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 Feb 26, 2023 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 An ontology in the domain of vaccine and vaccination Vaccine Ontology 1.1.218 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label BFO 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 BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not 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 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 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note 1 true editor_note editor note editor note definition editor term editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 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> definition editor definition editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes 1 true curator_notes curator note curator note curator notes 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 imported from expand expression to expand expression to 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 OBO foundry unique label 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 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(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) has associated axiom(fol) has axiom label 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 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 NCBI GeneID the NCBI LocusTag name of a gene Oliver He, Yue Liu NCBI LocusTag NCBI LocusTag a date of content modification Oliver He, Yue Liu modification date modification date The NCBITaxon ontology ID of an organism. Oliver He, Yue Liu organism NCBITaxon ID organism NCBITaxon ID A chromosome ID where a gene is located. Oliver He chromosome ID of gene chromosome ID of gene an annotation property that specifies the type of a gene Oliver He type of gene type of gene an annotation property that specifies a nomenclature status Oliver He nomenclature status nomenclature status An annotation property that represents a gene's association with PubMed publication(s). Yongqun He has PubMed association has PubMed association 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 temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime 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 logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations A logical macro assertion whose domain is an IRI for a property logical macro assertion on 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 logical macro assertion on an object property logical macro assertion on an annotation property logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall is indirect form of Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" cjm 2018-03-13T23:59:29Z is directional form of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 uberon development_notes true development_notes development_notes Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 uberon fma_set_term true fma_set_term 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 A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. uberon dc-contributor true dc-contributor An entity responsible for making contributions to the content of the resource. Contributor Contributor contributor Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Creator creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Mark Miller 2018-05-11T13:47:29Z has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand label label 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 https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes participates_in 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 This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 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 A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_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 inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant 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 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 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 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 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 disposition of penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. is allergic trigger for A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. is autoimmune trigger for penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. has allergic trigger A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. has autoimmune trigger 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 https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in 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. David Osumi-Sutherland 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 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). David Osumi-Sutherland regulates in other organism A part of relation that applies only between occurents. occurent part of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:36:08Z A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. has necessary component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, 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. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. 