en Shane Babcock The Bacteria Infectious Disease Ontology (BIDO) is an extension of IDO that will serve as a reference ontology concerning bacterial pathogens. In turn it will serve as a hub for IDO extensions concerning specific bacterial infectious diseases. It mirrors the Virus Infectious Disease Ontology in that respect. BIDO imports relevant molecular entities from CHEBI, proteins from PRO and cellular components and processes from GO, linking them together via new axioms. The relevance of imported terms to bacterial pathogenicity is highlighted by the addition of axioms linking them to key IDO terms such as 'virulence factor', 'toxin', 'invasion factor' and 'adhesion factor'. https://github.com/infectious-disease-ontology-extensions 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 metadata section term as in existing standard term source user interface 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 ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term 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 has measurement unit label This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about 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 process is result of The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR Is a relationship between a process and a preceding occurrent that directly caused the later one to occur is a relationship between a process and a preceding occurrent that directly caused the later one to occur Bjoern Peters, IEDB IEDB PERSON:Bjoern Peters process is result of bound_to A relationship between two material entities that form a complex based on a selective, non-covalent interaction. The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope. bound_to 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 David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets eco subset X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes 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 mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) eco subset capable of 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 A is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall http://purl.obolibrary.org/obo/ro.owl attached to pending final vetting a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel http://purl.obolibrary.org/obo/ro.owl eco subset Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a shortcut relation that equals to: processed material and (is_specified_output_of some vaccine preparation) and (has function some (vaccine function and (is realized by only (vaccine immunization and (realizes some ('immunization target role' and (role_of some 'MICROBE')))))))) The domain of this relation is a vaccine. The range of this relation is a microbe (a bacterium, a virus, a fungus, and a parasite) Yongqun He immunization against microbe vaccine immunization against microbe immunizes against http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.org/obo/owl/relationship OBO_REL:0000007 relationship has_proper_part http://purl.obolibrary.org/obo/ncbitaxon.owl fungi 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 asymptomatic carriers who have had contact with pathogens are prevented from having contact with other susceptible organisms. http://purl.obolibrary.org/obo/apollo-sv.owl quarantine control strategy A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms. Matthew Diller William R. Hogan http://purl.obolibrary.org/obo/apollo-sv.owl A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms. contact isolation control measure Objective specification whose endpoint is human awareness of the level of a 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 An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) 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 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 nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ; (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] http://purl.obolibrary.org/obo/bfo.owl quality 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]) Infection that has as part some bacterium. Shane Babcock bacterial infection Infectious disorder that has some bacterium as part, that exists as a result of a process of formation of disorder initiated by the bacterium. Note that this class does not include all disorders caused by bacterial pathogens. For instance, the disorder that is caused to an organism by c. botulinum toxins is not an infectious disorder. Is there any motivation for also introducing a separate class (as a direct child of 'disorder') with the label 'bacterial disorder' that includes non-infectious disorders caused by bacteria? I am not sure. Take the case of disorder caused by bacteria that do not localize? The disorder does not have bacteria as part. Is the fact that the toxins were produced by bacteria sufficient to make it a bacterial disorder? Concievably, the same disorder could have originated from the same toxins, but injected into the organism in a lab. Shane Babcock bacterial infectious disorder Infectious disease that has its material basis in some bacterial infectious disorder. Shane Babcock bacterial infectious disease Infectious disease course that is the realization of a bacterial infectious disease. Shane Babcock bacterial infectious disease course Antibiotic that is used to kill bacteria. This is an inferred subclass of 'bactericidal'. Shane Babcock bactericidal antibiotic Antibiotic that is used to inhibit the growth of bacteria. This is an inferred subclass of 'bacteriostatic'. Shane Babcock bacteriostatic antibiotic Justification for the introduction of this term. A variety of OBO ontologies import the term 'Firmicutes' from NCBITaxon, annotated with: 'alternative term: gram-positive bacteria'. Insofar that the intention is to use the NCBITaxon term to represent the class of all gram-positive bacteria, this is ontologically incorrect. Although most members of the phylum Firmicutes are gram-positive, not all are. Shane Babcock gram positive bacterium Shane Babcock gram negative bacterium Bacterium that is capable of growing and surviving in an oxygenated environment. Shane Babcock aerobic bacterium Mycobacterium tuberculosis Nocardia asteroides Aerobic bacterium that requires oxygen to survive and grow. Shane Babcock obligate aerobe bacterium Escherichia coli Salmonella Staphylococcus Anaerobic bacterium that is capable of anaerobic methods of energy production but uses aerobic respiration in the presence of oxygen. Note regarding the OWL definition, which may at first glance appear counterintuitive. Only PATO:anaerobic, and not PATO:aerobic, is included because although facultative anaerobe baceteria are capable of aerobic respiration, they do not depend upon it. Keep in mind that PATO:aerobic is defined as an organism's dependence upon oxygen. Thus aerobic organisms are only defined as being capable of aerobic respiration--and so they do not bear PATO:aerobic. This is an inferred subclass of anaerobic bacteria. That said, I am actually not sure whether facultative anaerobe bacteria should be primarily classified under aerobic bacteria or under anaerobic bacteria. Shane Babcock facultative anaerobe bacterium Bacterium that is capable of surviving and growing in the absence of oxygen. Shane Babcock anaerobic bacterium Actinomyces Bacteroides Clostridium Anaerobic bacterium that only uses anaerobic methods of energy production and is harmed by the presence of oxygen. Shane Babcock obligate anaerobe bacterium Bacterium that has a spherical or oval shape. Shane Babcock cocci bacterium Bacterium that is rod-shaped. Shane Babcock bacilli bacterium Bacterium that is flexible and has a thin, elongated, spiral shape. Shane Babcock Not to be confused with the bacterial phylum Spirochaetes. While most members of this phylum are spiral-shaped, this morphology is not universal in the phylum. [See: PMID: 22589287] spirochetes bacterium Bacterium that is rigid and has an elongated, spiral shape. Shane Babcock Not to be confused with the genus Spirillum, members of which are spirilla bacteria. Spirilla bacteria are also found within other genuses as well. spirilla bacterium Cutibacterium acnes Anaerobic bacterium that only uses fermentation for energy production but is unharmed by the presence of oxygen. Shane Babcock aerotolerant anaerobe bacterium Campylobacter Helicobacter pylori Obligate aerobic bacterium that requires oxygen for energy production but is harmed in atmospheric concentrations of oxygen (21% O2). Shane Babcock Since they are harmed by it, microaerophile bacteria require oxygen levels lower than that which are present in the atmosphere in order to grow. microaerophile bacterium Object aggregate whose members are bacteria. Shane Babcock bacteria aggregate Colony whose members are bacteria. Shane Babcock bacteria colony Organism population whose members are bacteria. Shane Babcock bacteria population Host whose extended organism has some bacterium part. Shane Babcock bacteria host Apperance of disorder by which a bacterial infectious disorder comes into existence. Shane Babcock appearance of bacterial infectious disorder Process of establishing an infection in which a bacterium participates. Shane Babcock process of establishing a bacterial infection Pathogenesis process realization of a pathogenic disposition inhering in some bacterium or bacteria population, having at least the proper process parts: (1) toxin biosynthetic process, and (2) appearance of disorder. We cannot assert that this class has 'establishment of localization in host', nor 'process of establishing an infection', as parts. That would exclude disease caused by toxins, produced by bacteria that never localize in the diseased organism. Shane Babcock bacterial pathogenesis Bacterial pathogenesis having at least the proper process parts: (1) establishment of localization in host, (2) process of establishing a bacterial infection, and (3) appearance of bacterial infectious disorder. Shane Babcock Note that this class and its sibling 'bacterial pathogenesis involving toxin production' are not disjoint. The pathogenesis processes associated with many bacteria are instances of both. By contrast, the bacterial pathogenesis process associated with mycobacterium tuberculosis is an example of bacterial pathogenesis that involves infection, but not toxin production. Some instances of this class may also have an instance of 'pathogen transmission process' as a part. But we cannot assert that 'bacterial pathogenesis involving an infection' has 'pathogen transmission process' as a process part. This would exclude bacterial pathogenesis involving infections caused by opportunistic pathogens, in which bacteria already established in a site in or on the host (e.g. bacteria colonizing the skin surface) are able to establish localization in a new site within that same host wherein they are able to realize their infectious disposition (e.g. when bacteria on the skin enter the host through a wound). bacterial pathogenesis involving an infection Process of bacterial infectious disease realizations for which there is a statistically significant increase in the bacterial infectious disease incidence of a population. Shane Babcock bacterial infectious disease epidemic Process in which multiple bacterial infectious disease epidemics of the same type of bacterial infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. Shane Babcock bacterial infectious disease pandemic Process boundary that marks the beginning of the lify cycle of a bacterium. Shane Babcock bacteria birth process boundary Process boundary that marks the end of the life cycle of some bacterium. Shane Babcock bacteria death process boundary Incubation process of some bacterium beginning with infection by the bacterium and ending with the manifestation of symptoms. Shane Babcock bacterium incubation process Latency process involving a bacterium, during which the bacterium lies dormant within the host, and ending when the bacterium starts to reproduce. Shane Babcock bacterial latency process Adhesion disposition borne by a macromolecule that is part of some bacterium that is the disposition to participate in the adhesion of the bacterium to a host. Shane Babcock bacterial adhesion disposition Biofilm consisting of an aggregate of surface-associated bacteria that are enveloped in a biofilm matrix produced by those bacteria. Shane Babcock Generally, many bacterial biofilms show protective resistance to the human immune system, as well as resistance to antibiotics. bacterial biofilm Adhesion factor that is part of some bacterium. Shane Babcock bacterial adhesion factor Disorder the formation of which involves some bacterial toxin. The idea is that this class will serve as a parent for any disorder involving bacterial toxins, including those that do not involve infection by the relevant toxin-producing bacteria. Thus, food botulism would have as its material basis a bacterial toxin disorder that is NOT a bacterial infectious disorder since the bacteria itself need not ever localize in the host. Of course, other bacterial toxin disorders are also infectious disorders. That is, cases where bacteria are infecting the host, and secreted toxins are a virulence factor aiding in the infection of the host by helping the bacteria bypass the innate and adaptive immune responses of the host. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243249/ I did at one point define this class as "Disorder caused by some bacterial toxin." But I wanted to avoid the potential suggestion that the toxin is in all cases the primary causative factor. It is the primary causative factor in food botulism where the bacteria need never be present in the host. But in cases involving infection, the toxin has more of a supporting role. Shane Babcock bacterial toxin disorder 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 A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. http://purl.obolibrary.org/obo/chebi.owl Phospholipid a phospholipid derivative phospholipids phospholipid Liposaccharide natural compounds consisting of a trisaccharide repeating unit (two heptose units and octulosonic acid) with oligosaccharide side chains and 3-hydroxytetradecanoic acid units (they are a major constituent of the cell walls of Gram-negative bacteria). This is an inferred subclass of 'virulence factor' and 'endotoxin'. (axiom editor) Shane Babcock http://purl.obolibrary.org/obo/chebi.owl LPS lipopolysaccharide Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. http://purl.obolibrary.org/obo/chebi.owl carbohydrate Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. http://purl.obolibrary.org/obo/chebi.owl Peptide peptides Peptid peptido peptidos peptide Nucleic acid composed of nucleotides containing deoxyribose and linked by phosphodiester bonds. http://purl.obolibrary.org/obo/chebi.owl deoxyribonucleic acid 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. http://purl.obolibrary.org/obo/chebi.owl lipid Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. http://purl.obolibrary.org/obo/chebi.owl Glycosaminoglycan glycosaminoglycan Glykosaminoglykan glicosaminoglicano glycosaminoglycane glycosaminoglycans glycosaminoglycan A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. http://purl.obolibrary.org/obo/chebi.owl Polysaccharide polysaccharides Glycan Glycane Glykan Glykane glycans polisacarido polisacaridos polysaccharide http://purl.obolibrary.org/obo/chebi.owl aminoglycans aminoglycan Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc. molecular entity Any phospholipid that contain both phosphate and carbohydrate as integral structural components. http://purl.obolibrary.org/obo/chebi.owl glycophospholipid glycophospholipids phosphoglycolipids glycophospholipid Role inhering in a molecular entity or part of that entity, realized in biological processes. http://purl.obolibrary.org/obo/chebi.owl biological role Glycophospholipids that are the components of endotoxins held responsible for the toxicity of Gram-negative bacteria. Lipid A is the innermost of the three regions of the lipopolysaccharide (LPS) molecule, and its hydrophobic nature allows it to anchor the LPS to the outer membrane. Four acyl chains attached directly to two (1->6)-linked glucosamine sugars are beta-hydroxy acyl chains usually between 10 and 16 carbons in length. Two additional acyl chains are often attached to the beta-hydroxy group. http://purl.obolibrary.org/obo/chebi.owl lipid A lipid As Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. http://purl.obolibrary.org/obo/chebi.owl metabolite http://purl.obolibrary.org/obo/chebi.owl peptide antibiotic Bacterial polysaccharide derivatives of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds, whose main function is to fortify the cell wall. In some parasites, they serve as a site of attachment to mucosal membranes. http://purl.obolibrary.org/obo/chebi.owl TAs teichoic acids Teichoic acids are present in the cell wall of Gram-positive bacteria. They are absent from the cell wall of Gram-negative bacteria. teichoic acid Any member of class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar part acylated by one or more fatty acids and the glycerol part may be absent. http://purl.obolibrary.org/obo/chebi.owl Glycolipid glycolipids glycolipid A macromolecule formed by a living organism. http://purl.obolibrary.org/obo/chebi.owl biopolymer Biopolymere biomacromolecules biopolymers biomacromolecule 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 A polysaccharide capsule that is found on the cell surface of a broad range of bacterial species and often involved in mediating direct interactions between the bacteria and its environment. Due to these interactions, capsular polysaccharides have been implicated as important virulence factors for many bacterial pathogens. The molecules are highly hydrated and composed of repeating single monosaccharide units which are joined together by glycosidic linkages. They can be homo- or heteropolymers and can be substituted with organic molecules such as acetyl groups, or or inorganic molecules such as phosphate. (BIDO axiom editor) Shane Babcock http://purl.obolibrary.org/obo/chebi.owl capsular polysaccharide Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion. http://purl.obolibrary.org/obo/chebi.owl complex protein conjugated protein 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 http://purl.obolibrary.org/obo/chebi.owl liposaccharides liposaccharide The glycolipid moiety of bacterial lipopolysaccharide (R can be either hydrogen or a fatty acyl group). (BIDO axiom editor) Shane Babcock http://purl.obolibrary.org/obo/chebi.owl Lipid A is the component of the lipopolysaccharide portion of the outer membrane of gram-negative bacteria which is responsible for its endotoxicity. When lipid A enters the circulatory system it causes a toxic reaction by activating toll like receptor TLR 4. lipid A Polypeptides synthesized by specific strains of bacteria that are lethal against other strains of the same or related species. This is an inferred subclass of 'toxin' and 'bactericidal' -SB BIDO axiom editor: Shane Babcock http://purl.obolibrary.org/obo/chebi.owl bacteriocins bacteriocin A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues. http://purl.obolibrary.org/obo/chebi.owl oligosaccharide Any molecular entity that contains carbon. http://purl.obolibrary.org/obo/chebi.owl organic molecular entity A biological role played by the molecular entity or part thereof within a biochemical context. http://purl.obolibrary.org/obo/chebi.owl biochemical role A peptidoglycan with a phosphate linkage to a lipid. http://purl.obolibrary.org/obo/chebi.owl PMID:18081839 lipid-linked peptidoglycans lipid-linked peptidoglycan Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. http://purl.obolibrary.org/obo/chebi.owl carbohydrate derivative A repetitive glycan polysaccharide contained within a lipopolysaccharide (LPS). The O-antigen is attached to the core oligosaccharide, and comprises the outermost domain of the LPS molecule. http://purl.obolibrary.org/obo/chebi.owl O antigen O-polysaccharide A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. http://purl.obolibrary.org/obo/chebi.owl Lipoprotein lipoproteins lipoprotein particle lipoprotein A carbohydrate derivative that is any derivative of a polysaccharide. http://purl.obolibrary.org/obo/chebi.owl polysaccharide derivatives polysaccharide derivative A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment. http://purl.obolibrary.org/obo/chebi.owl exopolysaccharides extracellular polymeric substance extracellular polymeric substances exopolysaccharide A bacterial gene that can produce a gene product that is at least partially responsible for enabling a bacterium to be pathogenic http://purl.obolibrary.org/obo/chebi.owl bacterial virulence gene B Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. http://purl.obolibrary.org/obo/chebi.owl prokaryotic metabolites prokaryotic metabolite Any prokaryotic metabolite produced during a metabolic reaction in bacteria. http://purl.obolibrary.org/obo/chebi.owl