source: PMID:9712824
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=264
VIOLIN vaccine ID: 264
in subset: vaccine
comment: A virG mutant (WRSS1) is attenuated in guinea pigs and induced significant protection from challenge with wild type Shigella sonnei
comment: An aroA and virG mutant (CVD 1203) is attenuated in guinea pigs, as shown by the Sereny test. Guinea pigs inoculated with CVD 1203 were also protected from challenge with wild type S. flexneri

Shigella sonnei vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Shigella sonnei
subclass of: VO_0000769
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella sonnei
term editor: Oliver He
in subset: vaccine

Shigella flexneri vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Shigella flexneri
subclass of: VO_0000769
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
term editor: Oliver He
in subset: vaccine

Shigella dysenteriae vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Shigella dysenteriae
subclass of: VO_0000769
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella dysenteriae
term editor: Oliver He
in subset: vaccine

Shigella flexneri 2a LPS vaccine complexed with Neisseria meningitidis proteosomes vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: S. flexneri 2a LPS vaccine complexed with N. meningitidis proteosomes
definition source: PMID:8500877
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=270
VIOLIN vaccine ID: 270
in subset: vaccine

vaccine regulation
type: Class
subclass of: planned process
definition: Process that regulates vaccine-related processes, such as vaccine trial, vaccine license application.
term editor: Oliver He
in subset: process

vaccine transportation
type: Class
subclass of: planned process
definition: Process of transporting vaccine from one place to another place.
term editor: Oliver He
in subset: process

obsolete recombinant bacterial vector vaccine role
type: Class
subclass of: Thing
definition: A recombinant vector vaccine role that inheres in a bacterium that carries a vaccine antigen for development of a particular vaccine
term editor: Oliver He
has obsolescence reason: IAO_0000226
deprecated: true

peptide vaccine role
type: Class
subclass of: subunit vaccine role
definition: A subunit vaccine role that indicates the vaccine being a peptide vaccine.
term editor: Jie Zheng
in subset: role

obsolete recombinant viral vector vaccine role
type: Class
subclass of: Thing
definition: A recombinant vector vaccine role that inheres in a virus that carries a vaccine antigen for development of a particular vaccine
term editor: Oliver He
has obsolescence reason: IAO_0000226
deprecated: true

antibiotics vaccine residual
type: Class
subclass of: VO_0000854
definition: a vaccine residual that is from antibiotics used during the manufacture process.
term editor: Asiyah Yu Lin
term editor: Oliver He
in subset: vaccine component

vaccine specific antibody test
type: Class
subclass of: immune response detection assay
term editor: Oliver He
in subset: assay

vaccine trial regulation
type: Class
subclass of: vaccine regulation
definition: A vaccine regulation process for vaccine clinical trials.
term editor: Oliver He
in subset: process

primary vaccination
type: Class
subclass of: vaccination
definition: A vaccination process that occurs at the first time to a host organization in a specified period.
term editor: Oliver He
alternative label: prime vaccination
in subset: vaccination

boost vaccination
type: Class
subclass of: vaccination
subclass of: Restriction
  on property: preceded by
  some values from: primary vaccination
definition: A vaccination process that occurs after the primer vaccination with a purpose to boost host immune response to vaccine antigen.
term editor: Oliver He
in subset: vaccination

Brucella melitensis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Brucella melitensis
subclass of: Brucella vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
term editor: Oliver He
in subset: vaccine

Brucella melitensis strain Rev. 1 vaccine
type: Class
subclass of: prophylactic vaccine
subclass of: licensed goat vaccine
subclass of: VO_0001135
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: has gene mutation
  some values from: VO_0010963
subclass of: Restriction
  on property: immunizes recipient
  some values from: Capra hircus
subclass of: Restriction
  on property: immunizes recipient
  some values from: Ovis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella melitensis
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: Brucella melitensis Rev 1
alternative label: Brucella melitensis Rev. 1B. melitensis strain Rev. 1
definition source: PMID:13416171
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=110
VIOLIN vaccine ID: 110
in subset: vaccine

inactivated viral vaccine
type: Class
equivalent class: Class
  intersection of: viral vaccine
  intersection of: Restriction
    on property: has role
    some values from: VO_0010008
subclass of: inactivated vaccine
subclass of: viral vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
definition: a viral vaccine that is inactivated
alternative label: killed viral vaccine
in subset: vaccine

vaccine allergen disposition
type: Class
subclass of: disposition
term editor: Oliver He
in subset: disposition

Canada licensed human vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has role
    some values from: VO_0000864
  intersection of: Restriction
    on property: immunizes recipient
    some values from: Homo sapiens
subclass of: licensed human vaccine
subclass of: Restriction
  on property: has role
  some values from: VO_0000864
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
definition: a licensed human vaccine that is licensed in Canada
term editor: Oliver He
in subset: vaccine

DNA vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: DNA vaccine
definition: A vaccine preparation that results in the generation of a DNA vaccine
term editor: Oliver He
in subset: vaccine preparation

conjugate vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: conjugate vaccine
definition: A vaccine preparation that results in the generation of a conjugate vaccine
term editor: Oliver He
in subset: vaccine preparation

subunit vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: subunit vaccine
definition: A vaccine preparation that results in the generation of a subunit vaccine
term editor: Oliver He
in subset: vaccine preparation

live attenuated vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: live attenuated vaccine
definition: A vaccine preparation that results in the generation of a live attenuated vaccine
term editor: Oliver He
in subset: vaccine preparation

RNA vaccine preparation
type: Class
subclass of: vaccine preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: RNA vaccine
definition: A vaccine preparation that results in the generation of a RNA vaccine
term editor: Oliver He
in subset: vaccine preparation

Brucella abortus strain RB51SOD vaccine
type: Class
subclass of: VO_0001134
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: expresses
  some values from: sodC from B. abortus strain 2308
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
alternative label: B. abortus strain RB51SOD
alternative label: Brucella abortus strain RB51SOD
definition source: PMID:10816475
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=11
VIOLIN vaccine ID: 11
in subset: vaccine

Brucella suis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Brucella suis
subclass of: Brucella vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella suis
definition: a Brucella vaccine against infection wtih B. suis
term editor: Oliver He
in subset: vaccine

Brucella suis strain 2 vaccine
type: Class
subclass of: licensed pig vaccine
subclass of: prophylactic vaccine
subclass of: VO_0001136
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Sus scrofa
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella suis
definition: An orally administrable brucellosis vaccine that was was developed in China. It is effective for oral vaccination of sheep, goats, cattle and pigs.
term editor: Oliver He
alternative label: Brucella suis S2
alternative label: Brucella suis strain 2
definition source: PMID:3541425
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=447
VIOLIN vaccine ID: 447
in subset: vaccine

Brucella abortus strain 45/20 vaccine
type: Class
subclass of: VO_0001134
subclass of: VO_0001466
subclass of: VO_0001476
subclass of: Restriction
  on property: immunizes against disease
  some values from: brucellosis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Bos taurus
subclass of: Restriction
  on property: immunizes recipient
  some values from: Ovis aries
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Brucella abortus
term editor: Oliver He
alternative label: B. abortus strain 45/20
alternative label: Brucella abortus strain 45/20
definition source: PMID:8236802
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=123
VIOLIN vaccine ID: 123
in subset: vaccine

cytomegalovirus vaccine
type: Class
subclass of: Herpesvirus vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Cytomegalovirus
term editor: Oliver He
in subset: vaccine

Dengue virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Dengue virus
subclass of: VO_0003546
subclass of: Restriction
  on property: immunizes against disease
  some values from: dengue disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Dengue virus
definition: A viral vaccine that protects against infection with Dengue virus.
term editor: Oliver He
alternative label: Dengue vaccine
in subset: vaccine

Ebola virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Ebola virus sp.
subclass of: viral vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: Ebola virus disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Ebola virus sp.
definition: A viral vaccine that protects against infection with Ebola virus.
term editor: Oliver He
alternative label: Ebola vaccine
in subset: vaccine

Herpesvirus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Herpesvirales
subclass of: viral vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Herpesvirales
definition: A viral vaccine that protects against infection with Herpesvirus.
term editor: Oliver He
in subset: vaccine

RNA vaccine role
type: Class
subclass of: vaccine role
definition: A vaccine role that indicates the vaccine being a RNA vaccine.
term editor: Oliver He
in subset: role

Herpes simplex virus vaccine
type: Class
subclass of: Herpesvirus vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Herpes Simplexvirus
term editor: Oliver He
in subset: vaccine

obsolete Marek disease vaccine
type: Class
subclass of: Thing
term editor: Oliver He
has obsolescence reason: IAO_0000227
term replaced by: VO_0012162
deprecated: true

Measles-Mumps-Rubella vaccine
type: Class
subclass of: prophylactic vaccine
subclass of: Measles-Mumps vaccine
subclass of: VO_0010441
subclass of: VO_0010442
subclass of: VO_0010450
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes against disease
  some values from: rubella
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rubella virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
definition: A Measles-Mumps vaccine that also protects against infection with Rubella virus.
term editor: Oliver He
alternative label: MMR
CVX code: 03
OMOP concept ID: 40213183
CVX full vaccine name: measles, mumps and rubella virus vaccine
CVX short description: MMR
in subset: vaccine
comment: MMR is usually live attenuated.

Diphtheria-Tetanus vaccine
type: Class
subclass of: Clostridium tetani vaccine
subclass of: Corynebacterium diphtheriae vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
definition: A Corynebacterium diphtheriae vaccine that also protect against infection with Clostridium tetani.
term editor: Oliver He
in subset: vaccine

CVD 1204(pGA1-CS2) vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: CVD 1204(pGA1-CS2)
definition source: PMID:11292735
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=265
VIOLIN vaccine ID: 265
in subset: vaccine

CVD 1204(pGA1-CS3) vaccine
type: Class
subclass of: Shigella flexneri vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
subclass of: Restriction
  on property: test in lab animal model
  some values from: Cavia porcellus
term editor: Oliver He
alternative label: CVD 1204(pGA1-CS3)
definition source: PMID:11292735
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=442
VIOLIN vaccine ID: 442
in subset: vaccine

Corynebacterium diphtheriae vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Corynebacterium diphtheriae
subclass of: VO_0003534
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
definition: A bacterial vaccine that protects against infection with Corynebacterium diphtheriae that causes Diphtheria.
term editor: Oliver He
alternative label: diphtheria vaccine
in subset: vaccine

Measles-Mumps vaccine
type: Class
subclass of: Measles virus vaccine
subclass of: Mumps virus vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
definition: A Measles virus vaccine that also protects against infection with Mumps virus.
term editor: Oliver He
in subset: vaccine

Measles-Mumps-Rubella-Varicella vaccine
type: Class
subclass of: Measles-Mumps-Rubella vaccine
subclass of: VO_0001220
subclass of: VO_0003537
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0010038
subclass of: Restriction
  on property: immunizes against disease
  some values from: mumps
subclass of: Restriction
  on property: immunizes against disease
  some values from: measles
subclass of: Restriction
  on property: immunizes against disease
  some values from: chickenpox
subclass of: Restriction
  on property: immunizes against disease
  some values from: rubella
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Human alphaherpesvirus 3
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rubella virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Measles morbillivirus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Mumps orthorubulavirus
definition: A Measles-Mumps-Rubella vaccine that also protects against Varicella.
term editor: Kallan Roan
term editor: Oliver He
definition source: https://www.cdc.gov/vaccines/hcp/vis/vis-statements/mmrv.html
CVX code: 94
OMOP concept ID: 40213184
CVX full vaccine name: measles, mumps, rubella, and varicella virus vaccine
in subset: vaccine

Diphtheria-Tetanus-Pertussis vaccine
type: Class
subclass of: prophylactic vaccine
subclass of: Diphtheria-Tetanus vaccine
subclass of: VO_0010435
subclass of: VO_0010436
subclass of: VO_0010445
subclass of: Restriction
  on property: has function
  some values from: preventive vaccine function
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
term editor: Oliver He
alternative label: DTP vaccine
CVX code: 01
OMOP concept ID: 40213291
CVX full vaccine name: diphtheria, tetanus toxoids and pertussis vaccine
CVX short description: DTP
in subset: vaccine

