From bac4af997b13e3dd43523b13053fa23f79e99329 Mon Sep 17 00:00:00 2001 From: Chris Grove Date: Fri, 28 Jun 2019 13:48:37 -0400 Subject: [PATCH 1/3] New pattern abnDecEfficOfBiolProc June 28 2019 --- ...yDecreasedEfficacyOfBiologicalProcess.yaml | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml diff --git a/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml b/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml new file mode 100644 index 00000000..b02a0234 --- /dev/null +++ b/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml @@ -0,0 +1,47 @@ +pattern_name: abnormallyDecreasedEfficacyOfBiologicalProcess +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml +description: "An abnormally decreased efficacy of a biological process compared to controls." + +contributors: + - https://orcid.org/0000-0001-9076-6015 + +classes: + decreased efficacy: PATO:0015003 + abnormal: PATO:0000460 + biological process: GO:0008150 + +relations: + inheres_in: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + biological_process: "'biological process'" + +name: + text: "decreased efficacy of %s" + vars: + - biological_process + +annotations: + - annotationProperty: exact_synonym + text: "Deficiency of %s" + vars: + - biological_process + - annotationProperty: exact_synonym + text: "Defective %s" + vars: + - biological_process + +def: + text: "Decreased efficacy of %s." + vars: + - biological_process + +equivalentTo: + text: "'has_part' some ('decreased efficacy' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" + vars: + - biological_process From b55ba3c4582981659d2a324634ec493e4ee9c066 Mon Sep 17 00:00:00 2001 From: Chris Grove Date: Mon, 1 Jul 2019 11:22:58 -0400 Subject: [PATCH 2/3] Update abnDecEfficOfBiolProc pattern July 1 2019 --- .../abnormallyDecreasedEfficacyOfBiologicalProcess.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml b/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml index b02a0234..7d664773 100644 --- a/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml +++ b/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml @@ -1,6 +1,6 @@ pattern_name: abnormallyDecreasedEfficacyOfBiologicalProcess pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml -description: "An abnormally decreased efficacy of a biological process compared to controls." +description: "An abnormally decreased efficacy (reduced ability to produce output) of a biological process compared to controls. For example, defective cytokinesis." contributors: - https://orcid.org/0000-0001-9076-6015 @@ -16,7 +16,8 @@ relations: has_part: BFO:0000051 annotationProperties: - exact_synonym: oio:hasExactSynonym + exact_synonym: oio:hasExactSynonym + narrow_synonym: oio:hasNarrowSynonym vars: biological_process: "'biological process'" @@ -27,7 +28,7 @@ name: - biological_process annotations: - - annotationProperty: exact_synonym + - annotationProperty: narrow_synonym text: "Deficiency of %s" vars: - biological_process From 613c516d676baab84a78d20a67aafb82135e926c Mon Sep 17 00:00:00 2001 From: Chris Grove Date: Wed, 3 Jul 2019 10:57:29 -0400 Subject: [PATCH 3/3] Update abnormallyDecreasedEfficacyOfBiologicalProcess.yaml July 3 2019 --- .../abnormallyDecreasedEfficacyOfBiologicalProcess.yaml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml b/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml index 7d664773..4c6f157d 100644 --- a/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml +++ b/src/patterns/dosdp-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml @@ -1,6 +1,6 @@ pattern_name: abnormallyDecreasedEfficacyOfBiologicalProcess pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedEfficacyOfBiologicalProcess.yaml -description: "An abnormally decreased efficacy (reduced ability to produce output) of a biological process compared to controls. For example, defective cytokinesis." +description: "An abnormally decreased efficacy (reduced ability to produce an output of normal amount and/or quality*) of a biological process compared to controls. *Here 'quality' refers specifically to the 'goodness', 'properness', or 'adequateness' of the output (as opposed to any characteristic in general) and 'output' can mean a particular physical entity (like metabolite as a product of a metabolic process) or state (or configuration) of a physical entity (like the fitness or health of a cell). This phenotype is usually inferred from more direct observations; for example, blood glucose levels may be measured by a colorimetric assay applied to a blood sample, which then is used to infer that blood glucose is high, low, or unstable, which can then itself be used to infer that blood glucose homeostasis is defective or has reduced efficacy." contributors: - https://orcid.org/0000-0001-9076-6015 @@ -17,7 +17,6 @@ relations: annotationProperties: exact_synonym: oio:hasExactSynonym - narrow_synonym: oio:hasNarrowSynonym vars: biological_process: "'biological process'" @@ -28,12 +27,8 @@ name: - biological_process annotations: - - annotationProperty: narrow_synonym - text: "Deficiency of %s" - vars: - - biological_process - annotationProperty: exact_synonym - text: "Defective %s" + text: "defective %s" vars: - biological_process