en Chris mungall Erica Marcos Ningxian Fan Paul Fabry Randi Vita Ryan R. Brinkman Shunzhou Deng Alan Ruttenburg Alexander D. Diehl Amogh Madireddi Anna Maria Masci Anthony Huffman Barry Smith Bjoern Peters Edison Ong Hong Yu Jason Hu Jie Zheng Kallan Roan Khadeejah Khan Lindsay Cowell Melanie Courtot Ningxian Fan Omar Tibi Philip Huang Randi Vita Rebecca Racz Richard H. Scheuermann Rohit Goru Ronak Sutariya Samantha G. Sayers (SGS) Thomas Todd Yongqun "Oliver" He (YH) Yu Lin (YL) Yuanyi (Penny) Pan Zuoshuang "Allen" Xiang 2023-11-17 The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. OWL-DL Vaccine Ontology 2023-11-17 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term A GeneID in the NCBI Gene database Oliver He, Yue Liu NCBI GeneID the NCBI LocusTag name of a gene Oliver He, Yue Liu NCBI LocusTag a date of content modification Oliver He, Yue Liu modification date The NCBITaxon ontology ID of an organism. Oliver He, Yue Liu organism NCBITaxon ID A chromosome ID where a gene is located. Oliver He chromosome ID of gene an annotation property that specifies the type of a gene Oliver He type of gene an annotation property that specifies a nomenclature status Oliver He nomenclature status An annotation property that represents a gene's association with PubMed publication(s). Yongqun He has PubMed association This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants 2023-03-03 UK spelling synonym A synonym type for common misspellings 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name 2023-07-27 legal name CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. 2023-09-30 INN International Nonproprietary Name nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. 2023-10-12 latin term NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. 2023-11-01 acronym An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . } never in taxon A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. non-overlapping with shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . } mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property A shortcut relationship that holds between two entities based on their identity criteria logical macro assertion involving identity A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. in approximate one to one relationship with 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is opposite of external_definition axiom_lost_from_external_ontology homology_notes has_relational_adjective taxon_notes development_notes external_ontology_notes fma_set_term Oliver He, Omar Tibi An annotation property that represents a matched vaccine identifier used in the VIOLIN database. VIOLIN vaccine ID VIOLIN vaccine ID An annotation property that represents the trade name of a product. YH trade name trade name An annotation property that represents the active ingredient of a vaccine. Oliver He has vaccine active ingredient has vaccine active ingredient An annotation property that represents the vaccine ingredient of a vaccine. Such an ingredient may not be active. Oliver He has vaccine ingredient has vaccine ingredient An annotation property that describes the dose information of a vaccine Oliver He vaccine dose annotation vaccine dose annotation The vaccine Prevnar (trade name) has a FDA-defined proper name: Pneumococcal 7-valent Conjugate Vaccine (Diphtheria CRM197 Protein). Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm An annotation property that represents the proper name of a vaccine, which is defined in an official way such as one defined by FDA. Oliver He, Kallan Roan vaccine proper name vaccine proper name The vaccine Prevnar has the manufacturer: Wyeth Pharmaceuticals Inc. Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm An annotation property that represents the manufacturer of a product such as vaccine Oliver He, Kallan Roan manufacturer manufacturer The vaccine Prevnar has the indications: - Immunization of infants 2, 4, 6 and 12-15 months of age to prevent invasive pneumococcal disease. - Immunization of infants and toddlers against otitis media caused by vaccine serotypes. Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm An annotation property that represents the indications of a vaccine defined by the USA FDA. Oliver He, Kallan Roan FDA vaccine indications FDA vaccine indications Prevnar has the package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM137038.pdf . Recorded on 11/26/2018. An annotation property that represents a URL of the package insert PDF document of a licensed vaccine Oliver He, Kallan Roan vaccine package insert PDF URL vaccine package insert PDF URL A number that is generated by FDA based on a request from an applicant of a product licensing. Oliver He, Kallan Roan vaccine submission’s tracking number https://www.fda.gov/downloads/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/ProceduresSOPPs/UCM461225.pdf BLA 101094 vaccine STN RxNORM ID RxNORM ID has Protegen id has Protegen id has Protegen annotation has Protegen annotation As seen: http://purl.bioontology.org/ontology/RXNORM/901644, the RxNORM vaccine term "Prevnar 13 vaccine 0.5 ML Prefilled Syringe" has Preferred Name of: 0.5 ML Streptococcus pneumoniae serotype 1 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 14 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 18C capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 19A capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 19F capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 23F capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 3 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 4 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 5 capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 6A capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 6B capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0088 MG/ML / Streptococcus pneumoniae serotype 7F capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML / Streptococcus pneumoniae serotype 9V capsular antigen diphtheria CRM197 protein conjugate vaccine 0.0044 MG/ML Prefilled Syringe [Prevnar 13]". In this case, the whole preferred name is annotated under the annotation property "RxNORM Preferred Name". RxNORM Preferred Name RxNORM Preferred Name An identifier assigned by the Vaccine Adjuvant Compendium (VAC: https://vac.niaid.nih.gov/) https://vac.niaid.nih.gov/ VAC adjuvant ID An annotation property that represents the annotated information about the antigens used for a specific vaccine. Oliver He, Penny Pan https://en.wikipedia.org/wiki/Antigen vaccine antigen annotation vaccine preparation annotation vaccine response annotation This is annotation property that refers to a specific CVX ID. Penny Pan, Oliver He https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx CVX code An annotation property that shows the status of vaccine developmeint including: clinical trial, research, licensed, or Emergency Use Authorization (EUA). Oliver He, Jie Zheng, Anthony Huffman, Penny Pan status of vaccine development has_rank An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification A relation between an organism and an organism that has vector role. obsolete_has vector true A relation between an organism and an organism that has host role. obsolete_has host true inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. x 'cell expresses' y iff: cell(x) AND gene(y) AND exists some 'transcription, DNA templated (GO_0006351)'(t) AND t occurs_in x AND t has_input y cell expresses David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during https://wiki.geneontology.org/Happens_during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Connects a biological entity to its taxon of origin. in taxon w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. gene product of every HOTAIR lncRNA is the gene product of some HOXC gene every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y has gene product 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process expressed in Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. over-expressed in g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. under-expressed in c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) has biological role c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) has application role c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) has chemical role x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. ubiquitously expressed in y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. expresses inverse of ubiquiotously expressed in ubiquitously expresses q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of A relationship that holds via some environmental process Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) ecologically related to holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y has host has vector depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. towards x is transcribed from y if and only if x is synthesized from template y http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed from inverse of transcribed from http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed to x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomal translation of inverse of ribosomal translation of http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomally translates to DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. DEPRECATED inheres in true DEPRECATED bearer of true a type of 'has vaccine component' relation that specifies a vaccine conjugate protein for a specific vaccine has vaccine conjugate protein YH a type of 'has vaccine vector' relation that specifies a bacterial vaccine vector has bacterial vaccine vector has_vaccine_contraindication is a relation that specifies contraindication of a vaccine. This relation may be replaced by has_vaccine_allergen. We need to determine if any vaccine contraindicator is not a vaccine allergen. YH has vaccine contraindication a type of 'has vaccine vector' that is specifically for viral vaccine vector has viral vaccine vector a 'has vaccine component' relation that specifies the plasmid used for development of a particular DNA vaccine. YH has DNA vaccine plasmid infection_of is a relation between a disorder and an infectious pathogen. The relation 'infection_of' is introduced to represent an infection caused by an infectious pathogen. A pathogen infection is a disorder. Since the number of pathogens is large, there are numerous infections. To make the description of a specific infection simple, the shortcut term 'infection_of' is defined: infection_of X = infection and has_part some (organism X and has_disposition some infectious disposition) YH, XZ, MC, BP, AR infection_of an object property that specifies a process that is induced by vaccination of a vaccine YH induced by vaccination of a 'has vaccine component' relation that specifies a gene inserted to DNA vaccine plasmid for development of a particular DNA vaccine, and this gene encodes for a protein antigen. YH has DNA vaccine antigen gene an object property that defines a relation between a vaccine and its component YL, YH has vaccine component an object property that specifies a vaccine antigen YL, YH This relation only works for those vaccine antigen that is physically part of a vaccine preparation. It does not include those antigens that are not part of vaccine. For example, a protein antigen expressed in a DNA vaccine is not a part of vaccine pe ser. In this case, the vaccine expresses the protein, but the gene is part of the vaccine, not the protein. For the case, we can use the relation 'DNA vaccine expresses protein antigen' under the relation 'expresses'. has vaccine antigen a type of 'has vaccine antigen' relation that is specifically for vaccine protective protein antigen used in subunit vaccine development YL, YH has subunit vaccine antigen a type of 'has vaccine antigen' relation that is specifically for vaccine protective antigen component YL, YH has vaccine protective antigen a type of 'has vaccine component' relation that is specifically for vaccine adjuvant component YL, YH has vaccine adjuvant a type of 'has vaccine component' relation that is specifically for vaccine vector component YL, YH has vaccine vector a object property that specifies a relation between a vaccine and a vaccine allergen YH has vaccine allergen an object property that indicates a secretion of a material (e.g., protein) from a vaccine organism. YH vaccine organism secretes YL, YH a 'has vaccine component' relation that is specifically used for vaccine preservative has vaccine preservative an object property that specifies a relation between a vaccine and a vaccinate route vaccinated in route an object property that specifies a relation between a vaccine and its vaccinee has vaccinee YH an 'expresses' relation that specifies a relation between a DNA vaccine and a protein antigen to be expressed by the DNA vaccine. DNA vaccine expresses