Projects stand up meeting 2021-07-07: Difference between revisions
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==Attendees== | ==Attendees== | ||
* Present: | * Present: Huaiyu, Kimberly, Pascale, Seth, David, Chris, Paul | ||
* Regrets: | * Regrets: | ||
* Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris | * Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris | ||
Line 8: | Line 8: | ||
=Discussion points= | =Discussion points= | ||
== TAIR Data Submission == | |||
* Any more feedback for Tanya? | |||
** We replied to her suggestion, the ball is in her court | |||
=Ongoing projects= | =Ongoing projects= | ||
Line 23: | Line 26: | ||
==SynGO Annotations== | ==SynGO Annotations== | ||
* There are some data issues with these annotations | * There are some data issues with these annotations | ||
** Use of an obsolete ECO code - https://github.com/geneontology/noctua/issues/726 | ** ''Use of an obsolete ECO code'' - https://github.com/geneontology/noctua/issues/726 | ||
** Use of IMP for CC in possibly a different way than standard annotations - RGD has asked about this | *** It would be good to at least update the obsolete ECO code in the GO-CAMs | ||
** | ** ''Use of IMP for CC in possibly a different way than standard annotations'' - RGD has asked about this | ||
** Try contacting SynGO about this before updating | ** ''Uniprot IDs from SYNGO models aren't in NEO'' - https://github.com/geneontology/noctua/issues/693 | ||
** Other places SynGO data resides, e.g. Protein2GO? | ** ''Harmonize SynGO's use of UniProt identifiers and MOD identifiers'' - https://github.com/geneontology/go-site/issues/1568 | ||
** Try contacting SynGO about this before updating any .ttl files in the noctua-models repo? | |||
*** Other places SynGO data resides, e.g. Protein2GO? | |||
* Where does all of this stand in our project priority list? | |||
* Wait until we've finished up other projects? | |||
* Add to the [https://github.com/orgs/geneontology/projects/37 existing project] but don't start on the work yet? | |||
* '''POSTPONE DISCUSSION UNTIL DUSTIN IS BACK''' | |||
==MOD imports== | ==MOD imports== | ||
* [https://github.com/orgs/geneontology/projects/52 GPAD output] | * [https://github.com/orgs/geneontology/projects/52 GPAD output] | ||
Kimberly and David described tasks - not all tickets are assigned yet; need Jim and probably Sierra | Kimberly and David described tasks - not all tickets are assigned yet; need Jim and probably Sierra | ||
** Jim will be assigned the tickets with the 'imports' label; this is high priority | |||
** Sierra will be tagged, so she can be trained | |||
* [https://github.com/orgs/geneontology/projects/58 MGI] -> waiting for GPAD | |||
* [https://github.com/orgs/geneontology/projects/58 MGI] | * [https://github.com/orgs/geneontology/projects/59 WormBase] -> waiting for GPAD and round trip before asking Alex changed to the GPAD export he produces | ||
* [https://github.com/orgs/geneontology/projects/59 WormBase] | |||
* [https://github.com/orgs/geneontology/projects/60 XenBase] | * [https://github.com/orgs/geneontology/projects/60 XenBase] | ||
* [https://github.com/orgs/geneontology/projects/61 SGD] (no tickets yet) | * [https://github.com/orgs/geneontology/projects/61 SGD] (no tickets yet) | ||
* ZFIN -> no project; all errors and bugs have been corrected; need to roll out | |||
==Ontology== | ==Ontology== | ||
* [https://github.com/orgs/geneontology/projects/64 ATPase jamboree ] | * [https://github.com/orgs/geneontology/projects/64 ATPase jamboree ] | ||
* Next: GO-Rhea alignment - week of July 26 | * Next: GO-Rhea alignment - week of July 26 | ||
