Difference between revisions of "Manager Call 2015-09-16"

From GO Wiki
Jump to: navigation, search
(Action Items from GOC)
(Action Items from GOC)
Line 39: Line 39:
 
*  Should GO have a protein complex branch and then if yes: At which level of granularity should it stop. if no How do we handle the subsequent migration out of GO. Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included.  
 
*  Should GO have a protein complex branch and then if yes: At which level of granularity should it stop. if no How do we handle the subsequent migration out of GO. Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included.  
  
Ontology <br>
+
'''Ontology''' <br>
 
* MF refactoring
 
* MF refactoring
 
** Make tickets for discussion of each requested new MF term as a place for agreeing logical definition.
 
** Make tickets for discussion of each requested new MF term as a place for agreeing logical definition.
Line 45: Line 45:
 
** David OS requests examples that demonstrate how crucial this is to Lego modeling (Suzi & PaulT)
 
** David OS requests examples that demonstrate how crucial this is to Lego modeling (Suzi & PaulT)
 
** GO PIs to determine how the required resources can be provided for required improvements to general MF axiomatisation.
 
** GO PIs to determine how the required resources can be provided for required improvements to general MF axiomatisation.
 +
** protein family binding terms will be removed from GO.  Annotations will be to ‘protein binding’ and the ‘with’ column (or, preferably, col. 16 using the has_input relation) will be required. 
 +
* Protein production
 +
** move protein production (and protein secretion?) to  regulation of production’. Tickets have already been generated (follow the link above)
 +
* External side of plasma membrane
 +
** Talk about the inconsistent annotations to external side of plasma membrane at an annotation call
 +
 +
'''gp2protein files, proteome sets'''<br>
 +
* GAF file renaming: Decision not documented
 +
* gp2protein file: MariaM's group already collaborates with MODS and produces a mapping file (gp2Acc file). That file can be used to populate gpi file. No need for groups to make gp2protein or gpi files moving forward.
 +
 +
'''Annotation Extension'''<br>
 +
* has_regulation_target  can all annotation with this relation be updated to regulates_transcription_of? Yes. We have to figure out who will do it.
 +
* Tony will send a list of annotations that have deprecated relations to all the groups.
 +
Action item: groups will take time to rehouse the annotations (we will not delete/drop those annotations)
 +
 +
'''Reactome Annotations'''<br>
 +
* contact a text miner to determine which papers (of the reactome set) correspond to which players (gene products) in the reactome annotations. Peter d’E will contact Jo McEntyre who may have already done this (cc-ing Claire).
 +
 +
'''Tracing the Annotation source''' <br>
 +
* We need to form a working group to figure this out.
 +
 +
'''Chromatin Binding''' <br>
 +
* In 2014 we decided to annotate ChiP experiments to chromatin (CC) and not chromatin binding (MF). We will continue with that practice. We should update documentation on this.

Revision as of 14:24, 15 September 2015

Agenda

The user wants to annotate their assembled transcripts using GO terms. We have always been down on blast2go yet offer no ready to use alternative on our website. (Chris)

  • Organise working group for working on chain of evidence: Tony S, Melanie, other volunteers? (MC)

Action Items from GOC

Github: Documentation on how to use github for curators, how to add curator initials when a new curator wants to make ontology changes (Paola has volunteered to bring this up in Ontology call)

GO survey:

  • Make sure we can track the survey respondent.
  • Use textpresso to get author emails from papers that cite or use GO.
  • Ask respondents if they want to participate in focus groups

User experience

  • training video for how to create a slim - build from existing training talks? Claire mentioned that EBI is making videos.
  • create a tool that would use a biology concept (angiogenesis) to select their slim terms (of the various slim flavors, this is the flavor made by gathering more granular terms related to and around the seeding term)
  • BD2K- Judy mentioned that there is some RFA to develop education resources/video tutorials. Here’s the link (http://grants.nih.gov/grants/guide/rfa-files/RFA-HG-14-009.html)

GOC Website

  • Ruth and Val to help Moni (+ perhaps Rama & Melanie) with composing the answer page for groups wishing to provide annotations. We’re only interested in manual annotations, not the output of Interpro2GO or other IEAs.
  • Improve Evidence code documentation so it isn’t as dispersed, but is all on one page. And more easily searchable.
  • Add a line item to renewal to support funding a dedicated user experience person to develop the web site.

Tools Registry:

  • Claire mentioned that UniProt has a checklist of questions to ask ourselves that will be very useful as we’re validating tools. Paola will get this list from Claire. It would be good expose tool validation rubric and data sets to public (could have the tangential effect of building the collection of gold-standard data sets for testing and comparing tools).

Noctua/Common curation environment

  • Documentation needed for defining annoton, model, etc.
  • Need to come with a consistent way to name models.
  • Work together with col-16 relations so they all align eventually
  • Organize Noctua workshop

Protein Complexes (IntAct)

  • new evidence code for capturing complexes, child of IPI (ECO:0000353)
  • new evidence code for reconstituted biological system consisting of components of more than one species
  • Should GO have a protein complex branch and then if yes: At which level of granularity should it stop. if no How do we handle the subsequent migration out of GO. Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included.

Ontology

  • MF refactoring
    • Make tickets for discussion of each requested new MF term as a place for agreeing logical definition.
    • Paul T proposes a two-day intensive effort to achieve this.
    • David OS requests examples that demonstrate how crucial this is to Lego modeling (Suzi & PaulT)
    • GO PIs to determine how the required resources can be provided for required improvements to general MF axiomatisation.
    • protein family binding terms will be removed from GO. Annotations will be to ‘protein binding’ and the ‘with’ column (or, preferably, col. 16 using the has_input relation) will be required.
  • Protein production
    • move protein production (and protein secretion?) to regulation of production’. Tickets have already been generated (follow the link above)
  • External side of plasma membrane
    • Talk about the inconsistent annotations to external side of plasma membrane at an annotation call

gp2protein files, proteome sets

  • GAF file renaming: Decision not documented
  • gp2protein file: MariaM's group already collaborates with MODS and produces a mapping file (gp2Acc file). That file can be used to populate gpi file. No need for groups to make gp2protein or gpi files moving forward.

Annotation Extension

  • has_regulation_target can all annotation with this relation be updated to regulates_transcription_of? Yes. We have to figure out who will do it.
  • Tony will send a list of annotations that have deprecated relations to all the groups.

Action item: groups will take time to rehouse the annotations (we will not delete/drop those annotations)

Reactome Annotations

  • contact a text miner to determine which papers (of the reactome set) correspond to which players (gene products) in the reactome annotations. Peter d’E will contact Jo McEntyre who may have already done this (cc-ing Claire).

Tracing the Annotation source

  • We need to form a working group to figure this out.

Chromatin Binding

  • In 2014 we decided to annotate ChiP experiments to chromatin (CC) and not chromatin binding (MF). We will continue with that practice. We should update documentation on this.