From afa762ae35acca1ac23aefdb4a8bf10d5bf31cc7 Mon Sep 17 00:00:00 2001 From: ybradford Date: Mon, 14 Feb 2022 12:02:57 -0800 Subject: [PATCH] add exp cond to AGR slim add experimental condition to AGR slim and fix typo --- imports/ro_import.owl | 804 ++++++++++++++---- reports/zeco-edit.owl-obo-report.tsv | 2 +- src/ontology/imports/ro_import.owl | 804 ++++++++++++++---- src/ontology/ontologyterms.txt | 4 +- .../reports/zeco-edit.owl-obo-report.tsv | 2 +- src/ontology/zeco-edit.owl | 3 +- zeco-base.json | 93 +- zeco-base.obo | 7 +- zeco-base.owl | 7 +- zeco-full.json | 773 +++++++++++++---- zeco-full.obo | 285 +++++-- zeco-full.owl | 794 +++++++++++++---- zeco-simple.json | 163 ++-- zeco-simple.obo | 11 +- zeco-simple.owl | 13 +- zeco.json | 119 +-- zeco.obo | 11 +- zeco.owl | 13 +- 18 files changed, 3009 insertions(+), 899 deletions(-) diff --git a/imports/ro_import.owl b/imports/ro_import.owl index 20372cf..d597f29 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -7,8 +7,8 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" @@ -16,8 +16,8 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2021-06-04 + + 2022-02-14 @@ -114,6 +114,15 @@ + + + + + term replaced by + + + + @@ -216,6 +225,12 @@ + + + + + + @@ -228,6 +243,12 @@ + + + + + + @@ -336,9 +357,9 @@ - + - + @@ -365,7 +386,7 @@ 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -401,7 +422,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -458,43 +479,38 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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 + + has characteristic @@ -538,6 +554,124 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + @@ -929,7 +1063,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall has function in capable of part of - + @@ -1110,6 +1244,39 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + q characteristic of 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 characteristic of part of + Chris Mungall + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + @@ -1154,7 +1321,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 @@ -1526,42 +1692,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - 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. 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 - - 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 - - - - @@ -1576,8 +1706,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different in pairwise interaction with interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 @@ -1593,7 +1723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 + http://purl.obolibrary.org/obo/MI_0915 @@ -1687,32 +1817,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - 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 - - - - @@ -1750,6 +1854,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + Chris Mungall + depends on + + + + + @@ -1785,7 +1899,7 @@ For example, A and B may be gene products and binding of B by A positively regul Chris Mungall interaction relation helper property - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -2096,6 +2210,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + + + + + disposition + + + + + + + + + + + + + + + + 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. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + 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. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + function + + + + @@ -2266,6 +2528,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + quality (PATO) + quality + + + + + + + + term replaced by + + + + @@ -216,6 +225,12 @@ + + + + + + @@ -228,6 +243,12 @@ + + + + + + @@ -336,9 +357,9 @@ - + - + @@ -365,7 +386,7 @@ 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -401,7 +422,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -458,43 +479,38 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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 + + has characteristic @@ -538,6 +554,124 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + @@ -929,7 +1063,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall has function in capable of part of - + @@ -1110,6 +1244,39 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + q characteristic of 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 characteristic of part of + Chris Mungall + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + @@ -1154,7 +1321,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 @@ -1526,42 +1692,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - 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. 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 - - 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 - - - - @@ -1576,8 +1706,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different in pairwise interaction with interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 @@ -1593,7 +1723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 + http://purl.obolibrary.org/obo/MI_0915 @@ -1687,32 +1817,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - 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 - - - - @@ -1750,6 +1854,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + Chris Mungall + depends on + + + + + @@ -1785,7 +1899,7 @@ For example, A and B may be gene products and binding of B by A positively regul Chris Mungall interaction relation helper property - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -2096,6 +2210,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + + + + + disposition + + + + + + + + + + + + + + + + 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. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + 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. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + function + + + + @@ -2266,6 +2528,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + quality (PATO) + quality + + + + + term replaced by + term replaced by @@ -265,6 +267,12 @@ + + + + + + @@ -413,9 +421,9 @@ - + - + @@ -442,7 +450,7 @@ 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -478,7 +486,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -535,43 +543,38 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + 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 + + has characteristic @@ -615,6 +618,124 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + @@ -1006,7 +1127,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall has function in capable of part of - + @@ -1187,6 +1308,39 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + q characteristic of 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 characteristic of part of + Chris Mungall + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + @@ -1231,7 +1385,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 @@ -1603,42 +1756,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - 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. 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 - - 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 - - - - @@ -1653,8 +1770,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different in pairwise interaction with interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 @@ -1670,7 +1787,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 + http://purl.obolibrary.org/obo/MI_0915 @@ -1764,32 +1881,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - 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 - - - - @@ -1827,6 +1918,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + Chris Mungall + depends on + + + + + @@ -1862,7 +1963,7 @@ For example, A and B may be gene products and binding of B by A positively regul Chris Mungall interaction relation helper property - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -2173,6 +2274,76 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + A diagnostic testing device utilizes a specimen. + X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y. + Asiyah Lin + https://orcid.org/0000-0001-9625-1899 Bill Duncan + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08 + utilizes + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + + + + + disposition + + + + + + + + + + + + + + + + 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. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + 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. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + function + + + + @@ -2343,6 +2592,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + quality (PATO) + quality + + + + @@ -2390,6 +2649,7 @@ For example, A and B may be gene products and binding of B by A positively regul Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition. + experimental conditions @@ -2482,7 +2742,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Experimental condition in which the availabity of food is manipulated. + Experimental condition in which the availability of food is manipulated. food availability @@ -4022,6 +4282,12 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + @@ -4076,6 +4342,15 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + @@ -4131,6 +4406,178 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -4389,51 +4836,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction @@ -5034,6 +5436,94 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/zeco-simple.json b/zeco-simple.json index 2284b1f..c2868ba 100644 --- a/zeco-simple.json +++ b/zeco-simple.json @@ -256,6 +256,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" @@ -295,9 +298,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." @@ -336,6 +336,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -354,9 +357,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this year has part this day (occurrent parthood)" @@ -538,7 +538,7 @@ "id" : "http://purl.obolibrary.org/obo/ZECO_0000113", "meta" : { "definition" : { - "val" : "Experimental condition in which the availabity of food is manipulated.", + "val" : "Experimental condition in which the availability of food is manipulated.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ZECO_0000267" ] @@ -849,6 +849,16 @@ }, "type" : "CLASS", "lbl" : "cauterization" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term replaced by" }, { "id" : "http://purl.obolibrary.org/obo/ZECO_0000139", "meta" : { @@ -859,10 +869,6 @@ }, "type" : "CLASS", "lbl" : "low glucose" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "type" : "PROPERTY", - "lbl" : "term replaced by" }, { "id" : "http://purl.obolibrary.org/obo/ZECO_0000253", "meta" : { @@ -1224,7 +1230,8 @@ "definition" : { "val" : "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.", "xrefs" : [ ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ZECO_0000267" ] }, "type" : "CLASS", "lbl" : "experimental conditions" @@ -1621,14 +1628,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000123", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000122" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000156", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000155" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000164", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000160" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000156", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000155" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000114", "pred" : "is_a", @@ -1657,14 +1664,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000216", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000209" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000133", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000132" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000122", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000121" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000133", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000132" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000144", "pred" : "is_a", @@ -1685,14 +1692,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000157", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000155" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000147", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000146" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000158", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000157" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000147", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000146" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000124", "pred" : "is_a", @@ -1709,14 +1716,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000255", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000253" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000243", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000131" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000201", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000200" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000243", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000131" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000223", "pred" : "is_a", @@ -1725,14 +1732,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000242", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000250" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000145", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000143" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000145", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000143" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000134", "pred" : "is_a", @@ -1793,14 +1800,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000126", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000125" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000137", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000136" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000148", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000147" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000137", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000136" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000128", "pred" : "is_a", @@ -1817,14 +1824,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000205", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000203" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000129", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000128" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000118", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000117" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000129", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000128" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000104", "pred" : "is_a", @@ -1838,17 +1845,17 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000110" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000138", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000116", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000136" + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000247" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000149", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000147" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000116", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000138", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000247" + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000136" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000127", "pred" : "is_a", @@ -1889,14 +1896,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000172", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000171" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000193", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000191" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000161", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000160" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000193", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000191" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000183", "pred" : "is_a", @@ -1921,14 +1928,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000222", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000104" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000130", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000250" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000141", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000130", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000250" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000152", "pred" : "is_a", @@ -1953,30 +1960,30 