From 6fbec5ee440c89becb3cda10f7b06612b6e9a49d Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 31 Aug 2021 10:12:42 +0100 Subject: [PATCH 1/4] removing reports no longer updated --- reports/chado_load_check_simple.txt | 0 reports/fbdv-edit-obo-report.tsv | 4 - reports/fbdv-edit.obo-obo-report.tsv | 100 --------- reports/fbdv.owl-obo-report.tsv | 197 ------------------ src/ontology/reports/basic-report.tsv | 2 - .../reports/class-count-by-prefix.tsv | 2 - src/ontology/reports/edges.tsv | 0 src/ontology/reports/fbdv-edit-obo-report.tsv | 4 - .../reports/fbdv-edit.obo-obo-report.tsv | 100 --------- src/ontology/reports/fbdv.owl-obo-report.tsv | 197 ------------------ src/ontology/reports/obsoletes.tsv | 0 src/ontology/reports/onto_metrics_calc.txt | 0 src/ontology/reports/synonyms.tsv | 2 - src/ontology/reports/xrefs.tsv | 0 14 files changed, 608 deletions(-) delete mode 100644 reports/chado_load_check_simple.txt delete mode 100644 reports/fbdv-edit-obo-report.tsv delete mode 100644 reports/fbdv-edit.obo-obo-report.tsv delete mode 100644 reports/fbdv.owl-obo-report.tsv delete mode 100644 src/ontology/reports/basic-report.tsv delete mode 100644 src/ontology/reports/class-count-by-prefix.tsv delete mode 100644 src/ontology/reports/edges.tsv delete mode 100644 src/ontology/reports/fbdv-edit-obo-report.tsv delete mode 100644 src/ontology/reports/fbdv-edit.obo-obo-report.tsv delete mode 100644 src/ontology/reports/fbdv.owl-obo-report.tsv delete mode 100644 src/ontology/reports/obsoletes.tsv delete mode 100644 src/ontology/reports/onto_metrics_calc.txt delete mode 100644 src/ontology/reports/synonyms.tsv delete mode 100644 src/ontology/reports/xrefs.tsv diff --git a/reports/chado_load_check_simple.txt b/reports/chado_load_check_simple.txt deleted file mode 100644 index e69de29..0000000 diff --git a/reports/fbdv-edit-obo-report.tsv b/reports/fbdv-edit-obo-report.tsv deleted file mode 100644 index 8a7c3f1..0000000 --- a/reports/fbdv-edit-obo-report.tsv +++ /dev/null @@ -1,4 +0,0 @@ -Level Rule Name Subject Property Value -WARN missing_definition FBDV:00000000 IAO:0000115 -WARN missing_definition FBDV:00000000 IAO:0000600 -INFO missing_superclass FBDV:00000000 rdfs:subClassOf diff --git a/reports/fbdv-edit.obo-obo-report.tsv b/reports/fbdv-edit.obo-obo-report.tsv deleted file mode 100644 index e8ab5b2..0000000 --- a/reports/fbdv-edit.obo-obo-report.tsv +++ /dev/null @@ -1,100 +0,0 @@ -Level Rule Name Subject Property Value -ERROR missing_ontology_description fbdv.owl dc11:description -ERROR missing_ontology_license fbdv.owl dc:license -ERROR missing_ontology_title fbdv.owl dc11:title -WARN missing_definition BFO:0000051 IAO:0000115 -WARN missing_definition BFO:0000062 IAO:0000115 -WARN missing_definition FBdv:00004886 IAO:0000115 -WARN missing_definition FBdv:00005287 IAO:0000115 -WARN missing_definition FBdv:00005288 IAO:0000115 -WARN missing_definition FBdv:00007000 IAO:0000115 -WARN missing_definition FBdv:00007009 IAO:0000115 -WARN missing_definition FBdv:00007024 IAO:0000115 -WARN missing_definition FBdv:00018001 IAO:0000115 -WARN missing_definition IAO:0000115 IAO:0000115 -WARN missing_definition IAO:0100001 IAO:0000115 -WARN missing_definition RO:0002012 IAO:0000115 -WARN missing_definition RO:0002087 IAO:0000115 -WARN missing_definition RO:0002090 IAO:0000115 -WARN missing_definition RO:0002131 IAO:0000115 -WARN missing_definition http://purl.obolibrary.org/obo/fbdv#systematic_synonym IAO:0000115 -WARN missing_definition oboInOwl:NamespaceIdRule IAO:0000115 -WARN missing_definition oboInOwl:SubsetProperty IAO:0000115 -WARN missing_definition oboInOwl:SynonymTypeProperty IAO:0000115 -WARN missing_definition oboInOwl:hasAlternativeId IAO:0000115 -WARN missing_definition oboInOwl:hasBroadSynonym IAO:0000115 -WARN missing_definition oboInOwl:hasDbXref IAO:0000115 -WARN missing_definition oboInOwl:hasExactSynonym IAO:0000115 -WARN missing_definition oboInOwl:hasNarrowSynonym IAO:0000115 -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:hasScope IAO:0000115 -WARN missing_definition oboInOwl:shorthand IAO:0000115 -WARN missing_obsolete_label FBdv:00005305 rdfs:label syncytial blastoderm stage -WARN missing_obsolete_label FBdv:00005310 rdfs:label cellular blastoderm stage -WARN missing_obsolete_label FBdv:00005320 rdfs:label germ band stage -WARN missing_obsolete_label FBdv:00005326 rdfs:label contracted germ band stage -WARN missing_obsolete_label FBdv:00005329 rdfs:label head involution stage -WARN missing_obsolete_label FBdv:00005412 rdfs:label gamete -WARN missing_obsolete_label FBdv:00007008 rdfs:label occurrent -INFO lowercase_definition FBdv:00007076 IAO:0000115 1st day after eclosion. -INFO lowercase_definition FBdv:00007077 IAO:0000115 2nd day after eclosion. -INFO lowercase_definition FBdv:00007078 IAO:0000115 3rd day after eclosion. -INFO lowercase_definition FBdv:00007079 IAO:0000115 4th day after eclosion. -INFO lowercase_definition FBdv:00007080 IAO:0000115 5th day after eclosion. -INFO lowercase_definition FBdv:00007081 IAO:0000115 6th day after eclosion. -INFO lowercase_definition FBdv:00007082 IAO:0000115 7th day after eclosion. -INFO lowercase_definition FBdv:00007083 IAO:0000115 8th day after eclosion. -INFO lowercase_definition FBdv:00007084 IAO:0000115 9th day after eclosion. -INFO lowercase_definition FBdv:00007085 IAO:0000115 10th day after eclosion. -INFO lowercase_definition FBdv:00007086 IAO:0000115 11th day after eclosion. -INFO lowercase_definition FBdv:00007087 IAO:0000115 12th day after eclosion. -INFO lowercase_definition FBdv:00007088 IAO:0000115 13th day after eclosion. -INFO lowercase_definition FBdv:00007089 IAO:0000115 14th day after eclosion. -INFO lowercase_definition FBdv:00007090 IAO:0000115 15th day after eclosion. -INFO lowercase_definition FBdv:00007091 IAO:0000115 16th day after eclosion. -INFO lowercase_definition FBdv:00007092 IAO:0000115 17th day after eclosion. -INFO lowercase_definition FBdv:00007093 IAO:0000115 18th day after eclosion. -INFO lowercase_definition FBdv:00007094 IAO:0000115 19th day after eclosion. -INFO lowercase_definition FBdv:00007095 IAO:0000115 20th day after eclosion. -INFO lowercase_definition FBdv:00007096 IAO:0000115 21st day after eclosion. -INFO lowercase_definition FBdv:00007097 IAO:0000115 22nd day after eclosion. -INFO lowercase_definition FBdv:00007098 IAO:0000115 23rd day after eclosion. -INFO lowercase_definition FBdv:00007099 IAO:0000115 24th day after eclosion. -INFO lowercase_definition FBdv:00007100 IAO:0000115 25th day after eclosion. -INFO lowercase_definition FBdv:00007101 IAO:0000115 26th day after eclosion. -INFO lowercase_definition FBdv:00007102 IAO:0000115 27th day after eclosion. -INFO lowercase_definition FBdv:00007103 IAO:0000115 28th day after eclosion. -INFO lowercase_definition FBdv:00007104 IAO:0000115 29th day after eclosion. -INFO lowercase_definition FBdv:00007105 IAO:0000115 30th day after eclosion. -INFO lowercase_definition FBdv:00007106 IAO:0000115 31st day after eclosion. -INFO lowercase_definition FBdv:00007107 IAO:0000115 32nd day after eclosion. -INFO lowercase_definition FBdv:00007108 IAO:0000115 33rd day after eclosion. -INFO lowercase_definition FBdv:00007109 IAO:0000115 34th day after eclosion. -INFO lowercase_definition FBdv:00007110 IAO:0000115 35th day after eclosion. -INFO lowercase_definition FBdv:00007111 IAO:0000115 36th day after eclosion. -INFO lowercase_definition FBdv:00007112 IAO:0000115 37th day after eclosion. -INFO lowercase_definition FBdv:00007113 IAO:0000115 38th day after eclosion. -INFO lowercase_definition FBdv:00007114 IAO:0000115 39th day after eclosion. -INFO lowercase_definition FBdv:00007115 IAO:0000115 40th day after eclosion. -INFO lowercase_definition FBdv:00007116 IAO:0000115 41st day after eclosion. -INFO lowercase_definition FBdv:00007117 IAO:0000115 42nd day after eclosion. -INFO lowercase_definition FBdv:00007118 IAO:0000115 43rd day after eclosion. -INFO lowercase_definition FBdv:00007119 IAO:0000115 44th day after eclosion. -INFO lowercase_definition FBdv:00007120 IAO:0000115 45th day after eclosion. -INFO lowercase_definition FBdv:00007121 IAO:0000115 46th day after eclosion. -INFO lowercase_definition FBdv:00007122 IAO:0000115 47th day after eclosion. -INFO lowercase_definition FBdv:00007123 IAO:0000115 48th day after eclosion. -INFO lowercase_definition FBdv:00007124 IAO:0000115 49th day after eclosion. -INFO lowercase_definition FBdv:00007125 IAO:0000115 50th day after eclosion. -INFO lowercase_definition FBdv:00007126 IAO:0000115 51st day after eclosion. -INFO lowercase_definition FBdv:00007127 IAO:0000115 52nd day after eclosion. -INFO lowercase_definition FBdv:00007128 IAO:0000115 53rd day after eclosion. -INFO lowercase_definition FBdv:00007129 IAO:0000115 54th day after eclosion. -INFO lowercase_definition FBdv:00007130 IAO:0000115 55th day after eclosion. -INFO lowercase_definition FBdv:00007131 IAO:0000115 56th day after eclosion. -INFO lowercase_definition FBdv:00007132 IAO:0000115 57th day after eclosion. -INFO lowercase_definition FBdv:00007133 IAO:0000115 58th day after eclosion. -INFO lowercase_definition FBdv:00007134 IAO:0000115 59th day after eclosion. -INFO lowercase_definition FBdv:00007135 IAO:0000115 60th day after eclosion. diff --git a/reports/fbdv.owl-obo-report.tsv b/reports/fbdv.owl-obo-report.tsv deleted file mode 100644 index 65630cb..0000000 --- a/reports/fbdv.owl-obo-report.tsv +++ /dev/null @@ -1,197 +0,0 @@ -Level Rule Name Subject Property Value -ERROR duplicate_label developmental process rdfs:label developmental process -ERROR duplicate_label developmental process rdfs:label developmental process -ERROR multiple_labels part of rdfs:label part of -ERROR multiple_labels part of rdfs:label part of@en -ERROR multiple_labels has part rdfs:label has part -ERROR multiple_labels has part rdfs:label has part@en -ERROR multiple_labels has part rdfs:label has_part -ERROR multiple_labels preceded_by rdfs:label preceded by@en -ERROR multiple_labels preceded_by rdfs:label preceded_by -ERROR multiple_labels occurent part of rdfs:label occurent part of -ERROR multiple_labels occurent part of rdfs:label occurent_part_of -ERROR multiple_labels immediately preceded by rdfs:label immediately preceded by@en -ERROR multiple_labels immediately preceded by rdfs:label immediately_preceded_by -ERROR multiple_labels immediately precedes rdfs:label ends_at_start_of -ERROR multiple_labels immediately precedes rdfs:label immediately precedes@en -ERROR multiple_labels happens during rdfs:label happens during -ERROR multiple_labels happens during rdfs:label happens during@en -ERROR multiple_labels ends_during rdfs:label ends during@en -ERROR multiple_labels ends_during rdfs:label ends_during -ERROR multiple_labels overlaps rdfs:label overlaps -ERROR multiple_labels overlaps rdfs:label overlaps@en -WARN annotation_whitespace ends_during rdfs:comment -WARN annotation_whitespace capable of definition 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 missing_definition anatomical entity definition -WARN missing_definition biological entity definition -WARN missing_definition oogenesis definition -WARN missing_definition unfertilized egg stage definition -WARN missing_definition fertilized egg stage definition -WARN missing_definition spermatogenesis definition -WARN missing_definition developmental process definition -WARN missing_definition biological process definition -WARN missing_definition substage_of definition -WARN missing_definition molecular_function definition -WARN missing_definition catalytic activity definition -WARN missing_definition kinase activity definition -WARN missing_definition transferase activity definition -WARN missing_definition transferase activity, transferring phosphorus-containing groups definition -WARN missing_definition definition definition -WARN missing_definition term replaced by definition -WARN missing_definition quality definition -WARN missing_definition has component activity definition -WARN missing_definition directly regulated by definition -WARN missing_definition during which ends definition -WARN missing_definition encompasses definition -WARN missing_definition ends after definition -WARN missing_definition immediately preceded by definition -WARN missing_definition during which starts definition -WARN missing_definition immediately precedes definition -WARN missing_definition starts during definition -WARN missing_definition happens during definition -WARN missing_definition ends_during definition -WARN missing_definition temporally related to definition -WARN missing_definition causally upstream of, positive effect definition -WARN missing_definition causally upstream of, negative effect definition -WARN missing_definition enables definition -WARN missing_definition immediately causally downstream of definition -WARN missing_definition phosphorylates definition -WARN missing_definition helper property (not for use in curation) definition -WARN missing_definition is kinase activity definition -WARN missing_definition depends on definition -WARN missing_definition causal relation between entities definition -WARN missing_definition causally influenced by definition -WARN missing_definition interaction relation helper property definition -WARN missing_definition molecular interaction relation helper property definition -WARN missing_definition acts upstream of or within, positive effect definition -WARN missing_definition acts upstream of or within, negative effect definition -WARN missing_definition causally upstream of or within, negative effect definition -WARN missing_definition causally upstream of or within, positive effect definition -WARN missing_definition Systematic synonym definition -WARN missing_definition namespace-id-rule definition -WARN missing_definition subset_property definition -WARN missing_definition synonym_type_property definition -WARN missing_definition has_alternative_id definition -WARN missing_definition has_broad_synonym definition -WARN missing_definition database_cross_reference definition -WARN missing_definition has_exact_synonym definition -WARN missing_definition has_narrow_synonym definition -WARN missing_definition has_obo_format_version definition -WARN missing_definition has_obo_namespace definition -WARN missing_definition has_related_synonym definition -WARN missing_definition has_scope definition -WARN missing_definition shorthand definition -WARN missing_obsolete_label syncytial blastoderm stage rdfs:label syncytial blastoderm stage -WARN missing_obsolete_label cellular blastoderm stage rdfs:label cellular blastoderm stage -WARN missing_obsolete_label germ band stage rdfs:label germ band stage -WARN missing_obsolete_label contracted germ band stage rdfs:label contracted germ band stage -WARN missing_obsolete_label head involution stage rdfs:label head involution stage -WARN missing_obsolete_label gamete rdfs:label gamete -WARN missing_obsolete_label occurrent rdfs:label occurrent -INFO lowercase_definition part of definition a core relation that holds between a part and its whole@en -INFO lowercase_definition has part definition a core relation that holds between a whole and its part@en -INFO lowercase_definition preceded_by definition -INFO lowercase_definition precedes definition -INFO lowercase_definition occurs in definition b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en -INFO lowercase_definition contains process definition [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en -INFO lowercase_definition day 1 of adulthood definition 1st day after eclosion. -INFO lowercase_definition day 2 of adulthood definition 2nd day after eclosion. -INFO lowercase_definition day 3 of adulthood definition 3rd day after eclosion. -INFO lowercase_definition day 4 of adulthood definition 4th day after eclosion. -INFO lowercase_definition day 5 of adulthood definition 5th day after eclosion. -INFO lowercase_definition day 6 of adulthood definition 6th day after eclosion. -INFO lowercase_definition day 7 of adulthood definition 7th day after eclosion. -INFO lowercase_definition day 8 of adulthood definition 8th day after eclosion. -INFO lowercase_definition day 9 of adulthood definition 9th day after eclosion. -INFO lowercase_definition day 10 of adulthood definition 10th day after eclosion. -INFO lowercase_definition day 11 of adulthood definition 11th day after eclosion. -INFO lowercase_definition day 12 of adulthood definition 12th day after eclosion. -INFO lowercase_definition day 13 of adulthood definition 13th day after eclosion. -INFO lowercase_definition day 14 of adulthood definition 14th day after eclosion. -INFO lowercase_definition day 15 of adulthood definition 15th day after eclosion. -INFO lowercase_definition day 16 of adulthood definition 16th day after eclosion. -INFO lowercase_definition day 17 of adulthood definition 17th day after eclosion. -INFO lowercase_definition day 18 of adulthood definition 18th day after eclosion. -INFO lowercase_definition day 19 of adulthood definition 19th day after eclosion. -INFO lowercase_definition day 20 of adulthood definition 20th day after eclosion. -INFO lowercase_definition day 21 of adulthood definition 21st day after eclosion. -INFO lowercase_definition day 22 of adulthood definition 22nd day after eclosion. -INFO lowercase_definition day 23 of adulthood definition 23rd day after eclosion. -INFO lowercase_definition day 24 of adulthood definition 24th day after eclosion. -INFO lowercase_definition day 25 of adulthood definition 25th day after eclosion. -INFO lowercase_definition day 26 of adulthood definition 26th day after eclosion. -INFO lowercase_definition day 27 of adulthood definition 27th day after eclosion. -INFO lowercase_definition day 28 of adulthood definition 28th day after eclosion. -INFO lowercase_definition day 29 of adulthood definition 29th day after eclosion. -INFO lowercase_definition day 30 of adulthood definition 30th day after eclosion. -INFO lowercase_definition day 31 of adulthood definition 31st day after eclosion. -INFO lowercase_definition day 32 of adulthood definition 32nd day after eclosion. -INFO lowercase_definition day 33 of adulthood definition 33rd day after eclosion. -INFO lowercase_definition day 34 of adulthood definition 34th day after eclosion. -INFO lowercase_definition day 35 of adulthood definition 35th day after eclosion. -INFO lowercase_definition day 36 of adulthood definition 36th day after eclosion. -INFO lowercase_definition day 37 of adulthood definition 37th day after eclosion. -INFO lowercase_definition day 38 of adulthood definition 38th day after eclosion. -INFO lowercase_definition day 39 of adulthood definition 39th day after eclosion. -INFO lowercase_definition day 40 of adulthood definition 40th day after eclosion. -INFO lowercase_definition day 41 of adulthood definition 41st day after eclosion. -INFO lowercase_definition day 42 of adulthood definition 42nd day after eclosion. -INFO lowercase_definition day 43 of adulthood definition 43rd day after eclosion. -INFO lowercase_definition day 44 of adulthood definition 44th day after eclosion. -INFO lowercase_definition day 45 of adulthood definition 45th day after eclosion. -INFO lowercase_definition day 46 of adulthood definition 46th day after eclosion. -INFO lowercase_definition day 47 of adulthood definition 47th day after eclosion. -INFO lowercase_definition day 48 of adulthood definition 48th day after eclosion. -INFO lowercase_definition day 49 of adulthood definition 49th day after eclosion. -INFO lowercase_definition day 50 of adulthood definition 50th day after eclosion. -INFO lowercase_definition day 51 of adulthood definition 51st day after eclosion. -INFO lowercase_definition day 52 of adulthood definition 52nd day after eclosion. -INFO lowercase_definition day 53 of adulthood definition 53rd day after eclosion. -INFO lowercase_definition day 54 of adulthood definition 54th day after eclosion. -INFO lowercase_definition day 55 of adulthood definition 55th day after eclosion. -INFO lowercase_definition day 56 of adulthood definition 56th day after eclosion. -INFO lowercase_definition day 57 of adulthood definition 57th day after eclosion. -INFO lowercase_definition day 58 of adulthood definition 58th day after eclosion. -INFO lowercase_definition day 59 of adulthood definition 59th day after eclosion. -INFO lowercase_definition day 60 of adulthood definition 60th day after eclosion. -INFO lowercase_definition participates in definition a relation between a continuant and a process, in which the continuant is somehow involved in the process@en -INFO lowercase_definition has participant definition a relation between a process and a continuant, in which the continuant is somehow involved in the process@en -INFO lowercase_definition has component process definition 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 overlaps definition 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 has component definition 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 develops from definition 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 develops into definition inverse of develops from -INFO lowercase_definition regulates definition -INFO lowercase_definition capable of part of definition 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 has input definition

-INFO lowercase_definition has developmental contribution from definition x has developmental contribution from y iff x has some part z such that z develops from y@en -INFO lowercase_definition developmentally contributes to definition inverse of has developmental contribution from -INFO lowercase_definition acts upstream of definition 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 acts upstream of or within definition 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 inheres in part of definition q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. -INFO lowercase_definition part of structure that is capable of definition this relation holds between c and p when c is part of some c', and c' is capable of p. -INFO lowercase_definition involved in definition c involved_in p if and only if c enables some process p', and p' is part of p -INFO lowercase_definition enabled by definition inverse of enables -INFO lowercase_definition regulated by definition inverse of regulates -INFO lowercase_definition negatively regulated by definition inverse of negatively regulates -INFO lowercase_definition positively regulated by definition inverse of positively regulates -INFO lowercase_definition input of definition inverse of has input -INFO lowercase_definition has developmental potential involving definition 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 has potential to developmentally contribute to definition 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 has potential to develop into definition 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 has potential to directly develop into definition 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 causally downstream of definition inverse of upstream of -INFO lowercase_definition causally upstream of definition p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain -INFO lowercase_definition immediately causally upstream of definition p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. -INFO lowercase_definition causally upstream of or within definition p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. -INFO lowercase_definition causally downstream of or within definition inverse of causally upstream of or within -INFO lowercase_definition involved in regulation of definition c involved in regulation of p if c is involved in some p' and p' regulates some p -INFO lowercase_definition involved in positive regulation of definition c involved in regulation of p if c is involved in some p' and p' positively regulates some p -INFO lowercase_definition involved in negative regulation of definition c involved in regulation of p if c is involved in some p' and p' negatively regulates some p -INFO lowercase_definition involved in or involved in regulation of definition 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 is active in definition c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. -INFO lowercase_definition has part that occurs in definition p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. -INFO lowercase_definition causal relation between processes definition p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. -INFO lowercase_definition has part structure that is capable of definition 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 acts upstream of, positive effect definition 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 acts upstream of, negative effect definition 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 diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv deleted file mode 100644 index 1ff3da9..0000000 --- a/src/ontology/reports/basic-report.tsv +++ /dev/null @@ -1,2 +0,0 @@ -?cls ?def ?xrefs - diff --git a/src/ontology/reports/class-count-by-prefix.tsv b/src/ontology/reports/class-count-by-prefix.tsv deleted file mode 100644 index 654449a..0000000 --- a/src/ontology/reports/class-count-by-prefix.tsv +++ /dev/null @@ -1,2 +0,0 @@ -?prefix ?numberOfClasses -"FBDV" 1 diff --git a/src/ontology/reports/edges.tsv b/src/ontology/reports/edges.tsv deleted file mode 100644 index e69de29..0000000 diff --git a/src/ontology/reports/fbdv-edit-obo-report.tsv b/src/ontology/reports/fbdv-edit-obo-report.tsv deleted file mode 100644 index 8a7c3f1..0000000 --- a/src/ontology/reports/fbdv-edit-obo-report.tsv +++ /dev/null @@ -1,4 +0,0 @@ -Level Rule Name Subject Property Value -WARN missing_definition FBDV:00000000 IAO:0000115 -WARN missing_definition FBDV:00000000 IAO:0000600 -INFO missing_superclass FBDV:00000000 rdfs:subClassOf diff --git a/src/ontology/reports/fbdv-edit.obo-obo-report.tsv b/src/ontology/reports/fbdv-edit.obo-obo-report.tsv deleted file mode 100644 index e8ab5b2..0000000 --- a/src/ontology/reports/fbdv-edit.obo-obo-report.tsv +++ /dev/null @@ -1,100 +0,0 @@ -Level Rule Name Subject Property Value -ERROR missing_ontology_description fbdv.owl dc11:description -ERROR missing_ontology_license fbdv.owl dc:license -ERROR missing_ontology_title fbdv.owl dc11:title -WARN missing_definition BFO:0000051 IAO:0000115 -WARN missing_definition BFO:0000062 IAO:0000115 -WARN missing_definition FBdv:00004886 IAO:0000115 -WARN missing_definition FBdv:00005287 IAO:0000115 -WARN missing_definition FBdv:00005288 IAO:0000115 -WARN missing_definition FBdv:00007000 IAO:0000115 -WARN missing_definition FBdv:00007009 IAO:0000115 -WARN missing_definition FBdv:00007024 IAO:0000115 -WARN missing_definition FBdv:00018001 IAO:0000115 -WARN missing_definition IAO:0000115 IAO:0000115 -WARN missing_definition IAO:0100001 IAO:0000115 -WARN missing_definition RO:0002012 IAO:0000115 -WARN missing_definition RO:0002087 IAO:0000115 -WARN missing_definition RO:0002090 IAO:0000115 -WARN missing_definition RO:0002131 IAO:0000115 -WARN missing_definition http://purl.obolibrary.org/obo/fbdv#systematic_synonym IAO:0000115 -WARN missing_definition oboInOwl:NamespaceIdRule IAO:0000115 -WARN missing_definition oboInOwl:SubsetProperty IAO:0000115 -WARN missing_definition oboInOwl:SynonymTypeProperty IAO:0000115 -WARN missing_definition oboInOwl:hasAlternativeId IAO:0000115 -WARN missing_definition oboInOwl:hasBroadSynonym IAO:0000115 -WARN missing_definition oboInOwl:hasDbXref IAO:0000115 -WARN missing_definition oboInOwl:hasExactSynonym IAO:0000115 -WARN missing_definition oboInOwl:hasNarrowSynonym IAO:0000115 -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:hasScope IAO:0000115 -WARN missing_definition oboInOwl:shorthand IAO:0000115 -WARN missing_obsolete_label FBdv:00005305 rdfs:label syncytial blastoderm stage -WARN missing_obsolete_label FBdv:00005310 rdfs:label cellular blastoderm stage -WARN missing_obsolete_label FBdv:00005320 rdfs:label germ band stage -WARN missing_obsolete_label FBdv:00005326 rdfs:label contracted germ band stage -WARN missing_obsolete_label FBdv:00005329 rdfs:label head involution stage -WARN missing_obsolete_label FBdv:00005412 rdfs:label gamete -WARN missing_obsolete_label FBdv:00007008 rdfs:label occurrent -INFO lowercase_definition FBdv:00007076 IAO:0000115 1st day after eclosion. -INFO lowercase_definition FBdv:00007077 IAO:0000115 2nd day after eclosion. -INFO lowercase_definition FBdv:00007078 IAO:0000115 3rd day after eclosion. -INFO lowercase_definition FBdv:00007079 IAO:0000115 4th day after eclosion. -INFO lowercase_definition FBdv:00007080 IAO:0000115 5th day after eclosion. -INFO lowercase_definition FBdv:00007081 IAO:0000115 6th day after eclosion. -INFO lowercase_definition FBdv:00007082 IAO:0000115 7th day after eclosion. -INFO lowercase_definition FBdv:00007083 IAO:0000115 8th day after eclosion. -INFO lowercase_definition FBdv:00007084 IAO:0000115 9th day after eclosion. -INFO lowercase_definition FBdv:00007085 IAO:0000115 10th day after eclosion. -INFO lowercase_definition FBdv:00007086 IAO:0000115 11th day after eclosion. -INFO lowercase_definition FBdv:00007087 IAO:0000115 12th day after eclosion. -INFO lowercase_definition FBdv:00007088 IAO:0000115 13th day after eclosion. -INFO lowercase_definition FBdv:00007089 IAO:0000115 14th day after eclosion. -INFO lowercase_definition FBdv:00007090 IAO:0000115 15th day after eclosion. -INFO lowercase_definition FBdv:00007091 IAO:0000115 16th day after eclosion. -INFO lowercase_definition FBdv:00007092 IAO:0000115 17th day after eclosion. -INFO lowercase_definition FBdv:00007093 IAO:0000115 18th day after eclosion. -INFO lowercase_definition FBdv:00007094 IAO:0000115 19th day after eclosion. -INFO lowercase_definition FBdv:00007095 IAO:0000115 20th day after eclosion. -INFO lowercase_definition FBdv:00007096 IAO:0000115 21st day after eclosion. -INFO lowercase_definition FBdv:00007097 IAO:0000115 22nd day after eclosion. -INFO lowercase_definition FBdv:00007098 IAO:0000115 23rd day after eclosion. -INFO lowercase_definition FBdv:00007099 IAO:0000115 24th day after eclosion. -INFO lowercase_definition FBdv:00007100 IAO:0000115 25th day after eclosion. -INFO lowercase_definition FBdv:00007101 IAO:0000115 26th day after eclosion. -INFO lowercase_definition FBdv:00007102 IAO:0000115 27th day after eclosion. -INFO lowercase_definition FBdv:00007103 IAO:0000115 28th day after eclosion. -INFO lowercase_definition FBdv:00007104 IAO:0000115 29th day after eclosion. -INFO lowercase_definition FBdv:00007105 IAO:0000115 30th day after eclosion. -INFO lowercase_definition FBdv:00007106 IAO:0000115 31st day after eclosion. -INFO lowercase_definition FBdv:00007107 IAO:0000115 32nd day after eclosion. -INFO lowercase_definition FBdv:00007108 IAO:0000115 33rd day after eclosion. -INFO lowercase_definition FBdv:00007109 IAO:0000115 34th day after eclosion. -INFO lowercase_definition FBdv:00007110 IAO:0000115 35th day after eclosion. -INFO lowercase_definition FBdv:00007111 IAO:0000115 36th day after eclosion. -INFO lowercase_definition FBdv:00007112 IAO:0000115 37th day after eclosion. -INFO lowercase_definition FBdv:00007113 IAO:0000115 38th day after eclosion. -INFO lowercase_definition FBdv:00007114 IAO:0000115 39th day after eclosion. -INFO lowercase_definition FBdv:00007115 IAO:0000115 40th day after eclosion. -INFO lowercase_definition FBdv:00007116 IAO:0000115 41st day after eclosion. -INFO lowercase_definition FBdv:00007117 IAO:0000115 42nd day after eclosion. -INFO lowercase_definition FBdv:00007118 IAO:0000115 43rd day after eclosion. -INFO lowercase_definition FBdv:00007119 IAO:0000115 44th day after eclosion. -INFO lowercase_definition FBdv:00007120 IAO:0000115 45th day after eclosion. -INFO lowercase_definition FBdv:00007121 IAO:0000115 46th day after eclosion. -INFO lowercase_definition FBdv:00007122 IAO:0000115 47th day after eclosion. -INFO lowercase_definition FBdv:00007123 IAO:0000115 48th day after eclosion. -INFO lowercase_definition FBdv:00007124 IAO:0000115 49th day after eclosion. -INFO lowercase_definition FBdv:00007125 IAO:0000115 50th day after eclosion. -INFO lowercase_definition FBdv:00007126 IAO:0000115 51st day after eclosion. -INFO lowercase_definition FBdv:00007127 IAO:0000115 52nd day after eclosion. -INFO lowercase_definition FBdv:00007128 IAO:0000115 53rd day after eclosion. -INFO lowercase_definition FBdv:00007129 IAO:0000115 54th day after eclosion. -INFO lowercase_definition FBdv:00007130 IAO:0000115 55th day after eclosion. -INFO lowercase_definition FBdv:00007131 IAO:0000115 56th day after eclosion. -INFO lowercase_definition FBdv:00007132 IAO:0000115 57th day after eclosion. -INFO lowercase_definition FBdv:00007133 IAO:0000115 58th day after eclosion. -INFO lowercase_definition FBdv:00007134 IAO:0000115 59th day after eclosion. -INFO lowercase_definition FBdv:00007135 IAO:0000115 60th day after eclosion. diff --git a/src/ontology/reports/fbdv.owl-obo-report.tsv b/src/ontology/reports/fbdv.owl-obo-report.tsv deleted file mode 100644 index 65630cb..0000000 --- a/src/ontology/reports/fbdv.owl-obo-report.tsv +++ /dev/null @@ -1,197 +0,0 @@ -Level Rule Name Subject Property Value -ERROR duplicate_label developmental process rdfs:label developmental process -ERROR duplicate_label developmental process rdfs:label developmental process -ERROR multiple_labels part of rdfs:label part of -ERROR multiple_labels part of rdfs:label part of@en -ERROR multiple_labels has part rdfs:label has part -ERROR multiple_labels has part rdfs:label has part@en -ERROR multiple_labels has part rdfs:label has_part -ERROR multiple_labels preceded_by rdfs:label preceded by@en -ERROR multiple_labels preceded_by rdfs:label preceded_by -ERROR multiple_labels occurent part of rdfs:label occurent part of -ERROR multiple_labels occurent part of rdfs:label occurent_part_of -ERROR multiple_labels immediately preceded by rdfs:label immediately preceded by@en -ERROR multiple_labels immediately preceded by rdfs:label immediately_preceded_by -ERROR multiple_labels immediately precedes rdfs:label ends_at_start_of -ERROR multiple_labels immediately precedes rdfs:label immediately precedes@en -ERROR multiple_labels happens during rdfs:label happens during -ERROR multiple_labels happens during rdfs:label happens during@en -ERROR multiple_labels ends_during rdfs:label ends during@en -ERROR multiple_labels ends_during rdfs:label ends_during -ERROR multiple_labels overlaps rdfs:label overlaps -ERROR multiple_labels overlaps rdfs:label overlaps@en -WARN annotation_whitespace ends_during rdfs:comment -WARN annotation_whitespace capable of definition 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 missing_definition anatomical entity definition -WARN missing_definition biological entity definition -WARN missing_definition oogenesis definition -WARN missing_definition unfertilized egg stage definition -WARN missing_definition fertilized egg stage definition -WARN missing_definition spermatogenesis definition -WARN missing_definition developmental process definition -WARN missing_definition biological process definition -WARN missing_definition substage_of definition -WARN missing_definition molecular_function definition -WARN missing_definition catalytic activity definition -WARN missing_definition kinase activity definition -WARN missing_definition transferase activity definition -WARN missing_definition transferase activity, transferring phosphorus-containing groups definition -WARN missing_definition definition definition -WARN missing_definition term replaced by definition -WARN missing_definition quality definition -WARN missing_definition has component activity definition -WARN missing_definition directly regulated by definition -WARN missing_definition during which ends definition -WARN missing_definition encompasses definition -WARN missing_definition ends after definition -WARN missing_definition immediately preceded by definition -WARN missing_definition during which starts definition -WARN missing_definition immediately precedes definition -WARN missing_definition starts during definition -WARN missing_definition happens during definition -WARN missing_definition ends_during definition -WARN missing_definition temporally related to definition -WARN missing_definition causally upstream of, positive effect definition -WARN missing_definition causally upstream of, negative effect definition -WARN missing_definition enables definition -WARN missing_definition immediately causally downstream of definition -WARN missing_definition phosphorylates definition -WARN missing_definition helper property (not for use in curation) definition -WARN missing_definition is kinase activity definition -WARN missing_definition depends on definition -WARN missing_definition causal relation between entities definition -WARN missing_definition causally influenced by definition -WARN missing_definition interaction relation helper property definition -WARN missing_definition molecular interaction relation helper property definition -WARN missing_definition acts upstream of or within, positive effect definition -WARN missing_definition acts upstream of or within, negative effect definition -WARN missing_definition causally upstream of or within, negative effect definition -WARN missing_definition causally upstream of or within, positive effect definition -WARN missing_definition Systematic synonym definition -WARN missing_definition namespace-id-rule definition -WARN missing_definition subset_property definition -WARN missing_definition synonym_type_property definition -WARN missing_definition has_alternative_id definition -WARN missing_definition has_broad_synonym definition -WARN missing_definition database_cross_reference definition -WARN missing_definition has_exact_synonym definition -WARN missing_definition has_narrow_synonym definition -WARN missing_definition has_obo_format_version definition -WARN missing_definition has_obo_namespace definition -WARN missing_definition has_related_synonym definition -WARN missing_definition has_scope definition -WARN missing_definition shorthand definition -WARN missing_obsolete_label syncytial blastoderm stage rdfs:label syncytial blastoderm stage -WARN missing_obsolete_label cellular blastoderm stage rdfs:label cellular blastoderm stage -WARN missing_obsolete_label germ band stage rdfs:label germ band stage -WARN missing_obsolete_label contracted germ band stage rdfs:label contracted germ band stage -WARN missing_obsolete_label head involution stage rdfs:label head involution stage -WARN missing_obsolete_label gamete rdfs:label gamete -WARN missing_obsolete_label occurrent rdfs:label occurrent -INFO lowercase_definition part of definition a core relation that holds between a part and its whole@en -INFO lowercase_definition has part definition a core relation that holds between a whole and its part@en -INFO lowercase_definition preceded_by definition -INFO lowercase_definition precedes definition -INFO lowercase_definition occurs in definition b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en -INFO lowercase_definition contains process definition [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en -INFO lowercase_definition day 1 of adulthood definition 1st day after eclosion. -INFO lowercase_definition day 2 of adulthood definition 2nd day after eclosion. -INFO lowercase_definition day 3 of adulthood definition 3rd day after eclosion. -INFO lowercase_definition day 4 of adulthood definition 4th day after eclosion. -INFO lowercase_definition day 5 of adulthood definition 5th day after eclosion. -INFO lowercase_definition day 6 of adulthood definition 6th day after eclosion. -INFO lowercase_definition day 7 of adulthood definition 7th day after eclosion. -INFO lowercase_definition day 8 of adulthood definition 8th day after eclosion. -INFO lowercase_definition day 9 of adulthood definition 9th day after eclosion. -INFO lowercase_definition day 10 of adulthood definition 10th day after eclosion. -INFO lowercase_definition day 11 of adulthood definition 11th day after eclosion. -INFO lowercase_definition day 12 of adulthood definition 12th day after eclosion. -INFO lowercase_definition day 13 of adulthood definition 13th day after eclosion. -INFO lowercase_definition day 14 of adulthood definition 14th day after eclosion. -INFO lowercase_definition day 15 of adulthood definition 15th day after eclosion. -INFO lowercase_definition day 16 of adulthood definition 16th day after eclosion. -INFO lowercase_definition day 17 of adulthood definition 17th day after eclosion. -INFO lowercase_definition day 18 of adulthood definition 18th day after eclosion. -INFO lowercase_definition day 19 of adulthood definition 19th day after eclosion. -INFO lowercase_definition day 20 of adulthood definition 20th day after eclosion. -INFO lowercase_definition day 21 of adulthood definition 21st day after eclosion. -INFO lowercase_definition day 22 of adulthood definition 22nd day after eclosion. -INFO lowercase_definition day 23 of adulthood definition 23rd day after eclosion. -INFO lowercase_definition day 24 of adulthood definition 24th day after eclosion. -INFO lowercase_definition day 25 of adulthood definition 25th day after eclosion. -INFO lowercase_definition day 26 of adulthood definition 26th day after eclosion. -INFO lowercase_definition day 27 of adulthood definition 27th day after eclosion. -INFO lowercase_definition day 28 of adulthood definition 28th day after eclosion. -INFO lowercase_definition day 29 of adulthood definition 29th day after eclosion. -INFO lowercase_definition day 30 of adulthood definition 30th day after eclosion. -INFO lowercase_definition day 31 of adulthood definition 31st day after eclosion. -INFO lowercase_definition day 32 of adulthood definition 32nd day after eclosion. -INFO lowercase_definition day 33 of adulthood definition 33rd day after eclosion. -INFO lowercase_definition day 34 of adulthood definition 34th day after eclosion. -INFO lowercase_definition day 35 of adulthood definition 35th day after eclosion. -INFO lowercase_definition day 36 of adulthood definition 36th day after eclosion. -INFO lowercase_definition day 37 of adulthood definition 37th day after eclosion. -INFO lowercase_definition day 38 of adulthood definition 38th day after eclosion. -INFO lowercase_definition day 39 of adulthood definition 39th day after eclosion. -INFO lowercase_definition day 40 of adulthood definition 40th day after eclosion. -INFO lowercase_definition day 41 of adulthood definition 41st day after eclosion. -INFO lowercase_definition day 42 of adulthood definition 42nd day after eclosion. -INFO lowercase_definition day 43 of adulthood definition 43rd day after eclosion. -INFO lowercase_definition day 44 of adulthood definition 44th day after eclosion. -INFO lowercase_definition day 45 of adulthood definition 45th day after eclosion. -INFO lowercase_definition day 46 of adulthood definition 46th day after eclosion. -INFO lowercase_definition day 47 of adulthood definition 47th day after eclosion. -INFO lowercase_definition day 48 of adulthood definition 48th day after eclosion. -INFO lowercase_definition day 49 of adulthood definition 49th day after eclosion. -INFO lowercase_definition day 50 of adulthood definition 50th day after eclosion. -INFO lowercase_definition day 51 of adulthood definition 51st day after eclosion. -INFO lowercase_definition day 52 of adulthood definition 52nd day after eclosion. -INFO lowercase_definition day 53 of adulthood definition 53rd day after eclosion. -INFO lowercase_definition day 54 of adulthood definition 54th day after eclosion. -INFO lowercase_definition day 55 of adulthood definition 55th day after eclosion. -INFO lowercase_definition day 56 of adulthood definition 56th day after eclosion. -INFO lowercase_definition day 57 of adulthood definition 57th day after eclosion. -INFO lowercase_definition day 58 of adulthood definition 58th day after eclosion. -INFO lowercase_definition day 59 of adulthood definition 59th day after eclosion. -INFO lowercase_definition day 60 of adulthood definition 60th day after eclosion. -INFO lowercase_definition participates in definition a relation between a continuant and a process, in which the continuant is somehow involved in the process@en -INFO lowercase_definition has participant definition a relation between a process and a continuant, in which the continuant is somehow involved in the process@en -INFO lowercase_definition has component process definition 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 overlaps definition 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 has component definition 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 develops from definition 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 develops into definition inverse of develops from -INFO lowercase_definition regulates definition -INFO lowercase_definition capable of part of definition 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 has input definition

-INFO lowercase_definition has developmental contribution from definition x has developmental contribution from y iff x has some part z such that z develops from y@en -INFO lowercase_definition developmentally contributes to definition inverse of has developmental contribution from -INFO lowercase_definition acts upstream of definition 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 acts upstream of or within definition 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 inheres in part of definition q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. -INFO lowercase_definition part of structure that is capable of definition this relation holds between c and p when c is part of some c', and c' is capable of p. -INFO lowercase_definition involved in definition c involved_in p if and only if c enables some process p', and p' is part of p -INFO lowercase_definition enabled by definition inverse of enables -INFO lowercase_definition regulated by definition inverse of regulates -INFO lowercase_definition negatively regulated by definition inverse of negatively regulates -INFO lowercase_definition positively regulated by definition inverse of positively regulates -INFO lowercase_definition input of definition inverse of has input -INFO lowercase_definition has developmental potential involving definition 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 has potential to developmentally contribute to definition 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 has potential to develop into definition 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 has potential to directly develop into definition 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 causally downstream of definition inverse of upstream of -INFO lowercase_definition causally upstream of definition p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain -INFO lowercase_definition immediately causally upstream of definition p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. -INFO lowercase_definition causally upstream of or within definition p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. -INFO lowercase_definition causally downstream of or within definition inverse of causally upstream of or within -INFO lowercase_definition involved in regulation of definition c involved in regulation of p if c is involved in some p' and p' regulates some p -INFO lowercase_definition involved in positive regulation of definition c involved in regulation of p if c is involved in some p' and p' positively regulates some p -INFO lowercase_definition involved in negative regulation of definition c involved in regulation of p if c is involved in some p' and p' negatively regulates some p -INFO lowercase_definition involved in or involved in regulation of definition 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 is active in definition c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. -INFO lowercase_definition has part that occurs in definition p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. -INFO lowercase_definition causal relation between processes definition p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. -INFO lowercase_definition has part structure that is capable of definition 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 acts upstream of, positive effect definition 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 acts upstream of, negative effect definition 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 diff --git a/src/ontology/reports/obsoletes.tsv b/src/ontology/reports/obsoletes.tsv deleted file mode 100644 index e69de29..0000000 diff --git a/src/ontology/reports/onto_metrics_calc.txt b/src/ontology/reports/onto_metrics_calc.txt deleted file mode 100644 index e69de29..0000000 diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv deleted file mode 100644 index d4dc070..0000000 --- a/src/ontology/reports/synonyms.tsv +++ /dev/null @@ -1,2 +0,0 @@ -?cls ?pred ?val ?synType - "root node"@en diff --git a/src/ontology/reports/xrefs.tsv b/src/ontology/reports/xrefs.tsv deleted file mode 100644 index e69de29..0000000 From d0e5c05e9846389296b5996cacaa5169e729453b Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 31 Aug 2021 10:14:07 +0100 Subject: [PATCH 2/4] error for multiple labels --- src/ontology/qc-profile.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/qc-profile.txt b/src/ontology/qc-profile.txt index 55fe4ba..c96533f 100644 --- a/src/ontology/qc-profile.txt +++ b/src/ontology/qc-profile.txt @@ -20,4 +20,4 @@ WARN missing_superclass WARN misused_obsolete_label ERROR multiple_definitions ERROR multiple_equivalent_classes -WARN multiple_labels +ERROR multiple_labels From 8d7c669460fdf8fbbec16cdbcb5a6bb1d8de6cb3 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 31 Aug 2021 10:14:18 +0100 Subject: [PATCH 3/4] release files 2021-08-31 --- fbdv-base.json | 100 +--- fbdv-base.obo | 30 +- fbdv-base.owl | 80 ++-- fbdv-full.json | 264 +---------- fbdv-full.obo | 172 +++---- fbdv-full.owl | 430 ++++++------------ fbdv-non-classified.json | 264 +---------- fbdv-non-classified.obo | 174 +++---- fbdv-non-classified.owl | 430 ++++++------------ fbdv-simple.json | 274 +---------- fbdv-simple.obo | 73 +-- fbdv-simple.owl | 171 +------ fbdv.json | 264 +---------- fbdv.obo | 71 +-- fbdv.owl | 430 ++++++------------ fly_development.obo | 48 +- imports/go_import.obo | 7 +- imports/go_import.owl | 7 +- imports/ro_import.obo | 57 +-- imports/ro_import.owl | 187 ++------ reports/fbdv-edit-release.owl-obo-report.tsv | 4 - reports/robot_simple_diff.txt | 89 +++- src/ontology/fbdv-non-classified.json | 264 +---------- src/ontology/fbdv-non-classified.obo | 174 +++---- src/ontology/fbdv-non-classified.owl | 430 ++++++------------ src/ontology/fly_development.obo | 48 +- src/ontology/imports/go_import.obo | 7 +- src/ontology/imports/go_import.owl | 7 +- src/ontology/imports/ro_import.obo | 57 +-- src/ontology/imports/ro_import.owl | 187 ++------ .../fbdv-edit-release.owl-obo-report.tsv | 4 - src/ontology/reports/robot_simple_diff.txt | 89 +++- src/patterns/definitions.owl | 4 +- src/patterns/pattern_owl_seed.txt | 4 +- 34 files changed, 1173 insertions(+), 3728 deletions(-) diff --git a/fbdv-base.json b/fbdv-base.json index 868bf41..632d4b4 100644 --- a/fbdv-base.json +++ b/fbdv-base.json @@ -3218,7 +3218,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "05:07:2021 10:41" + "val": "31:08:2021 09:05" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace", @@ -3230,64 +3230,14 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2021-07-05" + "val": "2021-08-31" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-07-05/fbdv-base.json", + "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-08-31/fbdv-base.json", "xrefs": [] }, "nodes": [ - { - "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has_part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "has_part" - } - ], - "xrefs": [ - { - "val": "BFO:0000051" - }, - { - "val": "OBO_REL:has_part" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded_by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "preceded_by" - } - ], - "xrefs": [ - { - "val": "BFO:0000062" - }, - { - "val": "OBO_REL:preceded_by" - } - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/FBdv_00000000", "lbl": "Drosophila life", @@ -8619,50 +8569,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002090", - "lbl": "ends_at_start_of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "ends_at_start_of" - } - ], - "xrefs": [ - { - "val": "RO:0002090" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002131", - "lbl": "overlaps", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "overlaps" - } - ], - "xrefs": [ - { - "val": "RO:0002131" - } - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/fbdv#systematic_synonym", "lbl": "Systematic synonym", diff --git a/fbdv-base.obo b/fbdv-base.obo index 0ed2ee9..5f457eb 100644 --- a/fbdv-base.obo +++ b/fbdv-base.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/fbdv-base.owl -date: 05:07:2021 10:41 +data-version: fbdv/releases/2021-08-31/fbdv-base.owl +date: 31:08:2021 09:05 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" @@ -30,7 +30,7 @@ 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 "2021-07-05" xsd:string +property_value: owl:versionInfo "2021-08-31" xsd:string [Term] id: FBdv:00000000 @@ -2007,18 +2007,6 @@ relationship: immediately_preceded_by FBdv:00005317 ! gastrula stage relationship: immediately_preceded_by FBdv:00005322 ! embryonic stage 8 relationship: substage_of FBdv:00005321 ! extended germ band stage -[Typedef] -id: ends_at_start_of -name: ends_at_start_of -xref: RO:0002090 - -[Typedef] -id: has_part -name: has_part -namespace: relationship -xref: BFO:0000051 -xref: OBO_REL:has_part - [Typedef] id: immediately_preceded_by name: immediately_preceded_by @@ -2029,18 +2017,6 @@ id: occurent_part_of name: occurent_part_of xref: RO:0002012 -[Typedef] -id: overlaps -name: overlaps -xref: RO:0002131 - -[Typedef] -id: preceded_by -name: preceded_by -namespace: relationship -xref: BFO:0000062 -xref: OBO_REL:preceded_by - [Typedef] id: substage_of name: substage_of diff --git a/fbdv-base.owl b/fbdv-base.owl index 245012e..9170243 100644 --- a/fbdv-base.owl +++ b/fbdv-base.owl @@ -12,7 +12,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -26,10 +26,10 @@ https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ - 05:07:2021 10:41 + 31:08:2021 09:05 FlyBase_development_CV 1.2 - 2021-07-05 + 2021-08-31 @@ -200,6 +200,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -357,32 +381,6 @@ - - - - BFO:0000051 - OBO_REL:has_part - relationship - has_part - has_part - has_part - - - - - - - - BFO:0000062 - OBO_REL:preceded_by - relationship - preceded_by - preceded_by - preceded_by - - - - @@ -423,36 +421,12 @@ - - - - RO:0002090 - FlyBase_development_CV - ends_at_start_of - ends_at_start_of - ends_at_start_of - - - - - - - - RO:0002131 - FlyBase_development_CV - overlaps - overlaps - overlaps - - - - + + term replaced by term replaced by @@ -506,18 +508,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -764,18 +790,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - OBO_REL:has_part + BFO:0000051 external - relationship - has_part + has_part - has_part + has_part has part has part - has_part @@ -806,14 +829,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by - BFO:0000062 - OBO_REL:preceded_by - relationship - preceded_by - preceded_by preceded by - preceded_by @@ -841,47 +858,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - @@ -1336,13 +1312,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. ends_at_start_of meets - RO:0002090 - FlyBase_development_CV - ends_at_start_of - ends_at_start_of X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - ends_at_start_of immediately precedes @@ -1430,15 +1401,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 - FlyBase_development_CV - overlaps - overlaps overlaps - overlaps @@ -2247,42 +2213,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - - - - @@ -2408,32 +2338,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - @@ -10357,6 +10261,7 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process single-multicellular organism process GO:0032501 + multicellular organismal process @@ -10824,118 +10729,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -11509,51 +11302,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction @@ -11954,6 +11702,118 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/fbdv-non-classified.json b/fbdv-non-classified.json index ced2359..dc9ef0d 100644 --- a/fbdv-non-classified.json +++ b/fbdv-non-classified.json @@ -103,15 +103,6 @@ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, - { - "domainClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000003" - ], - "predicateId": "http://purl.obolibrary.org/obo/BFO_0000066", - "rangeClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000004" - ] - }, { "domainClassIds": [ "http://purl.obolibrary.org/obo/BFO_0000003" @@ -148,15 +139,6 @@ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, - { - "domainClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000003" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002479", - "rangeClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000004" - ] - }, { "domainClassIds": [ "http://purl.obolibrary.org/obo/BFO_0000003" @@ -458,11 +440,6 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002411" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000067", - "pred": "inverseOf", - "sub": "http://purl.obolibrary.org/obo/BFO_0000066" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0030000", "pred": "is_a", @@ -3948,11 +3925,6 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/BFO_0000051" }, - { - "obj": "http://purl.obolibrary.org/obo/RO_0002131", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002432" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0002180", "pred": "subPropertyOf", @@ -4148,11 +4120,6 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002431" }, - { - "obj": "http://purl.obolibrary.org/obo/RO_0002328", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002432" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0002328", "pred": "subPropertyOf", @@ -4703,7 +4670,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "05:07:2021 10:41" + "val": "31:08:2021 09:06" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace", @@ -4715,11 +4682,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2021-07-05" + "val": "2021-08-31" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-07-05/fbdv-non-classified.json", + "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-08-31/fbdv-non-classified.json", "xrefs": [] }, "nodes": [ @@ -4921,7 +4888,7 @@ }, { "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has_part", + "lbl": "has part", "meta": { "basicPropertyValues": [ { @@ -4964,10 +4931,6 @@ "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "external" }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", "val": "has_part" @@ -4985,9 +4948,6 @@ "xrefs": [ { "val": "BFO:0000051" - }, - { - "val": "OBO_REL:has_part" } ] }, @@ -4995,7 +4955,7 @@ }, { "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded_by", + "lbl": "preceded by", "meta": { "basicPropertyValues": [ { @@ -5017,14 +4977,6 @@ { "pred": "http://purl.org/dc/elements/1.1/source", "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "preceded_by" } ], "definition": { @@ -5033,14 +4985,6 @@ }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ], - "xrefs": [ - { - "val": "BFO:0000062" - }, - { - "val": "OBO_REL:preceded_by" - } ] }, "type": "PROPERTY" @@ -5065,71 +5009,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl": "occurs in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "occurs in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "occurs_in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "unfolds in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "unfolds_in" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "comments": [ - "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" - ], - "definition": { - "val": "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl": "contains process", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "site of" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "comments": [ - "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" - ], - "definition": { - "val": "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/CARO_0000000", "lbl": "anatomical entity", @@ -11096,6 +10975,7 @@ ] }, "subsets": [ + "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms": [ @@ -11510,6 +11390,19 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl": "term replaced by", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + } + ] + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/PATO_0000001", "lbl": "quality", @@ -12213,7 +12106,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0002090", - "lbl": "ends_at_start_of", + "lbl": "immediately precedes", "meta": { "basicPropertyValues": [ { @@ -12231,14 +12124,6 @@ { "pred": "http://purl.obolibrary.org/obo/RO_0002575", "val": "http://purl.obolibrary.org/obo/BFO_0000063" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "ends_at_start_of" } ], "comments": [ @@ -12246,11 +12131,6 @@ ], "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ], - "xrefs": [ - { - "val": "RO:0002090" - } ] }, "type": "PROPERTY" @@ -12377,14 +12257,6 @@ { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "overlaps" } ], "definition": { @@ -12395,11 +12267,6 @@ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" - ], - "xrefs": [ - { - "val": "RO:0002131" - } ] }, "type": "PROPERTY" @@ -13618,44 +13485,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002432", - "lbl": "is active in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "A protein that enables activity in a cytosol." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "executes activity in" - } - ], - "comments": [ - "" - ], - "definition": { - "val": "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs": [ - "GOC:cjm", - "GOC:dos" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "enables activity in", - "xrefs": [] - } - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/RO_0002434", "lbl": "interacts with", @@ -13866,26 +13695,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002479", - "lbl": "has part that occurs in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/RO_0002481", "lbl": "is kinase activity", @@ -14582,11 +14391,6 @@ "lbl": "transferase activity, transferring phosphorus-containing groups", "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl": "term replaced by", - "type": "PROPERTY" - }, { "id": "http://www.geneontology.org/formats/oboInOwl#NamespaceIdRule", "lbl": "namespace-id-rule", @@ -14767,20 +14571,6 @@ ], "predicateId": "http://purl.obolibrary.org/obo/BFO_0000063" }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000050", - "http://purl.obolibrary.org/obo/BFO_0000066" - ], - "predicateId": "http://purl.obolibrary.org/obo/BFO_0000066" - }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000050", - "http://purl.obolibrary.org/obo/BFO_0000066" - ], - "predicateId": "http://purl.obolibrary.org/obo/BFO_0000066" - }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14837,13 +14627,6 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002331" }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000051", - "http://purl.obolibrary.org/obo/BFO_0000066" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002479" - }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/BFO_0000051", @@ -14914,13 +14697,6 @@ ], "predicateId": "http://purl.obolibrary.org/obo/BFO_0000063" }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000066", - "http://purl.obolibrary.org/obo/RO_0002327" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002432" - }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002017", diff --git a/fbdv-non-classified.obo b/fbdv-non-classified.obo index 2087fb3..08998e8 100644 --- a/fbdv-non-classified.obo +++ b/fbdv-non-classified.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/fbdv-non-classified.owl -date: 05:07:2021 10:41 +data-version: fbdv/releases/2021-08-31/fbdv-non-classified.owl +date: 31:08:2021 09:06 subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "" @@ -50,7 +50,7 @@ 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 "2021-07-05" xsd:string +property_value: owl:versionInfo "2021-08-31" xsd:string [Term] id: BFO:0000002 @@ -2342,6 +2342,7 @@ namespace: biological_process alt_id: GO:0044707 alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] @@ -2496,6 +2497,25 @@ name: quality is_a: BFO:0000020 ! specifically dependent continuant property_value: IAO:0000589 "quality (PATO)" xsd:string +[Typedef] +id: BFO:0000062 +name: preceded by +def: "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." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: happens_during BFO:0000062 +holds_over_chain: part_of BFO:0000062 +holds_over_chain: RO:0002091 BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + [Typedef] id: BFO:0000063 name: precedes @@ -2509,33 +2529,6 @@ holds_over_chain: part_of BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: BFO:0000066 -name: occurs in -def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: part_of BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: part_of ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Typedef] id: RO:0000052 name: characteristic of @@ -2787,7 +2780,7 @@ name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -holds_over_chain: ends_during preceded_by +holds_over_chain: ends_during BFO:0000062 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -2800,6 +2793,17 @@ property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: RO:0002222 ! temporally related to inverse_of: RO:0002091 ! starts during +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + [Typedef] id: RO:0002091 name: starts during @@ -2811,6 +2815,22 @@ domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: has_part RO:0002131 +holds_over_chain: part_of part_of +is_a: RO:0002323 ! mereotopologically related to +transitive_over: part_of ! part of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + [Typedef] id: RO:0002180 name: has component @@ -3215,7 +3235,7 @@ name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: preceded_by ! preceded_by +is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of @@ -3256,7 +3276,7 @@ def: "p is immediately causally upstream of q iff both (a) p immediately precede property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 -is_a: ends_at_start_of ! immediately precedes +is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of [Typedef] @@ -3322,18 +3342,6 @@ is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -[Typedef] -id: RO:0002432 -name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "executes activity in" xsd:string -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: overlaps ! overlaps -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002434 name: interacts with @@ -3412,16 +3420,6 @@ name: helper property (not for use in curation) property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - [Typedef] id: RO:0002481 name: is kinase activity @@ -3685,19 +3683,6 @@ domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences -[Typedef] -id: ends_at_start_of -name: ends_at_start_of -name: immediately precedes -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 -is_a: BFO:0000063 ! precedes - [Typedef] id: ends_during name: ends during @@ -3731,15 +3716,12 @@ is_a: RO:0002091 ! starts during [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: relationship def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -xref: OBO_REL:has_part property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string @@ -3750,7 +3732,7 @@ property_value: IAO:0000116 "Parthood requires the part and the whole to have co property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true -is_a: overlaps ! overlaps +is_a: RO:0002131 ! overlaps [Typedef] id: immediately_preceded_by @@ -3760,8 +3742,8 @@ comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "starts_at_end_of" xsd:string -is_a: preceded_by ! preceded_by -inverse_of: ends_at_start_of ! immediately precedes +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes [Typedef] id: occurent_part_of @@ -3774,23 +3756,6 @@ range: BFO:0000003 ! occurrent is_a: part_of ! part of is_a: RO:0002418 ! causally upstream of or within -[Typedef] -id: overlaps -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: part_of part_of -is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part of -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - [Typedef] id: part_of name: part of @@ -3821,32 +3786,9 @@ property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_a property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string is_transitive: true -is_a: overlaps ! overlaps +is_a: RO:0002131 ! overlaps inverse_of: has_part ! has part -[Typedef] -id: preceded_by -name: preceded by -name: preceded_by -namespace: relationship -def: "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." [] -subset: ro-eco -xref: BFO:0000062 -xref: OBO_REL:preceded_by -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: happens_during preceded_by -holds_over_chain: part_of preceded_by -holds_over_chain: RO:0002091 preceded_by -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - [Typedef] id: substage_of name: substage_of @@ -3855,5 +3797,5 @@ comment: Creating this relation as a temporary fix, pending adding the axiom occ xref: FBdv:00018001 is_transitive: true is_a: happens_during ! happens during -is_a: occurent_part_of ! occurent_part_of +is_a: occurent_part_of ! occurent part of diff --git a/fbdv-non-classified.owl b/fbdv-non-classified.owl index 11b6c4a..043ff62 100644 --- a/fbdv-non-classified.owl +++ b/fbdv-non-classified.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -31,10 +31,10 @@ FlyBase Developmental Ontology (FBdv) https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ - 05:07:2021 10:41 + 31:08:2021 09:06 FlyBase_development_CV 1.2 - 2021-07-05 + 2021-08-31 @@ -152,6 +152,8 @@ + + term replaced by term replaced by @@ -506,18 +508,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -764,18 +790,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - OBO_REL:has_part + BFO:0000051 external - relationship - has_part + has_part - has_part + has_part has part has part - has_part @@ -806,14 +829,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by - BFO:0000062 - OBO_REL:preceded_by - relationship - preceded_by - preceded_by preceded by - preceded_by @@ -841,47 +858,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - @@ -1336,13 +1312,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. ends_at_start_of meets - RO:0002090 - FlyBase_development_CV - ends_at_start_of - ends_at_start_of X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - ends_at_start_of immediately precedes @@ -1430,15 +1401,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 - FlyBase_development_CV - overlaps - overlaps overlaps - overlaps @@ -2247,42 +2213,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - - - - @@ -2408,32 +2338,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - @@ -10343,6 +10247,7 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process single-multicellular organism process GO:0032501 + multicellular organismal process @@ -10810,118 +10715,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -11495,51 +11288,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction @@ -11940,6 +11688,118 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/fbdv-simple.json b/fbdv-simple.json index 51ada2e..8f3d181 100644 --- a/fbdv-simple.json +++ b/fbdv-simple.json @@ -3,11 +3,6 @@ { "domainRangeAxioms": [], "edges": [ - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000062", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002087" - }, { "obj": "http://purl.obolibrary.org/obo/FBdv_00000000", "pred": "http://purl.obolibrary.org/obo/FBdv_00018001", @@ -3118,25 +3113,10 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/FBdv_00018001" }, - { - "obj": "http://purl.obolibrary.org/obo/RO_0002090", - "pred": "inverseOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002087" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0002092", "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/FBdv_00018001" - }, - { - "obj": "http://purl.obolibrary.org/obo/RO_0002131", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/BFO_0000051" - }, - { - "obj": "http://purl.obolibrary.org/obo/RO_0002131", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002012" } ], "equivalentNodesSets": [], @@ -3194,7 +3174,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "05:07:2021 10:41" + "val": "31:08:2021 09:05" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace", @@ -3206,140 +3186,14 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2021-07-05" + "val": "2021-08-31" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-07-05/fbdv-simple.json", + "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-08-31/fbdv-simple.json", "xrefs": [] }, "nodes": [ - { - "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has_part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "has part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my body has part my brain (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this year has part this day (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has_part" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "external" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "has_part" - } - ], - "definition": { - "val": "a core relation that holds between a whole and its part", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ], - "xrefs": [ - { - "val": "BFO:0000051" - }, - { - "val": "OBO_REL:has_part" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded_by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "is preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "preceded_by" - }, - { - "pred": "http://purl.org/dc/elements/1.1/source", - "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "preceded_by" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ], - "xrefs": [ - { - "val": "BFO:0000062" - }, - { - "val": "OBO_REL:preceded_by" - } - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/FBdv_00000000", "lbl": "Drosophila life", @@ -8640,6 +8494,19 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl": "term replaced by", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + } + ] + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/RO_0002012", "lbl": "occurent part of", @@ -8699,50 +8566,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002090", - "lbl": "immediately precedes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "David Osumi-Sutherland" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "ends_at_start_of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "meets" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0002575", - "val": "http://purl.obolibrary.org/obo/BFO_0000063" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "ends_at_start_of" - } - ], - "comments": [ - "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" - ], - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ], - "xrefs": [ - { - "val": "RO:0002090" - } - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/RO_0002092", "lbl": "happens during", @@ -8786,49 +8609,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002131", - "lbl": "overlaps", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000424", - "val": "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "overlaps" - } - ], - "definition": { - "val": "x overlaps y if and only if there exists some z such that x has part z and z part of y", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ], - "xrefs": [ - { - "val": "RO:0002131" - } - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/fbdv#systematic_synonym", "lbl": "Systematic synonym", @@ -8842,11 +8622,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl": "term replaced by", - "type": "PROPERTY" - }, { "id": "http://www.geneontology.org/formats/oboInOwl#NamespaceIdRule", "lbl": "namespace-id-rule", @@ -8998,22 +8773,7 @@ "type": "CLASS" } ], - "propertyChainAxioms": [ - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000051", - "http://purl.obolibrary.org/obo/RO_0002131" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002131" - }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000062", - "http://purl.obolibrary.org/obo/RO_0002092" - ], - "predicateId": "http://purl.obolibrary.org/obo/BFO_0000062" - } - ] + "propertyChainAxioms": [] } ] } diff --git a/fbdv-simple.obo b/fbdv-simple.obo index f57b9b4..b5e3152 100644 --- a/fbdv-simple.obo +++ b/fbdv-simple.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/fbdv-simple.owl -date: 05:07:2021 10:41 +data-version: fbdv/releases/2021-08-31/fbdv-simple.owl +date: 31:08:2021 09:05 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" @@ -33,7 +33,7 @@ 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 "2021-07-05" xsd:string +property_value: owl:versionInfo "2021-08-31" xsd:string [Term] id: FBdv:00000000 @@ -2003,17 +2003,6 @@ relationship: immediately_preceded_by FBdv:00005317 ! gastrula stage relationship: immediately_preceded_by FBdv:00005322 ! embryonic stage 8 relationship: substage_of FBdv:00005321 ! extended germ band stage -[Typedef] -id: ends_at_start_of -name: immediately precedes -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 - [Typedef] id: happens_during name: happens during @@ -2028,28 +2017,6 @@ property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string is_transitive: true -[Typedef] -id: has_part -name: has_part -namespace: relationship -def: "a core relation that holds between a whole and its part" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000051 -xref: OBO_REL:has_part -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: overlaps ! overlaps - [Typedef] id: immediately_preceded_by name: immediately_preceded_by @@ -2057,44 +2024,12 @@ comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "starts_at_end_of" xsd:string -is_a: preceded_by ! preceded_by -inverse_of: ends_at_start_of ! immediately precedes [Typedef] id: occurent_part_of name: occurent_part_of def: "A part of relation that applies only between occurents." [] xref: RO:0002012 -is_a: overlaps ! overlaps - -[Typedef] -id: overlaps -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part overlaps -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - -[Typedef] -id: preceded_by -name: preceded_by -namespace: relationship -def: "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." [] -subset: ro-eco -xref: BFO:0000062 -xref: OBO_REL:preceded_by -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -holds_over_chain: happens_during preceded_by -is_transitive: true [Typedef] id: substage_of @@ -2104,5 +2039,5 @@ comment: Creating this relation as a temporary fix, pending adding the axiom occ xref: FBdv:00018001 is_transitive: true is_a: happens_during ! happens during -is_a: occurent_part_of ! occurent part of +is_a: occurent_part_of ! occurent_part_of diff --git a/fbdv-simple.owl b/fbdv-simple.owl index dff3200..f63bc9d 100644 --- a/fbdv-simple.owl +++ b/fbdv-simple.owl @@ -13,7 +13,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -26,10 +26,10 @@ FlyBase Developmental Ontology (FBdv) https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ - 05:07:2021 10:41 + 31:08:2021 09:05 FlyBase_development_CV 1.2 - 2021-07-05 + 2021-08-31 @@ -45,18 +45,6 @@ - - - - - - - - - - - - @@ -72,12 +60,6 @@ - - - - - - @@ -96,12 +78,6 @@ - - - - - - @@ -111,23 +87,13 @@ + term replaced by + term replaced by - - - - - - - - - - - - @@ -287,9 +253,27 @@ - + + + + + + + + + + + + + + + + + + + - + @@ -456,65 +440,6 @@ - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - BFO:0000051 - OBO_REL:has_part - external - relationship - has_part - - - - has_part - has part - has part - has_part - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - BFO:0000062 - OBO_REL:preceded_by - relationship - preceded_by - - preceded_by - preceded by - preceded_by - - - - @@ -534,7 +459,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - A part of relation that applies only between occurents. RO:0002012 FlyBase_development_CV @@ -549,8 +473,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - David Osumi-Sutherland starts_at_end_of RO:0002087 @@ -564,25 +486,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - David Osumi-Sutherland - ends_at_start_of - meets - - RO:0002090 - FlyBase_development_CV - ends_at_start_of - - ends_at_start_of - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - ends_at_start_of - immediately precedes - - - - @@ -605,30 +508,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - RO:0002131 - FlyBase_development_CV - overlaps - - - - overlaps - overlaps - overlaps - - - - + + term replaced by term replaced by @@ -506,18 +508,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -764,18 +790,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - OBO_REL:has_part + BFO:0000051 external - relationship - has_part + has_part - has_part + has_part has part has part - has_part @@ -806,14 +829,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by - BFO:0000062 - OBO_REL:preceded_by - relationship - preceded_by - preceded_by preceded by - preceded_by @@ -841,47 +858,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - @@ -1336,13 +1312,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. ends_at_start_of meets - RO:0002090 - FlyBase_development_CV - ends_at_start_of - ends_at_start_of X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - ends_at_start_of immediately precedes @@ -1430,15 +1401,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 - FlyBase_development_CV - overlaps - overlaps overlaps - overlaps @@ -2247,42 +2213,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - - - - @@ -2408,32 +2338,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - @@ -10357,6 +10261,7 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process single-multicellular organism process GO:0032501 + multicellular organismal process @@ -10824,118 +10729,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -11509,51 +11302,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction @@ -11954,6 +11702,118 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/fly_development.obo b/fly_development.obo index e9101f3..24bcb7b 100644 --- a/fly_development.obo +++ b/fly_development.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: 2021-07-05 -date: 05:07:2021 10:41 +data-version: 2021-08-31 +date: 31:08:2021 09:06 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" @@ -1991,13 +1991,6 @@ relationship: immediately_preceded_by FBdv:00005317 ! gastrula stage relationship: immediately_preceded_by FBdv:00005322 ! embryonic stage 8 relationship: substage_of FBdv:00005321 ! extended germ band stage -[Typedef] -id: ends_at_start_of -name: ends_at_start_of -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -xref: RO:0002090 - [Typedef] id: happens_during name: happens_during @@ -2009,54 +2002,17 @@ subset: ro-eco xref: RO:0002092 is_transitive: true -[Typedef] -id: has_part -name: has_part -namespace: relationship -def: "a core relation that holds between a whole and its part" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000051 -xref_analog: OBO_REL:has_part -is_transitive: true -is_a: overlaps ! overlaps - [Typedef] id: immediately_preceded_by name: immediately_preceded_by comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -is_a: preceded_by ! preceded_by -inverse_of: ends_at_start_of ! ends_at_start_of [Typedef] id: occurent_part_of name: occurent_part_of def: "A part of relation that applies only between occurents." [] xref: RO:0002012 -is_a: overlaps ! overlaps - -[Typedef] -id: overlaps -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -holds_over_chain: has_part overlaps - -[Typedef] -id: preceded_by -name: preceded_by -namespace: relationship -def: "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." [] -subset: ro-eco -xref: BFO:0000062 -xref_analog: OBO_REL:preceded_by -holds_over_chain: happens_during preceded_by -is_transitive: true [Typedef] id: substage_of diff --git a/imports/go_import.obo b/imports/go_import.obo index d116145..37563cf 100644 --- a/imports/go_import.obo +++ b/imports/go_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/imports/go_import.owl +data-version: fbdv/releases/2021-08-31/imports/go_import.owl subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_manually_annotate "" subsetdef: goslim_agr "" @@ -16,8 +16,8 @@ subsetdef: goslim_plant "" subsetdef: goslim_pombe "" subsetdef: goslim_yeast "" ontology: fbdv/imports/go_import -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/go/releases/2021-06-16/go.owl -property_value: owl:versionInfo "2021-07-05" xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/go/releases/2021-08-18/go.owl +property_value: owl:versionInfo "2021-08-31" xsd:string [Term] id: GO:0000087 @@ -225,6 +225,7 @@ namespace: biological_process alt_id: GO:0044707 alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] diff --git a/imports/go_import.owl b/imports/go_import.owl index c5ebab2..3633d86 100644 --- a/imports/go_import.owl +++ b/imports/go_import.owl @@ -11,9 +11,9 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2021-07-05 + + + 2021-08-31 @@ -841,6 +841,7 @@ biological_process single-multicellular organism process GO:0032501 + multicellular organismal process diff --git a/imports/ro_import.obo b/imports/ro_import.obo index 14671f1..d1ad822 100644 --- a/imports/ro_import.obo +++ b/imports/ro_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/imports/ro_import.owl +data-version: fbdv/releases/2021-08-31/imports/ro_import.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -7,9 +7,9 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: fbdv/imports/ro_import -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/ro/releases/2021-06-23/ro.owl -property_value: owl:versionInfo "2021-07-05" xsd:string -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/ro/releases/2021-08-25/ro.owl +property_value: owl:versionInfo "2021-08-31" xsd:string +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Term] id: BFO:0000002 @@ -212,33 +212,6 @@ holds_over_chain: RO:0002092 BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: BFO:0000066 -name: occurs in -def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000050 BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Typedef] id: RO:0000052 name: characteristic of @@ -1095,18 +1068,6 @@ is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -[Typedef] -id: RO:0002432 -name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "executes activity in" xsd:string -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002434 name: interacts with @@ -1185,16 +1146,6 @@ name: helper property (not for use in curation) property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - [Typedef] id: RO:0002481 name: is kinase activity diff --git a/imports/ro_import.owl b/imports/ro_import.owl index 7531c1a..6d09cdb 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2021-07-05 + + + 2021-08-31 @@ -115,6 +115,15 @@ + + + + + term replaced by + + + + @@ -211,18 +220,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -467,47 +500,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - @@ -1827,42 +1819,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - - - - @@ -1988,32 +1944,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - @@ -3283,51 +3213,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction diff --git a/reports/fbdv-edit-release.owl-obo-report.tsv b/reports/fbdv-edit-release.owl-obo-report.tsv index 9ac9ab1..538b0f9 100644 --- a/reports/fbdv-edit-release.owl-obo-report.tsv +++ b/reports/fbdv-edit-release.owl-obo-report.tsv @@ -1,6 +1,4 @@ Level Rule Name Subject Property Value -WARN missing_definition has part definition -WARN missing_definition preceded by definition WARN missing_definition oogenesis definition WARN missing_definition unfertilized egg stage definition WARN missing_definition fertilized egg stage definition @@ -12,8 +10,6 @@ WARN missing_definition definition definition WARN missing_definition term replaced by definition WARN missing_definition occurent part of definition WARN missing_definition immediately preceded by definition -WARN missing_definition immediately precedes definition -WARN missing_definition overlaps definition WARN missing_definition Systematic synonym definition WARN missing_definition namespace-id-rule definition WARN missing_definition subset_property definition diff --git a/reports/robot_simple_diff.txt b/reports/robot_simple_diff.txt index 17e6610..1b74916 100644 --- a/reports/robot_simple_diff.txt +++ b/reports/robot_simple_diff.txt @@ -1,13 +1,78 @@ -5 axioms in left ontology but not in right ontology: -- Annotation( "2021-07-05"^^xsd:string) -- Annotation( "05:07:2021 10:41"^^xsd:string) -- AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"^^xsd:string) -- AnnotationAssertion(Annotation( "FlyBase:FBrf0089570"^^xsd:string) "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)."^^xsd:string) -- OntologyID(OntologyIRI() VersionIRI()) +3 axioms in left ontology but not in right ontology: +- Annotation( "2021-08-31"^^xsd:string) +- Annotation( "31:08:2021 09:05"^^xsd:string) +- OntologyID(OntologyIRI() VersionIRI()) -5 axioms in right ontology but not in left ontology: -+ Annotation( "2021-05-10"^^xsd:string) -+ Annotation( "10:05:2021 12:44"^^xsd:string) -+ AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"^^xsd:string) -+ AnnotationAssertion(Annotation( "FlyBase:FBrf0089570"^^xsd:string) "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)."^^xsd:string) -+ OntologyID(OntologyIRI() VersionIRI()) +72 axioms in right ontology but not in left ontology: ++ Annotation( "2021-07-05"^^xsd:string) ++ Annotation( "05:07:2021 10:41"^^xsd:string) ++ AnnotationAssertion( "has part"^^xsd:string) ++ AnnotationAssertion( "preceded by"^^xsd:string) ++ AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"^^xsd:string) ++ AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"^^xsd:string) ++ AnnotationAssertion( "this year has part this day (occurrent parthood)"^^xsd:string) ++ AnnotationAssertion( ) ++ AnnotationAssertion( "a core relation that holds between a whole and its part"^^xsd:string) ++ AnnotationAssertion( "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."^^xsd:string) ++ AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y"^^xsd:string) ++ AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."^^xsd:string) ++ AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"^^xsd:string) ++ AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."^^xsd:string) ++ AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."