Thread:Substantive changes (2)

From WikiPathways

That would be great if you could to that. There will be a supporting article explaining why we made these changes. We will submit this article this week. I do have some questions. The text under 'This pathway contains genes, proteins or metabolites with missing database annotations' is that automatically generated? I think I have most annotation except for the references to other pathways. Another question I have is that I now use "geneProduct", I am not sure if I should have used "protein"? Furthermore, the connection between reaction and geneproduct is "catalysis", but still the system seems to prefer gene IDs instead of protein IDs. And I cannot find a way to say which gene encodes for the protein. Last question, we looked up in ChEBI for most metabolites the version of the metabolite with the correct charge for the mitochondrion. We also have the HMDB IDs which I now used, but the automatic retrieval system then gives back the "neutral" versions of the metabolites in ChEBI. I do not seem to be able to annotate a metabolite with 2 IDs.--Mdstobbe 07:46, 3 April 2012 (UTC)