From 41a25db35a271399207ea00e375aff94e7d8f051 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Tue, 5 May 2020 12:59:16 -0700 Subject: [PATCH 1/6] Create abnormalProportionOfCellTypeInAnatomicalEntity.yaml Note- For HPO, we do not want to mention the location in the label, hope that is okay. --- ...roportionOfCellTypeInAnatomicalEntity.yaml | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml diff --git a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml new file mode 100644 index 00000000..21e23f27 --- /dev/null +++ b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml @@ -0,0 +1,44 @@ +pattern_name: abnormalProportionOfCellTypeInAnatomicalEntity +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml +description: "An abnormal proportion of a cell, in a location, like the blood. For example: HP_0020111 'Abnormal CD4+CD25+ regulatory T cell proportion'." + +contributors: +- https://orcid.org/0000-0001-5208-3432 + +classes: + proportionality to: PATO:0001470 + abnormal: PATO:0000460 + cell: CL:0000000 + independent continuant: BFO:0000004 + +relations: + inheres_in: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + part_of: BFO:0000050 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + cell: "cell" + location: "'independent continuant'" + +name: + text: "abnormal proportion of %s" + vars: + - cell + - location + +def: + text: "A deviation from the normal proportion of %s in the %s. + vars: + - chemical + - location + +equivalentTo: + text: "'has_part' some ('proportionality to' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" + vars: + - cell + - location + From e6dfbbb1dcdb6a1129802e744d7f860ef2d4ad09 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Tue, 5 May 2020 14:59:14 -0700 Subject: [PATCH 2/6] Update abnormalProportionOfCellTypeInAnatomicalEntity.yaml --- .../abnormalProportionOfCellTypeInAnatomicalEntity.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml index 21e23f27..004e1f56 100644 --- a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml @@ -25,15 +25,15 @@ vars: location: "'independent continuant'" name: - text: "abnormal proportion of %s" + text: "abnormal proportion of %s in %s" vars: - cell - location def: - text: "A deviation from the normal proportion of %s in the %s. + text: "A deviation from the normal proportion of %s in the %s." vars: - - chemical + - cell - location equivalentTo: From ab994fa67be8960ca8681ab8b665b5028e672a75 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Thu, 7 May 2020 08:57:52 -0700 Subject: [PATCH 3/6] Update abnormalProportionOfCellTypeInAnatomicalEntity.yaml --- .../abnormalProportionOfCellTypeInAnatomicalEntity.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml index 004e1f56..80c45bb1 100644 --- a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml @@ -16,6 +16,7 @@ relations: has_modifier: RO:0002573 has_part: BFO:0000051 part_of: BFO:0000050 + towards: annotationProperties: exact_synonym: oio:hasExactSynonym @@ -37,7 +38,7 @@ def: - location equivalentTo: - text: "'has_part' some ('proportionality to' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" + text: "'has_part' some ('proportionality to' and ('inheres_in' some (%s and ('part_of' some %s))) and ('towards' some 'cell') and ('has_modifier' some 'abnormal'))" vars: - cell - location From a7fc0c07ec845ac393958e2b0d4decb3346f0145 Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Thu, 7 May 2020 08:58:51 -0700 Subject: [PATCH 4/6] Update and rename abnormalProportionOfCellTypeInAnatomicalEntity.yaml to abnormalProportionOfCellTypeInLocation.yaml --- ...lEntity.yaml => abnormalProportionOfCellTypeInLocation.yaml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename src/patterns/dosdp-dev/{abnormalProportionOfCellTypeInAnatomicalEntity.yaml => abnormalProportionOfCellTypeInLocation.yaml} (98%) diff --git a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml similarity index 98% rename from src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml rename to src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml index 80c45bb1..cdbb69c0 100644 --- a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml @@ -16,7 +16,7 @@ relations: has_modifier: RO:0002573 has_part: BFO:0000051 part_of: BFO:0000050 - towards: + towards: towards annotationProperties: exact_synonym: oio:hasExactSynonym From 7bc420aa2207cf0179faec1873644bb0fc3c3d5d Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Thu, 7 May 2020 09:00:15 -0700 Subject: [PATCH 5/6] Update abnormalProportionOfCellTypeInLocation.yaml --- .../dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml index cdbb69c0..b8f58e45 100644 --- a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml @@ -16,7 +16,7 @@ relations: has_modifier: RO:0002573 has_part: BFO:0000051 part_of: BFO:0000050 - towards: towards + towards: RO:0002503 annotationProperties: exact_synonym: oio:hasExactSynonym From 9bad8fb63fdfa9206ec126c1bf497a6ca39e45ba Mon Sep 17 00:00:00 2001 From: Nicole Vasilevsky Date: Thu, 7 May 2020 09:07:36 -0700 Subject: [PATCH 6/6] Update abnormalProportionOfCellTypeInLocation.yaml --- .../dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml index b8f58e45..c0c7239f 100644 --- a/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalProportionOfCellTypeInLocation.yaml @@ -1,5 +1,5 @@ -pattern_name: abnormalProportionOfCellTypeInAnatomicalEntity -pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalProportionOfCellTypeInAnatomicalEntity.yaml +pattern_name: abnormalProportionOfCellTypeInLocation +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalProportionOfCellTypeInLocation.yaml description: "An abnormal proportion of a cell, in a location, like the blood. For example: HP_0020111 'Abnormal CD4+CD25+ regulatory T cell proportion'." contributors: