http://dx.doi.org/10.1186/2041-1480-4-30 http://orcid.org/0000-0002-1373-1705 http://orcid.org/0000-0002-7073-9172 https://orcid.org/0000-0001-5948-3092 https://orcid.org/0000-0002-0027-0858 An ontology for the description of Drosophila melanogaster phenotypes. Drosophila Phenotype Ontology (DPO) https://creativecommons.org/licenses/by/3.0/ 27:11:2019 11:30 FlyBase miscellaneous CV 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 class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage 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 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> IAO:0000116 uberon editor_note true editor_note editor note 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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=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 IAO:0000232 uberon curator_notes true curator_notes curator note curator notes imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from 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 expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO Foundry Uniquename OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation 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) 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 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 defined by inverse logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall Chris Mungall is direct form of If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). RO:0002604 quality is_opposite_of true true is_opposite_of is opposite of is_opposite_of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for 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 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. camcur CARO2 core class CARO2 plus class Manually annotated by ChEBI Team EmbDevSlim terms for FlyBase glossary page cur warning of impending obsoletion MGI ribbon terms Stanza contains hidden assertion. larval olfactory system BrainName official abbreviation BRAND NAME EmbDevSlim FORMULA FlyTed temp subset for edit tracking purposes Testis slim INN IUPAC NAME InChI InChIKey terms for rd test ontology SMILES Abnormal/normal slim Absent/present slim Attribute slim camcur cell_quality cur warning of impending obsoletion do not annotate fbcvsubset_mgiribbons larval olfactory system lethal phase terms Relational slim: types of quality that require an additional entity in order to exist Systematic synonym Value slim Term not to be used for direct annotation Term not to be used for direct manual annotation AGR slim Aspergillus GO slim Candida GO slim ChEMBL protein targets summary FlyBase Drosophila GO ribbon slim Generic GO slim Metagenomics GO slim Mouse GO slim PIR GO slim Plant GO slim Fission yeast GO slim Yeast GO slim oio:hasRelatedSynonym blast name oio:hasExactSynonym common name oio:hasExactSynonym equivalent name oio:hasExactSynonym genbank common name A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored has_rank oio:hasRelatedSynonym misspelling oio:hasExactSynonym scientific name oio:hasRelatedSynonym synonym Abnormal/normal slim Absent/present slim Attribute slim cell_quality Disposition slim Human phenotype slim Pathology slim Relational slim: types of quality that require an additional entity in order to exist Scalar slim Value slim Label appended to organism-specific terms in place of scientific name Unique short label for PRO terms for display purposes; based on orthology eco subset abstract upper-level terms not directly useful for analysis abstract upper-level terms not directly useful for analysis uberon dc-creator true dc-creator creator uberon dc-description true dc-description description uberon dc-source true dc-source derived from resource subset_property synonym_type_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope has_synonym_type in_subset in_subset shorthand uberon foaf-page true foaf-page page 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 BFO:0000050 OBO_REL:part_of part_of external protein quality relationship uberon part_of part_of part 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) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. 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 BFO:0000051 OBO_REL:has_part chebi_ontology external protein quality relationship uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by djs93 2009-10-09T10:00:53Z BFO:0000062 OBO_REL:preceded_by is preceded by takes place after relationship uberon preceded_by preceded_by preceded by preceded_by takes place after Allen:precedes is preceded by SIO:000249 precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external gene_ontology occurs_in occurs_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 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 BFO:0000067 uberon contains_process contains_process 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 contains process has_age FBdv:00018001 relationship substage_of substage_of Creating this relation as a temporary fix, pending adding the axiom occurent_part_of subpropertyof happens_during to RO substage_of inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in RO:0000052 fly_anatomy.ontology inheres_in inheres_in 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 RO:0000053 fly_anatomy.ontology uberon bearer_of bearer_of 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 RO:0000056 protein participates_in false participates_in 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 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 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 RO:0000086 protein uberon has_quality false has_quality has quality has quality has_quality 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 RO:0001015 uberon location_of location_of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains RO:0001019 uberon contains contains contains contains 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 RO:0001025 protein uberon located_in located_in 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. A part of relation that applies only between occurents. RO:0002012 FlyBase_development_CV occurent_part_of occurent_part_of occurent part of occurent_part_of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. GOC:dos dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of FlyBase_development_CV uberon immediately_preceded_by starts_at_end_of immediately_preceded_by starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland ends_at_start_of meets RO:0002090 FlyBase_development_CV ends_at_start_of ends_at_start_of X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) ends_at_start_of immediately precedes David Osumi-Sutherland io RO:0002091 external starts_during starts_during X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during starts_during David Osumi-Sutherland d during RO:0002092 external happens_during happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during happens during David Osumi-Sutherland o overlaps RO:0002093 external ends_during ends_during X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during ends_during A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 FlyBase_development_CV fly_anatomy.ontology uberon overlaps overlaps overlaps overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 protein uberon has_component false has_component For use in recording has_part with a cardinality constraint. Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? has component has component has_component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 fly_anatomy.ontology uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. A relation between a material entity (such as a cell) and a process. This is a shortcut relation, translation rule for which is: capable_of P <-> bearer_of (some realized_by only P). Example: osteoclast capable of bone resorption. Chris Mungall has function realized in PMID:20123131 PMID:21208450 For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". BFO_0000053 some (BFO_0000054 only ?Y) RO_0000053 some (RO_0000054 only ?Y) RO:0002215 fly_anatomy.ontology uberon capable_of capable_of capable of capable of capable_of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 fly_anatomy.ontology uberon capable_of_part_of capable_of_part_of capable of part of capable of part of capable_of_part_of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent has active participant obsolete has active participant true Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces has output Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. c involved in regulation of p if c enables 'p' and p' causally upstream of p acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within Inverse of developmentally preceded by Chris Mungall developmentally succeeded by p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall results_in_developmental_progression_of results in developmental progression of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of results in formation of cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of true 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 A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of RO:0002331 protein involved_in false involved_in involved in involved_in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by 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 RO:0002350 uberon member_of member_of member of member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output Chris Mungall RO:0002353 protein uberon output_of false output_of output of output of output_of Chris Mungall formed as result of A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of transitive form of directly_provides_input_for Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) transitively provides input for p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some 'p' and p' regulates some p c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall molecularly controls activity directly regulates activity of molecularly controls Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of molecularly decreases activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of molecularly increases activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property helper property (not for use in curation) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg Chris Mungall Pier Buttigieg determined by inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of true A relation that holds between two entities that have the property of being sequences or having sequences. Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. sequentially related to The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y Chris Mungall bounds sequence of inverse of bounds sequence of Chris Mungall is bound by sequence of x has subsequence y iff all of the sequence parts of x are sequence parts of y Chris Mungall contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 has subsequence inverse of has subsequence Chris Mungall contained by is subsequence of x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. Chris Mungall overlaps sequence of Chris Mungall causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. has modifier Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p results in breakdown of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' Inverse of 'causal agent in' has causal agent process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to related via dependence to true Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. Process(P1) directly regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. Process(P1) directly regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. cjm 2018-09-26T00:00:32Z disease relationship p has anatomical participant c iff p has participant c, and c is an anatomical entity cjm 2018-09-26T01:08:58Z has anatomical participant has_role has role quality correlates_with correlates_with q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM uberon transitively_connected_to transitively_connected to has participant 0 100 Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate dos Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. PMID:24138933 Wikipedia:Infant_mortality 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] 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] 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] bfo BFO:0000015 process 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] 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] 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] bfo BFO:0000019 quality 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 relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] 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] 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]) bfo BFO:0000030 object 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] 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] bfo BFO:0000040 material entity 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 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. anatomical entity anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CAROC:Brownsville2014 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. anatomical structure connected anatomical structure connected anatomical structure Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle. Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome. portion of organism substance CARO:0000004 Note - CARO explicitly declares organisms substances to be part of (some) organism. organism substance An Immaterial anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes and that is bounded by an anatomical surface. CARO:0000005 Original definition: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." The last clause. "contains one or more organism substances or anatomical structures" was dropped from the definition because it was an unnecessary restriction. anatomical space An anatomical entity that has mass. CARO:0000006 material anatomical entity material anatomical entity Anatomical entity that has no mass. CARO:0000007 immaterial anatomical entity Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. CARO:0000012 MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. multicellular organism 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 Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher. cell component cell part (CARO) CARO:0000014 This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. cell part Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism. CARO:0000032 organism subdivision 0 0 An anatomical structure that has no cells or cell parts as a part. CARO:0000040 Example. Insect cuticle, eggshell, hair. acellular anatomical structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. CARO:0000042 MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids? extraembryonic structure Anatomical space that is part of a cell. CARO:0000062 cell space 2 A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. multi-cell-component structure CARO:0001000 Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. multi-cell-part structure multi-cell-part structure Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. mah 10.7.2011 gross anatomical part Material anatomical entity that is a member of an individual species or is a viral or viroid particle. Melissa Haendel organism or virus Melissa Haendel 9/18/11 organism or virus or viroid An anatomical structure that has more than one cell as a part. djs93 Sun Feb 27 10:53:00 GMT 2011 CARO:0010000 multicellular anatomical structure There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS An individual member of a clade of cellular organisms. An individual member of a clade. mah organism mah 7.16.2011 CARO:0010004 A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. cellular organism organism 2 Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0000054 disconnected anatomical group An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure dos With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. Important for alignment with Darwin Core class "Organism". biological entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 cell The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:mah A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 cell in vivo cell To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). native cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:mah A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 cell secretory cell A cell that specializes in controlled release of one or more substances. GOC:tfm ISBN:0721662544 A cell that moves by its own activities. cell motile cell A cell that moves by its own activities. FB:ma A cell that lacks a nucleus. FMA:68647 non-nucleated cell cell anucleate cell A cell that lacks a nucleus. FB:ma A cell with a single nucleus. cell single nucleate cell A cell with a single nucleus. FB:ma GOC:tfm cell binucleate cell A cell with more than one nucleus. AEO:0000203 WBbt:0008074 syncitium syncytial cell syncytium cell multinucleate cell A cell with more than one nucleus. FB:ma A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. 2017-01-30T18:53:32Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 cell https://github.com/obophenotype/cell-ontology/issues/448 abnormal cell A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. GOC:add GOC:cg GOC:wdd An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism. 2017-01-30T19:16:26Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922 cell tumor cell tumour cell https://github.com/obophenotype/cell-ontology/issues/448 neoplastic cell An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism. GOC:add GOC:cg GOC:wdd A cell containing at least one nucleus. tmeehan 2010-09-07T03:32:33Z FMA:67513 cell nucleate cell A cell containing at least one nucleus. GOC:tfm A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. tmeehan 2009-12-23T10:53:24Z cell increased nucleus size A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. GOC:tfm A material entity which determines an environmental system. environmental feature A material entity which determines an environmental system. DOI:10.1186/2041-1480-4-43 NM:nm ORCID:0000-0002-4366-3088 A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. portion of environmental material environmental material A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. DOI:10.1186/2041-1480-4-43 MA:ma ORCID:0000-0002-4366-3088 URL:http://ontology.buffalo.edu/smith/articles/niches.html A system which has the disposition to environ one or more material entities. environment environmental system A system which has the disposition to environ one or more material entities. DOI:10.1186/2041-1480-4-43 An anthropogenic environment is an environmental system which is the product of human activity. anthropogenic environment An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. natural environment An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. https://en.wikipedia.org/wiki/Anthropization https://en.wikipedia.org/wiki/Natural_environment A process during which a natural environmental system is altered by human action. anthropization anthropisation A process during which a natural environmental system is altered by human action. https://en.wikipedia.org/wiki/Anthropization An environmental system which is determined by materials bearing roughly homogeneous qualities. environmental system determined by a quality An environmental system within which an environmental material strongly influences the system's composition and properties. environmental system determined by a material An environmental system which is determined by a living organism. host-associated environment environmental system determined by an organism An environmental system determined by an animal. animal environment Metazoan-associated environment animal-associated environment An environmental system determined by part of a living or dead animal, or a whole small animal. environment associated with an animal part or small animal An environmental system determined by part of a living or dead plant, or a whole small plant. environment associated with a plant part or small plant An environmental system which includes both living and non-living components. ecosystem An environmental system which includes both living and non-living components. https://en.wikipedia.org/wiki/Ecosystem A process in which includes the components of an environmental system as participants. environmental system process An environmental process which is driven by the action of humans. anthropogenic environmental process fly_anatomy.ontology FBbt:00000000 germ layer derivative An individual member of the species Drosophila melanogaster. CARO:0000012 NCBITaxon:7227 fly_anatomy.ontology Drosophila whole organism FBbt:00000001 organism An individual member of the species Drosophila melanogaster. FBC:DOS The three main divisions of the whole organism formed from groups of segments. fly_anatomy.ontology FBbt:00000002 tagma The three main divisions of the whole organism formed from groups of segments. FBC:GG One of the repeated divisions of the whole organism. fly_anatomy.ontology FBbt:00000003 segment One of the repeated divisions of the whole organism. FBC:GG fly_anatomy.ontology FBbt:00000004 head Any segment (FBbt:00000003) that is part of some head (FBbt:00000004). fly_anatomy.ontology FBbt:00000006 head segment Any segment (FBbt:00000003) that is part of some head (FBbt:00000004). FlyBase:FBrf0075072 A segment that is anterior to the gnathal segments. pregnathal segment preoral segment fly_anatomy.ontology cephalic segment procephalon FBbt:00000007 procephalic segment A segment that is anterior to the gnathal segments. FBC:GG Segment anterior to the intercalary segment. In the adult it bears the antennae. fly_anatomy.ontology FBbt:00000009 antennal segment Segment anterior to the intercalary segment. In the adult it bears the antennae. FBC:DOS . fly_anatomy.ontology FBbt:00000052 embryo . FlyBase:FBrf0039741 FlyBase:FBrf0041814 A collective term for stages 1-4. fly_anatomy.ontology FBbt:00000054 DEPRECATION WARNING cleavage stage embryo A collective term for stages 1-4. FBC:DOS Primordium that is a primary subdivision of the embryo into regions based on tissue and cell-type fate and specification. Germ layers first become morphologically distinct during gastrulation. As a result of gastrulation, the endoderm becomes the inner-most layer, the mesoderm becomes the middle layer and the ectoderm becomes the outer layer. fly_anatomy.ontology FBbt:00000110 germ layer Primordium that is a primary subdivision of the embryo into regions based on tissue and cell-type fate and specification. Germ layers first become morphologically distinct during gastrulation. As a result of gastrulation, the endoderm becomes the inner-most layer, the mesoderm becomes the middle layer and the ectoderm becomes the outer layer. FBC:DOS The outermost germ layer of the embryo. fly_anatomy.ontology FBbt:00000111 ectoderm The outermost germ layer of the embryo. FBC:GG The region of the ectoderm anterior to the cephalic furrow. fly_anatomy.ontology FBbt:00000119 anterior ectoderm The region of the ectoderm anterior to the cephalic furrow. FBC:DOS Any tagma (FBbt:00000002) that is part of some embryo (FBbt:00000052). fly_anatomy.ontology FBbt:00000137 embryonic tagma Any tagma (FBbt:00000002) that is part of some embryo (FBbt:00000052). FBC:Autogenerated Any segment (FBbt:00000003) that is part of some embryo (FBbt:00000052). fly_anatomy.ontology FBbt:00000154 embryonic segment Any segment (FBbt:00000003) that is part of some embryo (FBbt:00000052). FBC:Autogenerated Any head (FBbt:00000004) that is part of some embryo (FBbt:00000052). fly_anatomy.ontology FBbt:00000155 embryonic head Any head (FBbt:00000004) that is part of some embryo (FBbt:00000052). FBC:Autogenerated Any segment (FBbt:00000003) that is part of some embryonic head (FBbt:00000155). fly_anatomy.ontology FBbt:00000157 embryonic head segment Any segment (FBbt:00000003) that is part of some embryonic head (FBbt:00000155). FlyBase:FBrf0075072 Any procephalic segment (FBbt:00000007) that is part of some embryonic head (FBbt:00000155). fly_anatomy.ontology FBbt:00000158 embryonic procephalic segment Any procephalic segment (FBbt:00000007) that is part of some embryonic head (FBbt:00000155). FBC:Autogenerated Any antennal segment (FBbt:00000009) that is part of some embryonic head (FBbt:00000155). fly_anatomy.ontology FBbt:00000160 embryonic antennal segment Any antennal segment (FBbt:00000009) that is part of some embryonic head (FBbt:00000155). FBC:Autogenerated fly_anatomy.ontology FBbt:00001057 neurogenic region Primordium of the early extended germ band embryo that will give rise to the larval Bolwig organ, larval optic anlage and adult eye. It is a dorsoposterior strip of the embryonic procephalon that invaginates at stages 12-13. It can be subdivided into 4 different regions. The most anterior gives rise to the embryonic primordium of adult eye. Posterior to it, the anterior lip develops into the embryonic inner optic lobe primordium, that will give rise to the larval inner optic anlage. Posteriorly, the posterior lip develops into the embryonic outer optic lobe primordium, that will give rise to the larval outer optic anlage. The most posterior region will develop into the Bolwig organ primordium. optic lobe placode optic lobe primordium fly_anatomy.ontology P2 VisSys FBbt:00001059 visual primordium Primordium of the early extended germ band embryo that will give rise to the larval Bolwig organ, larval optic anlage and adult eye. It is a dorsoposterior strip of the embryonic procephalon that invaginates at stages 12-13. It can be subdivided into 4 different regions. The most anterior gives rise to the embryonic primordium of adult eye. Posterior to it, the anterior lip develops into the embryonic inner optic lobe primordium, that will give rise to the larval inner optic anlage. Posteriorly, the posterior lip develops into the embryonic outer optic lobe primordium, that will give rise to the larval outer optic anlage. The most posterior region will develop into the Bolwig organ primordium. FlyBase:FBrf0089570 FlyBase:FBrf0151275 optic lobe placode FlyBase:FBrf0151275 P2 VisSys FBC:DOS The ventrally/medially located ectodermal region of the trunk from which neuroblasts delaminate to form the ventral nerve cord. This region becomes distinct during stage 8 when its cells become enlarged compared to those in the adjacent dorsal ectoderm. FBbt:00000113 P2 VenEc VenEc ventral neurogenic region fly_anatomy.ontology neurectoderm neuroectoderm FBbt:00001061 ventral neurectoderm The ventrally/medially located ectodermal region of the trunk from which neuroblasts delaminate to form the ventral nerve cord. This region becomes distinct during stage 8 when its cells become enlarged compared to those in the adjacent dorsal ectoderm. FlyBase:FBrf0076117 FlyBase:FBrf0089570 An equivalence group of the neurectoderm where all cells can, although only one will, become a neural progenitor cell. fly_anatomy.ontology FBbt:00001135 proneural cluster An equivalence group of the neurectoderm where all cells can, although only one will, become a neural progenitor cell. FlyBase:FBrf0074477 FlyBase:FBrf0089570 fly_anatomy.ontology SOP sensillum precursor sensory organ mother cell sensory organ precursor cell FBbt:00001137 sensory mother cell Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993). embryonic imaginal precursor fly_anatomy.ontology FBbt:00001648 embryonic imaginal tissue Embryonic structure that will develop into a larval imaginal tissue, which will later form an adult structure (Cohen, 1993). FlyBase:FBrf0064789 Population of contiguous, morphologically distinct cells of the embryo that will proliferate to form an imaginal disc in the larva. During early embryogenesis the precursor is part of the epithelial sheet before segregating from the epithelial sheet by late embryogenesis (Cohen, 1993). fly_anatomy.ontology imaginal disc specific anlage FBbt:00001649 imaginal disc primordium Population of contiguous, morphologically distinct cells of the embryo that will proliferate to form an imaginal disc in the larva. During early embryogenesis the precursor is part of the epithelial sheet before segregating from the epithelial sheet by late embryogenesis (Cohen, 1993). FBC:SPR FlyBase:FBrf0064789 Primordium from which the eye-antennal disc develops. fly_anatomy.ontology eye-antennal disc specific anlage FBbt:00001652 eye-antennal disc primordium Primordium from which the eye-antennal disc develops. FBC:SPR fly_anatomy.ontology FBbt:00001727 larva Any tagma (FBbt:00000002) that is part of some larva (FBbt:00001727). fly_anatomy.ontology FBbt:00001728 larval tagma Any tagma (FBbt:00000002) that is part of some larva (FBbt:00001727). FBC:Autogenerated Any segment (FBbt:00000003) that is part of some larva (FBbt:00001727). fly_anatomy.ontology FBbt:00001729 larval segment Any segment (FBbt:00000003) that is part of some larva (FBbt:00001727). FBC:Autogenerated Any head (FBbt:00000004) that is part of some larva (FBbt:00001727). fly_anatomy.ontology FBbt:00001730 larval head Any head (FBbt:00000004) that is part of some larva (FBbt:00001727). FBC:Autogenerated Any segment (FBbt:00000003) that is part of some larval head (FBbt:00001730). fly_anatomy.ontology FBbt:00001732 larval head segment Any segment (FBbt:00000003) that is part of some larval head (FBbt:00001730). FlyBase:FBrf0075072 Any procephalic segment (FBbt:00000007) that is part of some larval head (FBbt:00001730). fly_anatomy.ontology FBbt:00001733 larval procephalic segment Any procephalic segment (FBbt:00000007) that is part of some larval head (FBbt:00001730). FBC:Autogenerated Any antennal segment (FBbt:00000009) that is part of some larval head (FBbt:00001730). fly_anatomy.ontology FBbt:00001735 larval antennal segment Any antennal segment (FBbt:00000009) that is part of some larval head (FBbt:00001730). FBC:Autogenerated Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis. embryonic/larval imaginal precursor larval imaginal precursor fly_anatomy.ontology FBbt:00001760 larval imaginal tissue Imaginal tissue that is found in the larva and will develop into an adult structure during metamorphosis. FlyBase:FBrf0064789 A sac shaped epithelial structure in the larva that gives rise to part of the adult integumentary system. One side of the sac consists of peripodial epithelium, the other of columnar epithelium. A single anterior-posterior compartment boundary bisects both peripodial membrane and columnar epithelium. Cells do not cross this boundary during growth and development of the disc. fly_anatomy.ontology imaginal disk FBbt:00001761 imaginal disc A sac shaped epithelial structure in the larva that gives rise to part of the adult integumentary system. One side of the sac consists of peripodial epithelium, the other of columnar epithelium. A single anterior-posterior compartment boundary bisects both peripodial membrane and columnar epithelium. Cells do not cross this boundary during growth and development of the disc. FBC:GG Imaginal disc that, in the adults, gives rise to the eye, antenna, head capsule (including all bristles and external membranes) and the maxillary palps (Cohen, 1993). fly_anatomy.ontology FBbt:00001766 Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc. eye-antennal disc Imaginal disc that, in the adults, gives rise to the eye, antenna, head capsule (including all bristles and external membranes) and the maxillary palps (Cohen, 1993). FlyBase:FBrf0064789 Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993). fly_anatomy.ontology FBbt:00001768 Figure 12 from Cohen (1993, Bate, Martinez Arias, 1993: 747--841) provides a fate map of the eye-antennal disc. eye disc Anterior, bulbous portion of the eye-antennal disc that gives rise to the eye as well as contributing to the head capsule (Cohen, 1993). FlyBase:FBrf0064789 Nervous system of the embryo/larva. FBbt:00005719 VFB:FBbt_00001911 larval nervous system fly_anatomy.ontology FBbt:00001911 embryonic/larval nervous system Nervous system of the embryo/larva. FlyBase:FBrf0045359 FlyBase:FBrf0075072 FlyBase:FBrf0105282 Any sense organ (FBbt:00005155) that is part of some larva (FBbt:00001727). VFB:FBbt_00002639 larval sense organ fly_anatomy.ontology FBbt:00002639 embryonic/larval sense organ Any sense organ (FBbt:00005155) that is part of some larva (FBbt:00001727). FBC:Autogenerated Any sense organ (FBbt:00005155) that is part of some larval antennal segment (FBbt:00001735). VFB:FBbt_00002654 larval antennal segment sensillum fly_anatomy.ontology FBbt:00002654 embryonic/larval antennal segment sensillum Any sense organ (FBbt:00005155) that is part of some larval antennal segment (FBbt:00001735). FBC:Autogenerated The prepupa is the name given to the organism at the period of the life cycle that begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C is approximately 12 hours. It occurs 120-132.2 hours after egg laying, and is the period of 0-12.2 hours after puparium formation. fly_anatomy.ontology PP FBbt:00002952 prepupa The prepupa is the name given to the organism at the period of the life cycle that begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C is approximately 12 hours. It occurs 120-132.2 hours after egg laying, and is the period of 0-12.2 hours after puparium formation. FlyBase:FBrf0036849 FlyBase:FBrf0048355 The pupa is the name given to