Entering edit mode
3.5 years ago
david.f.stein
▴
10
Is there a way to map rsIDs to KEGG variant IDs?
Traffic: 2109 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6
What have you tried? Can you give us a sample entry of something you have manually mapped (as in, you think they're connected)?
I've searched for a mapping tool and examined KEGGs API but there doesn't appear to be a programmatic way to map rsIDs to KEGG variant IDs. I have ~100,000 variants, so this cannot be done manually
Like I said, "give us a sample entry"
Once you outline your approach for a few variants, you can start to automate for the rest.
You want me to give you a sample rsID? Not really sure how that will help either of us answer the question. If you don't know how it's all good
I'm sorry that I wasn't clear before. Can you give us a sample rsID that you have mapped to a KEGG variant ID? For example, the KEGG variant 3845v1 can be mapped to rs121913529 because the KEGG website entry for the variant has this information (and so, it must be available to download as a flat file). However, dbSNP does not point to KEGG variant entries. Do you have a manual way of doing it for one sample rsID? If so, that could be automated.
I see, here is a link with a KEGG variant that maps to an rsID. https://www.kegg.jp/entry/hsa_var:4000v1 (rs58596362). It seems you can query using there dbget tool, but I'm just not sure how to search for the rsID and get back the KEGG ID rather than the other way around. For instance if I go here: https://www.genome.jp/dbget/ and search rs58596362 I don't get back any results. However, I can search the KEGG ID and get back to the first link.
Ah, I see. So you do not yet have any leads into going the other way (rsID -> KEGG variant entry) even manually. In that case, an approach would be to get a flat file mapping KEGG variants to rsIDs from the KEGG website, then using that to reverse-map the subset of your rsIDs that match the entries in that file.
I did some digging, and there seems to be no easy way to access their files; there is an ftp service though, which does not seem all that great. You could email them and check how to access their variant dataset.
Seems like I'll have to get in touch with them and see if I can get the flat file download. Thanks for the suggestion