Manager Call 2020-03-18

Agenda

• Agenda: Kimberly
• Minutes: Huaiyu
• Present:
• Regrets:

Discussion points

GO meeting Paris

• What do we need to do to prepare for a virtual meeting?

Proposed File Format Changes

• GPAD/GPI 2.0 specs released
• Also, we proposed last week to make an incremental update to GAF to allow for all gp2term relations.
  • Create specs for this and share internally as well as to users for comments?
  • How soon do we need to begin preparing for effects on GO products, tools?

Proposed data flow from Alex (GOA)

• Do we still need to discuss anything here?

• Based on decision at PI retreat to only show in AmiGO the 142 species also included in PANTHER, i.e. fewer species but all available annotations for those species.
• This would be a new pipeline to supplant the current UniProtGOA-all pipeline, i.e. the MODs will still be the source of their species annotations

1. All annotation sources/files are pulled to GO based on yaml files. (already implemented)

2. GOA pull them from GO based on yaml files data (partially implemented)

3. GOA perform all, so far known, sanity checks and constrains (already implemented)

4. GOA sends out reports to go-quality and group responsible for annotations (partially implemented)

5. GOA generate gpa/gpi (maybe gaf if you ask nicely) for 142 taxon for all annotations which are passed though step 3 (to be implemented)

6. GO using 142 taxon file for all their pipelines needs, no need to run their own set of checks, can be indexed directly to amigo and other tools. (to be implemented)

Pathway Genome Databases and the Alliance

See Chris' email

• Explore bringing in other existing curated pathways in a similar way that we did for Reactome
• Follow-up to Alliance call last week with Peter K.?

MGI and WB Imports

• Status updates
  • WB
    • Alex will work on preparing a test GPAD file with annotation history for WB - hopes to have it on the GOA ftp site some time next week