Annotation Conf. Call 2020-10-20: Difference between revisions

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= Agenda and Minutes =
= Agenda and Minutes =


== Planned site outage and system downtime for Berkeley site ==
== Infrastructure ==
* Friday the 23rd, at about 6pm PDT, to Saturday the 24th, at about 6pm PDT. These times are approximate.
 
=== Planned site outage and system downtime for Berkeley site - UPDATED ===
* The current planned downtime period is now from Friday the 30th, at about 6pm PDT, to Saturday the 31st, at about 6pm PDT. These times are approximate.
* Most services will continue during this downtime, but the following will be unavailable:
* Most services will continue during this downtime, but the following will be unavailable:
** Noctua (production and development)
** Noctua (production and development)
Line 11: Line 13:
**http://status.geneontology.org
**http://status.geneontology.org


== Tracker summary emails ==
=== Tracker summary emails ===
* https://github.com/geneontology/go-site/issues/1530
* https://github.com/geneontology/go-site/issues/1530
* Software team is working on this
* Software team is working on this
* ''Tracker summary emails for the go-annotation and go-ontology trackers will be sent to the go-consortium mailing list''
* ''Software group will soon start sending them out again - see ticket for sample email format''


== October Consortium Meeting - Follow-Up ==
=== GAF 2.2 and GPAD/GPI 2.0 ===
* Do any groups need help with this?
* Much discussion about this.  Key points below:
#''Question about the content of a gpi file from IntAct Molecular Interaction Database''
''IntAact curates physical interactions between gene products and chemicals.  However, in Column 5 of the gpi file specifications, there is no ontology 'type' listed for chemicals, as GO doesn't annotate chemicals and the purpose of the gpi file is to capture annotatable objects.''
# ''Question about achieving synchronicity amongst groups wrt applying gp2term relations in a GAF 2.2 file.  Note that this is distinct from harmonizing on using the same relations for gp2term for the same, or similar, annotations amongst different curation groups.''
  ''Proposal: dedicate the November 3rd annotation call to discussion solely to the timing of different groups wrt when they will be producing a GAF 2.2 or GPAD 2.0 that will allow all annotation groups to get gp2term relations from the annotation source.''


== Meetings ==


== GAF 2.2 and GPAD/GPI 2.0 ==
=== October Consortium Meeting - Follow-Up ===
=== GAF 2.2 ===
* [https://github.com/geneontology/go-annotation/issues/2917 github ticket]
* [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] 
* '''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 ===
=== Meeting Survey ===
* [https://github.com/geneontology/go-annotation/issues/2864 github ticket]
* Opportunity to give feedback on the meeting - please respond to [https://forms.gle/ZW3G1f4XQPKPofQt8 the survey] by end-of-day Tuesday, October 20th ('''''that's today''''')
* [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 ===
==== Annotation Resources Discussion ====
* GPAD 2.0 has an annotation property 'contributor-id' in which we'd ideally like to capture curators' orcids
* ''We didn't have much time to discuss this at the Baltimore consortium meeting, so would like to follow-up on this topic on future calls.
* 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
* ''Please review Judy Blakes' [https://docs.google.com/presentation/d/1CYbE8omvsGWcqSAjnlQdziq5NNrOqlRqRDSoEReQXxQ slides] on goals and need for annotation from the GOC virtual meeting and add your thoughts to the corresponding [https://docs.google.com/document/d/1UG833ux-2_o8_8nDevjH7ycffa01ys6anpH5eA6K71M Google doc].
* BUT, there are cases where a curator does not have an orcid and/or is no longer with the annotation group
* ''We will discuss the comments and feedback on a future annotation call, particularly in light of the upcoming GO grant renewal due in late January 2021.
* 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 ===
=== Action Items and Working Groups ===
* Have had some feedback requesting more specific information and examples about populating the file headers, e.g. optional ontology version fields
* Review with managers, but it would still be good to gauge interest
* Will add that to the documentation
* [https://docs.google.com/document/d/17Jo2qdNfbF58rIYI2K1dkrEWk4-JqT-2aVAb1_vgAHI/edit#heading=h.eg0ji6ooxn7f ACTION ITEMS/Future breakouts/projects]


