From 6ea2e6bbc207c97343b01793bef8865a663a404a Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 29 Aug 2016 14:25:49 -0700 Subject: [PATCH] patterns --- Makefile | 3 + modules/endochondral_cartilage.omn | 158 ++++++++++++++++++++++++--- patterns/endochondral_cartilage.yaml | 12 +- patterns/uberon_patterns.pro | 33 +++++- 4 files changed, 188 insertions(+), 18 deletions(-) diff --git a/Makefile b/Makefile index 3d11a585ac..e7e0a5704c 100644 --- a/Makefile +++ b/Makefile @@ -1391,6 +1391,9 @@ $(PATTERNDIR)/%.yaml: patterns/uberon_patterns.pro blip-findall -r uberonp -u odputil -i $(PATTERNDIR)/uberon_patterns.pro "write_yaml($*),fail" > $@.tmp && mv $@.tmp $@ .PRECIOUS: $(PATTERNDIR)/%.yaml +modules/conflict_analysis.tsv: + blip-findall -i uberon_edit.obo -r pext -u odputil -i patterns/uberon_patterns.pro conflicting_tuple_from_ldef/4 -label -no_pred -use_tabs > $@.tmp && mv $@.tmp $@ + modules/missing.txt: blip-findall -i uberon_edit.obo -r pext -u odputil -i $(PATTERNDIR)/uberon_patterns.pro "nomatch/3" -label -no_pred > $@ diff --git a/modules/endochondral_cartilage.omn b/modules/endochondral_cartilage.omn index 6849cf4555..ede1e09912 100644 --- a/modules/endochondral_cartilage.omn +++ b/modules/endochondral_cartilage.omn @@ -2,26 +2,26 @@ Prefix: : Prefix: IAO: Prefix: DOSDP: Prefix: oio: -Prefix: PR: Prefix: CL: +Prefix: NBO: +Prefix: ECTO: Prefix: SO: -Prefix: NPO: +Prefix: GOCHE: +Prefix: RO: Prefix: CHEBI: +Prefix: ExO: +Prefix: PO: +Prefix: UBERON: +Prefix: NPO: +Prefix: NCIT: Prefix: XCO: -Prefix: GOCHE: -Prefix: OBA: -Prefix: PATO: +Prefix: PR: +Prefix: BFO: Prefix: ENVO: -Prefix: PO: -Prefix: GO: +Prefix: PATO: Prefix: ZECO: -Prefix: BFO: -Prefix: NCIT: -Prefix: ExO: -Prefix: ECTO: -Prefix: NBO: -Prefix: UBERON: -Prefix: RO: +Prefix: GO: +Prefix: OBA: ## Auto-generated @@ -30,6 +30,8 @@ AnnotationProperty: IAO:0000115 AnnotationProperty: endochondral_cartilage/element AnnotationProperty: DOSDP:applies-pattern AnnotationProperty: oio:hasRelatedSynonym +AnnotationProperty: oio:hasExactSynonym +AnnotationProperty: oio:hasRelatedSynonym Class: UBERON:0002418 ## cartilage tissue ObjectProperty: RO:0002473 ## composed_primarily_of ## Auto-generated classes @@ -38,382 +40,510 @@ Class: UBERON:0004529 ## anatomical projection ## {"element": "UBERON:0004529"} Class: UBERON:0011769 Annotations: IAO:0000115 "A anatomical projection that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "anatomical projection cartilage" + Annotations: oio:hasRelatedSynonym "anatomical projection cartilage" EquivalentTo: UBERON:0004529 and RO:0002473 some UBERON:0002418 ## anatomical projection and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0004637 ## otic capsule ## {"element": "UBERON:0004637"} Class: UBERON:0005410 Annotations: IAO:0000115 "A otic capsule that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "otic capsule cartilage" + Annotations: oio:hasRelatedSynonym "otic capsule cartilage" EquivalentTo: UBERON:0004637 and RO:0002473 some UBERON:0002418 ## otic capsule and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0004765 ## skeletal element ## {"element": "UBERON:0004765"} Class: UBERON:0007844 Annotations: IAO:0000115 "A skeletal element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "skeletal element cartilage" + Annotations: oio:hasRelatedSynonym "skeletal element cartilage" EquivalentTo: UBERON:0004765 and RO:0002473 some UBERON:0002418 ## skeletal element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0010913 ## vertebral element ## {"element": "UBERON:0010913"} Class: UBERON:0011094 Annotations: IAO:0000115 "A vertebral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "vertebral element cartilage" + Annotations: oio:hasRelatedSynonym "vertebral element cartilage" EquivalentTo: UBERON:0010913 and RO:0002473 some UBERON:0002418 ## vertebral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0011134 ## nonsynovial joint ## {"element": "UBERON:0011134"} Class: UBERON:0002213 Annotations: IAO:0000115 "A nonsynovial joint that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "nonsynovial joint cartilage" + Annotations: oio:hasRelatedSynonym "nonsynovial joint cartilage" EquivalentTo: UBERON:0011134 and RO:0002473 some UBERON:0002418 ## nonsynovial joint and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0011248 ## procoracoid element ## {"element": "UBERON:0011248"} Class: UBERON:0011247 Annotations: IAO:0000115 "A procoracoid element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "procoracoid element cartilage" + Annotations: oio:hasRelatedSynonym "procoracoid element cartilage" EquivalentTo: UBERON:0011248 and RO:0002473 some UBERON:0002418 ## procoracoid element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0011608 ## hyomandibular element ## {"element": "UBERON:0011608"} Class: UBERON:0011607 Annotations: IAO:0000115 "A hyomandibular element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "hyomandibular element cartilage" + Annotations: oio:hasRelatedSynonym "hyomandibular element cartilage" EquivalentTo: UBERON:0011608 and RO:0002473 some UBERON:0002418 ## hyomandibular element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0011614 ## basihyal element ## {"element": "UBERON:0011614"} Class: UBERON:0011615 Annotations: IAO:0000115 "A basihyal element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "basihyal element cartilage" + Annotations: oio:hasRelatedSynonym "basihyal element cartilage" EquivalentTo: UBERON:0011614 and RO:0002473 some UBERON:0002418 ## basihyal element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0013631 ## sesamoid element ## {"element": "UBERON:0013631"} Class: UBERON:0013632 Annotations: IAO:0000115 "A sesamoid element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "sesamoid element cartilage" + Annotations: oio:hasRelatedSynonym "sesamoid element cartilage" EquivalentTo: UBERON:0013631 and RO:0002473 some UBERON:0002418 ## sesamoid element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0013746 ## basibranchial element ## {"element": "UBERON:0013746"} Class: UBERON:0013747 Annotations: IAO:0000115 "A basibranchial element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "basibranchial element cartilage" + Annotations: oio:hasRelatedSynonym "basibranchial element cartilage" EquivalentTo: UBERON:0013746 and RO:0002473 some UBERON:0002418 ## basibranchial element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015001 ## radius endochondral element ## {"element": "UBERON:0015001"} Class: UBERON:0006286 Annotations: IAO:0000115 "A radius endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "radius endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "radius endochondral element cartilage" EquivalentTo: UBERON:0015001 and RO:0002473 some UBERON:0002418 ## radius endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015002 ## radius-ulna endochondral element ## {"element": "UBERON:0015002"} Class: UBERON:0010848 Annotations: IAO:0000115 "A radius-ulna endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "radius-ulna endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "radius-ulna endochondral element cartilage" EquivalentTo: UBERON:0015002 and RO:0002473 some UBERON:0002418 ## radius-ulna endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015003 ## ulna endochondral element ## {"element": "UBERON:0015003"} Class: UBERON:0006306 Annotations: IAO:0000115 "A ulna endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "ulna endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "ulna endochondral element cartilage" EquivalentTo: UBERON:0015003 and RO:0002473 some UBERON:0002418 ## ulna endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015004 ## tibia endochondral element ## {"element": "UBERON:0015004"} Class: UBERON:0010849 Annotations: IAO:0000115 "A tibia endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "tibia endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "tibia endochondral element cartilage" EquivalentTo: UBERON:0015004 and RO:0002473 some UBERON:0002418 ## tibia endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015007 ## cervical vertebra endochondral element ## {"element": "UBERON:0015007"} Class: UBERON:0013505 Annotations: IAO:0000115 "A cervical vertebra endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "cervical vertebra endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "cervical vertebra endochondral element cartilage" EquivalentTo: UBERON:0015007 and RO:0002473 some UBERON:0002418 ## cervical vertebra endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015008 ## thoracic vertebra endochondral element ## {"element": "UBERON:0015008"} Class: UBERON:0013507 Annotations: IAO:0000115 "A thoracic vertebra endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "thoracic vertebra endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "thoracic vertebra endochondral element cartilage" EquivalentTo: UBERON:0015008 and RO:0002473 some UBERON:0002418 ## thoracic vertebra endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015009 ## lumbar vertebra endochondral element ## {"element": "UBERON:0015009"} Class: UBERON:0013509 Annotations: IAO:0000115 "A lumbar vertebra endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "lumbar vertebra endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "lumbar vertebra endochondral element cartilage" EquivalentTo: UBERON:0015009 and RO:0002473 some UBERON:0002418 ## lumbar vertebra endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015010 ## sacral vertebra endochondral element ## {"element": "UBERON:0015010"} Class: UBERON:0010745 Annotations: IAO:0000115 "A sacral vertebra endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "sacral vertebra endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "sacral vertebra endochondral element cartilage" EquivalentTo: UBERON:0015010 and RO:0002473 some UBERON:0002418 ## sacral vertebra endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015011 ## tibiotarsus endochondral element ## {"element": "UBERON:0015011"} Class: UBERON:0010902 Annotations: IAO:0000115 "A tibiotarsus endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "tibiotarsus endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "tibiotarsus endochondral element cartilage" EquivalentTo: UBERON:0015011 and RO:0002473 some UBERON:0002418 ## tibiotarsus endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015012 ## tarsometatarsus endochondral element ## {"element": "UBERON:0015012"} Class: UBERON:0010900 Annotations: IAO:0000115 "A tarsometatarsus endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "tarsometatarsus endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "tarsometatarsus endochondral element cartilage" EquivalentTo: UBERON:0015012 and RO:0002473 some UBERON:0002418 ## tarsometatarsus endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015013 ## fibula endochondral element ## {"element": "UBERON:0015013"} Class: UBERON:0010851 Annotations: IAO:0000115 "A fibula endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "fibula endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "fibula endochondral element cartilage" EquivalentTo: UBERON:0015013 and RO:0002473 some UBERON:0002418 ## fibula endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015014 ## calcaneum endochondral element ## {"element": "UBERON:0015014"} Class: UBERON:0010842 Annotations: IAO:0000115 "A calcaneum endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "calcaneum endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "calcaneum endochondral element cartilage" EquivalentTo: UBERON:0015014 and RO:0002473 some UBERON:0002418 ## calcaneum endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015015 ## supraoccipital endochondral element ## {"element": "UBERON:0015015"} Class: UBERON:0011162 Annotations: IAO:0000115 "A supraoccipital endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "supraoccipital endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "supraoccipital endochondral element cartilage" EquivalentTo: UBERON:0015015 and RO:0002473 some UBERON:0002418 ## supraoccipital endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015016 ## stapes endochondral element ## {"element": "UBERON:0015016"} Class: UBERON:0010055 Annotations: IAO:0000115 "A stapes endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "stapes endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "stapes endochondral element cartilage" EquivalentTo: UBERON:0015016 and RO:0002473 some UBERON:0002418 ## stapes endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015017 ## incus endochondral element ## {"element": "UBERON:0015017"} Class: UBERON:0007374 Annotations: IAO:0000115 "A incus endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "incus endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "incus endochondral element cartilage" EquivalentTo: UBERON:0015017 and RO:0002473 some UBERON:0002418 ## incus endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015018 ## malleus endochondral element ## {"element": "UBERON:0015018"} Class: UBERON:0010054 Annotations: IAO:0000115 "A malleus endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "malleus endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "malleus endochondral element cartilage" EquivalentTo: UBERON:0015018 and RO:0002473 some UBERON:0002418 ## malleus endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015019 ## rib endochondral element ## {"element": "UBERON:0015019"} Class: UBERON:0006288 Annotations: IAO:0000115 "A rib endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "rib endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "rib endochondral element cartilage" EquivalentTo: UBERON:0015019 and RO:0002473 some UBERON:0002418 ## rib endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015021 ## forelimb endochondral element ## {"element": "UBERON:0015021"} Class: UBERON:0010883 Annotations: IAO:0000115 "A forelimb endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "forelimb endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "forelimb endochondral element cartilage" EquivalentTo: UBERON:0015021 and RO:0002473 some UBERON:0002418 ## forelimb endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015022 ## hindlimb endochondral element ## {"element": "UBERON:0015022"} Class: UBERON:0010885 Annotations: IAO:0000115 "A hindlimb endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "hindlimb endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "hindlimb