Manager Call 2019-03-06

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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:

  1. 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 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?


Present

Pascale, David, Huaiyu, Judy, Laurent-Philippe, Suzi, Mike, Seth, Kimberly, Paul T