Annotation Conf. Call 2020-09-15: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(Created page with "= Agenda and Minutes = == October Consortium Meeting == * Virtual meeting * October 6th - 8th (SAB on October 9th) * [https://www.eventbrite.com/e/goc-meeting-fall-2020-regis...")
 
 
(20 intermediate revisions by one other user not shown)
Line 6: Line 6:
* [https://www.eventbrite.com/e/goc-meeting-fall-2020-registration-119369301795 Registration]
* [https://www.eventbrite.com/e/goc-meeting-fall-2020-registration-119369301795 Registration]
* [https://docs.google.com/document/d/17Jo2qdNfbF58rIYI2K1dkrEWk4-JqT-2aVAb1_vgAHI Draft agenda]
* [https://docs.google.com/document/d/17Jo2qdNfbF58rIYI2K1dkrEWk4-JqT-2aVAb1_vgAHI Draft agenda]
* We would like to have annotation groups give ~5' flash talks about what their groups is doing wrt GO curation (e.g. annotation, display, tools, outreach).  If you need more time, let us know.
* Please indicate if there are other topics you'd like to discuss and ideas for break-out groups
* Please indicate if there are other topics you'd like to discuss and ideas for break-out groups


== GAF 2.2 and GPAD/GPI 2.0 ==
== GAF 2.2 and GPAD/GPI 2.0 ==
* Check in to see if there is any additional feedback from groups
* PLEASE review the specs with your developers and provide feedback
** We will be asking groups to officially sign off on the specs on a github ticket
*** Ticket for signing off on specs:  https://github.com/geneontology/go-annotation/issues/2864
* The plan is still to switch to the new file formats by the end of 2020
=== GAF 2.2 ===
=== GAF 2.2 ===
* Naming: we won't be changing anything about naming the GAF files, but will need to communicate to users what the change is, i.e. the qualifier field is now mandatory and allowed values have increased
* [https://github.com/geneontology/go-annotation/issues/2917 github ticket]
* There will be a check for the actual relation label used and non-compliant annotations will be flagged/removed - need to confirm what the action will be
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications] 
* https://github.com/geneontology/go-annotation/issues/2917
* '''Summary:'''
** The qualifier field(Column 4) will be mandatory; accordingly, there are additional values for that field
** Also, required header fields include:
*** file format
*** generated-by
*** date-generated
* There will be a pipeline check for a value in the qualifier field
** Proposal: Non-compliant annotations (i.e. those with no value) will be assigned default relations as follows:
*** BP: acts_upstream_of_or_within
*** MF: enables
*** CC: located_in (for non-protein-containing complex terms)
*** CC: part_of (for protein-containing complex terms)
 
=== GPAD/GPI 2.0 ===
=== GPAD/GPI 2.0 ===
* https://github.com/geneontology/go-annotation/issues/2864
* [https://github.com/geneontology/go-annotation/issues/2864 github ticket]
* https://github.com/geneontology/go-annotation/issues/3031
* [https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md Specifications]
* Questions:
** What to do with curators that don't have an orcid?
 
=== Contributors/Users ===
* GPAD 2.0 has an annotation property 'contributor-id' in which we'd ideally like to capture curators' orcids
* orcids are captured as metadata (specifically the uri tag) in the [https://github.com/geneontology/go-site/blob/master/metadata/users.yaml users.yaml] file
* BUT, there are cases where a curator does not have an orcid and/or is no longer with the annotation group
* What to do?
** If a curator is still active within your group, please have them get an orcid and we can add it to users.yaml
** If a curator is no longer with your group, they don't have to get an orcid; we can use their GOC:xyz xref as their contributor-id
** Please DON'T remove anyone from the users.yaml file, though; this file allows us to keep some history of who was involved in GO and with what group in case we ever need to trace something down
** Organization, although often populated in the users.yaml file, is more of a legacy field.  Currently, we want curators to be associated with groups, designated with URLs.
** There is a tag, previous-groups, in the [https://github.com/geneontology/go-site/blob/master/metadata/users.schema.yaml users.yaml schema]
*** Will need to investigate further; sample PR this morning gave an error message
** 'Collective' users - double-check users.yaml entries for those
* users.yaml cleanup is fine - check in with Kimberly/Pascale/Seth if you have questions
 
=== Headers ===
* Have had some feedback requesting more specific information and examples about populating the file headers, e.g. optional ontology version fields
* Will add that to the documentation


=== Timing ===
* Wrt the timing and synchronicity of the GAF 2.2 and GPAD/GPI 2.0 changes, we will try to allow a period between the GOC release and when the new files are ingested so we can address any issues before the next release
* Wrt the timing and synchronicity of the GAF 2.2 and GPAD/GPI 2.0 changes, we will try to allow a period between the GOC release and when the new files are ingested so we can address any issues before the next release
* Groups will have to account for some possible asynchronicity in managing their local imports, but the file format should be in the header of each file so the expected format can be dealt with there
* Groups will have to account for some possible asynchronicity in managing their local imports, but the file format should be in the header of each file so the expected format can be dealt with there
* Berkeley will have parsing scripts available to share and can otherwise assist in helping groups with the transition
* Berkeley will have parsing scripts available to share and can otherwise assist in helping groups with the transition
== October Consortium Meeting ==
* Virtual meeting
* October 6th - 8th (SAB on October 9th)
* [https://docs.google.com/document/d/17Jo2qdNfbF58rIYI2K1dkrEWk4-JqT-2aVAb1_vgAHI Draft agenda]
* Please indicate if there are other topics you'd like to discuss and ideas for break-out groups


== GO-CAM Jamboree ==
== GO-CAM Jamboree ==
* We would like to hold a week-long GO-CAM jamboree this fall (exact dates TBD)
* Dates: Monday, November 16th - Friday, November 20th
* The purpose is to have focused discussions on GO-CAM modeling and to assess time and resources needed to create process-centric GO-CAM models
* Goal: focused discussions on GO-CAM modeling of specific topics to train more curators on making GO-CAM models and assess the time and resources needed to create process-centric GO-CAM models
* Format will be similar to transcription workshop and May GOC meeting, i.e. presentations, annotation, discussion, breakout rooms
* Format will be similar to transcription workshop and May GOC meeting, i.e. 1/2-day sessions of presentations, annotation, discussion, breakout rooms
* Ideally, we'd like to have a representative from each group (although it wouldn't have to be the same person every day)
* Ideally, we'd like to have a representative from each group (although it wouldn't have to be the same person every day)
* We want to work on processes that are as broadly relevant as possible, but also correspond to manageable chunks of biology. For example:
* [https://doodle.com/poll/z9s47yqwwrpnqnyv Doodle poll]  
** Signaling pathway
* [https://docs.google.com/spreadsheets/d/1RPyKWCsJ7SVnhBYBXJ7rIZ6H2HTtQK4rRLFMWjH9P_E Google spreadsheet] for suggesting biological processes to model
** Metabolic pathway
* Please fill out Doodle poll and spreadsheet if you'd like to attend
** Regulation of transcription
* Agenda will be forthcoming
** Small molecule activator/inhibitors that affect MFs
 
* [https://doodle.com/poll/z9s47yqwwrpnqnyv Doodle poll] for selecting a good week and a [https://docs.google.com/spreadsheets/d/1RPyKWCsJ7SVnhBYBXJ7rIZ6H2HTtQK4rRLFMWjH9P_E Google spreadsheet] for suggesting biological processes to model
== GO-CAM Modeling Calls ==
* Please fill out both by Friday, September 4th
* Reserve annotation call slot on the 2nd and 4th Tuesdays of each month for GO-CAM "office hours"
* Objective: answer specific questions that curators have about GO-CAM modeling
* Submit questions or tickets to [https://docs.google.com/document/d/1_ZIasvb0hhmJ1teEQ-wegvPob5T74-JeV4UGcZn_evE the agenda] by the Friday before the meeting, so we can make best/efficient use of everyone's time on the call


= Attendance =
= Attendance =
*On call:  
*On call: David, Dustin, Edith, Giulia, Harold, Judy, Karen, Kimberly, Li, Mahima, Malcolm, Mary, Midori, Pascale, Patrick, Penelope, Rob, Ruth, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi, Val


