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Create abnormalShapeOfPhysicalEntityInLocation.yaml #969

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Seems this was missing, can you check it?

@matentzn matentzn requested review from sbello and rays22 January 10, 2025 09:30
---
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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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.

@matentzn matentzn requested a review from rays22 January 11, 2025 08:16
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Thank you for your feedback! Can you check again?

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👍

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