protein antigen "A vaccinates B" means that the vaccine A is used for vaccinating the host B (e.g., human). A relationship between a vaccine instance and an organism type such that if the vaccine instance is given to an instance of the organism by the process vaccination, then it changes the organism's disposition to have an immune response against a disease. YH, AR, ZX, MC vaccinates has_vaccine_allegen is a relation that specifies an allegen to a vaccine. YH has_vaccine_allergen an object property that represents a mutational relation between a vaccine organism and another material (e.g., gene or protein). the mutated material initially exists in the original wildtype organism. YH vaccine organism has mutation YH an object property that specifies a relation between a vaccine and a vaccine virmugen. This is a short cut relation. Domain: vaccine Range: a gene Shortcut: is_specified_output_of some ('preparation of gene mutant vaccine' and (has_specified_input some gene)) has vaccine virmugen YH a 'has subunit vaccine antigen' relation that indicates the antigen is protective. has subunit vaccine protective antigen is_distributed_by is a relation that specifies a company that distributes a product (e.g., vaccine). The company is very likely not the manufacturer of the product. YH, ZX is_distributed_by a shortcut relation that equals to: 'processed material' and (is_specified_output_of some 'vaccine preparation') and ('has function' some ('vaccine function' and ('is realized by' only ('vaccine immunization' and (realizes some ('vaccine host role' and (role_of some 'organism' and has_disposition some disease)))))))). The domain of this relation is a vaccine. The range of this relation is a disease. Asiyah Yu Lin Oliver He immunization against disease vaccine immunization against disease immunizes against disease an object property that represents an organism has a mutation of a specific gene from the organism genome. Yongqun He has gene mutation a shortcut relation that equals to: 'processed material' and (is_specified_output_of some 'vaccine preparation') and ('has function' some ('vaccine function' and ('is realized by' only ('vaccine immunization' and (realizes some ('vaccine host role' and (role_of some 'organism')))))))). The domain of this relation is a vaccine. The range of this relation is a organism. YL Yongqun He immunization for host vaccine immunization for host immunizes host An object property that represents a relation between a vaccine with a prime-boost schedule and a vaccine used for priming. Oliver He has prime vaccine An object property that represents a relation between a vaccine with a prime-boost schedule and a vaccine used for boost. Oliver He has boost vaccine a shortcut relation that equals to: processed material and (is_specified_output_of some vaccine preparation) and (has function some (vaccine function and (is realized by only (vaccine immunization and (realizes some ('immunization target role' and (role_of some 'MICROBE')))))))) The domain of this relation is a vaccine. The range of this relation is a microbe (a bacterium, a virus, a fungus, and a parasite) Yongqun He immunization against microbe vaccine immunization against microbe immunizes against microbe a shortcut object property that represents a relation between a vaccine and a disease process where the vaccine immunizes a host against a disease process. Oliver He immunizes against disease process An object property that represents a relation between a material entity and biological process Anthony Huffman, Oliver He up-expressed as immune signature of An object property that represents a relation between a material entity (such as vaccine or vaccine adjuvant) and an immune profile where the material entity can induce the immune profile in a host. Oliver He, Amogh Madireddi induces immune profile A vaccine adjuvant T-vant has molecular receptor of TLR4. Reference: https://vac.niaid.nih.gov/view?id=61. An object property that represents a relation between a material entity and a molecular entitiy that serves as the molecular receptor to the material entity. Oliver He has molecular receptor A relationship between relationship between a material entity and a parasite where the material entity causes some processagainst some parasite such that transmitting to additional hosts or vectors. capable of blocking transmission (of life cycle) A relationship between relationship between a vaccine and a parasite where the vaccine immunizes against some parasite such that transmitting to additional hosts or vectors. Anthony Huffman, Anna Maria Masci, Oliver He, Jie Zheng blocks transmission of pathogen via vaccine A relationship between a vaccine X and organism Y where the vaccine X generates an immune response in a vaccinated organism and the immune product (e.g., antibody) can be transferred to the organism Y Anthony Huffman, Anna Maria Masci, Oliver He, Jie Zheng vaccine immunity response transferrable to organism entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) Digestive gland of crustaceans with functions approximately analogous to liver and pancreas of vertebrates - enzyme secretion, food absorption and storage. hepatopancreas 1: The trunk of an elephant; also: any long flexible snout. 2: Any of various elongated or extensible tubular processes as the sucking organ of a butterfly of the oral region of an invertebrate. proboscis An organic hydroxy compound that consists of benzene bearing a single hydroxy substituent. The parent of the class of phenols. 0 C6H6O InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H ISWSIDIOOBJBQZ-UHFFFAOYSA-N 94.11120 94.04186 Oc1ccccc1 CHEBI:14777 CHEBI:25966 CHEBI:43543 CHEBI:8071 Beilstein:969616 CAS:108-95-2 DrugBank:DB03255 Drug_Central:4266 Gmelin:2794 HMDB:HMDB0000228 KEGG:C00146 KEGG:C15584 KEGG:D00033 KEGG:D06536 KNApSAcK:C00002664 PDBeChem:IPH PMID:12058733 PMID:16953321 PMID:17852157 PMID:19029204 PMID:20886261 PMID:21492257 PMID:21689881 PMID:21809019 PMID:21822930 Reaxys:969616 UM-BBD_compID:c0128 Wikipedia:Phenol PHENOL Phenol phenol chebi_ontology Benzenol Carbolsaeure Hydroxybenzene Karbolsaeure Oxybenzene PhOH Phenic acid Phenylic acid Phenylic alcohol acide carbolique acide phenique carbolic acid CHEBI:15882 phenol A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O). 0 CH4N2O InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) XSQUKJJJFZCRTK-UHFFFAOYSA-N 60.05534 60.03236 NC(N)=O CHEBI:15292 CHEBI:27218 CHEBI:46379 CHEBI:9888 Beilstein:635724 CAS:57-13-6 DrugBank:DB03904 Drug_Central:4264 ECMDB:ECMDB04172 Gmelin:1378 HMDB:HMDB0000294 KEGG:C00086 KEGG:D00023 KNApSAcK:C00007314 MetaCyc:UREA PDBeChem:URE PMID:18037357 PMID:22770225 PPDB:1728 Reaxys:635724 UM-BBD_compID:c0165 Wikipedia:Urea YMDB:YMDB00003 UREA Urea urea chebi_ontology 1728 Carbamide E927b H2NC(O)NH2 Harnstoff Karbamid carbamide carbonyldiamide ur uree CHEBI:16199 urea Liposaccharide natural compounds consisting of a trisaccharide repeating unit (two heptose units and octulosonic acid) with oligosaccharide side chains and 3-hydroxytetradecanoic acid units (they are a major constituent of the cell walls of Gram-negative bacteria). CHEBI:14520 CHEBI:25062 CHEBI:6494 KEGG:C00338 PMID:15589368 PMID:24186868 PMID:24506665 PMID:24642373 PMID:24659348 Lipopolysaccharide chebi_ontology LPS lipopolysaccharides CHEBI:16412 lipopolysaccharide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. 0 (C2H2NOR)nC2H3NOR CHEBI:14753 CHEBI:25906 CHEBI:7990 KEGG:C00012 Peptide peptides chebi_ontology Peptid peptido peptidos CHEBI:16670 peptide An aldehyde resulting from the formal oxidation of methanol. 0 CH2O InChI=1S/CH2O/c1-2/h1H2 WSFSSNUMVMOOMR-UHFFFAOYSA-N 30.02598 30.01056 [H]C([H])=O CHEBI:14274 CHEBI:24077 CHEBI:337763 CHEBI:5142 Beilstein:1209228 CAS:50-00-0 DrugBank:DB03843 Drug_Central:3244 Gmelin:445 HMDB:HMDB0001426 KEGG:C00067 KEGG:D00017 MetaCyc:FORMALDEHYDE PDBeChem:FOR PMID:110589 PMID:12686735 PMID:15091529 PMID:16423181 PMID:17618393 PMID:18837732 PMID:25042713 PMID:7381846 PMID:7548723 PMID:7689168 PMID:7896413 PMID:9686972 PPDB:359 Reaxys:1209228 UM-BBD_compID:c0122 Wikipedia:Formaldehyde FORMALDEHYDE Formaldehyde formaldehyde chebi_ontology FORMALIN Formaldehyd Formalin Methanal Methylene oxide Oxomethane Oxomethylene CHEBI:16842 formaldehyde A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class 0 C21H39N7O12 InChI=1S/C21H39N7O12/c1-5-21(36,4-30)16(40-17-9(26-2)13(34)10(31)6(3-29)38-17)18(37-5)39-15-8(28-20(24)25)11(32)7(27-19(22)23)12(33)14(15)35/h4-18,26,29,31-36H,3H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/t5-,6-,7+,8-,9-,10-,11+,12-,13-,14+,15+,16-,17-,18-,21+/m0/s1 UCSJYZPVAKXKNQ-HZYVHMACSA-N 581.57434 581.26567 CN[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O[C@H]1[C@@H](O[C@@H](C)[C@]1(O)C=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](NC(N)=N)[C@@H](O)[C@@H]1NC(N)=N CHEBI:15119 CHEBI:26784 CHEBI:45745 CHEBI:9284 Beilstein:74498 CAS:57-92-1 DrugBank:DB01082 Drug_Central:2481 HMDB:HMDB0015214 KEGG:C00413 KEGG:D08531 MetaCyc:STREPTOMYCIN PDBeChem:SRY PMID:11228320 PMID:11905029 PMID:12118520 PMID:13030054 PMID:13116094 PMID:13136149 PMID:13596285 PMID:13691614 PMID:13985260 PMID:13990247 PMID:14623118 PMID:14828344 PMID:14852338 PMID:14939639 PMID:15081082 PMID:15137533 PMID:15207172 PMID:15686853 PMID:15736038 PMID:16904706 PMID:17105735 PMID:17238915 PMID:17429930 PMID:18173084 PMID:18916143 PMID:19052412 PMID:19335957 PMID:21350946 PMID:21362244 PMID:21593257 PMID:21937264 PMID:22101040 Pesticides:streptomycin Reaxys:74498 Wikipedia:Streptomycin N,N'''-[(1R,2R,3S,4R,5R,6S)-4-{5-deoxy-2-O-[2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl]-3-C-formyl-alpha-L-lyxofuranosyloxy}-2,5,6-trihydroxycyclohexane-1,3-diyl]diguanidine STREPTOMYCIN chebi_ontology 2,4-Diguanidino-3,5,6-trihydroxycyclohexyl 5-deoxy-2-O-(2-deoxy-2-methylamino-alpha-L-glucopyranosyl)-3-C-formyl-beta-L-lyxopentanofuranoside Kantrex SM [2-deoxy-2-(dimethylamino)-alpha-L-glucopyranosyl]-(1->2)-[5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl]-(1->4)-{N',N'''-[(1,3,5/2,4,6)-2,4,5,6-tetrahydroxycyclohexane-1,3-diyl]diguanidine} streomycin streptomycin CHEBI:17076 streptomycin A glycosylglucose disaccharide, found most notably in milk, that consists of D-galactose and D-glucose fragments bonded through a beta-1->4 glycosidic linkage. The glucose fragment can be in either the alpha- or beta-pyranose form, whereas the galactose fragment can only have the beta-pyranose form. 0 C12H22O11 InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10-,11?,12+/m1/s1 GUBGYTABKSRVRQ-QKKXKWKRSA-N 342.297 342.11621 OC[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](O)C(O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@H]1O CHEBI:10296 CHEBI:10380 CHEBI:14497 CHEBI:22460 CHEBI:22760 CHEBI:25005 CHEBI:27755 CHEBI:613009 Beilstein:1292745 CAS:63-42-3 GlyGen:G74621DY GlyTouCan:G74621DY Gmelin:882872 KEGG:C00243 KEGG:D00046 KEGG:G10504 KNApSAcK:C00001136 PMID:1292745 PMID:17329833 PMID:18300214 PMID:19053747 PMID:19846069 PMID:19913595 PMID:20094999 PMID:20503067 PMID:20699559 PMID:20873837 PMID:20961532 PMID:21403918 PMID:2432147 PMID:2456994 PMID:28690131 PMID:28807538 PMID:6194884 PMID:7574700 Reaxys:1292745 beta-D-galactopyranosyl-(1->4)-D-glucopyranose lactose chebi_ontology (+)-lactose (Gal)1 (Glc)1 1-beta-D-Galactopyranosyl-4-D-glucopyranose 4-(beta-D-galactosido)-D-glucose 4-O-beta-D-galactopyranosyl-D-glucose D-lactose Galbeta1-4Glc Lac Laktobiose Laktose Milchzucker Milk sugar WURCS=2.0/2,2,1/[a2122h-1x_1-5][a2112h-1b_1-5]/1-2/a4-b1 beta-D-Gal-(1->4)-D-Glc beta-D-Galp-(1->4)-D-Glcp beta-Gal1,4-Glc lactobiose milk sugar CHEBI:17716 lactose Any of a group of aminoglycoside antibiotics produced by fermentation of some Micromonospora spp. CHEBI:14293 CHEBI:24206 CHEBI:24212 CHEBI:5306 CAS:1403-66-3 DrugBank:DB00798 KEGG:C00505 4,6-diamino-3-[3-deoxy-4-C-methyl-3-(methylamino)pentopyranosyloxy]-2-hydroxycyclohexyl 2-amino-2,3,4,6,7-pentadeoxy-6-(methylamino)heptopyranoside chebi_ontology Gentamicin gentamycins CHEBI:17833 gentamycin A glycosyl glycoside formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose. 0 C12H22O11 InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1 CZMRCDWAGMRECN-UGDNZRGBSA-N 342.29650 342.11621 OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O CHEBI:15128 CHEBI:26812 CHEBI:45795 CHEBI:9314 Beilstein:90825 CAS:57-50-1 DrugBank:DB02772 Drug_Central:4610 Gmelin:97695 HMDB:HMDB0000258 KEGG:C00089 KEGG:D00025 KEGG:D06533 KEGG:G00370 KNApSAcK:C00001151 MetaCyc:SUCROSE PDBeChem:SUC PMID:11021636 PMID:11093712 PMID:11111003 PMID:12065720 PMID:12706980 PMID:13508893 PMID:15291457 PMID:15660210 PMID:15792978 PMID:15845855 PMID:16228482 PMID:16304615 PMID:16313996 PMID:16525719 PMID:16660545 PMID:16663947 PMID:16665852 PMID:17233733 PMID:17439666 PMID:17597061 PMID:18625236 PMID:19199566 PMID:19726178 PMID:21703290 PMID:21972845 PMID:22085755 PMID:22311778 PMID:22404833 PMID:22751876 Reaxys:1435311 Reaxys:90825 Wikipedia:Sucrose SUCROSE Sucrose beta-D-fructofuranosyl alpha-D-glucopyranoside sucrose chebi_ontology 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside Cane sugar Saccharose Sacharose White sugar beta-D-Fruf-(2<->1)-alpha-D-Glcp sacarosa table sugar CHEBI:17992 sucrose Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity An inorganic chloride salt having sodium(1+) as the counterion. 