Projects stand up meeting 2021-10-27: Difference between revisions
Jump to navigation
Jump to search
mNo edit summary |
|||
(28 intermediate revisions by the same user not shown) | |||
Line 8: | Line 8: | ||
==Discussion points== | ==Discussion points== | ||
* Alliance all hands: next meeting is early December; is there anything GO wants to present? | |||
* Chris: suggestion pathway widget | |||
* Kimberly; maybe present future plans? | |||
===Priorities & objectives for remainder of 2021=== | ===Priorities & objectives for remainder of 2021=== | ||
Line 28: | Line 30: | ||
==== Noctua==== | ==== Noctua==== | ||
* Technical | * Technical | ||
** Wrap up outstanding curator request tickets in current project | ** [https://github.com/orgs/geneontology/projects/65 Wrap up outstanding curator request tickets in current project] | ||
*** Resources needed: Tremayne (full time for xx time); Kimberly, Seth, Jim | |||
*** Will focus on fixing issues that create bad data and closing issues that are almost done | |||
** Implement annotation and model copy | ** Implement annotation and model copy | ||
** Clean up bad or incorrect data | *** Shallow model copy: Resources needed: Dustin + Kimberly | ||
*** Annotation copy: Tremayne has a prototype | |||
** '''Clean up bad or incorrect data''' highest priority | |||
*** Ontology terms | *** Ontology terms | ||
*** Relations | *** Relations | ||
*** Evidence codes | *** Evidence codes | ||
** Noctua visual editor: | |||
*** Resources needed: Tremayne 1 month (November 2021 ??) + Paul T | |||
* Documentation/Guidelines | * Documentation/Guidelines | ||
** Annotation extension usage | ** [https://github.com/orgs/geneontology/projects/67 Annotation extension usage] | ||
** Process-specific guidelines | ** Process-specific guidelines | ||
*** Signaling pathways | *** Signaling pathways | ||
*** Metabolism | *** Metabolism | ||
*** Gene expression | *** Gene expression | ||
** | ** Improve error reports when running the ShEx (that appear when running the reasoner) | ||
*** Resources needed: David, Kimberly, Jim, Seth | |||
==== MOD imports ==== | ==== MOD imports ==== | ||
* Import annotation sets from Protein2GO (SGD and WB) | |||
** Resolve outstanding GPAD output issues | ** Resources: Dustin, Kimberly | ||
** Put WB fully into production? | * Resolve outstanding GPAD output issues | ||
** Resources: Jim, Kimberly | |||
* Put WB fully into production? | |||
* Create roadmap for annotation data exchange amongst all relevant resources | |||
** Meeting today with GOA, FlyBase, wormbase, SGD to discuss dataflow | |||
==== Ontology ==== | ==== Ontology ==== | ||
* Boomer + Reports by Anne: errors in GO-RHEA mappings | |||
* ChEBI Roles: '''AI set up a jamboree to finish'''? | |||
*Other projects | |||
** transcription: | |||
*** epigenetic processes, miRNA, and related | |||
*** biological processes | |||
** multiorganism processes: | |||
*** remove MF in BP (modulation of host x activity) | |||
*** fix high level terms to make browsing more logical | |||
** Obsolete single step processes | |||
** Implement design patterns | |||
* Immunology/immune system processes + cytokine production terms | |||
==== Reactome2GO==== | ==== Reactome2GO==== | ||
* Peter got a grant for this project | |||
* There will be a meeting with people internal to the group | |||
==== ECO-GO alignment==== | ==== ECO-GO alignment==== | ||
==== PAINT==== | ==== PAINT==== | ||
==== Taxon constraints==== | New Panther release in PAINT in early spring 2022 | ||
* | |||
==== New Taxon constraints==== | |||
* Some terms need logical definitions | |||
* usage of occurs_in for inferences would add a number of constraints | |||
* '''AI set up a jamboree to complete taxon constraints'''? | |||
===GOC meeting follow up=== | ===GOC meeting follow up=== | ||
* Summary metrics workshop: https://docs.google.com/document/d/15tBWdDNQuw9IdfDKk0pxpuDjfrnW3vT-xKnwO8_c1D0/edit# | * Summary metrics workshop: https://docs.google.com/document/d/15tBWdDNQuw9IdfDKk0pxpuDjfrnW3vT-xKnwO8_c1D0/edit# | ||
* Summary subsets workshop | ** API redesign would facilitate this | ||
* Implementation documentation workshop suggestions | ** '''AI set up a meeting to discuss which of these metrics we'd like to use''' | ||
* [https://github.com/geneontology/go-ontology/issues/22294 Summary subsets workshop] | |||
* DONE Implementation documentation workshop suggestions - will discuss at the next annotation call | |||
===Project updates=== | ===Project updates=== |
Latest revision as of 12:31, 27 October 2021
Attendees
- Present:
- Regrets:
- Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris
Announcements
Discussion points
- Alliance all hands: next meeting is early December; is there anything GO wants to present?
