Pathway Talk:WP3880
From WikiPathways
Hi Agustin,
Great work on these now pathways. You are moving fast! A quick note before to get too far. Please use "GeneProduct" datanodes rather than "Protein" when planning to annotate with Entrez Gene. These identifiers don't actually specify a particular protein, but rather a gene, possible transcripts and possible protein products. That's what's meant by the "GeneProduct" type. Thanks! AlexanderPico 17:55, 17 August 2016 (UTC)
«no subject» (28)
There have been no changes to this discussion for at least 30 days. If it is concluded, you may want to write a summary.
Hi Alexander, thanks for the suggestion, I am also using the common protein names in the description. I would like to use this instead of the gen names to make the pathways easier to read for physiologist. Should I use a different annotation for that? Thanks!
It's fine to keep the labels and identifiers just as you have them. But the datanode type should be changed from "Protein" to "Gene Product". This sort of discrepancy won't make a different to human readers of the pathway, but when we try to submit this pathway to Pathway Commons and it's converted to BioPAX and other exchange formats it will be rejected simply because Entrez Gene IDs don't specific "Protein". Let me know if any of this is still unclear. Happy to help! AlexanderPico 18:09, 17 August 2016 (UTC)
Ah, I just noticed that you made the change. This is perfect. Thanks! AlexanderPico 18:10, 17 August 2016 (UTC)
«no subject» (27)
There have been no changes to this discussion for at least 30 days. If it is concluded, you may want to write a summary.
...and when you are done with each of your new pathways, let us know and we can review them for release and tag them as "Curated". You can send an email to [email protected], for example, with links and a short message saying new pathways are ready for review. AlexanderPico 18:04, 17 August 2016 (UTC)