Shigella ribosome-based vaccine (SRB)
type: Class
subclass of: Shigella flexneri vaccine
subclass of: Restriction
  on property: has role
  some values from: vaccine in research role
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Shigella flexneri
subclass of: Restriction
  on property: test in lab animal model
  some values from: Mus musculus
term editor: Oliver He
definition source: PMID:17507120
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=273
VIOLIN vaccine ID: 273
in subset: vaccine

Plasmodium falciparum vaccine combination B
type: Class
subclass of: Plasmodium falciparum vaccine
subclass of: combination vaccine
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has component
  some values from: VO_0010959
subclass of: Restriction
  on property: immunizes against disease
  some values from: malaria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Plasmodium
definition: A malaria vaccine that comprises recombinant Plasmodium falciparum (P. falciparum) blood-stage proteins MSP1, MSP2 and RESA, formulated with the adjuvant Montanide ISA 720.
term editor: Oliver He
alternative label: P. falciparum vaccine Combination B
definition source: PMID:14604568
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=206
VIOLIN vaccine ID: 206
in subset: vaccine

Haemophilus influenzae serotype b
type: Class
subclass of: Haemophilus influenzae
term editor: Oliver He
in subset: organism

Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
type: Class
subclass of: Bordetella pertussis vaccine
subclass of: VO_0000943
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
definition: A vaccine that protects against diphtheria, tetanus, pertussis, and poliovirus.
term editor: Kallan Roan
term editor: Oliver He
alternative label: DTaP/IPV vaccine
alternative label: diphtheria and tetanus toxoids and acellular pertussis adsorbed and inactivated poliovirus vaccine
in subset: vaccine

Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine
type: Class
subclass of: toxoid vaccine
subclass of: inactivated viral vaccine
subclass of: Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
subclass of: VO_0001214
subclass of: VO_0010435
subclass of: VO_0010436
subclass of: VO_0010439
subclass of: VO_0010445
subclass of: VO_0010447
subclass of: Restriction
  on property: has role
  some values from: combination vaccine role
subclass of: Restriction
  on property: has role
  some values from: recombinant vaccine vector role
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: has role
  some values from: VO_0000807
subclass of: Restriction
  on property: has role
  some values from: VO_0010008
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis B
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatitis B virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
definition: A vaccine used to prevent infections of diphtheria, tetanus (lockjaw), pertussis (whooping cough), hepatitis B, and poliovirus.
term editor: Kallan Roan
term editor: Oliver He
alternative label: DTaP/IPV/HepB vaccine
definition source: https://www.hendricks.org/HealthLibrary/default.aspx
CVX code: 110
OMOP concept ID: 40213286
CVX full vaccine name: DTaP-hepatitis B and poliovirus vaccine
CVX short description: DTaP-Hep B-IPV
in subset: vaccine

Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b vaccine
type: Class
subclass of: Haemophilus influenzae serotype b vaccine
subclass of: Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against disease
  some values from: tetanus
subclass of: Restriction
  on property: immunizes against disease
  some values from: diphtheria
subclass of: Restriction
  on property: immunizes against disease
  some values from: poliomyelitis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Enterovirus C
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Clostridium tetani
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Corynebacterium diphtheriae
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
definition: A vaccine that protects against, Diphtheria, Tetanus, Pertussis (whooping cough), Polio, and Haemophilus influenzae type b.
term editor: Kallan Roan
term editor: Oliver He
alternative label: DTaP/IPV/Hib vaccine
definition source: https://www.healthlinkbc.ca/healthlinkbc-files/dtap-ipv-hib-vaccine
in subset: vaccine

licensed human Hepatitis A & B vaccine
type: Class
subclass of: VO_0010438
subclass of: VO_0010439
subclass of: Restriction
  on property: has role
  some values from: licensed vaccine role
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis A
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis B
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatitis B virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatovirus A
term editor: Oliver He
CVX code: 104
OMOP concept ID: 40213303
CVX full vaccine name: hepatitis A and hepatitis B vaccine
in subset: vaccine

