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This is an umbrella ticket for discussion of cell death phenotypes. It is motivated by the Drosophila Phenotype Ontology definition:
[cell death defective](https://www.ebi.ac.uk/ols/ontologies/dpo…
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There turns out to be quite a number of what I want to call "complex phenotypes". A complex phenotype is a phenotype whose definition involves more than one entity. So far the Phenotype Editor have id…
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We merge diseases and phenotypes when the same term occurred in both MONDO and HP. But this isn't totally correct because diseases are not phenotypes (even if kinda they are). Sometimes for unclea…
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I would like to run TrajGWAS on some large-scale longitudinal phenotypes. Specifically, I have ``100,000`` observations, ``48`` covariates (+ intercept), and ``100`` phenotypes. I would like to get ef…
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I don't fully understand the difference between
abnormal actin cytoskeleton (FYPO:0005665)
A physical cellular phenotype in which the amount, distribution, or morphology of all or part of the act…
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So far the phenotypes and the SNPs are rather independent from each other, making it hard to link one to the other. But in principle we already have the information needed to link them, at least in a …
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We need to map the following terms the NCI thesaurus or the appropriate ontology, or create new ones as needed:
decreased sensitivity
detrimental effect
increased benefit
no response
no sensitivity
r…
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E.g., if a user assigns A-B to a species, then duplication of the coordinates occurs so that there's one set for phenotype A and one set for phenotype B. The code for this is already in the SIT librar…
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There is likely an error in `MED.py` causing certain medication codes to be skipped. See issue #4. Data can be found at `$OAK/users/magu/repos/rivas-lab/in_old_not_tools.txt`
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We should have the ability to see the unmatched phenotypes for the profile on the left list, as well as for any column. Basically, if you were interested in comparing a patient against a particular mo…