-
Notifications
You must be signed in to change notification settings - Fork 26
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
OBI:0100026 as taxon for variant objects #860
Comments
we originally attempted to infer taxon on genotype parts, instead of making an explicit edge for each (in retrospect maybe a mistake). Theres an inference path in the solr loader that has been broken for some time, in the sense that it either doesn't infer the taxa or infers 'organism'. tl;dr this should probably be fixed in dipper and likely won't be in the short term |
see also - SciGraph/golr-loader#10 |
Thats good to know. Thanks @kshefchek So this is blocked by Dipper or SciGraph loader? or both? |
The way it works now, this could either be fixed in dipper or the golr-loader code. We could also add something in scigraph but it would be some new post processor. I think the best thing to do is to add it in dipper. |
looking closer, many of these are transgenes, so which taxon applies? I would think the taxon in which the variant is studied but that is not entirely accurate. |
@mbrush Are you able to join the monarch-ui call on Tuesday November 12? This ticket is in relation to representation of variants, and we believe we need your help. |
Hi. Happy to join call on Tuesday. In the meantime, Appendix I of this document provides food for thought that I think is relevant to this topic. It gets pretty into the weeds concerning what it means to be a 'transgene' or an 'allele' from the GENO perspective. But the key bits are in the third paragraph that starts with "An allele . . . "). Copying key text below, but see document for broader context.
|
I am confused about why we are talking about an OBI ID in the first place. We shouldn't be using the OBI class for organism. |
@cmungall this comes from a multi integration issue, first from running elk on geno, then attempting to infer taxon via this graph path search: https://github.com/SciGraph/golr-loader/blob/master/src/main/java/org/monarch/golr/GolrLoader.java#L157 |
@kshefchek send along the list of troublesome IDs when you get a chance, and I"ll figure out what Dipper ingests needs to be corrected here |
This bug was originally raised by @iimpulse
For reference, the query: https://api-dev.monarchinitiative.org/api/bioentity/gene/MGI:98297/variants?fetch_objects=true&start=0&rows=10&facet=true&facet_fields=subject_taxon&taxon=OBI%3A0100026
yields gene to variant associations. But there are some associations where object has a
BNODE
prefix, and a taxon ofOBI:0100026 'organism'
. This makes it difficult to filter variants based on taxon since 'organism' is too generic of a taxon term.@cmungall @kshefchek Thoughts?
CC'ing @monicacecilia for her awesomeness!
The text was updated successfully, but these errors were encountered: