From 3acbac9ef281081bd8dd0b566e567f41be3f81d0 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Thu, 17 Mar 2022 22:05:38 +0000 Subject: [PATCH 01/20] Add new bone length from to DOSDP pattern template If applied, this commit will fix #73. --- .../dosdp-patterns/bone_length_from_to.yaml | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 src/patterns/dosdp-patterns/bone_length_from_to.yaml diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml new file mode 100644 index 00000000..8a125256 --- /dev/null +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -0,0 +1,81 @@ +--- +pattern_name: bone_length_from_to + +pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/bone_length_from_to.yaml + +description: 'A bone length trait that is the distance between two anatomical reference points measured in a straight line.' + +# examples: +# - http://purl.obolibrary.org/obo/FOVT_0001070 # femur length from caput to lateral condyle +# - http://purl.obolibrary.org/obo/FOVT_0001077 # length of talus along the midline +# - http://purl.obolibrary.org/obo/FOVT_0000007 # femur length from caput to medial condyle + +contributors: + - https://orcid.org/0000-0002-7073-9172 # David Osumi-Sutherland + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + - https://orcid.org/0000-0003-2699-3066 # Meghan A. Balk + +classes: + skeletal_element: UBERON:0004765 + anatomical_entity: UBERON:0001062 + length: PATO:0000122 + line: BFO:0000026 # one-dimensional spatial region + physical_object_quality: PATO:0001241 + +relations: + connected_to: RO:0002170 + characteristic_of: RO:0000052 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym + xref: oio:hasDbXref + +vars: + bone: "'skeletal_element'" + from: "'anatomical_entity'" + to: "'anatomical_entity'" + fovt: "'physical_object_quality'" + +name: + text: "%s length from %s to %s" + vars: + - bone + - from + - to + +annotations: + - annotationProperty: related_synonym + text: "%s length" + vars: + - bone + + - annotationProperty: xref + text: "FOVT:%s" + +def: + text: "The length of a line of %s from %s of a femur to %s." + vars: + - bone + - from + - to + + +subClassOf: + text: "'length' and 'characteristic_of' some %s" + vars: + - bone + multi_clause: + sep: "," + subClassOf: + text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + vars: + - from + multi_clause: + sep: "," + subClassOf: + text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + vars: + - to +... From 66185aa5b94bfebcc0354dd3ed550a54b3839d5d Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Mon, 21 Mar 2022 18:37:29 +0000 Subject: [PATCH 02/20] Fix multi_clause syntax in pattern template If applied, this commit will fix #73. --- .../dosdp-patterns/bone_length_from_to.yaml | 26 ++++++++----------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 8a125256..1942b695 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -61,21 +61,17 @@ def: - from - to - subClassOf: - text: "'length' and 'characteristic_of' some %s" - vars: - - bone multi_clause: - sep: "," - subClassOf: - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" - vars: - - from - multi_clause: - sep: "," - subClassOf: - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" - vars: - - to + sep: ' and ' + clauses: + - text: "'length' and 'characteristic_of' some %s" + vars: + - bone + - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + vars: + - from + - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + vars: + - to ... From 8d97a2afb13d8194c22fba5efc98c045da5736a6 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Tue, 22 Mar 2022 11:16:19 +0000 Subject: [PATCH 03/20] Add multiple subClassOf axioms Add multiple subClassOf axioms under the logical_axioms property instead of using one multi_clause axiom. If applied, this commit will fix #73. --- .../dosdp-patterns/bone_length_from_to.yaml | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 1942b695..d559a465 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -61,17 +61,17 @@ def: - from - to -subClassOf: - multi_clause: - sep: ' and ' - clauses: - - text: "'length' and 'characteristic_of' some %s" - vars: - - bone - - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" - vars: - - from - - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" - vars: - - to +logical_axioms: + - axiom_type: subClassOf + text: "'length' and 'characteristic_of' some %s" + vars: + - bone + - axiom_type: subClassOf + text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + vars: + - from + - axiom_type: subClassOf + text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + vars: + - to ... From 7e6c4cf5a2cf898ebbd15193e9374607b71eea0b Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Thu, 24 Mar 2022 20:11:39 +0000 Subject: [PATCH 04/20] Add missing fovt var --- src/patterns/dosdp-patterns/bone_length_from_to.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index d559a465..342e24f9 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -36,7 +36,7 @@ vars: bone: "'skeletal_element'" from: "'anatomical_entity'" to: "'anatomical_entity'" - fovt: "'physical_object_quality'" + fovt: "'physical_object_quality'" # FOVT id name: text: "%s length from %s to %s" @@ -52,7 +52,9 @@ annotations: - bone - annotationProperty: xref - text: "FOVT:%s" + text: "FOVT:%s" # give FOVT id here + vars: + - fovt def: text: "The length of a line of %s from %s of a femur to %s." From 113703e30b4413b62073ed1a04f9001fcddc5543 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Fri, 25 Mar 2022 10:28:19 +0000 Subject: [PATCH 05/20] Fix text definition --- src/patterns/dosdp-patterns/bone_length_from_to.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 342e24f9..b65a8ef5 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -57,10 +57,10 @@ annotations: - fovt def: - text: "The length of a line of %s from %s of a femur to %s." + text: "The length of a line from %s of a %s to %s." vars: - - bone - from + - bone - to logical_axioms: From 5877961aa6e8731fdae6e2dc8e51a07a53657233 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Fri, 1 Apr 2022 11:44:28 +0100 Subject: [PATCH 06/20] Add an xref on the definition --- src/patterns/dosdp-patterns/bone_length_from_to.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index b65a8ef5..6fdd57f0 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -37,6 +37,7 @@ vars: from: "'anatomical_entity'" to: "'anatomical_entity'" fovt: "'physical_object_quality'" # FOVT id + def_ref: "xsd:string" name: text: "%s length from %s to %s" @@ -52,7 +53,7 @@ annotations: - bone - annotationProperty: xref - text: "FOVT:%s" # give FOVT id here + text: "%s" # give FOVT IRI here vars: - fovt @@ -62,6 +63,12 @@ def: - from - bone - to + annotations: + - annotationProperty: xref + text: "%s" + vars: + - def_ref + logical_axioms: - axiom_type: subClassOf From b8211e9828b67c554aadf7c2d7937fa7e70f02c4 Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Fri, 1 Apr 2022 10:04:36 -0700 Subject: [PATCH 07/20] adding my edits --- .../dosdp-patterns/bone_length_from_to.yaml | 41 +++++++++++++++---- 1 file changed, 33 insertions(+), 8 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 6fdd57f0..faa6a832 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -22,6 +22,7 @@ classes: length: PATO:0000122 line: BFO:0000026 # one-dimensional spatial region physical_object_quality: PATO:0001241 + NCBITaxon: OBI:0100026 relations: connected_to: RO:0002170 @@ -30,7 +31,10 @@ relations: annotationProperties: exact_synonym: oio:hasExactSynonym related_synonym: oio:hasRelatedSynonym + broad_synonym: oio:hasBroadSynonym xref: oio:hasDbXref + measured_in_taxon: oio:measuredInTaxon + not_measured_in_taxon: oio:notMeasuredInTaxon vars: bone: "'skeletal_element'" @@ -38,25 +42,39 @@ vars: to: "'anatomical_entity'" fovt: "'physical_object_quality'" # FOVT id def_ref: "xsd:string" + taxa: "NCBITaxon" -name: - text: "%s length from %s to %s" - vars: - - bone - - from - - to - -annotations: +name:annotations: - annotationProperty: related_synonym text: "%s length" vars: - bone + - annotationProperty: exact_synonym + text: "%s length" + vars: + - bone + + - annotationProperty: broad_synonym + text: "%s length" + vars: + - bone + - annotationProperty: xref text: "%s" # give FOVT IRI here vars: - fovt + - annotationProperty: measured_in_taxon + text: "%s" + vars: + - taxa + + - annotationProperty: not_measured_in_taxon + text: "%s" + vars: + - taxa + def: text: "The length of a line from %s of a %s to %s." vars: @@ -70,6 +88,13 @@ def: - def_ref + text: "%s length from %s to %s" + vars: + - bone + - from + - to + + logical_axioms: - axiom_type: subClassOf text: "'length' and 'characteristic_of' some %s" From 82eb4448b9300bcfbf510cfa6c6730ded829d758 Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Thu, 28 Jul 2022 09:06:57 -0700 Subject: [PATCH 08/20] Update bone_length_from_to.yaml clarifying subclasses modifying definition --- .../dosdp-patterns/bone_length_from_to.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index faa6a832..00663df3 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -20,7 +20,7 @@ classes: skeletal_element: UBERON:0004765 anatomical_entity: UBERON:0001062 length: PATO:0000122 - line: BFO:0000026 # one-dimensional spatial region + anatomical_line: CARO:0000008 # one-dimensional, immaterial anatomical entity physical_object_quality: PATO:0001241 NCBITaxon: OBI:0100026 @@ -76,10 +76,10 @@ name:annotations: - taxa def: - text: "The length of a line from %s of a %s to %s." + text: "The length of a %s from %s to %s." vars: - - from - bone + - from - to annotations: - annotationProperty: xref @@ -97,15 +97,16 @@ def: logical_axioms: - axiom_type: subClassOf - text: "'length' and 'characteristic_of' some %s" + text: "'length' and ('characteristic_of' some %s)" #if along entire bone vars: - bone - axiom_type: subClassOf - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + text: "'length' and ('characteristic_of' some ('anatomical line' and ('connects' some %s) and ('connects' some %s)))" vars: - from + - to - axiom_type: subClassOf - text: "'characteristic_of' some ('line' and 'connected_to' some %s)" + text: "'length' and 'characteristic_of' ('part of' some %s)" #if along part of a bone [e.g., ('distal end' some humerus)] vars: - - to + - bone ... From 956219c18efd66563810da2842813708efd26596 Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Thu, 28 Jul 2022 09:13:23 -0700 Subject: [PATCH 09/20] Update bone_length_from_to.yaml adding part of --- src/patterns/dosdp-patterns/bone_length_from_to.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 00663df3..7fdabe84 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -27,6 +27,7 @@ classes: relations: connected_to: RO:0002170 characteristic_of: RO:0000052 + part_of: BFO:0000050 annotationProperties: exact_synonym: oio:hasExactSynonym @@ -106,7 +107,7 @@ logical_axioms: - from - to - axiom_type: subClassOf - text: "'length' and 'characteristic_of' ('part of' some %s)" #if along part of a bone [e.g., ('distal end' some humerus)] + text: "'length' and 'characteristic_of' some ('part of' some %s)" #if part of a bone [e.g., 'distalmost' ('part of' some humerus)] vars: - bone ... From ad9d851c1b56ace4594a537b80d1d31d3b4f4c25 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Fri, 19 Aug 2022 19:29:32 +0100 Subject: [PATCH 10/20] Implement data_lis_vars to help annotate definitions with external references. Addresses #73. --- .../dosdp-patterns/bone_length_from_to.yaml | 41 ++++++++++--------- 1 file changed, 22 insertions(+), 19 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 7fdabe84..51dd8e3e 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -3,7 +3,8 @@ pattern_name: bone_length_from_to pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/bone_length_from_to.yaml -description: 'A bone length trait that is the distance between two anatomical reference points measured in a straight line.' +description: 'A bone length trait that is the distance between two anatomical + reference points measured in a straight line.' # examples: # - http://purl.obolibrary.org/obo/FOVT_0001070 # femur length from caput to lateral condyle @@ -20,7 +21,7 @@ classes: skeletal_element: UBERON:0004765 anatomical_entity: UBERON:0001062 length: PATO:0000122 - anatomical_line: CARO:0000008 # one-dimensional, immaterial anatomical entity + anatomical_line: UBERON:0006800 physical_object_quality: PATO:0001241 NCBITaxon: OBI:0100026 @@ -28,6 +29,7 @@ relations: connected_to: RO:0002170 characteristic_of: RO:0000052 part_of: BFO:0000050 + connects: RO:0002176 annotationProperties: exact_synonym: oio:hasExactSynonym @@ -42,10 +44,13 @@ vars: from: "'anatomical_entity'" to: "'anatomical_entity'" fovt: "'physical_object_quality'" # FOVT id - def_ref: "xsd:string" taxa: "NCBITaxon" -name:annotations: +data_list_vars: + def_ref: "'xref'" # reference(s) to the source(s) of definition + + +annotations: - annotationProperty: related_synonym text: "%s length" vars: @@ -83,31 +88,29 @@ def: - from - to annotations: - - annotationProperty: xref - text: "%s" - vars: - - def_ref - - - text: "%s length from %s to %s" - vars: - - bone - - from - - to - + - annotationProperty: not_measured_in_taxon + value: def_ref logical_axioms: - axiom_type: subClassOf - text: "'length' and ('characteristic_of' some %s)" #if along entire bone + text: "'length' and ('characteristic_of' some %s)" # if along entire bone vars: - bone - axiom_type: subClassOf - text: "'length' and ('characteristic_of' some ('anatomical line' and ('connects' some %s) and ('connects' some %s)))" + text: "'length' and + ('characteristic_of' some + ('anatomical_line' and + ('connects' some %s) and + ('connects' some %s) + ) + )" vars: - from - to - axiom_type: subClassOf - text: "'length' and 'characteristic_of' some ('part of' some %s)" #if part of a bone [e.g., 'distalmost' ('part of' some humerus)] + text: "'length' and + ('characteristic_of' some ('part_of' some %s))" + # # if part of a bone [e.g., 'distalmost' ('part of' some humerus)] vars: - bone ... From 06e82cfe9430849e7260966b387ac5c3265bbd98 Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Fri, 19 Aug 2022 11:41:37 -0700 Subject: [PATCH 11/20] Update bone_length_from_to.yaml --- .../dosdp-patterns/bone_length_from_to.yaml | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 51dd8e3e..7c41a0f3 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -97,19 +97,7 @@ logical_axioms: vars: - bone - axiom_type: subClassOf - text: "'length' and - ('characteristic_of' some - ('anatomical_line' and - ('connects' some %s) and - ('connects' some %s) - ) - )" - vars: - - from - - to - - axiom_type: subClassOf - text: "'length' and - ('characteristic_of' some ('part_of' some %s))" + text: "'length' and ('characteristic_of' some ('part_of' some %s))" # # if part of a bone [e.g., 'distalmost' ('part of' some humerus)] vars: - bone From 1560a762b9a3c48e4ef4c149d1d28c769f775bcf Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Fri, 19 Aug 2022 20:08:54 +0100 Subject: [PATCH 12/20] Add comment field to template Addresses #73. --- src/patterns/dosdp-patterns/bone_length_from_to.