Manager Call 2019-03-06
Agenda
- Agenda: Huaiyu
- Minutes: Suzi
Management
- Update on all ongoing projects: https://github.com/orgs/geneontology/projects -
- Are goals clear for the GOC meeting next month?
- Is anyone encountering any roadblocks?
- We need % effort from the different people involved in project for all projects with a delivery date/active projects
- Created new projects for (1) GPAD/GPI specs (2) Documentation (to list items we have worked on during the current period)
- 'Gantt-chart' to manage projects: Hackathon tasks: how is that working ?
- The issues with the new input and output relations have been resolved. It is fine to make an official release.
GO meeting agenda
https://docs.google.com/document/d/1QiqfZ5eAwmljqt5Fh0Ooi1Pd-HKgMSGsYC_wx6-UEPY/edit#
Priorities:
- Moving existing annotations to GO-CAM
From last meeting minutes (by far not exhaustive)
- Create working group to coordinate integration of IEAs (single source ideally): priority?
- Handling redundant information: priority?
Discussion points
Fate of "unmanaged" external2go files
https://github.com/geneontology/go-ontology/issues/16989
New IEAs (not InterPro2GO)
https://github.com/geneontology/helpdesk/issues/195
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.
SynGO import
Long discussion last week - What's the next step ?
GPAD/GPI Specs
We were going to set up a call - has it be scheduled?
Model Copy
Update on the GO-CAM model copy (Laurent-Philippe). Further discuss user requirements (e.g. contributors and template aspect)
Examples (temporary URLs):
- original DBL-1 pathway | duplicated DBL-1 pathway
- original Signaling by BMP | duplicated Signaling by BMP
Original Tickets:
Minutes
Update on projects:
Documentation: this is just an ongoing list
- Pipeline [Seth]
- data issues, tend to be important for users
- PAINT pipeline: duplicated annotations for very few genes, some with slightly different withs, in last two releases. Cause likely evidence tracking issue. Dustin is working on this.
- Some genes missing from PANTHER upstream, Dustin/Seth will get to this.
- External2GO- remnant of domain switching.
- AmiGO is slowly being fully automated,
From Alliance call:
- Push GAF file to Alliance (right now for gene descriptions, probably other uses in future)
- [Judy] GO data put into a format that can be semi-automated, and in balance with what they're doing
- [Seth] Pushing data (annotation files) instead of pulling data
- Mapping human to HGNC in GO Central release
- [Paul] this has been the plan for a while, but hasn't been put in place
- [Pascale] How to get to the Uniprot entry page, may be more informative
- [PT] Consistent ID namespace whether they're protein coding or not
- [Judy] Alliance uses HGNC, so this would be consistent
- [MC] when to link to gene/protein, eg UniProt is explicitly protein
- [PT] Start with human, but also Xenopus and others need to have IDs clarified
- [Kimberly] Also need to address links in with/from throughout pipeline
- [PT] ...or of submission requirements
- need plan to act on- scope? all IDs or just with from, who we're working with, is this an internal exercise, etc.
[David] GPI file currently solves some of this, ties all entries to a GP
- GPAD-GPI specs
- headers- this will be addressed. Needs more attention in specs
- SO vs MSO [Judy] on agenda for Alliance all hands call in April
- Moving existing annots to GO-CAM
- [David] manually reviewing annotations to make rules
- [David] sometimes easier to make some changes in bulk import instead of one-by-one in Protein2GO, proposed a "special" GPAD for the initial load
- Noctua
- [Kimberly] in contact with LP and Tremayne
- [PT] time to bring newest (in-progress) version to dev for testing before release- Tremayne and Seth to work on this.
- [LP] model copying feature is ready for testing, URLs in agenda
- input as to requirements welcome
- [PT] future uses of copy function- all except EC and references, other uses, templates, etc.
- [David] Have add individual prompt templates?
- [Seth] very difficult now- keep this as requested feature for now
- [LP] also copies usable for teaching, no repos yet
- present this at GO meeting
Kimberly/David/Peter/Huaiyu in talks with Reactome, lots of details getting ironed out
QA rules: Eric hopefully getting to this, IBA getting filtered out
Website: few tickets remain, documentation and email for helpdesk remain
Other/off agenda: [David] release can be started today including PURLS pointing back at current. Everything defaults to release.
Prioritize projects/features because a user asks or shows a need?
- Eg term-ancestor table from https://github.com/geneontology/helpdesk/issues/165
- yes, this case- this will be needed for Alliance, internally, etc.
Present
Pascale, David, Huaiyu, Judy, Laurent-Philippe, Suzi, Mike, Seth, Kimberly, Paul T