Projects stand up meeting 2021-02-24: Difference between revisions
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** For future file testing, what can be automated? Is it worth it? | ** For future file testing, what can be automated? Is it worth it? | ||
** Testing these files raised some issues about how things actually happen wrt the pipeline, e.g. which PAINT files should be compared for input/output; we said we'd switch to GAF2.2 in March, what is happening with GPAD/GPI2.0 in March? If groups only produce a GPI2.0, will that break NEO production? | ** Testing these files raised some issues about how things actually happen wrt the pipeline, e.g. which PAINT files should be compared for input/output; we said we'd switch to GAF2.2 in March, what is happening with GPAD/GPI2.0 in March? If groups only produce a GPI2.0, will that break NEO production? | ||
*** Chris has updated NEO build pipeline to consume GPI2.0 as well as GPI1.2. | |||
** Once the documentation is on the website, what should we do with the documentation page in github? Add status update for other GAF file formats? Delete? | ** Once the documentation is on the website, what should we do with the documentation page in github? Add status update for other GAF file formats? Delete? | ||
** Where else should we announce the file format change? Other forums? Send email again? | ** Where else should we announce the file format change? Other forums? Send email again? |
Revision as of 13:25, 24 February 2021
Attendees
- Present: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Judy, Paul, Chris
- Regrets:
- Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Judy, Paul, Chris
Projects presentation
Template:
- Next deliverables + expected date
- Progress
- Issues / blockers
GAF2.2 migration status
- https://github.com/geneontology/pipeline/issues/211
- Kimberly manually testing GAF2.2 input, output WB files as well as GPAD1.2 output WB files
- Still going to double-check Protein2GO output gpad files
- Follow-up with UniProt
- Annotations to root nodes (Pascale emailed Alex 2021-02-24)
- Updated go-rule0000059 to account for annotations to root nodes (Kimberly will QC for WB files - should see this in rules report, when the code is updated - where/how do we know when go-rule0000059 is updated?)
- Annotations for external2go - make a proposal for each mapping and submit to groups that create the mappings for explicit approval (Pascale, Kimberly, David)
- Follow-up with UniProt
- Still going to double-check Protein2GO output gpad files
- David manually testing files that MGI ingest from all resources (e.g. GOC, UniProt) and subsequent release of MGI GAF2.2 (and also GPAD/GPI2.0)
- David will set up a meeting David, Darren, Kimberly, Seth to discuss issues with GPI2.0 specs
- Outstanding questions:
- How will GO handle different kinds of errors that may occur with gp2term relations in GAF2.2 files?
- Repair?
- For example, the gp2term relation for a root node annotation is not correct according to our GAF2.2 specifications.
- Remove?
- For example, the gp2term relation for non-protein-containing complex CC terms is 'part of'.
- This has not been addressed wrt rules yet. TBD
- For example, the gp2term relation for non-protein-containing complex CC terms is 'part of'.
- Repair?
- For future file testing, what can be automated? Is it worth it?
- Testing these files raised some issues about how things actually happen wrt the pipeline, e.g. which PAINT files should be compared for input/output; we said we'd switch to GAF2.2 in March, what is happening with GPAD/GPI2.0 in March? If groups only produce a GPI2.0, will that break NEO production?
- Chris has updated NEO build pipeline to consume GPI2.0 as well as GPI1.2.
- Once the documentation is on the website, what should we do with the documentation page in github? Add status update for other GAF file formats? Delete?
- Where else should we announce the file format change? Other forums? Send email again?
- Double-check what GAF file format each submitting group is actually submitting (roll this into broader outreach task).
- For upgrading GAF2.1, what is happening with root node annotations? The current upgrade may not address this.
- How will GO handle different kinds of errors that may occur with gp2term relations in GAF2.2 files?
Pathways2GO manuscript
ART1.0/Noctua3.0 plan
Items not discussed at last meeting
Imports
UniProt
- No plan yet
VEuPathDB
- Got in touch this week and would like to start using Noctua
Other resources (Yeast pathways)
History
GPAD export
=
Next sprint
https://docs.google.com/document/d/1AIuq8xxgV6bZZHFbXW-s3ln8PdUfZGNUuZcNFX1n7eQ/edit#