en Achchuthan Shanmugasundram Kitsos Louis Omar harb Satya Sahoo Anna Protasio Chris J. Janse Chris Stoeckert Flora Logan Jie Zheng Priti Parikh Shahid M. Khan 2010-08-04 The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. Ontology for Parasite Lifecycle The Parasite Life Cycle ontology was developed as part of the NIH-funded "Semantics and Services enabled Problem Solving Environment for Tcruzi" project (Grant#1R01HL087795-01A1). The Kno.e.sis center, Computer Science and Engineering Department, Wright State University, Center for Bioinformatics, Department of Genetics, University of Pennsylvania School of Medicine, USA and the Tarleton Lab, Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, USA collaborated to create this ontology. Resource page: http://knoesis.wright.edu/trykipedia 2021-01-28 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official 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 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 A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB 2018-09-21T16:43:39Z Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by 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 An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology true axiom_lost_from_external_ontology This annotation property may be replaced with an annotation property from an external ontology such as IAO axiom_lost_from_external_ontology Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 uberon function_notes true function_notes function_notes Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 uberon structure_notes true structure_notes structure_notes Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy has_rank uberon dc-contributor true dc-contributor contributor has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand label uberon seeAlso true seeAlso see also uberon depicted_by true depicted_by depicted by 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 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 A relation between an organism and an organism that has vector role. obsolete_has vector true A relation between an organism and an organism that has host role. obsolete_has host true inheres in this fragility 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 This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary lactation SubClassOf 'only in taxon' some 'Mammalia' x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall only in taxon A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y Chris Mungall has host Chris Mungall has vector entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth 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] A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. obsolete dependent continuant true s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella 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 specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) Digestive gland of crustaceans with functions approximately analogous to liver and pancreas of vertebrates - enzyme secretion, food absorption and storage. BrendaTissueOBO midgut gland BTO:0000597 hepatopancreas 1: The trunk of an elephant; also: any long flexible snout. 2: Any of various elongated or extensible tubular processes as the sucking organ of a butterfly of the oral region of an invertebrate. BrendaTissueOBO BTO:0001117 proboscis An anatomical entity that has mass. CARO:0000006 material anatomical entity An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CL:0000000 GO:0005623 CARO:0000013 deprecate and replace with CL or GO term? cell The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. BTO:0000575 CALOHA:TS-0454 FMA:14515 cell Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. hepatocyte A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. BTO:0000424 CALOHA:TS-0290 FMA:81100 RBC red blood cell cell erythrocyte A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. BTO:0000801 CALOHA:TS-0587 FMA:63261 FMA:83585 histiocyte cell 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 biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process 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. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division data item information content entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. cjm 2018-05-20T20:55:03Z ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. cjm 2018-05-20T20:55:30Z base ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module cjm 2018-05-20T20:55:47Z editors ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module cjm 2018-05-20T20:56:13Z main release ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. cjm 2018-05-20T20:56:23Z bridge ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file cjm 2018-05-20T20:56:47Z import ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology cjm 2018-05-20T20:58:11Z subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. cjm 2018-05-20T20:58:38Z curation subset ontology module An ontology module that is intended for usage in analysis or discovery applications. cjm 2018-05-20T20:58:49Z analysis subset ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset cjm 2018-05-20T20:59:19Z single layer subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim cjm 2018-05-20T20:59:57Z exclusion subset ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import cjm 2018-05-20T21:00:14Z external import ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset cjm 2018-05-20T21:14:16Z species subset ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. cjm 2018-05-20T21:20:33Z reasoned ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process cjm 2018-05-20T21:21:12Z generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. cjm 2018-05-20T21:21:21Z template generated ontology module cjm 2018-05-20T21:28:15Z taxonomic bridge ontology module cjm 2018-05-22T04:15:54Z ontology module subsetted by expressivity A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports cjm 2018-05-22T04:16:10Z obo basic subset ontology module cjm 2018-05-22T04:16:28Z ontology module subsetted by OWL profile cjm 2018-05-22T04:16:48Z EL++ ontology module A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. Albert Goldfain Alexander Diehl Lindsay Cowell In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen. The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction. parasite role A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent role A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles. pathogen role A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host. Albert Goldfain Alexander Diehl Lindsay Cowell primary host role The role is realized in developmental and reproduction processes of the host's partner in symbiosis. definitive host role A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle. Albert Goldfain Alexander Diehl Lindsay Cowell secondary host role The role is realized in developmental processes of the host's partner in symbiosis. intermediate host role A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced. Albert Goldfain Alexander Diehl Lindsay Cowell The partner in symbiosis bears the parasite role. The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the host's growth, survival, or fitness reduction. parasite host role An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role. infectious agent vector role An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector. Albert Goldfain Alexander Diehl Lindsay Cowell biological vector of infectious agent role NCBITaxon:85055 GC_ID:1 house mouse mouse ncbi_taxonomy Mus musculus GC_ID:1 ncbi_taxonomy Bulinus GC_ID:1 mammals ncbi_taxonomy mammals Mammalia GC_ID:1 true insects ncbi_taxonomy Insecta GC_ID:1 ncbi_taxonomy Oncomelania GC_ID:1 ncbi_taxonomy Trypanosomatidae GC_ID:1 Leishmania ncbi_taxonomy Leishmania <genus> GC_ID:1 ncbi_taxonomy Leishmania (Leishmania) major Leishmania tropica major Leishmania major GC_ID:1 ncbi_taxonomy Trypanosoma GC_ID:1 ncbi_taxonomy Trypanosoma (Trypanozoon) brucei Trypanosoma brucei subgroup Trypanosoma brucei GC_ID:1 ncbi_taxonomy Trypanosoma cruzi GC_ID:1 ncbi_taxonomy Plasmodium GC_ID:1 malaria parasite P. falciparum ncbi_taxonomy Plasmodium (Laverania) falciparum Plasmodium falciparum GC_ID:1 ncbi_taxonomy Schistosoma GC_ID:1 ncbi_taxonomy Schistosoma japonicum GC_ID:1 ncbi_taxonomy Schistosoma mansoni GC_ID:1 ncbi_taxonomy Schistosoma haematobium GC_ID:1 molluscs mollusks ncbi_taxonomy molluscs Mollusca GC_ID:1 ncbi_taxonomy Biomphalaria GC_ID:1 kissing bugs ncbi_taxonomy Triatominae GC_ID:1 Anopheles ncbi_taxonomy Anopheles <genus> GC_ID:1 PMID:9835021 sand flies sandflies ncbi_taxonomy Phlebotominae GC_ID:1 Glossina tsetse flies tsetse fly ncbi_taxonomy Glossina <genus> GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates Vertebrata <vertebrates> GC_ID:1 human man ncbi_taxonomy Homo sapiens GC_ID:1 dog dogs ncbi_taxonomy Canis canis Canis domesticus Canis familiaris Canis lupus familiaris host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism A Leishmania major promastigote that undergoes a second developmental transition yielding the metacyclic promastigote. This form of parasite is infective to its mammalian host. Chris Stoeckert Jie Zheng Priti Parikh L. major metacyclic promastigote PMID:11748963 Leishmania major metacyclic promastigote A hindgut that is a part of or originated from a Triatominae bug. Priti Parikh Triatominae hindgut A liver that is a part of or originated from a human (Homo sapiens). Priti Parikh human liver FMA:7197 Homo sapiens liver A promastigote stage of some kinetoplastids. Chris Stoeckert Jie Zheng Priti Parikh PMID:13129524 metacyclic promastigote stage An exflagellated microgametocyte stage in the lifecycle of Plasmodium falciparum that occurs in the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum exflagellated microgametocyte stage Plasmodium falciparum exflagellated microgametocyte stage A sporocyst stage in the Schistosoma haematobium lifecycle that occurs within the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium sporocyst stage Schistosoma haematobium sporocyst stage A cercaria stage in the lifecycle of Schistosoma japonicum that occurs in a freshwater snail and in fresh water. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum cercaria stage Schistosoma japonicum cercaria stage A microgametocyte stage in the Plasmodium falciparum lifecycle that occurs either in the bloodstream of a human host or the midgut of a mosquito vector. Chris Stoeckert Jie Zheng P. Parkh S. Khan. C. Janse P. falciparum microgametocyte stage Plasmodium falciparum microgametocyte stage A Schistosoma haematobium schistosomulum in a migratory larval form that is found within blood vessels of mammal, as definitive host, 3 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 3 hour schistosomulum Schistosoma haematobium 3 hour schistosomulum A Schistosoma haematobium in a free-living motile form that is covered with cilia and develops in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium miracidium Schistosoma haematobium miracidium A 3 days schistosomulum stage of Schistosoma mansoni that occurs in the definitive host 3 days post-infection. Chris Stoeckert Jie Zheng Priti Parikh S. mansoni 3 day schistosomulum stage Schistosoma mansoni 3 day schistosomulum stage A proboscis that is a part of or originated from a sand fly of genus Phlebotominae. Priti Parikh Phlebotominae proboscis A Leishmania major that is extracellular and motile form with an anterior flagellum. It grows and divides by longitudinal binary fission in the insect vector; i.e., sandfly. Chris Stoeckert Jie Zheng Priti Parikh L. major promastigote http://dna.kdna.ucla.edu/parasite_course-old/leish_files/introduction1.htm Leishmania major promastigote A schistosomulum stage that occurs in 3 hours after infection of the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng PMID:19885392 3 hour schistosomulum stage A parasite lifecycle stage of Trematodes where the parasite is in free-living motile form, covered with cilia and settles in the mollusc to become a sporocyst. Chris Stoeckert Jie Zheng Priti Parikh Wikipedia: Trematode lifecycle stages miracidium stage Cerebrospinal fluid that is a part of or originated from a human (Homo sapiens). Priti Parikh human CSF human cerebral spinal fluid human cerebrospinal fluid FMA:20935 Homo sapiens cerebrospinal fluid A Schistosoma japonicum schistosomulum in a migratory larval form that is found within blood vessels of the mammal, as definitive host, 3 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum 3 day schistosomulum Schistosoma japonicum 3 day schistosomulum A Schistosoma japonicum schistosomulum in a migratory larval form that is found within blood vessels of the mammal, as definitive host, 3 weeks post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum 3 hour schistosomulum Schistosoma japonicum 3 hour schistosomulum A trypomastigote stage where trypmastigote form of parasites are found in mammalian host blood stream. Chris Stoeckert Jie Zheng Priti Parikh bloodstream trypomastigote stage A miracidium stage in the Schistosoma japonicum lifecycle that occurs in the intermediate snail host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum miracidium stage Schistosoma japonicum miracidium stage A daughter sporocyst stage of Schistosoma japonicum that occurs in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum daughter sporocyst stage Schistosoma japonicum daughter sporocyst stage A Schistosoma mansoni schistosomulum in a migratory larval formi that is found within blood vessels of the definitive host, mammal, 24 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 24hour schistosomulum Schistosoma mansoni 24 hour schistosomulum A gamete stage in apicomplexan parasites when exflagellated microgametocyte divides into microgamete. Chris Stoeckert Jie Zheng Matt Berriman microgamete stage A skin that is a part of or originated from a human (Homo sapiens) body. Priti Parikh human skin FMA:7163 Homo sapiens skin A gametocyte stage where a cell differentiates into a female sexual form called macrogametocyte. Chris Stoeckert Jie Zheng Priti Parikh macrogametocyte stage A Schistosoma haematobium schistosomulum in a migratory larval form that is found within blood vessels of mammal, as definitive host, 24 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 24 hour schistosomulum Schistosoma haematobium 24 hour schistosomulum A Schistosoma japonicum sporocyst that develops into cercariae. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum daughter sporocyst Schistosoma japonicum daughter sporocyst A Trypanosoma brucei trypomastigote that is a dividing form of Trypanosoma brucei found in the midgut of an insect vector. Chris Stoeckert Jie Zheng Priti Parikh T. brucei procyclic trypomastigote Trypanosoma brucei procyclic trypomastigote A midgut that is a part of or originated from an Anopheles mosquito. Anopheles midgut A parasite lifecycle stage of trypanosomes. In trypomastigote stage, the kinetoplast is near the posterior end of the body, and the flagellum lies attached to the cell body for most of its length by an undulating membrane. Chris Stoeckert Jie Zheng Priti Parikh Wikipedia: Trypanosomatid trypomastigote stage A Trypanosoma brucei trypomastigote that is a non-dividing form infectious for the mammal host. It is found in the salivary gland of an insect vector or blood of a mammal host. Chris Stoeckert Jie Zheng Priti Parikh T. brucei metacyclic trypomastigote http://dna.kdna.ucla.edu/parasite_course-old/african%20tryps%20new_files/subchapters/Life%20cycle.htm Trypanosoma brucei metacyclic trypomastigote An erythrocytic schizont stage in the Plasmodium falciparum lifecycle that occurs in the infected erythrocytes of a human host. updated according to OPL terms Plasmodium final excel file from C. Janse, S. Khan C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum erythorcytic schizont stage Plasmodium falciparum erythrocytic schizont stage A parasite lifecycle stage of apicomplexan species where a daughter cell, called merozoite is produced from schizont through schizogony. adjusted to be more general Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarM.htm merozoite stage A Schistosoma haematobium is a mature form of Schistosoma haematobium and capable of sexual reproduction, which lives in the pelvic blood vessels of the vesicle plexis of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium worm Schistosoma haematobium worm A Schistosoma mansoni in a migratory larval form that is found within blood vessels of the definitive host, mammal, and develops into the worm. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni schistosomulum Schistosoma mansoni schistosomulum A Schistosoma japonicum schistosomulum in a migratory larval form that is found within blood vessels of the mammal, as definitive host, 6 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum 6 day schistosomulum Schistosoma japonicum 6 day schistosomulum A hepatocyte that is a part of or originated from a human (Homo sapiens). Priti Parikh human hepatocyte FMA:14515 Homo sapiens hepatocyte A sporocyst stage in the Schistosoma mansoni lifecycle that occurs in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni sporocyst stage Schistosoma mansoni sporocyst stage An erythrocytic ring trophozoite stage in the Plasmodium falciparum life cycle that occurs in erythrocytes of a human host. During this stage some Plasmodium falciparum merozoites undergo asexual reproduction cycle in erythrocytes and form young trophozoites that are referred to as "ring form" due to their morphology. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum erythrocytic ring trophozoite stage Wikipedia: Plasmodium falciparum biology Plasmodium falciparum erythrocytic ring trophozoite stage A Schistosoma japonicum in a parasitic larval form that develops in a freshwater snail and is released into the water. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum cercaria Schistosoma japonicum cercaria A promastigote stage where the form of parasite is short, ovoid, and slightly motile. Chris Stoeckert Jie Zheng Priti Parikh PMID:13129524 procyclic promastigote stage A 6 day schistosomulum stage of Schistosoma mansoni that occurs in the definitive host 6 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 6 day schistosomulum stage Schistosoma mansoni 6 day schistosomulum stage A schistosoma japonicum schistosomulum stage that occurs in the definitive host 6 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum 6 day schistosomulum stage Schistosoma japonicum 6 day schistosomulum stage A mesenteric vein that is a part of or originated from a human (Homo sapiens). Priti Parikh human mesenteric vein Homo sapiens mesenteric vein A lifecycle stage of Trypanosoma brucei. Chris Stoeckert Jie Zheng Priti Parikh T. brucei lifecycle stage Trypanosoma brucei lifecycle stage A Trypanosoma cruzi that is found in the intestinal tract of the insect vector. In this form, the kinetoplast is found anterior and adjacent to the nucleus. The flagellum emerges in the middle of the cell. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi epimastigote http://dna.kdna.ucla.edu/parasite_course-old/cruzi_files/intro.htm Trypanosoma cruzi epimastigote A Plasmodium falciparum gametocyte that is a male gametocyte and found in either bloodstream of a human host or midgut of a mosquito vector. The microgametocyte is a precursor cell of the microgamete. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum microgametocyte Plasmodium falciparum microgametocyte A Schistosoma japonicum worm is the mature form of Schistosoma japonicum and capable of sexual reproduction, which is found in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the human host 7 weeks after infection of the mammal host. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum 7 week worm Schistosoma japonicum 7 week worm A Schistosoma japonicum in an egg form that is laid by the female adult worm and released into the host gut where they leave the host in the faeces. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum egg Schistosoma japonicum egg A Schistosoma japonicum worm is capable of sexual reproduction, which is found in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammal host 3 weeks after infection of the human host. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum 3 week worm Schistosoma japonicum 3 week worm A metacyclic trypomastigote stage in the lifecycle of Trypanosoma brucei that occurs either in vertebrate host bloodstream or in salivary glands of an insect vector. Chris Stoeckert Jie Zheng Priti Parikh T. brucei metacyclic trypomastigote stage Trypanosoma brucei metacyclic trypomastigote stage A parasite lifecycle stage of some protozoan parasites that is a non-reproductive, feeding and growing stage. Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarT.htm trophozoite stage A procyclic promastigote stage in the Leishmania major lifecycle. Chris Stoeckert Jie Zheng Priti Parikh L. major procyclic promastigote stage Leishmania major procyclic promastigote stage A schizont stage that occurs in hepatocyte where sporozoites mature into a schizont. Chris Stoeckert Jie Zheng Matt Berriman and Priti Parikh PMID:11006474 hepatic schizont stage A Plasmodium falciparum divides through schizogony. Depending on its location, it is either called hepatic or erythrocytic schizont. The schizont is a dividing stage with 2 or more nuclei. C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum schizont Plasmodium falciparum schizont A Trypanosoma cruzi that is the intracellular dividing form in the cytoplasm of mammalian cells. It is a round/oval-shaped cell with no protruding flagellum. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi amastigote http://dna.kdna.ucla.edu/parasite_course-old/cruzi_files/intro.htm Trypanosoma cruzi amastigote A 3 days schistosomulum stage of Schistosoma haematobium occurs in the definitive host 3 days post-infection. Chris Stoeckert Jie Zheng Priti Parikh S. haematobium 3 day schistosomulum stage Schistosoma haematobium 3 day schistosomulum stage A 24 hours schistosomulum stage of Schistosoma mansoni that occurs in the definitive host 24 hours post-infection. Chris Stoeckert Jie Zheng Priti Parikh S. mansoni 24 hour schistosomulum stage Schistosoma mansoni 24 hour schistosomulum stage An amastigote stage in the lifecycle of Trypanosoma cruzi that occurs in mammalian hosts. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi amastigote stage Trypanosoma cruzi amastigote stage A schistosomulum stage that occurs in 6 days after infection of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh PMID:19885392 6 day schistosomulum stage A Schistosoma mansoni schistosomulum in a migratory larval formi that is found within blood vessels of the definitive host, mammal, 3 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 3hour schistosomulum Schistosoma mansoni 3 hour schistosomulum A macrogametocyte stage in the Plasmodium falciparum lifecycle that occurs either in the bloodstream of a human host or the midgut of a mosquito vector. gametocytes are mainly found in the blood C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum macrogametocyte stage Plasmodium falciparum macrogametocyte stage A miracidium stage in the Schistosoma haematobium lifecycle that occurs in the intermediate snail host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium miracidium stage Schistosoma haematobium miracidium stage A parasite lifecycle stage that is a free-living larval stage of Digenea, developed within the germinal cells of the sporocyst or redia. A cercaria has a tapering head with large penetration glands. It may or may not have a long swimming "tail", depending on the species. The motile cercaria finds and settles in a host where it will become either an adult, or a mesocercaria, or a metacercaria, according to species. Chris Stoeckert Jie Zheng Priti Parikh Wikipedia: Trematode lifecycle stages cercaria stage A worm stage of Schistosoma japonicum that is fully developed mature form and found in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum worm stage Schistosoma japonicum worm stage An egg stage in the lifecycle of Schistosoma japonicum that occurs in the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum egg stage Schistosoma japonicum egg stage A parasite lifecycle stage of sporozoa consisting of a zygote enclosed by cyst wall. Chris Stoeckert Jie Zheng Priti Parikh Mosby's Medical Dictionary, 8th edition. � 2009, Elsevier. (http://medical-dictionary.thefreedictionary.com/oocyst) oocyst stage A 3 hours schistosomulum stage of Schistosoma haematobium that occurs in the definitive host 3 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 3 hour schistosomulum stage Schistosoma haematobium 3 hour schistosomulum stage A macrogamete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum macrogamete stage Plasmodium falciparum macrogamete stage A trypomastigote stage where trypomastigote form of parasites are in dividing form. This stage occurs in fly vector. Chris Stoeckert Jie Zheng Priti Parikh procyclic trypomastigote stage A Schistosoma japonicum in a migratory larval form that is found within blood vessels of the definitive host and develops into the worm. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum schistosomulum Schistosoma japonicum schistosomulum A schizont stage that occurs in erythrocytes where trophozoites mature into a schizont and schizont produces daughter trophozoites or merozoites. Chris Stoeckert Jie Zheng Matt Berriman and Priti Parikh PMID: 11006474 erythrocytic schizont stage A Schistosoma haematobium is the parasitic larval form of the Schistosoma haematobium that develops in a freshwater snail and is released into the water. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium cercaria Schistosoma haematobium cercaria A parasite lifecycle stage that occurs in the liver of the host organism. For Plasmodium species these stages can include sporozoites, trophozoites, schizonts, and merozoites. Chris Stoeckert liver stage EuPathDB parasite lifecycle in host liver stage A procyclic promastigote stage in the Trypanosoma brucei lifecycle. Chris Stoeckert Jie Zheng Priti Parikh Trypanosoma brucei procyclic trypomastigote stage A parasite lifecycle stage of some parasites in which the parasite develops into a worm form, and undergoes maturation. Chris Stoeckert Jie Zheng Priti Parikh http://www.path.cam.ac.uk/~schisto/schistosoma/schisto_lifecycle_egg.html parasitic worm stage Hepatopancreas that is a part of or originated from a Bulinus snail. Priti Parikh Bulinus hepatopancreas A parasite lifecycle stage that is the multinucleate stage in the development of some members of the Sarcodina and some sporozoans during schizogony. Chris Stoeckert Jie Zheng Priti Parikh http://medical-dictionary.thefreedictionary.com/schizont schizont stage A gamete stage in parasites when macrogametocytes produce macrogametes through the process known as gametogenesis. Chris Stoeckert Jie Zheng Priti Parikh http://www.tulane.edu/~wiser/malaria/mal_lc.PDF macrogamete stage A sporocyst stage of Trematodes produced by a mother sporocyst; it lacks a gut and is capable of asexual production of either rediae or cercariae. Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarD.htm daughter sporocyst stage A Schistosoma haematobium worm is the mature form of Schistosoma haematobium and capable of sexual reproduction, which is found in the pelvic blood vessels of the vesicle plexis of the mammal host 7 weeks after infection of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 7 week worm Schistosoma haematobium 7 week worm A midgut that is a part of or originated from a Triatominae bug. Priti Parikh Triatominae midgut A Plasmodium falciparum that is a 'banana-shaped' form and originates from the round zygote. The ookinete is found in the midgut of a mosquito vector and traverses the midgut wall of a mosquito vector. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum ookinete Wikipedia: Plasmodium falciparum biology Plasmodium falciparum ookinete A Schistosoma mansoni worm that is capable of sexual reproduction, which is found in the small inferior mesenteric blood vessels surrounding the large intestine of the mammal host 3 weeks after infection of the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 3 week worm Schistosoma mansoni 3 week worm A worm stage of Schistosoma haematobium that is fully developed mature form and found in the pelvic blood vessels of the vesicle plexis of the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium worm stage Schistosoma haematobium worm stage A Trypanosoma brucei that is found in the salivary glands of tse-tse fly. In this form the kinetoplast is anterior to the nucleus with a short undulating membrane running about half the length of the body. Chris Stoeckert Jie Zheng Priti Parikh T. brucei epimastigote http://dna.kdna.ucla.edu/parasite_course-old/african%20tryps%20new_files/contents1.htm Trypanosoma brucei epimastigote A hepatic schizont stage in the lifecycle of Plasmodium falciparum that occurs in the infected hepatocytes of a human host. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum hepatic schizont stage Plasmodium falciparum hepatic schizont stage A Schistosoma japonicum is an elongated sac that develops from the miracidium within the snail indermediate host, and that either produces more sporocysts or develops into cercariae. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum sporocyst Schistosoma japonicum sporocyst A parasite lifecycle stage that is the migratory stage between cercaria and adult of the schistosomes; equivalent to the metacercarial stage in other digeneans. Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarS.htm schistomulum stage An erythrocyte that is a part of or originated from a human (Homo sapiens). Priti Parikh human RBC human erythrocyte human red blood cell FMA:62845 Homo sapiens erythrocyte Vesical venus plexus that is a part of or originated from a human (Homo sapiens). Priti Parikh human vesical venus plexus FMA:18934 Homo sapiens vesical venus plexus A parasite lifecycle stage that is the early developmental stage capable of asexual reproduction: in sporozoans it is usually enclosed within an oocyst; in digeneans it is an intramolluscan stage lacking a gut. Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarD.htm sporocyst stage A Schistosoma haematobium worm is the mature form of Schistosoma haematobium and capable of sexual reproduction, which is found in the pelvic blood vessels of the vesicle plexis of the human host 3 weeks after infection of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 3 week worm Schistosoma haematobium 3 week worm A schistosomulum stage of Schistosoma mansoni that occurs in the definitive host and is followed by the parasitic worm stage. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni schistosomulum stage Schistosoma mansoni schistosomulum stage A cercaria stage in the lifecycle of Schistosoma haematobium that occurs in a freshwater snail and in fresh water. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium cercaria stage Schistosoma haematobium cercaria stage A metacyclic promastigote stage in the lifecycle of Leishmania major. Chris Stoeckert Jie Zheng Priti Parikh L. major metacyclic promastigote stage Leishmania major metacyclic promastigote stage A merozoite stage in the Plasmodium falciparum lifecycle that occurs in the bloodstream or hepatocytes of a human host. C. Stoeckert Priti Parikh P. falciparum merozoite stage Plasmodium falciparum merozoite stage Hepatopancreas that is a part of or originated from a Biomphalaria snail. Priti Parikh Biomphalaria hepatopancreas A Schistosoma mansoni in an egg form that is laid by the female adult worm and released into the host gut where they leave the host in the faeces. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni egg Schistosoma mansoni egg A worm stage of Schistosoma japonicum that is found in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the definitive host 3 weeks after infection. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum 3 week worm stage Schistosoma japonicum 3 week worm stage A worm stage of Schistosoma mansoni that is found in the small inferior mesenteric blood vessels surrounding the large intestine of the definitive host 3 weeks after infection. Chris Stoeckert Jie Zheng Priti Parikh S. mansoni 3 week worm stage Schistosoma mansoni 3 week worm stage A parasite lifecycle stage of Trypanosomatids. During this stage, the undulating membrane is shortened and the flagellar pocket and the kinetoplast are anterior to the nucleus. This stage occurs in the insect host. Chris Stoeckert Jie Zheng Priti Parikh epimastigote stage A Schistosoma haematobium sporocyst that develops into cercariae. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium daughter sporocyst Schistosoma haematobium daughter sporocyst A Plasmodium falciparum schizont that is found in infected erythrocytes of a human host. C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum erythrocytic schizont Plasmodium falciparum erythrocytic schizont A 7 week worm stage of Schistosoma haematobium that is the mature stage of Schistosoma haematobium and found in the pelvic blood vessels of the vesicle plexis of the definitive host 7 weeks after weeks after infection . Chris Stoeckert Jie Zheng Priti Parikh S. haematobium 7 week worm stage Schistosoma haematobium 7 week worm stage A miracidium stage in the Schistosoma mansoni lifecycle that occurs in the intermediate snail host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni miracidium stage Schistosoma mansoni miracidium stage An oocyst stage in the Plasmodium falciparum lifecycle that occurs on the hemocoel side of the midgut of a mosquito vector. During this stage Plasmodium falciparum ookinete invades and escapes midgut wall of mosquito and embed itself onto the exterior of the gut membrane and develop encysted zygote, called oocyst. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum oocyst stage Plasmodium falciparum oocyst stage A parasite lifecycle stage is a nonflagellate intracellular developmental stage in the trypanosomatid parasites lifecycle that occurs in mammalian host. Chris Stoeckert Jie Zheng Priti Parikh amastigote stage A sporozoite stage in the Plasmodium falciparum lifecycle that occurs in the salivary glands of the mosquito and invades hepatocytes in the human host. C. Janse Chris Stoeckert Jie Zheng Matt Berrimen Priti Parikh S. Khan P. falciparum sporozoite stage Plasmodium falciparum sporozoite stage A Trypanosoma cruzi trypomastigote that is found in blood or cells of mammal hosts at the infectious stage for mammals. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi metacyclic trypomastigote http://dna.kdna.ucla.edu/parasite_course-old/cruzi_files/intro.htm Trypanosoma cruzi metacyclic trypomastigote Blood that is part of or originated from a human (Homo sapiens). previous def was: blood of human Chris Stoeckert human blood OPL Homo sapiens blood A schistosomulum stage of Schistosoma japonicum that occurs in the definitive host and is followed by the parasitic worm stage. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum schistosomulum stage Schistosoma japonicum schistosomulum stage A microgametocyte stage in some apicomplexan parasites where microgametocyte gets matured and form microgamete through the process known as exflagellation. Chris Stoeckert Jie Zheng Priti Parikh exflagellated microgametocyte stage A 3 hours schistosomulum stage of Schistosoma mansoni that occurs in the definitive host 3 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 3 hour schistosomulum stage Schistosoma mansoni 3 hour schistosomulum stage A salivary gland that is a part of or originated from an Anopheles mosquito. Priti Parikh Anopheles salivary gland A macrophage that is a part of or originated from a human (Homo sapiens). human macrophage FMA:63261 Homo sapiens macrophage A Schistosoma mansoni schistosomulum in a migratory larval formi that is found within blood vessels of the definitive host, mammal, 3 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 3day schistosomulum Schistosoma mansoni 3 day schistosomulum A 6 day schistosomulum stage of Schistosoma haematobium that occurs in the definitive host 6 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 6 day schistosomulum stage Schistosoma haematobium 6 day schistosomulum stage An egg stage in the lifecycle of Schistosoma haematobium that occurs in the mammalian host.. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium egg stage Schistosoma haematobium egg stage A Schistosoma japonicum is the mature form of Schistosoma japonicum and capable of sexual reproduction, which lives in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum worm Schistosoma japonicum worm An adult worm stage of a female parasitic worm. Chris Stoeckert Jie Zheng Priti Parikh http://www.path.cam.ac.uk/~schisto/schistosoma/schisto_lifecycle_egg.html adult female parasitic worm stage A Schistosoma mansoni in the mature form that is capable of sexual reproduction, which lives in the small inferior mesenteric blood vessels surrounding the large intestine of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni worm Schistosoma mansoni worm A 24 hours schistosomulum stage of Schistosoma haematobium that occurs in the definitive host 24 hours post-infection. Chris Stoeckert Jie Zheng Priti Parikh S. haematobium 24 hour schistosomulum stage Schistosoma haematobium 24 hour schistosomulum stage A Plasmodium falciparum that is produced in a schizont, found in the bloodstream of a human host and invades erythrocytes. Chris Stoeckert Jie Zheng P. Parkh P. falciparum merozoite Plasmodium falciparum merozoite A metacyclic trypomastigote stage in the lifecycle of Trypanosoma cruzi that occurs in a vertebrate host. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi metacyclic trypomastigote stage Trypanosoma cruzi metacyclic trypomastigote stage A Schistosoma japonicum schistosomulum in a migratory larval form that is found within blood vessels of the mammal, as definitive host, 24 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum 24 hour schistosomulum Schistosoma japonicum 24 hour schistosomulum A lung that is a part of or originated from a human (Homo sapiens). Priti Parikh human lung FMA:7195 Homo sapiens lung Hepatopancreas that is a part of or originated from a Oncomelania snail. Priti Parikh Oncomelania hepatopancreas An egg stage in the lifecycle of Schistosoma mansoni that occurs in the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni egg stage Schistosoma mansoni egg stage A Schistosoma mansoni worm is the mature form of Schistosoma mansoni and capable of sexual reproduction, which is found in the small inferior mesenteric blood vessels surrounding the large intestine of the mammal host 7 weeks after infection of the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 7 week worm Schistosoma mansoni 7 week worm A Plasmodium falciparum is formed in the oocyst. It migrates to and resides in the salivary glands of the mosquito vector. A distinction is made between oocyst-derived and salivary gland-derived sporozoites. Sporozoites invade hepatocytes in the vertebrate host. C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum sporozoite Wikipedia: Plasmodium falciparum biology Plasmodium falciparum sporozoite A Plasmodium falciparum that oocyst is formed, after traversal of the midgut wall by the ookinete stage, on the hemocoel side of the midgut wall of the mosquito vector. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum oocyst Plasmodium falciparum oocyst A 7 week worm stage of Schistosoma japonicum that is the mature stage of Schistosoma japonicum and found in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the definitive host 7 weeks after weeks after infection. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum 7 week worm stage Schistosoma japonicum 7 week worm stage An early trophozoite stage of Plasmodium sp. where a large central vacuole and peripheral nucleus give an appearance of a signet ring. Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarR.htm erythrocytic ring trophozoite stage An intestine that is a part of or originated from a human (Homo sapiens). Priti Parikh human intestine FMA:7199 Homo sapiens intestine A mother sporocyst stage in the Schistosoma mansoni lifecycle that occurs in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni mother sporocyst stage Schistosoma mansoni mother sporocyst stage A gametocyte stage where a cell differentiates into a male sexual form called microgametocyte. Chris Stoeckert Jie Zheng Priti Parikh microgametocyte stage A Schistosoma haematobium sporocyst that produces more sporocysts. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium mother sporocyst Schistosoma haematobium mother sporocyst A Schistosoma japonicum sporocyst that produces more sporocysts. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum mother sporocyst Schistosoma japonicum mother sporocyst A Plasmodium falciparum is a feeding form. The trophozoite stage has only 1 nucleus. Depending on its location, it is either called hepatic or erythrocytic trophozoite. C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum trophozoite Plasmodium falciparum trophozoite A Schistosoma mansoni is an elongated sac that develops from the miracidium within the snail indermediate host, and that either produces more sporocysts or develops into cercariae. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni sporocyst Schistosoma mansoni sporocyst A parasitic worm stage of development 7 weeks post differentiation into a worm form. Chris Stoeckert Jie Zheng Priti Parikh PMID:19885392 7 week parasitic worm stage A trypomastigote stage of Trypanosoma species which are nondividing forms resistant to mammalian complement that have the capacity to infect mammalian cells. Chris Stoeckert Jie Zheng Priti Parikh metacyclic trypomastigote stage A life cycle stage where a cell differentiates into male or female sexual forms. Chris Stoeckert Jie Zheng Priti Parikh gametocyte stage A parasite lifecycle stage of Trypanosomatids. In this stage, the flagellum is found anterior of nucleus and flagellum not attached to the cell body. The kinetoplast is located in front of the nucleus, near the anterior end of the body. (Wikipedia: Trypanosomatid) Chris Stoeckert Jie Zheng Priti Parikh promastigote stage A parasite lifecycle stage of some sporozoans where cells divide through sporogony producing daughter cells called sporozoites that infect new hosts. Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarS.htm sporozoite stage A parasite lifecycle stage of some sporozoans where motile and elongated zygote is formed by the fertilization of the macrogamete during the sexual reproductive phase of the sporozoan life cycle, specifically the malarial parasite Plasmodium. Chris Stoeckert Jie Zheng Priti Parikh Mosby's Medical Dictionary, 8th edition. � 2009, Elsevier. (http://medical-dictionary.thefreedictionary.com/ookinete) ookinete stage A salivary gland that is a part of or originated from a tsetse fly of genus Glossina. Priti Parikh Glossina salivary gland Plasmodium falciparum is a protozoan parasite, one of the species of Plasmodium that cause malignant malaria in humans. It is transmitted by the female Anopheles mosquito. Replaced by NCBITaxon term. Definition and axioms were added by OPL developers. P. falciparum Wikipedia: Plasmodium falciparum obsolete_Plasmodium falciparum true A lifecycle stage of Schistosoma japonicum. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum lifecycle stage Schistosoma japonicum lifecycle stage An amastigote stage in the lifecycle of Leishmania major that occurs in mammalian hosts. Chris Stoeckert Jie Zheng Priti Parikh L. major amastigote stage Leishmania major amastigote stage A schizont stage in the Plasmodium falciparum lifecycle that occurs in erythrocytes or in hepatocytes. updated according to OPL terms Plasmodium final excel file from C. Janse, S. Khan C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum schizont stage Plasmodium falciparum schizont stage A 3 days schistosomulum stage of Schistosoma japonicum that occurs in the definitive host 3 days post-infection. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum 3 day schistosomulum stage Schistosoma japonicum 3 day schistosomulum stage A Leishmania major promastigote that is found in the alimentary tract of an insect vector. It is non-infective to its mammalian host. Chris Stoeckert Jie Zheng Priti Parikh L. major procyclic promastigote PMID:11748963 Leishmania major procyclic promastigote A Plasmodium falciparum zygote is formed after fertilisation of the macrogamete by a microgamete in the midgut of the mosquito vector. This round form is the only diploid stage in the Plasmodium falciparum life cycle. C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum zygote Wikipedia: Plasmodium falciparum biology Plasmodium falciparum zygote A Plasmodium falciparum microgametocyte that is matured with flagellated motile microgametes still attached to its central body. Exflagellated microgametocyte of Plasmodium falciparum is found in the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Matt Berriman Priti Parikh P. falciparum exflagellated microgametocyte Plasmodium falciparum exflagellated microgametocyte A daughter sporocyst stage in the lifecycle of Schistosoma haematobium that occurs within the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium daughter sporocyst stage Schistosoma haematobium daughter sporocyst stage A Trypanosoma cruzi that is found in the bloodstream of infected mammals. It is a non-dividing form that is infectious for its insect vector. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi trypomastigote http://dna.kdna.ucla.edu/parasite_course-old/cruzi_files/intro.htm Trypanosoma cruzi trypomastigote A lifecycle stage of Plasmodium falciparum. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum lifecycle stage Plasmodium falciparum lifecycle stage A Schistosoma haematobium that is an elongated sac and develops from the miracidium within the snail indermediate host, and that either produces more sporocysts or develops into cercariae. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium sporocyst Schistosoma haematobium sporocyst A Plasmodium falciparum gamete that is a matured form of the macrogametocyte and is found in the midgut of a mosquito vector. The macrogamete is fertilized by the microgamete, forming the zygote Chris Stoeckert Jie Zheng P. falciparum macrogamete Plasmodium falciparum macrogamete A Schistosoma mansoni in a parasitic larval form that develops in a freshwater snail and is released into the water. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni cercaria Schistosoma mansoni cercaria A trypomastigote stage in the Trypanosoma cruzi lifecycle that occurs either in the vertebrate host or an insect vector. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi trypomastigote stage Trypanosoma cruzi trypomastigote stage A microgamete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum microgamete stage Plasmodium falciparum microgamete stage A parasite role which is realized only during parasitic infection of a human. previous def was not about a role. Priti Parikh, Chris Stoeckert human parasite role A schistosomulum stage that occurs in 24 hours after infection of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh PMID:19885392 24 hour schistosomulum stage A parasite lifecycle stage of some Plasmodium sp., such as Plasmodium vivax and Plasmodium ovale, the parasite in the liver cells do not achieve matuaration to a schizont immediately, but remain in a dormant form. This dormant form stage is called hypnozoite stage. Chris Stoeckert Jie Zheng Priti Parikh Wikipedia: Plasmodium hypnozoite stage A Plasmodium falciparum gamete that is a matured form of exflagellated microgametocyte and found in the midgut of a mosquito vector. The microgamete fertilizes the macrogamete, forming the zygote. Chris Stoeckert Jie Zheng P. falciparum microgamete Plasmodium falciparum microgamete A trypomastigote stage in the Trypanosoma brucei lifecycle that occurs in the vertebrate host. Chris Stoeckert Jie Zheng Priti Parikh T. brucei trypomastigote stage Trypanosoma brucei trypomastigote stage A ureter that is a part of or originated from a human (Homo sapiens). Priti Parikh human ureter FMA:9704 Homo sapiens ureter A lifecycle stage of Schistosoma haematobium. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium lifecycle stage Schistosoma haematobium lifecycle stage A Schistosoma haematobium in a migratory larval form that is found within blood vessels of the definitive host, mammal, and develops into the flatworm. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium schistosomulum Schistosoma haematobium schistosomulum A Schistosoma japonicum in a free-living motile form that is covered with cilia, and develops in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum miracidium Schistosoma japonicum miracidium A life cycle stage of some parasites in which a non-operculate egg emerges from the adult female worm. Chris Stoeckert Jie Zheng Priti Parikh http://www.path.cam.ac.uk/~schisto/schistosoma/schisto_lifecycle_egg.html egg stage A life cycle stage of a parasite. Chris Stoeckert Jie Zheng Priti Parikh parasite lifecycle stage A Trypanosoma brucei that is a Trypomastigote form of Trypanosoma brucei. In this form the large kinetoplast is postnuclear and is at the most posterior part of the body and the flagellum emerges from the flagellar pocket, and runs along the entire length of the body as an undulating membrane. Chris Stoeckert Jie Zheng Priti Parikh T. brucei trypomastigote http://dna.kdna.ucla.edu/parasite_course-old/african%20tryps%20new_files/contents1.htm Trypanosoma brucei trypomastigote A parasitic worm stage of development 3 weeks post differentiation into a worm form. Chris Stoeckert Jie Zheng Priti Parikh PMID:19885392 3 week parasitic worm stage A mother sporocyst stage in the Schistosoma japonicum lifecycle that occurs in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum mother sporocyst stage Schistosoma japonicum mother sporocyst stage A lifecycle stage of Trypanosoma cruzi. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi lifecycle stage Trypanosoma cruzi lifecycle stage A sporocyst stage in the Schistosoma japonicum lifecycle that is found within the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum sporocyst stage Schistosoma japonicum sporocyst stage An ookinete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector and on the outside of the midgut. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum ookinete stage Plasmodium falciparum ookinete stage Bloodstream trypomastigote stage in the lifecycle of Trypanosoma brucei. Priti Parikh T. brucei bloodstream trypomastigote stage obsolete_Trypanosoma brucei bloodstream trypomastigote stage true A promastigote stage in the Leishmania major lifecycle. Chris Stoeckert Jie Zheng Priti Parikh L. major promastigote stage Leishmania major promastigote stage A Plasmodium falciparum schizont that is found in infected hepatocytes (i.e., liver cells) of a human host. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum hepatic schizont Plasmodium falciparum hepatic schizont A Schistosoma mansoni sporocyst that develops into cercariae. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni daughter sporocyst Schistosoma mansoni daughter sporocyst A gametocyte stage in the lifecycle of Plasmodium falciparum. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum gametocyte stage Plasmodium falciparum gametocyte stage A 3 hours schistosomulum stage of Schistosoma japonicum that occurs in the definitive host 3 hours post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. japonicum 3 hour schistosomulum stage Schistosoma japonicum 3 hour schistosomulum stage A midgut that is a part of or originated from a sand fly of genus Phlebotominae. Priti Parikh Phlebotominae midgut A 24 hours schistosomulum stage of Schistosoma japonicum that occurs in the definitive host 24 hours post-infection. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum 24 hour schistosomulum stage Schistosoma japonicum 24 hour schistosomulum stage A Schistosoma mansoni sporocyst that produces more sporocysts. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni mother sporocyst Schistosoma mansoni mother sporocyst A schistosomulum stage of Schistosoma haematobium that occurs in the definitive host and is followed by the parasitic worm stage. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium schistosomulum stage Schistosoma haematobium schistosomulum stage A Schistosoma haematobium adult worm is a fully developed mature male form of Schistosoma haematobium and capable of sexual reproduction, which lives in the pelvic blood vessels of the vesicle plexis of the mammal host and has 4-5 testes. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium adult male worm http://www.path.cam.ac.uk/~schisto/schistosoma/schisto_lifecycle_egg.html Schistosoma haematobium adult male worm A zygote stage in the Plasmodium falciparum lifecycle that occurs in the midgut of the mosquito vector where a microgamete and a macrogamete fertilizes each other to produce a diploid cell. Chris Stoeckert Jie Zheng Priti Parikh P. falciparum zygote stage Wikipedia: Plasmodium falciparum biology Plasmodium falciparum zygote stage A Schistosoma haematobium in an egg form that is laid by the female adult worm and released into the host gut where they leave the host in the faeces. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium egg Schistosoma haematobium egg A Schistosoma haematobium schistosomulum in a migratory larval form that is found within blood vessels of mammal, as definitive host, 6 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 6 day schistosomulum Schistosoma haematobium 6 day schistosomulum A worm stage of Schistosoma haematobium that is found in the pelvic blood vessels of the vesicle plexis of the definitive host 3 weeks after infection. Chris Stoeckert Jie Zheng Priti Parikh S. haematobium 3 week worm stage Schistosoma haematobium 3 week worm stage A lifecycle stage of Schistosoma mansoni. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni lifecycle stage Schistosoma mansoni lifecycle stage A Leishmania major that is the intracellular, non-motile form of the parasite found in the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh L. major amastigote http://dna.kdna.ucla.edu/parasite_course-old/leish_files/introduction1.htm Leishmania major amastigote A Schistosoma haematobium schistosomulum in a migratory larval form that is found within blood vessels of mammal, as definitive host, 3 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium 3 day schistosomulum Schistosoma haematobium 3 day schistosomulum A Plasmodium falciparum gametocyte that is a female gametocyte and found either in bloodstream of a human host or midgut of mosquito vector. The macrogametocyte is a precursor of the macrogamete. C. Janse C. Stoeckert J. Zheng P. Parkh S. Khan P. falciparum macrogametocyte Plasmodium falciparum macrogametocyte An erythrocytic trophozoite stage in the Plasmodium falciparum life cycle that occurs in erythrocytes of a human host. C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum erythrocytic trophozoite stage Plasmodium falciparum erythrocytic trophozoite stage A Schistosoma mansoni in a free-living motile form that is covered with cilia and develops in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni miracidium Schistosoma mansoni miracidium A parasite lifecycle stage of Leishmania major. Chris Stoeckert Jie Zheng Priti Parikh L. major lifecycle stage Leishmania major lifecycle stage A cercaria stage in the lifecycle of Schistosoma mansoni that occurs in a freshwater snail and in fresh water. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni cercaria stage Schistosoma mansoni cercaria stage A worm stage of Schistosoma mansoni that is fully developed mature form and found in the small inferior mesenteric blood vessels surrounding the large intestine of the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni worm stage Schistosoma mansoni worm stage A mother sporocyst stage in the Schistosoma haematobium lifecycle that occurs in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium mother sporocyst stage Schistosoma haematobium mother sporocyst stage The vesical plexus envelops the lower part of the bladder and the base of the prostate and communicates with the pudendal and prostatic plexuses. Priti Parikh Wikipedia - Vesical venus plexus vesical venus plexus A sporocyst stage of Digenea formed after penetration of the miracidium into a mollusc; it lacks a gut and gives rise asexually to daughter sporocysts or rediae. Chris Stoeckert Jie Zheng Priti Parikh http://www.biology.ualberta.ca/parasites/parpub/text/text/glossarM.htm mother sporocyst stage A midgut that is a part of or originated from a tsetse fly of genus Glossina. Priti Parikh Glossina midgut An epimastigote stage in the lifecycle of Trypanosoma brucei. Chris Stoeckert Jie Zheng Priti Parikh T. brucei epimastigote stage Trypanosoma brucei epimastigote stage A 7 week worm stage of Schistosoma mansoni that is the mature stage of Schistosoma mansoni and found in the small inferior mesenteric blood vessels surrounding the large intestine of the definitive host 7 weeks after weeks after infection. Chris Stoeckert Jie Zheng Priti Parikh S. mansoni 7 week worm stage Schistosoma mansoni 7 week worm stage A Schistosoma mansoni schistosomulum in a migratory larval formi that is found within blood vessels of the definitive host, mammal, 6 days post-infection. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni 6day schistosomulum Schistosoma mansoni 6 day schistosomulum A urinary bladder that is a part of or originated from a human (Homo sapiens). Priti Parikh human bladder human urinary bladder FMA:15900 Homo sapiens urinary bladder A daughter sporocyst stage of Schistosoma mansoni that occurs in the snail intermediate host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni daughter sporocyst stage Schistosoma mansoni daughter sporocyst stage A schistosomulum stage that occurs in 3 days after infection of the mammalian host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng PMID:19885392 3 day schistosomulum stage A Plasmodium falciparum erythrocytic trophozoite that is found in erythrocytes. It is a young trophozoite stage that has a typical 'ring-like' appearance. Ring-form trophozoites of Plasmodium falciparum are often thin and delicate, measuring on average 1/5 the diameter of the red blood cell. C. Janse Chris Stoeckert Jie Zheng P. Parkh S. Khan P. falciparum erythrocytic ring trophozoite http://www.dpd.cdc.gov/dpdx/html/frames/m-r/malaria/falciparum/body_malariadffalcring.htm Plasmodium falciparum erythrocytic ring trophozoite An epimastigote stage in the lifecycle of Trypanosoma cruzi. Chris Stoeckert Jie Zheng Priti Parikh T. cruzi epimastigote stage Trypanosoma cruzi epimastigote stage An adult female worm stage of Schistosoma japonicum that is fully developed mature female stage of Schistosoma japonicum and occurs in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum adult female worm stage Schistosoma japonicum adult female worm stage An adult male worm stage of Schistosoma japonicum that is fully developed mature male stage of Schistosoma japonicum and occurs in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum adult male worm stage Schistosoma japonicum adult male worm stage A Schistosoma japonicum worm is a fully developed mature form of Schistosoma japonicum and capable of sexual reproduction, which lives in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammal host. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum adult worm Schistosoma japonicum adult worm A Schistosoma mansoni worm is the fully developed mature form of Schistosoma mansoni and capable of sexual reproduction, which lives in the small inferior mesenteric blood vessels surrounding the large intestine of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni adult worm Schistosoma mansoni adult worm An adult male worm stage of Schistosoma haematobium that is fully developed mature male stage of Schistosoma haematobium and found in the pelvic blood vessels of the vesicle plexis of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh S. haematobium adult male worm stage Schistosoma haematobium adult male worm stage A Schistosoma japonicum adult worm is a fully developed mature male form of Schistosoma japonicum and capable of sexual reproduction, which lives in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammal host and has 4-5 testes. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum adult male worm Schistosoma japonicum adult male worm An adult male worm stage of Schistosoma mansoni that is fully developed mature male stage of Schistosoma mansoni and found in the small inferior mesenteric blood vessels surrounding the large intestine of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh S. mansoni adult male worm stage Schistosoma mansoni adult male worm stage A Schistosoma mansoni adult worm is the fully developed mature female form of Schistosoma mansoni and capable of sexual reproduction, which lives within the gynacophoric canal of the adult male worm in the small inferior mesenteric blood vessels surrounding the large intestine of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni adult female worm Schistosoma mansoni adult female worm An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. Priti Parikh, Jie Zheng http://www.merriam-webster.com/dictionary/parasite?show=0&t=1310398415 parasite organism A Schistosoma haematobium worm is a fully developed mature form of Schistosoma haematobium and capable of sexual reproduction, which lives in the pelvic blood vessels of the vesicle plexis of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium adult worm Schistosoma haematobium adult worm An adult female worm stage of Schistosoma haematobium that is fully developed mature female stage of Schistosoma haematobium and found in the pelvic blood vessels of the vesicle plexis of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh S. haematobium adult female worm stage Schistosoma haematobium adult female worm stage A Schistosoma haematobium adult worm is a fully developed mature female form of Schistosoma haematobium and capable of sexual reproduction, which lives within the gynacophoric canal of the adult male worm in the pelvic blood vessels of the vesicle plexis of the mammal host. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. haematobium adult female worm Schistosoma haematobium adult female worm An adult female worm stage of Schistosoma mansoni that is fully developed mature female stage of Schistosoma mansoni and found in the small inferior mesenteric blood vessels surrounding the large intestine of the mammalian host. Chris Stoeckert Jie Zheng Priti Parikh S. mansoni adult female worm stage Schistosoma mansoni adult female worm stage A parasitic worm stage where the worm is matured and ready to pair up with another adult worm of the opposite gender, and reproduce. Chris Stoeckert Jie Zheng Priti Parikh http://www.path.cam.ac.uk/~schisto/schistosoma/schisto_lifecycle_egg.html adult parasitic worm stage A Schistosoma japonicum adult worm is a fully developed mature female form of Schistosoma japonicum and capable of sexual reproduction, which lives within the gynacophoric canal of the adult male worm in the small superior mesenteric blood vessels associated with the ileo-caecal area of the intestine of the mammal host. Chris Stoeckert Jie Zheng Priti Parikh S. japonicum adult female worm Schistosoma japonicum adult female worm An adult worm stage of a male parasitic worm. Chris Stoeckert Jie Zheng Priti Parikh http://www.path.cam.ac.uk/~schisto/schistosoma/schisto_lifecycle_egg.html adult male parasitic worm stage A Schistosoma mansoni adult worm is the fully developed mature male form of Schistosoma mansoni and capable of sexual reproduction, which lives in the small inferior mesenteric blood vessels surrounding the large intestine of the mammal host and has 4-5 testes. Anna Protasio Chris Stoeckert Flora Logan Jie Zheng S. mansoni adult male worm Schistosoma mansoni adult male worm A Plasmodium falciparum merozoite that is produced in a hepatic schizont and released into the bloodstream of a human host. These forms invade erythrocytes. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum hepatic merozoite Plasmodium falciparum hepatic merozoite A Plasmodium falciparum merozoite that is produced in an erythrocytic schizont and released into the bloodstream of a human host. These forms invade erythrocytes. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum erythrocytic merozoite Plasmodium falciparum erythrocytic merozoite A trophozoite stage in some protozoan parasite life cycle that occurs in erythrocytes. definition adapted from that for P. falciparum erythrocytic trophozoite stage and parent trophozoite stage C. Stoeckert erythrocytic trophozoite stage A Plasmodium falciparum trophozoite that is found in erythrocytes. It is a feeding stage with a single nucleus. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum erythrocytic trophozoite Plasmodium falciparum erythrocytic trophozoite An erythrocytic merozoite stage in the Plasmodium falciparum lifecycle that occurs in the bloodstream of a human host. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum erythrocytic merozoite stage Plasmodium falciparum erythrocytic merozoite stage A hepatic merozoite stage in the Plasmodium falciparum lifecycle that occurs in the hepatocyte of a human host. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum hepatic merozoite stage Plasmodium falciparum hepatic merozoite stage A merozoite stage in the Plasmodium lifecycle that occurs in the hepatocyte of a vertebrate host. definition adapted from that for P. falciparum hepatic merozoite stage C. Stoeckert Chris Stoeckert Jie Zheng hepatic merozoite stage A merozoite stage in the apicomplexan lifecycle that occurrs in the bloodstream of a vertebrate host. definition adapted from that for P. falciparum salivary erythrocytic merozoite stage and from the general merozoite definition C. Stoeckert Chris Stoeckert Jie Zheng erythrocytic merozoite stage A Plasmodium falciparum that is located either in the bloodstream of the human host or midgut of mosquito vector. Gametocytes are the precursor cells of the macro- or micro-gametes. C. Janse C. Stoeckert Chris Stoeckert Jie Zheng K. Louis S Khan Plasmodium falciparum gametocyte A hepatic trophozoite stage in the Plasmodium falciparum life cycle that occurs in hepatocytes of a human host. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum hepatic trophozoite stage Plasmodium falciparum hepatic trophozoite stage A trophozoite stage in the Plasmodium falciparum lifecycle that occurs in a human host. Chris Stoeckert Jie Zheng P. falciparum trophozoite stage Plasmodium falciparum trophozoite stage A sporozoite stage in the Plasmodium falciparum lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the human host. C. Janse Chris Stoeckert Jie Zheng S. Khan Plasmodium falciparum oocyst-derived sporozoite stage A sporozoite stage in the Plasmodium lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the vertebrate host. definition adapted from that for P. falciparum salivary gland derived sporozoite stage Chris Stoeckert salivary gland-derived sporozoite stage A salivary gland-derived sporozoite stage in the Plasmodium falciparum lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the human host. C. Janse Chris Stoeckert Jie Zheng S. Khan Plasmodium falciparum salivary gland-derived sporozoite stage A Plasmodium falciparum sporozoite that is formed in the oocyst. It migrates to and resides in the salivary glands of the mosquito vector. Sporozoites invade hepatocytes in a human host. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum salivary gland-derived sporozoite Plasmodium falciparum salivary gland-derived sporozoite A sporozoite stage in some parasite lifecycle that occurs in the hemocoel and the salivary glands of the mosquito. Sporozoites invade hepatocytes in the vertebrate host. definition adapted from that for P. falciparum oocyte derived sporozoite stage Chris Stoeckert oocyst-derived sporozoite stage A Plasmodium falciparum trophozoite that is found in hepatocytes of a human host. It is a feeding stage with a single nucleus C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum hepatic trophozoite Plasmodium falciparum hepatic trophozoite A Plasmodium falciparum that is found in midgut of mosquito vector. There are two forms of gametes: micro- and macrogametocytes. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum gamete Plasmodium falciparum gamete A Plasmodium falciparum sporozoite that is found in the infected hepatocytes of a human host. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum oocyst-derived sporozoite Plasmodium falciparum oocyst-derived sporozoite A life cycle stage of some parasites that develop into mature sexual cells. Jie Zheng gamete stage A trophozoite stage in some protozoan parasite life cycle that occurs in hepatocytes. definition adapted from that for P. falciparum hepatic trophozoite stage and from parent trophozoite stage Chris Stoeckert hepatic trophozoite stage A gamete stage in the Plasmodium falciparum lifecycle that occurs in the midgut of a mosquito vector. C. Janse Chris Stoeckert Jie Zheng S. Khan P. falciparum gamete stage Plasmodium falciparum gamete stage A parasite lifecycle stage that occurs as a result of asexual replication in the red blood cells of the host organism. For Plasmodium species these stages can include merozoites, trophozoites, and schizonts. Chris Stoeckert asexual blood stage EuPathDB asexual lifecycle in host red blood cell stage A Plasmodium that is found in the midgut of a mosquito vector during gamete lifecycle stage. There are two forms of gametes: micro- and macrogametocytes. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium gamete A Plasmodium gamete that is in a matured form of the macrogametocyte and found in the midgut of a mosquito vector. The macrogamete is fertilized by the microgamete, forming the zygote. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium macrogamete A Plasmodium gamete that is in a matured form of exflagellated microgametocyte and found in the midgut of a mosquito vector. The microgamete fertilises the macrogamete, forming the zygote. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium microgamete A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium gametocyte A Plasmodium gametocyte that is a female gametocyte of Plasmodium and found either in the bloodstream of the vertebrate host or midgut of mosquito vector. The macrogametocyte is a precursor of the macrogamete. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium macrogametocyte A Plasmodium gametocyte that is a male gametocyte of Plasmodium and found either in the bloodstream of a vertebrate host or midgut of a mosquito vector. The microgametocyte is a precursor cell of the microgamete Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium microgametocyte A Plasmodium that is during merozoite lifecycle stage, occurs in the bloodstream of a vertebrate host. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium merozoite A Plasmodium merozoite that is produced in an erythrocytic schizont and released into the bloodstream of a vertebrate host. These forms invade erythrocytes. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium erythrocytic merozoite A Plasmodium merozoite that is produced in a hepatic schizont and released into the bloodstream of a vertebrate host. These forms invade erythrocytes. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium hepatic merozoite A Plasmodium that is formed after traversal of the midgut wall by the ookinete stage, on the hemocoel side of the midgut wall of the mosquito vector. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium oocyst A Plasmodium that is a 'banana-shaped' form originates from the round zygote. The ookinete is found in the midgut of a mosquito vector and traverses the midgut wall of a mosquito vector. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium ookinete A Plasmodium that is a form divides through schizogony. Depending on its location, it is either called hepatic or erythrocytic schizont. The schizont is a dividing stage with 2 or more nuclei. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium schizont A Plasmodium schizont that is found in infected erythrocytes of a vertebrate host. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium erythrocytic schizont A Plasmodium schizont that is found in infected hepatocytes (i.e. liver cells) of a vertebrate host. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium hepatic schizont A Plasmodium that is formed in the oocyst and migrates to and reside in the salivary glands of the mosquito vector. A distinction is made between oocyst-derived and salivary gland-derived sporozoites. Sporozoites invade hepatocytes in the vertebrate host. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium sporozoite A Plasmodium sporozoite that is found in the infected hepatocytes of a vertebrate host. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium oocyst-derived sporozoite A Plasmodium sporozoite that is found in the salivary glands of the mosquito vector. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium salivary gland-derived sporozoite A Plasmodium that is a feeding form which has a single nucleus during the trophozoite stage. Depending on its location, it is either called hepatic or erythrocytic trophozoite. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium trophozoite A Plasmodium trophozoite that is found in erythrocytes of a vertebrate host. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium erythrocytic trophozoite A Plasmodium erythrocytic trophozoite that has a typical 'ring-like' appearance. Ring-form trophozoites of Plasmodium are often thin and delicate, measuring on average 1/5 the diameter of the red blood cell. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium erythrocytic ring trophozoite A Plasmodium trophozoite that is found in hepatocytes. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium hepatic trophozoite A Plasmodium that is formed after fertilization of the macrogamete by a microgamete in the midgut of the mosquito vector. This round form is the only diploid stage in the Plasmodium life cycle. Chris Stoeckert Jie Zheng Ulrike Boehme https://github.com/OPL-ontology/OPL/issues/2 GeneDB Plasmodium zygote A gamete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Plasmodium gamete stage A macrogamete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Plasmodium macrogamete stage A microgamete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Plasmodium microgamete stage A gametocyte stage in the lifecycle of Plasmodium. Chris Stoeckert Jie Zheng Plasmodium gametocyte stage A macrogametocyte stage in the Plasmodium lifecycle that occurs either in the bloodstream of a vertebrate host or the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Plasmodium macrogametocyte stage A microgametocyte stage in the Plasmodium lifecycle that occurs either in the bloodstream of a vertebrate host or the midgut of a mosquito vector. Chris Stoeckert Jie Zheng Plasmodium microgametocyte stage A merozoite stage in the Plasmodium lifecycle that occurs in the bloodstream or hepatocytes of a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium merozoite stage An erythrocytic merozoite stage in the Plasmodium lifecycle that occurs in the bloodstream of a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium erythrocytic merozoite stage A hepatic merozoite stage in the Plasmodium lifecycle that occurs in the hepatocyte of a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium hepatic merozoite stage An oocyst stage in the Plasmodium lifecycle that occurs on the hemocoel side of the midgut of a mosquito vector. During this stage Plasmodium ookinete invades and escapes midgut wall of mosquito and embed itself onto the exterior of the gut membrane and develop encysted zygote, called oocyst. Chris Stoeckert Jie Zheng Plasmodium oocyst stage An ookinete stage in the Plasmodium lifecycle that occurs in the midgut of a mosquito vector and on the outside of the midgut. Chris Stoeckert Jie Zheng Plasmodium ookinete stage A schizont stage in the Plasmodium lifecycle that occurs in erythrocytes or in hepatocytes. Chris Stoeckert Jie Zheng Plasmodium schizont stage An erythrocytic schizont stage in the Plasmodium lifecycle that occurs in the infected erythrocytes of a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium erythrocytic schizont stage A hepatic schizont stage in the Plasmodium lifecycle that occurs in the infected hepatocytes of a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium hepatic schizont stage A sporozoite stage in the Plasmodium lifecycle that occurs in the salivary glands of the mosquito and invades hepatocytes in the vertebrate host. Chris Stoeckert Jie Zheng Plasmodium sporozoite stage A sporozoite stage in the Plasmodium lifecycle that develops in oocysts of the mosquito midgut. Chris Stoeckert Jie Zheng Omar harb Plasmodium oocyst-derived sporozoite stage A salivary gland-derived sporozoite stage in the Plasmodium lifecycle that occurs in the salivary glands of the mosquito and invades hepatocytes in the vertebrate host. Chris Stoeckert Jie Zheng Omar harb Plasmodium salivary gland-derived sporozoite stage A trophozoite stage in the Plasmodium lifecycle that occurs in a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium trophozoite stage An erythrocytic trophozoite stage in the Plasmodium life cycle that occurs in erythrocytes of a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium erythrocytic trophozoite stage An erythrocytic ring trophozoite stage in the Plasmodium life cycle that occurs in erythrocytes of a vertebrate host. During this stage some Plasmodium merozoites undergo asexual reproduction cycle in erythrocytes and form young trophozoites that are referred to as "ring form" due to their morphology. Chris Stoeckert Jie Zheng Plasmodium erythrocytic ring trophozoite stage A hepatic trophozoite stage in the Plasmodium life cycle that occurs in hepatocytes of a vertebrate host. Chris Stoeckert Jie Zheng Plasmodium hepatic trophozoite stage A zygote stage in the Plasmodium lifecycle that occurs in the midgut of the mosquito vector where a microgamete and a macrogamete fertilizes each other to produce a diploid cell. Chris Stoeckert Jie Zheng Plasmodium zygote stage An adult worm stage in the Schistosoma haematobium lifecycle. Chris Stoeckert Jie Zheng Schistosoma haematobium adult worm stage An adult worm stage in the Schistosoma japonicum lifecycle. Chris Stoeckert Jie Zheng Schistosoma japonicum adult worm stage Blood that is part of or originated from a vertebrate. Jie Zheng OPL Vertebrate blood An erythrocyte that is a part of or originated from a vertebrate. Jie Zheng OPL Vertebrate erythrocyte A hepatocyte that is a part of or originated from a vertebrate. Jie Zheng OPL Vertebrate hepatocyte Cerebrospinal fluid that is a part of or originated from a mammal. Jie Zheng Mammalia cerebrospinal fluid A skin that is a part of or originated from a mammalian body. Jie Zheng Mammalia skin A liver that is a part of or originated from a mammal (Mammalia). Jie Zheng Mammalia liver A lung that is a part of or originated from a mammal (Mammalia). Jie Zheng Mammalia lung A mesenteric vein that is a part of or originated from a mammal (Mammalia). Jie Zheng Mammalia mesenteric vein An intestine that is a part of or originated from a mammal (Mammalia). Jie Zheng Mammalia intestine An adult worm stage in the Schistosoma mansoni lifecycle. Chris Stoeckert Jie Zheng Schistosoma mansoni adult worm stage Blood that is part of or originated from a mammalia. Jie Zheng Mammalia blood A macrophage that is a part of or originated from a mammalia. Jie Zheng Mammalia macrophage A parasite lifecycle stage of trypanosomatidae in which the organism is infectious and does not multiply. Chris Stoeckert Jie Zheng metacyclic stage https://microbewiki.kenyon.edu/index.php/Trypanosome_Life_Cycle https://web.stanford.edu/group/parasites/ParaSites2003/Leishmania/Leish%20Biology.html https://github.com/OPL-ontology/OPL/issues/9 Trypanosomatida metacyclic stage A parasite lifecycle stage of trypanosomatidae in which the organism is in dividing form and it occurs in fly vector. Achchuthan Shanmugasundram Chris Stoeckert Jie Zheng procyclic stage VEuPathDB https://github.com/OPL-ontology/OPL/issues/10 Trypanosomatida procyclic stage Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 BTO:0001409 CALOHA:TS-1084 EFO:0000930 EHDAA2:0002139 EHDAA:9341 EMAPA:17950 EV:0100097 FMA:9704 GAID:438 MA:0000378 MAT:0000120 MESH:D014513 MIAA:0000120 NCIT:C12416 OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA UMLS:C0041951 VHOG:0000605 XAO:0000144 galen:Ureter uberon metanephric duct UBERON:0000056 ureter Urinary:system.svg A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 NCIT:C12601 PdumDv:0000100 VHOG:0000745 XAO:1000001 ZFS:0000001 1-cell stage fertilized egg stage one cell stage uberon fertilized egg stage one-cell stage zygote zygotum UBERON:0000106 zygote stage Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. This class is probably too inclusive Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] intestinal In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:A03.492.411 MIAA:0000043 NCIT:C12736 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 galen:Intestine bowel uberon intestinal tract UBERON:0000160 intestine A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA TAO:0000007 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood saliva-secreting exocrine glands of the oral cavity[GO] currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands BTO:0001203 CALOHA:TS-0892 EFO:0000859 EHDAA2:0001775 EHDAA:7987 EMAPA:17751 EV:0100059 FBbt:00005382 FMA:9597 GAID:937 MA:0000346 MAT:0000079 MESH:D012469 MIAA:0000079 NCIT:C12426 OpenCyc:Mx4rvVjl5ZwpEbGdrcN5Y29ycA UMLS:C0036098 VHOG:0000376 galen:SalivaryGland salivary gland uberon glandulae salivariae UBERON:0001044 saliva-secreting gland http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 TGMA:0001036 UMLS:C0231052 VHOG:0000290 XAO:0000103 uberon mesenteron UBERON:0001045 midgut http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class the caudal portion of the primitive digestive tube of the embryo The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 TGMA:0001020 UMLS:C0231053 VHOG:0000459 XAO:0000104 uberon metenteron UBERON:0001046 hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] vesical The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] bladder AAO:0000623 BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 MA:0000380 MAT:0000122 MESH:A05.810.161 MIAA:0000122 NCIT:C12414 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA UMLS:C0005682 VHOG:0000740 XAO:0000154 galen:UrinaryBladder vesica urinaria uberon urocyst vesica UBERON:0001255 urinary bladder Urinary:system.svg A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6] Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] EHDAA2 models this as developing from CP, which is wrong the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. BIRNLEX:1798 BTO:0000237 CALOHA:TS-0130 EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 MA:0002503 MAT:0000499 MESH:A12.207.268 NCIT:C12692 TAO:0002184 UMLS:C0007806 VHOG:0001278 ZFA:0001626 CSF cerebral spinal fluid uberon liquor cerebrospinalis spinal fluid UBERON:0001359 cerebrospinal fluid Respiration organ that develops as an outpocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung https://github.com/obophenotype/uberon/issues/701 The organ covering the body that consists of the dermis and epidermis. consider 'integumentary system' for invertebrates MA uses the term skin to refer to what is called here: zone of skin BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA UMLS:C1123023 XAO:0000023 galen:Skin entire skin skin organ uberon entire integument integument integumental organ pelt skin UBERON:0002097 skin of body http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Organ which secretes bile and participates in formation of certain blood proteins.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] hepatic An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. AAO:0010111 BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 NCIT:C12392 OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA TAO:0000123 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 galen:Liver uberon iecur jecur UBERON:0002107 liver Leber:Schaf.jpg A vein that returns blood from the intestines. In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein BTO:0002781 EHDAA:4442 EMAPA:17348 MA:0002177 MESH:D008642 NCIT:C53055 RETIRED_EHDAA2:0001125 UMLS:C0025473 uberon intestinal vein UBERON:0005617 mesenteric vein DbXref Definition Obsolete Class Obsolete Class Subset Synonym SynonymType 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