^^xsd:string) ++ AnnotationAssertion( "David Osumi-Sutherland"^^xsd:string) ++ AnnotationAssertion( "has_part"^^xsd:string) ++ AnnotationAssertion( "is preceded by"^^xsd:string) ++ AnnotationAssertion( "preceded_by"^^xsd:string) ++ AnnotationAssertion( "ends_at_start_of"^^xsd:string) ++ AnnotationAssertion( "meets"^^xsd:string) ++ AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)"^^xsd:string) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"^^xsd:string) ++ AnnotationAssertion( "BFO:0000051"^^xsd:string) ++ AnnotationAssertion( "OBO_REL:has_part"^^xsd:string) ++ AnnotationAssertion( "BFO:0000062"^^xsd:string) ++ AnnotationAssertion( "OBO_REL:preceded_by"^^xsd:string) ++ AnnotationAssertion( "RO:0002090"^^xsd:string) ++ AnnotationAssertion( "RO:0002131"^^xsd:string) ++ AnnotationAssertion( "relationship"^^xsd:string) ++ AnnotationAssertion( "relationship"^^xsd:string) ++ AnnotationAssertion( "FlyBase_development_CV"^^xsd:string) ++ AnnotationAssertion( "FlyBase_development_CV"^^xsd:string) ++ AnnotationAssertion( "has_part"^^xsd:string) ++ AnnotationAssertion( "preceded_by"^^xsd:string) ++ AnnotationAssertion( "ends_at_start_of"^^xsd:string) ++ AnnotationAssertion( "overlaps"^^xsd:string) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( "has_part"^^xsd:string) ++ AnnotationAssertion( "preceded_by"^^xsd:string) ++ AnnotationAssertion( "ends_at_start_of"^^xsd:string) ++ AnnotationAssertion( "overlaps"^^xsd:string) ++ AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"^^xsd:string) ++ AnnotationAssertion(rdfs:label "has_part"^^xsd:string) ++ AnnotationAssertion(rdfs:label "preceded_by"^^xsd:string) ++ AnnotationAssertion(rdfs:label "expand expression to"^^xsd:string) ++ AnnotationAssertion(rdfs:label "immediately precedes"^^xsd:string) ++ AnnotationAssertion(rdfs:label "overlaps"^^xsd:string) ++ Declaration(AnnotationProperty()) ++ Declaration(ObjectProperty()) ++ Declaration(ObjectProperty()) ++ Declaration(ObjectProperty()) ++ Declaration(ObjectProperty()) ++ InverseObjectProperties( ) ++ OntologyID(OntologyIRI() VersionIRI()) ++ SubObjectPropertyOf( ) ++ SubObjectPropertyOf( ) ++ SubObjectPropertyOf( ) ++ SubObjectPropertyOf(ObjectPropertyChain( ) ) ++ SubObjectPropertyOf(ObjectPropertyChain( ) ) ++ TransitiveObjectProperty() ++ TransitiveObjectProperty() diff --git a/src/ontology/fbdv-non-classified.json b/src/ontology/fbdv-non-classified.json index ced2359..dc9ef0d 100644 --- a/src/ontology/fbdv-non-classified.json +++ b/src/ontology/fbdv-non-classified.json @@ -103,15 +103,6 @@ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, - { - "domainClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000003" - ], - "predicateId": "http://purl.obolibrary.org/obo/BFO_0000066", - "rangeClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000004" - ] - }, { "domainClassIds": [ "http://purl.obolibrary.org/obo/BFO_0000003" @@ -148,15 +139,6 @@ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, - { - "domainClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000003" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002479", - "rangeClassIds": [ - "http://purl.obolibrary.org/obo/BFO_0000004" - ] - }, { "domainClassIds": [ "http://purl.obolibrary.org/obo/BFO_0000003" @@ -458,11 +440,6 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002411" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000067", - "pred": "inverseOf", - "sub": "http://purl.obolibrary.org/obo/BFO_0000066" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0030000", "pred": "is_a", @@ -3948,11 +3925,6 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/BFO_0000051" }, - { - "obj": "http://purl.obolibrary.org/obo/RO_0002131", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002432" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0002180", "pred": "subPropertyOf", @@ -4148,11 +4120,6 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002431" }, - { - "obj": "http://purl.obolibrary.org/obo/RO_0002328", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002432" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0002328", "pred": "subPropertyOf", @@ -4703,7 +4670,7 @@ }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "05:07:2021 10:41" + "val": "31:08:2021 09:06" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace", @@ -4715,11 +4682,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2021-07-05" + "val": "2021-08-31" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-07-05/fbdv-non-classified.json", + "version": "http://purl.obolibrary.org/obo/fbdv/releases/2021-08-31/fbdv-non-classified.json", "xrefs": [] }, "nodes": [ @@ -4921,7 +4888,7 @@ }, { "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has_part", + "lbl": "has part", "meta": { "basicPropertyValues": [ { @@ -4964,10 +4931,6 @@ "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "external" }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, { "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", "val": "has_part" @@ -4985,9 +4948,6 @@ "xrefs": [ { "val": "BFO:0000051" - }, - { - "val": "OBO_REL:has_part" } ] }, @@ -4995,7 +4955,7 @@ }, { "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded_by", + "lbl": "preceded by", "meta": { "basicPropertyValues": [ { @@ -5017,14 +4977,6 @@ { "pred": "http://purl.org/dc/elements/1.1/source", "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "preceded_by" } ], "definition": { @@ -5033,14 +4985,6 @@ }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ], - "xrefs": [ - { - "val": "BFO:0000062" - }, - { - "val": "OBO_REL:preceded_by" - } ] }, "type": "PROPERTY" @@ -5065,71 +5009,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl": "occurs in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "occurs in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "occurs_in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "unfolds in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "unfolds_in" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "comments": [ - "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" - ], - "definition": { - "val": "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl": "contains process", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "site of" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "comments": [ - "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" - ], - "definition": { - "val": "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/CARO_0000000", "lbl": "anatomical entity", @@ -11096,6 +10975,7 @@ ] }, "subsets": [ + "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms": [ @@ -11510,6 +11390,19 @@ }, "type": "PROPERTY" }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl": "term replaced by", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + } + ] + }, + "type": "PROPERTY" + }, { "id": "http://purl.obolibrary.org/obo/PATO_0000001", "lbl": "quality", @@ -12213,7 +12106,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0002090", - "lbl": "ends_at_start_of", + "lbl": "immediately precedes", "meta": { "basicPropertyValues": [ { @@ -12231,14 +12124,6 @@ { "pred": "http://purl.obolibrary.org/obo/RO_0002575", "val": "http://purl.obolibrary.org/obo/BFO_0000063" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "ends_at_start_of" } ], "comments": [ @@ -12246,11 +12131,6 @@ ], "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ], - "xrefs": [ - { - "val": "RO:0002090" - } ] }, "type": "PROPERTY" @@ -12377,14 +12257,6 @@ { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "FlyBase_development_CV" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "overlaps" } ], "definition": { @@ -12395,11 +12267,6 @@ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" - ], - "xrefs": [ - { - "val": "RO:0002131" - } ] }, "type": "PROPERTY" @@ -13618,44 +13485,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002432", - "lbl": "is active in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "A protein that enables activity in a cytosol." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "executes activity in" - } - ], - "comments": [ - "" - ], - "definition": { - "val": "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs": [ - "GOC:cjm", - "GOC:dos" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "enables activity in", - "xrefs": [] - } - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/RO_0002434", "lbl": "interacts with", @@ -13866,26 +13695,6 @@ }, "type": "PROPERTY" }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002479", - "lbl": "has part that occurs in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, { "id": "http://purl.obolibrary.org/obo/RO_0002481", "lbl": "is kinase activity", @@ -14582,11 +14391,6 @@ "lbl": "transferase activity, transferring phosphorus-containing groups", "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl": "term replaced by", - "type": "PROPERTY" - }, { "id": "http://www.geneontology.org/formats/oboInOwl#NamespaceIdRule", "lbl": "namespace-id-rule", @@ -14767,20 +14571,6 @@ ], "predicateId": "http://purl.obolibrary.org/obo/BFO_0000063" }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000050", - "http://purl.obolibrary.org/obo/BFO_0000066" - ], - "predicateId": "http://purl.obolibrary.org/obo/BFO_0000066" - }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000050", - "http://purl.obolibrary.org/obo/BFO_0000066" - ], - "predicateId": "http://purl.obolibrary.org/obo/BFO_0000066" - }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/BFO_0000050", @@ -14837,13 +14627,6 @@ ], "predicateId": "http://purl.obolibrary.org/obo/RO_0002331" }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000051", - "http://purl.obolibrary.org/obo/BFO_0000066" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002479" - }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/BFO_0000051", @@ -14914,13 +14697,6 @@ ], "predicateId": "http://purl.obolibrary.org/obo/BFO_0000063" }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/BFO_0000066", - "http://purl.obolibrary.org/obo/RO_0002327" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002432" - }, { "chainPredicateIds": [ "http://purl.obolibrary.org/obo/RO_0002017", diff --git a/src/ontology/fbdv-non-classified.obo b/src/ontology/fbdv-non-classified.obo index 2087fb3..08998e8 100644 --- a/src/ontology/fbdv-non-classified.obo +++ b/src/ontology/fbdv-non-classified.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/fbdv-non-classified.owl -date: 05:07:2021 10:41 +data-version: fbdv/releases/2021-08-31/fbdv-non-classified.owl +date: 31:08:2021 09:06 subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "" @@ -50,7 +50,7 @@ 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 "2021-07-05" xsd:string +property_value: owl:versionInfo "2021-08-31" xsd:string [Term] id: BFO:0000002 @@ -2342,6 +2342,7 @@ namespace: biological_process alt_id: GO:0044707 alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] @@ -2496,6 +2497,25 @@ name: quality is_a: BFO:0000020 ! specifically dependent continuant property_value: IAO:0000589 "quality (PATO)" xsd:string +[Typedef] +id: BFO:0000062 +name: preceded by +def: "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." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: happens_during BFO:0000062 +holds_over_chain: part_of BFO:0000062 +holds_over_chain: RO:0002091 BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + [Typedef] id: BFO:0000063 name: precedes @@ -2509,33 +2529,6 @@ holds_over_chain: part_of BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: BFO:0000066 -name: occurs in -def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: part_of BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: part_of ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Typedef] id: RO:0000052 name: characteristic of @@ -2787,7 +2780,7 @@ name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -holds_over_chain: ends_during preceded_by +holds_over_chain: ends_during BFO:0000062 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -2800,6 +2793,17 @@ property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: RO:0002222 ! temporally related to inverse_of: RO:0002091 ! starts during +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + [Typedef] id: RO:0002091 name: starts during @@ -2811,6 +2815,22 @@ domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: has_part RO:0002131 +holds_over_chain: part_of part_of +is_a: RO:0002323 ! mereotopologically related to +transitive_over: part_of ! part of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + [Typedef] id: RO:0002180 name: has component @@ -3215,7 +3235,7 @@ name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: preceded_by ! preceded_by +is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of @@ -3256,7 +3276,7 @@ def: "p is immediately causally upstream of q iff both (a) p immediately precede property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 -is_a: ends_at_start_of ! immediately precedes +is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of [Typedef] @@ -3322,18 +3342,6 @@ is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -[Typedef] -id: RO:0002432 -name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "executes activity in" xsd:string -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: overlaps ! overlaps -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002434 name: interacts with @@ -3412,16 +3420,6 @@ name: helper property (not for use in curation) property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - [Typedef] id: RO:0002481 name: is kinase activity @@ -3685,19 +3683,6 @@ domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences -[Typedef] -id: ends_at_start_of -name: ends_at_start_of -name: immediately precedes -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 -is_a: BFO:0000063 ! precedes - [Typedef] id: ends_during name: ends during @@ -3731,15 +3716,12 @@ is_a: RO:0002091 ! starts during [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: relationship def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -xref: OBO_REL:has_part property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string @@ -3750,7 +3732,7 @@ property_value: IAO:0000116 "Parthood requires the part and the whole to have co property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true -is_a: overlaps ! overlaps +is_a: RO:0002131 ! overlaps [Typedef] id: immediately_preceded_by @@ -3760,8 +3742,8 @@ comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "starts_at_end_of" xsd:string -is_a: preceded_by ! preceded_by -inverse_of: ends_at_start_of ! immediately precedes +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes [Typedef] id: occurent_part_of @@ -3774,23 +3756,6 @@ range: BFO:0000003 ! occurrent is_a: part_of ! part of is_a: RO:0002418 ! causally upstream of or within -[Typedef] -id: overlaps -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: part_of part_of -is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part of -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - [Typedef] id: part_of name: part of @@ -3821,32 +3786,9 @@ property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_a property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string is_transitive: true -is_a: overlaps ! overlaps +is_a: RO:0002131 ! overlaps inverse_of: has_part ! has part -[Typedef] -id: preceded_by -name: preceded by -name: preceded_by -namespace: relationship -def: "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." [] -subset: ro-eco -xref: BFO:0000062 -xref: OBO_REL:preceded_by -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: happens_during preceded_by -holds_over_chain: part_of preceded_by -holds_over_chain: RO:0002091 preceded_by -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - [Typedef] id: substage_of name: substage_of @@ -3855,5 +3797,5 @@ comment: Creating this relation as a temporary fix, pending adding the axiom occ xref: FBdv:00018001 is_transitive: true is_a: happens_during ! happens during -is_a: occurent_part_of ! occurent_part_of +is_a: occurent_part_of ! occurent part of diff --git a/src/ontology/fbdv-non-classified.owl b/src/ontology/fbdv-non-classified.owl index 11b6c4a..043ff62 100644 --- a/src/ontology/fbdv-non-classified.owl +++ b/src/ontology/fbdv-non-classified.owl @@ -18,7 +18,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -31,10 +31,10 @@ FlyBase Developmental Ontology (FBdv) https://creativecommons.org/licenses/by/3.0/ * FBdv:$sequence(8,7000,10000)$ - 05:07:2021 10:41 + 31:08:2021 09:06 FlyBase_development_CV 1.2 - 2021-07-05 + 2021-08-31 @@ -152,6 +152,8 @@ + + term replaced by term replaced by @@ -506,18 +508,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -764,18 +790,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - OBO_REL:has_part + BFO:0000051 external - relationship - has_part + has_part - has_part + has_part has part has part - has_part @@ -806,14 +829,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by - BFO:0000062 - OBO_REL:preceded_by - relationship - preceded_by - preceded_by preceded by - preceded_by @@ -841,47 +858,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - @@ -1336,13 +1312,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. ends_at_start_of meets - RO:0002090 - FlyBase_development_CV - ends_at_start_of - ends_at_start_of X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - ends_at_start_of immediately precedes @@ -1430,15 +1401,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 - FlyBase_development_CV - overlaps - overlaps overlaps - overlaps @@ -2247,42 +2213,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - - - - @@ -2408,32 +2338,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - @@ -10343,6 +10247,7 @@ For example, A and B may be gene products and binding of B by A positively regul biological_process single-multicellular organism process GO:0032501 + multicellular organismal process @@ -10810,118 +10715,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -11495,51 +11288,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction @@ -11940,6 +11688,118 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/fly_development.obo b/src/ontology/fly_development.obo index e9101f3..24bcb7b 100644 --- a/src/ontology/fly_development.obo +++ b/src/ontology/fly_development.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: 2021-07-05 -date: 05:07:2021 10:41 +data-version: 2021-08-31 +date: 31:08:2021 09:06 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" @@ -1991,13 +1991,6 @@ relationship: immediately_preceded_by FBdv:00005317 ! gastrula stage relationship: immediately_preceded_by FBdv:00005322 ! embryonic stage 8 relationship: substage_of FBdv:00005321 ! extended germ band stage -[Typedef] -id: ends_at_start_of -name: ends_at_start_of -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -xref: RO:0002090 - [Typedef] id: happens_during name: happens_during @@ -2009,54 +2002,17 @@ subset: ro-eco xref: RO:0002092 is_transitive: true -[Typedef] -id: has_part -name: has_part -namespace: relationship -def: "a core relation that holds between a whole and its part" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000051 -xref_analog: OBO_REL:has_part -is_transitive: true -is_a: overlaps ! overlaps - [Typedef] id: immediately_preceded_by name: immediately_preceded_by comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -is_a: preceded_by ! preceded_by -inverse_of: ends_at_start_of ! ends_at_start_of [Typedef] id: occurent_part_of name: occurent_part_of def: "A part of relation that applies only between occurents." [] xref: RO:0002012 -is_a: overlaps ! overlaps - -[Typedef] -id: overlaps -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -holds_over_chain: has_part overlaps - -[Typedef] -id: preceded_by -name: preceded_by -namespace: relationship -def: "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." [] -subset: ro-eco -xref: BFO:0000062 -xref_analog: OBO_REL:preceded_by -holds_over_chain: happens_during preceded_by -is_transitive: true [Typedef] id: substage_of diff --git a/src/ontology/imports/go_import.obo b/src/ontology/imports/go_import.obo index d116145..37563cf 100644 --- a/src/ontology/imports/go_import.obo +++ b/src/ontology/imports/go_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/imports/go_import.owl +data-version: fbdv/releases/2021-08-31/imports/go_import.owl subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_manually_annotate "" subsetdef: goslim_agr "" @@ -16,8 +16,8 @@ subsetdef: goslim_plant "" subsetdef: goslim_pombe "" subsetdef: goslim_yeast "" ontology: fbdv/imports/go_import -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/go/releases/2021-06-16/go.owl -property_value: owl:versionInfo "2021-07-05" xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/go/releases/2021-08-18/go.owl +property_value: owl:versionInfo "2021-08-31" xsd:string [Term] id: GO:0000087 @@ -225,6 +225,7 @@ namespace: biological_process alt_id: GO:0044707 alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index c5ebab2..3633d86 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -11,9 +11,9 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2021-07-05 + + + 2021-08-31 @@ -841,6 +841,7 @@ biological_process single-multicellular organism process GO:0032501 + multicellular organismal process diff --git a/src/ontology/imports/ro_import.obo b/src/ontology/imports/ro_import.obo index 14671f1..d1ad822 100644 --- a/src/ontology/imports/ro_import.obo +++ b/src/ontology/imports/ro_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: fbdv/releases/2021-07-05/imports/ro_import.owl +data-version: fbdv/releases/2021-08-31/imports/ro_import.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -7,9 +7,9 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: fbdv/imports/ro_import -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/ro/releases/2021-06-23/ro.owl -property_value: owl:versionInfo "2021-07-05" xsd:string -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/ro/releases/2021-08-25/ro.owl +property_value: owl:versionInfo "2021-08-31" xsd:string +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Term] id: BFO:0000002 @@ -212,33 +212,6 @@ holds_over_chain: RO:0002092 BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: BFO:0000066 -name: occurs in -def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000050 BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Typedef] id: RO:0000052 name: characteristic of @@ -1095,18 +1068,6 @@ is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -[Typedef] -id: RO:0002432 -name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "executes activity in" xsd:string -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002434 name: interacts with @@ -1185,16 +1146,6 @@ name: helper property (not for use in curation) property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - [Typedef] id: RO:0002481 name: is kinase activity diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 7531c1a..6d09cdb 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2021-07-05 + + + 2021-08-31 @@ -115,6 +115,15 @@ + + + + + term replaced by + + + + @@ -211,18 +220,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -467,47 +500,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - @@ -1827,42 +1819,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - - - - @@ -1988,32 +1944,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - @@ -3283,51 +3213,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction diff --git a/src/ontology/reports/fbdv-edit-release.owl-obo-report.tsv b/src/ontology/reports/fbdv-edit-release.owl-obo-report.tsv index 9ac9ab1..538b0f9 100644 --- a/src/ontology/reports/fbdv-edit-release.owl-obo-report.tsv +++ b/src/ontology/reports/fbdv-edit-release.owl-obo-report.tsv @@ -1,6 +1,4 @@ Level Rule Name Subject Property Value -WARN missing_definition has part definition -WARN missing_definition preceded by definition WARN missing_definition oogenesis definition WARN missing_definition unfertilized egg stage definition WARN missing_definition fertilized egg stage definition @@ -12,8 +10,6 @@ WARN missing_definition definition definition WARN missing_definition term replaced by definition WARN missing_definition occurent part of definition WARN missing_definition immediately preceded by definition -WARN missing_definition immediately precedes definition -WARN missing_definition overlaps definition WARN missing_definition Systematic synonym definition WARN missing_definition namespace-id-rule definition WARN missing_definition subset_property definition diff --git a/src/ontology/reports/robot_simple_diff.txt b/src/ontology/reports/robot_simple_diff.txt index 17e6610..1b74916 100644 --- a/src/ontology/reports/robot_simple_diff.txt +++ b/src/ontology/reports/robot_simple_diff.txt @@ -1,13 +1,78 @@ -5 axioms in left ontology but not in right ontology: -- Annotation( "2021-07-05"^^xsd:string) -- Annotation( "05:07:2021 10:41"^^xsd:string) -- AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"^^xsd:string) -- AnnotationAssertion(Annotation( "FlyBase:FBrf0089570"^^xsd:string) "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)."^^xsd:string) -- OntologyID(OntologyIRI() VersionIRI()) +3 axioms in left ontology but not in right ontology: +- Annotation( "2021-08-31"^^xsd:string) +- Annotation( "31:08:2021 09:05"^^xsd:string) +- OntologyID(OntologyIRI() VersionIRI()) -5 axioms in right ontology but not in left ontology: -+ Annotation( "2021-05-10"^^xsd:string) -+ Annotation( "10:05:2021 12:44"^^xsd:string) -+ AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"^^xsd:string) -+ AnnotationAssertion(Annotation( "FlyBase:FBrf0089570"^^xsd:string) "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)."^^xsd:string) -+ OntologyID(OntologyIRI() VersionIRI()) +72 axioms in right ontology but not in left ontology: ++ Annotation( "2021-07-05"^^xsd:string) ++ Annotation( "05:07:2021 10:41"^^xsd:string) ++ AnnotationAssertion( "has part"^^xsd:string) ++ AnnotationAssertion( "preceded by"^^xsd:string) ++ AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"^^xsd:string) ++ AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"^^xsd:string) ++ AnnotationAssertion( "this year has part this day (occurrent parthood)"^^xsd:string) ++ AnnotationAssertion( ) ++ AnnotationAssertion( "a core relation that holds between a whole and its part"^^xsd:string) ++ AnnotationAssertion( "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."^^xsd:string) ++ AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y"^^xsd:string) ++ AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."^^xsd:string) ++ AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"^^xsd:string) ++ AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."^^xsd:string) ++ AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."^^xsd:string) ++ AnnotationAssertion( "David Osumi-Sutherland"^^xsd:string) ++ AnnotationAssertion( "has_part"^^xsd:string) ++ AnnotationAssertion( "is preceded by"^^xsd:string) ++ AnnotationAssertion( "preceded_by"^^xsd:string) ++ AnnotationAssertion( "ends_at_start_of"^^xsd:string) ++ AnnotationAssertion( "meets"^^xsd:string) ++ AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)"^^xsd:string) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by"^^xsd:string) ++ AnnotationAssertion( "BFO:0000051"^^xsd:string) ++ AnnotationAssertion( "OBO_REL:has_part"^^xsd:string) ++ AnnotationAssertion( "BFO:0000062"^^xsd:string) ++ AnnotationAssertion( "OBO_REL:preceded_by"^^xsd:string) ++ AnnotationAssertion( "RO:0002090"^^xsd:string) ++ AnnotationAssertion( "RO:0002131"^^xsd:string) ++ AnnotationAssertion( "relationship"^^xsd:string) ++ AnnotationAssertion( "relationship"^^xsd:string) ++ AnnotationAssertion( "FlyBase_development_CV"^^xsd:string) ++ AnnotationAssertion( "FlyBase_development_CV"^^xsd:string) ++ AnnotationAssertion( "has_part"^^xsd:string) ++ AnnotationAssertion( "preceded_by"^^xsd:string) ++ AnnotationAssertion( "ends_at_start_of"^^xsd:string) ++ AnnotationAssertion( "overlaps"^^xsd:string) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( ) ++ AnnotationAssertion( "has_part"^^xsd:string) ++ AnnotationAssertion( "preceded_by"^^xsd:string) ++ AnnotationAssertion( "ends_at_start_of"^^xsd:string) ++ AnnotationAssertion( "overlaps"^^xsd:string) ++ AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"^^xsd:string) ++ AnnotationAssertion(rdfs:label "has_part"^^xsd:string) ++ AnnotationAssertion(rdfs:label "preceded_by"^^xsd:string) ++ AnnotationAssertion(rdfs:label "expand expression to"^^xsd:string) ++ AnnotationAssertion(rdfs:label "immediately precedes"^^xsd:string) ++ AnnotationAssertion(rdfs:label "overlaps"^^xsd:string) ++ Declaration(AnnotationProperty()) ++ Declaration(ObjectProperty()) ++ Declaration(ObjectProperty()) ++ Declaration(ObjectProperty()) ++ Declaration(ObjectProperty()) ++ InverseObjectProperties( ) ++ OntologyID(OntologyIRI() VersionIRI()) ++ SubObjectPropertyOf( ) ++ SubObjectPropertyOf( ) ++ SubObjectPropertyOf( ) ++ SubObjectPropertyOf(ObjectPropertyChain( ) ) ++ SubObjectPropertyOf(ObjectPropertyChain( ) ) ++ TransitiveObjectProperty() ++ TransitiveObjectProperty() diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index eb9ed47..7dcd21c 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2021-07-05"^^xsd:string) + +Annotation(owl:versionInfo "2021-08-31"^^xsd:string) ) \ No newline at end of file diff --git a/src/patterns/pattern_owl_seed.txt b/src/patterns/pattern_owl_seed.txt index cd85817..b023c58 100644 --- a/src/patterns/pattern_owl_seed.txt +++ b/src/patterns/pattern_owl_seed.txt @@ -1,11 +1,11 @@ term -http://purl.obolibrary.org/obo/UBERON_0001062 -http://purl.obolibrary.org/obo/RO_0002314 http://purl.obolibrary.org/obo/PATO_0000460 http://purl.obolibrary.org/obo/RO_0002573 http://www.w3.org/1999/02/22-rdf-syntax-ns#nil http://purl.obolibrary.org/obo/BFO_0000051 http://purl.obolibrary.org/obo/PATO_0000001 +http://purl.obolibrary.org/obo/UBERON_0001062 +http://purl.obolibrary.org/obo/RO_0002314 http://purl.obolibrary.org/obo/upheno/patterns/abnormalAnatomicalEntity.yaml http://www.geneontology.org/formats/oboInOwl#hasExactSynonym http://purl.org/dc/terms/title From 95ae0b08d5439b9988983abf1002889eac0fdb72 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Tue, 31 Aug 2021 10:31:09 +0100 Subject: [PATCH 4/4] undo error for multiple labels --- src/ontology/qc-profile.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/qc-profile.txt b/src/ontology/qc-profile.txt index c96533f..55fe4ba 100644 --- a/src/ontology/qc-profile.txt +++ b/src/ontology/qc-profile.txt @@ -20,4 +20,4 @@ WARN missing_superclass WARN misused_obsolete_label ERROR multiple_definitions ERROR multiple_equivalent_classes -ERROR multiple_labels +WARN multiple_labels