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 51dd8e3e..8371ab72 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -38,6 +38,7 @@ annotationProperties: xref: oio:hasDbXref measured_in_taxon: oio:measuredInTaxon not_measured_in_taxon: oio:notMeasuredInTaxon + comment: rdfs:comment vars: bone: "'skeletal_element'" @@ -45,6 +46,7 @@ vars: to: "'anatomical_entity'" fovt: "'physical_object_quality'" # FOVT id taxa: "NCBITaxon" + your_comments: "xsd:string" # comments, clarifications for users data_list_vars: def_ref: "'xref'" # reference(s) to the source(s) of definition @@ -81,6 +83,11 @@ annotations: vars: - taxa + - annotationProperty: comment + text: "%s" + vars: + - your_comments + def: text: "The length of a %s from %s to %s." vars: From 2e912b9c0f25f1f15d8136c2a397f2e5e3339ac9 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Fri, 19 Aug 2022 21:02:26 +0100 Subject: [PATCH 13/20] Fix xref annotation Addresses #73. --- src/patterns/dosdp-patterns/bone_length_from_to.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index 5cfad0bf..eb54bdb2 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -95,7 +95,7 @@ def: - from - to annotations: - - annotationProperty: not_measured_in_taxon + - annotationProperty: xref value: def_ref logical_axioms: From 2d61e2cb49feadb3a454a68686c75f2bcd392f7d Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Fri, 19 Aug 2022 22:00:29 +0100 Subject: [PATCH 14/20] Delete redundant vars and axioms Addresses #73. --- .../dosdp-patterns/bone_length_from_to.yaml | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/bone_length_from_to.yaml index eb54bdb2..25406dac 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/bone_length_from_to.yaml @@ -21,30 +21,26 @@ classes: skeletal_element: UBERON:0004765 anatomical_entity: UBERON:0001062 length: PATO:0000122 - anatomical_line: UBERON:0006800 - physical_object_quality: PATO:0001241 NCBITaxon: OBI:0100026 relations: - connected_to: RO:0002170 characteristic_of: RO:0000052 part_of: BFO:0000050 - connects: RO:0002176 annotationProperties: exact_synonym: oio:hasExactSynonym related_synonym: oio:hasRelatedSynonym broad_synonym: oio:hasBroadSynonym xref: oio:hasDbXref - measured_in_taxon: oio:measuredInTaxon - not_measured_in_taxon: oio:notMeasuredInTaxon + measured_in_taxon: xsd:string + not_measured_in_taxon: xsd:string comment: rdfs:comment vars: bone: "'skeletal_element'" from: "'anatomical_entity'" to: "'anatomical_entity'" - fovt: "'physical_object_quality'" # FOVT id + fovt: "xsd:string" # FOVT id taxa: "NCBITaxon" your_comments: "xsd:string" # comments, clarifications for users @@ -99,13 +95,10 @@ def: value: def_ref logical_axioms: - - axiom_type: subClassOf - text: "'length' and ('characteristic_of' some %s)" # if along entire bone - vars: - - bone - axiom_type: subClassOf text: "'length' and ('characteristic_of' some ('part_of' some %s))" # # if part of a bone [e.g., 'distalmost' ('part of' some humerus)] + # # NOTE: Everything is part of itself. vars: - bone ... From 8e9ab15596fe93384b1d17bd70f1614c97b643d8 Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Fri, 26 Aug 2022 08:10:48 -0700 Subject: [PATCH 15/20] fixing pattern --- ...ength_from_to.yaml => length_from_to.yaml} | 47 ++++++++++--------- 1 file changed, 24 insertions(+), 23 deletions(-) rename src/patterns/dosdp-patterns/{bone_length_from_to.yaml => length_from_to.yaml} (74%) diff --git a/src/patterns/dosdp-patterns/bone_length_from_to.yaml b/src/patterns/dosdp-patterns/length_from_to.yaml similarity index 74% rename from src/patterns/dosdp-patterns/bone_length_from_to.yaml rename to src/patterns/dosdp-patterns/length_from_to.yaml index 25406dac..49bfb607 100644 --- a/src/patterns/dosdp-patterns/bone_length_from_to.yaml +++ b/src/patterns/dosdp-patterns/length_from_to.yaml @@ -1,9 +1,9 @@ --- -pattern_name: bone_length_from_to +pattern_name: length_from_to pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/bone_length_from_to.yaml -description: 'A bone length trait that is the distance between two anatomical +description: 'A length trait that is the distance between two anatomical reference points measured in a straight line.' # examples: @@ -18,10 +18,10 @@ contributors: - https://orcid.org/0000-0003-2699-3066 # Meghan A. Balk classes: - skeletal_element: UBERON:0004765 anatomical_entity: UBERON:0001062 length: PATO:0000122 - NCBITaxon: OBI:0100026 + taxon: OBI:0100026 + trait_term: PATO:0000051 relations: characteristic_of: RO:0000052 @@ -37,32 +37,28 @@ annotationProperties: comment: rdfs:comment vars: - bone: "'skeletal_element'" - from: "'anatomical_entity'" - to: "'anatomical_entity'" + element: 'anatomical_entity' + from: 'anatomical_entity' + to: 'anatomical_entity' + size_trait: 'trait_term' fovt: "xsd:string" # FOVT id - taxa: "NCBITaxon" + taxa: "taxon" your_comments: "xsd:string" # comments, clarifications for users data_list_vars: def_ref: "'xref'" # reference(s) to the source(s) of definition +name: + text: "%s length" + vars: + - element annotations: - - annotationProperty: related_synonym - text: "%s length" - vars: - - bone - annotationProperty: exact_synonym text: "%s length" vars: - - bone - - - annotationProperty: broad_synonym - text: "%s length" - vars: - - bone + - element - annotationProperty: xref text: "%s" # give FOVT IRI here @@ -87,18 +83,23 @@ annotations: def: text: "The length of a %s from %s to %s." vars: - - bone + - element - from - to annotations: - annotationProperty: xref value: def_ref +equivalentTo: + text: "'length' and ('characteristic_of' some ('part_of' some %s))" + # if part of a bone [e.g., 'distalmost' ('part of' some humerus)] + # NOTE: Everything is part of itself. + vars: + - element + logical_axioms: - axiom_type: subClassOf - text: "'length' and ('characteristic_of' some ('part_of' some %s))" - # # if part of a bone [e.g., 'distalmost' ('part of' some humerus)] - # # NOTE: Everything is part of itself. + text: "%s" vars: - - bone + - size_trait ... From ea7f682dde1c10867a6b866a1f72609f0fe17b2c Mon Sep 17 00:00:00 2001 From: megbalk Date: Fri, 26 Aug 2022 15:15:31 +0000 Subject: [PATCH 16/20] Update dosdp patterns file --- src/patterns/definitions.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index a364fb4f..b82e4c2b 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2022-08-03"^^xsd:string) + +Annotation(owl:versionInfo "2022-08-26"^^xsd:string) Declaration(Class()) Declaration(Class()) From 599e0a13641edeafb5a9ecb5b2055aa399058e2c Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Fri, 26 Aug 2022 08:40:32 -0700 Subject: [PATCH 17/20] getting rid of unneeded syn --- src/patterns/dosdp-patterns/length_from_to.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/patterns/dosdp-patterns/length_from_to.yaml b/src/patterns/dosdp-patterns/length_from_to.yaml index 49bfb607..b9463c3c 100644 --- a/src/patterns/dosdp-patterns/length_from_to.yaml +++ b/src/patterns/dosdp-patterns/length_from_to.yaml @@ -29,8 +29,6 @@ relations: annotationProperties: exact_synonym: oio:hasExactSynonym - related_synonym: oio:hasRelatedSynonym - broad_synonym: oio:hasBroadSynonym xref: oio:hasDbXref measured_in_taxon: xsd:string not_measured_in_taxon: xsd:string From 55481cbe8d3607cddb7aec3e979dbb6c5898eff7 Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Thu, 9 Feb 2023 13:14:01 -0700 Subject: [PATCH 18/20] Update length_from_to.yaml --- .../dosdp-patterns/length_from_to.yaml | 32 +++++++++++-------- 1 file changed, 18 insertions(+), 14 deletions(-) diff --git a/src/patterns/dosdp-patterns/length_from_to.yaml b/src/patterns/dosdp-patterns/length_from_to.yaml index