Manager Call 2019-03-13

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Agenda

  • Agenda: Suzi
  • Minutes: Seth

Management

Cambridge GOC Agenda

https://docs.google.com/document/d/1QiqfZ5eAwmljqt5Fh0Ooi1Pd-HKgMSGsYC_wx6-UEPY/edit


Discussion points

Implementation of taxon constraints

We'd like annotations failing taxon constraints to be excluded from AmiGO and all the files we export. Can we prioritize this task ? https://github.com/geneontology/go-ontology/issues/17025

'Redundant' PAINT annotations

  • Helen Atrill (and possibly others) would like to avoid making PAINT annotations from the same protein - ie would like to filter out GENE1 IBA with GENE1.
  • We had mentioned a while ago that there are 2 reasons to keep those:

1. Gives 'support' to the annotation in that it has been selected for PAINTing 2. (related to 1): could allow to display 'main' functions for each gene more prominently.

Do we want to implement anything relevant to that? If not, we might as well filter out these 'circular' annotations, which are certainly confusing for users.


Carried over form last week:

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?
    • Chris was going to review current specs, particularly wrt SO/MSO
  • Discuss expanding the gpi file to include other entities used in annotation, particularly the With/From field. e.g. variation IDs, RNAi experiment IDs, etc.
    • This has come up in discussions with several curation groups, including MGI, WB, and Zfin
    • How does the GO gpi file work fit in with Alliance data files?
    • Not all GO contributors are part of the Alliance, but it would be nice to have standardized file formats for other entities.

New topics

  • We need an SOP for how to handle annotation (or other?) files that have pipeline-blocking errors that can be fixed by GO
    • Is it okay to fix these errors?
    • If yes, then is it okay to point to a GO version of the file in the source URL in the datasets.yaml file until the source file is fixed?

Minutes

Minutes

  • Quick attempted pass at Cambridge agenda.
    • Remote access will get sorted
    • Tried to work out what to do for agenda
    • For next week, everybody take a look at what they want to report and what they want to ask add to document any information on action items as well
  • People: add percentages to effort for projects, if you have not done so
  • Gantt chart: generally usable?
    • Proposal gantt for breakout sessions; are there even breakout sessions
    • How granular is the information we need to plan? Vacation times?
    • Decision: maybe not gantt charts as a general tool, but first few managers calls after meeting devoted to draft of what they want their goals to be
  • Taxon constraints:
    • David: Do we even want to be filtering more generally?
    • Open question of whether filter or reporting is a better for this--some believe that this should be pushed upstream, with reporting only; some believe that these should be filtered from all products
    • May be continued on QC/QA call, likely need Chris
  • Costing:
    • Seth trying to get a handle on how we should be accounting for additional "overhead" in projects, such as taxon constraints or ontology fallout
      • Example, certain types of pipeline checks will cause more failures and false positives which must be dealt with; this marginal drag increases as more features are added to some products
      • Seth gestures a lot to make point, nobody sees as he is on the phone; point may not have been effectively made
    • Paul/Seth: marginal long-term overhead for features should be localized to the requesting group/project, this implies that projects must always roll forward and that overhead must be kept as a separate number per person.

Present

Seth, Kimberly, David, Huaiyu, Paul, Laurent, Pascale, Suzi,