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YuLab-SMU / ReactomePA

Reactome Pathway Analysis
https://yulab-smu.top/biomedical-knowledge-mining-book/
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enabling other organisms #1

Closed vladpetyuk closed 9 years ago

vladpetyuk commented 9 years ago

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'.

GuangchuangYu commented 9 years ago

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?