0 ClNa InChI=1S/ClH.Na/h1H;/q;+1/p-1 FAPWRFPIFSIZLT-UHFFFAOYSA-M 58.44247 57.95862 [Na+].[Cl-] Beilstein:3534976 CAS:7647-14-5 Gmelin:13673 KEGG:C13563 KEGG:D02056 MetaCyc:NACL PPDB:595 Reaxys:3534976 Wikipedia:Sodium_Chloride sodium chloride chebi_ontology Kochsalz NaCl Natriumchlorid chlorure de sodium cloruro sodico common salt halite natrii chloridum rock salt salt table salt CHEBI:26710 sodium chloride A dipeptide obtained by formal condensation of the alpha-carboxy group of L-aspartic acid with the amino group of methyl L-phenylalaninate. Commonly used as an artificial sweetener. 0 C14H18N2O5 InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1 IAOZJIPTCAWIRG-QWRGUYRKSA-N 294.304 294.12157 C(C[C@@H](C(N[C@@H](CC1=CC=CC=C1)C(=O)OC)=O)N)(=O)O CHEBI:45047 Beilstein:2223850 CAS:22839-47-0 DrugBank:DB00168 HMDB:HMDB0001894 KEGG:C11045 KEGG:D02381 PDBeChem:PME PMID:1771173 PMID:2013754 PMID:21150094 PMID:21372000 PMID:22354473 PMID:24355796 PMID:24925367 PMID:24944748 PMID:24965331 PMID:25431414 PMID:25543075 PMID:25786106 PMID:25951455 PMID:25991916 PMID:26015492 PMID:26099025 PMID:26159964 PMID:26247507 PMID:26308194 PMID:26321723 PMID:26377607 PMID:26582819 PMID:26593524 PMID:26912665 PMID:27015640 PMID:27038223 PMID:27088715 PMID:27127997 PMID:27216413 PMID:27298583 PMID:27492574 PMID:27565676 PMID:27614095 PMID:27640132 PMID:27699780 PMID:27728881 PMID:27840415 PMID:27845306 PMID:30000570 PMID:37291632 PMID:37297402 PMID:37454665 Patent:US3492131 Reaxys:2223850 Wikipedia:Aspartame Aspartame methyl L-alpha-aspartyl-L-phenylalaninate chebi_ontology 1-methyl N-L-alpha-aspartyl-L-phenylalanate 3-Amino-N-(alpha-carboxyphenethyl)succinamic acid N-methyl ester 3-Amino-N-(alpha-methoxycarbonylphenethyl) succinamic acid AminoSweet Asp-phe-ome Aspartylphenylalanine methyl ester E 951 L-Aspartyl-L-phenylalanine methyl ester NutraSweet Sanecta aspartam aspartamo aspartamum CHEBI:2877 aspartame 0 C6H14O6 182.172 182.07904 CHEBI:15093 CHEBI:26724 CHEBI:26726 CHEBI:33795 CHEBI:33796 CHEBI:9201 Beilstein:1721909 Gmelin:83165 Wikipedia:Sorbitol glucitol chebi_ontology Sorbitol gulitol rel-(2R,3R,4R,5S)-hexane-1,2,3,4,5,6-hexol CHEBI:30911 glucitol A 1,2-benzisothiazole having a keto-group at the 3-position and two oxo substituents at the 1-position. It is used as an artificial sweetening agent. 0 C7H5NO3S InChI=1S/C7H5NO3S/c9-7-5-3-1-2-4-6(5)12(10,11)8-7/h1-4H,(H,8,9) CVHZOJJKTDOEJC-UHFFFAOYSA-N 183.18500 182.99901 O=C1NS(=O)(=O)c2ccccc12 CHEBI:49717 Beilstein:6888 CAS:81-07-2 Gmelin:4203 HMDB:HMDB0029723 KEGG:D01085 MetaCyc:CPD-5581 PDBeChem:LSA PMID:24456165 PMID:24549104 PMID:24739358 PMID:24780866 Reaxys:6888 Wikipedia:Saccharin 1,2-benzisothiazol-3(2H)-one 1,1-dioxide Saccharin chebi_ontology 1,1-Dioxo-1,2-benzisothiazol-3(2H)-one 1,1-Dioxo-1,2-dihydro-benzo[d]isothiazol-3-one 1,2-Benzisothiazol-3(2H)-one 1,1-dioxide 1,2-Benzisothiazolin-3-one 1,1-dioxide 1,2-Dihydro-2-ketobenzisosulfonazole 1,2-Dihydro-2-ketobenzisosulphonazole 2,3-Dihydro-3-oxobenzisosulfonazole 2,3-Dihydro-3-oxobenzisosulphonazole 3-Hydroxybenzisothiazole-S,S-dioxide Anhydro-o-sulfaminebenzoic acid Benzo-2-sulphimide Benzoic acid sulfimide Benzoic sulfimide Benzoic sulphimide Benzosulfimide Benzosulphimide Benzoylsulfonic Imide Saccharimide Saccharine o-Benzoic sulfimide o-Benzosulfimide o-Sulfobenzimide o-Sulfobenzoic acid imide CHEBI:32111 saccharin 0 AlH3O3 H3AlO3 InChI=1S/Al.3H2O/h;3*1H2/q+3;;;/p-3 WNROFYMDJYEPJX-UHFFFAOYSA-K 78.00356 77.98976 [H]O[Al](O[H])O[H] CHEBI:30193 CHEBI:31195 CAS:21645-51-2 Drug_Central:4250 Gmelin:22216 KEGG:C13391 KEGG:D02859 Wikipedia:Aluminum_Hydroxide aluminium(3+) hydroxide aluminium(III) hydroxide trihydroxidoaluminium chebi_ontology Al(OH)3 Aluminiumhydroxid Aluminum hydroxide CHEBI:33130 aluminium hydroxide CAS:7632-05-5 Wikipedia:Sodium_phosphates sodium phosphate chebi_ontology phosphoric acid, sodium salt sodium orthophosphate sodium phosphates sodium salt of phosphoric acid CHEBI:37586 sodium phosphate A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages. CAS:9004-54-0 KEGG:C00372 KEGG:D00060 KEGG:D06541 KEGG:G10502 PMID:8154046 chebi_ontology (1,6-alpha-D-Glucosyl)m (1,6-alpha-D-Glucosyl)m+1 (1,6-alpha-D-Glucosyl)n (1,6-alpha-D-Glucosyl)n+1 1,6-alpha-D-Glucan Dextran 40 Dextran 70 Dextran 75 dextran dextrane dextrano dextrans dextranum CHEBI:52071 dextran A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a dodecanoyl group. 0 C58H114O26 1226.75977 1226.760 Beilstein:8973037 CAS:9005-64-5 KEGG:C11624 KEGG:D05565 Reaxys:8187252 Reaxys:8973037 Wikipedia:Polysorbate_20 chebi_ontology Polyoxyethylene (20) sorbitan monolaurate Polyoxyethylene sorbitan monolaurate Polysorbate Polysorbate 20 Tween 20 polisorbato polysorbate polysorbatum CHEBI:53424 polysorbate 20 A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by an oleoyl group. 0 C64H124O26 1308.83802 1308.838 CHEBI:9785 Beilstein:8187125 CAS:9005-65-6 KEGG:C11625 KEGG:D01067 Reaxys:8187125 Reaxys:8190601 Reaxys:8898414 Reaxys:9040798 Wikipedia:Polysorbate_80 chebi_ontology Glycol (polysorbate 80) Polyethylene oxide sorbitan mono-oleate Polyoxyethylene (20) sorbitan monooleate Polyoxyethylene sorbitan monooleate Polyoxyethylene sorbitan oleate Polysorbate 80 Tween 80 polisorbato polysorbate polysorbatum CHEBI:53426 polysorbate 80 An organic sodium salt that is the monosodium salt of glutamic acid. 0 C5H8NNaO4 InChI=1S/C5H9NO4.Na/c6-3(5(9)10)1-2-4(7)8;/h3H,1-2,6H2,(H,7,8)(H,9,10);/q;+1/p-1 LPUQAYUQRXPFSQ-UHFFFAOYSA-M 169.11110 169.03510 [Na+].[NH3+]C(CCC([O-])=O)C([O-])=O PMID:22293291 Reaxys:17003240 sodium 2-azaniumylpentanedioate chebi_ontology MSG sodium 2-ammoniopentanedioate sodium glutamate CHEBI:64220 monosodium glutamate A broad-spectrum highly toxic antibiotic or mixture of antibiotics produced by a streptomyces (Streptomyces fradiae) and used medically especially to treat local infections. CAS:1404-04-2 DrugBank:DB00994 KEGG:C00384 KEGG:D08260 Neomycin chebi_ontology CHEBI:7507 neomycin An alkylmercury compound (approximately 49% mercury by weight) used as an antiseptic and antifungal agent. 0 C9H9HgNaO2S C9H9HgO2S.Na InChI=1S/C7H6O2S.C2H5.Hg.Na/c8-7(9)5-3-1-2-4-6(5)10;1-2;;/h1-4,10H,(H,8,9);1H2,2H3;;/q;;2*+1/p-2 RTKIYNMVFMVABJ-UHFFFAOYSA-L 404.81233 405.99274 [Na+].CC[Hg]Sc1ccccc1C([O-])=O Beilstein:8169555 CAS:54-64-8 Gmelin:1677155 KEGG:D00864 PMID:18837732 PMID:21616561 PMID:21785120 PMID:22015977 PMID:22366633 PMID:22658806 PMID:22811707 PMID:23145070 PMID:23223227 PMID:23282150 PMID:23401210 PMID:23554557 PMID:23843785 PMID:23949514 PMID:23965928 PMID:23992327 PMID:25042713 PPDB:3062 Reaxys:8169555 VSDB:3062 Thimerosal sodium [(2-carboxylatophenyl)sulfanyl](ethyl)mercurate(1-) sodium ethyl[2-(sulfanyl-kappaS)benzoato(2-)]mercurate(1-) chebi_ontology Merthiolate Thiomersal [(o-carboxyphenyl)thio]ethylmercury sodium salt ethyl(2-mercaptobenzoato-S)mercury sodium salt ethylmercurithiosalicylate sodium ethylmercurithiosalicylic acid sodium salt mercurothiolate o-(ethylmercurithio)benzoic acid sodium salt sodium ethylmercurithiosalicylate sodium merthiolate thiomersal thiomersalate thiomersalum tiomersal CHEBI:9546 thimerosal A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. hepatocyte A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. macrophage A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions. infectious disease DOID:10115 DOID:11078 DOID:1304 DOID:1321 DOID:2040 DOID:2288 DOID:3099 DOID:4120 DOID:4620 DOID:5256 DOID:945 DOID:95 DOID:9532 DOID:9696 ICD9CM:079.0 UMLS_CUI:C0001485 infectious disease disease_ontology DOID:0050117 DO:wk disease by infectious agent A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread. disease_ontology DOID:0050338 primary bacterial infectious disease A cancer that is classified by the type of cell from which it is derived. snadendla 2011-06-13T03:28:50Z disease_ontology DOID:0050687 cell type cancer A disease by infectious agent that results_in infection, has_material_basis_in Bacteria. ICD10CM:A49.9 MESH:D001424 NCI:C2890 SNOMEDCT_US_2023_03_01:87628006 UMLS_CUI:C0004623 disease_ontology DOID:104 bacterial infectious disease A brucellosis that involves an infection caused by Brucella suis [NCBITaxon:29461] in swine and humans. The disease has_symptom fever, has_symptom chills, has_symptom malaise, has_symptom diaphoresis, has_symptom arthralgia, has_symptom myalgia, has_symptom headache, has_symptom anorexia, and has_symptom fatigue. disease_ontology DOID:11076 Brucella suis brucellosis A primary bacterial infectious disease that is caused by the bacteria of the genus Brucella, when humans come in contact with contaminated animals or animal products or ingestion of infected food products. The disease has_symptom fever, has_symptom sweat, has_symptom headache, has_symptom back pain, has_symptom physical weakness, has_symptom joint pain and has_symptom fatigue. DOID:0050060 GARD:5966 ICD10CM:A23 ICD9CM:023 MESH:D002006 NCI:C84602 SNOMEDCT_US_2023_03_01:154296006 UMLS_CUI:C0006309 Maltese fever undulant fever disease_ontology Bang's disease Gibraltar fever Malta fever Mediterranean fever DOID:11077 brucellosis A parasitic protozoa infectious disease characterized as a vector-borne infectious disease caused by the presence of protozoan parasites of the genus Plasmodium in the red blood cells, transmitted from an infected to an uninfected individual by the bite of anopheline mosquitoes, and characterized by periodic attacks of chills and fever that coincide with mass destruction of blood cells and the release of toxic substances by the parasite at the end of each reproductive cycle. DOID:12552 EFO:0001068 GARD:6961 ICD10CM:B54 ICD9CM:084 MESH:D008288 NCI:C34797 SNOMEDCT_US_2023_03_01:154374002 UMLS_CUI:C0024530 induced malaria disease_ontology DOID:12365 Xref MGI. malaria A disease by infectious agent that is carried out by a parasite which by definition is a pathogen that simultaneously injures and derives sustenance from its host. DOID:11681 DOID:13509 DOID:1396 DOID:1494 DOID:2114 DOID:2293 DOID:2922 DOID:3564 DOID:4191 DOID:886 DOID:948 DOID:9639 DOID:9644 ICD10CM:H44.12 ICD9CM:360.13 NCI:C34587 SNOMEDCT_US_2023_03_01:57100005 UMLS_CUI:C0014238 Ectoparasitic disease parasitemia disease_ontology DOID:1398 parasitic infectious disease A malaria described as a severe form of the disease caused by a parasite Plasmodium falciparum, which is marked by irrregular recurrence of paroxysms and prolonged or continuous fever. ICD10CM:B50 ICD9CM:084.0 MESH:D016778 NCI:C34798 SNOMEDCT_US_2023_03_01:62676009 UMLS_CUI:C0024535 Malaria fever, subtertian falciparum malaria malignant tertian fever disease_ontology DOID:14067 Plasmodium falciparum malaria A brucellosis that involves an infection caused by Brucella melitensis [NCBITaxon:29459] in cattle, goats, sheep and humans. The disease has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom limb pain and has_symptom back pain. ICD10CM:A23.0 ICD9CM:023.0 SNOMEDCT_US_2023_03_01:186305007 UMLS_CUI:C0302362 disease_ontology DOID:14456 Brucella melitensis brucellosis A brucellosis that involves an infection caused by Brucella abortus [NCBITaxon:235] in cattle and humans. The disease has_symptom fever, has_symptom chills, has_symptom sweats, has_symptom weight loss, has_symptom malaise, has_symptom headaches, has_symptom myalgia, and has_symptom arthralgia. ICD10CM:A23.1 ICD9CM:023.1 MESH:D002007 SNOMEDCT_US_2023_03_01:427795000 UMLS_CUI:C0302363 disease_ontology DOID:14457 Brucella abortus brucellosis A disease that is characterized by abnormally rapid cell division. neoplasm DOID:0000818 cell process disease neoplasm disease_ontology DOID:14566 disease of cellular proliferation A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. DOID:3226 ICD10CM:J98 ICD9CM:519 SNOMEDCT_US_2023_03_01:155603009 UMLS_CUI:C0029582 disease_ontology DOID:1579 respiratory system disease A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80.1 ICD9CM:199 ICDO:8000/3 MESH:D009369 NCI:C9305 SNOMEDCT_US_2023_03_01:269513004 UMLS_CUI:C0006826 malignant neoplasm malignant tumor primary cancer disease_ontology DOID:162 Updating out dated UMLS CUI. cancer A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from melanocytes which are found in skin, the bowel and the eye. EFO:0000756 ICDO:8720/3 KEGG:05218 MESH:D008545 NCI:C3224 SNOMEDCT_US_2023_03_01:2092003 UMLS_CUI:C0025202 Naevocarcinoma malignant melanoma disease_ontology DOID:1909 melanoma MESH:D008545 A parasitic infectious disease that is caused by parasitic protozoa which are microorganisms classified as