Annotation Conf. Call 2020-12-01: Difference between revisions
Jump to navigation
Jump to search
(Created page with "= Agenda and Minutes = == Infrastructure == === Planned site outage and system downtime for Berkeley site - UPDATED === * The current planned downtime period is now: from Fr...") |
|||
Line 1: | Line 1: | ||
= Agenda and Minutes = | = Agenda and Minutes = | ||
=== GAF 2.2 and GPAD/GPI 2.0 === | === GAF 2.2 and GPAD/GPI 2.0 === | ||
Line 27: | Line 15: | ||
== Meetings == | == Meetings == | ||
=== | === GO-CAM Jamboree === | ||
* Held from November 16th - 30th | |||
* ~30 people on and off throughout the week | |||
* Focused on generating process-centric models | |||
* Good discussions and feedback on process/workflow and tool | |||
* REMINDER: please send Paul and/or me your best estimate on how much time it took you to create a model, or begin to create a model with any additional thoughts on your individual experience | |||
==== Annotation Resources Discussion ==== | ==== Annotation Resources Discussion ==== |
Revision as of 10:36, 30 November 2020
Agenda and Minutes
GAF 2.2 and GPAD/GPI 2.0
- Discussion with groups about their current status with creating GAF 2.2 files
- Note that the specifications were updated to give guidelines on what relation to use with annotations to the root nodes:
- Biological Process -> involved_in
- Molecular Function -> enables
- Cellular Component -> is_active_in
- 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.
- Each annotation group should be applying their gp2term relations in accordance with the GAF 2.2 file specifications and their annotation practices, as well as the guidelines for root node annotation relations.
- Alex (UniProt - GOA) and Dustin (PAINT) are joining the call today to provide more information about the annotations from their groups/pipelines as these two annotations sources are a common upstream for many annotation groups.
- PAINT test files - ftp://ftp.pantherdb.org/downloads/paint/test/gaf2.2/
- Other outstanding issues/questions?
Meetings
GO-CAM Jamboree
- Held from November 16th - 30th
- ~30 people on and off throughout the week
- Focused on generating process-centric models
- Good discussions and feedback on process/workflow and tool
- REMINDER: please send Paul and/or me your best estimate on how much time it took you to create a model, or begin to create a model with any additional thoughts on your individual experience
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 want to discuss the comments and feedback, particularly in light of the upcoming GO grant renewal due in late January 2021.
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)
- Please add your name to the agenda and model topics to the spreadsheet if you'd like to attend
- Full agenda will be forthcoming
- November 17th annotation call will be cancelled due to the jamboree
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
- 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 interspecies interaction between organisms?
Attendance
- On call: