enabling other organisms #1
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ensure compatibility between graphite and GOSemSim.
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The organism translation is good. But their is a bug in ID conversion. Not all annotation db is org.X.eg.db, for example yeast is org.Sc.sgd.db. see https://support.bioconductor.org/p/64729/. The original version use EXTID2NAME from DOSE do import DB via GOSemSim::getDb and more compatible. Can you modify this part? |
string split by ": " is dangerous because sometimes colon is in the pathway names. For example (5752278): "Caenorhabditis elegans: Antigen processing: Ubiquitination & Proteasome degradation"
GuangchuangYu
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May 28, 2015
enabling other organisms
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may need explicitly add GOSemSim to Imports or expose getDb function (or similar function linking organism name to org.X.eg.db) in other way. I'll add organism name conversion to make sure 'graphite' compatible with 'GOSemSim'. E.g. homo sapiens is 'hsapiens' in 'graphite', but 'human' in 'GOSemSim'.