diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 20f6ab6..d17e4d2 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5 + container: obolibrary/odkfull:v1.5.1 # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/fbdv.obo b/fbdv.obo index 94eac23..67d1928 100644 --- a/fbdv.obo +++ b/fbdv.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2024-04-25 -date: 25:04:2024 05:20 +data-version: fbdv/releases/2024-06-13 +date: 13:06:2024 09:02 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: goslim_aspergillus "Aspergillus GO slim" @@ -16,19 +16,22 @@ subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" default-namespace: FlyBase_development_CV namespace-id-rule: * FBdv:$sequence(8,7000,10000)$ +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: terms http://purl.org/dc/terms/ ontology: fbdv.obo -property_value: http://purl.org/dc/elements/1.1/creator "http://orcid.org/0000-0002-1373-1705" xsd:string -property_value: http://purl.org/dc/elements/1.1/creator "http://orcid.org/0000-0002-7073-9172" xsd:string -property_value: http://purl.org/dc/elements/1.1/creator "https://orcid.org/0000-0001-5948-3092" xsd:string -property_value: http://purl.org/dc/elements/1.1/creator "https://orcid.org/0000-0002-0027-0858" xsd:string -property_value: http://purl.org/dc/elements/1.1/description "An ontology of Drosophila melanogaster developmental stages." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "Drosophila Developmental Ontology" xsd:string -property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string +property_value: dc:creator "http://orcid.org/0000-0002-1373-1705" xsd:string +property_value: dc:creator "http://orcid.org/0000-0002-7073-9172" xsd:string +property_value: dc:creator "https://orcid.org/0000-0001-5948-3092" xsd:string +property_value: dc:creator "https://orcid.org/0000-0002-0027-0858" xsd:string +property_value: dc:description "An ontology of Drosophila melanogaster developmental stages." xsd:string +property_value: dc:title "Drosophila Developmental Ontology" xsd:string property_value: IAO:0000700 FBdv:00000000 property_value: IAO:0000700 FBdv:00005259 property_value: IAO:0000700 FBdv:00007013 property_value: IAO:0000700 FBdv:00007024 -property_value: owl:versionInfo "2024-04-25" xsd:string +property_value: owl:versionInfo "2024-06-13" xsd:string +property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] id: FBdv:00000000 @@ -70,8 +73,8 @@ id: FBdv:00005259 name: developmental stage alt_id: FBdv:00007010 def: "A temporal subdivision of a developmental process." [FBC:DOS] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2009-10-01T05:56:56Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2009-10-01T05:56:56Z" xsd:string [Term] id: FBdv:00005261 @@ -827,8 +830,8 @@ comment: Temporal ordering number - 440. is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00005339 ! substage of third instar larval stage relationship: RO:0002087 FBdv:00005338 ! immediately preceded by second instar larval stage -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2008-11-13T11:51:56Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2008-11-13T11:51:56Z" xsd:string [Term] id: FBdv:00005341 @@ -840,8 +843,8 @@ synonym: "post-feeding larva" BROAD [] is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00007007 ! substage of late third instar larval stage relationship: RO:0002087 FBdv:00005340 ! immediately preceded by early third instar larval stage -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2008-11-13T11:55:46Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2008-11-13T11:55:46Z" xsd:string [Term] id: FBdv:00005342 @@ -1222,8 +1225,8 @@ def: "The developmental process by which male germ line stem cells self renew or comment: Temporal ordering number - 20000. xref: GO:0007283 is_a: FBdv:00007009 ! developmental process -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2008-06-05T04:51:08Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2008-06-05T04:51:08Z" xsd:string [Term] id: FBdv:00007001 @@ -1240,8 +1243,8 @@ relationship: RO:0002087 FBdv:00007007 ! immediately preceded by late third inst relationship: RO:0002090 FBdv:00005369 ! immediately precedes adult stage relationship: RO:0002090 FBdv:00005370 ! immediately precedes adult stage A1 relationship: RO:0002090 FBdv:00007025 ! immediately precedes immature adult stage -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2008-06-05T04:51:40Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2008-06-05T04:51:40Z" xsd:string [Term] id: FBdv:00007002 @@ -1287,8 +1290,8 @@ def: "Oogenesis stage during which the number of nurse cell nuclei at the anteri comment: Temporal ordering number - 10250. is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00005278 ! substage of oogenesis stage S13 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2008-11-13T06:27:57Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2008-11-13T06:27:57Z" xsd:string [Term] id: FBdv:00007007 @@ -1298,8 +1301,8 @@ comment: Temporal ordering number - 450. is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00005339 ! substage of third instar larval stage relationship: RO:0002087 FBdv:00005340 ! immediately preceded by early third instar larval stage -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2008-12-11T01:19:53Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2008-12-11T01:19:53Z" xsd:string [Term] id: FBdv:00007008 @@ -1312,16 +1315,16 @@ name: developmental process def: "A biological process whose specific outcome is the progression of an integrated living unit (an anatomical structure or an entire organism) over time from an initial condition to a later condition." [GO:0032502] xref: GO:0032502 is_a: FBdv:00007024 ! biological process -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2009-10-01T05:56:42Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2009-10-01T05:56:42Z" xsd:string [Term] id: FBdv:00007011 name: embryonic cycle def: "A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized." [FlyBase:FBrf0049535, FlyBase:FBrf0089570] is_a: FBdv:00007024 ! biological process -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2009-10-01T05:57:41Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2009-10-01T05:57:41Z" xsd:string [Term] id: FBdv:00007012 @@ -1330,23 +1333,23 @@ def: "A temporal subdivision of a Drosophila life, delimited by major transition synonym: "life cycle stage" EXACT [] is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00000000 ! substage of Drosophila life -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2009-10-01T05:59:22Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2009-10-01T05:59:22Z" xsd:string [Term] id: FBdv:00007013 name: age def: "Temporal subdivision of life based on time elapsed since some key developmental transition, such as fertilization, hatching or eclosion." [FBC:DOS] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2010-09-29T12:25:36Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2010-09-29T12:25:36Z" xsd:string [Term] id: FBdv:00007014 name: adult age in days def: "Temporal subdivision of adulthood in days post-eclosion." [FBC:DOS] is_a: FBdv:00007013 ! age -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2010-09-29T12:28:05Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2010-09-29T12:28:05Z" xsd:string [Term] id: FBdv:00007015 @@ -1356,8 +1359,8 @@ comment: Temporal ordering number - 391. Should not be used to stage embryos who is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00005335 ! substage of embryonic stage 17 relationship: RO:0002087 FBdv:00005334 ! immediately preceded by embryonic stage 16 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2011-04-26T11:57:15Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2011-04-26T11:57:15Z" xsd:string [Term] id: FBdv:00007016 @@ -1367,8 +1370,8 @@ comment: Temporal ordering number - 392. Should not be used to stage embryos who is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00005335 ! substage of embryonic stage 17 relationship: RO:0002087 FBdv:00007015 ! immediately preceded by embryonic stage 