Thread:Substantive changes (4)
From WikiPathways
Thank you for the answers. I tried now to annotate the geneproducts with the appropriate UniProt ID, but then in the "live" version it says that "Unable to load external references.", despite that this does work when I am the "editing mode". If I use the Entrez Gene IDs to annotate a protein then the external references can be loaded. A similar thing happens for metabolites, where HMDB IDs seem to work best. The curation tag "This pathway contains genes, proteins or metabolites with missing database annotations'" now only "complains" about the references to the other pathways andnd about the metabolite H+ and ubiquinol-10. I do not know why and how to correct this.
Use the ID you think is best. The "unable to load external refs" sounds like a bug on our end. If you found it in the database and it produces external references in edit mode, then you're all set. As for the curation tag, the "correction" is to simply remove it. Just click the little red 'x' after you're done making your edits. It won't appear again until it's triggered by future edits.
The pathway is final for now and the paper submitted. I picked the Entrez Gene IDs as we needed to submit the paper and the UniProt IDs did not generate links to other databases in the live version, only in the edit mode. I would prefer UniProt IDs though as it are enzymes and not genes, so if there is a fix let me know.
Great. In your paper, be aware of the difference between citing the pathway (e.g., http://wikipathways.org/index.php/Pathway:WP78) and citing your particular revision (e.g., http://wikipathways.org/index.php?title=Pathway:WP78&oldid=47741). The former may (and will) change over time... it's a wiki after all, and knowledge evolves; while the latter will always refer to that particular version no matter what changes follow. You may want to cite both depending on the purpose of the citation. AlexanderPico 21:03, 17 April 2012 (UTC)
