From 71234f6848f25c23309afef8b23ffa50e100b460 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 10 Jan 2025 11:30:17 +0200 Subject: [PATCH 01/10] Create abnormalShapeOfPhysicalEntityInLocation.yaml --- ...normalShapeOfPhysicalEntityInLocation.yaml | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml new file mode 100644 index 00000000..29c39045 --- /dev/null +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -0,0 +1,53 @@ +--- +pattern_name: abnormalShapeOfPhysicalEntityInLocation +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +description: "abnormal shape of an anatomical entity or a measurement of a process, such as an ECG wave, in a location" + +contributors: +- https://orcid.org/0000-0002-3528-5267 +- https://orcid.org/0000-0001-5208-3432 +- https://orcid.org/0000-0003-4148-4606 + +classes: + shape: PATO:0000052 + abnormal: PATO:0000460 + entity: BFO:0000002 + independent continuant: BFO:0000004 + +relations: + inheres_in: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + entity: "'entity'" + location: "'independent continuant'" + +name: + text: "abnormal shape of %s in %s" + vars: + - entity + - location + +annotations: +- annotationProperty: exact_synonym + text: "abnormally shaped %s in %s" + vars: + - entity + - location + +def: + text: "Any structural anomaly in the shape of the %s located in %s." + vars: + - entity + - location + +equivalentTo: + text: "'has_part' some ('shape' and (''inheres_in'' some (%s and (''part_of'' + some %s))) and ('has_modifier' some 'abnormal'))" + vars: + - entity + - location From 0b868f2af95fb3c51b988b7b5f5685aba29416a9 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:08:48 +0200 Subject: [PATCH 02/10] Update src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml Co-authored-by: Ray Stefancsik --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index 29c39045..66080652 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -4,9 +4,9 @@ pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalShapeOfP description: "abnormal shape of an anatomical entity or a measurement of a process, such as an ECG wave, in a location" contributors: -- https://orcid.org/0000-0002-3528-5267 -- https://orcid.org/0000-0001-5208-3432 -- https://orcid.org/0000-0003-4148-4606 + - https://orcid.org/0000-0002-3528-5267 # Sofia Robb + - https://orcid.org/0000-0001-5208-3432 # Nicole Vasilevsky + - https://orcid.org/0000-0003-4148-4606 # Midori A. Harris classes: shape: PATO:0000052 From 57a147a7efae2471d6fc34f7d4239a5ecf779f81 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:08:55 +0200 Subject: [PATCH 03/10] Update src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml Co-authored-by: Ray Stefancsik --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index 66080652..d82243b9 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -29,8 +29,8 @@ vars: name: text: "abnormal shape of %s in %s" vars: - - entity - - location + - entity + - location annotations: - annotationProperty: exact_synonym From 935f2788d849c34d649e70baef1902c0972d10b2 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:09:05 +0200 Subject: [PATCH 04/10] Update src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml Co-authored-by: Ray Stefancsik --- .../abnormalShapeOfPhysicalEntityInLocation.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index d82243b9..c6efb142 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -33,11 +33,11 @@ name: - location annotations: -- annotationProperty: exact_synonym - text: "abnormally shaped %s in %s" - vars: - - entity - - location + - annotationProperty: exact_synonym + text: "abnormally shaped %s in %s" + vars: + - entity + - location def: text: "Any structural anomaly in the shape of the %s located in %s." From ef679e5c749a136d7834597bb7af05fe5a00c72f Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:09:11 +0200 Subject: [PATCH 05/10] Update src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml Co-authored-by: Ray Stefancsik --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index c6efb142..92f52c21 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -42,8 +42,8 @@ annotations: def: text: "Any structural anomaly in the shape of the %s located in %s." vars: - - entity - - location + - entity + - location equivalentTo: text: "'has_part' some ('shape' and (''inheres_in'' some (%s and (''part_of'' From 25310540a1680cf371d55d3342627ed74bb13fe3 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:11:15 +0200 Subject: [PATCH 06/10] Update src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml Co-authored-by: Ray Stefancsik --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index 92f52c21..5d03648c 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -15,7 +15,7 @@ classes: independent continuant: BFO:0000004 relations: - inheres_in: RO:0000052 + characteristic_of: RO:0000052 has_modifier: RO:0002573 has_part: BFO:0000051 From cf83f5340a96e5a91d5eb51d6ea6484acc8e90b5 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:11:24 +0200 Subject: [PATCH 07/10] Update src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml Co-authored-by: Ray Stefancsik --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index 5d03648c..e249c649 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -46,7 +46,7 @@ def: - location equivalentTo: - text: "'has_part' some ('shape' and (''inheres_in'' some (%s and (''part_of'' + text: "'has_part' some ('shape' and (''characteristic_of'' some (%s and (''part_of'' some %s))) and ('has_modifier' some 'abnormal'))" vars: - entity From 43b21f44bab67d321a80f70aaa2059290ee22b5b Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:11:29 +0200 Subject: [PATCH 08/10] Update src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml Co-authored-by: Ray Stefancsik --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index e249c649..bb421c2a 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -49,5 +49,5 @@ equivalentTo: text: "'has_part' some ('shape' and (''characteristic_of'' some (%s and (''part_of'' some %s))) and ('has_modifier' some 'abnormal'))" vars: - - entity - - location + - entity + - location From 51496ea942961ba6934478f4c029e69df43fb33a Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 11 Jan 2025 10:16:32 +0200 Subject: [PATCH 09/10] Update abnormalShapeOfPhysicalEntityInLocation.yaml --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index bb421c2a..ab2dfc59 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -1,12 +1,13 @@ --- pattern_name: abnormalShapeOfPhysicalEntityInLocation pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalShapeOfPhysicalEntityInLocation.yaml -description: "abnormal shape of an anatomical entity or a measurement of a process, such as an ECG wave, in a location" +description: "abnormal shape of an anatomical entity in a location." contributors: - https://orcid.org/0000-0002-3528-5267 # Sofia Robb - https://orcid.org/0000-0001-5208-3432 # Nicole Vasilevsky - https://orcid.org/0000-0003-4148-4606 # Midori A. Harris + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik classes: shape: PATO:0000052 @@ -46,8 +47,7 @@ def: - location equivalentTo: - text: "'has_part' some ('shape' and (''characteristic_of'' some (%s and (''part_of'' - some %s))) and ('has_modifier' some 'abnormal'))" + text: '''has_part'' some (''shape'' and (''characteristic_of'' some (%s and (''part_of'' some %s))) and (''has_modifier'' some ''abnormal''))' vars: - entity - location From c19978fa7b60fb19991e47bacc4b8b0ae0a048da Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 18 Jan 2025 11:14:14 +0200 Subject: [PATCH 10/10] Update abnormalShapeOfPhysicalEntityInLocation.yaml --- .../dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml index ab2dfc59..8e8cc6da 100644 --- a/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml @@ -19,6 +19,7 @@ relations: characteristic_of: RO:0000052 has_modifier: RO:0002573 has_part: BFO:0000051 + part_of: BFO:0000050 annotationProperties: exact_synonym: oio:hasExactSynonym