Annotation Conf. Call 2020-10-20
From GO Wiki
- 1 Agenda and Minutes
- 1.1 Infrastructure
- 1.2 Meetings
- 1.3 Annotation Issues
- 2 Attendance
Agenda and Minutes
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
- 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:
- 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.
October Consortium Meeting - Follow-Up
- 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
- Review with managers, but it would still be good to gauge interest
- ACTION ITEMS/Future breakouts/projects
- 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
Capturing interacting taxon
- 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
- 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 interspecies interaction between organisms?
- 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