endochondral element cartilage" EquivalentTo: UBERON:0015022 and RO:0002473 some UBERON:0002418 ## hindlimb endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015048 ## basioccipital endochondral element ## {"element": "UBERON:0015048"} Class: UBERON:0006209 Annotations: IAO:0000115 "A basioccipital endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "basioccipital endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "basioccipital endochondral element cartilage" EquivalentTo: UBERON:0015048 and RO:0002473 some UBERON:0002418 ## basioccipital endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015051 ## exoccipital endochondral element ## {"element": "UBERON:0015051"} Class: UBERON:0010752 Annotations: IAO:0000115 "A exoccipital endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "exoccipital endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "exoccipital endochondral element cartilage" EquivalentTo: UBERON:0015051 and RO:0002473 some UBERON:0002418 ## exoccipital endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015052 ## femur endochondral element ## {"element": "UBERON:0015052"} Class: UBERON:0010129 Annotations: IAO:0000115 "A femur endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "femur endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "femur endochondral element cartilage" EquivalentTo: UBERON:0015052 and RO:0002473 some UBERON:0002418 ## femur endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015053 ## humerus endochondral element ## {"element": "UBERON:0015053"} Class: UBERON:0006245 Annotations: IAO:0000115 "A humerus endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "humerus endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "humerus endochondral element cartilage" EquivalentTo: UBERON:0015053 and RO:0002473 some UBERON:0002418 ## humerus endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015054 ## iliac endochondral element ## {"element": "UBERON:0015054"} Class: UBERON:0010714 Annotations: IAO:0000115 "A iliac endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "iliac endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "iliac endochondral element cartilage" EquivalentTo: UBERON:0015054 and RO:0002473 some UBERON:0002418 ## iliac endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015055 ## pubic endochondral element ## {"element": "UBERON:0015055"} Class: UBERON:0010718 Annotations: IAO:0000115 "A pubic endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "pubic endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "pubic endochondral element cartilage" EquivalentTo: UBERON:0015055 and RO:0002473 some UBERON:0002418 ## pubic endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015056 ## ischial endochondral element ## {"element": "UBERON:0015056"} Class: UBERON:0006254 Annotations: IAO:0000115 "A ischial endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "ischial endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "ischial endochondral element cartilage" EquivalentTo: UBERON:0015056 and RO:0002473 some UBERON:0002418 ## ischial endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015057 ## scapula endochondral element ## {"element": "UBERON:0015057"} Class: UBERON:0006290 Annotations: IAO:0000115 "A scapula endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "scapula endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "scapula endochondral element cartilage" EquivalentTo: UBERON:0015057 and RO:0002473 some UBERON:0002418 ## scapula endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015058 ## alisphenoid endochondral element ## {"element": "UBERON:0015058"} Class: UBERON:0010733 Annotations: IAO:0000115 "A alisphenoid endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "alisphenoid endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "alisphenoid endochondral element cartilage" EquivalentTo: UBERON:0015058 and RO:0002473 some UBERON:0002418 ## alisphenoid endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015059 ## orbitosphenoid endochondral element ## {"element": "UBERON:0015059"} Class: UBERON:0005687 Annotations: IAO:0000115 "A orbitosphenoid endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "orbitosphenoid endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "orbitosphenoid endochondral element cartilage" EquivalentTo: UBERON:0015059 and RO:0002473 some UBERON:0002418 ## orbitosphenoid endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015060 ## sphenoid endochondral element ## {"element": "UBERON:0015060"} Class: UBERON:0009193 Annotations: IAO:0000115 "A sphenoid endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "sphenoid endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "sphenoid endochondral element cartilage" EquivalentTo: UBERON:0015060 and RO:0002473 some UBERON:0002418 ## sphenoid endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015061 ## limb endochondral element ## {"element": "UBERON:0015061"} Class: UBERON:0010881 Annotations: IAO:0000115 "A limb endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "limb endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "limb endochondral element cartilage" EquivalentTo: UBERON:0015061 and RO:0002473 some UBERON:0002418 ## limb endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015063 ## autopod endochondral element ## {"element": "UBERON:0015063"} Class: UBERON:0015064 Annotations: IAO:0000115 "A autopod endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "autopod endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "autopod endochondral element cartilage" EquivalentTo: UBERON:0015063 and RO:0002473 some UBERON:0002418 ## autopod endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015067 ## centrale endochondral element ## {"element": "UBERON:0015067"} Class: UBERON:0015077 Annotations: IAO:0000115 "A centrale endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "centrale endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "centrale endochondral element cartilage" EquivalentTo: UBERON:0015067 and RO:0002473 some UBERON:0002418 ## centrale endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015068 ## distal carpal endochondral element ## {"element": "UBERON:0015068"} Class: UBERON:0015069 Annotations: IAO:0000115 "A distal carpal endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal carpal endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal carpal endochondral element cartilage" EquivalentTo: UBERON:0015068 and RO:0002473 some UBERON:0002418 ## distal carpal endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015078 ## proximal carpal endochondral element ## {"element": "UBERON:0015078"} Class: UBERON:0015079 Annotations: IAO:0000115 "A proximal carpal endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "proximal carpal endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "proximal carpal endochondral element cartilage" EquivalentTo: UBERON:0015078 and RO:0002473 some UBERON:0002418 ## proximal carpal endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015081 ## proximal tarsal endochondral element ## {"element": "UBERON:0015081"} Class: UBERON:0015082 Annotations: IAO:0000115 "A proximal tarsal endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "proximal tarsal endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "proximal tarsal endochondral element cartilage" EquivalentTo: UBERON:0015081 and RO:0002473 some UBERON:0002418 ## proximal tarsal endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015084 ## distal carpal bone 1 endochondral element ## {"element": "UBERON:0015084"} Class: UBERON:0015085 Annotations: IAO:0000115 "A distal carpal bone 1 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal carpal bone 1 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal carpal bone 1 endochondral element cartilage" EquivalentTo: UBERON:0015084 and RO:0002473 some UBERON:0002418 ## distal carpal bone 1 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015087 ## distal carpal bone 2 endochondral element ## {"element": "UBERON:0015087"} Class: UBERON:0015088 Annotations: IAO:0000115 "A distal carpal bone 2 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal carpal bone 2 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal carpal bone 2 endochondral element cartilage" EquivalentTo: UBERON:0015087 and RO:0002473 some UBERON:0002418 ## distal carpal bone 2 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015090 ## distal carpal bone 3 endochondral element ## {"element": "UBERON:0015090"} Class: UBERON:0015091 Annotations: IAO:0000115 "A distal carpal bone 3 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal carpal bone 3 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal carpal bone 3 endochondral element cartilage" EquivalentTo: UBERON:0015090 and RO:0002473 some UBERON:0002418 ## distal carpal bone 3 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015093 ## distal carpal bone 4 endochondral element ## {"element": "UBERON:0015093"} Class: UBERON:0015094 Annotations: IAO:0000115 "A distal carpal bone 4 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal carpal bone 4 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal carpal bone 4 endochondral element cartilage" EquivalentTo: UBERON:0015093 and RO:0002473 some UBERON:0002418 ## distal carpal bone 4 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015096 ## distal carpal bone 5 endochondral element ## {"element": "UBERON:0015096"} Class: UBERON:0015097 Annotations: IAO:0000115 "A distal carpal bone 5 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal carpal bone 5 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal carpal bone 5 endochondral element cartilage" EquivalentTo: UBERON:0015096 and RO:0002473 some UBERON:0002418 ## distal carpal bone 5 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015099 ## distal tarsal endochondral element ## {"element": "UBERON:0015099"} Class: UBERON:0015100 Annotations: IAO:0000115 "A distal tarsal endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal tarsal endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal tarsal endochondral element cartilage" EquivalentTo: UBERON:0015099 and RO:0002473 some UBERON:0002418 ## distal tarsal endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015102 ## distal tarsal bone 1 endochondral element ## {"element": "UBERON:0015102"} Class: UBERON:0015103 Annotations: IAO:0000115 "A distal tarsal bone 1 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal tarsal bone 1 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal tarsal bone 1 endochondral element cartilage" EquivalentTo: UBERON:0015102 and RO:0002473 some UBERON:0002418 ## distal tarsal bone 1 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015105 ## distal tarsal bone 2 endochondral element ## {"element": "UBERON:0015105"} Class: UBERON:0015106 Annotations: IAO:0000115 "A distal tarsal bone 2 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal tarsal bone 2 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal tarsal bone 2 endochondral element cartilage" EquivalentTo: UBERON:0015105 and RO:0002473 some UBERON:0002418 ## distal tarsal bone 2 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015108 ## distal tarsal bone 3 endochondral element ## {"element": "UBERON:0015108"} Class: UBERON:0015109 Annotations: IAO:0000115 "A distal tarsal bone 3 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal tarsal bone 3 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal tarsal bone 3 endochondral element cartilage" EquivalentTo: UBERON:0015108 and RO:0002473 some UBERON:0002418 ## distal tarsal bone 3 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015111 ## distal tarsal bone 4 endochondral element ## {"element": "UBERON:0015111"} Class: UBERON:0015112 Annotations: IAO:0000115 "A distal tarsal bone 4 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal tarsal bone 4 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal tarsal bone 4 endochondral element cartilage" EquivalentTo: UBERON:0015111 and RO:0002473 some UBERON:0002418 ## distal tarsal bone 4 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0015114 ## distal tarsal bone 5 endochondral element ## {"element": "UBERON:0015114"} Class: UBERON:0015115 Annotations: IAO:0000115 "A distal tarsal bone 5 endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal tarsal bone 5 endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal tarsal bone 5 endochondral element cartilage" EquivalentTo: UBERON:0015114 and RO:0002473 some UBERON:0002418 ## distal tarsal bone 5 endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0016491 ## vertebral centrum element ## {"element": "UBERON:0016491"} Class: UBERON:0009291 Annotations: IAO:0000115 "A vertebral centrum element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "vertebral centrum element cartilage" + Annotations: oio:hasRelatedSynonym "vertebral centrum element cartilage" EquivalentTo: UBERON:0016491 and RO:0002473 some UBERON:0002418 ## vertebral centrum element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0017750 ## proximal mesopodial endochondral element ## {"element": "UBERON:0017750"} Class: UBERON:0017751 Annotations: IAO:0000115 "A proximal mesopodial endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "proximal mesopodial endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "proximal mesopodial endochondral element cartilage" EquivalentTo: UBERON:0017750 and RO:0002473 some UBERON:0002418 ## proximal mesopodial endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0018099 ## distal mesopodial endochondral element ## {"element": "UBERON:0018099"} Class: UBERON:0018100 Annotations: IAO:0000115 "A distal mesopodial endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "distal mesopodial endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "distal mesopodial endochondral element cartilage" EquivalentTo: UBERON:0018099 and RO:0002473 some UBERON:0002418 ## distal mesopodial endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0018142 ## caudal vertebra endochondral element ## {"element": "UBERON:0018142"} Class: UBERON:0013503 Annotations: IAO:0000115 "A caudal vertebra endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "caudal vertebra endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "caudal vertebra endochondral element cartilage" EquivalentTo: UBERON:0018142 and RO:0002473 some UBERON:0002418 ## caudal vertebra endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0035130 ## auditory ossicle endochondral element ## {"element": "UBERON:0035130"} Class: UBERON:0035131 Annotations: IAO:0000115 "A auditory ossicle endochondral element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "auditory ossicle endochondral element cartilage" + Annotations: oio:hasRelatedSynonym "auditory ossicle endochondral element cartilage" EquivalentTo: UBERON:0035130 and RO:0002473 some UBERON:0002418 ## auditory ossicle endochondral element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0035561 ## styliform element ## {"element": "UBERON:0035561"} Class: UBERON:0008254 Annotations: IAO:0000115 "A styliform element that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "styliform element cartilage" + Annotations: oio:hasRelatedSynonym "styliform element cartilage" EquivalentTo: UBERON:0035561 and RO:0002473 some UBERON:0002418 ## styliform element and 'composed_primarily_of' some 'cartilage tissue' Class: UBERON:0035612 ## nasal turbinal ## {"element": "UBERON:0035612"} Class: UBERON:0035007 Annotations: IAO:0000115 "A nasal turbinal that is composed primarily of cartilage tissue" + Annotations: oio:hasExactSynonym "nasal turbinal cartilage" + Annotations: oio:hasRelatedSynonym "nasal turbinal cartilage" EquivalentTo: UBERON:0035612 and RO:0002473 some UBERON:0002418 ## nasal turbinal and 'composed_primarily_of' some 'cartilage tissue' diff --git a/patterns/endochondral_cartilage.yaml b/patterns/endochondral_cartilage.yaml index ac096dc047..ee554bbf3f 100644 --- a/patterns/endochondral_cartilage.yaml +++ b/patterns/endochondral_cartilage.yaml @@ -10,11 +10,19 @@ vars: element: "Thing" name: - text: "%s cartilage" + text: "%s cartilage element" vars: - element -annotations: [] +annotations: + - property: oio:hasExactSynonym + text: "%s cartilage" + vars: + - element + - property: oio:hasRelatedSynonym + text: "%s cartilage" + vars: + - element def: text: "A %s that is composed primarily of cartilage tissue" diff --git a/patterns/uberon_patterns.pro b/patterns/uberon_patterns.pro index 2ba29fd850..ab969dc2ae 100644 --- a/patterns/uberon_patterns.pro +++ b/patterns/uberon_patterns.pro @@ -1,9 +1,19 @@ -pattern(luminal_space_of,n('anatomical space'),[luminal_space_of=X],[structure],[X],[v(structure)-space], +pattern(luminal_space_of,n('anatomical space'),[luminal_space_of=X],[structure],[X], + [v(structure)-space, + v(structure)-lumen, + lumen-of-v(structure), + cavity-of-v(structure), + v(structure)-cavity + ], 'The luminal space within the %s.'-[structure]). pattern(endochondral_bone,G,[composed_primarily_of=n('bone tissue')],[element],[G],[v(element)-bone], 'A %s that is composed primarily of bone tissue'-[element]). -pattern(endochondral_cartilage,G,[composed_primarily_of=n('cartilage tissue')],[element],[G],[v(element)-cartilage], +pattern(endochondral_cartilage,G,[composed_primarily_of=n('cartilage tissue')],[element],[G], + [v(element)-cartilage-element, + v(element)-cartilage, + related=v(element)-cartilage + ], 'A %s that is composed primarily of cartilage tissue'-[element]). paired(endochondral_bone,endochondral_cartilage). @@ -14,8 +24,26 @@ pattern(mesenchyme,n(mesenchyme),[part_of=S],[element],[S], v(element)-mesenchyme ], 'The mesenchymal component of a %s'-[element]). + pattern(connective_tissue,n('connective tissue'),[part_of=S],[element],[S],[connective-tissue-of-v(element)], 'The connective tissue component of a %s'-[element]). + +pattern(skull_foramen_by_function,n('foramen of skull'),[conduit_for=S],[element],[S], + [v(element)-foramen, + foramen-of-v(element), + v(element)-canal], + 'An opening in the skull that through which the %s passes through.'-[element]). +pattern(skull_foramen_by_bone_and_function,n('foramen of skull'),[conduit_for=S, part_of=B],[element,bone],[S,B], + [v(element)-v(bone)-foramen], + 'An opening in the %s that through which the %s passes through.'-[bone,element]). + +pattern(bone_foramen,n('bone foramen'),[conduit_for=S],[element],[S], + [v(element)-foramen, + foramen-of-v(element), + v(element)-canal], + 'An opening in bone that through which the %s passes through.'-[element]). + + pattern(anatomical_line,n('anatomical line'),[connects=E1, connects=E2],[entity1, entity2],[E1,E2],[line-connecting-v(entity1)-and-v(entity2)], 'An anatomical line that connects a %s with a %s'-[entity1,entity2]). pattern(innervates_basic,G,[innervates=S],[innervator,innervatee],[G,S],[v(innervator)-v(innervatee)], @@ -24,6 +52,7 @@ pattern(innervates_branching,G,[branching_part_of=B,innervates=S],[innervator,in 'A %s that branches from a %s and innervates a %s'-[innervator,whole,innervatee]). paired(gland_acinus,gland_duct). + pattern(gland_acinus,n(glandular_acinus),[part_of=S],[gland],[S],[v(gland)-acinus], 'The acinar part of a %s.'-[gland]). pattern(gland_duct,n(duct),[part_of=S],[gland],[S],