[[Category:Annotation Working Group]]
[[Category:Annotation Working Group]]

Latest revision as of 11:56, 15 September 2020

Agenda and Minutes

October Consortium Meeting

  • Virtual meeting
  • October 6th - 8th (SAB on October 9th)
  • Registration
  • Draft agenda
  • We would like to have annotation groups give ~5' flash talks about what their groups is doing wrt GO curation (e.g. annotation, display, tools, outreach). If you need more time, let us know.
  • Please indicate if there are other topics you'd like to discuss and ideas for break-out groups

GAF 2.2 and GPAD/GPI 2.0

GAF 2.2

  • github ticket
  • Specifications
  • Summary:
    • The qualifier field(Column 4) will be mandatory; accordingly, there are additional values for that field
    • Also, required header fields include:
      • file format
      • generated-by
      • date-generated
  • There will be a pipeline check for a value in the qualifier field
    • Proposal: Non-compliant annotations (i.e. those with no value) will be assigned default relations as follows:
      • BP: acts_upstream_of_or_within
      • MF: enables
      • CC: located_in (for non-protein-containing complex terms)
      • CC: part_of (for protein-containing complex terms)

GPAD/GPI 2.0

Contributors/Users

  • GPAD 2.0 has an annotation property 'contributor-id' in which we'd ideally like to capture curators' orcids
  • orcids are captured as metadata (specifically the uri tag) in the users.yaml file
  • BUT, there are cases where a curator does not have an orcid and/or is no longer with the annotation group
  • What to do?
    • If a curator is still active within your group, please have them get an orcid and we can add it to users.yaml
    • If a curator is no longer with your group, they don't have to get an orcid; we can use their GOC:xyz xref as their contributor-id
    • Please DON'T remove anyone from the users.yaml file, though; this file allows us to keep some history of who was involved in GO and with what group in case we ever need to trace something down
    • Organization, although often populated in the users.yaml file, is more of a legacy field. Currently, we want curators to be associated with groups, designated with URLs.
    • There is a tag, previous-groups, in the users.yaml schema
      • Will need to investigate further; sample PR this morning gave an error message
    • 'Collective' users - double-check users.yaml entries for those
  • users.yaml cleanup is fine - check in with Kimberly/Pascale/Seth if you have questions

Headers

  • Have had some feedback requesting more specific information and examples about populating the file headers, e.g. optional ontology version fields
  • Will add that to the documentation

Timing

  • Wrt the timing and synchronicity of the GAF 2.2 and GPAD/GPI 2.0 changes, we will try to allow a period between the GOC release and when the new files are ingested so we can address any issues before the next release
  • Groups will have to account for some possible asynchronicity in managing their local imports, but the file format should be in the header of each file so the expected format can be dealt with there
  • Berkeley will have parsing scripts available to share and can otherwise assist in helping groups with the transition

GO-CAM Jamboree

  • Dates: Monday, November 16th - Friday, November 20th
  • Goal: focused discussions on GO-CAM modeling of specific topics to train more curators on making GO-CAM models and assess the time and resources needed to create process-centric GO-CAM models
  • Format will be similar to transcription workshop and May GOC meeting, i.e. 1/2-day sessions of presentations, annotation, discussion, breakout rooms
  • Ideally, we'd like to have a representative from each group (although it wouldn't have to be the same person every day)
  • Doodle poll
  • Google spreadsheet for suggesting biological processes to model
  • Please fill out Doodle poll and spreadsheet if you'd like to attend
  • Agenda will be forthcoming

GO-CAM Modeling Calls

  • Reserve annotation call slot on the 2nd and 4th Tuesdays of each month for GO-CAM "office hours"
  • Objective: answer specific questions that curators have about GO-CAM modeling
  • Submit questions or tickets to the agenda by the Friday before the meeting, so we can make best/efficient use of everyone's time on the call

Attendance

  • On call: David, Dustin, Edith, Giulia, Harold, Judy, Karen, Kimberly, Li, Mahima, Malcolm, Mary, Midori, Pascale, Patrick, Penelope, Rob, Ruth, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi, Val