en Gustavo Carvalho Regina Hurley Sebastian Deusing Shane Babcock Barry Smith John Beverley The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible. Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status 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> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Add as annotation triples in the granting ontology Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg is allocated id range has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime shorthand 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 preceded by 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 precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process John Beverley Not sure if this has an IRI yet, so I supplied a placeholder. occupies temporal region results in has_material_basis_in http://purl.obolibrary.org/obo/obi.owl has specified input Participates in relation between a planned process and a continuant participating in that process that is not created during the process, where the presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/obi.owl is specified input of http://purl.obolibrary.org/obo/obi.owl has specified output Participates in relation between a planned process and a continuant participating in that process where the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/obi.owl is specified output of 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 journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of 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 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 disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y 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 x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y Chris Mungall negatively regulates (process to process) negatively regulates x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall positively regulates (process to process) positively regulates p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of results in formation of An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member Infectious disease inhering in a virus disorder that is a disorder due to the presence of the virus. http://purl.obolibrary.org/obo/vido.owl John Beverley viral disease Objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population. http://purl.obolibrary.org/obo/apollo-sv.owl infectious disease control objective specification Plan specification whose objective specification is an infectious disease control objective specification. http://purl.obolibrary.org/obo/apollo-sv.owl infectious disease control strategy Algorithm that models the progress of a transmissible disease in a population. http://purl.obolibrary.org/obo/apollo-sv.owl disease transmission model Infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open. http://purl.obolibrary.org/obo/apollo-sv.owl place closure control strategy Infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious. http://purl.obolibrary.org/obo/apollo-sv.owl case isolation control strategy Infectious disease control strategy that has a vector control action specification as part. http://purl.obolibrary.org/obo/apollo-sv.owl vector control strategy Infectious disease control strategy whereby organisms who have had contact with infectious organisms but are not symptomatic or otherwise known to be infectious are prevented from having contact with other susceptible organisms. http://purl.obolibrary.org/obo/apollo-sv.owl quarantine control strategy Objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval. http://purl.obolibrary.org/obo/apollo-sv.owl disease surveillance objective specification Infectious disease control strategy that identifies and treats contacted organisms in a host population. http://purl.obolibrary.org/obo/apollo-sv.owl contact tracing entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] 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 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 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) temporal region Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. spatiotemporal region 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) process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) 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]) disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) 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]) realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] 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]) quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) 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 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. 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 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]) 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]) role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] 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 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]) site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 object 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. 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]) generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) 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. function the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) 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). 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 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] 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 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]) process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) Material entity part of or substance produced by a multicellular organism with granularity above the level of a protein complex. Anatomical entities - like other material entities - may have immaterial parts. anatomical entity Nucleic acid composed of nucleotides containing deoxyribose and linked by phosphodiester bonds. http://purl.obolibrary.org/obo/chebi.owl deoxyribonucleic acid Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc. molecular entity Role inhering in a molecular entity or part of that entity, realized in biological processes. http://purl.obolibrary.org/obo/chebi.owl biological role Macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases. http://purl.obolibrary.org/obo/chebi.owl nucleic acid Nucleic acid composed of nucleotides containing ribose and linked by phosphodiester bonds. http://purl.obolibrary.org/obo/chebi.owl ribonucleic acid Molecular entity of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/chebi.owl macromolecule Biological macromolecule consisting of one polypeptide chain synthesized at the ribosome. http://purl.obolibrary.org/obo/chebi.owl protein DNA consisting of two parallel strands joined by hydrogen bonds between complementary purines and pyrimidines. http://purl.obolibrary.org/obo/chebi.owl double-stranded DNA Material entity that is part of or derived from an organism, with maximally connected cell compartments surrounded by a plasma membrane. This should be an inferred subclass of BFO:object. -John cell Virus disorder that exists as a result of a process of formation of disorder initiated by a coronavirus or coronavirus population. This should be imported from: http://purl.obolibrary.org/obo/cido.owl John Beverley coronavirus disorder Coronavirus disorder that exists as a result of a process of formation of disorder initiated by SARS-CoV-2. John Beverley SARS-CoV-2 disorder Coronavirus disease inhering in a SARS-CoV-2 disorder, and which is realized in some COVID-19 disease course. John Beverley COVID-19 Viral disease course that is the realization of some coronavirus disease and has as a participant a coronavirus. This should be imported from: http://purl.obolibrary.org/obo/cido.owl John Beverley coronavirus disease course Coronavirus disease course that is the realization of some COVID-19 disease and has participant SARS-CoV-2 John Beverley COVID-19 disease course Virus aggregate whose members are all coronaviruses. This should be imported from: http://purl.obolibrary.org/obo/cido.owl John Beverley coronavirus aggregate Coronavirus aggregate whose members are all SARS-CoV-2. John Beverley SARS-CoV-2 aggregate Respiratory droplet virus fomite with coronavirus part. This should be imported from: http://purl.obolibrary.org/obo/cido.owl John Beverley respiratory droplet coronavirus fomite Respiratory droplet virus fomite with SARS-CoV-2 part. John Beverley respiratory droplet SARS-CoV-2 fomite Coronavirus process realization of an infectious structure disposition inhering in a coronavirus or coronavirus population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing a viral infection, and (4) appearance of a virus disorder. This should be imported from: http://purl.obolibrary.org/obo/cido.owl John Beverley coronavirus pathogenesis Coronavirus process realization of an infectious structure disposition inhering in a SARS-CoV-2 or a SARS-CoV-2 population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing a viral infection, and (4) appearance of a virus disorder. John Beverley SARS-CoV-2 pathogenesis This should be imported from: http://purl.obolibrary.org/obo/cido.owl Virus replication in which coronavirus is replicated. John Beverley coronavirus replication Coronavirus replication in which SARS-CoV-2 is replicated. John Beverley