the organism at the period of the life cycle that begins once larval/pupal apolysis is complete, as indicated by the expulsion of the larval armature. Early in this stage the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. The duration of this stage is approximately 32 hours at 25 degrees C, and spans from 132.2-164.3 hours after egg laying, or is the period of 12.2-44.3 hours after puparium formation. fly_anatomy.ontology P FBbt:00002953 pupa The pupa is the name given to the organism at the period of the life cycle that begins once larval/pupal apolysis is complete, as indicated by the expulsion of the larval armature. Early in this stage the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. The duration of this stage is approximately 32 hours at 25 degrees C, and spans from 132.2-164.3 hours after egg laying, or is the period of 12.2-44.3 hours after puparium formation. FlyBase:FBrf0036849 FlyBase:FBrf0048355 . fly_anatomy.ontology imago FBbt:00003004 adult . FlyBase:FBrf0036849 Any tagma (FBbt:00000002) that is part of some adult (FBbt:00003004). fly_anatomy.ontology FBbt:00003005 adult tagma Any tagma (FBbt:00000002) that is part of some adult (FBbt:00003004). FBC:Autogenerated Segment of the adult. fly_anatomy.ontology FBbt:00003006 adult segment Segment of the adult. FBC:SPR Head of the adult organism. fly_anatomy.ontology FBbt:00003007 adult head Head of the adult organism. FBC:SPR Segment of the adult head. fly_anatomy.ontology FBbt:00003009 adult head segment Segment of the adult head. FlyBase:FBrf0064788 Any procephalic segment (FBbt:00000007) that is part of some adult head (FBbt:00003007). fly_anatomy.ontology FBbt:00003010 adult procephalic segment Any procephalic segment (FBbt:00000007) that is part of some adult head (FBbt:00003007). FBC:Autogenerated Any antennal segment (FBbt:00000009) that is part of some adult head (FBbt:00003007). FBbt:00004512 adult antennal structure fly_anatomy.ontology FBbt:00003012 adult antennal segment Any antennal segment (FBbt:00000009) that is part of some adult head (FBbt:00003007). FBC:Autogenerated Any nervous system (FBbt:00005093) that is part of some adult (FBbt:00003004). VFB:FBbt_00003559 fly_anatomy.ontology FBbt:00003559 adult nervous system Any nervous system (FBbt:00005093) that is part of some adult (FBbt:00003004). FlyBase:FBrf0002482 FlyBase:FBrf0007196 FlyBase:FBrf0007735 FlyBase:FBrf0034076 Any sense organ (FBbt:00005155) that is part of some adult (FBbt:00003004). VFB:FBbt_00004113 fly_anatomy.ontology FBbt:00004113 adult sense organ Any sense organ (FBbt:00005155) that is part of some adult (FBbt:00003004). FlyBase:FBrf0007734 FlyBase:FBrf0031004 Any developing material anatomical entity (FBbt:00007006) that is part of some embryo (FBbt:00000052). fly_anatomy.ontology FBbt:00004208 developing embryonic structure Any developing material anatomical entity (FBbt:00007006) that is part of some embryo (FBbt:00000052). FBC:Autogenerated A collective term for stages 11 and 12. fly_anatomy.ontology FBbt:00004450 late extended germ band embryo A collective term for stages 11 and 12. FBC:DOS A bilaterally paired compound sense organ of the adult head that functions in visual perception. VFB:FBbt_00004508 fly_anatomy.ontology compound eye FBbt:00004508 eye A bilaterally paired compound sense organ of the adult head that functions in visual perception. FBC:DOS A division of the whole organism into specialized systems. fly_anatomy.ontology FBbt:00004856 organ system A division of the whole organism into specialized systems. FBC:GG All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems. VFB:FBbt_00005093 fly_anatomy.ontology FBbt:00005093 nervous system All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems. FlyBase:FBrf0166419 Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system. VFB:FBbt_00005155 fly_anatomy.ontology FBbt:00005155 sense organ Multicellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system. FBC:DOS A light sensitive sense organ. VFB:FBbt_00005162 fly_anatomy.ontology FBbt:00005162 photoreceptor A light sensitive sense organ. FBC:GG Any somatic cell (FBbt:00100318) that overlaps some sense organ (FBbt:00005155). fly_anatomy.ontology SOC FBbt:00005163 sensory organ cell Any somatic cell (FBbt:00100318) that overlaps some sense organ (FBbt:00005155). FBC:Autogenerated Precursor cell that gives rise to an external sensory organ. fly_anatomy.ontology FBbt:00005164 external sensory organ precursor cell Precursor cell that gives rise to an external sensory organ. FlyBase:FBrf0111371 Sensory organ that has external structures that detect mechanical or chemical stimuli. VFB:FBbt_00005168 eo es fly_anatomy.ontology sensillum FBbt:00005168 external sensory organ Sensory organ that has external structures that detect mechanical or chemical stimuli. FlyBase:FBrf0064796 es FlyBase:FBrf0064796 fly_anatomy.ontology FBbt:00005290 DEPRECATION WARNING pre-blastoderm embryo Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying). fly_anatomy.ontology FBbt:00005291 DEPRECATION WARNING stage 1 embryo Nuclear divisions 1 and 2. Duration at 25 degrees C: approximately 25 minutes (0-25 minutes after egg laying). FlyBase:FBrf0089570 Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL). fly_anatomy.ontology FBbt:00005293 DEPRECATION WARNING stage 2 embryo Nuclear divisions 3-8. The egg cytoplasm contracts producing a clear separation from the vitelline membrane and empty spaces at the anterior and posterior. The cleavage nuclei migrate towards the periphery. Duration at 25 degrees C approximately 40 minutes (25-65 minutes AEL). FlyBase:FBrf0089570 Nuclear division 9. The cleavage nuclei complete there migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying). fly_anatomy.ontology FBbt:00005301 DEPRECATION WARNING stage 3 embryo Nuclear division 9. The cleavage nuclei complete there migration to the periphery. Polar buds form at the posterior pole and divide once. Duration at 25 degrees C: approximately 15 minutes (65-80 minutes after egg laying). FlyBase:FBrf0089570 A collective term for stages 3-5. fly_anatomy.ontology FBbt:00005304 DEPRECATION WARNING blastoderm embryo A collective term for stages 3-5. FBC:DOS A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4). fly_anatomy.ontology FBbt:00005305 DEPRECATION WARNING syncytial blastoderm embryo A blastoderm embryo prior to cellularization (corresponds to embryonic stages 3 and 4). FBC:DOS FBC:GG Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying). fly_anatomy.ontology FBbt:00005306 DEPRECATION WARNING stage 4 embryo Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying). FlyBase:FBrf0089570 Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees C: approximately 40 minutes (130-170 minutes after egg laying). fly_anatomy.ontology cellular blastoderm embryo FBbt:00005311 DEPRECATION WARNING stage 5 embryo Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees C: approximately 40 minutes (130-170 minutes after egg laying). FBC:DOS FBC:MA FlyBase:FBrf0089570 A collective term for stages 6-8, during which complex morphogenetic movements result in the formation of the three germ layers; ectoderm, mesoderm and endoderm. fly_anatomy.ontology FBbt:00005317 DEPRECATION WARNING gastrula embryo A collective term for stages 6-8, during which complex morphogenetic movements result in the formation of the three germ layers; ectoderm, mesoderm and endoderm. FBC:DOS FBC:GG A collective term for stages 9-12. fly_anatomy.ontology FBbt:00005321 DEPRECATION WARNING extended germ band embryo A collective term for stages 9-12. FBC:DOS A collective term for stages 13-15. fly_anatomy.ontology contracted germ band embryo head involution embryo FBbt:00005331 DEPRECATION WARNING dorsal closure embryo A collective term for stages 13-15. FBC:DOS A collective term for stages 16 and 17. fly_anatomy.ontology FBbt:00005333 DEPRECATION WARNING late embryo A collective term for stages 16 and 17. FBC:DOS "anlagen in statu nascendi" are domains that do not yet coincide 1:1 with a later organ. Anlagen in statu nascendi are typically defined for the early blastoderm by the expression domains of genes which, in the late blastoderm or later, are expressed in specific anlagen, but initially come on in larger domains. fly_anatomy.ontology A0 FBbt:00005413 anlage in statu nascendi "anlagen in statu nascendi" are domains that do not yet coincide 1:1 with a later organ. Anlagen in statu nascendi are typically defined for the early blastoderm by the expression domains of genes which, in the late blastoderm or later, are expressed in specific anlagen, but initially come on in larger domains. FlyBase:FBrf0155831 FlyBase:FBrf0178740 Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage. Asn VisSys fly_anatomy.ontology A0Vis FBbt:00005425 visual anlage in statu nascendi Anlage in statu nascendi of the visual system in a stage 5 embryo that will give rise to the visual system anlage. FBC:VH Asn VisSys FBC:DOS Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. fly_anatomy.ontology FBbt:00005426 anlage Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. FlyBase:FBrf0089570 FlyBase:FBrf0178740 fly_anatomy.ontology FBbt:00005427 ectoderm anlage Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium. A VisSys fly_anatomy.ontology AVis FBbt:00005434 visual anlage Anlage of the visual system in the gastrula embryo that will give rise to the visual primordium. FBC:VH A VisSys FBC:DOS Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. fly_anatomy.ontology P placode FBbt:00005495 primordium Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue. FBC:DOS FlyBase:FBrf0089570 FlyBase:FBrf0178740 Early primordium of the late extended germ band and dorsal closure embryo that will give rise to the adult eye. It develops from the visual primordium. adult eye primordium early fly_anatomy.ontology FBbt:00005515 early embryonic primordium of adult eye Early primordium of the late extended germ band and dorsal closure embryo that will give rise to the adult eye. It develops from the visual primordium. FBC:DOS FBC:VH FlyBase:FBrf0089570 FlyBase:FBrf0151275 fly_anatomy.ontology P2 iVenEp venEpiP2 FBbt:00005533 ventral epidermis primordium P2 iVenEp FBC:DOS . fly_anatomy.ontology P2 VenEc venEc FBbt:00005558 ventral ectoderm . FlyBase:FBrf0089570 P2 VenEc FBC:DOS Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009). FBbt:00004171 VFB:FBbt_00005806 antennal sensillum fly_anatomy.ontology FBbt:00005806 antennal sense organ Any sense organ (FBbt:00005155) that is part of some antennal segment (FBbt:00000009). FBC:Autogenerated The developing adult after pupal-adult apolysis, i.e. from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. fly_anatomy.ontology FBbt:00006011 pharate adult The developing adult after pupal-adult apolysis, i.e. from stage P8 (when yellow eye color first becomes visible through the pupal case), to eclosion. FlyBase:FBrf0049147 Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. CARO:0000003 fly_anatomy.ontology FBbt:00007001 anatomical structure Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. CARO:MAH FBC:DOS Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:0000013 CL:0000000 GO:0005623 fly_anatomy.ontology FBbt:00007002 cell Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:MAH Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. CARO:0000043 fly_anatomy.ontology FBbt:00007003 portion of tissue Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. CARO:MAH Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions. CARO:0000066 fly_anatomy.ontology FBbt:00007005 epithelium Portion of tissue, that consists of one or more layers of cells with distinct apical-basal polarity, connected to each other by cell junctions. CARO:MAH fly_anatomy.ontology FBbt:00007006 developing material anatomical entity fly_anatomy.ontology FBbt:00007008 somatic precursor cell Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism. CARO:0000032 fly_anatomy.ontology FBbt:00007009 organism subdivision Anatomical structure that is a primary subdivision of whole organism. The mereological sum of these is the whole organism. CARO:MAH Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which, through specific morphogenetic processes, forms a single distinct structural unit demarcated by bona fide boundaries from other distinct structural units of different types. CARO:0000055 fly_anatomy.ontology FBbt:00007010 multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which, through specific morphogenetic processes, forms a single distinct structural unit demarcated by bona fide boundaries from other distinct structural units of different types. CARO:MAH CARO:0000006 fly_anatomy.ontology FBbt:00007016 material anatomical entity The region of the ectoderm posterior to the cephalic furrow. fly_anatomy.ontology FBbt:00007045 trunk ectoderm The region of the ectoderm posterior to the cephalic furrow. FBC:DOS An anatomical structure consisting of multiple cell cluster organs and which does not contain portions of tissue. david 2008-10-21T12:20:23Z fly_anatomy.ontology FBbt:00007230 compound cell cluster organ An anatomical structure consisting of multiple cell cluster organs and which does not contain portions of tissue. FBC:DOS Any compound cell cluster organ (FBbt:00007230) that capable of some detection of stimulus involved in sensory perception (GO:0050906). david 2008-10-21T02:09:38Z FBbt:00002653 VFB:FBbt_00007234 compound sensillum fly_anatomy.ontology FBbt:00007234 compound sense organ Any compound cell cluster organ (FBbt:00007230) that capable of some detection of stimulus involved in sensory perception (GO:0050906). FBC:Autogenerated Compound sense organ that is located within the epidermis. david 2008-10-21T02:23:08Z VFB:FBbt_00007235 fly_anatomy.ontology FBbt:00007235 external compound sense organ Compound sense organ that is located within the epidermis. FlyBase:FBrf0089570 Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all connected to each other. david 2008-11-04T03:09:28Z fly_anatomy.ontology FBbt:00007276 anatomical group Material anatomical entity generated by coordinated expression of the organism's own genome and whose component parts are not all connected to each other. FBC:DOS An anatomical group whose component structures share a common function. david 2008-11-04T03:18:01Z fly_anatomy.ontology FBbt:00007278 non-connected functional system An anatomical group whose component structures share a common function. FBC:DOS Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730). david 2008-11-05T10:34:14Z VFB:FBbt_00007280 larval head sense organ fly_anatomy.ontology FBbt:00007280 embryonic/larval head sense organ Any sense organ (FBbt:00005155) that is part of some larval head (FBbt:00001730). FBC:Autogenerated An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of sound. fly_anatomy.ontology FBbt:00007685 auditory system An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of sound. FBC:DOS An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of mechanical stimuli. fly_anatomy.ontology FBbt:00007687 mechanosensory system An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of mechanical stimuli. FBC:DOS An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of smell. fly_anatomy.ontology FBbt:00007688 olfactory system An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of smell. FBC:DOS An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of chemical stimuli. fly_anatomy.ontology FBbt:00007689 chemosensory system An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of chemical stimuli. FBC:DOS An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of taste. fly_anatomy.ontology FBbt:00007690 gustatory system An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of taste. FBC:DOS An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception. fly_anatomy.ontology FBbt:00007692 Note - the relationship of this class to the nervous system is overlap. This allows for sense organ components that function in the transduction of sensory signals but that are not considered to be part of the nervous system to be part of sensory systems. sensory system An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception. FBC:DOS A collective term for stages 9 and 10. fly_anatomy.ontology FBbt:00014201 early extended germ band embryo A collective term for stages 9 and 10. FBC:DOS Any germ layer derivative (FBbt:00000000) that develops from some ectoderm (FBbt:00000111). FBbt:00005253 fly_anatomy.ontology FBbt:00025990 ectodermal derivative Any germ layer derivative (FBbt:00000000) that develops from some ectoderm (FBbt:00000111). FBC:DOS . fly_anatomy.ontology FBbt:00025991 anterior ectoderm derivative . FBC:DOS . fly_anatomy.ontology FBbt:00025993 ventral ectoderm derivative . FBC:DOS Any group of similar imaginal cells, such as an imaginal disc, imaginal ring or imaginal island, or a precursor tissue that forms one of them. These tissues develop separately from other embryonic and larval tissues and they generate adult structures during metamorphosis. http://orcid.org/0000-0002-1373-1705 2018-08-15T09:31:08Z imaginal structure fly_anatomy.ontology FBbt:00047552 imaginal tissue Any group of similar imaginal cells, such as an imaginal disc, imaginal ring or imaginal island, or a precursor tissue that forms one of them. These tissues develop separately from other embryonic and larval tissues and they generate adult structures during metamorphosis. FlyBase:FBrf0064789 imaginal structure FlyBase:FBrf0053815 An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light. http://orcid.org/0000-0002-1373-1705 2018-09-18T13:08:28Z fly_anatomy.ontology FBbt:00047735 visual system An anatomical system consisting of all of the anatomical entities that function in some part of the sensory perception of light. FBC:CP david 2008-06-30T04:15:23Z fly_anatomy.ontology FBbt:00057001 anterior-posterior subdivision of organism Anatomical structure that has multiple cells as parts. djs93 2010-11-02T02:25:04Z fly_anatomy.ontology FBbt:00100313 multicellular structure Anatomical structure that has multiple cells as parts. FBC:DOS Any multicellular structure (FBbt:00100313) that capable of some secretion (GO:0046903). djs93 2010-11-02T05:39:45Z fly_anatomy.ontology FBbt:00100317 gland Any multicellular structure (FBbt:00100313) that capable of some secretion (GO:0046903). FBC:Autogenerated djs93 2010-11-04T08:35:02Z fly_anatomy.ontology FBbt:00100318 somatic cell Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye. adult eye primordium late fly_anatomy.ontology FBbt:00105515 late embryonic primordium of adult eye Primordium of the late embryo that develops from the early primordium, and will give rise to the adult eye. FBC:DOS FBC:VH FlyBase:FBrf0089570 FlyBase:FBrf0151275 Nervous system of the pupa. mmc46 2013-01-04T10:01:28Z VFB:FBbt_00110192 fly_anatomy.ontology FBbt:00110192 pupal nervous system Nervous system of the pupa. FBC:MMC fly_anatomy.ontology FBbt:01000119 anterior ectoderm anlage Anatomical entity which is part_of Drosophila melanogaster. FBbt_root:00000000 fly_anatomy.ontology Drosophila FBbt:10000000 anatomical entity Anatomical entity which is part_of Drosophila melanogaster. CARO:MAH Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium. P1 Eye adult eye primordium fly_anatomy.ontology FBbt:10005249 embryonic primordium of adult eye Primordium of the embryo that will give rise to the adult eye. It corresponds to the most anterior region that develops from the visual primordium. FlyBase:FBrf0089570 FlyBase:FBrf0151275 P1 Eye FBC:DOS Phenotype that is a defect in thermotaxis (GO:0043052). 'thermotaxis' is defined as: 'The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.' thermotaxis behaviour defective phenotypic_class FBcv:0000002 thermotaxis behavior defective Phenotype that is a defect in thermotaxis (GO:0043052). 'thermotaxis' is defined as: 'The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.' FBC:DOS GOC:cab1 WB_REF:cgc467 Phenotype of males that is a reduction in the proportion of fertilized eggs produced, but only to > 50% of wild-type. phenotypic_class FBcv:0000006 male semi-fertile Phenotype of females that is a reduction in the proportion of fertilized eggs produced, but only to > 50% of wild-type. phenotypic_class FBcv:0000007 female semi-fertile Genotype g1 is a modifier of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is significantly different from that caused by g2 alone. phenotypic_class variegation FBcv:0000008 modifier of variegation Genotype g1 is a modifier of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is significantly different from that caused by g2 alone. FBC:DOS variegation FBC:DOS Phenotype that is the partial or full transformation of one or more segments (FBbt:00000003) or segmental appendages from one identity to another. For example, in antennapedia an antenna is partially or fully transformed into a leg. phenotypic_class FBcv:0000316 homeotic Phenotype that is the partial or full transformation of one or more segments (FBbt:00000003) or segmental appendages from one identity to another. For example, in antennapedia an antenna is partially or fully transformed into a leg. FBC:DOS Phenotype that is a defect in dorsal/ventral axis specification (GO:0009950). 'dorsal/ventral axis specification' is defined as: 'The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.' phenotypic_class dorsal-ventral polarity FBcv:0000324 dorsal/ventral axis specification defective Phenotype that is a defect in dorsal/ventral axis specification (GO:0009950). 