unicellular eukaryotes. DOID:0060003 DOID:10553 DOID:3734 DOID:3804 DOID:947 ICD10CM:B64 MESH:D011528 NCI:C34953 SNOMEDCT_US_2023_03_01:95896000 UMLS_CUI:C0033740 mastigophora infectious disease sarcomastigophora infectious disease disease_ontology DOID:2789 parasitic protozoa infectious disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MESH:D004194 NCI:C2991 SNOMEDCT_US_2023_03_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease A viral infectious disease that results in destruction of immune system, leading to life-threatening opportunistic infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted by sexual contact, transmitted by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted by congenital method, and transmitted by contaminated needles. The virus infects helper T cells (CD4+ T cells) which are directly or indirectly destroyed, macrophages, and dendritic cells. The infection has symptom diarrhea, has symptom fatigue, has symptom fever, has symptom vaginal yeast infection, has symptom headache, has symptom mouth sores, has symptom muscle aches, has symptom sore throat, and has symptom swollen lymph glands. ICD10CM:B20 ICD9CM:042-042.99 MESH:D015658 NCI:C3108 SNOMEDCT_US_2023_03_01:86406008 UMLS_CUI:C0019693 HIV infection disease_ontology DOID:526 human immunodeficiency virus infectious disease A disease that manifests in a defined anatomical structure. DOID:1 DOID:2 DOID:5 DOID:71 DOID:72 DOID:8 disease_ontology DOID:7 disease of anatomical entity A viral infectious disease that results in infection, located in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness. DOID:8468 ICD10CM:J11.1 ICD9CM:487 MESH:D007251 NCI:C53482 SNOMEDCT_US_2023_03_01:155559006 UMLS_CUI:C0021400 Influenza with other manifestations flu influenza with non-respiratory manifestation disease_ontology DOID:8469 influenza A disease by infectious agent that results in infection, has_material_basis_in Viruses. DOID:1329 ICD10CM:A94 ICD10CM:B34.9 ICD9CM:060-066.99 MESH:D001102 MESH:D014777 NCI:C3439 NCI:C34396 SNOMEDCT_US_2023_03_01:34014006 SNOMEDCT_US_2023_03_01:40610006 UMLS_CUI:C0003723 UMLS_CUI:C0042769 Viral Infection Viral disease virus infection disease_ontology DOID:934 viral infectious disease fma FMA:12278 Hormone An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). Wikipedia:Adaptive_immune_system acquired immune response immune memory response biological_process GO:0002250 adaptive immune response An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract. GO:0002386 GO:0002422 immune response in MALT immune response in mucosal-associated lymphoid tissue immune response in urogenital tract biological_process GO:0002385 mucosal immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. biological_process GO:0006955 immune response A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. antibody cellular_component GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein-containing complex Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. cell division A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z IgG1 IgG2 IgG2a IgG2b IgG2c IgG3 IgG4 cellular_component GO:0071735 Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. IgG immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z cellular_component GO:0071738 Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgD immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z cellular_component GO:0071742 Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgE immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z IgA1 antibody IgA2 antibody cellular_component GO:0071745 Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgA immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z cellular_component GO:0071753 Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgM immunoglobulin complex conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. A report that is published in a journal. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert OBI_0000159 group:OBI journal article data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI OBI_0000099 report data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document publication journal article, newspaper story, book, etc. A document that is the output of a publishing process. PERSON: Chris Stoeckert PERSON: Jie Zheng PERSON: Lawrence Hunter published document Revisit the term in Octorber 2020. Improve the defintion. publication denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. Albert Goldfain Alexander Diehl Lindsay Cowell In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen. The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction. parasite role A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized. infectious agent role A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. pathogen role A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host. Albert Goldfain Alexander Diehl Lindsay Cowell primary host role The role is realized in developmental and reproduction processes of the host's partner in symbiosis. definitive host role A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle. intermediate host role A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced. parasite host role An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role. infectious agent vector role An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector. Albert Goldfain Alexander Diehl Lindsay Cowell biological vector of infectious agent role A disposition to initiate processes that result in a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell pathogenicity A pathogenic disposition is realized in processes that create a disorder. The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. pathogenic disposition A material entity with a pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen A biological macromolecule produced by a pathogen and that has a virulence factor disposition. Albert Goldfain Alexander Diehl Lindsay Cowell virulence factor house mouse mouse NCBITaxon:85055 GC_ID:1 house mouse mouse ncbi_taxonomy Mus musculus GC_ID:1 rat rats ncbi_taxonomy Rattus NCBITaxon:84274 GC_ID:1 domestic guinea pig guinea pig ncbi_taxonomy Cavia aperea porcellus Cavia cobaya Mus porcellus Cavia porcellus GC_ID:1 chinchillas chinchillas and viscachas ncbi_taxonomy Chinchillidae GC_ID:1 ncbi_taxonomy Vira Viridae viruses Viruses GC_ID:1 ncbi_taxonomy Poxviridae GC_ID:1 ncbi_taxonomy Chordopoxvirinae GC_ID:1 ncbi_taxonomy Orthopoxvirus NCBITaxon:130669 NCBITaxon:130670 GC_ID:1 monkey pox virus ncbi_taxonomy Monkeypox virus GC_ID:1 vaccinia virus VV ncbi_taxonomy Vaccinia virus NCBITaxon:12871 GC_ID:1 small pox virus smallpox smallpox virus variola virus VAR ncbi_taxonomy Variola virus GC_ID:1 Contagious pustular dermatitis virus ncbi_taxonomy Orf virus GC_ID:1 ncbi_taxonomy Avipoxvirus FWPV GC_ID:1 Avipoxvirus clade A1 Fowlpoxvirus fowl poxvirus fowlpox virus FP fowlpox virus FPV ncbi_taxonomy Fowlpox virus GC_ID:1 Pigeon pox virus Pigeon poxvirus pigeonpox virus PPV ncbi_taxonomy Pigeonpox virus GC_ID:1 H5N1 ncbi_taxonomy H5N1 subtype GC_ID:1 ncbi_taxonomy Herpesviridae GC_ID:1 Alphaherpesviruses ncbi_taxonomy Alphaherpesvirinae GC_ID:1 ncbi_taxonomy Simplexvirus HSV-1 HSV1 GC_ID:1 Herpes simplex virus type 1 Human herpesvirus type 1 herpes simplex virus 1 HSV-1 herpes simplex virus HSV-1 herpes simplex virus type 1 HSV-1 herpes simplex virus type 1 HSV1 herpes simplex virus type-1 HSV-1 ncbi_taxonomy Herpes simplex virus 1 Human herpesvirus 1 Human alphaherpesvirus 1 HSV2 GC_ID:1 Herpes simplex virus (type 2) Herpes simplex virus II Herpes simplex virus type 2 Herpes simplex virus type 2 (HSV-2) Human herpesvirus 2 ncbi_taxonomy Herpes simplex virus 2 herpes simplex virus type 2 HSV-2 Human alphaherpesvirus 2 GC_ID:1 ncbi_taxonomy Varicellovirus NCBITaxon:11265 NCBITaxon:12738 BoHV-1 GC_ID:1 Bovine herpesvirus 1 Bovine herpesvirus type 1 Bovine herpesvirus-1 Bovine rhinotracheitis virus bovine herpesvirus 1 BHV 1 bovine herpesvirus 1 BHV-1 bovine herpesvirus 1 BHV1 bovine herpesvirus BHV-1 bovine herpesvirus type 1 BHV-1 bovine herpesvirus type-1 BHV-1 infectious bovine rhinotracheitis virus BHV-1 ncbi_taxonomy Infectious bovine rhinotracheitis virus Bovine alphaherpesvirus 1 EHV-1 GC_ID:1 Equid herpesvirus 1 Equine herpesvirus 1 Equine herpesvirus type 1 Equine herpesvirus-1 equine abortion virus equine herpesvirus 1 EHV-1 equine herpesvirus type-1 ncbi_taxonomy equine herpesvirus type 1 EHV-1 Equid alphaherpesvirus 1 GC_ID:1 Felid herpesvirus 1 Feline alphaherpesvirus 1 Feline herpesvirus 1 Feline herpesvirus type 1 feline herpesvirus feline herpesvirus type 1 FHV-1 feline herpesvirus-1 feline herpesvirus-1 FHV-1 ncbi_taxonomy Felid alphaherpesvirus 1 HHV-3 VZV GC_ID:1 Human herpes virus 3 Human herpesvirus 3 Varicella Zoster Virus Varicella-zoster virus varicella zoster virus VZV varicella-zoster virus VZV ncbi_taxonomy Human alphaherpesvirus 3 NCBITaxon:44156 PRV GC_ID:1 Alphaherpesvirus pseudorabies virus PRV Aujeszky's disease virus Pseudorabies Virus PRV Pseudorabies virus Suid herpesvirus 1 Suid herpesvirus type 1 ncbi_taxonomy Suid alphaherpesvirus 1 GC_ID:1 Betaherpesviruses ncbi_taxonomy Betaherpesvirinae HHV-5 GC_ID:1 Human cytomegalovirus Human herpesvirus 5 human herpesvirus type 5 ncbi_taxonomy Human betaherpesvirus 5 GC_ID:1 Mouse cytomegalovirus 1 Murid herpesvirus 1 Murine cytomegalovirus murine cytomegalovirus (MCMV) murine cytomegalovirus MCMV murine herpesvirus 1 ncbi_taxonomy Murid betaherpesvirus 1 NCBITaxon:10342 NCBITaxon:12743 NCBITaxon:46620 GaHV-1 ILTV GC_ID:1 Avian infectious laryngotracheitis virus Gallid herpesvirus 1 Gallid herpesvirus type 1 Laryngotracheitis virus infectious laryngotracheitis virus ILTV ncbi_taxonomy Infectious laryngotracheitis virus Gallid alphaherpesvirus 1 NCBITaxon:38013 NCBITaxon:39111 NCBITaxon:43684 GaHV-2 MDV1 GC_ID:1 Gallid herpesvirus 2 Gallid herpesvirus type 2 Marek disease virus Marek disease virus type 1 Marek's disease herpesvirus Marek's disease herpesvirus 1 Marek's disease virus Marek's disease virus (MDV) Marek's disease virus MDV Marek's disease virus MDV1 Marek's disease virus serotype 1 MDV-1 Marek's disease virus type 1 MDV1 Mareks disease virus ncbi_taxonomy Marek's disease virus type 1 Gallid alphaherpesvirus 2 GC_ID:1 mammalian hepatitis B-type viruses ncbi_taxonomy Orthohepadnavirus HBV GC_ID:1 Human hepatitis B virus hepatitis B virus (HBV) hepatitis B virus HBV hepatitis B virus, HBV human hepatitis B virus HBV ncbi_taxonomy Hepatitis B virus NCBITaxon:72150 GC_ID:1 Anatid Herpes virus-1 Anatid herpesvirus 1 Duck enteritis virus Duck plague virus ncbi_taxonomy Anatid alphaherpesvirus 1 GC_ID:1 Baculovirus Baculovirus sp. ncbi_taxonomy unidentified baculovirus ASFV GC_ID:1 African swine fever virus ASF African swine fever virus ASFV African swine fever virus, ASFV ncbi_taxonomy African swine fever virus GC_ID:1 ncbi_taxonomy Adenoviridae GC_ID:1 ncbi_taxonomy Mastadenovirus NCBITaxon:12607 GC_ID:1 Canine adenovirus type 1 Canine adenovirus type 1 Cav-1 Mastadenovirus c1 Mastadenovirus can1 canine adenovirus type 1 Can1 dog adenovirus 1 ncbi_taxonomy Canine adenovirus 1 GC_ID:1 Canine adenovirus type 2 Canine adenovirus type 2 Cav-1 Mastadenovirus c2 Mastadenovirus can2 dog adenovirus 2 ncbi_taxonomy Canine adenovirus 2 GC_ID:1 Adenovirus ncbi_taxonomy unidentified adenovirus GC_ID:1 Canine adenovirus Canine adenovirus A ncbi_taxonomy Canine mastadenovirus A GC_ID:1 Human Papilloma Virus human papillomavirus HPV ncbi_taxonomy Human papillomavirus GC_ID:1 ncbi_taxonomy Bovine papillomavirus GC_ID:11 ncbi_taxonomy Clostridium perfringens (type D) Clostridium perfringens D FPLV GC_ID:1 Feline panleucopenia virus Feline panleukopaenia virus ncbi_taxonomy Feline panleukopenia virus GC_ID:1 ncbi_taxonomy Feline panleukopenia virus (strain 193) CPV GC_ID:1 ncbi_taxonomy Canine parvovirus MEV GC_ID:1 ncbi_taxonomy Mink enteritis virus PPV GC_ID:1 porcine parvovirus PPV ncbi_taxonomy Porcine parvovirus GC_ID:1 Orbiviridae Orbiviruses ncbi_taxonomy Orbivirus GC_ID:1 Rotaviruses ncbi_taxonomy Rotavirus GC_ID:1 ncbi_taxonomy Porcine rotavirus GC_ID:1 bovine rotavirus BRV ncbi_taxonomy Bovine rotavirus GC_ID:1 ncbi_taxonomy Equine rotavirus GC_ID:1 ncbi_taxonomy Birnaviridae NCBITaxon:12740 IBDV GC_ID:1 Avian infectious bursal disease virus Gumboro virus Infectious bursal disease virus of chickens infectious bursal disease virus IBDV ncbi_taxonomy Infectious bursal disease virus NCBITaxon:12744 IPNV GC_ID:1 infectious pancreatic necrosis virus IPNV ncbi_taxonomy Infectious pancreatic necrosis virus GC_ID:1 Alphaviridae arboviruses group A ncbi_taxonomy Alphavirus GC_ID:1 Eastern equine encephalomyelitis virus eastern equine encephalomyelitis EEE eastern equine encephalomyelitis virus EEEV ncbi_taxonomy Eastern equine encephalitis virus GC_ID:1 ncbi_taxonomy Sindbis virus VEE VEEV GC_ID:1 Venezuelan equine encephalitis VEE Venezuelan equine encephalitis virus VEE Venezuelan equine encephalomyelitis virus ncbi_taxonomy Venezuelan equine encephalitis virus GC_ID:1 ncbi_taxonomy Western equine encephalomyelitis virus Western equine encephalitis virus GC_ID:1 ncbi_taxonomy Rubivirus GC_ID:1 ncbi_taxonomy Rubella virus EAV GC_ID:1 ncbi_taxonomy Equine arteritis virus GC_ID:1 Flavivirus (arbovirus group B) ncbi_taxonomy Flaviviridae GC_ID:1 arboviruses group B ncbi_taxonomy Flavivirus GC_ID:1 Japanese encephalitis (JE) virus Japanese encephalitis virus JE Japanese encephalitis virus JEV ncbi_taxonomy Japanese encephalitis virus WNV GC_ID:1 ncbi_taxonomy West Nile virus TBEV GC_ID:1 FSME virus Tick born encephalitis virus tick-borne encephalitis virus TBE virus tick-borne encephalitis virus TBEV ncbi_taxonomy Tick-borne encephalitis virus YFV GC_ID:1 Flavivirus febricis yellow fever virus YFV ncbi_taxonomy Yellow fever virus GC_ID:1 PMID:12832207 PMID:7747470 ncbi_taxonomy Pestivirus NCBITaxon:12625 NCBITaxon:54314 GC_ID:1 PMID:7747470 Hog cholera virus Pestivirus type 2 classical swine fever virus CSFV swine fever virus ncbi_taxonomy Classical swine fever virus NCBITaxon:121864 BVDV BVDV-1 GC_ID:1 PMID:7747470 Bovine viral diarrhea virus Bovine viral diarrhea virus type 1 Bovine viral diarrhea virus-1 Mucosal disease virus Pestivirus type 1 bovine viral diarrhea virus BVDV bovine viral diarrhea virus type I ncbi_taxonomy Bovine viral diarrhea virus 1 GC_ID:11 PMID:11411686 PMID:28066339 ncbi_taxonomy Porphyromonas gulae GC_ID:1 ncbi_taxonomy Coronaviridae IBV GC_ID:1 Avian infectious bronchitis virus avian infectious bronchitis coronavirus IBV avian infectious bronchitis virus IBV avian infectious bronchitis virus, IBV infectious bronchitis virus IBV ncbi_taxonomy Infectious bronchitis virus BCV BECV GC_ID:1 Bovine enteritic coronavirus Bovine enteritic coronavirus BECV bovine coronavirus BCV bovine enteric coronavirus calf diarrheal coronavirus neonatal calf diarrhea virus ncbi_taxonomy Bovine coronavirus FIPV GC_ID:1 ncbi_taxonomy Feline infectious peritonitis virus NCBITaxon:12859 TGEV GC_ID:1 Porcine transmissable gastroenteritis coronavirus Porcine transmissible gastroenteritis coronavirus porcine transmissible gastroenteritis virus transmissible gastroenteritis coronavirus transmissible gastroenteritis virus TGEV ncbi_taxonomy Transmissible gastroenteritis virus GC_ID:1 Canine enteric coronavirus canine coronavirus CCV ncbi_taxonomy Canine coronavirus GC_ID:1 negative-sense genome single-stranded RNA viruses ncbi_taxonomy Mononegavirales GC_ID:1 ncbi_taxonomy Paramyxoviridae GC_ID:1 Morbilliviruses ncbi_taxonomy Morbillivirus NCBITaxon:11230 GC_ID:1 Cell-associated subacute sclerosing panencephalitis Measles virus Subacute sclerosing panencephalitis virus measles virus MV rougeole virus rubeola virus subacute sclerose panencephalitis virus subacute sclerosing panencephalitis virus, SSPEV ncbi_taxonomy Measles morbillivirus RDV GC_ID:1 Rinderpest virus rinderpest virus RPV rinderpest virus RV ncbi_taxonomy Rinderpest morbillivirus GC_ID:1 Pneumovirinae ncbi_taxonomy Pneumoviridae NCBITaxon:12604 BRS BRSV GC_ID:1 Bovine respiratory syncytial virus bovine RSV bovine respiratory syncytial virus BRSV ncbi_taxonomy Bovine orthopneumovirus HRSV GC_ID:1 Human respiratory syncytial virus human RSV ncbi_taxonomy Human orthopneumovirus NCBITaxon:11267 GC_ID:1 Filovirus ncbi_taxonomy Filoviridae GC_ID:1 PMID:16186241 ncbi_taxonomy Rhabdoviridae GC_ID:1 ncbi_taxonomy Lyssavirus NCBITaxon:12873 NCBITaxon:12874 VHSV GC_ID:1 Haemorrhagic septicemia virus Hemorrhagic septicemia virus Viral haemorrhagic septicaemia virus hemorragic septicemy virus of fish viral haemorrhagic scepticaemia virus VHS viral haemorrhagic septicaemia virus VHSV viral hemorrhagic septicemia virus VHSV ncbi_taxonomy Viral hemorrhagic septicemia virus IHNV GC_ID:1 ncbi_taxonomy Infectious hematopoietic necrosis virus GC_ID:1 Rabies lyssavirus Rabies virus ncbi_taxonomy Lyssavirus rabies GC_ID:1 ncbi_taxonomy Orthomyxoviridae GC_ID:1 Influenza virus Influenza virus sp. Influenzavirus avian influenza virus ncbi_taxonomy unidentified influenza virus GC_ID:1 Dhori thogotovirus Dhori virus Tick-borne virus ncbi_taxonomy Thogotovirus dhoriense FLUAV GC_ID:1 Human Influenza A Virus Influenza virus type A influenza A virus ncbi_taxonomy Influenza A virus GC_ID:1 H1N1 ncbi_taxonomy H1N1 subtype RVFV GC_ID:1 ncbi_taxonomy Rift Valley fever virus NCBITaxon:11835 NCBITaxon:11872 NCBITaxon:36380 GC_ID:1 Avian reticuloendotheliosis virus reticuloendotheliosis virus A REV-A reticuloendotheliosis virus REV-A ncbi_taxonomy Reticuloendotheliosis virus GC_ID:1 Lentivirinae ncbi_taxonomy Lentivirus FIV GC_ID:1 feline immunodeficiency virus FIV ncbi_taxonomy Feline immunodeficiency virus NCBITaxon:11677 NCBITaxon:11739 NCBITaxon:11740 CIV SIV GC_ID:1 Chimpanzee immunodeficiency virus Chimpanzee immunodeficiency virus (SIV(CPZ)) Simian immunodeficiency virus SIVcpz simian immunodeficiency virus SIV simian immunodeficiency virus, SIV simian immunodeficiency viruses SIV ncbi_taxonomy Simian immunodeficiency virus GC_ID:1 fish fishes ncbi_taxonomy Agnatha Hyperotreti Myxini NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy Euteleostomi NCBITaxon:11920 GC_ID:1 Feline leukemia provirus feline leukemia virus FeLV ncbi_taxonomy Feline leukemia virus BLV GC_ID:1 bovine leukemia virus BLV bovine leukemia virus, BLV ncbi_taxonomy Bovine leukemia virus GC_ID:1 ncbi_taxonomy Enoplea GC_ID:1 ncbi_taxonomy Caliciviridae NCBITaxon:12806 NCBITaxon:31701 RHDV GC_ID:1 Rabbit haemorrhagic disease virus rabbit hemorrhagic disease virus RHDV ncbi_taxonomy Rabbit hemorrhagic disease virus FCV GC_ID:1 Feline vesivirus feline calicivirus FCV ncbi_taxonomy Feline calicivirus GC_ID:1 ncbi_taxonomy Picornavirus Picornaviridae NCBITaxon:12128 GC_ID:1 Enteroviruses ncbi_taxonomy Enterovirus GC_ID:1 ncbi_taxonomy Coxsackievirus GC_ID:1 ncbi_taxonomy Ecdysozoa HPV-1 PV1 GC_ID:1 Human poliovirus 1 Human poliovirus type 1 Polio virus 1 Poliovirus type 1 poliovirus type 1 PV1 ncbi_taxonomy Poliovirus 1 HPV-2 GC_ID:1 Human Poliovirus type 2 Human poliovirus 2 Poliovirus type 2 ncbi_taxonomy Poliovirus 2 HPV-3 GC_ID:1 Human poliovirus 3 Human poliovirus type 3 Polio virus 3 ncbi_taxonomy Poliovirus serotype 3 Poliovirus type 3 Poliovirus 3 GC_ID:1 ncbi_taxonomy Hepatovirus HAV GC_ID:1 Hepatitis A virus ncbi_taxonomy Hepatovirus A FMDV GC_ID:1 Foot and mouth disease virus foot and mouth disease virus FMDV foot-and-mouth disease virus FMDV ncbi_taxonomy Foot-and-mouth disease virus GC_ID:11 PMID:11321122 PMID:11837318 purple photosynthetic bacteria and relatives ncbi_taxonomy "Alphaproteobacteriota" Whitman et al. 2018 Alphaproteobacteriota Proteobacteria Proteobacteriota proteobacteria Pseudomonadota GC_ID:11 PMID:23334881 ncbi_taxonomy Proteobacteria gamma subdivision Pseudomonadia Purple bacteria, gamma subdivision g-proteobacteria gamma proteobacteria gamma subdivision gamma subgroup Gammaproteobacteria GC_ID:11 PMID:1371057 ncbi_taxonomy Piscirickettsia salmonis NCBITaxon:31968 GC_ID:11 PMID:10555317 PMID:11034484 PMID:11542017 PMID:15143038 PMID:25403554 PMID:37409558 Firmicutes low G+C Gram-positive bacteria low GC Gram+ ncbi_taxonomy "Firmicutes" corrig. Gibbons and Murray 1978 (Approved Lists 1980) Bacillaeota Bacillota corrig. Gibbons and Murray 2021 Bacillus/Clostridium group Clostridium group firmicutes Firmicuteota Low G+C firmicutes clostridial firmicutes firmicutes Bacillota BDV GC_ID:1 PMID:25449305 Borna disease virus BDV ncbi_taxonomy Borna disease virus NCBITaxon:12682 HDV GC_ID:1 Hepatitis D virus hepatitis delta virus HDV ncbi_taxonomy Hepatitis delta virus CAV GC_ID:1 Chicken infectious anemia virus chicken anaemia agent CAA chicken anemia virus CAV chicken anemia virus, CAV ncbi_taxonomy chicken anaemia agent virus CAA Chicken anemia virus GC_ID:1 ncbi_taxonomy Dengue virus HIV GC_ID:1 ncbi_taxonomy AIDS virus Human immunodeficiency virus GC_ID:11 PMID:10319469 PMID:10319495 PMID:10425778 PMID:10758876 PMID:12656157 PMID:17220435 PMID:9734063 ncbi_taxonomy Aurococcus Staphylococcus NCBITaxon:325213 NCBITaxon:46170 NCBITaxon:72759 GC_ID:11 PMID:31023808 PMID:8573498 ncbi_taxonomy Micrococcus aureus Micrococcus pyogenes Staphlococcus pyogenes citreus Staphylococcus aureus subsp. anaerobius Staphylococcus pyogenes aureus Staphylococcus aureus RSV GC_ID:1 respiratory syncytial virus RS respiratory syncytial virus RS virus respiratory syncytial virus RSV ncbi_taxonomy Respiratory syncytial virus GC_ID:1 ncbi_taxonomy Swine influenza virus GC_ID:11 PMID:10555340 PMID:14657115 PMID:1720654 PMID:19620365 PMID:19880633 PMID:7537076 PMID:8995803 ncbi_taxonomy Streptococcus GC_ID:11 PMID:23245487 PMID:5220563 PMID:9731300 PMID:9734065 ncbi_taxonomy Streptococcus suis NCBITaxon:76757 GC_ID:11 PMID:15774692 PMID:8995807 ncbi_taxonomy Streptoccocus de la mammite Streptococcus agalactiae contagiosae Streptococcus difficile Streptococcus difficilis Streptococcus mastitidis Streptococcus agalactiae GC_ID:11 ncbi_taxonomy Diplococcus pneumoniae Micrococcus pneumoniae Streptococcus pneumoniae GC_ID:11 ncbi_taxonomy Micrococcus scarlatinae Streptococcus erysipelatos Streptococcus hemolyticus Streptococcus scarlatinae Streptococcus pyogenes MERS MERS-CoV GC_ID:1 MERS coronavirus MERS virus Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Middle East respiratory syndrome coronavirus ncbi_taxonomy Middle East respiratory syndrome-related coronavirus GC_ID:11 ncbi_taxonomy Streptococcus equi GC_ID:1 ncbi_taxonomy Dicentrarchus GC_ID:1 European sea bass European seabass ncbi_taxonomy Labrax labrax Morone labrax Perca labrax Roccus labrax Sciaena labrax Dicentrarchus labrax GC_ID:11 PMID:11075904 PMID:11542017 PMID:16558735 PMID:1917844 PMID:23908650 ncbi_taxonomy spirochetes Spirochaetales NCBITaxon:2954866 GC_ID:11 ncbi_taxonomy Bacillus/Staphylococcus group Caryophanales Bacillales GC_ID:11 PMID:10843090 PMID:11491334 PMID:1742196 PMID:2223602 PMID:23475340 PMID:7727277 PMID:8138135 PMID:8863420 Bacillus Bacillus rRNA group 1 ncbi_taxonomy Bacillus <firmicutes> NCBITaxon:138953 GC_ID:1 Enterovirus EV-C Human enterovirus C Poliovirus ncbi_taxonomy Enterovirus C GC_ID:11 PMID:1380285 PMID:1503971 PMID:24744012 PMID:7699027 PMID:7981102 PMID:8995796 PMID:9336916 Lyme disease spirochete ncbi_taxonomy Borrelia burgdorferi Borreliella burgdorferi NCBITaxon:1494525 NCBITaxon:1494531 NCBITaxon:1494577 GC_ID:11 PMID:8123566 anthrax anthrax bacterium ncbi_taxonomy Bacillus cereus var. anthracis Bacteridium anthracis Bacillus anthracis GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria Boreoeutheria NCBITaxon:69207 GC_ID:11 PMID:26643615 PMID:27488356 ncbi_taxonomy Anaerobacter Clostridium GC_ID:1 ncbi_taxonomy Euteleosteomorpha NCBITaxon:29368 GC_ID:11 PMID:10028279 PMID:15244052 ncbi_taxonomy Bacillus botulinus Bacillus putrificus Botulobacillus botulinus Clostridium putrificum Ermengemillus botulinus Pacinia putrifica Clostridium botulinum NCBITaxon:2588446 NCBITaxon:2588447 NCBITaxon:41533 NCBITaxon:592 GC_ID:11 PMID:10758910 Salmonella enterica serovar Enteritidis ncbi_taxonomy Bacillus enteritidis Salmonella enteritidis Salmonella enterica subsp. enterica serovar Enteritidis GC_ID:1 ncbi_taxonomy Canine parainfluenza virus GC_ID:11 PMID:11043982 ncbi_taxonomy Yersinia enterocolitica subsp. enterocolitica NCBITaxon:1683536 GC_ID:11 PMID:1374625 PMID:184898 ncbi_taxonomy 'Clostridium plagarum' Bacillus perfringens Bacterium welchii Clostridium plagarum Clostridium perfringens NCBITaxon:10781 GC_ID:1 Parvovirus Parvoviruses ncbi_taxonomy Protoparvovirus GC_ID:11 ncbi_taxonomy Bacillus tetani Clostridium tetani GC_ID:1 PMID:20206957 Papillomavirus ncbi_taxonomy Papillomaviridae GC_ID:1 ncbi_taxonomy Polyomaviridae NCBITaxon:11762 GC_ID:1 MLV-related viruses Mammalian type C retrovirus group Mammalian type C retroviruses mammalian type C oncoviruses type C oncoviruses ncbi_taxonomy Gammaretrovirus GC_ID:1 ncbi_taxonomy Galloanseri ducks, geese, chickens, fowl, quail, currasows and allies Galloanserae Bulinus GC_ID:11 ncbi_taxonomy Microspironema pallidum Spirillum pallidum Spirochaeta pallida Spironema pallidum Treponema pallidum HMPV GC_ID:1 ncbi_taxonomy Human metapneumovirus GC_ID:1 ncbi_taxonomy Metapneumovirus NCBITaxon:1634566 NCBITaxon:2293539 NCBITaxon:2293540 NCBITaxon:2293541 NCBITaxon:2293542 NCBITaxon:2293543 NCBITaxon:2293544 NCBITaxon:2293545 NCBITaxon:2293546 NCBITaxon:2293547 NCBITaxon:2364651 NCBITaxon:2364652 NCBITaxon:2364653 NCBITaxon:2364654 NCBITaxon:2364655 NCBITaxon:2364656 NCBITaxon:2364657 NCBITaxon:2364658 NCBITaxon:2364659 NCBITaxon:2364660 NCBITaxon:2482733 NCBITaxon:2482734 NCBITaxon:2482735 NCBITaxon:2482736 NCBITaxon:2482737 NCBITaxon:2482738 NCBITaxon:2482739 NCBITaxon:2482740 NCBITaxon:2482741 NCBITaxon:2482742 NCBITaxon:2482743 NCBITaxon:2482744 NCBITaxon:2482745 NCBITaxon:2482746 NCBITaxon:2482747 NCBITaxon:2482748 NCBITaxon:2482749 