Manager Call 2019-03-20
- Agenda: Suzi
- Minutes: Pascale
Cambridge GOC Agenda
Start to firm up the agenda for GO meeting:
March release status
As as March 19th, release was from Feb 2nd (AmiGO). but Version 2019-03-10 in zenodo Why the discrepancy ?
PURLs from the public website
PURLs for the ontology need to point to 'current' rather than 'snapshot' -> https://github.com/geneontology/go-site/issues/873 When will we do that ?
Carried over from previous agendas:
'Redundant' PAINT annotations
- Helen Atrill (and others) would like to avoid making PAINT annotations from the same protein - ie would like to filter out GENE1 IBA with GENE1.
- We had mentioned a while ago that there are 2 reasons to keep those:
- 1. Gives 'support' to the annotation in that it has been selected for PAINTing
- 2. (related to 1): could allow to display 'main' functions for each gene more prominently.
Do we want to implement anything relevant to that? If not, we might as well filter out these 'circular' annotations, which are certainly confusing for users. -> Paul says (offline discussion with Pascale) that we don't plan to remove this. Databases can filter them out of they want.
Fate of "unmanaged" external2go files
Note that there has been a discussion of why the Reactome file hasn't been updated. https://github.com/geneontology/go-site/issues/1031
New IEAs (not InterPro2GO)
We decided earlier to not accept IEAs from outside groups, as all sequences would be run through the dependable InterPro2GO after uploading- but this group/method *seems* like they have more accurate annotations and higher coverage.
Long discussion last week - What's the next step ?
- I created a github project stub for this - Kimberly
- We were going to set up a call - has it be scheduled?
- Chris was going to review current specs, particularly wrt SO/MSO
- Discuss expanding the gpi file to include other entities used in annotation, particularly the With/From field. e.g. variation IDs, RNAi experiment IDs, etc.
- This has come up in discussions with several curation groups, including MGI, WB, and Zfin
- How does the GO gpi file work fit in with Alliance data files?
- Not all GO contributors are part of the Alliance, but it would be nice to have standardized file formats for other entities.
- BioLink availability: plan to durably solve those issues (last week we had timeout, this morning internal server error) ?
- We need an SOP for how to handle annotation (or other?) files that have pipeline-blocking errors that can be fixed by GO
- Is it okay to fix these errors?
- If yes, then is it okay to point to a GO version of the file in the source URL in the datasets.yaml file until the source file is fixed?
- Seth to visit MGI in July? Do we have the funds to bring Seth out so he can sit with the software engineer at MGI who handles all of our loads? If we are going to create the uber-gafs at the GOC it would be nice for him to learn the ins and outs of what we do.