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 A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall has phenotype 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. Chris Mungall 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 Chris Mungall 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 Chris Mungall expressed in process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. ExO:0000001 has exposure receptor A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. ExO:0000000 has exposure stressor A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 has exposure route A broad relationship between an exposure event or process and the course takes from the source to the target. http://purl.obolibrary.org/obo/ExO_0000004 has exposure transport path Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure 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 A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c involved in regulation of p if c enables f and f causally upstream of p acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within 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. Chris Mungall ubiquitously expressed in Inverse of 'expressed in' Chris Mungall expresses inverse of ubiquiotously expressed in Chris Mungall ubiquitously expresses Inverse of 'is substance that treats' cjm is treated by substance cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. Austin Meier Chris Mungall Marie Angelique Laporte cjm 2017-06-05T17:35:04Z has exposure stimulus q inheres in 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 inheres in part of Chris Mungall inheres in part of A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of 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. Chris Mungall 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 c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall directly positively regulates directly activates (process to process) directly activates p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall indirectly positively regulates indirectly activates Chris Mungall directly negatively regulates directly inhibits (process to process) directly inhibits Chris Mungall indirectly negatively regulates indirectly inhibits This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall directly provides input for (process to process) directly provides input for transitive form of directly_provides_input_for Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) transitively provides input for p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of Chris Mungall involved in positive regulation of Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p Chris Mungall involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls activity directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall 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. Chris Mungall towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg determined by inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of x is transcribed from y if and only if x is synthesized from template y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 transcribed from inverse of transcribed from Chris Mungall 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 Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomal translation of inverse of ribosomal translation of Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 ribosomally translates to Chris Mungall causally influenced by (material entity to material entity) causally influenced by Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating pazopanib -> pathological angiogenesis Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. treats The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. capable of inhibiting or preventing pathological process benzene -> cancer [CHEBI] Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. causes disease capable of upregulating or causing pathological process c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. treats is substance that treats c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI is marker for Inverse of 'causal agent in process' process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. related via dependence to A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in represses expression of Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in increases expression of The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. causes or contributes to condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. causes condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. contributes to condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. contributes to expressivity of condition contributes to severity of condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. contributes to penetrance of condition contributes to frequency of condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. is preventative for condition Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. ameliorates condition A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. correlated with condition A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. exacerbates condition A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. condition ameliorated by A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. condition exacerbated by Do not use this relation directly. It is intended as a grouping for a more specific relations cjm 2017-11-05T02:38:20Z condition has genetic basis in cjm 2017-11-05T02:45:20Z has material basis in gain of function germline mutation in cjm 2017-11-05T02:45:37Z has material basis in loss of function germline mutation in cjm 2017-11-05T02:45:54Z has material basis in germline mutation in cjm 2017-11-05T02:46:07Z has material basis in somatic mutation in cjm 2017-11-05T02:46:26Z has major susceptibility factor cjm 2017-11-05T02:46:57Z has partial material basis in germline mutation in Do not use this relation directly. It is intended as a grouping for a more specific relations cjm 2017-11-05T02:53:08Z is genetic basis for condition Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. cjm 2017-11-05T02:55:51Z is causal gain of function germline mutation of in Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. cjm 2017-11-05T02:56:06Z is causal loss of function germline mutation of in Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. cjm 2017-11-05T02:56:40Z