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Update the EQ in abnormalLevelOfChemicalEntity#982

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rays22 wants to merge 2 commits into
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issue981
Open

Update the EQ in abnormalLevelOfChemicalEntity#982
rays22 wants to merge 2 commits into
masterfrom
issue981

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@rays22

@rays22 rays22 commented Apr 14, 2025

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This commit intends to restrict the scope of the abnormalLevelOfChemicalEntity pattern to apply to chemical qualities only in anatomical entities. To achieve this, the logical definition will be updated.

If applied, this commit will fix #981.

This commit intends to restrict the scope of the abnormalLevelOfChemicalEntity pattern to apply to chemical qualities only in anatomical entities. To achieve this, the logical definition will be updated.

If applied, this commit will fix #981.
@rays22 rays22 self-assigned this Apr 14, 2025
@rays22 rays22 requested a review from matentzn April 14, 2025 15:10

@sbello sbello left a comment

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@matentzn

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These changes make this identical to http://purl.obolibrary.org/obo/upheno/patterns/abnormalLevelOfChemicalEntityInLocation.yaml

No, not identical - there is no filler class in this pattern! Only the chemical entity and the fact that it is measured in some part of an organism (anatomical entity)

@sbello

sbello commented Apr 14, 2025

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Ah, okay. This needs to be made very clear, maybe add a note to the top.
I still have the question of what this means for phenotypes related to levels in exhaled gases. But I think we could probably just leave these without eqs.

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Everything is correct about this PR but I am scared that if I merge it, I lose a lot of cross species mappings..

  • This this pattern with a uPheno build

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Restrict the abnormalLevelOfChemicalEntity pattern to anatomical entities

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