phenoscape / rphenoscape

R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.
https://rphenoscape.phenoscape.org/
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Adds Resnik (MICA) similarity #142

Closed hlapp closed 4 years ago

hlapp commented 4 years ago

At present unfortunately the "taxon_annotations" corpus can take quite a while (0.5-1 hour or more) to compute term frequencies, because they are not pre-computed in the database. It does work though. For entity terms, many pre-generated post-compositions in the subsumer list incorrectly receive a count of zero from the API, but this may not necessarily matter, because if terms with higher IC are also shared, they will masquerade this problem.