Manager Call 2015-09-16

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Agenda

  1. Start of preparation of 2015 Progress Report - google doc and wiki PR reports (Judy)
    Minutes
    • Judy: A google doc has been created, and the address was sent out to everyone. The due date is Jan. 1st, but probably get it ready by mid-December.
    • Kimberly asked about the grant application update.
    • Judy: The deadline is Jan. 25th, but it could change. Will get update. There will be 4 separate aims. Different sections will go to different reviewers, so there will be repeated sections, such as budget, etc. Will need input from all managers.
    • It will be submitted to NHGRI.
    • Paul T. SAB members are still working on the report. Will wait for their feedback.
    • Chris asked whether we should prepare to publish papers.
    • July: Maybe some usage and metrics paper.
    • Paul T.: GO is broadly used, probably not needed to publish any paper about utilities. It will be help to get the word out on LEGO, etc.
  2. User email- http://jira.geneontology.org/browse/GO-949
    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)
    Minutes
    • Paul T.: This probably should be handled by InterproScan.
  3. Organise working group for working on chain of evidence: Tony S, Melanie, other volunteers? (MC)
    Minutees
    • Chris would like to join.
    • Rama and David H would like to also, but both of them have busy schedule, so not sure how much time they can commit.

Action Items from GOC

Github: 1) Documentation on how to use github for curators, 2) how to add curator initials when a new curator wants to make ontology changes (Paola has volunteered to bring this up in Ontology call). UPDATE ON 2): discussed here: http://jira.geneontology.org/browse/GO-952. Last question remaining: Chris, can editors stop editing the GO.curator_dbxref file then?

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
  • Paola will incorporate feedback from SGD and send round a revised version.
    Minutes
    • Target date: Paul T.: It would be nice to include the results in the grant proposal.
    • Paola: Then the survey should be circulated in October, so there will be enough time to analyze the results for the proposal.

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). UPDATE - discussed at last week's editors call, see http://wiki.geneontology.org/index.php/Ontology_meeting_2015-09-10#User_experience_.28UX.29
  • 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)
    Minutes
    • Chris: It will be helpful to get user feedback about user-created GO slim, and whether it is repeatable or ad-hoc.

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. (UPDATE: UniProt's checklist is about validating other resources (rather than just tools) in order to cross-reference them. Paola has list now.) 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). (UPDATE: We will prepare a list of criteria based on UniProt's suggestions and on ELIXIR's requirements for inclusion in their data registry, and will then discuss those on a manager call.)
    Minutes
    • Paola: It would be important for us to provide a checklist, and validate the resources.
    • Judy: It is a question about priority. At this point, this can be on the to-do list, but probably not in high priority.
    • Paola: Maybe it can be coupled with other work, such as enrichment tools.
    • Paul T.: Agree with Judy about the prioritization. We have our own enrichment tools, and probably should encourage users to use them.
    • Rama: Maybe create a FAQ to help users.

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
    Minutes
    • Melanie: There are relationships in Noctua that are not in col-16. Should there be a separate relationship file, or they should be incorporated into col-16?
    • Paul T.: We should discuss about this. We should make sure that the semantics are correctly captured. For example, directly activate in LEGO means the function of a gene product on another function. So probably should not put everything into col-16. Will need to discuss and see how to better store it.
    • There was a question about whether to organize Noctua workshop before or after the grant renewal submission.
    • Paul T.: It should be helpful to have do it before, but will see whether it is technically feasible. Will discuss it at the next LEGO call.
    • Judy: We have fund to organize it, probably in Feb 2016, which will be after the grant submission.
    • Rama: We can do two phases, just like those for PAINT. The first will be a small focus group mainly working on documentations, and tool test and feedback.
    • Paul T.: The tool is getting together with most of the features. It needs to be at the production level for the community to use it.

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 + Birgit (IntAct), Paola + David OS + Helen + Melanie + Chris (GO), Peter (Reactome) should be included.
    Minutes
    • Judy: Will need to form a working group to address this question. Probably should involve Harold also.
    • David H>: This is sucking a lot of ontology editors' resources. The faster this can be resolved, the better.
    • Chris agrees with David.


The call adjourned at this point. The remaining items will be discussed at the next call.


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.