** Participants + goals: | ** Participants + goals: | ||
https://docs.google.com/document/d/1Ki1xnWU29OkQZSScZ-ge-U_90Ql3-Ni5HbAvFktephs/edit# | |||
==Noctua== | |||
* [https://github.com/orgs/geneontology/projects/65 Noctua enhancements, bug fixes, user support 6/2021 - 12/2021] | |||
Tremayne, Laurent-Philippe, Kimberly, David | |||
=Priorities= | |||
* GPAD project | * GPAD project | ||
* NEO | * NEO : fix/refactor to make more robust and add more species/chains(?) (and maybe automate some parts like periodic reloading) | ||
** '''NEXT: schedule a planning meeting''' | |||
https://docs.google.com/spreadsheets/d/19-i43w0mGQdFYmKXqskVIgrDO-pVTWo1YgjaWa5PI1o/edit#gid=68094648 | * Other priorities: https://docs.google.com/spreadsheets/d/19-i43w0mGQdFYmKXqskVIgrDO-pVTWo1YgjaWa5PI1o/edit#gid=68094648 | ||
==GOC meeting Action Points== | ==GOC meeting Action Points== |
Latest revision as of 11:55, 7 July 2021
Attendees
- Present: Huaiyu, Kimberly, Pascale, Seth, David, Chris, Paul
- Regrets:
- Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris
Announcements
GOC meeting dates: Oct 13-15 (Wed to Friday)
Discussion points
TAIR Data Submission
- Any more feedback for Tanya?
- We replied to her suggestion, the ball is in her court
Ongoing projects
Urgent bug
NEO - not loading all MGI entities: https://github.com/geneontology/neo/issues/70 Jim needed to help fix this
This seems to be fixed.
GAF2.2 Migration
- Can we close this project?
- Are all GO upstreams in compliance?
- https://github.com/orgs/geneontology/projects/51
SynGO Annotations
- There are some data issues with these annotations
- Use of an obsolete ECO code - https://github.com/geneontology/noctua/issues/726
- It would be good to at least update the obsolete ECO code in the GO-CAMs
- Use of IMP for CC in possibly a different way than standard annotations - RGD has asked about this
- Uniprot IDs from SYNGO models aren't in NEO - https://github.com/geneontology/noctua/issues/693
- Harmonize SynGO's use of UniProt identifiers and MOD identifiers - https://github.com/geneontology/go-site/issues/1568
- Try contacting SynGO about this before updating any .ttl files in the noctua-models repo?
- Other places SynGO data resides, e.g. Protein2GO?
- Use of an obsolete ECO code - https://github.com/geneontology/noctua/issues/726
- Where does all of this stand in our project priority list?
- Wait until we've finished up other projects?
- Add to the existing project but don't start on the work yet?
- POSTPONE DISCUSSION UNTIL DUSTIN IS BACK
MOD imports
Kimberly and David described tasks - not all tickets are assigned yet; need Jim and probably Sierra
- Jim will be assigned the tickets with the 'imports' label; this is high priority
- Sierra will be tagged, so she can be trained
- MGI -> waiting for GPAD
- WormBase -> waiting for GPAD and round trip before asking Alex changed to the GPAD export he produces
- XenBase
- SGD (no tickets yet)
- ZFIN -> no project; all errors and bugs have been corrected; need to roll out
Ontology
- ATPase jamboree
- Next: GO-Rhea alignment - week of July 26
- Participants + goals:
https://docs.google.com/document/d/1Ki1xnWU29OkQZSScZ-ge-U_90Ql3-Ni5HbAvFktephs/edit#
Noctua
Tremayne, Laurent-Philippe, Kimberly, David
Priorities
- GPAD project
- NEO : fix/refactor to make more robust and add more species/chains(?) (and maybe automate some parts like periodic reloading)
- NEXT: schedule a planning meeting
- Other priorities: https://docs.google.com/spreadsheets/d/19-i43w0mGQdFYmKXqskVIgrDO-pVTWo1YgjaWa5PI1o/edit#gid=68094648
GOC meeting Action Points
- Are any of these items high priority?