NCBITaxon:2484857 NCBITaxon:2484858 NCBITaxon:2485082 NCBITaxon:2485083 NCBITaxon:2485084 NCBITaxon:2485085 NCBITaxon:2485086 NCBITaxon:2485087 NCBITaxon:2485088 NCBITaxon:2485089 NCBITaxon:2485090 NCBITaxon:2485091 NCBITaxon:2485092 NCBITaxon:2485093 NCBITaxon:2485094 NCBITaxon:2485095 NCBITaxon:2485096 NCBITaxon:2486732 NCBITaxon:2486733 NCBITaxon:2486734 NCBITaxon:2486735 NCBITaxon:2486736 NCBITaxon:2486737 NCBITaxon:2486738 NCBITaxon:2486739 NCBITaxon:2486740 NCBITaxon:2486741 GC_ID:11 PMID:17773427 PMID:1906732 PMID:8782698 ncbi_taxonomy Bacterium monocytogenes Bacterium monocytogenes hominis Corynebacterium infantisepticum Corynebacterium parvulum Erysipelothrix monocytogenes Listerella hepatolytica Listeria monocytogenes GC_ID:11 PMID:1503975 PMID:8427802 ncbi_taxonomy Bacillus insidiosus Bacillus rhusiopathiae suis Bacterium rhusiopathiae Erysipelothrix erysipeloides Erysipelothrix insidiosa Erysipelothrix murisepticus Erysipelothrix porci Erysipelothrix rhusiopathiae GC_ID:11 ncbi_taxonomy Yersinia pseudotuberculosis complex GC_ID:1 ncbi_taxonomy Mammarenavirus NCBITaxon:12461 NCBITaxon:2953663 GC_ID:1 ncbi_taxonomy Orthohepevirus A Paslahepevirus balayani NCBITaxon:29512 NCBITaxon:29514 NCBITaxon:29516 GC_ID:11 PMID:10425768 PMID:1581182 PMID:19868121 PMID:9103653 ncbi_taxonomy Leptospira NCBITaxon:144193 GC_ID:11 PMID:10425754 PMID:19661509 PMID:29760685 PMID:30186281 PMID:7547284 PMID:7547291 PMID:7547293 PMID:8186090 ncbi_taxonomy Turicella Corynebacterium GC_ID:11 PMID:7729671 ncbi_taxonomy Bacillus diphtheriae Bacterium diphtheriae Microsporon diphthericum Microsporon diphtheriticum Mycobacterium diphtheriae Pacinia loeffleri Corynebacterium diphtheriae GC_ID:11 ncbi_taxonomy Bacillus pseudotuberculosis Bacillus pseudotuberculosis-ovis Corynebacterium ovis Corynebacterium preisz-nocardi Corynebacterium pseudotuberculosis-ovis Mycobacterium tuberculosis-ovis Corynebacterium pseudotuberculosis NCBITaxon:2843297 NCBITaxon:2843299 GC_ID:11 PMID:15545494 PMID:19867994 PMID:19868337 PMID:19972157 PMID:25288661 PMID:9542090 ncbi_taxonomy Leptospira icteroides Spirochaeta biflexa Spirochaeta icterogenes Spirochaeta icterohaemorrhagiae Spirochaeta interrogans Spirochaeta nodosa Leptospira interrogans GC_ID:1 ncbi_taxonomy Passeroidea GC_ID:11 ncbi_taxonomy Leptospira hardjo Leptospira interrogans serovar Hardjo GC_ID:11 PMID:1380284 PMID:1581193 PMID:16014496 PMID:1883713 PMID:2275850 PMID:31296783 PMID:31649146 PMID:31649147 PMID:34554081 PMID:7547284 PMID:7547304 PMID:7907223 PMID:8863452 ncbi_taxonomy Mycobacterium Lehmann and Neumann 1896 (Approved Lists 1980) Mycobacterium GC_ID:11 PMID:2397193 PMID:8347508 ncbi_taxonomy Bacillus tuberculosis gallinarum Mycobacterium tuberculosis avium Mycobacterium tuberculosis typus gallinaceus Tuberculose des oiseaux Mycobacterium avium NCBITaxon:115863 GC_ID:11 PMID:10618079 PMID:11931153 PMID:14657105 PMID:29205127 ncbi_taxonomy Mycobacterium bovis Mycobacterium tuberculosis typus bovinus Mycobacterium tuberculosis var. bovis Mycobacterium tuberculosis variant bovis GC_ID:11 ncbi_taxonomy Bacillus leprae Mycobacterium leprae NCBITaxon:2528440 GC_ID:11 PMID:29205127 ncbi_taxonomy Bacillus tuberculosis Bacterium tuberculosis Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis Mycobacterium tuberculosis variant tuberculosis Mycobacterium tuberculosis GC_ID:11 PMID:12089250 PMID:20668542 ncbi_taxonomy Mycobacterium balnei Mycobacterium platypoecilus Mycobacterium marinum GC_ID:11 PMID:18988685 PMID:23851394 ncbi_taxonomy Terrabacteria group GC_ID:1 Marek's disease-like viruses ncbi_taxonomy Mardivirus GC_ID:1 Infectious laryngo-tracheitis-like viruses Infectious laryngotracheitis-like viruses ncbi_taxonomy Iltovirus GC_ID:1 Marburg-like viruses ncbi_taxonomy Marburgvirus GC_ID:1 ncbi_taxonomy Clupeocephala GC_ID:1 ncbi_taxonomy Novirhabdovirus GC_ID:1 ncbi_taxonomy Orthopneumovirus NCBITaxon:10625 BFPyV GC_ID:1 Aves polyomavirus 1 BFDV Budgerigar fledgling disease polyomavirus Budgerigar fledgling disease virus Budgerigar fledgling polyomavirus ncbi_taxonomy Gammapolyomavirus avis GC_ID:11 PMID:27620848 ncbi_taxonomy Yersiniaceae GC_ID:11 PMID:11542086 PMID:12361288 PMID:16627635 PMID:1704793 PMID:19801389 PMID:29034857 ncbi_taxonomy Campylobacter GC_ID:11 PMID:11321120 PMID:1354478 ncbi_taxonomy Spirillum fetus Vibrio fetus Campylobacter fetus NCBITaxon:2172531 NCBITaxon:2182326 NCBITaxon:2201165 NCBITaxon:2211407 NCBITaxon:2211408 NCBITaxon:2211409 NCBITaxon:2293848 NCBITaxon:2293849 NCBITaxon:2293850 NCBITaxon:2303571 NCBITaxon:2305452 NCBITaxon:2305453 NCBITaxon:2305454 NCBITaxon:2305455 NCBITaxon:2305456 NCBITaxon:2305457 NCBITaxon:2305458 NCBITaxon:2305459 NCBITaxon:2340789 NCBITaxon:2478524 NCBITaxon:2572055 NCBITaxon:2572062 NCBITaxon:2572070 NCBITaxon:2572072 NCBITaxon:2572075 NCBITaxon:2572080 NCBITaxon:2572086 NCBITaxon:3042472 NCBITaxon:3042475 NCBITaxon:3042476 NCBITaxon:3042477 NCBITaxon:3042478 NCBITaxon:3042479 NCBITaxon:3042480 NCBITaxon:3042481 NCBITaxon:3042482 NCBITaxon:3042483 NCBITaxon:3042484 NCBITaxon:3042485 NCBITaxon:3042486 NCBITaxon:3042488 GC_ID:11 PMID:11321120 ncbi_taxonomy Campylobacter fetus subsp. jejuni Vibrio hepaticus Vibrio jejuni Campylobacter jejuni GC_ID:1 Influenzavirus A ncbi_taxonomy Alphainfluenzavirus GC_ID:1 Influenzavirus B ncbi_taxonomy Betainfluenzavirus GC_ID:1 Influenzavirus C ncbi_taxonomy Gammainfluenzavirus GC_ID:1 ncbi_taxonomy Bunyavirales NCBITaxon:11598 GC_ID:1 ncbi_taxonomy Hantavirus Orthohantavirus NCBITaxon:38142 HIRRV GC_ID:1 Hirame novirhabdovirus Hirame rhabdovirus ncbi_taxonomy Novirhabdovirus hirame GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:32628106 PMID:36748408 PMID:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes Bacteria GC_ID:11 ncbi_taxonomy Flavobacteriales GC_ID:11 PMID:11837318 PMID:25288668 PMID:26654112 ncbi_taxonomy "Leptospiria" Cavalier-Smith 2020 Spirochaetes Spirochaetia GC_ID:11 PMID:12271122 Brucella suis str. 1330 ncbi_taxonomy Brucella melitensis biovar Suis str. 1330 Brucella suis ATCC 23444 Brucella suis NCTC 10316 Brucella suis 1330 NCBITaxon:11268 GC_ID:1 Ebola virus EBO unidentified Ebola virus ncbi_taxonomy Ebola virus sp. GC_ID:11 PMID:23575986 ncbi_taxonomy Neisseriales GC_ID:4 PMID:13403276 PMID:16350067 ncbi_taxonomy Borrelomycetaceae Parasitaceae Pleuropneumoniaceae Mycoplasmataceae NCBITaxon:29500 NCBITaxon:57371 GC_ID:4 PMID:10826816 PMID:11321109 PMID:11411711 PMID:11931184 PMID:13403276 PMID:15176735 PMID:16350067 PMID:16403858 PMID:25288662 PMID:8863441 PMID:8995799 ncbi_taxonomy Asterococcus Asteromyces Borrelomyces Bovimyces Eperythrozoon Haemobartonella Pleuropneumonia Mycoplasma GC_ID:4 ncbi_taxonomy Mycoplasma gallisepticum Mycoplasmoides gallisepticum GC_ID:4 PMID:11491338 PMID:1316139 PMID:1374621 PMID:8573513 ncbi_taxonomy Mycoplasma suipneumoniae Mesomycoplasma hyopneumoniae NCBITaxon:219 GC_ID:11 PMID:11931154 PMID:1995031 PMID:8186097 PMID:8494747 ncbi_taxonomy Campylobacter pylori Campylobacter pylori subsp. pylori Campylobacter pyloridis Helicobacter nemestrinae Helicobacter pylori GC_ID:4 ncbi_taxonomy Mycoplasma synoviae Mycoplasmopsis synoviae GC_ID:11 ncbi_taxonomy Leptospira canicola Leptospira interrogans serovar Canicola GC_ID:11 PMID:16403855 ncbi_taxonomy Campylobacterales GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:32628106 PMID:36748408 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea NCBITaxon:11619 GC_ID:1 Argentinian mammarenavirus Junin arenavirus Junin mammarenavirus Junin virus Junn mammarenavirus ncbi_taxonomy Mammarenavirus juninense GC_ID:11 PMID:11756688 ncbi_taxonomy Brucella melitensis ATCC 23456 Brucella melitensis bv. 1 str. 16M GC_ID:11 PMID:28066370 PMID:32373076 PMID:35335701 PMID:37395662 PMID:8573514 ncbi_taxonomy Brucella GC_ID:11 Brucella melitensis bv. Abortus ncbi_taxonomy "Bacillus of abortion" Bang 1897 Bacterium abortus Brucella melitensis biovar Abortus Brucella abortus GC_ID:11 Brucella melitensis bv. Ovis ncbi_taxonomy Brucella melitensis biovar Ovis Brucella ovis GC_ID:1 Negative-strand RNA viruses ncbi_taxonomy Negarnaviricota GC_ID:1 ncbi_taxonomy Polyploviricotina GC_ID:1 ncbi_taxonomy Orthocoronavirinae GC_ID:1 RNA viruses RNA viruses and viroids ncbi_taxonomy Riboviria GC_ID:1 ncbi_taxonomy Avulavirinae GC_ID:1 ncbi_taxonomy Orthoparamyxovirinae GC_ID:1 ncbi_taxonomy Rubulavirinae NCBITaxon:11176 NDV GC_ID:1 Avian Paramyxovirus Serotype I Avian paramyxovirus type 1 Avian paramyxovirus type-1 Newcastle disease virus Newcastle disease virus NDV avian paramyxovirus 1 ncbi_taxonomy Avian avulavirus 1 Avian orthoavulavirus 1 NCBITaxon:11161 NCBITaxon:1979165 GC_ID:1 Mumps virus ncbi_taxonomy Mumps rubulavirus Mumps orthorubulavirus GC_ID:1 ncbi_taxonomy Avulavirus GC_ID:1 ncbi_taxonomy Henipavirus GC_ID:1 PMID:30257078 ncbi_taxonomy Metamonada GC_ID:1 ncbi_taxonomy Discoba GC_ID:11 PMID:15805518 Brucella abortus biovar 1 str. 9-941 Brucella abortus bv. 1 strain 9-941 ncbi_taxonomy Brucella abortus bv. 1 str. 9-941 GC_ID:11 ncbi_taxonomy Bacterium tularense Brucella tularensis Francisella tularense Pasteurella tularensis Francisella tularensis SARS-CoV-2 GC_ID:1 2019-nCoV COVID-19 virus HCoV-19 Human coronavirus 2019 SARS-2 SARS-CoV2 SARS2 ncbi_taxonomy Severe acute respiratory syndrome coronavirus 2 GC_ID:1 ncbi_taxonomy Bamfordvirae GC_ID:1 ncbi_taxonomy Shotokuvirae GC_ID:1 ncbi_taxonomy Orthornavirae GC_ID:1 ncbi_taxonomy Kitrinoviricota GC_ID:1 ncbi_taxonomy Cossaviricota GC_ID:1 ncbi_taxonomy Papovaviricetes GC_ID:1 ncbi_taxonomy Alsuviricetes GC_ID:1 ncbi_taxonomy Pisoniviricetes GC_ID:1 ncbi_taxonomy Revtraviricetes GC_ID:1 ncbi_taxonomy Pokkesviricetes NCBITaxon:10880 GC_ID:1 ncbi_taxonomy Reoviridae Reovirales GC_ID:1 ncbi_taxonomy Hepelivirales GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota GC_ID:1 ncbi_taxonomy Bovinae NCBITaxon:29525 GC_ID:11 PMID:1503973 ncbi_taxonomy Bacteroides macacae Bacteroides melaninogenicus subsp. macacae Bacteroides salivosus Porphyromonas salivosa Porphyromonas macacae NCBITaxon:707 GC_ID:11 ncbi_taxonomy Listonella ordalii Vibrio ordalii GC_ID:11 PMID:11541974 PMID:11837318 PMID:16166687 PMID:16403855 PMID:19060069 ncbi_taxonomy Alphabacteria Proteobacteria alpha subdivision Purple bacteria, alpha subdivision a-proteobacteria alpha proteobacteria alpha subdivision alpha subgroup Alphaproteobacteria GC_ID:11 PMID:16403855 PMID:28581923 ncbi_taxonomy Proteobacteria beta subdivision Purple bacteria, beta subdivision b-proteobacteria beta proteobacteria beta subdivision beta subgroup Betaproteobacteria NCBITaxon:12796 NCBITaxon:70172 PRRSV GC_ID:1 Porcine reproductive and respiratory syndrome virus (PRRSV) Porcine respiratory and reproductive syndrome virus porcine reproductive and respiratory syndrome virus PRRSV porcine reproductive and respiratory syndrome virus, PRRSV ncbi_taxonomy Porcine reproductive and respiratory syndrome virus NCBITaxon:1435366 NCBITaxon:1435368 NCBITaxon:1435988 NCBITaxon:1439853 NCBITaxon:1487954 NCBITaxon:1487955 GC_ID:11 PMID:12734250 PMID:1283774 ncbi_taxonomy Bacillus pseudomallei Bacterium whitmori Loefflerella pseudomallei Malleomyces pseudomallei Pseudomonas pseudomallei Burkholderia pseudomallei NCBITaxon:212745 GC_ID:11 PMID:10758879 PMID:10939664 PMID:15950132 PMID:18048745 PMID:23918787 PMID:7727274 PMID:9103607 ncbi_taxonomy "Chlorobacterium" Guillebeau 1890, nom. rejic. Opin. 6 (not "Chlorobacterium" Lauterborn 1916) Liquidomonas Loefflerella RNA similarity group I Pseudomonas NCBITaxon:1224290 NCBITaxon:1437768 NCBITaxon:1437769 NCBITaxon:1437770 NCBITaxon:1508364 NCBITaxon:1607811 NCBITaxon:1607813 NCBITaxon:1683559 NCBITaxon:1683561 NCBITaxon:1851858 NCBITaxon:1851865 NCBITaxon:1860124 NCBITaxon:665948 NCBITaxon:912077 NCBITaxon:931955 NCBITaxon:931956 NCBITaxon:931957 NCBITaxon:931958 NCBITaxon:932477 GC_ID:11 ncbi_taxonomy Bacillus aeruginosus Bacillus pyocyaneus Bacterium aeruginosum Bacterium pyocyaneum Micrococcus pyocyaneus Pseudomonas polycolor Pseudomonas pyocyanea probable synonym or variety: "Pseudomonas polycolor" Clara 1930 Pseudomonas aeruginosa GC_ID:1 ncbi_taxonomy Neospora caninum GC_ID:11 PMID:8573514 ncbi_taxonomy Micrococcus melitensis Streptococcus Miletensis Brucella melitensis GC_ID:11 Brucella melitensis bv. Suis ncbi_taxonomy Brucella melitensis biovar Suis Brucella suis NCBITaxon:689832 GC_ID:1 ncbi_taxonomy Sedoreovirinae Sedoreoviridae GC_ID:1 ncbi_taxonomy Heptrevirinae GC_ID:11 ncbi_taxonomy Yersinia ruckeri GC_ID:11 PMID:7547305 PMID:7857801 PMID:7981108 PMID:8123559 PMID:8347512 PMID:9226893 ncbi_taxonomy Candidatus intracellularis Ileal symbiont intracellularis Lawsonia intracellularis GC_ID:1 ncbi_taxonomy Orthoherpesviridae GC_ID:1 ncbi_taxonomy Orthoflavivirus NCBITaxon:45337 NCBITaxon:63330 GC_ID:1 PMID:7701348 Equine morbillivirus Hendra henipavirus Hendra virus ncbi_taxonomy Henipavirus hendraense NCBITaxon:121791 GC_ID:1 Nipah henipavirus Nipah virus Nipah-virus