bacterial metabolite A peptidoglycosaminoglycan formed by alternating residues of beta-(1->4)-linked N-acetylglucosamine and N-acetylmuramic acid {2-amino-3-O-[(S)-1-carboxyethyl]-2-deoxy-D-glucose} residues. Attached to the carboxy group of the muramic acid is a peptide chain of three to five amino acids. http://purl.obolibrary.org/obo/chebi.owl Peptidoglycan peptidoglycan Mucopeptide Murein Peptideglycan peptidoglycan A family of glycosaminoglycan formed by alternating residues of D-glucosamine and either muramic acid {2-amino-3-O-[(S)-1-carboxyethyl]-2-deoxy-D-glucose} or L-talosaminuronic acid (2-amino-2-deoxy-L-taluronic acid), which are usually N-acetylated or N-glycoloylated. Those containing muramic acid residues are known as peptidoglycans while those containing L-talosaminuronic acid residues are known as pseudopeptidoglycans. The carboxyl group of the muramic acid is commonly substituted by a peptide containing residues of both L- and D-amino acids, whereas that of L-talosaminuronic acid is substituted by a peptide consisting of L-amino acids only. http://purl.obolibrary.org/obo/chebi.owl peptidoglycosaminoglycans peptidoglycosaminoglycan A short chain of sugar residues within a lipopolysaccharide, containing an oligosaccharide component which attaches directly to a lipid A component. {External definition} (BIDO axiom editor) Shane Babcock Core oligosaccharide http://purl.obolibrary.org/obo/chebi.owl LPS core A biological process that presents the survival of a microbe inside a cell line cell. Yongqun He http://purl.obolibrary.org/obo/clo.owl microbial survival inside cell line cell A microbial survival inside cell line cell where the microbe is a bacterium. Yongqun He http://purl.obolibrary.org/obo/clo.owl bacterial survival inside cell line cell 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 A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). http://purl.obolibrary.org/obo/cl.owl CARO:0000013 To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). native cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. http://purl.obolibrary.org/obo/cl.owl T lymphocyte T-cell T-lymphocyte T cell A leukocyte with abundant granules in the cytoplasm. http://purl.obolibrary.org/obo/cl.owl granular leucocyte granular leukocyte polymorphonuclear leukocyte granulocyte A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive. http://purl.obolibrary.org/obo/cl.owl polymorphonuclear leukocyte Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)). mature neutrophil A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. http://purl.obolibrary.org/obo/cl.owl Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5. mast cell A cell that moves by its own activities. http://purl.obolibrary.org/obo/cl.owl motile cell Any cell capable of ingesting particulate matter via phagocytosis. http://purl.obolibrary.org/obo/cl.owl phagocyte A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. http://purl.obolibrary.org/obo/cl.owl histiocyte Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. http://purl.obolibrary.org/obo/cl.owl B lymphocyte B-cell B-lymphocyte B cell A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). http://purl.obolibrary.org/obo/cl.owl interdigitating cell veiled cell dendretic cell http://purl.obolibrary.org/obo/cl.owl prokaryotic cell A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. http://purl.obolibrary.org/obo/cl.owl lymphocyte A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged. [database_cross_reference: GOC:tfm][database_cross_reference: ISBN:0618947256] http://purl.obolibrary.org/obo/cl.owl BTO:0002779 bacterial spore endospore Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. http://purl.obolibrary.org/obo/cl.owl monocyte A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. http://purl.obolibrary.org/obo/cl.owl dust cell alveolar macrophage A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. http://purl.obolibrary.org/obo/cl.owl large granular lymphocyte null cell NK cell natural killer cell An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. http://purl.obolibrary.org/obo/cl.owl immune cell leucocyte white blood cell leukocyte A cell of the monocyte, granulocyte, or mast cell lineage. http://purl.obolibrary.org/obo/cl.owl myeloid leukocyte Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. http://purl.obolibrary.org/obo/cl.owl polymorphonuclear leukocyte neutrophil Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. http://purl.obolibrary.org/obo/cl.owl immature neutrophil A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. http://purl.obolibrary.org/obo/cl.owl mature B cell A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. http://purl.obolibrary.org/obo/cl.owl Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive. plasma cell A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative. http://purl.obolibrary.org/obo/cl.owl Memory B-cells are also reportedly CD5-negative, CD10-negative, CD21-positive, CD22-positive, CD23-negative, CD24-positive, CD25-positive, CD27-positive, CD34-negative, CD38-negative, CD40-positive, CD43-negative, CD44-positive, CD45-positive, CD53-positive, CD80-negative, CD81-negative, CD86-positive, and CD196/CCR6-positive. memory B cell A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure. http://purl.obolibrary.org/obo/cl.owl memory T cell A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive. http://purl.obolibrary.org/obo/cl.owl cytotoxic T lymphocyte cytotoxic T cell A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. http://purl.obolibrary.org/obo/cl.owl effector T cell A effector T cell that provides help in the form of secreted cytokines to other immune cells. http://purl.obolibrary.org/obo/cl.owl helper T cell A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. http://purl.obolibrary.org/obo/cl.owl Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. http://purl.obolibrary.org/obo/cl.owl antibody secreting cell A long lived plasma cell that secretes IgE. http://purl.obolibrary.org/obo/cl.owl cell IgE plasma cell true A long lived plasma cell that secretes IgE. GOC:msz GO_REF:0000031 ISBN:781735149 A short lived plasma cell that secretes IgE. http://purl.obolibrary.org/obo/cl.owl cell IgE short lived plasma cell true A short lived plasma cell that secretes IgE. GOC:msz GO_REF:0000031 ISBN:781735149 A mature B cell that produces cytokines that can influence CD4 T cell differentiation. http://purl.obolibrary.org/obo/cl.owl B effector cell Be cell A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow. http://purl.obolibrary.org/obo/cl.owl long lived plasma cell A fully differentiated plasma cell that lives for months. http://purl.obolibrary.org/obo/cl.owl short lived plasma cell A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system. http://purl.obolibrary.org/obo/cl.owl cell IgA short lived plasma cell true A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system. GOC:msz GO_REF:0000031 ISBN:781735149 A short lived plasma cell that secretes IgG. http://purl.obolibrary.org/obo/cl.owl cell IgG short lived plasma cell true A short lived plasma cell that secretes IgG. GOC:msz GO_REF:0000031 ISBN:781735149 A short lived plasma cell that secretes IgM. http://purl.obolibrary.org/obo/cl.owl cell IgM short lived plasma cell true A short lived plasma cell that secretes IgM. GOC:msz GO_REF:0000031 ISBN:781735149 A fully differentiated plasma cell that secretes IgG. http://purl.obolibrary.org/obo/cl.owl cell IgG plasma cell true A fully differentiated plasma cell that secretes IgG. GOC:msz GO_REF:0000031 ISBN:781735149 A fully differentiated plasma cell that secretes IgM. http://purl.obolibrary.org/obo/cl.owl cell IgM plasma cell true A fully differentiated plasma cell that secretes IgM. GOC:msz GO_REF:0000031 ISBN:781735149 A fully differentiated plasma cell that secretes IgA. http://purl.obolibrary.org/obo/cl.owl cell IgA plasma cell true A fully differentiated plasma cell that secretes IgA. GOC:msz GO_REF:0000031 ISBN:781735149 A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses. http://purl.obolibrary.org/obo/cl.owl innate lymphoid cell An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines. http://purl.obolibrary.org/obo/cl.owl group 1 innate lymphoid cell A T cell that expresses a T cell receptor complex and has completed T cell selection. http://purl.obolibrary.org/obo/cl.owl mature T cell Any measurement of the degree to which the presentation of a disease state has caused pain or damage, established one or more lesions or infectious colonies, and/or taken over or interfered with the normal functioning of the body as a whole, or of one or more organs, tissues, cells or subcellular mechanisms of an organism. JSmith http://purl.obolibrary.org/obo/cmo.owl disease severity measurement Any measurement of the degree to which the presentation of a bacterial infection has caused pain or damage, or of the degree to which bacteria has established lesions or infectious colonies, and/or taken over or interfered with the normal functioning of the body as a whole, or of one or more organs, tissues, cells or subcellular mechanisms of an organism. BIDO axiom editor: Shane Babcock http://purl.obolibrary.org/obo/cmo.owl JSmith 2015-04-29T08:31:47Z bacterial infection severity measurement A measurement of bacterial infection severity which is derived from a combination of multiple measurements and/or an objective or subjective ranking or rating system according to a specified formula or set of criteria. http://purl.obolibrary.org/obo/cmo.owl JSmith 2015-04-29T08:33:04Z composite score for bacterial infection severity bacterial infection severity score A ranking or rating of bacterial infection severity which is based on or derived from the ratio of the number of leukocytes in a sample of mucosal membrane to total number of cells the that sample. http://purl.obolibrary.org/obo/cmo.owl JSmith 2015-04-29T08:35:02Z bacterial infection severity score based on the percentage of leukocyte infiltration leukocyte infiltrate in mucosa (% total cellularity) bacterial infection severity score based on mucosal leukocyte infiltration A ranking or rating of bacterial infection severity which is based on or derived from the number and/or size of foci of inflammatory cells (that is, leukocytes, especially neutrophils, macrophages, monocytes, eosinophils, and/or basophils) in a sample of exudate from an infected tissue or organ. An exudate is a fluid with a high content of protein and cellular debris which has escaped from blood vessels and has been deposited in tissues or on tissue surfaces, usually as a result of inflammation. http://purl.obolibrary.org/obo/cmo.owl JSmith 2015-04-29T08:37:29Z score of inflammatory exudate in tympanic cavity bacterial infection severity score based on inflammatory foci in exudate The enumeration, i.e. measurement of the total number, of bacteria in a specified sample of an infected tissue or bodily fluid, or in the entire body of the host. http://purl.obolibrary.org/obo/cmo.owl JSmith 2015-04-29T08:39:34Z bacterial count bacteria count The enumeration, i.e. measurement of the total number, of bacterial colony forming units (CFUs) in a specified sample of fluid removed from and/or solution used to wash the interior of a cavity in a body or an organ. A bacterial CFU is an individual bacterium which is able to clonally propagate itself into an entire colony of identical cells. http://purl.obolibrary.org/obo/cmo.owl JSmith 2015-04-29T08:41:38Z recovered CFU total number of CFU in effusion plus wash total number of bacterial colony forming units recovered The logarithm of the enumeration, i.e. measurement of the total number, of bacterial colony forming units (CFUs) in a specified sample of fluid removed from and/or solution used to wash the interior of a cavity in a body or an organ. A logarithm is the power to which a base, such as 10, must be raised to produce a given number. A bacterial CFU is an individual bacterium which is able to clonally propagate itself into an entire colony of identical cells. http://purl.obolibrary.org/obo/cmo.owl JSmith 2015-04-29T08:46:53Z Log recovered CFU logarithm of the total number of CFU in effusion plus wash logarithm of the total number of bacterial colony forming units recovered The role of a material entity to prevent, diagnose, treat, or study disease and/or its effects William Hogan http://purl.obolibrary.org/obo/dron.owl William Hogan clinical drug role A material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role William Hogan http://purl.obolibrary.org/obo/dron.owl William Hogan drug product A role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism William R. Hogan http://purl.obolibrary.org/obo/dron.owl active ingredient A role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes William R. Hogan http://purl.obolibrary.org/obo/dron.owl role of scattered molecular aggregate A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism William R. Hogan http://purl.obolibrary.org/obo/dron.owl drug administration A biome is an ecosystem to which resident ecological communities have evolved adaptations. http://purl.obolibrary.org/obo/envo.owl major habitat type EcosytemType There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar. biome A complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix; usually adhering to a substratum. Move this to under 'colony'? http://purl.obolibrary.org/obo/envo.owl biofilm A system which has the disposition to environ one or more material entities. http://purl.obolibrary.org/obo/envo.owl environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. enviromental system An environmental system which includes both living and non-living components. http://purl.obolibrary.org/obo/envo.owl This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem Processed material bearing a reagent role. http://purl.obolibrary.org/obo/ero.owl reagent An antibody is used to detect proteins in a Western blot assay. A reagent that is comprised of immunoglobulins produced by B cells in response to an antigen. Antibody reagents can be engineered to have specificity for specific antigens. Nicole Vasilevsky http://www.nlm.nih.gov/medlineplus/ency/article/002223.htm http://purl.obolibrary.org/obo/ero.owl antibody reagent An mouse anti-human Mad4 antibody. Antibody reagent that recognizes a single epitope. Melissa Haendel http://purl.obolibrary.org/obo/ero.owl monoclonal antibody reagent 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 Beta barrel membrane transport protein that acts as a diffusion channel for small molecules. [This is an external definition] Imported from FMA because we needed a general class for porins, as opposed to the specific types found in the Protein Ontology -SB [12/18/2020] Shane Babcock (external definition and axioms) http://purl.obolibrary.org/obo/fma.owl Porins are present in the outer membrane of gram-negative bacteria and some gram-positive mcyobacteria. Porins serve as specific receptors for some bacteriophages. porin Environmental Isolate Fecal Indicator Bacteria Number Environment Canada Metadata 12,456 cfu Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens. URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf http://purl.obolibrary.org/obo/genepio.owl fecal indicator bacteria count OD reading or cfu's or cells per millilitre Number of bacteria in sample GROUP: Environment Canada Metadata http://purl.obolibrary.org/obo/genepio.owl bacteria density http://purl.obolibrary.org/obo/genepio.owl environmental datum 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 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. [database_cross_reference: GOC:go_curators][database_cross_reference: GOC:isa_complete][database_cross_reference: GOC:jl][database_cross_reference: ISBN:0198506732] GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process reproduction Enables the energy independent passage of toxins, sized less than 1000 Da, across a membrane towards the outside of the cell. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. http://purl.obolibrary.org/obo/go.owl toxin export channel activity The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells. [database_cross_reference: GOC:mtg_cell_cycle] http://purl.obolibrary.org/obo/go.owl GO:0007104 GO:0016288 GO:0033205 Wikipedia:Cytokinesis cell cycle cytokinesis cytokinesis involved in cell cycle Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other. cytokinesis Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a bacterial-type specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/go.owl krc 2010-10-19T03:36:01Z bacterial-type RNA polymerase activity Any process involved in the transition from the initiation to the elongation phases of transcription by a DNA-dependent RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors. [database_cross_reference: PMID:15020047][database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH] Add axiom: has part some protein-DNA-RNA complex remodeling http://purl.obolibrary.org/obo/go.owl krc 2010-12-01T02:13:09Z promoter escape promoter clearance during DNA-dependent transcription promoter clearance during DNA-templated transcription Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble. [database_cross_reference: PMID:15020047][database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/go.owl krc 2010-12-02T02:15:04Z promoter melting DNA-dependent transcriptional open complex formation DNA-templated transcriptional open complex formation DNA-templated transcription open complex formation The synthesis of RNA from a DNA template by a bacterial-type RNA polymerase, originating at a bacterial-type promoter. [database_cross_reference: GOC:txnOH] https://github.com/geneontology/go-ontology/issues/14854 http://purl.obolibrary.org/obo/go.owl transcription from bacterial-type RNA polymerase promoter bacterial transcription Any process involved in the transition from the initiation to the elongation phase of transcription by a bacterial-type RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance generally involves dissociation of the sigma initiation factor. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/go.owl krc 2010-12-06T03:38:10Z promoter clearance from bacterial-type RNA polymerase promoter Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/go.owl krc 2010-12-06T03:40:12Z transcription initiation from bacterial-type RNA polymerase promoter The extension of an RNA molecule after transcription initiation and promoter clearance at a bacterial-type RNA polymerase promoter by the addition of ribonucleotides catalyzed by a bacterial-type RNA polymerase. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/go.owl krc 2010-12-06T03:46:27Z RNA elongation from bacterial-type RNA polymerase promoter transcription elongation from bacterial-type RNA polymerase promoter The process in which the synthesis of an RNA molecule by a bacterial-type RNA polymerase using a DNA template is completed. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/go.owl krc 2010-12-06T03:47:43Z transcription termination from bacterial-type RNA polymerase promoter The aggregation, arrangement and bonding together of proteins on a bacterial-type RNA polymerase promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/go.owl krc 2010-12-06T03:54:45Z bacterial-type RNA polymerase transcription PIC biosynthesis bacterial-type RNA polymerase transcription PIC formation bacterial-type RNA polymerase transcriptional preinitiation complex formation bacterial-type RNA polymerase preinitiation complex assembly Any process involved in the melting of the DNA hybrid of the core promoter region within a bacterial-type RNA polymerase promoter to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/go.owl krc 2010-12-06T04:04:16Z transcriptional open complex formation at bacterial-type RNA polymerase promoter transcription open complex formation at bacterial-type RNA polymerase promoter Any process involved in the selection of the specific location within the template strand of a DNA-dependent RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript. [database_cross_reference: PMID:16826228][database_cross_reference: PMID:18846104][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/go.owl krc 2011-06-20T12:44:11Z DNA-dependent transcriptional start site selection DNA-templated transcriptional start site selection Any process involved in the selection of the specific location within the template strand of a bacterial-type RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript. [database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/go.owl krc 2011-06-20T01:48:56Z transcriptional start site selection at bacterial-type RNA polymerase promoter Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. http://purl.obolibrary.org/obo/go.owl ciliary/flagellar motility ciliary or bacterial-type flagellar motility Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC. cilium or flagellum-dependent cell motility The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/go.owl NK cell differentiation natural killer cell development Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. natural killer cell differentiation The expansion of a natural killer cell population by cell division. [database_cross_reference: GOC:add][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/go.owl NK cell proliferation natural killer cell proliferation The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl cytokine production The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. http://purl.obolibrary.org/obo/go.owl T cell mediated apoptosis T cell mediated cell death T cell mediated cell killing T lymphocyte mediated cytotoxicity T-cell mediated apoptosis T-cell mediated cell death T-cell mediated cell killing T-cell mediated cytotoxicity T-lymphocyte mediated cytotoxicity T cell mediated cytolysis Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in the induction of apoptosis in the target cell. Note that both CD4 and CD8 positive T cells can mediate apoptosis of target cells, independently of their definition as 'helper' T cells or not. T cell mediated cytotoxicity The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. GOC:add GOC:pr ISBN:0781735149 PMID:11911826 The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. http://purl.obolibrary.org/obo/go.owl NK cell mediated immunity natural killer cell mediated immunity 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 The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/go.owl T cell activation during immune response T lymphocyte activation during immune response T-cell activation during immune response T-lymphocyte activation during immune response T cell activation involved in immune response The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. [database_cross_reference: GOC:add][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/go.owl T cell development involved in immune response T cell differentiation during immune response T lymphocyte differentiation during immune response T-cell differentiation during immune response T-lymphocyte differentiation during immune response Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T cell differentiation involved in immune response The expansion of a T cell population by cell division as part of an immune response. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/go.owl T cell proliferation during immune response T lymphocyte proliferation during immune response T-cell proliferation during immune response T-lymphocyte proliferation during immune response T cell proliferation involved in immune response The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. [database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/go.owl B cell activation during immune response B lymphocyte activation during immune response B-cell activation during immune response B-lymphocyte activation during immune response B cell activation involved in immune response The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response. [database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/go.owl mature B cell development involved in immune response mature B cell differentiation during immune response mature B lymphocyte differentiation during immune response mature B-cell differentiation during immune response mature B-lymphocyte differentiation during immune response Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. mature B cell differentiation involved in immune response The process in which a B cell acquires the specialized features of a memory B cell. Memory B cells are cells that can respond rapidly to antigen re-exposure by production of high-affinity antibody. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/go.owl memory B lymphocyte differentiation memory B-cell differentiation memory B-lymphocyte differentiation memory B cell development Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. memory B cell differentiation The expansion of a B cell population by cell division following B cell activation during an immune response. [database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/go.owl B cell proliferation during immune response B lymphocyte proliferation during immune response B-cell proliferation during immune response B-lymphocyte proliferation during immune response B cell proliferation involved in immune response The change in morphology and behavior of a natural killer cell resulting from exposure a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. [database_cross_reference: PMID:15032583][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/go.owl NK cell activation during immune response natural killer cell activation during immune response natural killer cell activation involved in immune response http://purl.obolibrary.org/obo/go.owl NK cell proliferation during immune response natural killer cell proliferation during immune response natural killer cell proliferation involved in immune response The process in which a naive natural killer cell acquires the specialized features of an effector natural killer T cell as part of an immune response. [database_cross_reference: GOC:add][database_cross_reference: PMID:11698225] http://purl.obolibrary.org/obo/go.owl NK cell differentiation during immune response natural killer cell development involved in immune response natural killer cell differentiation during immune response Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. natural killer cell differentiation involved in immune response The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/go.owl mature B lymphocyte differentiation mature B-cell differentiation mature B-lymphocyte differentiation mature cell development Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. mature B cell differentiation The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl cytokine production involved in immune response Any process that contributes to cytokine production by a B cell. http://purl.obolibrary.org/obo/go.owl B cell cytokine production Any process that contributes to cytokine production by a T cell. http://purl.obolibrary.org/obo/go.owl T cell cytokine production Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. http://purl.obolibrary.org/obo/go.owl immune system process Process involved in the carrying out of an immune response by a leukocyte. leukocyte mediated immunity The process in which a B cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/go.owl B lymphocyte antigen processing and presentation B-cell antigen processing and presentation B-lymphocyte antigen processing and presentation B cell antigen processing and presentation Any process involved in the carrying out of an immune response by a T cell. http://purl.obolibrary.org/obo/go.owl cell-mediated immunity cellular immune response T lymphocyte mediated immunity T-cell mediated immunity T-lymphocyte mediated immunity T cell mediated immunity Any process involved in the carrying out of an immune response by a T cell. GOC:add GO_REF:0000022 ISBN:0781735149 The process in which a T cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/go.owl T lymphocyte antigen processing and presentation T-cell antigen processing and presentation T-lymphocyte antigen processing and presentation T cell antigen processing and presentation An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. http://purl.obolibrary.org/obo/go.owl adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. GOC:add GOC:mtg_sensu ISBN:0781735149 ISBN:1405196831 The process in which a dendritic cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/go.owl dendritic cell antigen processing and presentation The process in which a monocyte expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/go.owl monocyte antigen processing and presentation The process in which a macrophage expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/go.owl macrophage antigen processing and presentation A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. http://purl.obolibrary.org/obo/go.owl molecular_function Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. http://purl.obolibrary.org/obo/go.owl antigen binding Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [database_cross_reference: GOC:vw][database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/go.owl Wikipedia:Enzyme enzyme activity catalytic activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [database_cross_reference: GOC:pf][database_cross_reference: EC:2.7.7.6] http://purl.obolibrary.org/obo/go.owl transcriptase; DNA-directed RNA polymerase activity Reactome:R-HSA-174425; Reactome:R-HSA-111264; Reactome:R-HSA-427366; Reactome:R-HSA-75850; Reactome:R-HSA-167115; Reactome:R-HSA-167121; Reactome:R-HSA-74986; Reactome:R-HSA-68913; EC:2.7.7.6; Reactome:R-HSA-167117; Reactome:R-HSA-167136; Reactome:R-HSA-9670149; Reactome:R-HSA-6781824; Reactome:R-HSA-75869; Reactome:R-HSA-167113; MetaCyc:DNA-DIRECTED-RNA-POLYMERASE-RXN; Reactome:R-HSA-76576; Reactome:R-HSA-203901; Reactome:R-HSA-5601926; Reactome:R-HSA-75873 DNA-directed RNA polymerase I activity; DNA-directed RNA polymerase III activity; RNA polymerase I activity; RNA polymerase II activity; RNA polymerase III activity; DNA-directed RNA polymerase II activity C RNA formation factors DNA-dependent RNA nucleotidyltransferase activity DNA-dependent RNA polymerase activity DNA-dependent ribonucleate nucleotidyltransferase activity RNA nucleotidyltransferase (DNA-directed) activity deoxyribonucleic acid-dependent ribonucleic acid polymerase activity nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed) activity DNA-directed 5'-3' RNA polymerase activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. http://purl.obolibrary.org/obo/go.owl carrier Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. transporter activity A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). http://purl.obolibrary.org/obo/go.owl cellular_component The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. http://purl.obolibrary.org/obo/go.owl extracellular Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. extracellular region The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins. http://purl.obolibrary.org/obo/go.owl cell wall All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. http://purl.obolibrary.org/obo/go.owl cytoplasm An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/go.owl free ribosome membrane bound ribosome ribosomal RNA ribosome Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [database_cross_reference: GOC:mah][database_cross_reference: ISBN:0198547684][database_cross_reference: PMID:16959967] http://purl.obolibrary.org/obo/go.owl cytoskeleton The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. http://purl.obolibrary.org/obo/go.owl juxtamembrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane plasma membrane lipid bilayer plasma membrane The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. http://purl.obolibrary.org/obo/go.owl integral to plasma membrane integral component of plasma membrane The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP). http://purl.obolibrary.org/obo/go.owl fermentation Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. http://purl.obolibrary.org/obo/go.owl DNA metabolism cellular DNA metabolism DNA metabolic process The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. http://purl.obolibrary.org/obo/go.owl DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. DNA replication A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands. http://purl.obolibrary.org/obo/go.owl DNA-dependent DNA replication The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase. http://purl.obolibrary.org/obo/go.owl DNA ligation The cellular synthesis of RNA on a template of DNA. [database_cross_reference: GOC:txnOH][database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/go.owl cellular transcription transcription Wikipedia:Transcription_(genetics) DNA-dependent transcription cellular transcription, DNA-dependent transcription, DNA-dependent transcription regulator activity transcription, DNA-templated Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription. [database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH][database_cross_reference: GOC:jid] http://purl.obolibrary.org/obo/go.owl DNA-dependent RNA polymerase complex assembly at promoter DNA-dependent transcription, initiation initiation of DNA-dependent transcription initiation of transcription, DNA-dependent transcription initiation factor activity transcription initiation, DNA-dependent Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation. DNA-templated transcription, initiation The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA. [database_cross_reference: PMID:15020047][database_cross_reference: ISBN:0716720094][database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/go.owl transcriptional complex disassembly DNA-dependent transcription, termination termination of DNA-dependent transcription termination of transcription, DNA-dependent transcription termination factor activity transcription termination, DNA-dependent DNA-templated transcription, termination The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase. [database_cross_reference: PMID:15020047][database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl RNA elongation DNA-dependent transcription, elongation transcription elongation, DNA-dependent transcriptional elongation, DNA-dependent DNA-templated transcription, elongation The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. http://purl.obolibrary.org/obo/go.owl small molecule transport solute:solute exchange single-organism transport Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. http://purl.obolibrary.org/obo/go.owl phagocytosis Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. http://purl.obolibrary.org/obo/go.owl defense response The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. http://purl.obolibrary.org/obo/go.owl inflammatory response 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 The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. http://purl.obolibrary.org/obo/go.owl cell cycle A form of asexual reproduction, occurring in certain bacteria and fungi (e.g. yeasts) and some primitive animals in which an individual arises from a daughter cell formed by pinching off a part of the parent cell. The budlike outgrowths so formed may sometimes remain attached to the parent cell. http://purl.obolibrary.org/obo/go.owl budding cell budding Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. http://purl.obolibrary.org/obo/go.owl cell communication Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. http://purl.obolibrary.org/obo/go.owl cell-cell signalling cell-cell signaling Process specifically pertinent to the functioning of functionally integrated units. biological process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. http://purl.obolibrary.org/obo/go.owl metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process single-organism metabolic process metabolic process The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor. http://purl.obolibrary.org/obo/go.owl aerobic respiration The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor. http://purl.obolibrary.org/obo/go.owl anaerobic respiration The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli. [database_cross_reference: GOC:go_curators] http://purl.obolibrary.org/obo/go.owl cell envelope biosynthesis cell envelope biosynthetic process cell wall anabolism cell wall assembly cell wall biosynthetic process cell wall formation cell wall synthesis peptidoglycan-based cell wall biogenesis A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli. http://purl.obolibrary.org/obo/go.owl envelope peptidoglycan murein sacculus peptidoglycan-based cell wall A layer of peptidoglycan found outside of the cytoplasmic membrane. The peptidoglycan is relatively thick (20-80nm) and retains the primary stain of the Gram procedure, thus cells appear blue after Gram stain. The cell walls often contain teichoic acids (acidic anionic polysaccharides) bound to the peptidoglycan. Examples of this component are found in Gram-positive bacteria. http://purl.obolibrary.org/obo/go.owl 20-80nm peptidoglycan-based cell wall cell wall of Gram-positive Bacteria Gram-positive-bacterium-type cell wall The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain. http://purl.obolibrary.org/obo/go.owl Gram-negative-bacterium-type cell wall A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. bacterial outer membrane http://purl.obolibrary.org/obo/go.owl outer membrane of cell To annotate the plasma (cytoplasmic) membrane, see instead GO:0005886. cell outer membrane A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope. http://purl.obolibrary.org/obo/go.owl flagellin-based flagellum bacterial-type flagellum A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter. In GO, pilus is a subclass of 'cell projection'. It was necessary to also assert it as a subclass of 'macromolecule' in order to add axioms ensuring that pilus is also an inferred subclass of 'adhesion factor' and 'virulence factor'. It should be noted that 'pilus' is sometimes used for any hair-like appendage on bacteria or archaea. But some researchers reserve the term 'pilus' for the appendage of bacteria. GO seems to be following the latter usage. -SB (axiom editor) Shane Babcock http://purl.obolibrary.org/obo/go.owl fimbria fimbriae fimbrium pili pilus The controlled release of proteins from a cell. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/go.owl glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment protein secretion The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms. http://purl.obolibrary.org/obo/go.owl quorum sensing system cell-cell signaling involved in quorum sensing detection of cell density by secreted molecule quorum sensing The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. http://purl.obolibrary.org/obo/go.owl toxin anabolism toxin biosynthesis toxin formation toxin synthesis toxin biosynthetic process The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. http://purl.obolibrary.org/obo/go.owl toxin metabolism toxin metabolic process 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, which in the most common case has at least all of the following proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing an infection, and (4) appearance of disorder. Pathogenesis does not involve all of (1)-(4) in every case. For instance, in the case of various bacterial pathogens, pathogenesis occurs without (1)-(3) via the secretion of toxins which subsequently cause disorder in some organism. http://purl.obolibrary.org/obo/go.owl John Beverley Shane Babcock pathogenesis The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. [database_cross_reference: GOC:go_curators] http://purl.obolibrary.org/obo/go.owl toxin breakdown toxin catabolism toxin degradation toxin catabolic process The long (approximately 20 nm), thin external structure of the bacterial-type flagellum, which acts as a propeller. http://purl.obolibrary.org/obo/go.owl flagellar filament flagellin-based flagellum filament bacterial-type flagellum filament The proteinaceous structure at the distal tip of the bacterial-type flagellar filament. http://purl.obolibrary.org/obo/go.owl flagellar filament cap flagellin-based flagellum filament cap bacterial-type flagellum filament cap The region of the bacterial-type flagellum where the hook and filament meet. http://purl.obolibrary.org/obo/go.owl flagellar hook-filament junction bacterial-type flagellum hook-filament junction The portion of the bacterial-type flagellum that connects the filament to the basal body. http://purl.obolibrary.org/obo/go.owl flagellar hook flagellin-based flagellum hook bacterial-type flagellum hook One of the three major substructures of the bacterial-type flagellum, the basal body is embedded in the cell envelope (the plasma membrane, peptidoglycan cell wall, and, if one is present, the outer membrane); it houses the secretion apparatus that exports the more distal components and the flagellar motor. http://purl.obolibrary.org/obo/go.owl flagellar basal body flagellin-based flagellum basal body bacterial-type flagellum basal body The portion of the central rod of the bacterial-type flagellar basal body that is distal to the cell membrane; spans most of the distance between the inner and outer membranes. http://purl.obolibrary.org/obo/go.owl flagellar basal body, distal rod flagellin-based flagellum basal body, distal rod bacterial-type flagellum basal body, distal rod One of the rings of the bacterial-type flagellar basal body; anchors the basal body to the outer membrane. http://purl.obolibrary.org/obo/go.owl flagellar basal body, distal rod, L ring flagellin-based flagellum basal body, distal rod, L ring bacterial-type flagellum basal body, distal rod, L ring One of the rings of the bacterial-type flagellar basal body; anchors the basal body to the peptidoglycan layer. http://purl.obolibrary.org/obo/go.owl flagellin-based flagellum basal body, distal rod, P ring flagellar basal body, distal rod, P ring bacterial-type flagellum basal body, distal rod, P ring The portion of the central rod of the bacterial-type flagellar basal body that is proximal to the cell membrane; the proximal rod connects the distal rod to the flagellar motor. http://purl.obolibrary.org/obo/go.owl flagellar basal body, proximal rod flagellin-based flagellum basal body, proximal rod bacterial-type flagellum basal body, proximal rod One of the rings of the bacterial-type flagellar basal body; a double-flanged ring that anchors the basal body to the cytoplasmic membrane. [database_cross_reference: GOC:cilia][database_cross_reference: GOC:mtg_sensu][database_cross_reference: PMID:10572114][database_cross_reference: PMID:12624192] http://purl.obolibrary.org/obo/go.owl flagellar basal body, mounting plate flagellar basal body, MS ring flagellin-based flagellum basal body, MS ring bacterial-type flagellum basal body, MS ring Cytoplasmic ring located at the base of the bacterial-type flagellar basal body; acts as a rotor; includes three switch proteins, which generate torque and can change their conformational state in a bimodal fashion, so that the motor direction can switch between clockwise and counterclockwise. [database_cross_reference: GOC:cilia][database_cross_reference: GOC:mtg_sensu][database_cross_reference: PMID:10572114][database_cross_reference: PMID:12624192] http://purl.obolibrary.org/obo/go.owl flagellar basal body, C ring flagellin-based flagellum basal body, C ring bacterial-type flagellum basal body, C ring A response to non-pathogenic bacteria that confers broad spectrum systemic resistance to disease that does not depend upon salicylic acid signaling. http://purl.obolibrary.org/obo/go.owl induced systemic resistance Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/go.owl cellular process The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [database_cross_reference: GOC:dph][database_cross_reference: GOC:tb] http://purl.obolibrary.org/obo/go.owl Wikipedia:Gene_expression gene expression The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/go.owl enzyme transport protein transport Enables the transfer of polysaccharides from one side of a membrane to the other. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. http://purl.obolibrary.org/obo/go.owl polysaccharide transmembrane transporter activity Enables the transfer of capsular-polysaccharides from one side of a membrane to the other. Capsular polysaccharides make up the capsule, a protective structure surrounding some species of bacteria and fungi. http://purl.obolibrary.org/obo/go.owl capsule polysaccharide transporter activity capsular polysaccharide transmembrane transporter activity Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. http://purl.obolibrary.org/obo/go.owl pore activity channel/pore class transporter activity nonselective channel activity alpha-type channel activity channel-forming toxin activity pore class transporter activity substrate-specific channel activity channel activity Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. http://purl.obolibrary.org/obo/go.owl porin activity http://purl.obolibrary.org/obo/go.owl protein secretion by the T2S protein secretion by the T2SS protein secretion by the type II protein secretion system type II protein secretion system protein secretion by the general secretion pathway protein secretion by the general secretory pathway Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type II protein secretion system complex ; GO:0015627'. This process refers specifically to secretion across the outer membrane. For components of the Sec and Tat pathways, consider annotating to 'protein transport by the Sec complex ; GO:0043952' and 'protein transport by the Tat complex ; GO:0043953'. Note that this term is used for annotation of proteins that compose the secretion complex but not the proteins being secreted. protein secretion by the type II secretion system The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. http://purl.obolibrary.org/obo/go.owl polysaccharide transport The directed movement of capsular polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Capsular polysaccharides make up the capsule, a protective structure surrounding some species of bacteria and fungi. http://purl.obolibrary.org/obo/go.owl capsular polysaccharide transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/go.owl peptide transport A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. http://purl.obolibrary.org/obo/go.owl membrane region region of membrane whole membrane membrane A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. [ GOC:jl GOC:ai GOC:mah ] http://purl.obolibrary.org/obo/go.owl cellular component organization An immune response mediated by immunoglobulins, whether cell-bound or in solution. http://purl.obolibrary.org/obo/go.owl antibody-mediated immune response immunoglobulin mediated immune response The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/go.owl RNA metabolism RNA metabolic process A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. http://purl.obolibrary.org/obo/go.owl vesicle transport vesicular transport protein sorting along secretory pathway vesicle trafficking vesicle-mediated transport Enables the transfer of a toxin from one side of a membrane to the other. A toxin is a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. http://purl.obolibrary.org/obo/go.owl toxin transmembrane transporter activity Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. http://purl.obolibrary.org/obo/go.owl B lymphocyte mediated immune effector process B lymphocyte mediated immunity B-cell mediated immune effector process B-cell mediated immunity B-lymphocyte mediated immune effector process B-lymphocyte mediated immunity B cell mediated immunity Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. GOC:add GO_REF:0000022 ISBN:0781735149 An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus. http://purl.obolibrary.org/obo/go.owl antimicrobial humoral response An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster. http://purl.obolibrary.org/obo/go.owl antibacterial humoral response 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 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. http://purl.obolibrary.org/obo/go.owl outer membrane The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/go.owl antigen presentation antigen processing antigen processing and presentation The biological process in which new individuals are produced by either a single cell or a group of cells, in the absence of any sexual process. [database_cross_reference: ISBN:0387520546] http://purl.obolibrary.org/obo/go.owl Wikipedia:Asexual_reproduction parthenogenesis asexual reproduction Any process involved in the biological strategy of changing antigenic determinants on the surface that are exposed to another organism's immune system. http://purl.obolibrary.org/obo/go.owl surface antigen variation antigenic variation The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. [database_cross_reference: GOC:isa_complete][database_cross_reference: GOC:mtg_cell_cycle] http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate cell cycle process The aggregation, arrangement and bonding together of a cellular component. [database_cross_reference: GOC:isa_complete] http://purl.obolibrary.org/obo/go.owl cell structure assembly cellular component assembly at cellular level cellular component assembly The attachment of a cell, organism or acellular structure to a substrate, another cell, organism or acellular structure. The textual definition has been modified in IDO to encompass acellular structures. http://purl.obolibrary.org/obo/go.owl biological adhesion Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged. http://purl.obolibrary.org/obo/go.owl porters uniporter activity z facilitated diffusion passive transmembrane transporter activity Enables the transport of a solute across a membrane via a large pore, un-gated channel. Examples include gap junctions, which transport substances from one cell to another; and porins which transport substances in and out of bacteria, mitochondria and chloroplasts. http://purl.obolibrary.org/obo/go.owl non-gated, wide pore channel activity gap junction activity wide pore channel activity Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. http://purl.obolibrary.org/obo/go.owl substrate-specific transmembrane transporter activity substrate-specific transporter activity uptake permease activity uptake transmembrane transporter activity transmembrane transporter activity A thylakoid that is derived from and attached to, but not necessarily continuous with, the plasma membrane, and is not enclosed in a plastid. It bears the photosynthetic pigments in photosynthetic cyanobacteria. http://purl.obolibrary.org/obo/go.owl bacterial thylakoid The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor. [database_cross_reference: GOC:mgi_curators][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/go.owl NK cell activation natural killer cell activation A carbohydrate rich layer at the outermost periphery of a cell. [database_cross_reference: GOC:krc][database_cross_reference: ISBN:0815316208][database_cross_reference: GOC:mlg][database_cross_reference: PMID:28876829] Note, that it is only asserted that glycolax bears an 'adhesion disposition' because glycolax is a component of cells other than bacteria. The same applies to its subclasses. -SB http://purl.obolibrary.org/obo/go.owl Wikipedia:Glycocalyx glycocalyx A slime layer is an easily removed, diffuse, unorganized layer of extracellular material that surrounds a cell. Specifically this consists mostly of exopolysaccharides, glycoproteins, and glycolipids. [database_cross_reference: GOC:mlg][database_cross_reference: Wikipedia:Slime_layer] http://purl.obolibrary.org/obo/go.owl Wikipedia:Slime_layer While this structure is found most commonly in bacteria, it is also found in Archaea as well: Wikipedia:Slime_layer slime layer A crystalline protein layer surrounding some bacteria. [database_cross_reference: GOC:mlg][database_cross_reference: ISBN:0815108893] http://purl.obolibrary.org/obo/go.owl Wikipedia:S-layer S-layer The chemical reactions and pathways resulting in the formation of a bacteriocin, any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary. http://purl.obolibrary.org/obo/go.owl bacteriocin anabolism bacteriocin biosynthesis bacteriocin formation bacteriocin synthesis bacteriocin biosynthetic process The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. [database_cross_reference: GO_REF:0000022][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl B lymphocyte differentiation B-cell differentiation B-lymphocyte differentiation B cell development B cell development B cell differentiation A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. http://purl.obolibrary.org/obo/go.owl extracellular matrix organisation extracellular matrix organization and biogenesis extracellular matrix organization The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. [database_cross_reference: GOC:mah][database_cross_reference: GO_REF:0000022][database_cross_reference: GOC:jid] http://purl.obolibrary.org/obo/go.owl T lymphocyte differentiation T-cell differentiation T-lymphocyte differentiation T cell development Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T cell differentiation The process in which proteins are secreted into the extracellular milieu via the type I secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/go.owl protein secretion by the TOSS protein secretion by the type I protein secretion system type I protein secretion system Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type I protein secretion system complex ; GO:0030256'. protein secretion by the type I secretion system The process in which proteins are transferred into the extracellular milieu or directly into host cells by the bacterial type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/go.owl protein secretion by the T3S protein secretion by the T3SS protein secretion by the TTSS protein secretion by the type III protein secretion system type III protein secretion system Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type III protein secretion system complex ; GO:0030257'. Note that this term is used for annotation of proteins that compose the secretion complex but not the proteins being secreted. protein secretion by the type III secretion system The process in which proteins are transferred into the extracellular milieu or directly into host cells, via the type IV protein secretion system. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/go.owl protein secretion by the T4SS protein secretion by the type IV protein secretion system type IV protein secretion system Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type IV protein secretion system complex ; GO:0043684'. protein secretion by the type IV secretion system A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space. [database_cross_reference: PMID:9618447] http://purl.obolibrary.org/obo/go.owl ABC translocator complex type I protein secretion system complex A complex of approximately 20 proteins, most of which are located in the cytoplasmic membrane that carries out protein secretion in the bacterial type III secretion system; type III secretion also requires a cytoplasmic, probably membrane-associated ATPase. [database_cross_reference: PMID:9618447] http://purl.obolibrary.org/obo/go.owl T3SS complex TTSS complex type III protein secretion system complex A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space. http://purl.obolibrary.org/obo/go.owl The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'. external encapsulating structure An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present. http://purl.obolibrary.org/obo/go.owl cell envelope The central portion of the bacterial-type flagellar basal body, which spans the periplasm and threads through the rings. http://purl.obolibrary.org/obo/go.owl flagellar basal body, rod flagellin-based flagellum basal body, rod bacterial-type flagellum basal body, rod A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. http://purl.obolibrary.org/obo/go.owl proteinaceous extracellular matrix matrisome extracellular matrix The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. http://purl.obolibrary.org/obo/go.owl Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent. intrinsic component of membrane An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy. [database_cross_reference: GOC:js][database_cross_reference: PMID:10498708][database_cross_reference: PMID:11844753][database_cross_reference: PMID:12923081] http://purl.obolibrary.org/obo/go.owl BAC bacterial microcompartment polyhedral organelle An organelle consisting of a proteinaceous coat and enzymes for the fixation of CO(2). It augments the concentration of CO(2) in the vicinity of RuBisCO to increase the efficiency of CO(2) fixation under atmospheric conditions. [database_cross_reference: GOC:js][database_cross_reference: PMID:8157606][database_cross_reference: PMID:8491708][database_cross_reference: PMID:28934381] https://github.com/geneontology/go-ontology/issues/19743 http://purl.obolibrary.org/obo/go.owl carboxysome An organelle found in bacteria consisting of a proteinaceous coat containing enzymes for the degradation of ethanolamine whose purpose is the protection of the rest of the cell from the toxic acetaldehyde product of the enzyme ethanolamine ammonia lyase. [database_cross_reference: GOC:js][database_cross_reference: PMID:11844753] http://purl.obolibrary.org/obo/go.owl ethanolamine metabolosome ethanolamine degradation polyhedral organelle An organelle found in bacteria consisting of a proteinaceous coat containing enzymes for the degradation of 1,2-propanediol whose purpose is the protection of the rest of the cell from the toxic propionaldehyde product of the enzyme diol dehydratase. [database_cross_reference: GOC:js][database_cross_reference: PMID:10498708][database_cross_reference: PMID:11844753][database_cross_reference: PMID:12923081] http://purl.obolibrary.org/obo/go.owl propanediol degradation polyhedral organelle A transmembrane protein complex involved in the translocation of proteins across the cytoplasmic membrane. In Gram-negative bacteria, Sec-translocated proteins are subsequently secreted via the type II, IV, or V secretion systems. Sec complex components include SecA, D, E, F, G, Y and YajC. [database_cross_reference: GOC:mtg_sensu][database_cross_reference: PMID:15223057] http://purl.obolibrary.org/obo/go.owl Sec complex Sec secretion complex Sec translocation complex plasma membrane Sec complex Note that this term represents the protein complex involved in transport of proteins across the cytoplasmic membrane. For proteins involved in bacterial type II secretion across the outer membrane, consider annotating to 'type II protein secretion complex ; GO:0015628'. For proteins involved in Sec-complex dependent translocation into the eukaryotic endoplasmic reticulum, consider annotating to 'endoplasmic reticulum Sec complex ; GO:0031205'. cell envelope Sec protein transport complex A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. http://purl.obolibrary.org/obo/go.owl envelope Any small, fluid-filled, spherical organelle enclosed by membrane. http://purl.obolibrary.org/obo/go.owl membrane-bounded vesicle membrane-enclosed vesicle vesicle Biological process whose specific outcome is the progression of a functional, integrated, unit. developmental process The biological process in which new individuals are produced by one or two single-celled organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. [database_cross_reference: GOC:isa_complete] http://purl.obolibrary.org/obo/go.owl reproduction of a single-celled organism The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria. http://purl.obolibrary.org/obo/go.owl chemokine production The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. http://purl.obolibrary.org/obo/go.owl interferon type I production type I IFN production type I interferon biosynthetic process type I interferon secretion Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. type I interferon production The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IFN-alpha production IFNA production interferon-alpha biosynthetic process interferon-alpha secretion Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. interferon-alpha production The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IFNB production; IFN-beta production interferon-beta secretion; interferon-beta biosynthetic process Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. interferon-beta production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. http://purl.obolibrary.org/obo/go.owl type II IFN production type II interferon production IFNG production interferon-gamma biosynthetic process interferon-gamma secretion interferon-gamma production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-1 production interleukin-1 biosynthetic process interleukin-1 secretion interleukin-1 production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-10 production interleukin-10 biosynthetic process interleukin-10 secretion interleukin-10 production The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-11 production interleukin-11 biosynthetic process interleukin-11 secretion interleukin-11 production The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-12 production CLMF production NKSF production interleukin-12 biosynthetic process interleukin-12 secretion interleukin-12 production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-13 production interleukin-13 biosynthetic process interleukin-13 secretion interleukin-13 production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-14 production interleukin-14 biosynthetic process interleukin-14 secretion interleukin-14 production The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-15 production interleukin-15 biosynthetic process interleukin-15 secretion interleukin-15 production The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-16 production pro-interleukin-16 production LCF production interleukin-16 biosynthetic process interleukin-16 secretion interleukin-16 production The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl CTLA-8 production Cytotoxic T-lymphocyte-associated antigen 8 production IL-17 production interleukin-17 biosynthetic process interleukin-17 secretion interleukin-17 production The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah GOC:rv Wikipedia:Interleukin_17 CTLA-8 production GOC:BHF Cytotoxic T-lymphocyte-associated antigen 8 production GOC:BHF The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-2 production interleukin-2 biosynthetic process interleukin-2 secretion interleukin-2 production The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-3 production interleukin-3 biosynthetic process interleukin-3 secretion interleukin-3 production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-4 production interleukin-4 biosynthetic process interleukin-4 secretion interleukin-4 production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-5 production interleukin-5 biosynthetic process interleukin-5 secretion interleukin-5 production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-6 production interleukin-6 biosynthetic process interleukin-6 secretion interleukin-6 production The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-8 production interleukin-8 biosynthetic process interleukin-8 secretion interleukin-8 production The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/go.owl IL-9 production interleukin-9 biosynthetic process interleukin-9 secretion interleukin-9 production The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:mah RNA biosynthesis; RNA formation; RNA anabolism; RNA synthesis The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. [database_cross_reference: GOC:mah][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/go.owl Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study. RNA biosynthetic 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-containing complex The process in which proteins are transferred into the extracellular milieu or directly into host cells by the type VI secretion system. Proteins secreted by this system do not require an N-terminal signal sequence. [database_cross_reference: GOC:mlg][database_cross_reference: PMID:16432199][database_cross_reference: PMID:16763151] http://purl.obolibrary.org/obo/go.owl protein secretion by the T6SS protein secretion by the type VI protein secretion system type VI protein secretion system Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type VI protein secretion system complex ; GO:0033104'. protein secretion by the type VI secretion system A complex of proteins that permits the transfer of proteins into the extracellular milieu or directly into host cells via the type VI secretion system. Proteins secreted by this complex do not require an N-terminal signal sequence. [database_cross_reference: GOC:mlg][database_cross_reference: PMID:16432199][database_cross_reference: PMID:16763151] http://purl.obolibrary.org/obo/go.owl T6SS complex type VI protein secretion system complex A complex of three proteins integral to the cytoplasmic membrane of bacteria and membranes of organelles derived from bacteria (chloroplasts and mitochondria) involved in membrane transport of folded proteins. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/go.owl TAT protein secretion complex TAT protein translocation system complex Twin-arginine translocation complex TAT protein transport complex Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template, via extension of the 3'-end. [database_cross_reference: EC:2.7.7.6][database_cross_reference: GOC:pf][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl RNA polymerase activity ribonucleic acid nucleotidyltransferase transcriptase Reactome:R-HSA-5696807 Reactome:R-HSA-6786881 C RNA formation factors C ribonucleic acid formation factors RNA nucleotidyltransferase activity RNA transcriptase activity ribonucleate nucleotidyltransferase activity ribonucleate polymerase activity ribonucleic acid polymerase activity ribonucleic acid transcriptase activity ribonucleic polymerase activity ribonucleic transcriptase activity 5'-3' RNA polymerase activity The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/go.owl cellular protein complex assembly cellular macromolecule complex assembly cellular protein-containing complex assembly The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule 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, carried out by individual cells. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl cellular biopolymer biosynthetic process cellular macromolecule anabolism cellular macromolecule biosynthesis cellular macromolecule formation cellular macromolecule synthesis cellular macromolecule biosynthetic process The process in which a bacterium enters a host cell. http://purl.obolibrary.org/obo/go.owl bacterial entry into host cell invasion of bacteria into host cell entry of bacterium into host cell A mycolic acid-rich cell outer membrane containing a lipid bilayer and long-chain mycolic acids (hydroxylated branched-chain fatty acids) that are covalently linked to the cell wall peptidoglycan via an arabinogalactan network. Found in mycobacteria and related genera (e.g. corynebacteria). http://purl.obolibrary.org/obo/go.owl MOM mycobacterial outer membrane mycomembrane mycolate outer membrane A heterodimeric protein complex that binds a type I interferon and transmits the signal across the membrane into the cell. Consists of an alpha subunit (IFNAR1) and a beta subunit (IFNAR2). http://purl.obolibrary.org/obo/go.owl interferon-alpha/beta receptor complex type I interferon receptor complex The directed movement of peptides or proteins produced by an organism to a location inside its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. [database_cross_reference: GOC:cc] http://purl.obolibrary.org/obo/go.owl translocation of peptides or proteins into other organism during symbiotic interaction translocation of peptides or proteins into other organism involved in symbiotic interaction transport of peptides or proteins into other organism during symbiotic interaction transport of peptides or proteins into host translocation of peptides or proteins into host The expansion of a T cell population by cell division. Follows T cell activation. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/go.owl T lymphocyte proliferation T-cell proliferation T-lymphocyte proliferation T cell proliferation The expansion of a B cell population by cell division. Follows B cell activation. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/go.owl B lymphocyte proliferation B-cell proliferation B-lymphocyte proliferation B cell proliferation 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 T cell activation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. T cell activation The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. [database_cross_reference: GOC:mgi_curators][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/go.owl B lymphocyte activation B-cell activation B-lymphocyte activation B cell activation A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall. Includes biosynthesis of constituent macromolecules, such as proteins and polysaccharides, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. A cell wall is the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. [database_cross_reference: GOC:jl][database_cross_reference: GOC:mah][database_cross_reference: GOC:mtg_sensu][database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/go.owl cell wall assembly cell wall biogenesis immunoglobulin complex, circulating An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. antibody antibody immunoglobulin complex, circulating A protective structure surrounding some fungi and bacteria, attached externally to the cell wall and composed primarily of polysaccharides. Capsules are highly organized structures that adhere strongly to cells and cannot be easily removed. Capsules play important roles in pathogenicity, preventing phagocytosis by other cells, adherance, and resistance to dessication. [database_cross_reference: GOC:mlg] Add an axiom to the effect that this is the material basis for protective resistance? -SB http://purl.obolibrary.org/obo/go.owl capsule MHC protein complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. MHC protein complex A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules. http://purl.obolibrary.org/obo/go.owl MHC class I protein complex A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. http://purl.obolibrary.org/obo/go.owl MHC class II protein complex A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription. http://purl.obolibrary.org/obo/go.owl biofilm formation Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. http://purl.obolibrary.org/obo/go.owl defence response to bacteria defence response to bacterium defense response to bacteria defense response to bacterium, incompatible interaction resistance response to pathogenic bacteria resistance response to pathogenic bacterium antibacterial peptide activity defense response to bacterium Process by which an organism or acellular structure avoids the effects of the host organism's immune response. http://purl.obolibrary.org/obo/go.owl immune evasion evasion of host immune response A prolongation or process extending from a cell, e.g. a flagellum or axon. http://purl.obolibrary.org/obo/go.owl cellular projection cell projection A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells. [database_cross_reference: GOC:mah][database_cross_reference: ISBN:0815108893][database_cross_reference: PMID:12626683] http://purl.obolibrary.org/obo/go.owl Wikipedia:Binary_fission cytokinesis by binary fission prokaryote-type cytokinesis prokaryotic fission Note that this term is intended for the annotation of prokaryotic gene products. FtsZ-dependent cytokinesis Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility. http://purl.obolibrary.org/obo/go.owl TFP-dependent motility TFP-dependent movement type 4 pilus-dependent motility type four pilus-dependent motility social gliding motility twitching motility type IV pilus-dependent motility Any process in which infecting bacteria are clumped together by a host organism. http://purl.obolibrary.org/obo/go.owl induction of bacterial agglutination A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Gram-negative bacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane. [database_cross_reference: GOC:jl][database_cross_reference: GOC:mtg_sensu][database_cross_reference: ISBN:0815108893] http://purl.obolibrary.org/obo/go.owl cell wall anabolism cell wall assembly cell wall biosynthetic process cell wall formation cell wall synthesis 1-2nm peptidoglycan-based cell wall biogenesis Gram-negative-bacterium-type cell wall biogenesis The chemical reactions and pathways involving macromolecules, any molecule 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. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process macromolecule metabolic process Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. http://purl.obolibrary.org/obo/go.owl organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. http://purl.obolibrary.org/obo/go.owl membrane-enclosed organelle membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. http://purl.obolibrary.org/obo/go.owl non-membrane-enclosed organelle non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. http://purl.obolibrary.org/obo/go.owl intracellular non-membrane-enclosed organelle intracellular non-membrane-bounded organelle The process in which a newly activated T cell acquires specialized features of a memory T cell. [database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/go.owl memory T lymphocyte differentiation memory T-cell differentiation memory T-lymphocyte differentiation memory T cell development Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. memory T cell differentiation A protein complex that is composed of an interleukin-12 alpha (p35, product of the IL12A gene) and an interleukin-12 beta subunit (p40, product of the IL12B gene) and is secreted into the extracellular space. http://purl.obolibrary.org/obo/go.owl IL-12 complex Note that this heterodimeric cytokine utilizes the IL-12p35 subunit as its alpha chain, which is also used by IL-35 as its alpha chain, and utilizes the IL-12p40 subunit as its beta chain, which is also used by IL-23 as its beta chain. interleukin-12 complex The region of a bacterial cell to which the DNA is confined. http://purl.obolibrary.org/obo/go.owl bacterial nucleoid A complex of proteins related to those involved in bacterial DNA conjugative transfer, that permits the transfer of DNA or proteins into the extracellular milieu or directly into host cells. In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s). [database_cross_reference: GOC:ml] http://purl.obolibrary.org/obo/go.owl T4SS complex type IV protein secretion system complex type IV secretion system complex Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl mah 2010-09-08T10:01:42Z protein complex subunit organisation protein complex subunit organization cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation macromolecular complex subunit organization protein-containing complex subunit organization The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/go.owl protein secretion by the Sec complex protein translocation by the Sec complex Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular structure term 'cell envelope Sec protein transport complex ; GO:0031522'. For proteins involved in bacterial type II secretion across the outer membrane, consider annotating to 'protein secretion by the type II secretion system ; GO:0015628'. For proteins involved in Sec-complex dependent translocation into the eukaryotic endoplasmic reticulum, consider annotating to 'SRP-dependent cotranslational protein targeting to membrane, translocation ; GO:0006616'. Note that this term is used for annotation of proteins that compose the transport complex but not the proteins being transported. protein transport by the Sec complex The process in which folded proteins are transported across cytoplasmic membranes of bacteria and membranes of organelles derived from bacteria (chloroplasts and mitochondria) by the TAT complex. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/go.owl twin-arginine translocation pathway protein secretion by the TAT complex protein translocation by the TAT complex protein translocation by the twin-arginine translocation complex Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular structure term 'TAT protein translocation system complex ; GO:0033281'. Note that this term is used for annotation of proteins that compose the transport complex but not the proteins being transported. protein transport by the Tat complex The directed movement of peptides or proteins produced by a symbiont organism to a location within the host cell cytoplasm. [database_cross_reference: MITRE:tk] http://purl.obolibrary.org/obo/go.owl translocation of symbiont peptides or proteins into host cell cytoplasm transport of peptides or proteins into host cell cytoplasm translocation of peptides or proteins into host cell cytoplasm A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. [database_cross_reference: GOC:jl][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl cellular component biogenesis at cellular level cellular component biogenesis The chemical reactions and pathways involving macromolecules, any molecule 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, as carried out by individual cells. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl cellular biopolymer metabolic process cellular macromolecule metabolism cellular macromolecule metabolic process The process in which proteins are transferred into the extracellular milieu or directly into host cells, via the type VII protein secretion system. [database_cross_reference: PMID:17922044][database_cross_reference: PMID:19876390] http://purl.obolibrary.org/obo/go.owl protein secretion by the type VII secretion system 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, or acellular structure, into the body, tissues, or cells of the host organism. entry into host The directed movement of a molecule(s) produced by an organism to a location inside its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. [database_cross_reference: GOC:cc] http://purl.obolibrary.org/obo/go.owl translocation of molecules into other organism during symbiotic interaction translocation of molecules into other organism involved in symbiotic interaction transport of molecules into other organism during symbiotic interaction transport of molecules into host translocation of molecules into host The DNA-dependent DNA replication that takes place as part of the cell cycle. http://purl.obolibrary.org/obo/go.owl cell cycle DNA replication The DNA-dependent DNA replication, exemplified by prokaryotes, that occurs as part of the cell cycle. Prokaryotic DNA replication is bi-directional and originates at a single origin of replication on the circular genome. http://purl.obolibrary.org/obo/go.owl bacterial-type cell cycle DNA replication bacterial-type DNA replication Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. innate immune response The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration). http://purl.obolibrary.org/obo/go.owl respiration oxidative metabolic process oxidative metabolism cellular respiration The chemical reactions and pathways involving bacteriocins, any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/go.owl bacteriocin metabolism bacteriocin metabolic process The chemical reactions and pathways resulting in the breakdown of a bacteriocin, any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/go.owl bacteriocin breakdown bacteriocin catabolism bacteriocin degradation bacteriocin catabolic process A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. [database_cross_reference: GOC:mgi_curators][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/go.owl lymphocyte activation The process in which proteins mediate their own secretion across the outer membrane through a beta-barrel pore structure formed by the C-terminal domain of the protein precursor. Following passage across the outer membrane, the mature protein is released from the pore by an autocatalytic activity. Proteins secreted by the Type V system are first translocated across the plasma membrane by the Sec pathway. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/go.owl autotransporter system protein secretion by the autotransporter system protein secretion by the type V protein secretion system type V protein secretion system protein secretion by the type V secretion system An intracellular, often complex, membranous structure, sometimes with additional membranous lamellae inside, found in bacteria. They are associated with synthesis of DNA and secretion of proteins. http://purl.obolibrary.org/obo/go.owl mesosome A complex of protein and RNA which facilitates translocation of proteins across membranes. [database_cross_reference: GOC:mlg] Add subclasses? -SB http://purl.obolibrary.org/obo/go.owl signal recognition particle 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. Should only be in VIDO, and not in IDO. -SB negative regulation of viral process Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. http://purl.obolibrary.org/obo/go.owl cell locomotion cell movement cell motility Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/go.owl down regulation of phagocytosis down-regulation of phagocytosis downregulation of phagocytosis inhibition of phagocytosis negative regulation of phagocytosis 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 Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism. http://purl.obolibrary.org/obo/go.owl defence response to Gram-negative bacteria defence response to Gram-negative bacterium defense response to Gram-negative bacteria Gram-negative antibacterial peptide activity defense response to Gram-negative bacterium Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism. http://purl.obolibrary.org/obo/go.owl defence response to Gram-positive bacteria defence response to Gram-positive bacterium defense response to Gram-positive bacteria Gram-positive antibacterial peptide activity defense response to Gram-positive bacterium 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 The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA-dependent DNA replication. http://purl.obolibrary.org/obo/go.owl DNA ligation involved in DNA-dependent DNA replication DNA ligation during DNA-dependent DNA replication DNA-dependent DNA replication DNA ligation Process that localizes a substance or cellular component via movement, tethering or selective degradation. establishment of localization The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. http://purl.obolibrary.org/obo/go.owl Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division Attachment of bacterial clusters to the surface of the host in a type IV pili dependent manner. The host is defined as the larger of the organisms involved in a symbiotic interaction. [database_cross_reference: GOC:ml] http://purl.obolibrary.org/obo/go.owl type IV pili-dependent localized adherence to host Flagellar filaments located in the periplasmic space; characterized in spirochetes, in which they are essential for shape and motility. Composed of a core surrounded by two sheath layers, the flagella rotate to allow migration of the cell through viscous media, which would not be possible using external flagella. http://purl.obolibrary.org/obo/go.owl periplasmic flagellum A spherical, bilayered proteolipid vesicle released from gram-negative bacterial outer membranes. [database_cross_reference: GOC:dph][database_cross_reference: GOC:pr][database_cross_reference: PMID:20596524] http://purl.obolibrary.org/obo/go.owl bacterial outer membrane vesicle A structure lying external to microbial cells. A biofilm is an aggregate of surface-associated cells, and the biofilm matrix is the envelope of polymeric substances that surrounds the cells. http://purl.obolibrary.org/obo/go.owl biofilm matrix The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/go.owl chaperone activity macromolecular complex assembly macromolecule complex assembly protein complex assembly protein complex formation protein-containing complex assembly The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/go.owl DNA-protein complex assembly protein-DNA complex assembly Process that modulates a measurable attribute of any biological process, quality or function. biological regulation An extracellular region part that consists of a protective layer of mucus secreted by epithelial cells lining tubular organs of the body such as the colon or secreted into fluids such as saliva. Mucus is a viscous slimy secretion consisting of mucins (i.e. highly glycosylated mucin proteins) and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. [database_cross_reference: GOC:krc][database_cross_reference: GOC:mah][database_cross_reference: GOC:mm2][database_cross_reference: PMID:18806221][database_cross_reference: PMID:19432394][database_cross_reference: Wikipedia:Mucin] http://purl.obolibrary.org/obo/go.owl extracellular proteinaceous gel mucous mucous layer mucus Musin proteins in the mucus layer have an important function in the defense against bacterial infection, as they can reduce attachment and biofilm formation. mucus layer The inner of two mucus layers secreted by epithelial cells in the colon; the inner mucus layer is firmly attached to the epithelium, is densely packed with a compact stratified appearance and is devoid of bacteria. [database_cross_reference: GOC:mah][database_cross_reference: GOC:mm2][database_cross_reference: PMID:18806221][database_cross_reference: PMID:19432394] http://purl.obolibrary.org/obo/go.owl inner mucus layer The aggregation, arrangement and bonding together of a cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl cell wall assembly The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription. [database_cross_reference: GOC:txnOH][database_cross_reference: GOC:jp] http://purl.obolibrary.org/obo/go.owl mah 2009-09-01T04:33:47Z transcription PIC biosynthesis transcription PIC formation transcriptional preinitiation complex formation DNA-dependent transcriptional preinitiation complex assembly DNA-templated transcriptional preinitiation complex assembly transcription preinitiation complex assembly The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/go.owl mah 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism organic substance metabolic process A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/go.owl mah 2010-03-24T01:44:53Z IgG antibody IgG1 antibody IgG2 antibody IgG2a antibody IgG2b antibody IgG2c antibody IgG3 antibody IgG4 antibody Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. IgG immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 IgG antibody GOC:add IgG1 antibody GOC:add IgG2 antibody GOC:add IgG2a antibody GOC:add IgG2b antibody GOC:add IgG2c antibody GOC:add IgG3 antibody GOC:add IgG4 antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/go.owl mah 2010-03-24T01:44:53Z IgD antibody Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgD immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 PMID:11282392 IgD antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/go.owl mah 2010-03-24T01:44:53Z IgE antibody Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgE immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 IgE antibody GOC:add A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/go.owl mah 2010-03-24T01:44:53Z IgA antibody IgA1 antibody IgA2 antibody Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgA immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 PMID:16362985 IgA antibody GOC:add IgA1 antibody GOC:add IgA2 antibody GOC:add A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph. http://purl.obolibrary.org/obo/go.owl mah 2010-03-24T01:44:53Z IgM antibody Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgM immunoglobulin complex, circulating A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph. GOC:add ISBN:0781765196 PMID:20176268 IgM antibody GOC:add A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Actinobacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane. Actinobacterial cell walls contain characteristic mycolic acids, of which some are covalently linked to the cell wall peptidoglycan and others accumulate at the cell surface. [database_cross_reference: GOC:mah][database_cross_reference: PMID:15653820][database_cross_reference: PMID:3149973] http://purl.obolibrary.org/obo/go.owl mah 2010-03-29T04:12:51Z Actinobacterium-type cell wall biogenesis The process in which a protein is transported across a membrane. [database_cross_reference: GOC:mah][database_cross_reference: GOC:vw] http://purl.obolibrary.org/obo/go.owl protein membrane transport Note that this term is not intended for use in annotating lateral movement within membranes. protein transmembrane transport A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. [ GOC:mah ] http://purl.obolibrary.org/obo/go.owl cellular component organization or biogenesis Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope. http://purl.obolibrary.org/obo/go.owl flagellin-based flagellar cell motility bacterial-type flagellar cell motility bacterial-type flagellum-dependent cell motility Bacterial-type flagellum-dependent cell motility that results in the smooth movement of a cell through a liquid medium. http://purl.obolibrary.org/obo/go.owl bacterial-type flagellum-mediated cell swimming bacterial-type flagellar swimming motility bacterial-type flagellum-dependent swimming motility Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria. http://purl.obolibrary.org/obo/go.owl bacterial-type flagellum-mediated cell swarming bacterial-type flagellar swarming motility bacterial-type flagellum-dependent swarming motility Any process in which an organism disseminates its spores. [database_cross_reference: Wikipedia:Spore] https://github.com/geneontology/go-ontology/issues/18823 GO:0075326 GO:0075327 spore dispersal on or near host during symbiotic interaction active spore dispersal on or near host active spore dispersal on or near host during symbiotic interaction passive spore dispersal on or near host spore dispersal on or near host spore dispersal Any cellular metabolic process involving nucleic acids. [database_cross_reference: GOC:dph][database_cross_reference: GOC:tb] http://purl.obolibrary.org/obo/go.owl tb 2010-04-07T10:18:47Z nucleic acid metabolic process An immune response directed against a previously encountered antigen, being quicker and quantitatively better compared with the primary response. http://purl.obolibrary.org/obo/go.owl adaptive immune memory response An immune response mediated by reactivated memory T cells and B cells and directed against a previously encountered antigen, being quicker and quantitatively better compared with the primary response. http://purl.obolibrary.org/obo/go.owl adaptive immune memory response involving T cells and B cells An adaptive immune response against an antigen not previously encountered by immune system. http://purl.obolibrary.org/obo/go.owl primary adaptive immune response Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom. http://purl.obolibrary.org/obo/go.owl toxin receptor binding toxin activity immune complex formation The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. immune complex formation immunoglobulin-mediated neutralization The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. [database_cross_reference: GOC:add][database_cross_reference: GOC:rv] http://purl.obolibrary.org/obo/go.owl pr 2012-03-26T01:55:24Z antibody-mediated neutralization immunoglobulin-mediated neutralization A structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria. http://purl.obolibrary.org/obo/go.owl bacterial biofilm matrix The external part of the biofilm matrix, a structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria. http://purl.obolibrary.org/obo/go.owl bacterial biofilm matrix surface A heterooligomeric protein complex that spans the bacterial periplasm and enables the secretion of adhesin proteins in Gram-negative bacteria. In Citrobacter rodentium, Salmonella enterica and Escherichia coli, the TAM complex consists of an Omp85-family protein, TamA, in the outer membrane and TamB in the inner membrane. [database_cross_reference: GOC:am][database_cross_reference: PMID:22466966] http://purl.obolibrary.org/obo/go.owl translocation and assembly module protein complex TAM protein secretion complex Cell motility due to movement of bacterial- or archaeal-type flagella. http://purl.obolibrary.org/obo/go.owl Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. This term was added for mapping to the UniProt keyword "flagellar rotation". For manual annotation, please use one of the child terms of GO:0097588 that refer specifically to either archaeal- or bacterial-type flagella. archaeal or bacterial-type flagellum-dependent cell motility The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA). [database_cross_reference: GOC:pr][database_cross_reference: GOC:txnOH][database_cross_reference: GOC:vw] http://purl.obolibrary.org/obo/go.owl Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. nucleic acid-templated transcription Small membrane vesicle (< 1 um) that buds off a prokaryotic cell plasma membrane, able to carry proteins, phospholipids, lipopolysaccharides, nucleic acids, viruses, and more. Important in intercellular communication and pathogenesis; can exist within host cells. http://purl.obolibrary.org/obo/go.owl bacterial extracellular vesicle Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template. [database_cross_reference: GOC:pf] http://purl.obolibrary.org/obo/go.owl pr 2016-12-02T11:48:55Z RNA polymerase activity A complex of proteins that permits the translocation of proteins across the outer membrane via a transmembrane pore, formed by a beta-barrel, into the extracellular milieu or directly into host cells; the secreted proteins contain all the information required for translocation of an effector molecule through the cell envelope. The type V secretion systems includes the autotransporters (type Va), the two-partner secretion system (type Vb) and the Oca family (type Vc). [database_cross_reference: PMID:15590781][database_cross_reference: GOC:bf][database_cross_reference: GOC:bhm][database_cross_reference: PMID:15119822] http://purl.obolibrary.org/obo/go.owl T5SS complex autotransporter system complex Note that the type II protein secretion system complex does not include components of the Sec or Tat pathways. For components of these pathways, consider annotating to 'cell envelope Sec complex ; GO:0031522' or 'TAT protein translocation system complex ; GO:0033281'. type V protein secretion system complex The clustering together of unicellular organisms in suspension form aggregates. http://purl.obolibrary.org/obo/go.owl aggregation of single cell organisms aggregation of unicellular organisms The clustering together and adhesion of initially separate cells to form an aggregate. Examples include the clustering of unicellular organisms or blood cells in suspension and the condensation of mesenchymal cells during cartilage formation. http://purl.obolibrary.org/obo/go.owl cell aggregation A proteinaceous extracellular fiber, produced by an enteric bacterium, that is involved in surface and cell-cell contacts that promote community behavior and host colonization. http://purl.obolibrary.org/obo/go.owl tafi thin aggregative fimbrae curli The directed movement of proteins across the cell outer membrane. [database_cross_reference: GOC:dos] http://purl.obolibrary.org/obo/go.owl protein transport across the cell outer membrane Protein secretion through the outer membrane via the mechanism used for the secretion of curli subunits. [database_cross_reference: PMID:24080089][database_cross_reference: PMID:19299134] http://purl.obolibrary.org/obo/go.owl T8SS This term is defined so as to leave open the possibility that things other than curli subunits are secreted via same secretory system as that used by curli subunits. protein secretion by the type VIII secretion system A process that results in the assembly, arrangement of constituent parts, or disassembly of a biofilm matrix. http://purl.obolibrary.org/obo/go.owl biofilm matrix organization and biogenesis biofilm matrix organization A process that results in the assembly of a biofilm matrix. http://purl.obolibrary.org/obo/go.owl biofilm matrix assembly A process that results in the disassembly of a biofilm matrix. http://purl.obolibrary.org/obo/go.owl biofilm matrix disassembly Any protein complex that is part of a membrane. http://purl.obolibrary.org/obo/go.owl membrane protein complex Any protein complex that is part of the plasma membrane. [database_cross_reference: GOC:dos] http://purl.obolibrary.org/obo/go.owl plasma membrane protein complex Any protein complex that is part of the bacterial outer membrane. An example In E.coli, is RcsF associated with any one of several outer membrane beta-barrel proteins (OMPs), such as OmpA, OmpF, or OmpcC. http://purl.obolibrary.org/obo/go.owl outer membrane protein complex A bacterial protein complex that neutralises its own toxin by complexing the toxin with the antitoxin. The antitoxin can be either a protein or an RNA. The neutralising toxin-antitoxin complex also acts as a transcriptional repressor of the toxin-antitoxin operon. http://purl.obolibrary.org/obo/go.owl An example is YoeB (P69348) in Escherichia coli in PMID:16109374 (inferred by direct evidence). toxin-antitoxin complex A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. http://purl.obolibrary.org/obo/go.owl cellular anatomical entity A transmembrane complex embedded in the cytoplasmic membrane which is the motor force, or torque, generator of the bacterial-type flagellum. The motor consists of a membrane-anchored rotor complex surrounded by one or more stator complexes in the cytoplasmic membrane. The stator consists of a hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. Examples are the H+ driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ driven PomA-PomB stator complex of Vibrio and Shewanella species. The rotor complex consists of a membrane-anchored ring and the motor switch complex, which controls the direction of flagellar rotation. http://purl.obolibrary.org/obo/go.owl bacterial-type flagellum motor A hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. The A and B proteins form a channel through which flow the ions that power the bacterial-type flagellum. They form the stator, or nonrotating portion, of the flagellum motor with the B protein apparently attached to the peptidoglycan cell wall. Examples include the H+ driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ driven PomA-PomB stator complex of Vibrio and Shewanella species. http://purl.obolibrary.org/obo/go.owl bacterial-type flagellum motor force generator complex bacterial-type flagellum torque generator complex bacterial-type flagellum stator complex A part of the bacterial-type flagellum that is located at the cytoplasmic side of the MS ring and composed of six membrane proteins (FlhA, FlhB, FliP, FliQ, FliR, and FliO, or orthologs thereof) and three soluble proteins (FliI, FliH, and FliJ, or orthologs thereof) in the cytoplasm. It is responsible for secretion of flagellar type III protein substrates, including the proteins of the flagellar rod, hook, and filament. [database_cross_reference: GOC:cilia][database_cross_reference: PMID:10572114][database_cross_reference: PMID:12624192][database_cross_reference: PMID:24697492][database_cross_reference: DOI:10.1002/9780470015902.a0000744.pub4][database_cross_reference: PMID:25251856] Annotations http://purl.obolibrary.org/obo/go.owl bacterial-type flagellum export apparatus bacterial-type flagellum secretion apparatus The rotor complex of the bacterial-type flagellum consists of a membrane-anchored ring and the motor switch complex, which participates in the conversion of proton/Na+ energy into the mechanical work of rotation and controls the direction of flagellar rotation. http://purl.obolibrary.org/obo/go.owl bacterial-type flagellum rotor complex An defense response against a bacteria mediated through an innate immune response. An innate immune response is mediated by germline encoded components that directly recognize components of potential pathogens. http://purl.obolibrary.org/obo/go.owl antibacterial innate immune response The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/go.owl toxin transport Any DNA ligation that is involved in cell cycle DNA replication. http://purl.obolibrary.org/obo/go.owl DNA ligation involved in cell cycle DNA replication cell cycle DNA replication DNA ligation Any DNA ligation that is involved in bacterial-type DNA replication. http://purl.obolibrary.org/obo/go.owl DNA ligation involved in bacterial-type DNA replication bacterial-type DNA replication DNA ligation Any vesicle that is part of the extracellular region. http://purl.obolibrary.org/obo/go.owl microparticle extracellular vesicle A macromolecular complex that contains both RNA and protein molecules. [database_cross_reference: GOC:krc][database_cross_reference: GOC:vesicles] http://purl.obolibrary.org/obo/go.owl RNA-protein complex RNP protein-RNA complex ribonucleoprotein complex extracellular ribonucleoprotein complex intracellular ribonucleoprotein complex ribonucleoprotein complex Any process that modulates the frequency, rate or extent of entry of bacterium into host cell. [database_cross_reference: GOC:obol] http://purl.obolibrary.org/obo/go.owl regulation of bacterial entry into host cell regulation of invasion of bacteria into host cell regulation of entry of bacterium into host cell Any process that stops, prevents or reduces the frequency, rate or extent of entry of bacterium into host cell. [database_cross_reference: GOC:obol] http://purl.obolibrary.org/obo/go.owl negative regulation of bacterial entry into host cell negative regulation of invasion of bacteria into host cell negative regulation of entry of bacterium into host cell measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot http://purl.obolibrary.org/obo/iao.owl measurement unit label 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 datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. http://purl.obolibrary.org/obo/iao.owl datum label data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data http://purl.obolibrary.org/obo/iao.owl data item 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 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI http://purl.obolibrary.org/obo/iao.owl measurement datum 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 whose 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 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 Disposition borne by a macromolecule that is the disposition to participate in an adhesion process. Shane Babcock http://purl.obolibrary.org/obo/ido.owl adhesion disposition 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 http://purl.obolibrary.org/obo/ido.owl 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 part of a symbiont that is the disposition to participate in adherence to a host. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl symbiont 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 pathogen 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 pathogen 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 pathogen 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 pathogen Disposition borne by a material entity to establish localization in or produce toxins that can be transmitted to an organism or acellular structure, either or which may form disorder in the entity or immunocompetent members of the entity's species. Albert Goldfain Alexander Diehl Lindsay Cowell pathogenicity http://purl.obolibrary.org/obo/ido.owl This textual definition refers to 'organism or acellular structure' rather than 'host' so as to not exclude cases, such as food botulism, where previously formed toxins, but not the producing pathogen itself, are present in the entity.' -Shane Babcock 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 likelihood 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 a pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl susceptibility to pathogen 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 pathogen and is the degree to which the infectious pathogen 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 pathogen 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. Site occupied by an organism population lacking any infectious disease incidences. 