=== Timing ===
=== GO-CAM Jamboree ===
* 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
* 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
* 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
Line 74: Line 53:
* Agenda will be forthcoming
* Agenda will be forthcoming


== GO-CAM Modeling Calls ==
=== GO-CAM Modeling Calls ===
* Reserve annotation call slot on the 2nd and 4th Tuesdays of each month for GO-CAM "office hours"
* 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
* 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
* 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
== Annotation Issues ==
=== Capturing interacting taxon ===
** [https://github.com/geneontology/go-shapes/issues/237 How to capture in GO-CAM (and the MOD imports)?]
** [https://github.com/geneontology/go-ontology/issues/19693 New ontology terms and the scope of GO]
* Currently, a second taxa is just captured in a separate field in the GAF (Taxon, pipe separated when more than one) or GPAD (Interacting taxon) with no relation.
* Proposal: capture dual taxon information using the annotation extension field and a 'has input' relation
* Questions:
** Does everyone who uses the existing Taxon or Interacting taxon fields for dual taxon annotations also use annotation extensions?
** Would this apply to all children of [http://amigo.geneontology.org/amigo/term/GO:0044419 interspecies interaction between organisms]?


= Attendance =
= Attendance =
*On call:  
*On call: Antonia, Birgit, Chris M, Colin, David, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Malcolm, Mary K, Michele, Midori, Noemi, Pascale, Patrick M, Penelope, Petra, Rob N, Robert D, Sabrina, Stacia, Seth, Suzi, Val


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

Latest revision as of 12:18, 22 October 2020

Agenda and Minutes

Infrastructure

Planned site outage and system downtime for Berkeley site - UPDATED

  • The current planned downtime period is now from Friday the 30th, at about 6pm PDT, to Saturday the 31st, at about 6pm PDT. These times are approximate.
  • Most services will continue during this downtime, but the following will be unavailable:
    • Noctua (production and development)
    • GO-CAM site (latest models component)
    • RDF endpoint
  • Noctua curators will need to save any work they wish to be preserved before the scheduled downtime.
  • The current status of all of the main GO systems can be found at:

Tracker summary emails

  • https://github.com/geneontology/go-site/issues/1530
  • Software team is working on this
  • Tracker summary emails for the go-annotation and go-ontology trackers will be sent to the go-consortium mailing list
  • Software group will soon start sending them out again - see ticket for sample email format

GAF 2.2 and GPAD/GPI 2.0

  • Do any groups need help with this?
  • Much discussion about this. Key points below:
  1. Question about the content of a gpi file from IntAct Molecular Interaction Database
IntAact curates physical interactions between gene products and chemicals.  However, in Column 5 of the gpi file specifications, there is no ontology 'type' listed for chemicals, as GO doesn't annotate chemicals and the purpose of the gpi file is to capture annotatable objects.
  1. Question about achieving synchronicity amongst groups wrt applying gp2term relations in a GAF 2.2 file. Note that this is distinct from harmonizing on using the same relations for gp2term for the same, or similar, annotations amongst different curation groups.
 Proposal: dedicate the November 3rd annotation call to discussion solely to the timing of different groups wrt when they will be producing a GAF 2.2 or GPAD 2.0 that will allow all annotation groups to get gp2term relations from the annotation source.

Meetings

October Consortium Meeting - Follow-Up

Meeting Survey

  • Opportunity to give feedback on the meeting - please respond to the survey by end-of-day Tuesday, October 20th (that's today)

Annotation Resources Discussion

  • We didn't have much time to discuss this at the Baltimore consortium meeting, so would like to follow-up on this topic on future calls.
  • Please review Judy Blakes' slides on goals and need for annotation from the GOC virtual meeting and add your thoughts to the corresponding Google doc.
  • We will discuss the comments and feedback on a future annotation call, particularly in light of the upcoming GO grant renewal due in late January 2021.

Action Items and Working Groups

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

Annotation Issues

Capturing interacting taxon

Attendance

  • On call: Antonia, Birgit, Chris M, Colin, David, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Malcolm, Mary K, Michele, Midori, Noemi, Pascale, Patrick M, Penelope, Petra, Rob N, Robert D, Sabrina, Stacia, Seth, Suzi, Val