Haemophilus b and Hepatitis B vaccine
type: Class
equivalent class: Class
  intersection of: Hepatitis B virus vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Haemophilus influenzae serotype b
subclass of: Hepatitis B virus vaccine
subclass of: Haemophilus influenzae serotype b vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: haemophilus meningitis
subclass of: Restriction
  on property: immunizes against disease
  some values from: hepatitis B
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Hepatitis B virus
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Haemophilus influenzae serotype b
definition: a viral vaccine against Hepatitis B virus and at the same time against bacterial H. influenzae serotype b.
term editor: Oliver He
in subset: vaccine

DNA and MVA encoding ME-TRAP vaccine
type: Class
subclass of: DNA vaccine
subclass of: Plasmodium falciparum vaccine
subclass of: Restriction
  on property: has role
  some values from: DNA vaccine role
subclass of: Restriction
  on property: expresses
  some values from: VO_0010920
subclass of: Restriction
  on property: immunizes against disease
  some values from: malaria
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Plasmodium
definition: A vaccine that contains DNA and modified vaccinia virus Ankara (MVA) encoding thrombospondin-related adhesion protein (TRAP) with a multiple-epitope string ME (ME-TRAP). This vaccine is used with a prime-boost regime by DNA priming and MVA boosting.
term editor: Oliver He
alternative label: DNA and MVA encoding ME-TRAP
definition source: PMID:16988273
definition source: VIOLIN: https://violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=210
VIOLIN vaccine ID: 210
in subset: vaccine

obsolete Papillomavirus vaccine
type: Class
subclass of: Thing
definition: A viral vaccine that protects against infection with Papillomavirus.
term editor: Oliver He
has obsolescence reason: IAO_0000227
term tracker item: https://github.com/vaccineontology/VO/issues/688
term replaced by: VO_0003538
see also: MeSH: D053918
deprecated: true

Parainfluenza virus vaccine
type: Class
subclass of: viral vaccine
definition: A viral vaccine that protects against infection with Parainfluenza virus.
term editor: Oliver He
alternative label: parainfluenza vaccine
in subset: vaccine

Pseudorabies virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Suid alphaherpesvirus 1
subclass of: VO_0003537
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Suid alphaherpesvirus 1
definition: A viral vaccine that protects against infection with Pseudorabies virus.
term editor: Oliver He
alternative label: pseudorabies vaccine
in subset: vaccine

Simian immunodeficiency virus vaccine
type: Class
subclass of: viral vaccine
definition: A viral vaccine that prevents against infection with Simian immunodeficiency virus.
term editor: Oliver He
alternative label: SAIDS vaccine
in subset: vaccine

West Nile virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: West Nile virus
subclass of: VO_0003546
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: West Nile virus
definition: A viral vaccine that protects against West Nile virus infection.
term editor: Oliver He
in subset: vaccine

Respiratory syncytial virus vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Respiratory syncytial virus
subclass of: VO_0001507
subclass of: Restriction
  on property: immunizes against disease
  some values from: respiratory syncytial virus infectious disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Respiratory syncytial virus
definition: A viral vaccine that prevents infection with Respiratory syncytial virus.
term editor: Oliver He
in subset: vaccine

marker vaccine
type: Class
subclass of: vaccine
definition: A vaccine that is used in conjunction with diagnostic tests to differentiate vaccinated animals from carrier animals. It can be a subunit or a gene-deleted vaccine.
term editor: Oliver He
has cross-reference: MeSH: D022581
in subset: vaccine

edible vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: has quality
    some values from: edible
subclass of: vaccine
subclass of: Restriction
  on property: has quality
  some values from: edible
definition: A vaccine that is edible and derived from an edible plant. The transgenic plant is used as recombinant protein production system. The edible plant tissue functions as an oral vaccine.
term editor: Oliver He
has cross-reference: MeSH: D022462
in subset: vaccine

acellular vaccine
type: Class
subclass of: subunit vaccine
definition: A subunit vaccine that is produced by using only the antigenic part of the disease causing organism. It often requires a "booster" every few years to maintain their effectiveness.
term editor: Oliver He
in subset: vaccine