17(i) -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2011-04-26T12:00:15Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2011-04-26T12:00:15Z" xsd:string [Term] id: FBdv:00007017 @@ -1378,8 +1381,8 @@ comment: Temporal ordering number - 393. Should not be used to stage embryos who is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00005335 ! substage of embryonic stage 17 relationship: RO:0002087 FBdv:00007016 ! immediately preceded by embryonic stage 17(ii) -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2011-04-26T12:01:18Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2011-04-26T12:01:18Z" xsd:string [Term] id: FBdv:00007018 @@ -1389,8 +1392,8 @@ comment: Temporal ordering number - 394. Should not be used to stage embryos who is_a: FBdv:00005259 ! developmental stage relationship: FBdv:00018001 FBdv:00005335 ! substage of embryonic stage 17 relationship: RO:0002087 FBdv:00007017 ! immediately preceded by embryonic stage 17(iii) -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2011-04-26T12:03:14Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2011-04-26T12:03:14Z" xsd:string [Term] id: FBdv:00007019 @@ -1449,8 +1452,8 @@ relationship: FBdv:00018001 FBdv:00007075 ! substage of day 0 of adulthood relationship: RO:0002087 FBdv:00006011 ! immediately preceded by pharate adult stage relationship: RO:0002087 FBdv:00007001 ! immediately preceded by P-stage relationship: RO:0002090 FBdv:00007026 ! immediately precedes mature adult stage -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2013-01-08T20:06:59Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2013-01-08T20:06:59Z" xsd:string [Term] id: FBdv:00007026 @@ -1459,8 +1462,8 @@ def: "Life stage from the end of adult stage A3, when tanning is complete, to de is_a: FBdv:00007012 ! life stage relationship: RO:0002087 FBdv:00006012 ! immediately preceded by adult stage A3 relationship: RO:0002087 FBdv:00007025 ! immediately preceded by immature adult stage -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/date "2013-01-10T13:03:54Z" xsd:string +property_value: terms:contributor http://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2013-01-10T13:03:54Z" xsd:string [Term] id: FBdv:00007075 @@ -2032,8 +2035,8 @@ comment: Temporal ordering number - 1410. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:00007135 ! immediately preceded by day 60 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010002 @@ -2043,8 +2046,8 @@ comment: Temporal ordering number - 1420. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010001 ! immediately preceded by day 61 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010003 @@ -2054,8 +2057,8 @@ comment: Temporal ordering number - 1430. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010002 ! immediately preceded by day 62 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010004 @@ -2065,8 +2068,8 @@ comment: Temporal ordering number - 1440. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010003 ! immediately preceded by day 63 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010005 @@ -2076,8 +2079,8 @@ comment: Temporal ordering number - 1450. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010004 ! immediately preceded by day 64 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010006 @@ -2087,8 +2090,8 @@ comment: Temporal ordering number - 1460. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010005 ! immediately preceded by day 65 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010007 @@ -2098,8 +2101,8 @@ comment: Temporal ordering number - 1470. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010006 ! immediately preceded by day 66 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010008 @@ -2109,8 +2112,8 @@ comment: Temporal ordering number - 1480. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010007 ! immediately preceded by day 67 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010009 @@ -2120,8 +2123,8 @@ comment: Temporal ordering number - 1490. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010008 ! immediately preceded by day 68 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Term] id: FBdv:0010010 @@ -2131,8 +2134,8 @@ comment: Temporal ordering number - 1500. is_a: FBdv:00007014 ! adult age in days relationship: FBdv:00018001 FBdv:00005369 ! substage of adult stage relationship: RO:0002087 FBdv:0010009 ! immediately preceded by day 69 of adulthood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2024-01-15T17:54:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2024-01-15T17:54:59Z" xsd:dateTime [Typedef] id: FBdv:00018001 diff --git a/fly_development.obo b/fly_development.obo index ef4077d..c67358e 100644 --- a/fly_development.obo +++ b/fly_development.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: 2024-04-25 -date: 25:04:2024 05:20 +data-version: 2024-06-13 +date: 13:06:2024 09:02 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: goslim_aspergillus "Aspergillus GO slim" diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 4197d27..8a2180b 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for fbdv # Generated using ontology-development-kit -# ODK Version: v1.5 +# ODK Version: v1.5.1 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use fbdv.Makefile instead @@ -45,8 +45,8 @@ REPORT_LABEL = -l true REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties -SPARQL_EXPORTS = basic-report edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.5 +SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms +ODK_VERSION_MAKEFILE = v1.5.1 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 29e4ac3..aa6d22d 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,26 +7,16 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-04-25") + +Annotation(owl:versionInfo "2024-06-13") Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -34,9 +24,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -55,28 +42,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -87,92 +53,23 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -182,7 +79,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -193,44 +89,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty(rdfs:comment)) -Declaration(AnnotationProperty(rdfs:label)) -############################ -# Annotation Properties -############################ - -# Annotation Property: (definition) - -AnnotationAssertion(rdfs:label "definition") - -# Annotation Property: (subset_property) - -AnnotationAssertion(rdfs:label "subset_property") - -# Annotation Property: (has_broad_synonym) - -AnnotationAssertion(rdfs:label "has_broad_synonym") - -# Annotation Property: (database_cross_reference) - -AnnotationAssertion(rdfs:label "database_cross_reference") - -# Annotation Property: (has_exact_synonym) - -AnnotationAssertion(rdfs:label "has_exact_synonym") - -# Annotation Property: (has_narrow_synonym) - -AnnotationAssertion(rdfs:label "has_narrow_synonym") - -# Annotation Property: (has_obo_format_version) - -AnnotationAssertion(rdfs:label "has_obo_format_version") - -# Annotation Property: (has_related_synonym) - -AnnotationAssertion(rdfs:label "has_related_synonym") - ############################ # Object Properties @@ -270,101 +128,6 @@ TransitiveObjectProperty() ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (characteristic of) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:comment "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.") -AnnotationAssertion(rdfs:label "characteristic of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -FunctionalObjectProperty() - -# Object Property: (has characteristic) - -AnnotationAssertion( "Inverse of characteristic_of"@en) -AnnotationAssertion(rdfs:label "has characteristic"@en) -InverseFunctionalObjectProperty() -ObjectPropertyRange( ) - -# Object Property: (participates in) - -AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion(rdfs:label "participates in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has participant) - -AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion(rdfs:label "has participant"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (function of) - -AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:comment "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.") -AnnotationAssertion(rdfs:label "function of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (quality of) - -AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:comment "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.") -AnnotationAssertion(rdfs:label "quality of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (role of) - -AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:comment "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.") -AnnotationAssertion(rdfs:label "role of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has function) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has function"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has quality) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has quality"@en) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - -# Object Property: (has role) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has role"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion(rdfs:comment "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.") -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - # Object Property: (occurrent part of) AnnotationAssertion( "A part of relation that applies only between occurrents.") @@ -374,72 +137,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (has regulatory component activity) - -AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion(rdfs:label "has regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has negative regulatory component activity) - -AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") -AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") -AnnotationAssertion(rdfs:label "has negative regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has positive regulatory component activity) - -AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") -AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") -AnnotationAssertion(rdfs:label "has positive regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has component activity) - -AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") -AnnotationAssertion(rdfs:label "has component activity") -SubObjectPropertyOf( ) - -# Object Property: (has component process) - -AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") -AnnotationAssertion(rdfs:label "has component process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulated by) - -AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") -AnnotationAssertion(rdfs:label "directly regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly negatively regulated by) - -AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") -AnnotationAssertion(rdfs:label "directly negatively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly positively regulated by) - -AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") -AnnotationAssertion(rdfs:label "directly positively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has effector activity) - -AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") -AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") -AnnotationAssertion(rdfs:label "has effector activity") -SubObjectPropertyOf( ) -FunctionalObjectProperty() - # Object Property: (during which ends) AnnotationAssertion(rdfs:comment "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.") @@ -511,12 +208,6 @@ AnnotationAssertion(rdfs:label "over SubObjectPropertyOf( ) SymmetricObjectProperty() -# Object Property: (has component) - -AnnotationAssertion( "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") -AnnotationAssertion(rdfs:label "has component"@en) -SubObjectPropertyOf( ) - # Object Property: (develops from) AnnotationAssertion( "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") @@ -538,48 +229,6 @@ SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (regulates) - -AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") -AnnotationAssertion(rdfs:label "regulates"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulates) - -AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion(rdfs:label "negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (positively regulates) - -AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion(rdfs:label "positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (capable of) - -AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") -AnnotationAssertion(rdfs:label "capable of"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of part of) - -AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") -AnnotationAssertion(rdfs:label "capable of part of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (temporally related to) AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") @@ -587,14 +236,6 @@ AnnotationAssertion(rdfs:label "temp ObjectPropertyDomain( ) ObjectPropertyRange( ) -# Object Property: (has input) - -AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") -AnnotationAssertion(rdfs:label "has input"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - # Object Property: (has developmental contribution from) AnnotationAssertion( "x has developmental contribution from y iff x has some part z such that z develops from y"@en) @@ -619,46 +260,12 @@ InverseObjectProperties( ) ObjectPropertyRange( ) -# Object Property: (acts upstream of) - -AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") -AnnotationAssertion(rdfs:label "acts upstream of") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within) - -AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") -AnnotationAssertion( "affects") -AnnotationAssertion(rdfs:label "acts upstream of or within") -SubObjectPropertyOf( ) - # Object Property: (developmentally succeeded by) AnnotationAssertion( "Inverse of developmentally preceded by") AnnotationAssertion(rdfs:label "developmentally succeeded by"@en) SubObjectPropertyOf( ) -# Object Property: (causally upstream of, positive effect) - -AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") -AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") -AnnotationAssertion(rdfs:label "causally upstream of, positive effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, negative effect) - -AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") -AnnotationAssertion(rdfs:label "causally upstream of, negative effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (characteristic of part of) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "characteristic of part of"@en) -SubObjectPropertyOf( ) - # Object Property: (mereotopologically related to) AnnotationAssertion( "A mereological relationship or a topological relationship") @@ -669,66 +276,6 @@ AnnotationAssertion(rdfs:label "mere AnnotationAssertion( "A relationship that holds between entities participating in some developmental process (GO:0032502)") AnnotationAssertion(rdfs:label "developmentally related to"@en) -# Object Property: (enables) - -AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion(rdfs:label "enables"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (functionally related to) - -AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") -AnnotationAssertion(rdfs:label "functionally related to"@en) - -# Object Property: (part of structure that is capable of) - -AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") -AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) -SubObjectPropertyOf( ) - -# Object Property: (involved in) - -AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion(rdfs:label "involved in"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enabled by) - -AnnotationAssertion( "inverse of enables") -AnnotationAssertion(rdfs:label "enabled by"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (regulated by) - -AnnotationAssertion( "inverse of regulates") -AnnotationAssertion(rdfs:label "regulated by"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulated by) - -AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion(rdfs:label "negatively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (positively regulated by) - -AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion(rdfs:label "positively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (input of) - -AnnotationAssertion( "inverse of has input") -AnnotationAssertion(rdfs:label "input of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (has developmental potential involving) AnnotationAssertion( "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)."@en) @@ -753,57 +300,11 @@ AnnotationAssertion( "has potential to directly develop into"@en) SubObjectPropertyOf( ) -# Object Property: (causally downstream of) - -AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion(rdfs:label "causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately causally downstream of) - -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (indirectly positively regulates) - -AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (indirectly negatively regulates) - -AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - # Object Property: (causally related to) AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") AnnotationAssertion(rdfs:label "causally related to"@en) -# Object Property: (causally upstream of) - -AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") -AnnotationAssertion(rdfs:label "causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately causally upstream of) - -AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (causally upstream of or within) AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") @@ -820,102 +321,6 @@ AnnotationAssertion(rdfs:label "caus SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (involved in regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion(rdfs:label "involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (involved in positive regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion(rdfs:label "involved in positive regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in negative regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion(rdfs:label "involved in negative regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in or involved in regulation of) - -AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") -AnnotationAssertion(rdfs:label "involved in or involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (interacts with) - -AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "in pairwise interaction with") -AnnotationAssertion(rdfs:label "interacts with") -SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (molecularly interacts with) - -AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") -AnnotationAssertion(rdfs:label "molecularly interacts with") -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (phosphorylates) - -AnnotationAssertion(rdfs:label "phosphorylates") -SubObjectPropertyOf( ) - -# Object Property: (directly regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") -AnnotationAssertion( "molecularly controls") -AnnotationAssertion(rdfs:label "directly regulates activity of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly negatively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") -AnnotationAssertion( "molecularly decreases activity of") -AnnotationAssertion(rdfs:label "directly negatively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly positively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") -AnnotationAssertion( "molecularly increases activity of") -AnnotationAssertion(rdfs:label "directly positively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (helper property (not for use in curation)) - -AnnotationAssertion(rdfs:label "helper property (not for use in curation)") - -# Object Property: (is kinase activity) - -AnnotationAssertion(rdfs:label "is kinase activity") -SubObjectPropertyOf( ) - -# Object Property: (causal agent in process) - -AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion(rdfs:label "causal agent in process") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - # Object Property: (causal relation between processes) AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") @@ -924,272 +329,20 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (depends on) - -AnnotationAssertion(rdfs:label "depends on") - -# Object Property: (causal relation between entities) - -AnnotationAssertion(rdfs:label "causal relation between entities") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (causally influenced by) - -AnnotationAssertion(rdfs:label "causally influenced by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (interaction relation helper property) - -AnnotationAssertion(rdfs:label "interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (molecular interaction relation helper property) - -AnnotationAssertion(rdfs:label "molecular interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (causally influences) - -AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") -AnnotationAssertion(rdfs:label "causally influences") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulates) - -AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion(rdfs:label "directly regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has part structure that is capable of) - -AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") -AnnotationAssertion(rdfs:label "has part structure that is capable of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causal relation between material entity and a process) - -AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") -AnnotationAssertion(rdfs:label "causal relation between material entity and a process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") -AnnotationAssertion(rdfs:label "capable of regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of negatively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion(rdfs:label "capable of negatively regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of positively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") -AnnotationAssertion(rdfs:label "capable of positively regulating") -SubObjectPropertyOf( ) - -# Object Property: (process has causal agent) - -AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion(rdfs:label "process has causal agent") -SubObjectPropertyOf( ) - -# Object Property: (directly positively regulates) - -AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion(rdfs:label "directly positively regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (directly negatively regulates) - -AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion(rdfs:label "directly negatively regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enables subfunction) - -AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") -AnnotationAssertion(rdfs:label "enables subfunction") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, positive effect) - -AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, negative effect) - -AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, positive effect) - -AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") -AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, negative effect) - -AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") -AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, negative effect) - -AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, positive effect) - -AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") -SubObjectPropertyOf( ) - -# Object Property: (regulates activity of) - -AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") -AnnotationAssertion(rdfs:label "regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (indirectly causally upstream of) - -AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) -SubObjectPropertyOf( ) - -# Object Property: (indirectly regulates) - -AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion(rdfs:label "indirectly regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (device utilizes material) - -AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( "utilizes") -AnnotationAssertion(rdfs:label "device utilizes material"@en) - -# Object Property: (regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates characteristic") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) - -# Object Property: (positively regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates characteristic") -SubObjectPropertyOf( ) - -# Object Property: (negatively regulates characteristic) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates characteristic") -SubObjectPropertyOf( ) - ############################ # Classes ############################ -# Class: (continuant) +# Class: () -AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (occurrent) +# Class: () -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) -AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (independent continuant) - -AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) -AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (process) - -AnnotationAssertion( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) -AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) -AnnotationAssertion(rdfs:label "process"@en) -SubClassOf( ) - -# Class: (disposition) - -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (realizable entity) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (specifically dependent continuant) - -AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) -AnnotationAssertion(rdfs:comment "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."@en) -AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (role) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "role"@en) -SubClassOf( ) - -# Class: (function) - -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) - -# Class: (material entity) - -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) -AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) - # Class: (mitotic M phase) AnnotationAssertion(Annotation( "GOC:mtg_cell_cycle") "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle.") @@ -1237,26 +390,6 @@ AnnotationAssertion( "nuclear division") SubClassOf( ) -# Class: (molecular_function) - -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") -AnnotationAssertion( "GO:0005554") -AnnotationAssertion( "molecular function") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003674") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") -AnnotationAssertion(rdfs:label "molecular_function") - -# Class: (catalytic activity) - -AnnotationAssertion(Annotation( "GOC:vw") Annotation( "ISBN:0198506732") "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.") -AnnotationAssertion( "Wikipedia:Enzyme") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "enzyme activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003824") -AnnotationAssertion(rdfs:label "catalytic activity") -SubClassOf( ) - # Class: (organelle organization) AnnotationAssertion(Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") @@ -1353,42 +486,6 @@ AnnotationAssertion( "cellular component organization") SubClassOf( ) -# Class: (kinase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") -AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") -AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") -AnnotationAssertion( "phosphokinase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016301") -AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") -AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) -SubClassOf( ObjectHasSelf()) - -# Class: (transferase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") -AnnotationAssertion( "EC:2.-.-.-") -AnnotationAssertion(Annotation(rdfs:label "PE is converted to PS by PTDSS2") "Reactome:R-HSA-1483089") -AnnotationAssertion(Annotation(rdfs:label "PC is converted to PS by PTDSS1") "Reactome:R-HSA-1483186") -AnnotationAssertion(Annotation(rdfs:label "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK") "Reactome:R-HSA-5668414") -AnnotationAssertion(Annotation(rdfs:label "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248") "Reactome:R-HSA-8868783") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016740") -AnnotationAssertion(rdfs:label "transferase activity") -SubClassOf( ) - -# Class: (transferase activity, transferring phosphorus-containing groups) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "EC:2.7.-.-") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016772") -AnnotationAssertion(rdfs:comment "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.") -AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") -SubClassOf( ) - # Class: (cell cycle process) AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:mtg_cell_cycle") "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.") @@ -1540,83 +637,15 @@ SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "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.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv index 488f6de..40eb906 100644 --- a/src/ontology/reports/basic-report.tsv +++ b/src/ontology/reports/basic-report.tsv @@ -29,12 +29,10 @@ "11th day after eclosion." "24th day after eclosion." "The developmental stage that lasts from eclosion of the adult from the pupal case until tanning is complete (the end of adult stage A3)." - "An entity that has temporal parts and that happens, unfolds or develops through time."@en "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." "Wikipedia:Mitosis" "The 16th cell cycle division of embryogenesis. Asynchronous." "The M-phase of embryonic cycle 14. This is asynchronous across the embryo, but occurs synchronously within discrete domains, known as mitotic domains." "Oogenesis stage that begins when nurse cell chromosomes are no longer bulbous - the association between homologs weakens so that these chromosomes no longer have a polytene structure. During this stage, posterior nurse cell nuclei have a higher ploidy (64C) than anterior ones." - "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en "Pale yellow pigmentation spreads inwards across the eye. Eye color becomes bright yellow, then changes to amber. Duration at 25 degrees C: approximately 12 hours 20 minutes. (164.3-176.6 hours after egg laying; 44.3-56.6 hours after puparium formation)." "Thoracic bristles become visible, and the tips of the wings turn grey. Duration at 25 degrees C: approximately 2 hours. (194.6-196.6 hours after egg laying; 74.6-76.6 hours after puparium formation)." "39th day after eclosion." @@ -58,19 +56,16 @@ "The 11th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." "The anterior spiracles are fully everted, with 7-9 finger-like projections. The body shortens, withdrawing three apparent abdominal segments and the larva sticks to its substrate." "19th day after eclosion." - "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."@en "16th day after eclosion." "13th day after eclosion." "Oogenesis stage during which polyploidation and enlargement of follicle cells begins. Nurse cell ploidy ranges from 256C (anterior) to 512C (posterior) and the egg chamber gains an elongated shape." "Malpighian tubules become prominent and green. Duration at 25 degrees C: approximately 5 hours, 25 minutes. (133.3-138.7 hours after egg laying; 13.3-18.7 hours after puparium formation)." "The 12th mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." "Embryonic stage 1-3." - "Stage 8 starts with the rapid phase of germ band extension and ends with the beginning of mesodermal segmentation. By the end of this stage germ band extension has progressed to the point where the proctodeal opening is at about 60% egg length and the dorsal folds (transverse furrows) are no longer visible. Duration at 25 degrees C: approximately 30 minutes (190-220 minutes after egg laying)." "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." "The M-phase (GO:0000279) of an embryonic cycle." "47th day after eclosion." - "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."@en "36th day after eclosion." "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase." "Wikipedia:M_phase" "Oogenesis stage that begins when the centripetal follicle cells begin to migrate. As a result, the vitelline membrane extends into the opercular region. This stage ends when nurse cell dumping begins." @@ -94,7 +89,6 @@ "61st day after eclosion." "Tips of folded wings become grey. Duration at 25 degrees C: approximately 45 minutes (195.5-196.6 hours after egg laying; 75.9-76.6 hours after puparium formation)." "46th day after eclosion." - "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." "Reactome:R-HSA-8868783 EC:2.