- Chris: suggestion pathway widget
- Kimberly; maybe present future plans?
Priorities & objectives for remainder of 2021
API redesign
- Right now we have multiple little APIs all over the place.
- Main GO API, Noctua API and xx
- Modernize API
- Integrate GO-CAM API
- AI Chris and Seth: will write up objective for project - what can be done in 1st month, and resources needed
Technical debt / refactoring
- Projects to be defined - this may fit within other projects
Test units
Noctua
- Technical
- Wrap up outstanding curator request tickets in current project
- Resources needed: Tremayne (full time for xx time); Kimberly, Seth, Jim
- Will focus on fixing issues that create bad data and closing issues that are almost done
- Implement annotation and model copy
- Shallow model copy: Resources needed: Dustin + Kimberly
- Annotation copy: Tremayne has a prototype
- Clean up bad or incorrect data highest priority
- Ontology terms
- Relations
- Evidence codes
- Noctua visual editor:
- Resources needed: Tremayne 1 month (November 2021 ??) + Paul T
- Wrap up outstanding curator request tickets in current project
- Documentation/Guidelines
- Annotation extension usage
- Process-specific guidelines
- Signaling pathways
- Metabolism
- Gene expression
- Improve error reports when running the ShEx (that appear when running the reasoner)
- Resources needed: David, Kimberly, Jim, Seth
MOD imports
- Import annotation sets from Protein2GO (SGD and WB)
- Resources: Dustin, Kimberly
- Resolve outstanding GPAD output issues
- Resources: Jim, Kimberly
- Put WB fully into production?
- Create roadmap for annotation data exchange amongst all relevant resources
- Meeting today with GOA, FlyBase, wormbase, SGD to discuss dataflow
Ontology
- Boomer + Reports by Anne: errors in GO-RHEA mappings
- ChEBI Roles: AI set up a jamboree to finish?
- Other projects
- transcription:
- epigenetic processes, miRNA, and related
- biological processes
- multiorganism processes:
- remove MF in BP (modulation of host x activity)
- fix high level terms to make browsing more logical
- Obsolete single step processes
- Implement design patterns
- transcription:
- Immunology/immune system processes + cytokine production terms
Reactome2GO
- Peter got a grant for this project
- There will be a meeting with people internal to the group
ECO-GO alignment
PAINT
New Panther release in PAINT in early spring 2022
New Taxon constraints
- Some terms need logical definitions
- usage of occurs_in for inferences would add a number of constraints
- AI set up a jamboree to complete taxon constraints?
GOC meeting follow up
- Summary metrics workshop: https://docs.google.com/document/d/15tBWdDNQuw9IdfDKk0pxpuDjfrnW3vT-xKnwO8_c1D0/edit#
- API redesign would facilitate this
- AI set up a meeting to discuss which of these metrics we'd like to use
- Summary subsets workshop
- DONE Implementation documentation workshop suggestions - will discuss at the next annotation call
Project updates
Clean up Google drive, calendar, and GH to remove part project members
https://github.com/orgs/geneontology/people
Asynchrony issues in the release pipeline
https://github.com/geneontology/go-site/issues/1742