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000162", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000161" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000184", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000183" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000195", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000194" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000184", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000183" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000253", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000252" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000255", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000264", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000111" + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000154" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000241", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000251" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000264", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000255", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000154" + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000111" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000180", "pred" : "is_a", @@ -1986,25 +1993,25 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000229" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000155", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000142", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000131" + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000153", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000151" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000142", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000165", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000155", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000164" + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000131" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000186", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000184" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000165", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000198", "pred" : "is_a", @@ -2017,14 +2024,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000241", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000240" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000259", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000229" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000215", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000209" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000259", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000229" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000194", "pred" : "is_a", @@ -2233,14 +2240,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000209", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000208" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000219", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000217" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000174", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000229" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000219", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000217" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000227", "pred" : "is_a", @@ -2324,9 +2331,9 @@ "val" : "zebrafish_experimental_conditions_ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2021-06-04" + "val" : "2022-02-14" } ], - "version" : "http://purl.obolibrary.org/obo/zeco/releases/2021-06-04/zeco-simple.json" + "version" : "http://purl.obolibrary.org/obo/zeco/releases/2022-02-14/zeco-simple.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], diff --git a/zeco-simple.obo b/zeco-simple.obo index df65987..d31cdfb 100644 --- a/zeco-simple.obo +++ b/zeco-simple.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: zeco/releases/2021-06-04/zeco-simple.owl +data-version: zeco/releases/2022-02-14/zeco-simple.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -11,7 +11,7 @@ ontology: zeco/zeco-simple property_value: http://purl.org/dc/elements/1.1/description "Ontology of Zebrafish Experimental Conditions" xsd:string property_value: http://purl.org/dc/elements/1.1/title "Zebrafish Experimental Conditions Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ -property_value: owl:versionInfo "2021-06-04" xsd:string +property_value: owl:versionInfo "2022-02-14" xsd:string [Term] id: ZECO:0000100 @@ -43,6 +43,7 @@ is_a: ZECO:0000100 ! conditions id: ZECO:0000104 name: experimental conditions def: "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition." [] +subset: ZECO:0000267 is_a: ZECO:0000100 ! conditions [Term] @@ -99,7 +100,7 @@ is_a: ZECO:0000104 ! experimental conditions [Term] id: ZECO:0000113 name: food availability -def: "Experimental condition in which the availabity of food is manipulated." [] +def: "Experimental condition in which the availability of food is manipulated." [] subset: ZECO:0000267 is_a: ZECO:0000104 ! experimental conditions @@ -985,7 +986,7 @@ property_value: IAO:0000112 "my brain is part of my body (continuant parthood, t property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 @@ -1014,7 +1015,7 @@ property_value: IAO:0000112 "my body has part my brain (continuant parthood, two property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 diff --git a/zeco-simple.owl b/zeco-simple.owl index 4271e08..e661321 100644 --- a/zeco-simple.owl +++ b/zeco-simple.owl @@ -12,12 +12,12 @@ xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Ontology of Zebrafish Experimental Conditions Zebrafish Experimental Conditions Ontology zebrafish_experimental_conditions_ontology - 2021-06-04 + 2022-02-14 @@ -105,7 +105,9 @@ + term replaced by + term replaced by @@ -336,7 +338,7 @@ 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -371,7 +373,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -466,6 +468,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition. + experimental conditions @@ -558,7 +561,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Experimental condition in which the availabity of food is manipulated. + Experimental condition in which the availability of food is manipulated. food availability diff --git a/zeco.json b/zeco.json index e4cf16d..acc80cc 100644 --- a/zeco.json +++ b/zeco.json @@ -256,6 +256,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" @@ -295,9 +298,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." @@ -336,6 +336,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -354,9 +357,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this year has part this day (occurrent parthood)" @@ -538,7 +538,7 @@ "id" : "http://purl.obolibrary.org/obo/ZECO_0000113", "meta" : { "definition" : { - "val" : "Experimental condition in which the availabity of food is manipulated.", + "val" : "Experimental condition in which the availability of food is manipulated.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ZECO_0000267" ] @@ -849,6 +849,16 @@ }, "type" : "CLASS", "lbl" : "cauterization" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term replaced by" }, { "id" : "http://purl.obolibrary.org/obo/ZECO_0000139", "meta" : { @@ -859,10 +869,6 @@ }, "type" : "CLASS", "lbl" : "low glucose" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "type" : "PROPERTY", - "lbl" : "term replaced by" }, { "id" : "http://purl.obolibrary.org/obo/ZECO_0000253", "meta" : { @@ -1224,7 +1230,8 @@ "definition" : { "val" : "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.", "xrefs" : [ ] - } + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ZECO_0000267" ] }, "type" : "CLASS", "lbl" : "experimental conditions" @@ -1621,14 +1628,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000123", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000122" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000164", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000160" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000156", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000155" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000164", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000160" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000114", "pred" : "is_a", @@ -1697,14 +1704,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000147", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000146" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000169", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000168" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000122", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000251" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000169", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000168" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000255", "pred" : "is_a", @@ -1725,14 +1732,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000242", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000250" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000187", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000183" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000145", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000143" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000183" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000134", "pred" : "is_a", @@ -1769,14 +1776,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000159", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000157" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000224", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000247", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000113" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000224", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000202", "pred" : "is_a", @@ -1921,10 +1928,6 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000222", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000104" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000152", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000151" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000130", "pred" : "is_a", @@ -1933,6 +1936,10 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000141", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000152", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000151" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000185", "pred" : "is_a", @@ -1965,6 +1972,10 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000253", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000252" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000264", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000154" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000241", "pred" : "is_a", @@ -1973,10 +1984,6 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000255", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000111" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000264", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000154" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000180", "pred" : "is_a", @@ -1997,14 +2004,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000142", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000186", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000184" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000165", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000164" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000186", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000184" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000198", "pred" : "is_a", @@ -2017,14 +2024,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000241", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000240" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000259", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000229" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000215", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000209" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000259", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000229" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000194", "pred" : "is_a", @@ -2101,14 +2108,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000200", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000190" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000171", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000176" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000171", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000176" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000131", "pred" : "is_a", @@ -2158,11 +2165,11 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000209" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000254", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000231", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000106" }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000231", + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000254", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000106" }, { @@ -2233,14 +2240,14 @@ "sub" : "http://purl.obolibrary.org/obo/ZECO_0000209", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000208" - }, { - "sub" : "http://purl.obolibrary.org/obo/ZECO_0000219", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ZECO_0000217" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000174", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ZECO_0000229" + }, { + "sub" : "http://purl.obolibrary.org/obo/ZECO_0000219", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/ZECO_0000217" }, { "sub" : "http://purl.obolibrary.org/obo/ZECO_0000227", "pred" : "is_a", @@ -2324,9 +2331,9 @@ "val" : "zebrafish_experimental_conditions_ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2021-06-04" + "val" : "2022-02-14" } ], - "version" : "http://purl.obolibrary.org/obo/zeco/releases/2021-06-04/zeco.json" + "version" : "http://purl.obolibrary.org/obo/zeco/releases/2022-02-14/zeco.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], diff --git a/zeco.obo b/zeco.obo index 4456f6e..a62b448 100644 --- a/zeco.obo +++ b/zeco.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2021-06-04 +data-version: releases/2022-02-14 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -11,7 +11,7 @@ ontology: zeco property_value: http://purl.org/dc/elements/1.1/description "Ontology of Zebrafish Experimental Conditions" xsd:string property_value: http://purl.org/dc/elements/1.1/title "Zebrafish Experimental Conditions Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ -property_value: owl:versionInfo "2021-06-04" xsd:string +property_value: owl:versionInfo "2022-02-14" xsd:string [Term] id: ZECO:0000100 @@ -43,6 +43,7 @@ is_a: ZECO:0000100 ! conditions id: ZECO:0000104 name: experimental conditions def: "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition." [] +subset: ZECO:0000267 is_a: ZECO:0000100 ! conditions [Term] @@ -99,7 +100,7 @@ is_a: ZECO:0000104 ! experimental conditions [Term] id: ZECO:0000113 name: food availability -def: "Experimental condition in which the availabity of food is manipulated." [] +def: "Experimental condition in which the availability of food is manipulated." [] subset: ZECO:0000267 is_a: ZECO:0000104 ! experimental conditions @@ -985,7 +986,7 @@ property_value: IAO:0000112 "my brain is part of my body (continuant parthood, t property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 @@ -1014,7 +1015,7 @@ property_value: IAO:0000112 "my body has part my brain (continuant parthood, two property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 diff --git a/zeco.owl b/zeco.owl index 877b2ba..5aef499 100644 --- a/zeco.owl +++ b/zeco.owl @@ -12,12 +12,12 @@ xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Ontology of Zebrafish Experimental Conditions Zebrafish Experimental Conditions Ontology zebrafish_experimental_conditions_ontology - 2021-06-04 + 2022-02-14 @@ -105,7 +105,9 @@ + term replaced by + term replaced by @@ -336,7 +338,7 @@ 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -371,7 +373,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -466,6 +468,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition. + experimental conditions @@ -558,7 +561,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - Experimental condition in which the availabity of food is manipulated. + Experimental condition in which the availability of food is manipulated. food availability