-.-.- Reactome:R-HSA-5668414 Reactome:R-HSA-1483186 Reactome:R-HSA-1483089" "51st day after eclosion." "31st day after eclosion." "The pupal stage starts once larval/pupal apolysis is complete as indicated by the expulsion of the larval armature. Early in this stage, the legs and wings reach full extension along the abdomen. The stage ends when the pupal cuticle separates from the underlying epidermis (pupal/adult apolysis), and the eye cup becomes yellow at its periphery. Duration at 25 degrees C: approximately 32 hours. (132.2-164.3 hours after egg laying; 12.2-44.3 hours after puparium formation)." @@ -124,7 +118,6 @@ "7th day after eclosion." "Oogenesis stage during which follicle cell division ceases." "3rd day after eclosion." - "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en "Cellularization. Stage 5 begins when cellularization starts. Near the end of this stage the pole cells begin to migrate dorsally and ventral midline cells acquire an irregular, wavy appearance. Stage 5 ends when ventral furrow formation becomes apparent. Duration at 25 degrees: approximately 40 minutes (130-170 minutes after egg laying)." "The day of eclosion." "2nd day after eclosion." @@ -158,7 +151,6 @@ "Third instar larva prior to the wandering stage (approximately the first 24 hours of the third instar larval stage under standard conditions at 25'C.)." "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." "40th day after eclosion." - "Stage 9 begins when mesodermal segmentation becomes (transiently) visible, and ends with the appearance of the stomodeal invagination slightly ventral to the anterior pole. Duration at 25 degrees C: approximately 40 minutes (220-260 minutes after egg laying)." "A cycle of nuclear division during the embryogenesis of Drosophila melanogaster. The first 13 cycles are synchronous throughout the embryo and occur their timing relative to other developmental processes is invariant. Later nuclear division cycles are asynchronous across the embryo although may be more locally synchronized." "The creation of two or more organelles by division of one organelle." @@ -175,7 +167,6 @@ "4th day after eclosion." "6th day after eclosion." - "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." "EC:2.7.-.-" "Oogenesis stage that begins when the oocyte chromosomes condense into a karyosome attached to a distinctive spherical structure known as an endobody. The oocyte nucleolus disappears completely. During this stage, nurse cell ploidy reaches 16C." "A collective term for stages 9 and 10." "20th day after eclosion." @@ -210,7 +201,6 @@ "55th day after eclosion." "Stage of the third larval instar during which the larva wanders out of the food and climbs. Under optimum conditions at 25'C, this occurs approximately 24 hours after the start of the third instar larval stage." "Dark green 'yellow body' appears between the anterior ends of the two Malpighian tubule segments, mid-dorsally at the anterior of the abdomen. Duration at 25 degrees C: approximately 13 hours, 45 minutes. (138.7-152.4 hours after egg laying; 18.7-32.4 hours after puparium formation)." - "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." "Reactome:R-HSA-6788855 Reactome:R-HSA-6788867" "The prepupal stage begins at puparium formation and ends when larval/pupal apolysis is complete, as indicated by the completion of imaginal head sac eversion and the expulsion of the oral armature of the larva. Duration at 25 degrees C: approximately 12 hours. (120-132.2 hours after egg laying; 0-12.2 hours after puparium formation)." "63rd day after eclosion." "Oogenesis stage during which only 5-6 nurse cell nuclei remain at the anterior of the oocyte. The oocyte nucleus is in late prometaphase:the bivalents arrange themselves in on the equatorial plane of the spindle; homologous centromeres are pulled towards the poles." @@ -219,6 +209,7 @@ "62nd day after eclosion." "28th day after eclosion." + "42nd day after eclosion." "The fourth mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." @@ -239,26 +230,22 @@ "The substage of the wandering third instar larval stage when the larva has cleared its gut contents." "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." "Tarsal bristles darken and claws become black. Duration at 25 degrees C: approximately 3 hours, 20 minutes. (198.6-201.9 hours after egg laying; 78.6-81.9 hours after puparium formation)." - "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en "Eye color darkens to deep amber, then becomes pale pink. Duration at 25 degrees C: approximately 18 hours. (176.6-194.5 hours after egg laying; 56.6-74.5 hours after puparium formation)." "The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoon." "GO:0007283" - "Germ band retraction. Stage 12 begins when germ-band retraction starts and ends when this process is complete so that the prospective anal plate occupies the posterior pole. During this stage the posterior and anterior midgut primordia meet and fuse and the tracheal pits fuse to form the tracheal tree. Duration at 25 degrees C: approximately 120 minutes (440-560 minutes after egg laying)." - "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." "44th day after eclosion." + "The stage of the Drosophila life-cycle from hatching to the beginning of puparium formation." "18th day after eclosion." "Stage 10 begins with the appearance of the stomodeal invagination, slightly ventral to the anterior pole. Periodic furrows appear in the embryonic epidermis around the middle of the stage. The germ band continues to extend, reaching its maximum extent of 75% egg length towards the end of the stage. The end of the stage is marked by the beginning of invagination of the tracheal placodes. Duration at 25 degrees : approximately 60 minutes (260-320 minutes after egg laying)." "Stage 15 begins with the appearance of the second midgut constriction. During this stage the 1st and 3rd midgut constrictions form, dorsal closure is completed, and epidermal segmentation is accomplished. This stage ends when the intersegmental grooves can be distinguished at mid-dorsal level. Duration at 25 degrees C: approximately 100 minutes (680-780 minutes after egg laying)." "Life stage from the end of adult stage A3, when tanning is complete, to death." - "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." "Wikipedia:Enzyme" - "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en "Stage which starts when the operculum opens and ends when eclosion is completed. Duration at 25 degrees C: approximately 24 minutes. (219.6-220 hours after egg laying; 99.6-100 hours after puparium formation)." "50th day after eclosion." "34th day after eclosion." "The complete process of formation and maturation of an ovum or female gemate from a primordial female germ cell." "GO:0048477" "5th day after eclosion." "The second mitotic cell cycle of embryogenesis. This occurs synchronously across the embryo." + "45th day after eclosion." "Formation of specialized endochorion structures in the anterior of the follicle: branches in the developing dorsal appendages; compact endochorion lacking the pillars seen in the rest of the follicle." - "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en diff --git a/src/ontology/reports/class-count-by-prefix.tsv b/src/ontology/reports/class-count-by-prefix.tsv new file mode 100644 index 0000000..c73ff95 --- /dev/null +++ b/src/ontology/reports/class-count-by-prefix.tsv @@ -0,0 +1,4 @@ +?prefix ?numberOfClasses +"FBdv" 222 +"BFO" 3 +"GO" 25 diff --git a/src/ontology/reports/edges.tsv b/src/ontology/reports/edges.tsv index 09bc563..34ce829 100644 --- a/src/ontology/reports/edges.tsv +++ b/src/ontology/reports/edges.tsv @@ -1,472 +1,472 @@ ?x ?p ?y - - - - - - - - - - - - - - - - - - - - - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - + + + + + + - - - - - - - - - - + + + + + + + - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - + + + + + + + + - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + + - - - - - - - - + + + - - - - - - + + + + + + + + + + + + + + + + + - - + + + + - - + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + - - - - - + + + + - - - - - - - - - - - + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - - - + + + - - + + + + - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + - - - - - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + @@ -678,44 +678,31 @@ - - - - - - - - - - - - - - - - - - - + - - - - + + + - - - - - - + + + + + + - + + + + - + + + + + + - - - + diff --git a/src/ontology/reports/obo_qc_fbdv.owl.txt b/src/ontology/reports/obo_qc_fbdv.owl.txt index 2852304..1e53dab 100644 --- a/src/ontology/reports/obo_qc_fbdv.owl.txt +++ b/src/ontology/reports/obo_qc_fbdv.owl.txt @@ -1,16 +1,10 @@ Level Rule Name Subject Property Value WARN annotation_whitespace RO:0002093 rdfs:comment X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). @en -WARN annotation_whitespace RO:0002215 IAO:0000115 A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. WARN duplicate_label FBdv:00007009 rdfs:label developmental process WARN duplicate_label GO:0032502 rdfs:label developmental process WARN duplicate_label_synonym FBdv:00007024 oboInOwl:hasExactSynonym biological process -WARN missing_definition BFO:0000016 IAO:0000115 -WARN missing_definition BFO:0000019 IAO:0000115 -WARN missing_definition BFO:0000034 IAO:0000115 WARN missing_definition IAO:0000115 IAO:0000115 WARN missing_definition IAO:0100001 IAO:0000115 -WARN missing_definition RO:0002017 IAO:0000115 -WARN missing_definition RO:0002022 IAO:0000115 WARN missing_definition RO:0002084 IAO:0000115 WARN missing_definition RO:0002085 IAO:0000115 WARN missing_definition RO:0002086 IAO:0000115 @@ -21,19 +15,6 @@ WARN missing_definition RO:0002091 IAO:0000115 WARN missing_definition RO:0002092 IAO:0000115 WARN missing_definition RO:0002093 IAO:0000115 WARN missing_definition RO:0002222 IAO:0000115 -WARN missing_definition RO:0002405 IAO:0000115 -WARN missing_definition RO:0002447 IAO:0000115 -WARN missing_definition RO:0002464 IAO:0000115 -WARN missing_definition RO:0002481 IAO:0000115 -WARN missing_definition RO:0002502 IAO:0000115 -WARN missing_definition RO:0002506 IAO:0000115 -WARN missing_definition RO:0002559 IAO:0000115 -WARN missing_definition RO:0002563 IAO:0000115 -WARN missing_definition RO:0002564 IAO:0000115 -WARN missing_definition RO:0004032 IAO:0000115 -WARN missing_definition RO:0004033 IAO:0000115 -WARN missing_definition RO:0004046 IAO:0000115 -WARN missing_definition RO:0004047 IAO:0000115 WARN missing_definition oboInOwl:NamespaceIdRule IAO:0000115 WARN missing_definition oboInOwl:SubsetProperty IAO:0000115 WARN missing_definition oboInOwl:hasAlternativeId IAO:0000115 @@ -45,73 +26,21 @@ WARN missing_definition oboInOwl:hasOBOFormatVersion IAO:0000115 WARN missing_definition oboInOwl:hasOBONamespace IAO:0000115 WARN missing_definition oboInOwl:hasRelatedSynonym IAO:0000115 WARN missing_definition oboInOwl:id IAO:0000115 -WARN missing_superclass GO:0003674 rdfs:subClassOf WARN missing_superclass GO:0008150 rdfs:subClassOf -INFO lowercase_definition BFO:0000004 IAO:0000115 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])@en -INFO lowercase_definition BFO:0000015 IAO:0000115 p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])@en -INFO lowercase_definition BFO:0000020 IAO:0000115 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en INFO lowercase_definition BFO:0000050 IAO:0000115 a core relation that holds between a part and its whole@en INFO lowercase_definition BFO:0000051 IAO:0000115 a core relation that holds between a whole and its part@en INFO lowercase_definition BFO:0000062 IAO:0000115 x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.@en INFO lowercase_definition BFO:0000063 IAO:0000115 x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.@en -INFO lowercase_definition RO:0000052 IAO:0000115 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.@en -INFO lowercase_definition RO:0000056 IAO:0000115 a relation between a continuant and a process, in which the continuant is somehow involved in the process@en -INFO lowercase_definition RO:0000057 IAO:0000115 a relation between a process and a continuant, in which the continuant is somehow involved in the process@en -INFO lowercase_definition RO:0000079 IAO:0000115 a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence@en -INFO lowercase_definition RO:0000080 IAO:0000115 a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence@en -INFO lowercase_definition RO:0000081 IAO:0000115 a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence@en -INFO lowercase_definition RO:0000085 IAO:0000115 a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence@en -INFO lowercase_definition RO:0000086 IAO:0000115 a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence@en -INFO lowercase_definition RO:0000087 IAO:0000115 a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence@en -INFO lowercase_definition RO:0000091 IAO:0000115 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence@en -INFO lowercase_definition RO:0000092 IAO:0000115 inverse of has disposition -INFO lowercase_definition RO:0002018 IAO:0000115 w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. INFO lowercase_definition RO:0002131 IAO:0000115 x overlaps y if and only if there exists some z such that x has part z and z part of y -INFO lowercase_definition RO:0002180 IAO:0000115 w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. INFO lowercase_definition RO:0002202 IAO:0000115 x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y INFO lowercase_definition RO:0002203 IAO:0000115 inverse of develops from -INFO lowercase_definition RO:0002211 IAO:0000115 p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. -INFO lowercase_definition RO:0002212 IAO:0000115 p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. -INFO lowercase_definition RO:0002213 IAO:0000115 p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. -INFO lowercase_definition RO:0002216 IAO:0000115 c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. -INFO lowercase_definition RO:0002233 IAO:0000115 p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. INFO lowercase_definition RO:0002254 IAO:0000115 x has developmental contribution from y iff x has some part z such that z develops from y@en INFO lowercase_definition RO:0002255 IAO:0000115 inverse of has developmental contribution from -INFO lowercase_definition RO:0002263 IAO:0000115 c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. -INFO lowercase_definition RO:0002264 IAO:0000115 c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. -INFO lowercase_definition RO:0002304 IAO:0000115 p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. -INFO lowercase_definition RO:0002305 IAO:0000115 p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. -INFO lowercase_definition RO:0002314 IAO:0000115 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. -INFO lowercase_definition RO:0002327 IAO:0000115 c enables p iff c is capable of p and c acts to execute p. -INFO lowercase_definition RO:0002329 IAO:0000115 this relation holds between c and p when c is part of some c', and c' is capable of p. -INFO lowercase_definition RO:0002331 IAO:0000115 c involved_in p if and only if c enables some process p', and p' is part of p -INFO lowercase_definition RO:0002333 IAO:0000115 inverse of enables -INFO lowercase_definition RO:0002334 IAO:0000115 inverse of regulates -INFO lowercase_definition RO:0002335 IAO:0000115 inverse of negatively regulates -INFO lowercase_definition RO:0002336 IAO:0000115 inverse of positively regulates -INFO lowercase_definition RO:0002352 IAO:0000115 inverse of has input INFO lowercase_definition RO:0002384 IAO:0000115 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).