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matentzn / trait-phenotype-ontology-patterns

The goal of this repo is to reconcile our discussions on trait & phenotype modelling patterns, including measurements and other entities.
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phenome.jax.org use case #4

Open matentzn opened 3 years ago

matentzn commented 3 years ago

From Elissa: [In the Phenome Database], you can see some potential mapping, e.g. measurement 1501 has "altered susceptibility to bacterial infection" phenotype (MP) and "response to bacterial infection trait" in VT. The VT annotation is likely more appropriate. MA is mouse anatomy--not relevant to your project. In both cases, we would like to map these to HPO and MonDO, as traits that are used to characterize human disease, or traits that are aspects of human disease.

We use trait-based meta-analysis to find variants associated with all measurements annotated to the same VT or MP term. We intend (and have built infrastructure) to map these results directly onto human variant GWAS associations to the same traits through gene orthology.

matentzn commented 3 years ago

From Elissa: we’d want to use ontology annotations to match the mouse and human traits.