Manager Call 2015-10-07

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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.
    • Minutes: Chris will bring MF refactoring up at ontology call tomorrow
  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
    • Minutes: Melanie to talk to Tony about only changing the GOA file names - if no issue go ahead, if issue organise call.
  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.
    • Kimberly - I did some preliminary Textpresso searches for 'Gene Ontology' on the PMC open access papers we currently have in the development version of Textpresso Central. I restricted searches to papers published over the past five years. There are lots of hits. Some of the corresponding authors are likely to already be on GO mailing lists (i.e., they're on our SAB or they are members or collaborators of the GOC); others I don't know. One of the nice things is that there is a range of organisms represented in the papers.
    • What will the logistics be for sending out the survey? If we wanted to try to collate some of the corresponding author emails from these papers, where would they then go for emailing?
    • Minutes: Plan to send out by October 15, analysis before grant renewal. Kim did basic search on GO, watch out for overlap with existing lists. Nice range of species, geo locations. Kim will send list of emails by Monday. As it is a targeted user group, we should say sthg like “as the author of paper citing GO, we selected you to answer this survey”. Rama will send example.
  • 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?
    • Minutes: Complexes working group. Darren/Harold part of working group which meets every Thursday.
    • Group reports for Progress Reports - in addition to google doc, need team reports posted on the wiki.
    • Minutes: Group progress reports: reminder to all to update the wiki. Put placeholders for stats/metrics etc which will be only complete in December.
    • From Rama: there are two working groups on Complexes: first one to come up with guidelines on how to annotate complexes as objects (Sandra presented about this at the GOC meeting, http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects) and the second one is an ontology group to figure out what complexes should be in GO and what should be in PRO/IntAct. This latter working group has met twice so far (

https://drive.google.com/folderview?id=0B0BzQEtrvNZlfnUzWXJJaG9oREpYN2JteG84RlhBQldUdkRZekFxUUgyUFNnaWNLYlZtcGs&usp=sharing)

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.
    • Minutes see above
  • Protein production
    • move protein production (and protein secretion?) to regulation of production’. Tickets have already been generated (follow the link above)
    • Minutes (discussed in previous call) retain protein production terms (mark as “do not annotate”), add missing regulation of production terms which will be children of them. Annotations will be moved to a regulation of production term or removed.
  • External side of plasma membrane
    • Talk about the inconsistent annotations to external side of plasma membrane at an annotation call
    • Minutes Rama will put on agenda for next annotation call. She and Pascale are working on this.

gp2protein files, proteome sets

  • GAF file renaming: Decision not documented
    • Minutes see above
  • 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.
    • Minutes UniProt (Tony) working on this. Chris will produce documentation on what his pipeline is and where to go for the various files. Engage dialog with Maria's group to understand dependencies.


Rama is leaving :( - but she will remain in touch. She will be on organising committee for Biocuration.

Below not discussed:

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)