Manager Call 2015-10-07

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Revision as of 05:31, 7 October 2015 by MC (talk | contribs) (→‎Agenda)
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Agenda

  1. Action item from Ontology call (Melanie) - MF refactoring
    • GO PIs + Chris M. to determine whether resources can be provided for required improvements to general MF axiomatisation prior to refactoring. This mainly consists of pulling in mappings to ChEBI from Rhea - possibly from other resources #*via EC. Could be simple subclassing axioms if full logical definitions prove problematic. Without this work we will not be able to automate classification under new classes requested by Paul T.
  2. File names and content (Melanie)
    • There was a proposal to update the content of the files the GOA team is producing, specifically the current goa_"species" file would disappear, and the current goa_ref would be renamed as goa_"species". To minimize confusion for users, we thought it would be best for this change to happen in concert with Kimberly's proposed file renaming.
    • Generic proposal from Tony: <submitting group or database>[_<species>].(gaf|gpa)
    • Note that for groups that are submitting a file for more than one species, we could substitute 'species' for an appropriate grouping term, like 'nematode' or 'flatworm'.
    • We (Tony, Melanie, Kimberly) have looked through the current list of GAFs and have a proposed name for each; would need approval from all submitting groups. See Media:Suggested file name changes-1.xlsx
  3. Survey status
    • It's been revised according to all feedback; currently going through last round of sanity check
    • Ready to be sent out by October 15th. EBI will then start analysis around November 15th. This will ensure enough time to collect responses and have results in time for grant application.
  • Judy's things to fit somewhere
    • Complexes - working group who/when is regular call?, what complexes for GO what for PRO? still some challenges to philosophy for annotating to complexes. Who is working to move relevant complexes to PRO?
    • Group reports for Progress Reports - in addition to google doc, need team reports posted on the wiki.

Action Items from GOC (cont.)

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.

Other topics

  1. Follow-up: collaboration with Trey Ideker's group on autophagy (David)
    • This would be really good to show community engagement. Status update, publication plans, etc.
  2. Moving tickets from Jira (EBI instance, NOT Jira helpdesk) to GitHub (David)