is causal germline mutation in Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. cjm 2017-11-05T02:57:07Z is causal somatic mutation in Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. cjm 2017-11-05T02:57:43Z is causal susceptibility factor for Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. cjm 2017-11-05T02:58:43Z is causal germline mutation partially giving rise to cjm 2017-11-05T03:20:01Z realizable has basis in cjm 2017-11-05T03:20:29Z is basis for realizable cjm 2017-11-05T03:26:47Z disease has basis in A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. cjm 2017-11-05T03:29:32Z disease has basis in dysfunction of A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. cjm 2017-11-05T03:37:52Z disease has basis in disruption of A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z disease has basis in feature After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm 2017-11-05T03:50:54Z causal relationship with disease as subject A relationship between a disease and a process where the disease process disrupts the execution of the process. cjm 2017-11-05T03:51:09Z disease causes disruption of cjm 2017-11-05T03:58:20Z disease causes dysfunction of A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. cjm 2017-11-05T04:06:02Z disease has location A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z disease has inflammation site A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. cjm 2017-12-26T19:45:49Z realized in response to stimulus A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. cjm 2017-12-26T19:50:53Z disease has feature A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. cjm 2017-12-26T19:58:44Z disease arises from structure cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. Austin Meier Chris Mungall David Osumi-Sutherland Marie Angelique Laporte triggered by process realized in response to 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 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 continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. 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 occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant 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 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 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity quality Quality quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant function 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 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 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 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 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 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 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity 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 sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. 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 MetaCyc:CPD-5583 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 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 is an artificial sweetener. The basic substance, benzoic sulfilimine, has effectively no food energy and is much sweeter than sucrose, but has a bitter or metallic aftertaste, especially at high concentrations. It is used to sweeten products such as drinks, candies, cookies, medicines, and toothpaste. (wikipedia) 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 sodium phosphate 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 (brand names include Alkest, Canarcel and Tween, which is a registered trademark of ICI Americas, Inc.) is a nonionic surfactant and emulsifier derived from polyethoxylated sorbitan and oleic acid, and is often used in foods. Polysorbate 80 is a viscous, water-soluble yellow liquid. The hydrophilic groups in this compound are polyethers also known as polyoxyethylene groups which are polymers of ethylene oxide. In the nomenclature of polysorbates, the numeric designation following polysorbate refers to the lipophilic group, in this case the oleic acid (see polysorbate for more detail). Polysorbate 80 is often used in food and other products as an emulsifier. (wikipedia) 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 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. 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 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 ICD10CM:A49.9 MSH:D001424 NCI:C2890 SNOMEDCT_US_2015_03_01:154318005 SNOMEDCT_US_2015_03_01:186470002 SNOMEDCT_US_2015_03_01:187347000 SNOMEDCT_US_2015_03_01:266182006 SNOMEDCT_US_2015_03_01:266187000 SNOMEDCT_US_2015_03_01:301811001 SNOMEDCT_US_2015_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 ICD10CM:A23 ICD10CM:A23.9 ICD9CM:023 ICD9CM:023.9 MSH:D002006 NCI:C84602 SNOMEDCT_US_2015_03_01:111804008 SNOMEDCT_US_2015_03_01:154296006 SNOMEDCT_US_2015_03_01:186310006 SNOMEDCT_US_2015_03_01:187304000 SNOMEDCT_US_2015_03_01:75702008 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 ICD10CM:B54 ICD9CM:084 ICD9CM:084.6 MSH:D008288 NCI:C34797 OMIM:609148 SNOMEDCT_US_2015_03_01:105649009 SNOMEDCT_US_2015_03_01:154374002 SNOMEDCT_US_2015_03_01:186797008 SNOMEDCT_US_2015_03_01:187510004 SNOMEDCT_US_2015_03_01:248437004 SNOMEDCT_US_2015_03_01:61462000 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_2015_03_01:193273005 SNOMEDCT_US_2015_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 ICD10CM:B50.9 ICD9CM:084.0 MSH:D016778 NCI:C34798 SNOMEDCT_US_2015_03_01:186802002 SNOMEDCT_US_2015_03_01:187504004 SNOMEDCT_US_2015_03_01:248441000 SNOMEDCT_US_2015_03_01:62676009 UMLS_CUI:C0024535 Falciparum Malaria Falciparum malaria (disorder) Falciparum malaria [malignant tertian] Malaria fever, subtertian Plasmodium falciparum malaria, unspecified Plasmodium falciparum malaria, unspecified (disorder) malignant tertian fever (finding) 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_2015_03_01:186305007 SNOMEDCT_US_2015_03_01:30789005 SNOMEDCT_US_2015_03_01:427999003 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 MSH:D002007 SNOMEDCT_US_2015_03_01:186306008 SNOMEDCT_US_2015_03_01:427795000 SNOMEDCT_US_2015_03_01:9060000 UMLS_CUI:C0302363 disease_ontology DOID:14457 Brucella abortus brucellosis A disease that is characterized by abnormally rapid cell division. DOID:0000818 cell process disease disease_ontology DOID:14566 disease of cellular proliferation A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80 ICD10CM:C80.1 ICD9CM:199 MSH:D009369 NCI:C9305 SNOMEDCT_US_2015_03_01:154432008 SNOMEDCT_US_2015_03_01:154433003 SNOMEDCT_US_2015_03_01:154577008 SNOMEDCT_US_2015_03_01:187597000 SNOMEDCT_US_2015_03_01:188475001 SNOMEDCT_US_2015_03_01:188482002 SNOMEDCT_US_2015_03_01:190150006 SNOMEDCT_US_2015_03_01:269513004 SNOMEDCT_US_2015_03_01:269623003 SNOMEDCT_US_2015_03_01:269626006 SNOMEDCT_US_2015_03_01:269634000 SNOMEDCT_US_2015_03_01:363346000 SNOMEDCT_US_2015_03_01:38807002 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 derived_from melanocytes which are found in skin, the bowel and the eye. EFO:0000756 KEGG:05218 MSH:D008545 NCI:C3224 OMIM:155600 SNOMEDCT_US_2015_03_01:154501005 SNOMEDCT_US_2015_03_01:189749008 SNOMEDCT_US_2015_03_01:2092003 SNOMEDCT_US_2015_03_01:269503007 SNOMEDCT_US_2015_03_01:269577007 SNOMEDCT_US_2015_03_01:372244006 UMLS_CUI:C0025202 Naevocarcinoma malignant melanoma disease_ontology DOID:1909 melanoma 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:B50-B64 ICD10CM:B64 MSH:D011528 NCI:C34953 SNOMEDCT_US_2015_03_01:187247003 SNOMEDCT_US_2015_03_01:187502000 SNOMEDCT_US_2015_03_01:187517001 SNOMEDCT_US_2015_03_01:240627001 SNOMEDCT_US_2015_03_01:367372008 SNOMEDCT_US_2015_03_01:89933001 SNOMEDCT_US_2015_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. MSH:D004194 NCI:C2991 SNOMEDCT_US_2015_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 ICD10CM:B20-B20 ICD9CM:042 ICD9CM:042-042.99 MSH:D015658 NCI:C3108 SNOMEDCT_US_2015_03_01:123321001 SNOMEDCT_US_2015_03_01:186705005 SNOMEDCT_US_2015_03_01:187438009 SNOMEDCT_US_2015_03_01:187453001 SNOMEDCT_US_2015_03_01:86406008 UMLS_CUI:C0019693 HIV infection disease_ontology DOID:526 Human immunodeficiency virus infectious disease 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 MSH:D007251 NCI:C53482 SNOMEDCT_US_2015_03_01:155559006 SNOMEDCT_US_2015_03_01:155562009 SNOMEDCT_US_2015_03_01:195931008 SNOMEDCT_US_2015_03_01:266353003 SNOMEDCT_US_2015_03_01:266393000 SNOMEDCT_US_2015_03_01:6142004 UMLS_CUI:C0021400 Influenza with non-respiratory manifestation (disorder) Influenza with other manifestations Influenza with other manifestations (disorder) Influenza with other manifestations NOS (disorder) 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 ICD10CM:B34.9 ICD9CM:060-066.99 ICD9CM:066.9 MSH:D001102 MSH:D014777 NCI:C3439 NCI:C34396 SNOMEDCT_US_2015_03_01:154319002 SNOMEDCT_US_2015_03_01:154345006 SNOMEDCT_US_2015_03_01:154372003 SNOMEDCT_US_2015_03_01:186619002 SNOMEDCT_US_2015_03_01:186754003 SNOMEDCT_US_2015_03_01:187471008 SNOMEDCT_US_2015_03_01:266116004 SNOMEDCT_US_2015_03_01:266188005 SNOMEDCT_US_2015_03_01:266194002 SNOMEDCT_US_2015_03_01:34014006 SNOMEDCT_US_2015_03_01:40610006 UMLS_CUI:C0003723 UMLS_CUI:C0042769 Viral Infection Viral disease Viral disease (disorder) Viral infection NOS Viral infection NOS (disorder) Viral infection, unspecified (disorder) Viral: [infection NOS] or [illness] arbovirus infectious disease virus infection disease_ontology arthropod-borne viruses DOID:934 viral infectious disease fma FMA:12278 Hormone An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). Wikipedia:Adaptive_immune_system acquired immune response biological_process GO:0002250 This term was added by GO_REF:0000022. 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. biological_process GO:0002385 This term was added by GO_REF:0000022. mucosal immune response 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 This term was improved by GO_REF:0000022. It was redefined and moved. immune response biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological_process 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. 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 macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. Wikipedia:Protein_complex protein-protein complex cellular_component GO:0043234 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 complex response to stimulus 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. response to stimulus 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. midori 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. midori 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. midori 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. midori 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. midori 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. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item 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: Melanie Courtot PERSON:Chris Stoeckert 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 that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum 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 pathogen A material entity with a pathogenic disposition. pathogen virulence factor A biological macromolecule produced by a pathogen and that has a virulence factor disposition. virulence factor 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 Cavia porcellus GC_ID:1 chinchillas chinchillas and viscachas ncbi_taxonomy Chinchillidae Viruses 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 GC_ID:1 monkey pox virus ncbi_taxonomy Monkeypox virus 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 Feline viral rhinotracheitis virus 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 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 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 ncbi_taxonomy Reoviridae 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 VEE virus 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 Bovine parainfluenza 3 virus Bovine parainfluenza virus 3 Bovine parainfluenza virus type 3 ncbi_taxonomy Bovine respirovirus 3 GC_ID:1 Morbilliviruses ncbi_taxonomy Morbillivirus CDV GC_ID:1 Canine distemper virus canine distemper virus CDV ncbi_taxonomy Canine 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 virus ncbi_taxonomy Rabies lyssavirus 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 virus Tick-borne virus ncbi_taxonomy Dhori thogotovirus FLUAV GC_ID:1 Human Influenza A Virus Influenza virus type A ncbi_taxonomy Influenza A virus GC_ID:1 H1N1 ncbi_taxonomy H1N1 subtype RVFV GC_ID:1 ncbi_taxonomy Rift Valley fever virus GC_ID:1 Lassa virus ncbi_taxonomy Lassa mammarenavirus NCBITaxon:12748 LCMV GC_ID:1 Lymphocytic choriomeningitis virus lymphocytic choriomeningitis virus LCMV ncbi_taxonomy Lymphocytic choriomeningitis mammarenavirus 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 Euteleostomi bony vertebrates 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 HPV-1 PV1 GC_ID:1 Human poliovirus type 1 Polio virus 1 Poliovirus 1 Poliovirus type 1 poliovirus type 1 PV1 ncbi_taxonomy Human poliovirus 1 HPV-2 GC_ID:1 Human Poliovirus type 2 Poliovirus 2 Poliovirus type 2 ncbi_taxonomy Human poliovirus 2 HPV-3 GC_ID:1 Human poliovirus type 3 Polio virus 3 Poliovirus 3 ncbi_taxonomy Poliovirus type 3 Human 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:1 Nipah virus Nipah-virus ncbi_taxonomy Nipah henipavirus GC_ID:11 PMID:11321122 PMID:11542017 PMID:11837318 PMID:26654112 PMID:29458499 purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives ncbi_taxonomy Alphaproteobacteraeota Alphaproteobacteriota proteobacteria Proteobacteria GC_ID:11 PMID:23334881 ncbi_taxonomy Proteobacteria gamma subdivision 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:26654112 PMID:29458499 low G+C Gram-positive bacteria low GC Gram+ ncbi_taxonomy Bacillaeota Bacillota Bacillus/Clostridium group Clostridium group firmicutes Firmacutes Low G+C firmicutes clostridial firmicutes firmicutes Firmicutes 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 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 GC_ID:11 ncbi_taxonomy Bacillus/Staphylococcus group 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 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 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: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:29497402 PMID:31296783 PMID:31649146 PMID:31649147 PMID:34554081 PMID:7547284 PMID:7547304 PMID:7907223 PMID:8863452 ncbi_taxonomy 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 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 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 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 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 Bacteria eubacteria 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: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 GC_ID:4 PMID:11491338 PMID:1316139 PMID:1374621 PMID:14323369 PMID:8573513 ncbi_taxonomy Mycoplasma suipneumoniae Mycoplasma 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 Archaea 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:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea GC_ID:11 PMID:11756688 ncbi_taxonomy Brucella melitensis ATCC 23456 Brucella melitensis bv. 1 str. 16M GC_ID:11 PMID:28066370 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 Orthoparamyxovirinae 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 HCoV-19; COVID-19 virus; SARS-2; Human coronavirus 2019; SARS-CoV2; SARS2; 2019-nCoV 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 Alsuviricetes GC_ID:1 ncbi_taxonomy Pisoniviricetes GC_ID:1 ncbi_taxonomy Revtraviricetes GC_ID:1 ncbi_taxonomy Pokkesviricetes Eukaryota eucaryotes eukaryotes 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 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 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy Laurasiatheria Euarchontoglires 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 Tetrapoda tetrapods Tetrapoda Amniota amniotes 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 Opisthokonta GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts Opisthokonta Bilateria 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 GC_ID:1 ncbi_taxonomy H1N1 swine influenza virus 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 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 Mammalia 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 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 PMID:19346311 Brucella melitensis str. ATCC 23457 Brucella melitensis strain ATCC 23457 ncbi_taxonomy Brucella melitensis ATCC 23457 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 ncbi_taxonomy Salmon isavirus GC_ID:1 ncbi_taxonomy Dintheria 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 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 GC_ID:1 ncbi_taxonomy Eimeria tenella GC_ID:1 ncbi_taxonomy Eimeria maxima 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 GC_ID:1 malaria parasite P. falciparum ncbi_taxonomy Plasmodium (Laverania) falciparum Plasmodium falciparum 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: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 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 NCBITaxon:45337 GC_ID:1 PMID:7701348 Equine morbillivirus Hendra virus ncbi_taxonomy Hendra henipavirus 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