'dorsal/ventral axis specification' is defined as: 'The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.' FBC:DOS GOC:dph GOC:go_curators GOC:tb dorsal-ventral polarity FBC:DOS A phenotype that is an expansion of the developing embryonic nervous system at the expense of developing ventral epidermis. djs93 2011-09-13T02:42:10Z phenotypic_class FBcv:0000325 Typically this is caused by and expansion of the population of neuroblasts at the expense of prospective epidermis, both of which originate in the ventral ectoderm. neurogenic phenotype A phenotype that is an expansion of the developing embryonic nervous system at the expense of developing ventral epidermis. FlyBase:FBrf0040185 phenotypic_class FBcv:0000347 phenotypic class The canonical phenotype of a wild-type Drosophilid. phenotypic_class FBcv:0000348 wild-type The canonical phenotype of a wild-type Drosophilid. FBC:DOS A phenotype that is survival to mature adulthood, where mature is defined as after adult stage A3 (FBdv:00006012). phenotypic_class FBcv:0000349 Note, this term should not be used with the qualifier 'partially'. Use semi-viable or semi-lethal instead. viable A phenotype that is survival to mature adulthood, where mature is defined as after adult stage A3 (FBdv:00006012). FBC:DOS 5 50 5 50 A phenotype of a population that is the death of some significant proportion of animals in that population, but less that half, prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012). semi-viable phenotypic_class FBcv:0000350 partially lethal - majority live A phenotype of a population that is the death of some significant proportion of animals in that population, but less that half, prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012). FBC:DOS 98 98 A phenotype of a population that is the death of all animals in that population at some stage or stages prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012). phenotypic_class FBcv:0000351 Note on usage: lethal is appropriate in cases where escaper adults are very rare. The lethal phase prior to becoming a mature adult may be further specified using children terms which specify stage. lethal A phenotype of a population that is the death of all animals in that population at some stage or stages prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012). FBC:DOS FBC:KM 50 98 50 98 A phenotype of a population that is the death of a majority of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012). semi-lethal phenotypic_class FBcv:0000352 Stages during which there is significant death prior to mature adulthood can be indicated using one or more stage qualifiers. partially lethal - majority die A phenotype of a population that is the death of a majority of animals in that population prior to becoming a mature adult, where mature is defined as after adult stage A3 (FBdv:00006012). FBC:DOS FBC:KM FBC:NB A phenotype that is a failure of mutant cells to survive. phenotypic_class FBcv:0000353 Typically, this phenotype is assayed in clones of cells. cell lethal A phenotype that is a failure of mutant cells to survive. FBC:DOS A post-embryonic, macroscopic, anatomical phenotype. phenotypic_class FBcv:0000354 visible A post-embryonic, macroscopic, anatomical phenotype. FBC:DOS Phenotype that is a defect in eye color compared to wild-type. eye colour defective phenotypic_class FBcv:0000355 eye color defective Phenotype that is a defect in eye color compared to wild-type. FBC:DOS A phenotype that is a defect in body color compared to wild-type. body colour defective phenotypic_class FBcv:0000356 body color defective A phenotype that is a defect in body color compared to wild-type. FBC:DOS A phenotype that is a defect in the size of the whole body or some body part compared to wild-type. phenotypic_class FBcv:0000357 size defective A phenotype that is a defect in the size of the whole body or some body part compared to wild-type. FBC:DOS Phenotype that is a decrease in body size compared to identically raised wild-type controls. phenotypic_class FBcv:0000358 small body Phenotype that is a decrease in body size compared to identically raised wild-type controls. FBC:DOS Phenotype that is a decrease in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth - there may be fewer cells in an otherwise normal volume of tissue. reduced cell number phenotypic_class FBcv:0000359 decreased cell number Phenotype that is a decrease in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth - there may be fewer cells in an otherwise normal volume of tissue. FBC:DOS Phenotype that is a decrease in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth of a tissue - there may be more cells in an otherwise normal volume of tissue. reduced cell size phenotypic_class FBcv:0000360 Note that defects in cell size are not necessarily the result of defects in cell growth. A change in the rate of cell division in the absence of any change in cell growth rate can result in smaller or larger cells. decreased cell size Phenotype that is a decrease in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. This phenotype is not necessarily accompanied by decreased growth of a tissue - there may be more cells in an otherwise normal volume of tissue. FBC:DOS Phenotype that is an increase in body size compared to identically raised wild-type controls. phenotypic_class FBcv:0000361 large body Phenotype that is an increase in body size compared to identically raised wild-type controls. FBC:DOS Phenotype that is an increase in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. phenotypic_class FBcv:0000362 This phenotype is not necessarily accompanied by overgrowth of a tissue - there may be more cells in an otherwise normal volume of tissue. It is not necessarily due to an increase in cell growth -it may be the result of an increase in the division rate at normal growth rates. It may not even be due to an increase in the cell division rate - a reduced rate of cell death while the division rate is normal could also achieve it. increased cell number Phenotype that is an increase in the number of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. FBC:DOS Phenotype that is an increase in the size of cells compared to wild-type. phenotypic_class FBcv:0000363 May be due to an increase in the cell growth rate or to a reduced rate of cell division along with a normal rate of cell growth. increased cell size Phenotype that is an increase in the size of cells compared to wild-type. FBC:DOS A phenotype that is the inability to produce a zygote. phenotypic_class FBcv:0000364 The cause of sterility may be physical or behavioral. Note, this term should not be used with the qualifier 'partially'. Use semi-sterile or semi-fertile instead. sterile A phenotype that is the inability to produce a zygote. FBC:DOS A phenotype that is a reduction in the proportion of fertilized eggs produced to below 50% of wild-type. phenotypic_class FBcv:0000365 semi-sterile A phenotype that is a reduction in the proportion of fertilized eggs produced to below 50% of wild-type. FBC:DOS A phenotype that is the inability of females to mate and produce fertilized offspring. phenotypic_class FBcv:0000366 The cause of sterility may be physical or behavioral. Note: this term should not be used with the qualifier 'partially' - use semi-sterile or semi-fertile instead. female sterile A phenotype that is the inability of females to mate and produce fertilized offspring. FBC:DOS A phenotype that is a reduction in the proportion of fertilized eggs produced by females to below 50% of wild-type. phenotypic_class FBcv:0000367 female semi-sterile A phenotype that is a reduction in the proportion of fertilized eggs produced by females to below 50% of wild-type. FBC:DOS A phenotype of female sterility due to defects in the female germline. female sterile germ-line-dependent phenotypic_class FBcv:0000368 female sterile germline-dependent A phenotype of female sterility due to defects in the female germline. FBC:DOS A phenotype of female sterility due to defects in somatic cells of the ovary (FBbt:00006030), or of the products of these cells (such as eggshell). phenotypic_class FBcv:0000369 female sterile soma-dependent A phenotype of female sterility due to defects in somatic cells of the ovary (FBbt:00006030), or of the products of these cells (such as eggshell). FBC:DOS A phenotype that is the inability of males to mate and produce fertilized offspring. phenotypic_class FBcv:0000370 The cause of sterility may be physical or behavioral. Note - this term should not be used with the qualifier 'partially' - use semi-sterile or semi-fertile instead. male sterile A phenotype that is the inability of males to mate and produce fertilized offspring. FBC:DOS A phenotype that is a reduction in the proportion of fertilized eggs produced by males to below 50% of wild-type. phenotypic_class FBcv:0000371 male semi-sterile A phenotype that is a reduction in the proportion of fertilized eggs produced by males to below 50% of wild-type. FBC:DOS A phenotype of male sterility due to defects in the male germline. male sterile germ-line-dependent phenotypic_class FBcv:0000372 male sterile germline-dependent A phenotype of male sterility due to defects in the male germline. FBC:DOS A phenotype of male sterility due to defects in somatic cells of the testis (FBbt:00006031) or of the products of these cells. phenotypic_class FBcv:0000373 male sterile soma-dependent A phenotype of male sterility due to defects in somatic cells of the testis (FBbt:00006031) or of the products of these cells. FBC:DOS A phenotype that is the ability to mate and as a result produce fertilized eggs. phenotypic_class FBcv:0000374 Note, this term should not be used with the qualifier 'partially'. Use semi-sterile or semi-fertile instead. fertile A phenotype that is the ability to mate and as a result produce fertilized eggs. FBC:DOS Phenotype that is a reduction in the proportion of fertilized eggs produced, but only to > 50% of wild-type. phenotypic_class FBcv:0000375 semi-fertile Phenotype that is a reduction in the proportion of fertilized eggs produced, but only to > 50% of wild-type. FBC:DOS A phenotype that is the ability of males to mate and as a result produce fertilized eggs. phenotypic_class FBcv:0000376 Note - this term should not be used with the qualifier 'partially' - use male semi-sterile or male semi-fertile instead. male fertile A phenotype that is the ability of males to mate and as a result produce fertilized eggs. FBC:DOS A phenotype that is the ability of females to mate and as a result produce fertilized eggs. phenotypic_class FBcv:0000377 Note - this term should not be used with the qualifier 'partially' - use female semi-sterile or female semi-fertile instead. female fertile A phenotype that is the ability of females to mate and as a result produce fertilized eggs. FBC:DOS A phenotype in which all offspring are sterile. Typically, this is due to maternal effect sterility resulting from defects in pole cell development. phenotypic_class FBcv:0000378 grandchildless A phenotype in which all offspring are sterile. Typically, this is due to maternal effect sterility resulting from defects in pole cell development. ISBN:978-0-87969-321-3 Genotype g1 is an enhancer of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is greater than that caused by g2 alone. phenotypic_class FBcv:0000379 Typically, g2 is a chromosomal aberration or an insertion. enhancer of variegation Genotype g1 is an enhancer of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is greater than that caused by g2 alone. FBC:DOS Genotype g1 is a non-enhancer of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not greater than that caused by g2 alone. phenotypic_class FBcv:0000380 non-enhancer of variegation Genotype g1 is a non-enhancer of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not greater than that caused by g2 alone. FBC:DOS Genotype g1 is a suppressor of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is less than that caused by to g2 alone. phenotypic_class FBcv:0000381 Typically, g2 is a chromosomal aberration or an insertion. suppressor of variegation Genotype g1 is a suppressor of variegation if, and only if, some genotype g2 has a variegated phenotype and the degree of variegation caused by g1g2 is less than that caused by to g2 alone. FBC:DOS Genotype g1 is a non-suppressor of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not less than that caused by g2 alone. phenotypic_class FBcv:0000382 non-suppressor of variegation Genotype g1 is a non-suppressor of variegation of the phenotype due to genotype g2 if, and only if, g2 has a variegated phenotype and the degree of variegation caused by g1g2 is not less than that caused by g2 alone. FBC:DOS A phenotype that is the inability to synthesize some organic compound that can be synthesized by wild-type animals, and that is required for normal growth and/or development. phenotypic_class FBcv:0000383 auxotroph A phenotype that is the inability to synthesize some organic compound that can be synthesized by wild-type animals, and that is required for normal growth and/or development. http://en.wikipedia.org/wiki/Auxotrophic Phenotype that is a defect in aging (GO:0007568). 