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uPheno integration issues #965
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A question. What does "nucleus phenotype" actually mean? If it means any phenotype that is observed in the nucleus, it would be tricky. So does this term really mean "nucleus organization phenotype"? or "nucleus morphology phenotype (size and shape)" |
@ValWood nucleus phenotype is meant to be the grouping class that collects all morphological and physiological abnormalities in the nucleus. The removal of the word abnormal from the uPheno labels without replacing it with another word with a similar if less negative connotations is I think contributing to the confusion. Both organization and morphology terms should fall under this term. If this isn't a useful grouping class than we should also discuss that. We can add that to the potential workshop topics. |
got it! In FYPO, due to a historic design decision, we keep abnormal morphology and abnormal process phenotypes distinct. Despite being (probably) ontologically correct I think that searches would benefit from such a grouping term (because often the genes annotated to such terms obviously often overlap). In fact, in some cases, it is difficult to distinguish, and really only depends on the method of observation (for example, we were recently unable to justify abnormal cytoskeleton organization from abnormal cytoskeleton morphology). I'm still considering what to do here. |
We've done a similar thing in the MP and have a similar issue, are they talking about the process or the outcome of the process is frequently tricky to decide. |
Same reason as above.
Can you give an example of a term that should but does not classify under its abnormallyDecreasedRateOfBiologicalProcess counterpart term?
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I think we need to review the use of 'characteristic of part of' and 'characteristic of' and how these integrate in uPheno. The MP is using 'characteristic of part of' in the pattern for decreased T cell apoptosis since we want to be able to infer that any decrease in T cell apoptosis, either specific T cell types or parts of the apoptosis process in T cells will fall under this term. The question I have is can we agree on only a single pattern using either 'characteristic of part of' or 'characteristic of' for each type of pattern. Right now I think we have some cases where we have both 'characteristic of part of' and 'characteristic of' for some pattern types (see Abnormal morphology of anatomical entity and Abnormal morphology of part of anatomical entity for example). It seems like if we could agree on a single pattern to use then integration could be improved. With both patterns in use we're getting some weird/confusing results in the integrated ontology. |
@anna-anagnostop I fixed some issues in the latest release: https://github.com/obophenotype/upheno-dev/releases/tag/2025-01-11 can you look at upheno.owl in Protege and confirm you are satisfied? I would also ask you if possible to create individual issues for everything you observe and assign to me, and close this compound issue. It is very hard to deal with multiple disjoint issues in a single thread! @sbello @anna-anagnostop thank you so much for your feedback so far, please keep them coming as I want to be in really good shape for biocuration! Nico |
While searching for cellular phenotypes in uPheno I have come across a number of integration issues, including:
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