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 An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally. infectious disease hyper-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 a pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl immunization against pathogen Immunization that begins with exposure of an organism to antigen and results in immunity against a pathogen Albert Goldfain Alexander Diehl Lindsay Cowell inoculation http://purl.obolibrary.org/obo/ido.owl active immunization against pathogen 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 pathogen 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 a pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl passive immunization against pathogen Process of infectious disease realizations 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 extended organism which has an infectious pathogen part, that exists as a result of a process of formation of disorder initiated by the infectious pathogen. 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 establishment 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 More commonly referred to as an 'infectious agent reservoir', we use the label 'pathogen reservoir' so as to not exclude infectious structures. -SB pathogen 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. In bacteriology, the term endotoxin is properly reserved to refer to the lipopolysaccharide complex associated with gram-negative bacteria. Note that the IDO term is being used in a wider sense, to cover endotoxic entities other than lipopolysaccharides. 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 Material entity that is used to treat bacterial infections and which bears either a bactericidal disposition or a bacteriostatic disposition. During John's cleanup of IDO's coverage of treatment agents, this term was obsoleted from IDO Core. But it but it is needed in BIDO to pair with terms like 'antibiotic resistance'. Not sure if my revised treatment of this term is how we should proceed. Originally, 'antibiotic' was defined as "A material entity bearing an antibacterial disposition". The latter disposition was defined as "A disposition to kill or inhibit the reproduction of bacteria", and was replaced by John's 'bactericidal disposition' and 'bacteriostatic disposition'. Simply defining an antibiotic as a material entity that has one of these two dispositions doesn't really work. It is true that antibiotics are usually classified under either 'bactericidal' or 'bacteriostatic'. But classifying an antibiotic merely as a material entity wouldn't capture how 'antibiotic' is exclusively used for substances that are used as drugs to treat bacterial infections. Certain chemical disinfectants are also classified as bactericidals. So we need a way of distinguishing antibiotics from other material entities, like disenfectants, that bear one of these dispositions. Albert Goldfain Alex Diehl Lindsay Cowell Shane Babcock antibacterial antibiotic 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 pathogen 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 pathogen 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 pathogen 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 pathogen 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 Material entity that is part of an extended organism that has some pathogen as part, which participates in the formation of the material entity by invading tissues of the organism. 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 conferred 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 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 pathogen 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 Process in which a material entity reaches a site in or on a host in which it can survive, grow, multiply, or mature and establishes itself there. 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 distinct material entity, or organism whose extended organism contains a distinct material entity, 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 While hosts are usually classified as organisms, in line with our classification of viruses as acellular structures, this definition has been curated to accomodate the case of a virus serving as host to an infecting virophage. -Shane Babcock 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 with a human infectious disposition. 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 or structure and lacks protective immunity to the infectious agent or structure. Alex Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl susceptible organism Process which is necessary for the survival of an organism. Alex Diehl, Lindsay Cowell http://purl.obolibrary.org/obo/ido.owl life-sustaining process 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 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 cfu/100mL requires discussion A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid. Should this be deprecated? Need to find working examples that actually use / 100mL. Damion Dooley http://purl.obolibrary.org/obo/genepio.owl colony forming unit per 100 milliliter Disposition inhering in a material entity, that is realized in a process of killing fungi. http://purl.obolibrary.org/obo/ido.owl John Beverley fungicidal disposition Disposition inhering in a material entity, that is realized in a process of killing bacteria. http://purl.obolibrary.org/obo/ido.owl John Beverley bactericidal disposition Disposition inhering in a material entity, that is realized in a process of inhibiting the reproduction of bacteria. http://purl.obolibrary.org/obo/ido.owl John Beverley bacteriostatic disposition Disposition inhering in a material entity, that is realized in a process of killing 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 inhering in a material entity, that is realized in a process of inhibiting 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. This class will be moved to IDO Bacteria once that ontology has been created. -SB 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 consisting of an arrangement of interrelated acellular parts forming an acellular biological unit that is able to initiate replication of the structure in a host. http://purl.obolibrary.org/obo/ido.owl John Beverley acellular structure Material entity with a cidal agent disposition. http://purl.obolibrary.org/obo/ido.owl John Beverley cidal agent Material entity with a static agent disposition. http://purl.obolibrary.org/obo/ido.owl John Beverley static agent Disposition inhering in a material entity, that is realized in a process of inhibiting the reproduction of bacteria, fungi, or parasites, or inhibiting the replication of viruses. http://purl.obolibrary.org/obo/ido.owl John Beverley static agent disposition Disposition inhering in a material entity, that is realized in a process of killing 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 While the definition of 'pathogen transporter role' requires the bearer to have a pathogen located in or on it, bearers also have certain dispositions that enable them to play the role. Thus, while a mosquito bears this role only when a malaria parasite is located in or on it, there also inheres in its physical structure a disposition to transfer the parasites, which it has whether or not it contains any parasites. -SB 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 Temporal subdivision of a developmental process. John Beverley http://purl.obolibrary.org/obo/ido.owl 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 bearing an asymptomatic carrier role. 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 The outer of two mucus layers secreted by epithelial cells in the colon; the outer mucus layer is loosely packed and can be colonized by bacteria. [database_cross_reference: GOC:mah][database_cross_reference: GOC:mm2][database_cross_reference: PMID:18806221][database_cross_reference: PMID:19432394] http://purl.obolibrary.org/obo/go.owl outer mucus layer 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 Site part of an antigen that is recognized by immune system cells and to which antibodies attach. John Beverley epitope site Biological role borne by a material 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 more pathogens, with the purpose of managing those pathogens. Shane Babcock http://purl.obolibrary.org/obo/ido.owl pathogen surveillance Surveillance process aiming to produce information about changes in the geographical distribution and density of one or several pathogen vectors, with the purpose of facilitating appropriate and timely desisions regarding interventions. Shane Babcock http://purl.obolibrary.org/obo/ido.owl vector surveillance Objective specification whose endpoint is human awareness of the level of an infectious disease in a particular population of a given biological taxon during some time interval. Shane Babcock infectious disease surveillance objective specification Infectious disposition that is the disposition to become part of a disorder in a host of the species Homo Sapiens. Shane Babcock human infectious disposition Developmental process whose specific outcome is the progression of a pathogen. Shane Babcock http://purl.obolibrary.org/obo/ido.owl pathogen developmental process Developmental process whose specific outcome is the progression of an infectious agent. Shane Babcock http://purl.obolibrary.org/obo/ido.owl infectious agent developmental process Developmental process whose specific outcome is the progression of an infectious structure. Shane Babcock http://purl.obolibrary.org/obo/ido.owl infectious structure developmental process Process beginning with the establishing of an infection in a host and ending with the onset of symptoms by the host, during which pathogens are multiplying in the host. John Beverley Shane Babcock http://purl.obolibrary.org/obo/ido.owl Wasn't sure where this goes in the hierarchy. May need to be moved. -SB incubation process Process beginning with the establishing of an infection in a host and ending when the host becomes contagious, during which pathogens are multiplying in the host. John Beverley Shane Babcock http://purl.obolibrary.org/obo/ido.owl latency process Process profile comprised of a series of determinate infectious disease incidence qualities caused by a specific pathogen in a population over time. Shane Babcock infectious disease incidence profile Process profile comprised of a series of infectious disease rate qualities caused by a specific pathogen per unit time. Shane Babcock infectious disease incidence rate profile Process profile comprised of a series of infectious disease incidence proportion qualities caused by a specific pathogen per unit time. Shane Babcock Infectious disease proportion profile Process profile comprised of a series of determinate infection prevalence qualities in a population over time. Shane Babcock infection prevalence process profile Process profile comprised of a series of determinate infectious disease prevalence qualities in a population over time. Shane Babcock infectious disease prevalence process profile Infectious disease endemicity that inheres in an organism population in virtue of the fact that intra-population transmission occurs with an extremely high frequency, where most of population's older members are asymptomatic carriers due to adaptive immunity, whereas its younger members are more likely to be symptomatic carriers. This is a working definition which will require further vetting. See also: https://github.com/infectious-disease-ontology-extensions/ido-core/issues/4 -SB Shane Babcock infectious disease holoendemicity To do Shane Babcock infectious disease mesoendemicity Host that has been hospitalized. This class has been moved from here from the Influenza Ontology, with a simplified textual definition. -SB Shane Babcock hospitalized host A population of memory B cells and memory T cells which bears an immunological memory disposition. This is a placeholder class. There is a term 'cell population', but it belongs to an ontology in which it is out of scope [http://purl.obolibrary.org/obo/GSSO_005261] This term doesn't seem to have a home in the Cell Ontology as it does not import BFO:disposition -SB Shane Babcock immunological memory Collective disposition inhering in some population of memory B cells and memory T cells, that is the ability of the immune system to quickly recognize a previously encountered antigen and to initiate a quicker and quantitatively better secondary immune response upon subsequent exposures to that same antigen. Shane Babcock immunological memory disposition Infection for which the infectious agents or structures that are part of the infection are not multiplying in the host. Shane Babcock latent infection Site occupied by an organism population bearing an infectious disease endemicity. Shane Babcock Yu Lin This textual definition still needs vetting. infectious disease endemic site Site occupied by an organism population lacking any infectious disease incidences. Shane Babcock Yu Lin Not sure about this definition. Can it be defined in terms of any of the existing IDO epidemiology qualities? infectious disease free site Site occupied by an organism population lacking infectious disease endemicity. Shane Babcock Yu Lin This textual definition needs vetting. infectious disease non-endemic site Planned process that is the realization of an infectious disease surveillance objective specification. Shane Babcock Yu Lin infectious disease surveillance bacterium eukaryota homo sapiens The complement system is a complex system of serum proteins that interact in a cascade. Many of the early components are serine proteases that activate each other sequentially. This complement system consists of three separate activation triggers: (1) Ab binding to a cell surface, (2) formation of immune complexes, and (3) a carbohydrate component of a microbe's cell membrane. Along with this triggers, there are also two sets of mechanisms. Both of these mechanisms, classical pathway and alternative or properdin pathway, make MAC (Membrane Attack Complex), which can lyse and destroy the cell. This term has the label 'complement' in NCIT. -SB http://purl.obolibrary.org/obo/ncit.owl complement system A class of soluble glycoproteins which act nonenzymatically through specific receptors to regulate immune responses. Cytokines are derived from both immune and non-immune cells and are intercellular mediators that differ from hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. http://purl.obolibrary.org/obo/ncit.owl cytokine Chemokines constitute a superfamily of small (8-10 kDa), inducible, secreted, pro-inflammatory cytokines that are involved in a variety of immune and inflammatory responses as well as in viral infection. Chemokines act primarily as chemoattractants and activators of specific types of leukocytes. Some members of this family were initially identified on the basis of their biological activities (e.g., IL-8, GRO), others were discovered using subtractive hybridization (e.g., RANTES) or signal sequence trap (e.g., PBSF/SDF-1)11 cloning strategies. They attract and activate leukocytes and regulate diverse cellular systems and organs ranging from blood vessels to the central nervous system. http://purl.obolibrary.org/obo/ncit.owl chemokine A pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'. YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device. YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention. YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623. YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740. YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events. YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'. Yongqun He adverse reaction; AE WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm; WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068; WEB: http://en.wikipedia.org/wiki/Adverse_event http://purl.obolibrary.org/obo/oae.owl The OAE official website is: http://www.oae-ontology.org/. adverse event An adverse event that has an outcome of a pathogen infection, i.e., an infection caused by a pathogen such as a virus, bacterium, or parasite. change of name from 'infection adverse event' to 'infectious adverse event' on 09/23/13 for a better clinical relevance, move 'infection adverse event' as an alternative term - SS YH, JX infectious adverse event WEB: http://medical-dictionary.thefreedictionary.com/infection http://purl.obolibrary.org/obo/oae.owl infection AE An infection AE that results in detrimental colonization of a host organism by bacteria YH, SS bacterial infection AE WEB: http://en.wikipedia.org/wiki/Bacterial_infection http://purl.obolibrary.org/obo/oae.owl HPO: HP_0002718; SIDER: C0004623 bacterial infection AE 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 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation 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 the sodium and chloride ions in a glass of salt water A material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates Alan Ruttenberg Collective Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 http://purl.obolibrary.org/obo/obi.owl scattered molecular aggregate categorical measurement datum A measurement datum that is reported on a categorical scale. Bjeorn Peters 'nominal measurement datum' Bjeorn Peters http://purl.obolibrary.org/obo/obi.owl categorical measurement datum disposition to be bound by an MHC protein complex Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters MHC ligand disposition IEDB disposition to be bound by an MHC protein complex MHC protein complex binding to ligand The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex. The process in which a ligand binds to an MHC molecule to form a stable complex 6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. PERSON: Bjoern Peters; Randi Vita IEDB MHC protein complex binding to ligand disposition to be a product of antigen processing and presentation The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER. A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. IEDB IEDB disposition to be a product of antigen processing and presentation The process of material entities forming complexes. 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. binding immunoglobulin binding to epitope Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). PERSON: Bjoern Peters, Randi Vita IEDB immunoglobulin binding to epitope B cell epitope specific immunoglobulin-mediated neutralization immunoglobulin-mediated neutralization resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl http://purl.obolibrary.org/obo/obi.owl B cell epitope specific immunoglobulin-mediated neutralization B cell epitope specific immune complex formation immune complex formation resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific immune complex formation surveillance process An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. Chris Stoeckert Shane Babcock, OBI IDO, VEuPathDB http://purl.obolibrary.org/obo/obi.owl surveillance process 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 entity entity bearing the epitope role. http://purl.obolibrary.org/obo/obi.owl John Beverley epitope epitope binding by adaptive immune receptor is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. IEDB IEDB epitope binding by adaptive immune receptor adaptive immune receptor Receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB http://purl.obolibrary.org/obo/obi.owl adaptive immune receptor An antigen bearing the immunogen role. This is a suggested definition. The original OBI definition does not specify that an immunogen is a specific type of antigen. -SB IEDB Shane Babcock http://purl.obolibrary.org/obo/obi.owl immunogen Molecular entity bearing an antigen role. http://purl.obolibrary.org/obo/obi.owl antigen disposition to be bound by an adaptive immune receptor Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. IEDB epitope disposition IEDB disposition to be bound by an adaptive immune receptor MHC:epitope complex binding to TCR a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule. IEDB IEDB MHC:epitope complex binding to TCR Biological role inhering in some molecular entity, that is capable on its own of eliciting an immune response when identified by the immune system cells. This is a suggested definition. The definitions of this term and antigen role need to be made more precise in order to distinguish them. -SB IEDB Shane Babcock http://purl.obolibrary.org/obo/obi.owl immunogen role restricting MHC role The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. IEDB IEDB restricting MHC role organizational term A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. This term does not belong in OBI. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. CD8 WEB: http://en.wikipedia.org/wiki/CD8 http://purl.obolibrary.org/obo/obi.owl CD8 receptor 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 Albert Goldfain creation date: 2009-06-23T11:53:49Z http://purl.obolibrary.org/obo/ogms.owl bodily process A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z http://purl.obolibrary.org/obo/ogms.owl pathological bodily process 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 A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z http://purl.obolibrary.org/obo/ogms.owl treatment A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18 health care process health care encounter A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z health care encounter hospitalization TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z hospitalization An abnormal material entity that is part of a patient and hypothesized to be clinically relevant. Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension http://purl.obolibrary.org/obo/ogms.owl physical sign An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant. http://purl.obolibrary.org/obo/ogms.owl processual sign An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant. Example: the color of a rash; the shape of a melanoma http://purl.obolibrary.org/obo/ogms.owl qualitative sign A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside. Oliver He, Jie Zheng, Jihad Obeid, Anna Maria Masci https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/ microbiome A microbiome that includes a collective population of bacterial organisms. YH, JZ, JO, AA http://purl.obolibrary.org/obo/ohmi.owl bacterial microbiome http://purl.obolibrary.org/obo/omit.owl bacterial outer membrane proteins This imported term was given a new axiom that makes it an inferred subclass of 'bacterial adhesion factor'. -SB http://purl.obolibrary.org/obo/omit.owl adhesins, bacterial This imported term was given a new axiom that makes it an inferred subclass of 'bacterial adhesion factor'. -SB http://purl.obolibrary.org/obo/omit.owl fimbriae proteins The observable manifestation of the genotype of a microbial cell or group of cells in an environment. http://purl.obolibrary.org/obo/omp.owl microbial phenotype A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth but will utilize O2 in metabolic reactions when it is present. http://purl.obolibrary.org/obo/omp.owl facultative aerobe facultative anaerobe A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth and doesn't utilize O2 even when it is present. http://purl.obolibrary.org/obo/omp.owl External comment: This definition does not logically rule out the ability to use oxygen for energy production, whereas aerotolerant organisms cannot use oxygen (although they tolerate its presence). -SB aerotolerant anaerobe An oxygen growth range phenotype where growth and reproduction requires oxygen but at levels below that found in air (approx. 21%). A microbial phenotype that describes a microorganism that requires O2 for growth, but doesn't grow in the presence of atmospheric levels of O2. Optimal growth of a microaerophile occurs in environments with xx% - xx% O2. http://purl.obolibrary.org/obo/omp.owl Optimal oxygen levels for growth of typical microaerophilic bacteria is 2 to 10% O2, and growth is impaired by atmospheric oxygen levels (approx. 21%). microaerophile A microbial phenotype that describes a microorganism that does not grow in the presence of oxygen gas (O2). http://purl.obolibrary.org/obo/omp.owl strict anaerobe obligate anaerobe A microbial phenotype that describes a microorganism that requires the presence of oxygen gas (O2) for growth. http://purl.obolibrary.org/obo/omp.owl strict aerobe obligate aerobe A gram stain phenotype where a cell or cells retain crystal violet stain when decolorized with an organic solvent such as ethanol. http://purl.obolibrary.org/obo/omp.owl GO:0009275 (Gram-positive-bacterium-type cell wall) gram positive A gram stain phenotype where a cell or cells do not retain crystal violet stain when decolorized with an organic solvent such as ethanol. http://purl.obolibrary.org/obo/omp.owl GO:0009276 (Gram-negative-bacterium-type cell wall) gram negative A cell staining phenotype where microorganisms are grouped based on their ability to retain crystal violet stain when decolorized with an organic solvent such as ethanol. http://purl.obolibrary.org/obo/omp.owl This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. gram stain phenotype A cell-staining phenotype where a cell or cells are classified based on whether they are decolorized by an acid-alcohol mixture after staining, typically with carbolfuchsin. http://purl.obolibrary.org/obo/omp.owl acid-fast staining phenotype A microbial phenotype where a cell or cells are treated with a dye or dyes for purposes of identification and classification. http://purl.obolibrary.org/obo/omp.owl This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. cell staining phenotype Material entity that is a human made structure with firm connection between its foundation and the ground. http://purl.obolibrary.org/obo/OMRSE architectural 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 A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. http://purl.obolibrary.org/obo/pato.owl morphology A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). http://purl.obolibrary.org/obo/pato.owl shape A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals). http://purl.obolibrary.org/obo/pato.owl spiral helical helicoid helicoidal helix-shaped coiled A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. http://purl.obolibrary.org/obo/pato.owl bowing curled curved A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. http://purl.obolibrary.org/obo/pato.owl elongated A quality which inheres in a continuant. http://purl.obolibrary.org/obo/pato.owl physical object quality A shape quality inhering in a cell by virtue of the bearer's ability to take on two or more different shapes during its life cycle. http://purl.obolibrary.org/obo/pato.owl pleomorphic A quality inhering in a bearer by virtue of the bearer's dependence on oxygen. http://purl.obolibrary.org/obo/pato.owl This term is problematic. It seems to blur the distinction between aerobes more generally and obligate aerobes. aerobic A quality inhering in a bearer by virtue of the bearer's independence on oxygen. http://purl.obolibrary.org/obo/pato.owl anaerobic A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter). http://purl.obolibrary.org/obo/pato.owl globular rotund spherical A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. http://purl.obolibrary.org/obo/pato.owl bendy flexible A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. http://purl.obolibrary.org/obo/pato.owl stiff stiffness inflexible A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. http://purl.obolibrary.org/obo/pato.owl rod-like rod-shaped cylindrical A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a continuous convex surface with an axis of symmetry and one axis longer than the other; egg-shaped. http://purl.obolibrary.org/obo/pato.owl egg-shaped oval ovoid ovate A quality that inheres in an entire organism or part of an organism. http://purl.obolibrary.org/obo/pato.owl organismal quality An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. http://purl.obolibrary.org/obo/pr.owl protein A type II interferon that is a translation product of the human IFNG gene or a 1:1 ortholog thereof. The core domain structure consists of an Interferon gamma domain (Pfam:PF00714) that is four-helical cytokine domain with an additional helix in one of the crossover connections. It is a cytokine produced by lymphocytes activated by specific antigens or mitogens that has important immunoregulatory functions. http://purl.obolibrary.org/obo/pr.owl IFN-gamma IFNG http://purl.obolibrary.org/obo/pr.owl immune interferon interferon gamma A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. http://purl.obolibrary.org/obo/pr.owl T-cell differentiation antigen L3T4 T-cell surface antigen T4/Leu-3 T-cell surface glycoprotein CD4 CD4 molecule A protein with a core domain composition consisting of a propeptide region and an Interleukin-1 / 18 domain. http://purl.obolibrary.org/obo/pr.owl interleukin-1 A protein that is a T cell-derived cytokine that may play an important role in the initiation or maintenance of the proinflammatory response. Except for IL-17B, all other IL-17 family members are homodimers containing five highly conserved cysteine residues forming characteristic cystein-knot structure, similar to that found in the TGF-beta-like cystine-knot (PR:000000008). This class consists of six cytokines. Among them, interleukin 17A (IL-17) and IL-17F are expressed by a novel subset of CD4+ helper T (Th) cells and play a critical role in inflammation and autoimmunity. On the other hand, IL-17E, also called IL-25, has been associated with allergic responses. http://purl.obolibrary.org/obo/pr.owl IL17 fam:IL-17 interleukin-17 A protein with a core domain composition consisting of a signal peptide, an extracellular domain with multiple Leucine rich repeat (Pfam:PF13855) domain (LRR), a cysteine-rich region, a single-pass transmembrane domain and a C-terminal cytoplasmic tail containing a TIR domain (Pfam:PF01582). http://purl.obolibrary.org/obo/pr.owl fam:TLR Category=family. Toll-like receptor A protein that is a translation product of the human IL7 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl IL-7 IL7 interleukin-7 A protein with a core domain architecture consisting of an N-terminal Interleukin 10 (Pfam:PF00726) domain. http://purl.obolibrary.org/obo/pr.owl class 2 cytokine, IL-10 type A type III interferon that is distantly related to type I interferons (IFNs) and the interleukin-10 family. It comprises the translation product of the IL28A, IL28B and IL29 genes. Generally induced by viral infection and exert their antiviral and immunomodulatory activities through a unique receptor complex composed of IFN-lambdaR1 and interleukin 10 receptor 2. http://purl.obolibrary.org/obo/pr.owl Note: Some references consider 'lambda' and 'type III' to be synonyms. This is likely because lambda is the only type III interferon identified. However, the classification criteria for each nomenclature system differ. interferon lambda A protein that is a translation product of the human IL11 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl AGIF IL-11 IL11 adipogenesis inhibitory factor oprelvekin interleukin-11 A protein that is a translation product of the human IL12A gene or a 1:1 ortholog thereof. It associates with interleukin-12 subunit beta to form the interleukin-23. Interleukin-12 subunit alpha associates with interleukin-27 subunit beta to form the interleukin-35. http://purl.obolibrary.org/obo/pr.owl CLMF p35 IL-12 subunit p35 IL-12A IL12A NK cell stimulatory factor chain 1 NKSF1 cytotoxic lymphocyte maturation factor 35 kDa subunit interleukin-12 subunit alpha A protein that is a translation product of the human IL12B gene or a 1:1 ortholog thereof. Interleukin-12 subunit beta associates with interleukin-12 subunit alpha or interleukin-23 subunit alpha to form the interleukin-23. http://purl.obolibrary.org/obo/pr.owl CLMF p40 IL-12 subunit p40 IL-12B IL12B NK cell stimulatory factor chain 2 NKSF2 cytotoxic lymphocyte maturation factor 40 kDa subunit interleukin-12 subunit beta protein that is a translation product of the human IL13 gene or a 1:1 ortholog thereof. Interleukin-13 is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related. http://purl.obolibrary.org/obo/pr.owl IL-13 IL13 T-cell activation protein P600 NC30 interleukin-13 A protein that is a translation product of the human IL15 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl IL-15 IL15 interleukin-15 A protein that is a translation product of the human IL16 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl IL16 interleukin-16 A protein that is a translation product of the human IL2 gene or a 1:1 ortholog thereof. Interleukin-2 has a dual role in maintaining tolerance and contributing to immunity. http://purl.obolibrary.org/obo/pr.owl IL-2 IL2 T-cell growth factor TCGF aldesleukin interleukin-2 A protein that is a translation product of the human IL3 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl IL-3 IL3 MCGF P-cell-stimulating factor hematopoietic growth factor multipotential colony-stimulating factor Csfmu mast cell growth factor interleukin-3 A protein that is a translation product of the human IL4 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl B-cell IgG differentiation factor B-cell growth factor 1 B-cell stimulatory factor 1 BSF-1 IGG1 induction factor IL-4 IL4 binetrakin lymphocyte stimulatory factor 1 pitrakinra interleukin-4 A protein that is a translation product of the human IL5 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl B-cell differentiation factor I B-cell growth factor II BCGF-II IL-5 IL5 T-cell replacing factor TRF cytotoxic T-lymphocyte inducer eosinophil differentiation factor interleukin-5 A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl B-cell hybridoma growth factor B-cell stimulatory factor 2 BSF-2 CDF CTL differentiation factor IFN-beta-2 IL-6 IL6 interferon beta-2 interleukin HP-1 interleukin-6 A protein that is a translation product of the human CXCL8 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl C-X-C motif chemokine 8 CXCL8 IL-8 MDNCF MONAP NAP-1 T-cell chemotactic factor emoctakin granulocyte chemotactic protein 1 monocyte-derived neutrophil chemotactic factor monocyte-derived neutrophil-activating peptide neutrophil-activating protein 1 protein 3-10C interleukin-8 A protein that is a translation product of the human IL9 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl IL-9 IL9 T-cell growth factor P40 cytokine P40 interleukin-9 A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof. Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds. http://purl.obolibrary.org/obo/pr.owl CSIF IL-10 IL10 cytokine synthesis inhibitory factor interleukin-10 A protein that is a translation product of the Escherichia coli K-12 secA gene or a 1:1 ortholog thereof. [database_cross_reference: PRO:DNx] http://purl.obolibrary.org/obo/pr.owl secA azi pea prlD protein translocase subunit SecA http://purl.obolibrary.org/obo/pr.owl fam:IFNA Category=Family interferon alpha http://purl.obolibrary.org/obo/pr.owl IFBN Category=Family interferon beta A protein that binds to a specific cell surface receptor complex known as the IFN-gamma receptor (IFNGR), a complex of two IFNGR1 and two IFNGR2 chains. http://purl.obolibrary.org/obo/pr.owl IFN type II interferon gamma Category=family. Note: Some references consider 'gamma' and 'type II' to be synonyms. This is likely because gamma is the only type II interferon identified. However, the classification criteria for each nomenclature system differ. type II interferon A protein that consists solely of an Interferon alpha/beta domain (Pfam:PF00143) and which binds to a specific cell surface receptor complex known as the IFN-alpha receptor (IFNAR), a heterodimer of IFNAR1 and IFNAR2 chains. http://purl.obolibrary.org/obo/pr.owl IFN type I Category=Family type I interferon A class 2 cytokine, IL-10 type that binds to a specific cell surface receptor complex known as the IFN type III receptor, a heterodimer consisting of IFNLR1 and IL-10R2. http://purl.obolibrary.org/obo/pr.owl Note: Some references consider 'lambda' and 'type III' to be synonyms. This is likely because lambda is the only type III interferon identified. However, the classification criteria for each nomenclature system differ. type III interferon A protein that is encoded in the genome of some Bacteria <prokaryote>. http://purl.obolibrary.org/obo/pr.owl Bacteria <prokaryote> protein bacterial protein An immunoglobulin complex whose components are encoded in the genome of human. http://purl.obolibrary.org/obo/pr.owl immunoglobulin complex (human) Material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 http://purl.obolibrary.org/obo/ro.owl system ready for release A count is a data item denoted by an integer and represented the number of instances or occurences of an entity Damion Dooley's note: Unfortunately an IAO "count" cannot be a subclass of immaterial entity "linear coordinate" as this leads to disjoint conflict. STATO http://purl.obolibrary.org/obo/stato.owl Damion Dooley's note: The result of the act of counting is a scalar number whose unit is a description of the thing being counted. One can count 10 oranges and compare that to a count of 5 oranges. One can generalize that a count of 5 oranges is a count of pieces of fruit. One can then compare 5 oranges and 5 apples, fruitfully!; Damion Dooley's note: A count datum often implicity carries a date range for which the count is ascertained, or estimated, or simulated for. count 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 Indirect pathogen transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an animate intermediary vector to another host. http://purl.obolibrary.org/obo/trans.owl vector-borne 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 Vector-borne pathogen transmission process during which the pathogen is transported, from a reservoir, source or host to another host, within the vector and undergoes part of it's lifecycle, or replication cycle, in the vector. http://purl.obolibrary.org/obo/trans.owl biologic pathogen transmission process Biological pathogen transmission process during which the pathogen that is ingested with the blood meal undergoes simple multiplication in the body of the vector. http://purl.obolibrary.org/obo/trans.owl propagative 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 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. http://purl.obolibrary.org/obo/uberon.owl anatomical system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. http://purl.obolibrary.org/obo/uberon.owl immune system A soft, thin film of food debris, mucin, and dead epithelial cells deposited on the teeth, providing the medium for the growth of various bacteria. The main inorganic components are calcium and phosphorus, with small amounts of magnesium, potassium, and sodium; the organic matrix consists of polysaccharides, proteins, carbohydrates, lipids, and other components. Plaque plays an important etiologic role in the development of dental caries and periodontal and gingival diseases and provides the base for the development of materia alba; calcified plaque forms dental calculus. Note that 'dental plaque' is classified in UBERON as an 'organism substance'. But dental plaque is commonly recognized as a type of biofilm. -SB http://purl.obolibrary.org/obo/uberon.owl bacterial plaque plaque dental plaque "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] http://purl.obolibrary.org/obo/uo.owl unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. http://purl.obolibrary.org/obo/uo.owl concentration unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. http://purl.obolibrary.org/obo/uo.owl dimensionless unit A dimensionless unit which denotes a simple count of things. http://purl.obolibrary.org/obo/uo.owl count unit A dimensionless count unit which is a measure of viable bacterial numbers. http://purl.obolibrary.org/obo/uo.owl CFU colony forming unit A concentration unit which a measure of viable bacterial numbers in a given volume. http://purl.obolibrary.org/obo/uo.owl colony forming unit per volume cfu/mL requires discussion A colony forming unit which a measure of viable bacterial numbers in one milliliter. Damion Dooley http://purl.obolibrary.org/obo/uo.owl colony forming unit per milliliter A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. Many vaccines are developed to protect against infectious pathogens that causes infectious diseases. Many vaccines are also being developed against other diseases such as cancer, allergy, and autoimmune diseases. YH, BP, BS, MC, LC, XZ, RS, a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo. http://purl.obolibrary.org/obo/vo.owl vaccine MeSH: D014612 A vaccine that targets against a bacterial disease. YH http://purl.obolibrary.org/obo/vo.owl bacterial vaccine MeSH: D001428 A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex. [database_cross_reference: PMID:16448494] http://purl.obolibrary.org/obo/go.owl MTB T2SS-associated complexes main terminal branch Sec-dependent secretion system-associated complex general secretion pathway-associated complex Note that the type II protein secretion system complex does not include components of the Sec or Tat pathways. For components of these pathways, consider annotating to 'cell envelope Sec complex ; GO:0031522' or 'TAT protein translocation system complex ; GO:0033281'. type II protein secretion system complex 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 Disposition inhering in a material entity, that is realized in a process of inhibiting 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 then 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 An assay for detecting bacteria by subjecting them to strain-specific bacteriophages. Damion Dooley https://en.wikipedia.org/wiki/Phage_typing http://snomed.info/sct/900000000000207008 Bacterial bacteriophage typing http://phinvads.cdc.gov/vads/http:/phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.96&code=22642004 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])