b9463c3c..522d1f00 100644 --- a/src/patterns/dosdp-patterns/length_from_to.yaml +++ b/src/patterns/dosdp-patterns/length_from_to.yaml @@ -28,7 +28,7 @@ relations: part_of: BFO:0000050 annotationProperties: - exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym xref: oio:hasDbXref measured_in_taxon: xsd:string not_measured_in_taxon: xsd:string @@ -42,22 +42,27 @@ vars: fovt: "xsd:string" # FOVT id taxa: "taxon" your_comments: "xsd:string" # comments, clarifications for users + your_synonym: "xsd:string" #related synonymn for what other references may call the measurement data_list_vars: def_ref: "'xref'" # reference(s) to the source(s) of definition + syn_ref: "'xref" # reference(s) to the source(s) of the measurement name name: - text: "%s length" + text: "%s length" #e.g., humerus length vars: - - element - + - element #e.g., humerus + annotations: - - annotationProperty: exact_synonym - text: "%s length" + - annotationProperty: related_synonym + text: "%s" vars: - - element - + - your_synonym + annotations: + - annotatinProperty: xref + value: syn_ref + - annotationProperty: xref text: "%s" # give FOVT IRI here vars: @@ -79,11 +84,11 @@ annotations: - your_comments def: - text: "The length of a %s from %s to %s." + text: "The length of a %s from %s to %s." #The length of a humerus from ventral tubercule of humerus to caput of humerus vars: - - element - - from - - to + - element #humerus + - from #ventral tubercule of humerus + - to #caput of humerus annotations: - annotationProperty: xref value: def_ref @@ -99,5 +104,4 @@ logical_axioms: - axiom_type: subClassOf text: "%s" vars: - - size_trait -... + - size_trait \ No newline at end of file From 4869992706ed7ac827583737944dfb5fcf53637d Mon Sep 17 00:00:00 2001 From: Meghan Balk Date: Thu, 9 Feb 2023 13:23:12 -0700 Subject: [PATCH 19/20] Update length_from_to.yaml --- src/patterns/dosdp-patterns/length_from_to.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-patterns/length_from_to.yaml b/src/patterns/dosdp-patterns/length_from_to.yaml index 522d1f00..36ae615e 100644 --- a/src/patterns/dosdp-patterns/length_from_to.yaml +++ b/src/patterns/dosdp-patterns/length_from_to.yaml @@ -41,6 +41,7 @@ vars: size_trait: 'trait_term' fovt: "xsd:string" # FOVT id taxa: "taxon" + position: "xsd:string" #e.g., lateral, medial your_comments: "xsd:string" # comments, clarifications for users your_synonym: "xsd:string" #related synonymn for what other references may call the measurement @@ -48,10 +49,12 @@ data_list_vars: def_ref: "'xref'" # reference(s) to the source(s) of definition syn_ref: "'xref" # reference(s) to the source(s) of the measurement name + name: - text: "%s length" #e.g., humerus length + text: "%s %s length" #e.g., humerus length vars: - - element #e.g., humerus + - element + - position annotations: From e3dc2fe52a15b31672153dae6be0ed7bb1f79592 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Thu, 2 Mar 2023 11:51:38 +0000 Subject: [PATCH 20/20] Update pattern templates This commit intends to 1. add DOS-DP data filler 2. update DOS-DP yaml template --- src/patterns/data/default/length_from_to.tsv | 2 + .../dosdp-patterns/length_from_to.yaml | 69 ++++++++++--------- 2 files changed, 38 insertions(+), 33 deletions(-) create mode 100644 src/patterns/data/default/length_from_to.tsv diff --git a/src/patterns/data/default/length_from_to.tsv b/src/patterns/data/default/length_from_to.tsv new file mode 100644 index 00000000..a2729ca0 --- /dev/null +++ b/src/patterns/data/default/length_from_to.tsv @@ -0,0 +1,2 @@ +defined_class defined_class_name element element_name from from_name to to_name fovt fovt_name taxa taxa_name position your_comments your_synonym def_ref +OBA:2069999 UBERON:0000981 femur UBERON:0006767 head of femur UBERON:0009985 lateral condyle of