ISCOM vaccine adjuvant
type: Class
subclass of: VO_0001356
subclass of: Restriction
  on property: induces immune profile
  some values from: VO_0005311
definition: A particulate antigen delivery system vaccine adjuvant that consists of an assembly of antigens in multimeric form and presents an antigen to induce specific immunologic responses. The assembly is attached to a matrix with a built-in adjuvant, saponin. ISCOMs induce strong serum antibody responses, and are used as highly immunogenic forms of subunit vaccines. MeSH term: D20.215.894.860.449.
term editor: Oliver He
alternative label: ISCOM
alternative label: ISCOM(s)™
alternative label: The immunostimulating complex
has cross-reference: https://violinet.org/vaxjo/vaxjo_detail.php
in subset: vaccine adjuvant

Plasmodium vivax vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Plasmodium vivax
subclass of: malaria vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: malaria
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Plasmodium vivax
term editor: Oliver He
in subset: vaccine

contraceptive vaccine
type: Class
subclass of: vaccine
definition: A vaccine that is used to prevent conception.
term editor: Oliver He
alternative label: antifertility vaccine
has cross-reference: MeSH: D022642
in subset: vaccine

Alzheimer vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against disease
    some values from: Alzheimer's disease
subclass of: VO_0005503
subclass of: Restriction
  on property: immunizes against disease
  some values from: Alzheimer's disease
subclass of: Restriction
  on property: immunizes recipient
  some values from: Homo sapiens
definition: A vaccine that prevents or treats Alzheimer disease.
term editor: Oliver He
has cross-reference: MeSH: D023582
in subset: vaccine

malaria vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Plasmodium
subclass of: protozoan vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: malaria
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Plasmodium
definition: Plasmodium vaccine is a vaccine that prevents against Plasmodium species causing malaria. It is made from antigens arising from any of the four strains of Plasmodium which cause malaria in humans, or from P. berghei which causes malaria in rodents.
term editor: Oliver He
alternative label: Plasmodium vaccine
alternative label: malarial Vaccine
in subset: vaccine

Leishmania vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Leishmania <subgenus>
subclass of: protozoan vaccine
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Leishmania <subgenus>
definition: a protozoan vaccine that prevents against infection with Leishmania.
term editor: Oliver He
alternative label: Leishmaniasis vaccine
in subset: vaccine

Vibrio cholerae vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Vibrio cholerae
subclass of: Vibrio vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: cholera
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Vibrio cholerae
definition: A bacterial vaccine that prevents infection with Vibrio cholera.
term editor: Oliver He
alternative label: cholera vaccine
in subset: vaccine

Borrelia burgdorferi vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Borreliella burgdorferi
subclass of: VO_0003518
subclass of: Restriction
  on property: immunizes against disease
  some values from: Lyme disease
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Borreliella burgdorferi
definition: Vaccine that protects against Borrelia burgdorferi infection causing Lyme disease.
term editor: Oliver He
alternative label: Lyme disease vaccine
has cross-reference: MeSH: D022123
in subset: vaccine

Bordetella pertussis vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Bordetella pertussis
subclass of: Bordetella vaccine
subclass of: Restriction
  on property: immunizes against disease
  some values from: pertussis
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Bordetella pertussis
definition: A bacterial vaccine that prevents against Bordetella pertussis infection that causes pertussis or whooping cough.
term editor: Khadeejah Khan
term editor: Oliver He
alternative label: Acellular Pertussis Vaccine
alternative label: Pertussis vaccine
in subset: vaccine

Pseudomonas vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Pseudomonas
subclass of: VO_0003535
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Pseudomonas
definition: Vaccine that protects against Pseudomonas infection.
term editor: Oliver He
has cross-reference: MeSH: D054406
in subset: vaccine

Rickettsial vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Rickettsia
subclass of: VO_0003550
subclass of: Restriction
  on property: immunizes against pathogen
  some values from: Rickettsia
definition: Vaccine that protects against Rickettsia infection. Typhus is any of several similar diseases caused by Rickettsia bacteria. So Rickettsial vaccine is also called typhus vaccine.
term editor: Oliver He
alternative label: typhus vaccine
definition source: WEB: http://en.wikipedia.org/wiki/Typhus_vaccine
has cross-reference: MeSH: D012290
in subset: vaccine

Salmonella vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: immunizes against pathogen
    some values from: Salmonella
subclass of: VO_0003552
definition: Vaccine that protects against Salmonella species infection.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Salmonella
has cross-reference: MeSH: D022562
in subset: vaccine