Manager Call 2020-07-08

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Agenda

  • Agenda: Huaiyu
  • Minutes: Suzi
  • Present: Chris, David, Huaiyu, Judy, Kimberly, Laurent-Philippe, Pascale, Paul T, Seth, Suzi


Project plans for remainder of 2020

Kimberly should be here for this discussion - what are the items we need to deliver for GO-CAM and Noctua ? So we can select what we can do from https://docs.google.com/document/d/1URLkEQBewlzD-NVAjbPLWD5Gu-5xq0RysTrm1GMbuiM/edit#

  • Please also see the Noctua 3.0 planning Google doc
  • Kimberly in talks about what is needed for next development cycle- add to future manager's call
  • MOD imports still priority
*List of resources needed for each task is still missing; Review tool (ART) is still missing.  LP to put together a technical implementation plan for that tool.

Pascale would like to know what everyone's priorities and time estimates (delivery estimates) are for next cycle- bioinformatics outreach, fixing website, GO-CAM stats, everything else. may be doubly listed or not in this doc. What can reasonably get done by next grant cycle?

Project Priorities for calendar year 2020= goals for next grant, unless marked as de-prioritized. Maybe list other personnel expected on project? 1.a.1): Mouse/worm/yeast pathways. May not need expert on organism, just someone to look over ontology terms. IMP-> multicellular processes exclusion: trying to figure out how many GO CAMs must be curated. IMP is part of or causally upstream of- if upstream, isn't required for import on a pathway. Not final list, just trying to estimate bounds (number of models, time per model) on the problem. Potentially get list of items to exclude.

1.a.ii): Maybe get top 20 processes from major mods, then compare- apoptosis, development, etc. Any groups interested should participated. de novo curation using both Form and GE, could be sped up by using existing annotations. Expect discussions on modelling biology, so takes longer. Estimate time to create new template vs. create own model without template.

Also need to know overall effort for curators/contributors

1.b: consensus on rules and paper has been started. Most statements have been converted to pathways, but needs closer look before being releasable. Val's review is for import of Pombase annotations.

2: not yet ready to assign times.

3: same as doc Kimberly showed for 3.0, plus MOD migration.

4: conversion to new formats and ongoing pipeline work. 4c- item in planning and likely de-prioritized or not yet discussed. 4h- NEO into main pipeline- nice but not required 4j- optimization- may become requirement

GO-CAM

  • Discussion on whiteboard (was photographed) and in Alliance proposal in December

URL GO ribbon

Proposals:

  • ribbon.geneontology.org
  • www.geneontology.org/ribbon-sandbox (pas besoin de Seth).
  • doc : www.geneontology.org/docs/ribbon.

Current Mockup:


LP needs feedback:


Tickets to comment:

Loading 142 species

Can someone get the list of species for the 204 (?) with > 1000 EXP annotations ? (Laurent-Philippe/Hauiyu?)

LP can bring to next meeting This is in planning doc.

UMBC-hosted meeting will be virtual

  • Action from last week: Dates have been finalized. Pascale will first confirm with Michelle, and then send out the announcement.

-> Michelle is on vacation; we'll send the announcement next week.


Any other business?

Release- missing 500k IBAs (taxon problems maybe??). Going to push off release and get stats in now.