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Create abnormalShapeOfPhysicalEntityInLocation.yaml #969
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Create abnormalShapeOfPhysicalEntityInLocation.yaml
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src/patterns/dosdp-dev/abnormalShapeOfPhysicalEntityInLocation.yaml
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| 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" | ||
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| contributors: | ||
| - https://orcid.org/0000-0002-3528-5267 | ||
| - https://orcid.org/0000-0001-5208-3432 | ||
| - https://orcid.org/0000-0003-4148-4606 | ||
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| classes: | ||
| shape: PATO:0000052 | ||
| abnormal: PATO:0000460 | ||
| entity: BFO:0000002 | ||
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| independent continuant: BFO:0000004 | ||
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| relations: | ||
| inheres_in: RO:0000052 | ||
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| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
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| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
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| vars: | ||
| entity: "'entity'" | ||
| location: "'independent continuant'" | ||
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| name: | ||
| text: "abnormal shape of %s in %s" | ||
| vars: | ||
| - entity | ||
| - location | ||
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| annotations: | ||
| - annotationProperty: exact_synonym | ||
| text: "abnormally shaped %s in %s" | ||
| vars: | ||
| - entity | ||
| - location | ||
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| def: | ||
| text: "Any structural anomaly in the shape of the %s located in %s." | ||
| vars: | ||
| - entity | ||
| - location | ||
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| equivalentTo: | ||
| text: "'has_part' some ('shape' and (''inheres_in'' some (%s and (''part_of'' | ||
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| some %s))) and ('has_modifier' some 'abnormal'))" | ||
| vars: | ||
| - entity | ||
| - location | ||
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I have a serious problem with a statement like ""shape of ... measurement of a process ...", because PATO:0000052 shape is clearly defined as being a physical object quality.
An electrocardiogram (ECG) can be viewed as a measurement datum, or a timed stamped measurement datum, and then it may come in many different forms, and you could attribute some "shape" characteristics to some of its forms. However, the shape of a measurement datum does not look like one to be included in a phenotype ontology.
However, we can view an ECG as some sort of a quality of the electrophysiological characteristics of a physical object, the heart. In that case, it does not make sense at all to talk about the "shape quality" of another very specific quality.
In summary, PATO:0000052 shape should be reserved for characterising physical objects like anatomical entities, but not processes, or worse, measurement datums.
We need a better description here with better examples of when and how to use this phenotype pattern.