femur FOVT:0001070 femur length from caput to lateral condyle diff --git a/src/patterns/dosdp-patterns/length_from_to.yaml b/src/patterns/dosdp-patterns/length_from_to.yaml index 36ae615e..fa9361c5 100644 --- a/src/patterns/dosdp-patterns/length_from_to.yaml +++ b/src/patterns/dosdp-patterns/length_from_to.yaml @@ -1,15 +1,18 @@ --- pattern_name: length_from_to -pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/bone_length_from_to.yaml +pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/length_from_to.yaml description: 'A length trait that is the distance between two anatomical reference points measured in a straight line.' # examples: -# - http://purl.obolibrary.org/obo/FOVT_0001070 # femur length from caput to lateral condyle -# - http://purl.obolibrary.org/obo/FOVT_0001077 # length of talus along the midline -# - http://purl.obolibrary.org/obo/FOVT_0000007 # femur length from caput to medial condyle +# - http://purl.obolibrary.org/obo/FOVT_0001070 +# # femur length from caput to lateral condyle +# - http://purl.obolibrary.org/obo/FOVT_0001077 +# # length of talus along the midline +# - http://purl.obolibrary.org/obo/FOVT_0000007 +# # femur length from caput to medial condyle contributors: - https://orcid.org/0000-0002-7073-9172 # David Osumi-Sutherland @@ -20,12 +23,14 @@ contributors: classes: anatomical_entity: UBERON:0001062 length: PATO:0000122 + distance: PATO:0000040 taxon: OBI:0100026 - trait_term: PATO:0000051 relations: characteristic_of: RO:0000052 part_of: BFO:0000050 + characteristic_of_part_of: RO:0002314 + towards: RO:0002503 annotationProperties: related_synonym: oio:hasRelatedSynonym @@ -38,34 +43,30 @@ vars: element: 'anatomical_entity' from: 'anatomical_entity' to: 'anatomical_entity' - size_trait: 'trait_term' fovt: "xsd:string" # FOVT id taxa: "taxon" - position: "xsd:string" #e.g., lateral, medial + position: "xsd:string" # e.g., lateral, medial your_comments: "xsd:string" # comments, clarifications for users - your_synonym: "xsd:string" #related synonymn for what other references may call the measurement + your_synonym: "xsd:string" # related synonym + # for what other references may call the measurement data_list_vars: def_ref: "'xref'" # reference(s) to the source(s) of definition - syn_ref: "'xref" # reference(s) to the source(s) of the measurement name - name: - text: "%s %s length" #e.g., humerus length + text: "%s length from %s to %s" vars: - element - - position - + - from + - to + annotations: - annotationProperty: related_synonym text: "%s" vars: - your_synonym - annotations: - - annotatinProperty: xref - value: syn_ref - + - annotationProperty: xref text: "%s" # give FOVT IRI here vars: @@ -87,24 +88,26 @@ annotations: - your_comments def: - text: "The length of a %s from %s to %s." #The length of a humerus from ventral tubercule of humerus to caput of humerus + text: "The length of a %s from %s to %s." # The length of a humerus from + # ventral tubercule of humerus to caput of humerus vars: - - element #humerus - - from #ventral tubercule of humerus - - to #caput of humerus + - element # humerus + - from # ventral tubercule of humerus + - to # caput of humerus annotations: - annotationProperty: xref value: def_ref -equivalentTo: - text: "'length' and ('characteristic_of' some ('part_of' some %s))" - # if part of a bone [e.g., 'distalmost' ('part of' some humerus)] - # NOTE: Everything is part of itself. - vars: - - element - -logical_axioms: - - axiom_type: subClassOf - text: "%s" - vars: - - size_trait \ No newline at end of file +subClassOf: + multi_clause: + sep: ' and ' + clauses: + - text: "'length' and ('characteristic_of_part_of' some %s)" + vars: + - element + - text: "'distance' and + ('characteristic_of' some %s) and + ('towards' some %s)" + vars: + - from + - to