ncbi_taxonomy Henipavirus nipahense NCBITaxon:11103 HCV GC_ID:1 Hepacivirus C Hepatitis C virus hepatitis C virus HCV human hepatitis C virus human hepatitis C virus HCV human hepatitis virus C HCV post-transfusion hepatitis non A non B virus ncbi_taxonomy Hepacivirus hominis NCBITaxon:11623 NCBITaxon:12748 LCMV GC_ID:1 Lymphocytic choriomeningitis mammarenavirus Lymphocytic choriomeningitis virus lymphocytic choriomeningitis virus LCMV ncbi_taxonomy Mammarenavirus choriomeningitidis NCBITaxon:11620 GC_ID:1 Lassa mammarenavirus Lassa virus ncbi_taxonomy Mammarenavirus lassaense NCBITaxon:11232 CDV GC_ID:1 Canine distemper virus Canine morbillivirus canine distemper virus CDV ncbi_taxonomy Morbillivirus canis NCBITaxon:11593 NCBITaxon:1980519 CCHFV GC_ID:1 Crimean-Congo haemorrhagic fever virus Crimean-Congo hemorrhagic fever nairovirus Crimean-Congo hemorrhagic fever orthonairovirus Crimean-Congo hemorrhagic virus ncbi_taxonomy Crimean-Congo hemorrhagic fever virus Orthonairovirus haemorrhagiae NCBITaxon:1511906 GC_ID:1 Carnivore protoparvovirus 1 ncbi_taxonomy Protoparvovirus carnivoran1 NCBITaxon:11215 GC_ID:1 Bovine parainfluenza 3 virus Bovine parainfluenza virus 3 Bovine parainfluenza virus type 3 Bovine respirovirus 3 ncbi_taxonomy Respirovirus bovis GC_ID:1 ncbi_taxonomy Musteloidea GC_ID:1 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy Laurasiatheria GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:15522813 Rodents and rabbits ncbi_taxonomy Glires GC_ID:1 ncbi_taxonomy Anthropoidea Simiiformes GC_ID:1 amniotes ncbi_taxonomy Amniota GC_ID:1 diapsids ncbi_taxonomy Diapsida Sauria GC_ID:1 ncbi_taxonomy Orthoretrovirinae NCBITaxon:186155 GC_ID:1 Canine parvovirus-1 Minute virus of canines ncbi_taxonomy Canine minute virus GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts Opisthokonta GC_ID:1 ncbi_taxonomy Bilateria GC_ID:1 ncbi_taxonomy Protostomia GC_ID:1 ncbi_taxonomy unclassified Papillomaviridae GC_ID:1 guinea pigs and others ncbi_taxonomy Hystricognathi Hystricomorpha GC_ID:1 carnivores ncbi_taxonomy carnivores Carnivora GC_ID:11 PMID:13200095 PMID:22427448 PMID:8240957 PMID:9103649 ncbi_taxonomy Moraxella anatipestifer Pasteurella anapestifer Pasteurella anatipestifer Pfeifferella anatipestifer Riemerella anatipestifer GC_ID:1 ncbi_taxonomy Replication competent viruses GC_ID:1 ncbi_taxonomy unclassified Orthomyxoviridae GC_ID:1 ncbi_taxonomy Pecora GC_ID:11 PMID:16299333 PMID:20462421 ncbi_taxonomy Brucella melitensis biovar Abortus 2308 Brucella abortus 2308 NCBITaxon:10624 GC_ID:1 Polyomavirus Polyomaviruses ncbi_taxonomy Polyomavirus sp. GC_ID:1 ncbi_taxonomy H1N1 swine influenza virus GC_ID:11 ncbi_taxonomy Streptococcus sp. (group A) group A streptococci group A streptococcus Streptococcus sp. 'group A' GC_ID:11 Brucella melitensis bv. Canis ncbi_taxonomy Brucella melitensis biovar Canis Brucella canis GC_ID:1 ncbi_taxonomy Chikungunya virus GC_ID:1 ncbi_taxonomy Caniformia GC_ID:1 Avian reovirus ncbi_taxonomy Avian orthoreovirus GC_ID:11 PMID:1581182 ncbi_taxonomy Leptospira grippotyphosa Leptospira kirschneri serovar Grippotyphosa GC_ID:1 Avian pneumovirus ncbi_taxonomy Avian metapneumovirus GC_ID:1 Leishmania ncbi_taxonomy Leishmania <subgenus> GC_ID:1 ncbi_taxonomy Leishmania donovani species complex NCBITaxon:109679 GC_ID:1 ncbi_taxonomy Murinae GC_ID:1 ncbi_taxonomy Bos bubalis bubalis Bubalus bubalis bubalis GC_ID:11 Yersinia enterocolitica subsp. enterocolitica str. 8081 Yersinia enterocolitica subsp. enterocolitica strain 8081 ncbi_taxonomy Yersinia enterocolitica subsp. enterocolitica 8081 GC_ID:1 ncbi_taxonomy Rubulavirus CpHV-1 GC_ID:1 Caprine herpesvirus 1 Caprine herpesvirus type 1 goat herpesvirus ncbi_taxonomy Caprine alphaherpesvirus 1 NCBITaxon:10896 AHSV GC_ID:1 African horse sickness group African horse sickness virus (AHSV) African horsesickness virus ncbi_taxonomy African horse sickness virus AHSV African horse sickness virus NCBITaxon:12591 GC_ID:1 Bluetongue virus group bluetongue virus BTV ncbi_taxonomy Bluetongue virus GC_ID:1 ncbi_taxonomy Quailpox virus GC_ID:1 ncbi_taxonomy Parvovirinae GC_ID:11 PMID:18048732 ncbi_taxonomy Vibrio salmonicida Aliivibrio salmonicida mammals GC_ID:1 mammals ncbi_taxonomy mammals Mammalia TAdV-3 GC_ID:1 Marble spleen disease virus Turkey adenovirus serotype 3 Turkey haemorrhagic enteritis virus Turkey hemorrhagic enteritis virus hemorrhagic enteritis virus ncbi_taxonomy Turkey adenovirus 3 GC_ID:1 ncbi_taxonomy Vinckeia Plasmodium (Vinckeia) GC_ID:1 ncbi_taxonomy Hematozoa Vivier 1982 Aconoidasida GC_ID:1 ncbi_taxonomy Eimeriorina GC_ID:1 ncbi_taxonomy Sarcocystis neurona GC_ID:11 Brucella abortus str. S19 Brucella abortus strain S19 ncbi_taxonomy Brucella abortus S19 CNPV GC_ID:1 Avipoxvirus clade B1 Canary poxvirus ncbi_taxonomy Canarypox virus NCBITaxon:399128 GC_ID:11 PMID:18218934 ncbi_taxonomy Brucella microti GC_ID:11 Brucella ovis str. ATCC 25840 Brucella ovis strain ATCC 25840 ncbi_taxonomy Brucella ovis ATCC 25840 GC_ID:1 ncbi_taxonomy Picornavirales GC_ID:11 PMID:19346311 Brucella suis str. ATCC 23445 Brucella suis strain ATCC 23445 ncbi_taxonomy Brucella suis ATCC 23445 GC_ID:1 PMID:11062127 PMID:12684019 ncbi_taxonomy Mycota fungi Fungi GC_ID:11 PMID:19346311 Brucella canis str. ATCC 23365 Brucella canis strain ATCC 23365 ncbi_taxonomy Brucella canis ATCC 23365 GC_ID:11 ncbi_taxonomy Diplokokkus intracellularis meningitidis Micrococcus intracellularis Micrococcus meningitidis Micrococcus meningitidis cerebrospinalis Neisseria weichselbaumii Neisseria meningitidis PsHV-1 GC_ID:1 Pacheco's disease virus Psittacid herpesvirus 1 ncbi_taxonomy Psittacid alphaherpesvirus 1 GC_ID:1 trouts, salmons & chars ncbi_taxonomy Salmoninae true insects Insecta GC_ID:11 PMID:11491321 ncbi_taxonomy Bordetella NCBITaxon:514 GC_ID:11 PMID:8240949 PMID:8782670 PMID:9226899 ncbi_taxonomy Alcaligenes bronchicanis Alcaligenes bronchisepticus Bacillus bronchicanis Bacillus bronchisepticus Bacterium bronchisepticus Brucella bronchiseptica Haemophilus bronchisepticus Bordetella bronchiseptica GC_ID:11 PMID:8240949 ncbi_taxonomy Bacterium tussis-convulsivae Haemophilus pertussis Hemophilus pertussis Microbe de la coqueluche Bordetella pertussis GC_ID:11 PMID:4074238 ncbi_taxonomy Bordetella avium GC_ID:11 PMID:10555323 PMID:10555334 PMID:16166704 PMID:27620848 ncbi_taxonomy Enterobacteraceae enterobacteria gamma-3 proteobacteria Enterobacteriaceae NCBITaxon:136447 NCBITaxon:64986 NCBITaxon:96055 BVDV type II BVDV-2 GC_ID:1 PMID:7747470 Bovine viral diarrhea virus genotype 2 Bovine viral diarrhea virus type 2 Bovine viral diarrhea virus-2 bovine viral diarrhea virus type II pestivirus type 4 ncbi_taxonomy Bovine viral diarrhea virus 2 GC_ID:11 Tenericutes ncbi_taxonomy "Mollicutaeota" Oren et al. 2015 "Tenericutes" Murray 1984 Mollicutota Mycoplasmatota GC_ID:11 PMID:19346311 Brucella melitensis str. ATCC 23457 Brucella melitensis strain ATCC 23457 ncbi_taxonomy Brucella melitensis ATCC 23457 GC_ID:1 ncbi_taxonomy Herpesvirales GC_ID:1 ncbi_taxonomy Coccidioides NCBITaxon:28167 NCBITaxon:665 GC_ID:11 PMID:21296930 ncbi_taxonomy Achromobacter ichthyodermis Listonella anguillara Listonella anguillarum Pseudomonas ichthyodermis Vibrio ichthyodermis Vibrio piscium Vibrio piscium var. japonicus Vibrio anguillarum NCBITaxon:155284 NCBITaxon:86501 GC_ID:1 Salmon isavirus ncbi_taxonomy Isavirus salaris GC_ID:1 ncbi_taxonomy Dintheria Oncomelania NCBITaxon:1637691 NCBITaxon:1806490 NCBITaxon:469598 NCBITaxon:662101 NCBITaxon:662104 GC_ID:11 PMID:10319482 E. coli Escherichia/Shigella coli ncbi_taxonomy Bacillus coli Bacterium coli Bacterium coli commune Enterococcus coli Escherichia coli GC_ID:1 ncbi_taxonomy Trypanosomatidae Leishmania GC_ID:1 Leishmania ncbi_taxonomy Leishmania <genus> NCBITaxon:31284 GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) amazonensis Leishmania mexicana amazonensis Leishmania amazonensis GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) donovani Leishmania donovani GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) major Leishmania tropica major Leishmania major NCBITaxon:33701 NCBITaxon:5724 GC_ID:1 PMID:12046599 PMID:15734659 PMID:22000167 ncbi_taxonomy Tritrichomonas suis NCBITaxon:5662 GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) infantum Leishmania donovani infantum Leishmania infantum NCBITaxon:399127 GC_ID:11 PMID:19653890 Brucella microti str. CCM 4915 Brucella microti strain CCM 4915 ncbi_taxonomy Brucella sp. CCM 4915 Brucella microti CCM 4915 GC_ID:1 ncbi_taxonomy Trypanosoma GC_ID:1 ncbi_taxonomy Trypanosoma (Trypanozoon) brucei Trypanosoma brucei subgroup Trypanosoma brucei GC_ID:1 ncbi_taxonomy Trypanosoma cruzi GC_ID:1 PMID:11432808 PMID:19135417 ncbi_taxonomy Giardia duodenalis Giardia lamblia Lamblia intestinalis Giardia intestinalis GC_ID:1 ncbi_taxonomy Entamoeba histolytica GC_ID:1 ncbi_taxonomy Naegleria GC_ID:1 ncbi_taxonomy Naegleria gruberi GC_ID:1 brain-eating amoeba ncbi_taxonomy Naegleria fowleri GC_ID:1 apicomplexans ncbi_taxonomy apicomplexans Apicomplexa GC_ID:1 ncbi_taxonomy Eimeria Eimeria acervulina GC_ID:1 ncbi_taxonomy Eimeria tenella GC_ID:1 ncbi_taxonomy Eimeria maxima Cryptosporidium NCBITaxon:2200815 NCBITaxon:2200816 NCBITaxon:2200817 NCBITaxon:2200818 NCBITaxon:2200819 NCBITaxon:2200820 NCBITaxon:2200821 NCBITaxon:2200822 NCBITaxon:2200823 NCBITaxon:2200824 NCBITaxon:2200825 NCBITaxon:2200826 GC_ID:1 ncbi_taxonomy Cryptosporidium parvum GC_ID:1 ncbi_taxonomy Sarcocystids Sarcocystidae GC_ID:1 ncbi_taxonomy Toxoplasma gondii GC_ID:1 ncbi_taxonomy Plasmodium GC_ID:1 ncbi_taxonomy Plasmodium berghei Plasmodium chabaudi malaria parasite P. falciparum GC_ID:1 malaria parasite P. falciparum ncbi_taxonomy Plasmodium (Laverania) falciparum Plasmodium falciparum Plasmodium knowlesi malaria parasite P. vivax GC_ID:1 malaria parasite P. vivax ncbi_taxonomy Haemamoeba vivax Haemamoeba vivax Grassi and Feletti, 1890 Plasmodium vivax GC_ID:1 ncbi_taxonomy Plasmodium yoelli Plasmodium yoelii GC_ID:1 Piroplasmids ncbi_taxonomy Piroplasmida GC_ID:1 ncbi_taxonomy Babesia GC_ID:1 ncbi_taxonomy Babesia bovis GC_ID:1 ncbi_taxonomy Babesia bigemina GC_ID:1 ncbi_taxonomy Babesia canis GC_ID:1 ncbi_taxonomy Theileria GC_ID:1 ncbi_taxonomy Theileria annulata GC_ID:1 ncbi_taxonomy Theileria parva GC_ID:11 PMID:10319519 PMID:10939679 PMID:12072558 PMID:15653929 PMID:15653930 PMID:3231714 PMID:37486130 PMID:9731304 ncbi_taxonomy Salmonella NCBITaxon:149049 GC_ID:11 PMID:15653929 PMID:15653930 PMID:7149525 ncbi_taxonomy Salmonella cholerae-suis subsp. cholerae-suis Salmonella choleraesuis subsp. choleraesuis Salmonella enterica I Salmonella enterica subsp. I Salmonella enterica subsp. Subsp. I Salmonella enterica subsp. Subsp. Ixxx Salmonella enterica subsp. enterica NCBITaxon:41510 GC_ID:11 ncbi_taxonomy Salmonella enterica serovar Gallinarum Salmonella gallinarum Salmonella enterica subsp. enterica serovar Gallinarum GC_ID:1 ncbi_taxonomy Schistosoma GC_ID:1 ncbi_taxonomy Schistosoma japonicum GC_ID:1 ncbi_taxonomy Schistosoma mansoni Schistosoma haematobium GC_ID:1 ncbi_taxonomy Monkeypox virus Zaire-96-I-16 GC_ID:11 PMID:26834722 ncbi_taxonomy Shigella GC_ID:11 PMID:12054222 Escherichia/Shigella dysenteriae ncbi_taxonomy Bacillus dysenteriae Bacillus dysentericus Bacillus shigae Eberthella dysenteriae Shigella shigae Shigella dysenteriae GC_ID:11 Escherichia flexneri Escherichia/Shigella flexneri ncbi_taxonomy Shigella paradysenteriae Shigella flexneri GC_ID:11 ncbi_taxonomy Bacterium sonnei Shigella sonnei GC_ID:11 Yersinia ncbi_taxonomy Yersinia <enterobacteria> GC_ID:11 PMID:15084509 ncbi_taxonomy Bacillus pestis Bacterium pestis Pasteurella pestis Pestisella pestis Yersinia pseudotuberculosis subsp. pestis Yersinia pestis NCBITaxon:1161941 GC_ID:11 PMID:2223608 PMID:23919959 ncbi_taxonomy Bacillus pseudotuberkulosis Bacterium pseudotuberculosis Pasteurella lymphangitidis Pasteurella pseudotuberculosis Shigella pseudotuberculosis Yersinia pseudotuberculosis GC_ID:1 ncbi_taxonomy Trichinella spiralis GC_ID:11 Edwardsiella ncbi_taxonomy Asakusa group Bartholomew group Edwardsiella <enterobacteria> NCBITaxon:1471792 NCBITaxon:1471793 GC_ID:11 PMID:27539016 ncbi_taxonomy Edwardsiella anguillimortifera Paracolobactrum anguillimortiferum Edwardsiella tarda GC_ID:11 PMID:15143042 PMID:4954820 PMID:8427811 ncbi_taxonomy gamma-3 proteobacteria Vibrionaceae GC_ID:11 PMID:11155981 PMID:12067377 PMID:12807216 PMID:1380286 PMID:1380289 PMID:15388703 PMID:16560691 PMID:17012583 PMID:17158971 PMID:19567585 PMID:7520733 PMID:8347521 PMID:8934910 ncbi_taxonomy Aeromonas NCBITaxon:1471787 NCBITaxon:1471788 NCBITaxon:329135 NCBITaxon:329140 NCBITaxon:346633 NCBITaxon:346634 NCBITaxon:582196 NCBITaxon:582198 NCBITaxon:582214 NCBITaxon:582215 NCBITaxon:582216 NCBITaxon:582217 NCBITaxon:582218 NCBITaxon:582219 NCBITaxon:582220 NCBITaxon:582221 NCBITaxon:582222 NCBITaxon:582223 NCBITaxon:582224 NCBITaxon:582225 