SARS-CoV-2 replication Virus attachment stage involving SARS-CoV-2 that bonds with a host cell John Beverley SARS-CoV-2 attachment stage Virus penetration stage involving SARS-CoV-2 that penetrates a host cell John Beverley SARS-CoV-2 penetration stage Virus release stage during which SARS-CoV-2 is released from a host cell John Beverley SARS-CoV-2 release stage John Beverley SARS-CoV-2 genome replication stage John Beverley SARS-CoV-2 transcription stage John Beverley SARS-CoV-2 synthesis stage Virus uncoating stage during which SARS-CoV-2 uncoats outer proteins to release genetic material into host cell. John Beverley SARS-CoV-2 uncoating stage Virus adhesion susceptible cell bearing a SARS-COV-2 adhesion disposition John Beverley SARS-COV-2 adhesion susceptible cell Viral adhesion disposition borne by a macromolecule part of SARS-CoV-2 that is the disposition to participate in a SARS-COV-2 attachment process John Beverley SARS-COV-2 adhesion disposition Infection prevalence involving agents infected by SARS-COV-2. John Beverley SARS-COV-2 prevalence Infectious disease prevalence where the infectious disease is COVID-19. John Beverley COVID-19 prevalence Infectious disease mortality rate where the infectious disease is COVID-19. John Beverley COVID-19 mortality rate Infectious disease lifetime prevalence where the infectious disease is COVID-19. John Beverley COVID-19 lifetime prevalence Infectious disease incidence rate where the infectious disease is COVID-19. John Beverley COVID-19 incidence rate Infectious disease incidence where the infectious disease is COVID-19. John Beverley COVID-19 disease incidence proportion Infectious disease incidence where the infectious disease is COVID-19. John Beverley COVID-19 incidence Infectious disease endemicity where the infectious disease is COVID-19. John Beverley COVID-19 endemicity Infectious pathogen transmissibility involving SARS-CoV-2. John Beverley SARS-CoV-2 transmissibility Pathogen seroprevalence where the pathogen is SARS-CoV-2. John Beverley SARS-CoV-2 seroprevalence Infection incidence rate involving agents infected by SARS-CoV-2. John Beverley SARS-CoV-2 incidence rate John Beverley Infection incidence proportion involving organisms infected by SARS-CoV-2. SARS-CoV-2 incidence proportion John Beverley Infection incidence that is the number of organisms in the population that become infected by SARS-CoV-2 during a specified period of time. SARS-CoV-2 incidence Infectivity where the pathogen is SARS-CoV-2. John Beverley SARS-CoV-2 infectivity Virulence where the pathogen is SARS-CoV-2. John Beverley SARS-CoV-2 virulence Infectious disease sporadicity where the infectious disease is COVID-19. John Beverley COVID-19 sporadicity Processed material bearing a reagent role. http://purl.obolibrary.org/obo/ero.owl reagent Reagent that is comprised of immunoglobulins produced by B cells in response to an antigen. http://purl.obolibrary.org/obo/ero.owl antibody reagent Assay used to determine viral titers. http://purl.obolibrary.org/obo/ero.owl viral plaque assay Planned process used to influence one or more factors in a research study, and the independent variable in an interventional study wherein the influence is measured or evaluated. http://purl.obolibrary.org/obo/ero.owl John Beverley intervention Assay analyzing blood serum and other bodily fluids, to detect the presence of serum antibodies. http://purl.obolibrary.org/obo/ero.owl serology assay Assay measuring the concentration of a substance in a material by exploiting binding between an analyte and a corresponding detection antibody. http://purl.obolibrary.org/obo/ero.owl immunoassay Temporal subdivision of a developmental process. John Beverley http://purl.obolibrary.org/obo/ido.owl generative stage Material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface). http://purl.obolibrary.org/obo/GEO geographical entity Geographical entity that has at least one bona fide boundary. http://purl.obolibrary.org/obo/GEO geographical feature Geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. http://purl.obolibrary.org/obo/GEO geographical region Immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). adaptive immune response Process involved in the carrying out of an immune response by a leukocyte. leukocyte mediated immunity Immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response Immune response mediated through a body fluid. humoral immune response Process specifically pertinent to the functioning of functionally integrated units. biological process Protein surrounding virion nucleic acid in some virus particles. http://purl.obolibrary.org/obo/go.owl viral capsid Macromolecule lipid bilayer of a virion surrounding capsid. http://purl.obolibrary.org/obo/go.owl viral envelope Virus generative stage during which an incoming virus is disassembled in the host cell to release a replication-competent viral genome. http://purl.obolibrary.org/obo/go.owl virus uncoating stage Virus generative stage during which a virion protein binds to molecules on the host surface or host cell surface projection. http://purl.obolibrary.org/obo/go.owl virus attachment stage Virus developmental stage during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed. http://purl.obolibrary.org/obo/go.owl virus synthesis stage Virus generative stage during which viral mRNA is translated into viral protein, using the host cellular machinery. http://purl.obolibrary.org/obo/go.owl virus translation stage Virus developmental stage during which a viral genome, or part of a viral genome, is transcribed within the host cell. http://purl.obolibrary.org/obo/go.owl virus transcription stage 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. immunoglobulin complex Immunoglobulin complex present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. B cell receptor complex Biological process whose specific outcome is the progression of a functional, integrated, unit. developmental process Stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. macromolecular complex Protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. T cell receptor complex Process carried out by gene products in an organism or acellular structure that enables the entity to engage in a symbiotic relationship with an organism. John Beverley http://purl.obolibrary.org/obo/go.owl symbiotic process Attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. adhesion of symbiont to host Penetration by an organism into the body, tissues, or cells of the host organism. entry into host Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism. entry into host through host barriers Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. innate immune response Virus generative stage during which a virion or viral nucleic acid breaches the barriers of a host. http://purl.obolibrary.org/obo/go.owl virus penetration stage Protein subunit comprising viral capsid. http://purl.obolibrary.org/obo/go.owl capsomere Process that stops, prevents, or reduces the frequency, rate or extent of a biological process. negative regulation of biological process Process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant. negative regulation of viral process Process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. negative regulation of immune response Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). negative regulation of developmental process Process that localizes a substance or cellular component via movement, tethering or selective degradation. establishment of localization Process that modulates a measurable attribute of any biological process, quality or function. biological regulation Virus generative stage involving dissemination of mature virus particles from the host cell, by cell lysis or the budding of virus particles from the cell membrane. http://purl.obolibrary.org/obo/go.owl virus release stage 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. http://purl.obolibrary.org/obo/iao.owl objective specification Directive information entity that describes an action the bearer will take http://purl.obolibrary.org/obo/iao.owl action specification information content entity 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. http://purl.obolibrary.org/obo/iao.owl algorithm Directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications. http://purl.obolibrary.org/obo/iao.owl plan specification Virus which infects and replicates within or on fungi. http://purl.obolibrary.org/obo/vido.owl John Beverley mycovirus Process in which multiple COVID-19 epidemics caused by SARS-CoV-2 unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. John Beverley COVID-19 pandemic Process of COVID-19 realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. John Beverley COVID-19 epidemic A role borne by an organism in symbiosis. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl symbiont role Symbiont role borne by an organism in which both symbionts derive a growth, survival, or fitness advantage from symbiosis. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl mutualist role Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis, while the other symbiont is neither advantaged nor disadvantaged. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl commensal role Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl parasite role Infectious disposition to become part of a disorder only in organisms whose defenses are compromised. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl opportunistic infectious disposition Infectious disposition to become part of a disorder in immunocompetent organisms. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. primary infectious disposition Host role borne by an organism whose extended organism provides an environment supportive for the survival, growth, maturation, or reproduction of an object contained as a proper part. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl symbiont host role Symbiont host role borne by an organism iwhose partner in symbiosis reaches developmental maturity or reproduces sexually in the host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl definitive host role Symbiont host role borne by an organism whose partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl intermediate host role Symbiont host role borne by an organism whose partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl dead-end host role Pathogen host role borne by an organism whose extended organism contains an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious agent host role Host role borne by an object having a pathogen as part or an borne by an organism having a pathogen as part of its extended organism. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathogen host role A pathogen vector role borne by an organism in virtue of the fact that the pathogen does not multiply in or on the vector. Albert Goldfain Alexander Diehl Lindsay Cowell passive carrier mechanical vector role A pathogen vector role borne by an organism in virtue of the fact that the pathogen multiplies in the vector. Albert Goldfain Alexander Diehl Lindsay Cowell biological vector role A pathogen transporter role borne by an entity in virtue of the fact that the entity is not a complete organism. I don't understand the rdfs comment indicating drinking water bears the infected agent vehicle role, but neither of the subtypes. Presumably, if an infectious agent is present in drinking water, then it bears a fomite role. Drinking water is, in fact, a classic example. -John Beverley I've expanded this definition and label to cover infectious agent pathogens and infectious structure pathogens. -John Beverley Albert Goldfain Alexander Diehl Lindsay Cowell Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles. pathogen vehicle role A pathogen vehicle role borne by an entity in virtue of the fact that the entity is living or contains living cells other than those that have the infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell Examples include blood, serum, tissue, or fresh produce. biological vehicle role An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive. Albert Goldfain Alexander Diehl Lindsay Cowell fomite role Role borne by a material entity in which pathogens can persist, and from which they can be transmitted to hosts. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl reservoir of pathogen role Disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host. virulence factor disposition Disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl toxin disposition Toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl exotoxin disposition Role borne by an anatomical entity that serves as the site through which a pathogen enters a host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathogen portal of entry role Role borne by an anatomical entity that serves as the site through which a pathogen exits a host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathogen portal of exit role Role borne by an infectious disorder whose host has another, distinct, infectious disorder - neither arising from the other through metastasis - which emerged after this infectious disorder was established due to increased host susceptibility to infectious disorders. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl primary infection role Role borne by an infectious disorder whose host has another, distinct, primary infectious disorder - neither arising from the other through metastasis - which emerged after the primary infectious disorder was established due to increased host susceptibility to infectious disorders. Albert Goldfain Alexander Diehl Lindsay Cowell secondary infection role Disease whose physical basis is an infectious disorder. Albert Goldfain Alexander Diehl Lindsay Cowell tranmissible disease http://purl.obolibrary.org/obo/ido.owl infectious disease Disposition borne by a macromolecule that is the disposition to participate in adherence to a host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl adhesion disposition Disposition borne by a biological macromolecule that is the disposition to facilitate breach of and entry through host barriers. Albert Goldfain Alexander Diehl Lindsay Cowell Invasion factor; invasin http://purl.obolibrary.org/obo/ido.owl invasion disposition Disposition inhering in an acellular structure or organism, with a part having a disposition to mitigate damage to the entity from invasive or internal threats, which is realized in one or more negative biological regulation process. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide. protective resistance Protective resistance that mitigates the damaging effects of a drug. http://purl.obolibrary.org/obo/ido.owl Albert Goldfain Alexander Diehl Lindsay Cowell resistance to drug Protective resistance that inheres in an organism and mitigates the damaging effects of a pathogen. http://purl.obolibrary.org/obo/ido.owl Albert Goldfain Alexander Diehl Lindsay Cowell resistance to pathogen Collective resistance disposition that inheres in an organism population where the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts to susceptible individuals. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl herd immunity to infectious organism Resistance to pathogen that inheres in an organism due to immune system components in its extended organism. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunity to pathogen Immunity to pathogen that results in elimination of the infectious agent from the host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Sterilizing immunity is typically conferred by neutralizing antibodies. sterilizing immunity to infectious agent Disposition borne by a material entity to establish localization in and result in formation of disorder in a host or immunocompetent members of the same species as the host. Albert Goldfain Alexander Diehl Lindsay Cowell pathogenicity http://purl.obolibrary.org/obo/ido.owl pathogenic disposition Disposition borne by a pathogen that is the disposition to penetrate the epithelial barriers of an organism of another species. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl invasive disposition Infectious disposition to be transmitted from an infected, non-human host to a human host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl zoonotic disposition Infectious disposition to be transmitted from an infected, human host to a non-human host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. reverse zoonotic disposition Disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. Albert Goldfain Alexander Diehl Lindsay Cowell This should be pushed up to: http://purl.obolibrary.org/obo/bfo.owl collective disposition Organism that is experiencing immunosuppression. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunosuppressed organism Organism that has immunocompetence. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunocompetent organism Disposition that inheres in a pathogen host and is a disposition to horizontally transmit that pathogen to organisms of the same species as the host, through casual contact, with a high likelihood of realization. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl contagiousness Host that contains a colony in or on its extended organism. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl colonized host Quality that inheres in an infectious agent or infectious structure and is the likelihood that the agent or structure will undergo a horizontal transmission process. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. infectious pathogen transmissibility Quality that inheres in a pathogen and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl This quality is measured by the proportion of exposed who become infected. infectivity Quality that inheres in a pathogen and is the degree to which realizations of the infectious disease caused by the pathogen become severe or fatal. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl This quality is measured by the proportion of clinically apparent cases that are severe or fatal. virulence Quality that inheres in an entity and is the degree to which it can be harmed by another entity. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. susceptibility Susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl susceptibility to infectious agent Susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl drug susceptibility Drug susceptibility that inheres in an infectious agent and is the degree to which the infectious agent can be harmed or inhibited from surviving by a drug. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl drug susceptibility of infectious agent Infection comprised of infectious organisms from different species. John Beverley complex infection Infection in which pathogen parts persist in the extracellular space of the host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl extracellular infection Infection in which pathogen parts persist inside host cells. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl intracellular infection Infection for which the infectious agents or structures that are part of the infection are distributed throughout the host. John Beverley systematic infection Infection for which the infectious agents or structures that are part of the infection are limited to a relatively small area of the host's body. local infection Infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl acute infectious disease course Quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. infectious disease incidence Quality that inheres in an organism population and is the number of organisms in the population that become infected with a pathogen during a specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. infection incidence Quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell cumulative incidence of infectious disease http://purl.obolibrary.org/obo/ido.owl An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured. infectious disease incidence proportion Quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell cumulative incidence of infection http://purl.obolibrary.org/obo/ido.owl An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured. infection incidence proportion Quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured. infectious disease incidence rate Quality that inheres in an organism population and is the infection incidence proportion per unit time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured. infection incidence rate Quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. infectious disease prevalence Quality that inheres in an organism population and is the number of organisms in the population infected with a pathogen at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. infection prevalence Quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. infectious disease lifetime prevalence Quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for a pathogen in their serum at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics. pathogen seroprevalence Quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year. infectious disease mortality rate Quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic. infectious disease endemicity Quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Sporadic quality of infectious disease is relational to previous prevalence of the disease. infectious disease sporadicity Disease course that is the realization of an infectious disease. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease course Chronic infectious disease course that does not progress to severe stages for a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl long-term non-progressing infectious disease course Process by which an organism acquires immunity to an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunization against infectious agent Immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell inoculation http://purl.obolibrary.org/obo/ido.owl active immunization against infectious agent Active immunization that begins with exposure of an organism to a vaccine. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl vaccination against infectious agent Active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl variolation Immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl passive immunization against infectious agent Process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious disease epidemic Process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious disease pandemic Disorder that is part of an organism whose extended organism has some infectious agent or structure as part, which participates in the formation of infection. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious disorder Infection that has as part bacteria located in the blood. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl bacteremia Aggregate of organisms of the same species. Albert Goldfain Alexander Diehl Lindsay Cowell The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. organism population Organism population whose members have an infection. Albert Goldfain Alexander Diehl Lindsay Cowell infected population Organism population in whose members an infectious disease is being realized. Albert Goldfain Alexander Diehl Lindsay Cowell diseased population Organism population whose members each have an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent population Organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell at-risk population susceptible population Organism population whose members are participating in non-parasitic symbiosis with a particular host. Albert Goldfain Alexander Diehl Lindsay Cowell normal resident microflora population An infectious organism population (IDO:0000513) (1) that is not part of any infection (IDO:0000586), (2) whose members are participating in a process of symbiosis (GO:0044403) with the same host, and (3) whose members are organisms of types among the normal resident microbiota for the type of host organism. normal resident microbiota population One-dimensional temporal region beginning with the extablishment of an infectious agent or structure in a host and ending with the onset of symptoms in the host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl incubation interval One-dimensional temporal region during which a pathogen host bears a contagiousness disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl communicability interval Organism bearing a symbiont role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl symbiont Organism that can only reach developmental maturity, replicate, or persist in symbiosis. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl obligatory symbiont Symbiont bearing a mutualist role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl mutualist Symbiont bearing a commensal role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl commensal Symbiont bearing a parasite role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl parasite Material entity bearing a pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathogen Pathogen bearing a primary infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell principal pathogen http://purl.obolibrary.org/obo/ido.owl primary pathogen Object bearing a host role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl This should be pushed to an upper-level ontology. host Host bearing a definitive host role. Albert Goldfain Alexander Diehl Lindsay Cowell primary host http://purl.obolibrary.org/obo/ido.owl definitive host Host bearing an intermediate host role. Albert Goldfain Alexander Diehl Lindsay Cowell secondary host http://purl.obolibrary.org/obo/ido.owl intermediate host Host bearing a dead-end host role. Albert Goldfain Alexander Diehl Lindsay Cowell incidental host http://purl.obolibrary.org/obo/ido.owl dead-end host Pathogen host bearing an infectious agent host role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious agent host Host bearing a pathogen host role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathogen host Infectious agent host bearing the infectious agent carrier role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl asymptomatic infectious agent carrier Pathogen transporter bearing a pathogen vehicle role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathogen vehicle Pathogen vehicle bearing a fomite role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl fomite Material entity bearing a pathogen reservoir role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious agent reservoir A macromolecule produced by a pathogen and that has a virulence factor disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl virulence factor Biological macromolecule that has an invasion disposition. Albert Goldfain Alexander Diehl Lindsay Cowell invasin http://purl.obolibrary.org/obo/ido.owl invasion factor Molecular entity that has a toxin disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl toxin Toxin bearing an exotoxin disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl exotoxin Exotoxin bearing an enterotoxin disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl enterotoxin Toxin bearing an endotoxin disposition that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl endotoxin Anatomical entity bearing a pathogen portal of entry role. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen portal of entry Anatomical entity bearing a pathogen portal of exit role. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen portal of exit Biological macromolecule that has an adhesion disposition. Albert Goldfain Alexander Diehl Lindsay Cowell adhesin adhesion molecule http://purl.obolibrary.org/obo/ido.owl adhesion factor Infectious disorder bearing a primary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl primary infection Infectious disorder bearing a secondary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl secondary infection Infectious disease inhering in an infectious disorder composed of pathogens having zoonotic dispositions. Albert Goldfain Alexander Diehl Lindsay Cowell zoonosis Infection that is part of an asymptomatic carrier. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl subclinical infection Material entity bearing protective resistance. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl resistant entity Immunity to pathogen that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl innate immunity to infectious agent Immunity to pathogen that inheres in an organism in virtue of components of its circulating body fluid, e.g. blood, lymph, hemolymph. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl "Circulating body fluid" refers to blood, lymph, and hemolymph. humoral immunity to infectious agent Immunity to pathogen that inheres in an organism in virtue of its leukocytes. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl leukocyte-mediated immunity to infectious agent Immunity to pathogen that inheres in an organism in virtue of antibodies not produced by that organism. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl passive immunity to infectious agent Resistance to drug that mitigates the damaging effects of an antibiotic. http://purl.obolibrary.org/obo/ido.owl Albert Goldfain Alexander Diehl Lindsay Cowell antibiotic resistance Pathogen whose infection incidence is increasing following its first introduction into a new host Species. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl emerging pathogen Toxin bearing a cytotoxin disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl cytotoxin Collective disposition to initiate processes that result in a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl collective pathogenic disposition Part of an organism that itself is part of an extended organism with a pathogen as part, which participates in the formation of the infection. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infection Resistance to pathogen that inheres in an organism due to an allele or combination of alleles in its genome. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl The resistance of individuals to HIV invasion oonferred by particular CCR5 alleles is an example. Resistance against malaria conferred by the sickle cell gene is another. genetic resistance to pathogen Collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl collective resistance disposition Organism that has an immunodeficiency. Albert Goldfain Alexander Diehl Lindsay Cowell immunocompromised organism http://purl.obolibrary.org/obo/ido.owl immunodeficient organism Infectious disease course that unfolds over a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl chronic infectious disease course Organism population whose members have acquired immunity to an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell immune population One-dimensional temporal region during which a transmission process occurs. Albert Goldfain Alexander Diehl Lindsay Cowell This should be imported from: http://purl.obolibrary.org/obo/trans.owl transmission interval Organism that has an infectious disposition. This is an inferred subclass of pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious agent Process by which an infectious agent or infectious structure, established in a host, becomes part of an infection in the host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl process of establishing an infection Establishment of localization in host process in which an organism or acellular structure establishes a colony in or on a host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl colonization of host Colonization of host process that results in a clinically abnormal colony. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl establishment of a clinically abnormal colony Process in which an entity comes into being as a result of the process. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl production Production process in which a participant creates a copy of itself. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl replication Process that attenuates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunosuppression Immunosuppression which unfolds as part of the natural self-regulation of an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl physiologic immunosuppression Immunosuppression process which arises as the result of a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathologic immunosuppression Organism population persisting in a site it has colonized. Albert Goldfain Alexander Diehl Lindsay Cowell colony Colony whose members are infectious agents. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent colony Disorder of an immune system component that results in defective functioning of the immune system. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunodeficiency Disposition inhering in an organism that is the disposition to mount a normal immune response. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunocompetence Disposition whose realization negatively regulates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunosuppressive disposition Immunity to pathogen that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism. Albert Goldfain Alexander Diehl Lindsay Cowell adaptive immunity to infectious agent http://purl.obolibrary.org/obo/ido.owl acquired immunity to infectious agent Infectious disposition to be transmitted from one organism to another of the same species by horizontal transmission. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl communicability Establishment of localization process in which a material entity reaches a site in or on a host in which it can survive, grow, multiply, or mature. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl establishment of localization in host Process by which a disorder comes into existence. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl appearance of disorder Infectious disorder that is the physical basis for an unfolding acute infectious disease course. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl acute infection Infection that persists for an extended period of time. John Beverley chronic infection Role borne by an acellular structure containing a material entity other than the structure, or organism whose extended organism contains a material entity other than the organism, realized in use of that structure or organism as a site of reproduction or replication. Albert Goldfain Alexander Diehl Lindsay Cowell This should be pushed to: http://purl.obolibrary.org/obo/ogms.owl host role Infection resulting from a transmission process that unfolds in a hospital. Albert Goldfain Alexander Diehl Lindsay Cowell nosocomial infection http://purl.obolibrary.org/obo/ido.owl hospital-acquired infection Infection resulting from a transmission process that did not unfold in a health care facility. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl community-acquired infection Toxin bearing a neurotoxin disposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl neurotoxin Infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host. John Beverley metastatic infection Role borne by a material entity that contains a site from which an infectious agent is transmitted. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl source of infection role Infection resulting from a transmission process that unfolds in a nursing home. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl nursing-home acquired infection Pathogen disposed to infect human hosts. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl infectious human pathogen Immunodeficiency that is not caused by a genetic predisposition. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy). acquired immunodeficiency Infection comprised of infectious organisms or structures all of the same Species. simple infection Pathogen whose infection incidence is increasing in a host population as a result of changes in the biology of the host or pathogen, or changes in their interactions. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl re-emerging pathogen Colonization of host in a human. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl colonization of human Immunodeficiency that exists in an organism because of a genetic predisposition. Albert Goldfain Alex Diehl Lindsay Cowell congenital immunodeficiency http://purl.obolibrary.org/obo/ido.owl primary immunodeficiency Infectious disease inhering in an infectious disorder composed of pathogens bearing reverse zoonotic dispositions. Albert Goldfain Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl reverse zoonosis Pathogen with an opportunistic infectious disposition. Albert Goldfain Alex Diehl Lindsay Cowell opportunist http://purl.obolibrary.org/obo/ido.owl opportunistic pathogen Disposition to undergo a transmission process. Albert Goldfain Alex Diehl Lindsay Cowell This should be pushed to: http://purl.obolibrary.org/obo/trans.owl transmissibility disposition Pathogen transmission process in which a pathogen is transmitted from one host to another of the same species, and the two hosts are not in a parent-child relationship. http://purl.obolibrary.org/obo/ido.owl horizontal pathogen transmission process Process that results in death. Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl process that results in death Organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl susceptible organism Process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process. Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl negative regulation of life-sustaining process Material entity bearing a source of infection role. Albert Goldfain Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl source of infection John Beverley http://purl.obolibrary.org/obo/ido.owl infection incidence profile John Beverley http://purl.obolibrary.org/obo/ido.owl infection incidence proportion profile John Beverley http://purl.obolibrary.org/obo/ido.owl infection incidence rate profile Immunosuppressed organism that is experiencing pathologic immunosuppression. Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl negative regulation of establishment of localization pathologically immunosuppressed organism Process that stops, prevents, or reduces the frequency, rate or extent of a production process. John Beverley http://purl.obolibrary.org/obo/ido.owl negative regulation of production Process that stops, prevents, or reduces the frequency, rate or extent of a replication process. John Beverley http://purl.obolibrary.org/obo/ido.owl negative regulation of replication Process boundary that marks the start of the life cycle of a pathogen. Alex Diehl John Beverley Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl pathogen birth process boundary Process boundary that marks the end of the life cycle of a pathogen. John Beverley http://purl.obolibrary.org/obo/ido.owl pathogen death process boundary Pathologically immunosuppressed organism that is experiencing drug-based immunosuppression. Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl drug-based immunosuppressed organism Disposition to kill fungi. http://purl.obolibrary.org/obo/ido.owl John Beverley fungicidal disposition Disposition to kill bacteria. http://purl.obolibrary.org/obo/ido.owl John Beverley bactericidal disposition Disposition to inhibit the reproduction of bacteria. http://purl.obolibrary.org/obo/ido.owl John Beverley bacteriostatic disposition Disposition to kill parasites. We use parasite in the sense of organisms that are parasitic in humans. http://purl.obolibrary.org/obo/ido.owl John Beverley parasiticidal disposition Disposition to inhibit the reproduction of parasites. 'Parasite' is used in the sense of eukaryotic organisms that are parasitic in humans. http://purl.obolibrary.org/obo/ido.owl John Beverley parasitostatic disposition Static agent bearing a bacteriostatic disposition. http://purl.obolibrary.org/obo/ido.owl John Beverley bacteriostatic Cidal agent with a bactericidal disposition that is realized in a process of killing bacteria. http://purl.obolibrary.org/obo/ido.owl John Beverley bactericidal Acellular structure that has an infectious disposition. This is an inferred subclass of pathogen. http://purl.obolibrary.org/obo/ido.owl John Beverley infectious structure Aggregate of acellular structures. John Beverley acellular structure aggregate Zero-dimensional temporal region occupied by a pathogen birth process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley pathogen birth temporal region Zero-dimensional temporal region occupied by a pathogen death process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley pathogen death temporal region prions viruses Object that is an arrangement of interrelated acellular parts forming a biological unit. http://purl.obolibrary.org/obo/ido.owl John Beverley acellular structure Material entity with a cidal agent disposition that is realized in a process of killing bacteria, fungi, parasites, or viruses. http://purl.obolibrary.org/obo/ido.owl John Beverley cidal agent Material entity bearing a static agent disposition. http://purl.obolibrary.org/obo/ido.owl John Beverley static agent Disposition to inhibit the reproduction of bacteria, fungi, or parasites, or inhibit the replication of viruses. http://purl.obolibrary.org/obo/ido.owl John Beverley static agent disposition Disposition to kill bacteria, fungi, parasites, or viruses. http://purl.obolibrary.org/obo/ido.owl John Beverley cidal agent disposition Pathogen host bearing an infectious structure host role. http://purl.obolibrary.org/obo/ido.owl John Beverley infectious structure host Pathogen host role borne by an object or organism whose extended organism contains an infectious structure. http://purl.obolibrary.org/obo/ido.owl John Beverley infectious structure host role Material entity bearing a pathogen transporter role. http://purl.obolibrary.org/obo/ido.owl John Beverley pathogen transporter Role borne by a material entity in or on which a pathogen is located, from which the pathogen may be transmitted to a new host. John Beverley pathogen transporter role Pathogen generative stage that is a temporal subdivision of an infectious agent developmental process. http://purl.obolibrary.org/obo/ido.owl John Beverley infectious agent generative stage Pathogen generative stage that is a temporal subdivision of an infectious structure developmental process. http://purl.obolibrary.org/obo/ido.owl John Beverley infectious structure generative stage Generative stage that is a temporal subdivision of a pathogen developmental process. http://purl.obolibrary.org/obo/ido.owl John Beverley pathogen generative stage Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the pathogen. http://purl.obolibrary.org/obo/ido.owl John Beverley asymptomatic carrier role Pathogen host with an infection as part but exhibits no signs or symptoms. http://purl.obolibrary.org/obo/ido.owl John Beverley asymptomatic carrier Infectious structure host bearing an asymptomatic carrier role. http://purl.obolibrary.org/obo/ido.owl John Beverley asymptomatic infectious structure carrier Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has manifested symptoms of the infectious disease caused by the pathogen. http://purl.obolibrary.org/obo/ido.owl John Beverley symptomatic carrier role Pathogen host with infection as part that exhibits symptoms. http://purl.obolibrary.org/obo/ido.owl John Beverley symptomatic carrier Toxin disposition realized in processes resulting in damage to host cells. http://purl.obolibrary.org/obo/ido.owl John Beverley cytotoxin disposition Toxin disposition realized in damaging or interfering with the function of nerve tissue. http://purl.obolibrary.org/obo/ido.owl John Beverley neurotoxin disposition Toxin disposition that is a structural component of a pathogen and is realized only during cytolsis. http://purl.obolibrary.org/obo/ido.owl John Beverley endotoxin disposition Exotoxin disposition ithat is realized in a process of damaging intestinal mucosa cells. http://purl.obolibrary.org/obo/ido.owl John Beverley enterotoxin disposition Infectious structure host bearing a symptomatic carrier role. http://purl.obolibrary.org/obo/ido.owl John Beverley symptomatic infectious structure carrier Infectious agent host bearing an infectious agent carrier role. http://purl.obolibrary.org/obo/ido.owl John Beverley symptomatic infectious agent carrier Acellular structure aggregate whose members are infectious structures. John Beverley infectious structure aggregate Pathogen transporter bearing a pathogen vector role. http://purl.obolibrary.org/obo/ido.owl John Beverley pathogen vector Pathogen vector bearing a biological vector role. http://purl.obolibrary.org/obo/ido.owl John Beverley biological vector Pathogen vector bearing a mechanical vector role. http://purl.obolibrary.org/obo/ido.owl John Beverley mechanical vector Pathogen vehicle bearing a biological vehicle role. http://purl.obolibrary.org/obo/ido.owl John Beverley biological vehicle Establishment of localization in or on a human host. http://purl.obolibrary.org/obo/ido.owl John Beverley establishment of localization in human host One-dimensional temporal region beginning with the establishing of an infection in a host and ending when the host becomes contagious. http://purl.obolibrary.org/obo/ido.owl John Beverley latency interval Process boundary that marks the start of an infection, latency process, and incubation process. http://purl.obolibrary.org/obo/ido.owl John Beverley infection start process boundary Process boundary marking the end of a latency period. http://purl.obolibrary.org/obo/ido.owl John Beverley latency end process boundary Process boundary marking the end of an incubation period. http://purl.obolibrary.org/obo/ido.owl John Beverley incubation end process boundary Zero-dimensional temporal region occupied by an infection start process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley infection start temporal region Zero-dimensional temporal region occupied by an infection end process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley infection end temporal region Zero-dimensional temporal region occupied by a latency end process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley latency end temporal region Zero-dimensional temporal region occupied by a communicability end process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley communicability end temporal region Zero-dimensional temporal region occupied by an incubation end process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley incubation end temporal region Zero-dimensional temporal region occupied by a communicability start process boundary. http://purl.obolibrary.org/obo/ido.owl John Beverley communicability start temporal region Process boundary marking the start of a latency interval. http://purl.obolibrary.org/obo/ido.owl John Beverley latency start process boundary Process boundary marking the start of an incubation interval. http://purl.obolibrary.org/obo/ido.owl John Beverley incubation start process boundary Process boundary marking the start of a communicability interval. http://purl.obolibrary.org/obo/ido.owl John Beverley communicability start process boundary Process boundary marking the end of a communicability interval. http://purl.obolibrary.org/obo/ido.owl John Beverley communicability