'aging' is defined as: 'A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).' phenotypic_class FBcv:0000384 aging defective Phenotype that is a defect in aging (GO:0007568). 'aging' is defined as: 'A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).' GOC:PO_curators 5 5 Phenotype that is a shorter adult life-span than wild-type. increased adult mortality phenotypic_class FBcv:0000385 short lived Phenotype that is a shorter adult life-span than wild-type. FBC:DOS Phenotype that is a longer adult life-span than wild-type. phenotypic_class FBcv:0000386 long lived Phenotype that is a longer adult life-span than wild-type. FBC:DOS Phenotype that is a defect in behavior (GO:0007610). 'behavior' is defined as: 'The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.' behaviour defective behavioural phenotypic_class behavioral FBcv:0000387 behavior defective Phenotype that is a defect in behavior (GO:0007610). 'behavior' is defined as: 'The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.' GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 Phenotype that is a change in the strong tendency, seen in wild-type Drosophila melanogaster, to climb - a behavior otherwise known as negative gravitaxis (GO:0048060 ; movement away from the source of gravity). phenotypic_class geotaxis behaviour defective gravitaxis behavior defective FBcv:0000388 Note, this term should not be used when flies have climbing defects purely as a consequence of locomotion defects, use 'locomotor behavior defective' instead. gravitaxis defective Phenotype that is a change in the strong tendency, seen in wild-type Drosophila melanogaster, to climb - a behavior otherwise known as negative gravitaxis (GO:0048060 ; movement away from the source of gravity). FBC:DOS Phenotype that is a disposition to paralysis under conditions that do not cause paralysis in a wild-type animal. Paralysis is defined as an inability to exhibit `multicellular organismal movement` (GO:0050879) phenotypic_class FBcv:0000389 paralytic Phenotype that is a disposition to paralysis under conditions that do not cause paralysis in a wild-type animal. Paralysis is defined as an inability to exhibit `multicellular organismal movement` (GO:0050879) FBC:DOS A phenotype consisting of decreased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type. phenotypic_class FBcv:0000390 hypoactive A phenotype consisting of decreased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type. FBC:DOS A phenotype exhibited following mechanical shock and consisting of a brief period of intense, uncoordinated motor activity (legs and wings flailing, abdomen coiling) followed by a prolonged period of paralysis. phenotypic_class easily shocked FBcv:0000391 bang sensitive A phenotype exhibited following mechanical shock and consisting of a brief period of intense, uncoordinated motor activity (legs and wings flailing, abdomen coiling) followed by a prolonged period of paralysis. FlyBase:FBrf0022877 easily shocked FlyBase:FBrf0022877 A phenotype consisting of increased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type. phenotypic_class FBcv:0000392 hyperactive A phenotype consisting of increased frequency of `multicellular organismal movement` (GO:0050879) compared to wild-type. FBC:DOS Phenotype that is a defect in response to pain (GO:0048265). 'response to pain' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.' phenotypic_class FBcv:0000393 pain response defective Phenotype that is a defect in response to pain (GO:0048265). 'response to pain' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.' FBC:DOS GOC:jid PMID:10203867 PMID:12723742 PMID:12843304 Wikipedia:Pain Phenotype that is a defect in circadian rhythm (GO:0007623). 'circadian rhythm' is defined as: 'Any biological process in an organism that recurs with a regularity of approximately 24 hours.' phenotypic_class FBcv:0000394 circadian rhythm defective Phenotype that is a defect in circadian rhythm (GO:0007623). 'circadian rhythm' is defined as: 'Any biological process in an organism that recurs with a regularity of approximately 24 hours.' FBC:DOS GOC:bf GOC:go_curators Phenotype that is a defect in locomotor rhythm (GO:0045475). 'locomotor rhythm' is defined as: 'The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.' phenotypic_class FBcv:0000395 locomotor rhythm defective Phenotype that is a defect in locomotor rhythm (GO:0045475). 'locomotor rhythm' is defined as: 'The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.' FBC:DOS GOC:go_curators Phenotype that is a defect in eclosion rhythm (GO:0008062). 'eclosion rhythm' is defined as: 'The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.' phenotypic_class FBcv:0000396 eclosion rhythm defective Phenotype that is a defect in eclosion rhythm (GO:0008062). 'eclosion rhythm' is defined as: 'The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.' FBC:DOS PMID:11715043 Phenotype that is a defect in learning (GO:0007612). 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.' phenotypic_class FBcv:0000397 learning defective Phenotype that is a defect in learning (GO:0007612). 'learning' is defined as: 'Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.' FBC:DOS ISBN:0582227089 ISBN:0721662544 Phenotype that is a defect in memory (GO:0007613). 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).' phenotypic_class FBcv:0000398 memory defective Phenotype that is a defect in memory (GO:0007613). 'memory' is defined as: 'The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).' FBC:DOS GOC:curators ISBN:0582227089 http://www.onelook.com/ Phenotype that is a defect in courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.' phenotypic_class FBcv:0000399 courtship behavior defective Phenotype that is a defect in courtship behavior (GO:0007619). 'courtship behavior' is defined as: 'The behavior of an organism for the purpose of attracting sexual partners.' FBC:DOS GOC:ai GOC:dph Phenotype that is a defect in mating (GO:0007618). 'mating' is defined as: 'The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.' phenotypic_class FBcv:0000400 mating defective Phenotype that is a defect in mating (GO:0007618). 'mating' is defined as: 'The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes.' FBC:DOS GOC:jl ISBN:0387520546 Phenotype that is a defect in circadian mating behavior (GO:0035648). 'circadian mating behavior' is defined as: 'The fluctuation in mating behavior that occurs over an approximately 24 hour cycle.' phenotypic_class FBcv:0000401 mating rhythm defective Phenotype that is a defect in circadian mating behavior (GO:0035648). 'circadian mating behavior' is defined as: 'The fluctuation in mating behavior that occurs over an approximately 24 hour cycle.' FBC:DOS GOC:bf GOC:dos PMID:11470898 PMID:17276917 Phenotype that is a defect in male courtship behavior, veined wing generated song production (GO:0045433). This is defined as 'The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.' singing defective song production defective phenotypic_class FBcv:0000402 song defective Phenotype that is a defect in male courtship behavior, veined wing generated song production (GO:0045433). This is defined as 'The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.' FBC:DOS GOC:mtg_sensu PMID:11092827 singing defective FBC:SM song production defective FBC:SM Phenotype that is a defect in chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.' chemosensitive behaviour defective phenotypic_class FBcv:0000403 chemosensitive behavior defective Phenotype that is a defect in chemosensory behavior (GO:0007635). 'chemosensory behavior' is defined as: 'Behavior that is dependent upon the sensation of chemicals.'.' FBC:DOS GOC:go_curators Phenotype that is a defect in sensory perception of smell (GO:0007608). 'sensory perception of smell' is defined as: 'The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.' olfaction defective phenotypic_class FBcv:0000404 smell perception defective Phenotype that is a defect in sensory perception of smell (GO:0007608). 'sensory perception of smell' is defined as: 'The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.' FBC:DOS GOC:ai http://www.onelook.com/ Phenotype that is a defect in sensory perception of taste (GO:0050909). 'sensory perception of taste' is defined as: 'The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.' gustation defective taste defective phenotypic_class FBcv:0000405 taste perception defective Phenotype that is a defect in sensory perception of taste (GO:0050909). 'sensory perception of taste' is defined as: 'The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.' FBC:DOS GOC:ai http://www.onelook.com/ Phenotype that is a failure to exhibit proboscis extension reflex in response to a sugar stimulus via taste sensilla on the tarsus. phenotypic_class FBcv:0000406 tarsal response defective Phenotype that is a failure to exhibit proboscis extension reflex in response to a sugar stimulus via taste sensilla on the tarsus. FBC:DOS Phenotype that is a defect in sensory perception of sound (GO:0007605). 'sensory perception of sound' is defined as: 'The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.' phenotypic_class auditory system defective FBcv:0000407 auditory perception defective Phenotype that is a defect in sensory perception of sound (GO:0007605). 'sensory perception of sound' is defined as: 'The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.' FBC:DOS GOC:ai Phenotype that is a defect in response to stress (GO:0006950). 'response to stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).' environmental stress response defective phenotypic_class FBcv:0000408 stress response defective Phenotype that is a defect in response to stress (GO:0006950). 'response to stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).' FBC:DOS GOC:mah Phenotype that is a defect in response to osmotic stress (GO:0006970). 