@en INFO lowercase_definition RO:0002385 IAO:0000115 x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y@en INFO lowercase_definition RO:0002387 IAO:0000115 x has the potential to develop into y iff x develops into y or if x is capable of developing into y@en INFO lowercase_definition RO:0002388 IAO:0000115 x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y@en -INFO lowercase_definition RO:0002404 IAO:0000115 inverse of upstream of -INFO lowercase_definition RO:0002407 IAO:0000115 p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. -INFO lowercase_definition RO:0002409 IAO:0000115 p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. INFO lowercase_definition RO:0002410 IAO:0000115 relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. -INFO lowercase_definition RO:0002411 IAO:0000115 p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. -INFO lowercase_definition RO:0002412 IAO:0000115 p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. INFO lowercase_definition RO:0002418 IAO:0000115 p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. INFO lowercase_definition RO:0002427 IAO:0000115 inverse of causally upstream of or within -INFO lowercase_definition RO:0002428 IAO:0000115 c involved in regulation of p if c is involved in some p' and p' regulates some p -INFO lowercase_definition RO:0002429 IAO:0000115 c involved in regulation of p if c is involved in some p' and p' positively regulates some p -INFO lowercase_definition RO:0002430 IAO:0000115 c involved in regulation of p if c is involved in some p' and p' negatively regulates some p -INFO lowercase_definition RO:0002431 IAO:0000115 c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p INFO lowercase_definition RO:0002501 IAO:0000115 p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. -INFO lowercase_definition RO:0002578 IAO:0000115 p directly regulates q iff p is immediately causally upstream of q and p regulates q. -INFO lowercase_definition RO:0002584 IAO:0000115 s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p -INFO lowercase_definition RO:0002629 IAO:0000115 p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. -INFO lowercase_definition RO:0002630 IAO:0000115 p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. -INFO lowercase_definition RO:0004034 IAO:0000115 c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive -INFO lowercase_definition RO:0004035 IAO:0000115 c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative -INFO lowercase_definition RO:0012011 IAO:0000115 p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. -INFO lowercase_definition RO:0012012 IAO:0000115 p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. diff --git a/src/ontology/reports/obsoletes.tsv b/src/ontology/reports/obsoletes.tsv index ffacc1c..7459792 100644 --- a/src/ontology/reports/obsoletes.tsv +++ b/src/ontology/reports/obsoletes.tsv @@ -3,7 +3,7 @@ - "FBdv:00005330" + diff --git a/src/ontology/reports/robot_simple_diff.txt b/src/ontology/reports/robot_simple_diff.txt index c1c27c4..e80e40f 100644 --- a/src/ontology/reports/robot_simple_diff.txt +++ b/src/ontology/reports/robot_simple_diff.txt @@ -1,9 +1,9 @@ 3 axioms in left ontology but not in right ontology: -- Annotation( "25:04:2024 05:20") -- Annotation( "2024-04-25") -- OntologyID(OntologyIRI() VersionIRI()) +- Annotation( "13:06:2024 09:02") +- Annotation( "2024-06-13") +- OntologyID(OntologyIRI() VersionIRI()) 3 axioms in right ontology but not in left ontology: -+ Annotation( "18:04:2024 09:08") -+ Annotation( "2024-04-18") -+ OntologyID(OntologyIRI() VersionIRI()) ++ Annotation( "25:04:2024 05:20") ++ Annotation( "2024-04-25") ++ OntologyID(OntologyIRI() VersionIRI()) diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv index 5445287..6fe77c3 100644 --- a/src/ontology/reports/synonyms.tsv +++ b/src/ontology/reports/synonyms.tsv @@ -216,63 +216,47 @@ "day 0 of adulthood" "pharate adult stage P11(i)" "day 32 of adulthood" - "catalytic activity" - "mitotic cell cycle phase" - "M phase" "interphase" - "specifically dependent continuant"@en - "multicellular organismal process" - "process"@en - "quality"@en - "independent continuant"@en - "biological_process" + "M phase" + "cell cycle" + "organelle organization" + "mitotic cell cycle process" + "cell cycle phase" + "nuclear division" "cellular process" - "material entity"@en + "mitotic cell cycle, embryonic" + "biological phase" + "mitotic nuclear division" + "developmental process" + "organelle fission" + "mitotic cell cycle phase" "mitotic cell cycle" - "function"@en - "realizable entity"@en "cell cycle process" - "mitotic cell cycle, embryonic" - "continuant"@en - "mitotic cell cycle process" + "embryo development" + "multicellular organism development" + "mitotic interphase" "anatomical structure development" "mitotic M phase" "cellular component organization or biogenesis" - "nuclear division" - "mitotic interphase" - "occurrent"@en - "organelle fission" + "biological_process" + "multicellular organismal process" "cellular component organization" - "transferase activity, transferring phosphorus-containing groups" - "biological phase" - "organelle organization" - "transferase activity" - "embryo development" - "role"@en - "molecular_function" - "cell cycle" - "mitotic nuclear division" - "multicellular organism development" - "cell cycle phase" - "kinase activity" - "developmental process" - "disposition"@en "adult stage II" "pupal stage" "adult stage I" "third instar larva" "adult stage III" "white prepupa" - "single-multicellular organism process" - "single-organism process" - "single organism process" - "single-organism cellular process" - "mitosis" - "karyokinesis" - "cell organization and biogenesis" "single-organism organelle organization" "organelle organization and biogenesis" + "karyokinesis" + "single-organism cellular process" "single-organism developmental process" + "mitosis" + "single-organism process" + "single organism process" + "single-multicellular organism process" + "cell organization and biogenesis" "pupal stage P0" "white prepupa" "cell growth and/or maintenance" @@ -350,31 +334,28 @@ "head involution stage" "pupal stage P11(i)" "head bristles stage" - "enzyme activity" - "M-phase" "karyostasis" - "organismal physiological process" - "physiological process" - "biological process" + "M-phase" + "cell-division cycle" + "single organism organelle organization" + "organelle organisation" "cellular physiological process" "cell physiology" + "mitosis" + "embryogenesis" + "embryonal development" + "interphase of mitotic cell cycle" "development of an anatomical structure" "M-phase of mitotic cell cycle" "M phase of mitotic cell cycle" "cellular component organisation or biogenesis" "cellular component organization or biogenesis at cellular level" "cellular component organisation or biogenesis at cellular level" - "interphase of mitotic cell cycle" + "physiological process" + "biological process" + "organismal physiological process" "cellular component organisation at cellular level" "cell organisation" "cellular component organization in other organism" "cellular component organization at cellular level" "cellular component organisation in other organism" - "single organism organelle organization" - "organelle organisation" - "embryogenesis" - "embryonal development" - "molecular function" - "cell-division cycle" - "mitosis" - "phosphokinase activity" diff --git a/src/ontology/reports/xrefs.tsv b/src/ontology/reports/xrefs.tsv index 538a364..5f9c91f 100644 --- a/src/ontology/reports/xrefs.tsv +++ b/src/ontology/reports/xrefs.tsv @@ -6,18 +6,9 @@ "GO:0008150" "UBERON:8000002" "UBERON:8000001" - "Wikipedia:Enzyme" - "Wikipedia:M_phase" "Wikipedia:Interphase" - "Wikipedia:Biological_process" + "Wikipedia:M_phase" + "Wikipedia:Cell_cycle" "Wikipedia:Mitosis" - "EC:2.7.-.-" - "Reactome:R-HSA-8868783" - "EC:2.-.-.-" - "Reactome:R-HSA-5668414" - "Reactome:R-HSA-1483186" - "Reactome:R-HSA-1483089" "Wikipedia:Embryogenesis" - "Wikipedia:Cell_cycle" - "Reactome:R-HSA-6788855" - "Reactome:R-HSA-6788867" + "Wikipedia:Biological_process" diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql index 0c4d284..a6a4851 100644 --- a/src/sparql/class-count-by-prefix.sparql +++ b/src/sparql/class-count-by-prefix.sparql @@ -7,4 +7,4 @@ SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE FILTER (!isBlank(?cls)) BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) } -GROUP BY ?prefix +GROUP BY ?prefix \ No newline at end of file