Projects update meeting 2022-06-29: Difference between revisions

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* Members:  David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
* Members:  David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
* Present:  
* Present: Huaiyu, Kimberly, Pascale, Seth, Suzi, Cynthia
* Regrets: David
* Regrets: David, Paul, Chris
 
==GOC meeting==
Only 15 people would attend in person, out of 30 responses:
https://docs.google.com/forms/d/14pCJd-tiYtVB0prij_EXc1F80Vqfvnuc0sBe_Gdolf4/edit#responses


== Ongoing work updates ==
== Ongoing work updates ==


===Google drive move===
https://github.com/orgs/geneontology/projects/90
* Status: will check and report next week


=== Adding SO terms as valid range for 'occurs in' annotation extension ===
=== Adding SO terms as valid range for 'occurs in' annotation extension ===
Line 16: Line 23:
=== [https://github.com/orgs/geneontology/projects/37 SynGO Updates] ===
=== [https://github.com/orgs/geneontology/projects/37 SynGO Updates] ===
* Actions
* Actions
** PO: Paul T
*Pascale to check annotations
** TL: Dustin
* If looks OK, request feedback from Frank
** Ask Frank at SynGO to check
** Do we have some SOP? sanity checks?
*** David to provide list of MGI checks
# Dustin will generate stats on the json to ttl conversion
# Ask Frank at SynGO to check models on dev, proposed date to get feedback by: June 23rd
# Make a syngo-specific pipeline to give them a report
# We will put the models on prod no matter what in 2 weeks (whether or not we are able to do this work)
# Produce a MOU (see below)


===[https://github.com/orgs/geneontology/projects/80 Model copy]===
===[https://github.com/orgs/geneontology/projects/80 Model copy]===
* Tasks required before moving to production
* Status
* Project meeting tomorrow on the Noctua work benches call, to know:
* Tremayne submitted PR; Seth updated noctua-dev
** schedule final round of testing - planned for this week
* Tomorrow morning - Kimberly will systematically test
** deploy on prod - end of this week, early next week?
** This is a large PR with changes to multiple workbenches besides model copy; will require some pretty thorough testing
* Workbenches at 10am PDT Thursday - aiming to make a call on moving to production by then - Tuesday, July 5th target date?


===[https://github.com/orgs/geneontology/projects/87 Automated Minerva updates]===
==Loading widgets into AmiGO==
* To do: review models that sometimes use regulates and other times directly regulates (23 models). Were curators trying to capture something specific that is now missing since we only use regulates?  
* [https://github.com/geneontology/amigo/issues/650 Preliminary work indicates that this is not too much work] 
* Note also that regulates does not have to be direct, according to the RO transitivity rules. We need to make sure this is clear and see how this impact annotation guidelines
What's next? How high of a priority is this?
* Should this be a new project ? what is the priority on this?
* Need to decide exactly what we want - needs have a proper project and propose some specs and deliverables (and PI, PO, TL)


===Review relation documentation===
==Distinction_between_'has_input'_and_'with/from'==
* We need a to generate a list of all relations currently used in Noctua and in P2GO
https://wiki.geneontology.org/Annotation_Extension_Relation:has_input#Distinction_between_'has_input'_and_'with/from'
* We need to clearly list which relations are slated for obsoletion/not allowed for GO/GO-CAM curation
* We need to document usage for all valid relations (like we have started for has input, has output and occurs in)


===MOU draft===
===MOU draft===

Latest revision as of 11:43, 29 June 2022

Attendees

  • Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
  • Present: Huaiyu, Kimberly, Pascale, Seth, Suzi, Cynthia
  • Regrets: David, Paul, Chris

GOC meeting

Only 15 people would attend in person, out of 30 responses: https://docs.google.com/forms/d/14pCJd-tiYtVB0prij_EXc1F80Vqfvnuc0sBe_Gdolf4/edit#responses

Ongoing work updates

Google drive move

https://github.com/orgs/geneontology/projects/90

  • Status: will check and report next week

Adding SO terms as valid range for 'occurs in' annotation extension

  • Curators would like to be able to specify chromosomal regions where MFs occur
  • Right now, SO terms are not a valid range for 'occurs in'
  • Any reason(s) not to add SO terms as a valid range?
    • A few years ago, there was discussion of MSO vs SO that might have had some bearing on this, but that discussion seems to have tailed off.

SynGO Updates

  • Actions
  • Pascale to check annotations
  • If looks OK, request feedback from Frank

Model copy

  • Status
  • Tremayne submitted PR; Seth updated noctua-dev
  • Tomorrow morning - Kimberly will systematically test
    • This is a large PR with changes to multiple workbenches besides model copy; will require some pretty thorough testing
  • Workbenches at 10am PDT Thursday - aiming to make a call on moving to production by then - Tuesday, July 5th target date?

Loading widgets into AmiGO

What's next? How high of a priority is this?

  • Need to decide exactly what we want - needs have a proper project and propose some specs and deliverables (and PI, PO, TL)

Distinction_between_'has_input'_and_'with/from'

https://wiki.geneontology.org/Annotation_Extension_Relation:has_input#Distinction_between_'has_input'_and_'with/from'

MOU draft

Can this be automated from the yaml?

  • CHRIS: YES!!!!

Potential priorities short list

https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.nntgv5th4cph