NCBITaxon:582226 NCBITaxon:582228 NCBITaxon:582229 NCBITaxon:582231 NCBITaxon:582236 NCBITaxon:582237 NCBITaxon:582240 NCBITaxon:582250 NCBITaxon:582251 NCBITaxon:582253 NCBITaxon:582254 NCBITaxon:582265 NCBITaxon:582266 NCBITaxon:582267 NCBITaxon:582279 NCBITaxon:582282 NCBITaxon:582284 NCBITaxon:582286 NCBITaxon:582287 NCBITaxon:582289 NCBITaxon:582290 NCBITaxon:582291 NCBITaxon:582292 NCBITaxon:582295 NCBITaxon:582297 NCBITaxon:582299 NCBITaxon:582300 NCBITaxon:582302 NCBITaxon:582303 NCBITaxon:582304 NCBITaxon:582305 NCBITaxon:582306 NCBITaxon:582307 NCBITaxon:582308 NCBITaxon:582309 NCBITaxon:582310 NCBITaxon:582311 NCBITaxon:582312 NCBITaxon:582313 NCBITaxon:582314 NCBITaxon:582315 NCBITaxon:582316 NCBITaxon:582317 NCBITaxon:582318 NCBITaxon:582319 NCBITaxon:582320 NCBITaxon:582321 NCBITaxon:582322 NCBITaxon:582323 NCBITaxon:582324 NCBITaxon:98358 GC_ID:11 PMID:16560691 PMID:19965992 PMID:23485124 PMID:932684 ncbi_taxonomy Aeromonas dourgesi Aeromonas hydrophila (Chester 1901) Stanier 1943 (Approved Lists 1980) Aeromonas liquefaciens Bacillus hydrophilus fuscus Bacterium hydrophilum Proteus hydrophilus Proteus ichthyosmius Pseudomonas hydrophila Aeromonas hydrophila molluscs mollusks Mollusca NCBITaxon:1055664 NCBITaxon:697046 GC_ID:11 PMID:19965992 ncbi_taxonomy Bacillus salmonicida Bacterium salmonicida Proteus salmonicida Aeromonas salmonicida NCBITaxon:1618316 GC_ID:11 PMID:10515907 PMID:10758897 PMID:16585709 PMID:24744012 PMID:27930271 PMID:28141502 PMID:30154058 PMID:30586413 PMID:31454394 PMID:31722850 PMID:31836459 PMID:32320380 PMID:35816828 PMID:36748499 PMID:7981102 PMID:8573491 PMID:8934900 PMID:8995795 PMID:9336916 Lyme Disease Borrelia ncbi_taxonomy Borrelia burgdorferi group Borrelia burgdorferi sensu lato Borreliella Biomphalaria NCBITaxon:705 GC_ID:11 PMID:1371064 PMID:17978204 PMID:21057054 PMID:21296930 PMID:24409173 PMID:4935323 PMID:7520733 PMID:8590667 ncbi_taxonomy Beneckea Listonella Microspira Pacinia Vibrio NCBITaxon:140100 NCBITaxon:376726 GC_ID:11 PMID:1015934 PMID:9272984 ncbi_taxonomy Bacillo virgola del Koch Bacillus cholerae Bacillus cholerae-asiaticae Kommabacillus Liquidivibrio cholerae Microspira comma Pacinia cholerae-asiaticae Spirillum cholerae Spirillum cholerae-asiaticae Vibrio albensis Vibrio cholera Vibrio cholerae biovar albensis Vibrio cholerae bv. albensis Vibrio cholerae-asiaticae Vibrio comma Vibrio cholerae GC_ID:11 ncbi_taxonomy Edwardsiella ictaluri NCBITaxon:352473 DHV-1 GC_ID:1 Duck hepatitis A virus Duck hepatitis virus 1 Duck hepatitis virus type 1 ncbi_taxonomy Avihepatovirus A GC_ID:1 ncbi_taxonomy Coronavirinae GC_ID:1 Alphacoronavirus-1 ncbi_taxonomy Alphacoronavirus 1 NCBITaxon:156439 GC_ID:1 Coronavirus group 2 Group 2 species ncbi_taxonomy Coronavirus Betacoronavirus NCBITaxon:227859 NCBITaxon:311178 HCoV-SARS SARS SARSr-CoV SARSrCoV GC_ID:1 Human coronavirus (strain SARS) SARS-like coronavirus SARS-related coronavirus ncbi_taxonomy Severe acute respiratory syndrome-related coronavirus GC_ID:1 ncbi_taxonomy Tremovirus A kissing bugs Triatominae GC_ID:11 PMID:10843050 PMID:15280320 PMID:15388716 PMID:17220461 PMID:2223605 PMID:29923825 ncbi_taxonomy Pasteurellaceae GC_ID:11 PMID:1847295 ncbi_taxonomy Haemophilus pleuropneumoniae Actinobacillus pleuropneumoniae Anopheles GC_ID:1 Anopheles ncbi_taxonomy Anopheles <genus> sand flies sandflies Phlebotominae GC_ID:11 ncbi_taxonomy Thiomicrospira group Thiothrix/Francisella group Thiotrichales GC_ID:11 PMID:1736960 ncbi_taxonomy Haemophilus GC_ID:11 ncbi_taxonomy Bacterium influenzae Coccobacillus pfeifferi Haemophilus meningitidis Influenza-bacillus Mycobacterium influenzae Haemophilus influenzae NCBITaxon:163489 NCBITaxon:214923 GC_ID:11 PMID:13130032 PMID:4333932 ncbi_taxonomy Haemophilus agni Haemophilus ovis Haemophilus somnifer Haemophilus somnus Hemophilus agni Histophilus ovis Histophilus somni GC_ID:11 PMID:5821848 ncbi_taxonomy Haemophilus parasuis Glaesserella parasuis Glossina tsetse flies tsetse fly Glossina <genus> GC_ID:11 PMID:15184562 ncbi_taxonomy Bacterium multocidum Micrococcus gallicidus Pasteurella cholerae-gallinarum Pasteurella gallicida Pasteurella multocida NCBITaxon:746 GC_ID:11 PMID:10028248 PMID:8782683 ncbi_taxonomy Pasteurella haemolytica Newsom and Cross 1932 (Approved Lists 1980) Mannheimia haemolytica GC_ID:11 PMID:11760958 PMID:8240958 rickettsias ncbi_taxonomy alpha-1 proteobacteria Rickettsiales GC_ID:1 ncbi_taxonomy Arteriviridae GC_ID:1 ncbi_taxonomy Nidovirales NCBITaxon:61430 GC_ID:1 ncbi_taxonomy Theileria hirci Theileria lestoquardi Vertebrata vertebrates GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates Vertebrata <vertebrates> GC_ID:11 PMID:9226923 ncbi_taxonomy Rickettsia burneti Rickettsia diaporica Coxiella burnetii GC_ID:11 PMID:10939649 PMID:11491333 PMID:14662925 PMID:9103608 ncbi_taxonomy Rickettsia GC_ID:1 fish fishes ray-finned fishes ncbi_taxonomy Actinopterygi Osteichthyes bony fishes Actinopterygii GC_ID:11 ncbi_taxonomy Clostridium perfringens C GC_ID:1 catfishes ncbi_taxonomy Siluriformes GC_ID:1 PMID:15062801 salmonids ncbi_taxonomy Salmonidae NCBITaxon:1311475 GC_ID:1 rainbow trout ncbi_taxonomy Oncorhynchus nerka mykiss Parasalmo mykiss Salmo mykiss Oncorhynchus mykiss GC_ID:11 PMID:16403855 ncbi_taxonomy Burkholderia/Oxalobacter/Ralstonia group Burkholderiales NCBITaxon:83553 GC_ID:11 PMID:10319462 PMID:11211265 PMID:21048221 PMID:21048222 PMID:23620152 PMID:25618261 PMID:9103632 PMID:9103637 ncbi_taxonomy "Prowazekia" Coles 1953 Bedsonia Chlamydophila Miyagawanella Rakeia Rickettsiaformis Chlamydia GC_ID:11 PMID:10192388 PMID:10319462 PMID:8102247 PMID:8347519 ncbi_taxonomy Chlamydozoon trachomatis Rickettsia trachomae Rickettsia trachomatis Chlamydia trachomatis GC_ID:11 ncbi_taxonomy Escherichia coli O157:H7 NCBITaxon:812 GC_ID:11 PMID:10319462 PMID:12807198 PMID:8102247 PMID:8347519 ncbi_taxonomy Chlamydophila psittaci Chlamydozoon psittaci Ehrlichia psittaci Rickettsia psittaci Rickettsiaformis psittacosis Chlamydia psittaci GC_ID:11 PMID:10319462 PMID:12807198 PMID:25618261 ncbi_taxonomy Chlamydia psittaci (Lillie 1930) Page 1968 Chlamydia psittaci serotype 1 Chlamydophila abortus Chlamydia abortus NCBITaxon:811 GC_ID:11 PMID:10319462 PMID:8102247 PMID:8347519 ncbi_taxonomy Chlamydophila pneumoniae Chlamydia pneumoniae GC_ID:11 PMID:10319462 agent of mouse pneumonitis ncbi_taxonomy Chlamydia trachomatis MoPn Chlamydia muridarum GC_ID:11 PMID:15774632 PMID:24158948 PMID:25481042 PMID:8186083 PMID:8590687 ncbi_taxonomy Porphyromonas NCBITaxon:1761 GC_ID:11 PMID:11837321 PMID:1736962 PMID:19244447 PMID:31157615 ncbi_taxonomy Corynebacteriales Corynebacteriales Goodfellow and Jones 2015 Corynebacterineae Mycobacteriales Janke 1924 (Approved Lists 1980) Mycobacteriales PCV2 GC_ID:1 Porcine circovirus Type II Porcine circovirus type 2 Porcine circovirus-2 ncbi_taxonomy Porcine circovirus 2 GC_ID:1 birds ncbi_taxonomy avian birds Aves GC_ID:1 ncbi_taxonomy Neognathae GC_ID:1 ducks ncbi_taxonomy Anas NCBITaxon:9099 GC_ID:1 turkeys ncbi_taxonomy Phasianidae GC_ID:11 ncbi_taxonomy Leptospira interrogans serovar Icterohaemorrhagiae Gallus domesticus bantam chicken chickens GC_ID:1 Gallus domesticus bantam chicken chickens ncbi_taxonomy Gallus gallus domesticus Phasianus gallus Gallus gallus NCBITaxon:41530 NCBITaxon:601 NCBITaxon:72667 GC_ID:11 PMID:10319519 PMID:10758910 PMID:15653930 PMID:16558776 PMID:9336938 ncbi_taxonomy Bacillus typhi Bacterium (subgen. Eberthella) typhi Salmonella choleraesuis serovar Typhi Salmonella choleraesuis typhi Salmonella enterica ser. typhi Salmonella enterica serotype Typhi Salmonella enterica serovar Typhi Salmonella typhi Salmonella enterica subsp. enterica serovar Typhi NCBITaxon:41532 NCBITaxon:59210 NCBITaxon:602 GC_ID:11 PMID:10758910 PMID:15653930 PMID:9336938 ncbi_taxonomy Bacillus typhimurium Salmonella choleraesuis serotype typhimurium Salmonella enterica 1,4,[5],12,:i:1,2 Salmonella enterica ser. typhimurium Salmonella enterica serotype Typhimurium Salmonella enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:1,2 Salmonella typhi-murium Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium GC_ID:1 common turkey turkey wild turkey ncbi_taxonomy Meleagris gallopavo GC_ID:11 ncbi_taxonomy Bacillus/Lactobacillus/Streptococcus group Firmibacteria Bacilli GC_ID:11 PMID:27620848 ncbi_taxonomy Enterobacteriaceae and related endosymbionts Enterobacteriaceae group Enterobacteriales gamma-3 proteobacteria Enterobacterales GC_ID:1 whales, hippos, ruminants, pigs, camels etc. ncbi_taxonomy Cetartiodactyla even-toed ungulates Artiodactyla GC_ID:1 parrot parrots ncbi_taxonomy Psittacidae GC_ID:11 ncbi_taxonomy Leptospira sp. Pomona primate Primates GC_ID:1 New World monkeys monkey monkeys ncbi_taxonomy Platyrrhini GC_ID:11 PMID:11760958 PMID:1736961 PMID:7537065 Potomac horse fever agent equine monocytic ehrlichiosis agent ncbi_taxonomy Ehrlichia risticii Neorickettsia risticii GC_ID:1 ncbi_taxonomy Catarrhini GC_ID:1 African green monkey African green monkeys grivet savanah monkey ncbi_taxonomy Cercopithecus aethiops Ceropithecus aethiops Simia aethiops Chlorocebus aethiops human GC_ID:1 human ncbi_taxonomy Homo sapiens GC_ID:1 dog, coyote, wolf, fox ncbi_taxonomy Canidae GC_ID:1 ncbi_taxonomy Canis GC_ID:1 gray wolf grey wolf ncbi_taxonomy Canis lupus dog dogs GC_ID:1 dog dogs ncbi_taxonomy Canis canis Canis domesticus Canis familiaris Canis lupus familiaris NCBITaxon:68731 NCBITaxon:9609 GC_ID:1 ncbi_taxonomy Fennecus Vulpes GC_ID:1 northern raccoon raccoon ncbi_taxonomy Ursus lotor Procyon lotor NCBITaxon:77150 GC_ID:1 black ferret domestic ferret ferret ncbi_taxonomy Mustela furo Mustela putorius furo GC_ID:1 ncbi_taxonomy Felis NCBITaxon:36475 GC_ID:1 PMID:17600185 PMID:8581300 PMID:8603894 cat cats domestic cat ncbi_taxonomy Felis domesticus Felis silvestris catus Felis catus NCBITaxon:171554 GC_ID:11 PMID:11541229 PMID:11542017 PMID:28066339 BCF group Bacteroides-Cytophaga-Flexibacter group CFB group Cytophaga-Flexibacter-Bacteroides phylum ncbi_taxonomy "Bacteroidota" Whitman et al. 2018 Bacteroidetes CFB group bacteria Sphingobacteria Bacteroidota GC_ID:1 sei whale ncbi_taxonomy Balaenoptera borealis GC_ID:1 horses ncbi_taxonomy Equidae GC_ID:1 domestic horse equine horse ncbi_taxonomy Equus przewalskii f. caballus Equus przewalskii forma caballus Equus caballus GC_ID:1 pig pigs swine wild boar ncbi_taxonomy Sus scrofa GC_ID:1 deer ncbi_taxonomy Cervidae white-tailed deer Odocoileus virginianus GC_ID:1 ncbi_taxonomy Bovidae GC_ID:1 ncbi_taxonomy Bison GC_ID:1 American bison Bison ncbi_taxonomy Bos (Bison) bison Bos bison Bison bison bovine cattle cow dairy cow domestic cattle domestic cow ox oxen NCBITaxon:272461 GC_ID:1 bovine cattle cow dairy cow domestic cattle domestic cow ox oxen ncbi_taxonomy Bos bovis Bos primigenius taurus Bos taurus NCBITaxon:57076 GC_ID:1 domestic goat goat goats ncbi_taxonomy Capra aegagrus hircus Capra hircus GC_ID:1 ncbi_taxonomy Ovis NCBITaxon:9936 GC_ID:1 domestic sheep lambs sheep wild sheep ncbi_taxonomy Ovis ammon aries Ovis orientalis aries Ovis ovis Ovis aries NCBITaxon:29531 GC_ID:11 PMID:11594628 PMID:16560903 PMID:29593693 ncbi_taxonomy Chondrococcus columnaris Cytophaga columnaris Flavobacterium columnare (Bernardet and Grimont 1989) Bernardet et al. 1996 Flexibacter columnaris Flexibacter columnaris (ex Davis 1922) Bernardet and Grimont 1989 Flavobacterium columnare GC_ID:1 ncbi_taxonomy Caprinae NCBITaxon:34833 NCBITaxon:9985 GC_ID:1 European rabbit Japanese white rabbit domestic rabbit rabbit rabbits ncbi_taxonomy Lepus cuniculus Oryctolagus cuniculus GC_ID:1 rodent ncbi_taxonomy rodents Rodentia a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'. YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device. YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention. YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623. YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740. YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events. YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'. Yongqun He AE adverse reaction WEB: http://en.wikipedia.org/wiki/Adverse_event WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068 The OAE official website is: http://www.oae-ontology.org/. adverse event an adverse event that occurs after a vaccination. YH vaccine adverse event A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment. Yongqun He, Sirarat Sarntivijai, Mathias Brochhausen, William Hogan, ‎Philip E. Empey http://en.wikipedia.org/wiki/Contraindication contraindication an adverse event that is induced by a vaccination. YH vaccine-induced adverse event planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role regulation-assigned role Approval letter Regulation-assigned role is a regulatory role defined by legislation or governmental orders Person: Jennifer Fostel regulation-assigned role regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role