Manager Call 2020-05-27

From GO Wiki
Jump to navigation Jump to search

Agenda

  • Agenda: Suzi
  • Minutes: Seth
  • Present: David, Kimberly, Huaiyu, Suzi, Laurent, Judy, Chris, Pascale, PaulT, Suzi, Seth
  • Regrets:


SARSCoV2 status

Patrick says the entries are still not loaded - what is blocking ?

Discussion

Chris: GPI is still problematic--duplicate entries. Maybe just PRO? But then data flow hard. And on and on, still not resolved. NEO load. Just picking one should be fine.
Chris: let’s make a decision about the duplicates here today.
Pascale: This is PI-level
David: PRO is used by Reactome and MGI
Judy: Let’s push on using PRO IDs
Pascale: Just tell Patrick to annotate to PRO?
PaulT: Just ask them for the level of granularity--technically doesn’t have to be PRO. Can’t be mandated, but… Talk to Alex/Alan.
Chris: For the directors call then.


Load the 142 Panther species in NEO and AmiGO

(Pascale)

https://github.com/geneontology/pipeline/issues/178

  • Discussion from the multiorg group.
  • We had proposed loading all reviewed entries for bacteria and viruses, see https://github.com/geneontology/neo/issues/49, but the 35 bacterial species (+ their substrains) are probably sufficient for the needs of bacterial annotation.
  • Other species could be added if needed, to be discussed for each species and also with Panther.

Discussion

Pascale: Talked about this on multi-organism. Right now, PANTHER has one E. coli, but eight are being annotated. So, plus species subspecies/strains.
Chris: “GO reference genomes”
Laurent: What about all species in GO over 1000 annotation
Pascale: should at least check. And we need to add viruses
Laurent: Do we want more feedback? Ask Pasteur?
Judy: Start with this set, then go ask.
PaulT: What genomes will have experimental studies?
Pascale: Can you send the list of bacterial species?
Huaiyu: It changes build to build. Sometimes replace.
Chris: TSV or YAML.
Pascale: I’ll take care of it.
Chris: Still need to schedule pipeline changes.
Pascale: Alex is ready to go.
Chris: Just SwissProt? Most in QfO set? For majority, in reference. What about others?
PaulT: Ask for reference proteome. Have them for all species.
Chris: What about our super-set?
PaulT: Should be available in reference proteome. The pan-genome is still an open question.
Chris: GO can follow PANTHER and QfO.

ECO

  • To decide whether we need to hold a meeting with Michelle, and how soon that will be, we need to know
    • Are we using ECO anywhere ? For example it shows up in AmiGO
    • How do we WANT to use it ? Do we want to allow the full ECO, a subset, or just the current 3-letter ones ?
Retrieved from "https://wiki.geneontology.org/index.php?title=Manager_Call_2020-05-27&oldid=78252"