'response to osmotic stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.' phenotypic_class FBcv:0000409 osmotic stress response defective Phenotype that is a defect in response to osmotic stress (GO:0006970). 'response to osmotic stress' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.' FBC:DOS GOC:jl Phenotype that is a defect in response to heat (GO:0009408). 'response to heat' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.' phenotypic_class FBcv:0000410 heat stress response defective Phenotype that is a defect in response to heat (GO:0009408). 'response to heat' is defined as: 'Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.' FBC:DOS GOC:lr Phenotype that is a defect in visual behavior (GO:0007632). 'visual behavior' is defined as: 'The behavior of an organism in response to a visual stimulus.' visual behaviour defective phenotypic_class FBcv:0000411 visual behavior defective Phenotype that is a defect in visual behavior (GO:0007632). 'visual behavior' is defined as: 'The behavior of an organism in response to a visual stimulus.' FBC:DOS GOC:jid GOC:pr Phenotype that is a defect in optomotor response: a motor response during flight or walking that serves to stabilize both image formation on the retina and locomotor course. optomotor behaviour defective phenotypic_class FBcv:0000412 optomotor response defective Phenotype that is a defect in optomotor response: a motor response during flight or walking that serves to stabilize both image formation on the retina and locomotor course. FBC:DOS Phenotype that is a defect in phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.' phenotypic_class phototaxis behaviour defective FBcv:0000413 phototaxis defective Phenotype that is a defect in phototaxis (GO:0042331). 'phototaxis' is defined as: 'The directed movement of a motile cell or organism in response to light.' FBC:DOS GOC:jl ISBN:0192800981 Phenotype that is a defect in locomotory behavior (GO:0007626). 'locomotory behavior' is defined as: 'The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.' locomotor behaviour defective phenotypic_class FBcv:0000414 locomotor behavior defective Phenotype that is a defect in locomotory behavior (GO:0007626). 'locomotory behavior' is defined as: 'The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.' FBC:DOS GOC:dph Phenotype that is a reduced ability to jump or a reduced jump response. This may be due to neurological or muscular defects. phenotypic_class FBcv:0000415 jumping defective Phenotype that is a reduced ability to jump or a reduced jump response. This may be due to neurological or muscular defects. FBC:DOS Phenotype that is a lack of normal co-ordination in locomotor activity. phenotypic_class FBcv:0000416 uncoordinated Phenotype that is a lack of normal co-ordination in locomotor activity. FBC:DOS Phenotype that is a defect in flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.' flight behaviour defective phenotypic_class FBcv:0000417 This term is agnostic as to the causes of defects in flight. An animal's flight may be defective for mechanical, behavioral or sensory reasons. flight defective Phenotype that is a defect in flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.' FBC:DOS GOC:dph Phenotype that is the absence of flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.' phenotypic_class FBcv:0000418 This term is agnostic as to the causes of flightlessness. An animal may be flightless for mechanical or behavioral reasons. flightless Phenotype that is the absence of flight (GO:0060361). 'flight' is defined as: 'Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.' FBC:DOS GOC:dph Phenotype that is a defect in feeding behavior (GO:0007631). 'feeding behavior' is defined as: 'Behavior associated with the intake of food.' feeding behaviour defective phenotypic_class FBcv:0000419 feeding behavior defective Phenotype that is a defect in feeding behavior (GO:0007631). 'feeding behavior' is defined as: 'Behavior associated with the intake of food.' FBC:DOS GOC:mah Phenotype that is a defect in grooming behavior (GO:0007625). 'grooming behavior' is defined as: 'The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.' grooming behaviour defective phenotypic_class FBcv:0000420 grooming behavior defective Phenotype that is a defect in grooming behavior (GO:0007625). 'grooming behavior' is defined as: 'The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.' FBC:DOS GOC:jl GOC:pr Phenotype that is reduction in or loss of a stereotypical behavioral response to touch. touch sensitivity defective phenotypic_class FBcv:0000421 This phenotype is commonly assayed by scoring larval avoidance responses following stroking of the thoracic segments (see Kernan et al., 1994). On its own, this is not sufficient evidence for a defect in sensory perception of touch, as motor defects can also cause this phenotype. touch response defective Phenotype that is reduction in or loss of a stereotypical behavioral response to touch. FlyBase:FBrf0073546 Phenotype that is a defect in entrainment of circadian clock by photoperiod (GO:0043153), which is defined as: 'The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).' phenotypic_class FBcv:0000422 photoperiod response variant Phenotype that is a defect in entrainment of circadian clock by photoperiod (GO:0043153), which is defined as: 'The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).' FBC:DOS GOC:jl Phenotype that is a defect in DNA repair (GO:0006281). 'DNA repair' is defined as: 'The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.' phenotypic_class FBcv:0000423 DNA repair defective Phenotype that is a defect in DNA repair (GO:0006281). 'DNA repair' is defined as: 'The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.' FBC:DOS PMID:11563486 Phenotype that is a change in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. This may be due to effects on the regulation of cell death (GO:0010941) or in cell death (GO:0008219) pathways themselves. apoptosis defective pcd defective programmed cell death defective phenotypic_class FBcv:0000424 cell death defective Phenotype that is a change in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. This may be due to effects on the regulation of cell death (GO:0010941) or in cell death (GO:0008219) pathways themselves. FBC:DOS Phenotype that is an increase in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. pcd increase programmed cell death increase phenotypic_class FBcv:0000425 increased cell death Phenotype that is an increase in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. FBC:DOS Phenotype that is a decrease in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. pcd decrease programmed cell death decrease phenotypic_class FBcv:0000426 decreased cell death Phenotype that is a decrease in the amount of cell death in a whole animal or in some specific organ tissue or clone of cells compared to wild-type. FBC:DOS Phenotype that is a defect in cell growth (GO:0016049). 'cell growth' is defined as: 'The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.' phenotypic_class FBcv:0000427 Note that defects in cell size are not necessarily the result of defects in cell growth. A change in the rate of cell division in the absence of any change in cell growth rate can result in smaller or larger cells. cell growth defective Phenotype that is a defect in cell growth (GO:0016049). 'cell growth' is defined as: 'The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.' FBC:DOS GOC:ai Phenotype that is a defect in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. phenotypic_class FBcv:0000428 cell size defective Phenotype that is a defect in the size of cells in a whole animal or in some specific organ, tissue or clone of cells compared to wild-type. FBC:DOS Phenotype that is a defect in the shape (PATO:0000052) of some cell compared to wild-type. phenotypic_class FBcv:0000429 cell shape defective Phenotype that is a defect in the shape (PATO:0000052) of some cell compared to wild-type. FBC:DOS Phenotype that is a defect in the asymmetric distribution of components within a cell. For example an epithelial cell is 'cell polarity defective' if it lacks the normal asymmetric distribution of proteins or cell components such as junctions or villi along its apical-basal axis. phenotypic_class FBcv:0000430 cell polarity defective Phenotype that is a defect in the asymmetric distribution of components within a cell. For example an epithelial cell is 'cell polarity defective' if it lacks the normal asymmetric distribution of proteins or cell components such as junctions or villi along its apical-basal axis. FBC:DOS Phenotype that is a defect in meiotic cell cycle (GO:0051321). 'meiotic cell cycle' is defined as: 'Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.' phenotypic_class meiotic FBcv:0000431 meiotic cell cycle defective Phenotype that is a defect in meiotic cell cycle (GO:0051321). 'meiotic cell cycle' is defined as: 'Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.' FBC:DOS GOC:ai Phenotype that is a defect in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: 'Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.' phenotypic_class mitotic FBcv:0000432 mitotic cell cycle defective Phenotype that is a defect in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: 'Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.' FBC:DOS GOC:mah ISBN:0815316194 Reactome:69278 Phenotype that is a defect in cytokinesis (GO:0000910). 'cytokinesis' is defined as: 'The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.' phenotypic_class FBcv:0000433 cytokinesis defective Phenotype that is a defect in cytokinesis (GO:0000910). 'cytokinesis' is defined as: 'The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.' FBC:DOS GOC:mtg_cell_cycle Phenotype that is a defect in the electrophysiological properties of some class of neurons, muscles or anatomical structure of the nervous system. Examples of these phenotypes at the neuron class level include defects in spontaneous or evoked excitatory junction potential. Examples at a more gross anatomical level include abnormal retinal electrophysiology (e.g.- measured by an electroretinogram). phenotypic_class FBcv:0000434 neurophysiology defective Phenotype that is a defect in the electrophysiological properties of some class of neurons, muscles or anatomical structure of the nervous system. Examples of these phenotypes at the neuron class level include defects in spontaneous or evoked excitatory junction potential. Examples at a more gross anatomical level include abnormal retinal electrophysiology (e.g.- measured by an electroretinogram). FBC:DOS Phenotype that is a defect in nervous system (FBbt:00005093). 'nervous system' is defined as: 'All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.' phenotypic_class FBcv:0000435 neuroanatomy defective Phenotype that is a defect in nervous system (FBbt:00005093). 'nervous system' is defined as: 'All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.' FBC:DOS FlyBase:FBrf0166419 Phenotype that is a defect in sex determination (GO:0007530). 'sex determination' is defined as: 'Any process that establishes and transmits the specification of sexual status of an individual organism.' phenotypic_class FBcv:0000436