end process boundary Biological role borne by a molecular entity that serves as the site on an antigen realized in immune system recognition and binding by antibodies. http://purl.obolibrary.org/obo/ido.owl John Beverley epitope role Surveillance process aiming to produce information about one or several objects, in the form of microorganisms, which have the role of pathogen. http://purl.obolibrary.org/obo/ido.owl pathogen surveillance Surveillance process aiming to produce information about one or several objects, in the form of arthropods, which have the role of serving as biological pathogen vectors. http://purl.obolibrary.org/obo/ido.owl vector surveillance Acellular structure with RNA or DNA genetic material which uses host metabolic resources for RNA or DNA replication. The mass noun term label imported from the NCBITaxon "Viruses" has been replaced with the count noun "virus", to align with BFO. virus Positive-sense single-stranded RNA virus with a helically symmetrical nucleocapsid, lipid bilayer viral envelope, and surface spike peplomers. http://purl.obolibrary.org/obo/NCBITaxon_11118 John Beverley coronavirus http://purl.obolibrary.org/obo/NCBITaxon_1335626 John Beverley MERS-CoV bacteria Human Immunodeficiency Virus Virus with genetic material encoded in single-stranded RNA that replicates using reverse transcriptase to convert positive-sense RNA to DNA. http://purl.obolibrary.org/obo/NCBITaxon_2169561 Baltimore Classification Group VI John Beverley single-stranded RNA retrovirus http://purl.obolibrary.org/obo/NCBITaxon_227859 John Beverley SARS-CoV-2 Parvovirus Virus with genetic material encoded in single-stranded DNA and replicates using DNA polymerase. http://purl.obolibrary.org/obo/NCBITaxon_2731342 Baltimore Classification Group II John Beverley single-stranded DNA virus eukaryota Adenovirus Poxvirus Virus that has its genetic material encoded in double-stranded DNA and replicates using DNA polymerase. http://purl.obolibrary.org/obo/NCBITaxon_35237 Baltimore Classification Group I John Beverley double-stranded DNA virus Hepatitus B Virus Virus with genetic material that is encoded in double-stranded DNA and replicates through single-stranded RNA intermediate. http://purl.obolibrary.org/obo/NCBITaxon_35268 Baltimore Classification Group VII Pararetrovirus John Beverley double-stranded DNA retrovirus Coronavirus Picornavirus Virus with genetic material encoded in single-stranded RNA that can be translated directly into proteins. http://purl.obolibrary.org/obo/NCBITaxon_35278 Baltimore Classification Group IV John Beverley positive-sense single-stranded RNA virus Rhabdovirus Virus with genetic material encoded in single-stranded RNA that can be translated into proteins only after transcription by RNA polymerase. http://purl.obolibrary.org/obo/NCBITaxon_35301 Baltimore Classification Group V John Beverley negative-sense single-stranded RNA virus Reovirus Virus with genetic material encoded in double-stranded RNA. http://purl.obolibrary.org/obo/NCBITaxon_35325 Baltimore Classification Group III John Beverley double-stranded RNA virus Acellular structure that consists of an abnormally folded protein which replicates by by transmitting its abnormal structure to other proteins. John Beverley http://purl.obolibrary.org/obo/ncbitaxon.owl prion homo sapiens Process that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/obi.owl planned process Material entity that is created or changed during material processing. http://purl.obolibrary.org/obo/obi.owl processed material Planned process with the objective to produce information about some evaluant. http://purl.obolibrary.org/obo/obi.owl assay Role inhering in a molecular entity when the molecular entity is used to produce a chemical reaction to detect, measure, or produce other substances. http://purl.obolibrary.org/obo/obi.owl reagent role Planned process which results in physical changes in a specified input material. http://purl.obolibrary.org/obo/obi.owl material processing Biological role inhering in some molecular entity, that stimulates an immune response when identified by the immune systems cells. http://purl.obolibrary.org/obo/obi.owl John Beverley antigen role Double stranded DNA that is the specified output of a polymerase chain reaction http://purl.obolibrary.org/obo/obi.owl PCR product Enzymatic amplification in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. http://purl.obolibrary.org/obo/obi.owl polymerase chain reaction Material processing amplifying cDNA during a PCR reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. http://purl.obolibrary.org/obo/obi.owl reverse transcribed PCR Object that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. organism Material processing using enzymes to increase the number of molecules of a material entity. http://purl.obolibrary.org/obo/obi.owl enzymatic amplification Molecular entity bearing the epitope role. http://purl.obolibrary.org/obo/obi.owl John Beverley epitope Molecular entity bearing an antigen role. http://purl.obolibrary.org/obo/obi.owl antigen Process experienced by a patient which can only be experienced by the patient, that is hypothesized to be clinically relevant. symptom Disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease Material entity that is a clinically abnormal part of an extended organism. disorder Totality of all processes through which a given disease instance is realized. disease course Object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. extended organism Material entity that is a human made structure with firm connection between its foundation and the ground. http://purl.obolibrary.org/obo/OMRSE architectual structure Architectural structure that bears some function. http://purl.obolibrary.org/obo/OMRSE facility Facility that is run by a hospital organization and is the bearer of a hospital function. http://purl.obolibrary.org/obo/OMRSE hospital facility Facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population. http://purl.obolibrary.org/obo/OMRSE healthcare facility Protein complex consisting of an N-terminal peptidase M2 domain and a C-terminal collectrin renal amino acid transporter domain, which is attached to surface of alveolar, enterocyte cells, arterial and venous endothelial cells, and cortical neurons. http://purl.obolibrary.org/obo/uniprot.owl angiotensin-converting enzyme 2 Process in which a pathogen is transmitted directly or indirectly to a new host. TRANS includes a sibling class of 'indirect' labeled 'direct', and these terms mirror standard definitions of 'direct transmission' and 'indirect transmission' in the literature. However, in the literature and in TRANS the definitions seem confused. For example, direct transmission is claimed to involve direct contact, yet respiratory droplet spread from a host - which plausibly involves a vehicle - is counted as direct rather than indirect transmission. We will follow standard use in part, adopting indirect transmission, but not direct, and defining a term for contact transmission. pathogen transmission process Pathogen transmission process in which a pathogen is indirectly transferred to a host by intermediary vehicles or vectors. John Beverley indirect pathogen transmission process Pathogen transmission process in which a pathogen is transferred to a host through surface-to-surface contact. http://purl.obolibrary.org/obo/trans.owl John Beverley contact pathogen transmission process Indirect pathogen transmission process in which a pathogen is transmitted from a host expelling respiratory droplets to another host. http://purl.obolibrary.org/obo/trans.owl John Beverley droplet pathogen transmission process A fluid that is composed of blood plasma and erythrocytes. blood Anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://purl.obolibrary.org/obo/uberon.owl organism substance Organism substance that is secreted by a respiratory system. http://purl.obolibrary.org/obo/uberon.owl respiratory secretion Matter ejected from the lungs, bronchi, and trachea, through the mouth. http://purl.obolibrary.org/obo/uberon.owl sputum Macromolecule glycoprotein component of SARS-CoV-2 membrane. http://purl.obolibrary.org/obo/uniprot.owl SARS-CoV-2 spike glycoprotein Macromolecule consisting of positive stranded viral RNA of SARS-CoV-2. http://purl.obolibrary.org/obo/uniprot.owl John Beverley SARS-CoV-2 nucleoside protein Macromolecule component of SARS-CoV-2 envelope. http://purl.obolibrary.org/obo/uniprot.owl John Beverley SARS-CoV-2 membrane protein Infection that has as part virus particles located in the blood. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl viremia Virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules. Albert Goldfain Alexander Diehl Lindsay Cowell virion Cidal agent with a viricidal disposition that is realized in a process of killing viruses. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl viricide Static agent bearing a viostatic disposition. John Beverley http://purl.obolibrary.org/obo/vido.owl virostatic Replication process in which a virus containing some portion of genetic material inherited from a parent virus is replicated. John Beverley http://purl.obolibrary.org/obo/vido.owl virus replication Disposition to kill viruses. http://purl.obolibrary.org/obo/vido.owl John Beverley viricidal disposition A disposition to inhibit the reproduction of viruses. http://purl.obolibrary.org/obo/vido.owl John Beverley virostatic disposition Acellular structure aggregate whose members are viruses http://purl.obolibrary.org/obo/vido.owl John Beverley virus aggregate Acellular infectious aggregate whose members are viroids. http://purl.obolibrary.org/obo/vido.owl John Beverley viroid aggregate Acellular infectious aggregate whose members are prions. http://purl.obolibrary.org/obo/vido.owl John Beverley prion aggregate Replication process in which a prion facilitates abnormal folding in proteins resulting in additional, identical, abnormally folded proteins. http://purl.obolibrary.org/obo/vido.owl John Beverley prion replication Infectious structure generative stage that is a temporal subdivision of a virus developmental process. http://purl.obolibrary.org/obo/vido.owl John Beverley virus generative stage Infectious disease whose physical basis is a virus disorder that is clinically abnormal in virtue of the presence of the relevant virus population. http://purl.obolibrary.org/obo/vido.owl John Beverley viral disease course Infectious disorder that exists as a result of a process of formation of disorder initiated by a virus or virus population. http://purl.obolibrary.org/obo/vido.owl John Beverley virus disorder Infectious structure host whose extended organism has some virus part. http://purl.obolibrary.org/obo/vido.owl John Beverley virus host Viral disease inhering in a coronavirus disorder which is realized in some coronavirus disease course This should be imported from: http://purl.obolibrary.org/obo/cido.owl John Beverley coronavirus disease Subclinical infection that is part of a virus host. http://purl.obolibrary.org/obo/vido.owl John Beverley subclinical virus infection Respiratory secretion composed of a small column of liquid, bounded completely or almost completely by free surfaces which maintains its shape due to the surface tension of the liquid. http://purl.obolibrary.org/obo/vido.owl John Beverley respiratory droplet Respiratory droplet bearing a fomite role. http://purl.obolibrary.org/obo/vido.owl John Beverley respiratory droplet fomite Respiratory droplet fomite with virus part. http://purl.obolibrary.org/obo/vido.owl John Beverley respiratory droplet virus fomite Pathogenesis process realization of a pathogenic disposition inhering in a virus or virus population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing a viral infection, and (4) appearance of a virus disorder. http://purl.obolibrary.org/obo/vido.owl John Beverley viral pathogenesis Process of establishing an infection in which a virus participates. http://purl.obolibrary.org/obo/vido.owl John Beverley process of establishing viral infection Cell with an adhesion factor part bearing a viral adhesion disposition John Beverley virus adhesion susceptible cell Adhesion disposition borne by a macromolecule part of a virus that is the disposition to participate in a virus attachment process http://purl.obolibrary.org/obo/vido.owl John Beverley viral adhesion disposition Quality inhering in a portion of fluid that is the proportion of virions to volume of that portion of fluid http://purl.obolibrary.org/obo/vido.owl John Beverley viral load Virus which infects and replicates within or on bacteria or archea. http://purl.obolibrary.org/obo/vido.owl This is an inferred subclass of pathogen. John Beverley bacteriophage Virus which infects and replicates within or on viruses. This is an inferred subclass of pathogen. http://purl.obolibrary.org/obo/vido.owl John Beverley virophage http://purl.obolibrary.org/obo/vido.owl John Beverley establishment of localization in virus host Virus that causes cancer in hosts. http://purl.obolibrary.org/obo/vido.owl John Beverley oncovirus Acellular structure having some arrangement of viral components (e.g. viral capsid, viral DNA/RNA), that is clinically abnormal. http://purl.obolibrary.org/obo/vido.owl John Beverley disordered virus Acellular structure having some arrangement of protein components, that is clinically abnormal. http://purl.obolibrary.org/obo/vido.owl John Beverley disordered prion One-dimensional temporal region beginning with the establishment of a virus in a host and ending with the first appearance of a virion following viral release. http://purl.obolibrary.org/obo/vido.owl John Beverley eclipse interval Site part of an antigen that is recognized by immune system cells and to which antibodies attach. John Beverley epitope site Process in which multiple viral disease epidemics of the same type of viral disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. http://purl.obolibrary.org/obo/vido.owl John Beverley viral disease pandemic Process of viral disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. http://purl.obolibrary.org/obo/vido.owl John Beverley viral disease epidemic Planned process with the objective to produce information about some evaluant with the purpose of, if justified by the information gathered, managing, directing, or protecting. http://purl.obolibrary.org/obo/vsmo.owl surveillance process Site generated by morphogenetic or physiologic processes that is bounded by an anatomical surface. http://purl.obolibrary.org/obo/caro.owl John Beverley anatomical space Anatomical space that is part of a cell. http://purl.obolibrary.org/obo/caro.owl cell space Subclinical virus infection with coronavirus as part. This should be imported from: http://purl.obolibrary.org/obo/cido.owl John Beverley subclinical coronavirus infection Subclinical coronavirus infection with SARS-CoV-2 as part. John Beverley subclinical SARS-CoV-2 infection Disposition to inhibit the reproduction of fungi. http://purl.obolibrary.org/obo/ido.owl John Beverley fungistatic disposition Anatomical space through which a pathogen enters an organism. http://purl.obolibrary.org/obo/ido.owl John Beverley pathogen portal of entry site Anatomical space through which a pathogen exits an organism. http://purl.obolibrary.org/obo/ido.owl John Beverley pathogen portal of exit site Anatomical space in which an infection is located. http://purl.obolibrary.org/obo/ido.owl John Beverley site of infection Anatomical space in which an infection appears in a host organism. http://purl.obolibrary.org/obo/ido.owl John Beverley source of infection site A pathogen transporter role that is borne by an organism active in the transfer of an infectious agent or infectious structure to an organism of another species in which it can realize its infectious disposition. John Beverley The role is realized in a process that transfers an infectious organism from one location to another. pathogen vector role Pathogenic disposition borne by a pathogen to be transmitted to a host and become part of an infection in that host or immunocompetent members of the same species as the host. http://purl.obolibrary.org/obo/ido.owl John Beverley infectious disposition Disease that occurs in different organs functioning in respiration and consisting especially of the nose, nasal passages, nasopharynx, larynx, trachea, bronchi, and lungs. http://www.ebi.ac.uk/efo/efo.owl respiratory system disease Respiratory system disease located in the lower respiratory tract. http://www.ebi.ac.uk/efo/efo.owl lower respiratory tract disease Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. http://www.ebi.ac.uk/efo/efo.owl acute respiratory distress syndrome Process that generates the ability of a pathogen to induce disorder in an organism. Process that is the realization of a pathogenic disposition inhering in an pathogen or pathogen population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing an infection, and (4) appearance of disorder. http://purl.obolibrary.org/obo/go.owl John Beverley pathogenesis A Geopolitical Entity that delimits a Government with effective internal and external sovereignty over the region and its population, and which is not dependent on or subject to any other power or Geopolitical Entity. http://www.ontologyrepository.com/CommonCoreOntologies/ country Information Content Entity that consists of a set of propositions that describe some Entity. http://www.ontologyrepository.com/CommonCoreOntologies/ descriptive information content entity Information Content Entity that consists of a set of symbols that denote some Entity. http://www.ontologyrepository.com/CommonCoreOntologies/ designative information content entity Information Content Entity that consists of a set of propositions or images (as in the case of a blueprint) that prescribe some Entity. http://www.ontologyrepository.com/CommonCoreOntologies/ directive information content entity A Geospatial Region that is a fiat division of a Geopolitical Entity and not a Geopolitical Entity. http://www.ontologyrepository.com/CommonCoreOntologies/ division of geopolitical entity A geospatial region that delimits the authority of a formally constituted government to exercise its control within the bounded area. http://www.ontologyrepository.com/CommonCoreOntologies/ geopolitical entity A Geospatial Region at which an Entity or Event is located. http://www.ontologyrepository.com/CommonCoreOntologies/ geospatial location A site at or near the surface of the Earth. http://www.ontologyrepository.com/CommonCoreOntologies geospatial region example to be eventually removed The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion John Beverley SARS-COV-2 Infection John Beverley United States John Beverley Canada ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) relation has no temporal argument Person:Alan Ruttenberg To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])