Managers 2June06

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GO Managers call 2 June 2006

Minutes by Jennifer Clark.

Present: Michael Ashburner, Judy Blake, Rex Chisholm, Jennifer Clark, Midori Harris, David Hill, Eurie Hong, Suzi Lewis, Jane Lomax.

Absent: Mike Cherry, Chris Mungall.

Contents

  1. Action items from last time.
  2. Agenda for this meeting.
  3. Action items from this meeting
  4. Call content.
  5. Questions and answers with rationale.

    Includes all action items as they occurred.

  1. Action items from last time
    1. Newly merged ontology development group report - done
    2. Advocacy group to change to include Jane Lomax as joint leader - done
    3. Management group mailing list creation - done
    4. Release of newsletter - done
    5. Show outreach database to Chris - done
    6. Mike to begin planning IEA standards meeting - little progress, but September date planned
    7. Annotation consistency report - done
  2. Agenda
    1. Status of GO wiki and who will do what.
    2. Status of St Croix minutes, and posting on GO.
    3. Discussion of CASP7 proposal - should GO be involved ?
    4. Proposed Web Group - should this be devolved to Jane & Eurie's Group ?
    5. Next GO meeting. Suggestion is January 2007 in Cambridge or Hinxton. Could GOA group take responsibility ?
    6. Reference Genomes, Is it a problem for the "gold standard" metric to limit annotations to just those that have a PubMed ID.
    7. Reference genomes and ISS checks.
    8. A proposal for ensuring all emails to gohelp are being answered (Jane/Eurie).
    9. Users meeting (Seattle, Sept. '06) update
    10. Revised Ontology Working Group Proposal
    11. E. coli Collaboration
    12. Next Meeting
  3. Action Items from this meeting.
    1. Status of GO wiki and who will do what.
    2. Action items (for Mike, Chris, Eurie and possibly Amelia):

      1. Add calendar.
      2. Make it possible to edit navigation features.
      3. Add place for people to post random jottings and ideas.
      4. Place for conference call agendas and minutes. (Like CBio wiki.)
      5. Add place to list conferences that people have been to and info about what they have presented.
      6. Move wiki to permanent location. (URL will change.)
      7. Ask Amelia to do inital design with Eurie.
    3. Status of St Croix minutes, and posting on GO.
    4. Action items:

      1. Judy to send text to complete minutes.
      2. Minutes to be sent to Amelia to be put on website. (Kimberley)
    5. Discussion of CASP7 proposal
    6. Action:

      1. GO should be involved.
      2. We should try to have some control over which genes are annotated. Preferably some that are prioritised by the reference genomes group.
      3. Rex + Evelyn + GO-Top to take the discussion forward.
    7. Proposed Web Group
    8. Action:

      1. All decision making on this devolved to Advocacy group. Jane and Eurie to take forward.
    9. Next GO Consortium meeting.
      1. Who?
      2. Action:

          i)GO-top will approach possible organisers in order:
          1. GOA
          2. GOA + Val Wood
          3. GOA + GO Editorial Office
          4. GO Editorial Office.
      3. When?
      4. Action: Meeting set for 7th-10th January.

      5. Where?
      6. Action: Ask if we can get Lucy Cavendish College.

    10. Do we need a PubMed id for a GO annotation?
    11. Action:

      Implement this policy:

      1. We cannot restrict just to PubMed ids.
      2. If data from a large scale experiment is taken into a database like MGI or FlyBase and manually curated then we would accept that as equivalent to peer review and publication (publically accessible id to be provided).
    12. Reference genomes and ISS checks.
    13. Action:

      1. Implement policy that if the source annotation for an ISS is found to be wrong then the ISS must be rechecked.
      2. David to write a paragraph about what he writes in the structured notes field when he does an ISS annotation and about how he sends annotations to GOA via the ftp site.
      3. David + Rex to make a proposal to present before the annotation camp on how we can improve the system of feeding annotations through to GOA.
      4. Mike and Chris to make a script to check ISS annotations to see if corrections have been made to the annotation from which ISS was inferred.
      5. Reference Genome group to work out standards for ISS.
    14. Ensuring all emails to gohelp are being answered
    15. Action:

      1. People volunteer to be on rota, one week each. Put calendar on wiki. (Advocacy group to co-ordinate.)
    16. Users meeting (Seattle, Sept. '06) update
    17. Action:

      1. Midori will open abstract submission (with technical help from Amelia and Mike), and will review and select abstracts.
      2. Midori is to document how she sets up the user meeting so that others can do it next year.
      3. Try to avoid having gaps between adjacent meetings and overlaps with other meetings in future.
      4. Midori to contact Judy with MGED9 contact info.
    18. Revised proposal for Ontology Working Group.
    19. Action:

      1. For mailing list issues we have decided for now just to have groups form and unform as required with conclusios to be sent to the mailing list or put on sourceforge.
      2. Jen to set up voice recording on laptop for neurogenesis meeting.
    20. New E. coli Collaboration
    21. Action:

      1. Rex to send more details of new E. coli group (name spellings, database name and e-mail address) to Jennifer to go in the anntotation-outreach records.
    22. Next Call
    23. Action:

      1. Next meeting to be 21st June, 8 am Pacific, 11 noon Eastern, 10 am Central, 4 pm UK.
      2. Jennifer to compile agenda.


  4. Main questions, answers and action items.
    1. Status of GO wiki and who will do what.
    2. Wiki: http://www-dev.godatabase.org/wiki/

      Q/What to do?

      See action items below.

      Q/Who to do it?

      Action items for Mike, Chris, Eurie and possibly Amelia. (Below)

      Q/External or internal

      Wiki is a means to communicate internally in consortium so will be internal only. Editing will require login and password.

      Action items:

      1. Add calendar.
      2. Make it possible to edit navigation features.
      3. Add place for people to post random jottings and ideas.
      4. Place for conference call agendas and minutes. (Like CBio wiki.)
      5. Add place to list conferences that people have been to and info about what they have presented.
      6. Move wiki to permanent location. (URL will change.)
      7. Ask Amelia to do inital design with Eurie.
    3. Status of St Croix minutes, and posting on GO.
    4. The minutes are nearly ready to go. Judy has a bit of text to add but will do that.

      Action items:

      1. Judy to send text to complete minutes (Judy)
      2. Minutes to be sent to Amelia to be put on website. (Kimberley)
    5. Discussion of CASP7 proposal
    6. CASP7: "7th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction Asilomar Conference Center, Pacific Grove, CA November 26-30, 2006"

      Q/ Should GO be involved ?

      Yes.

      Reasons for:

      1. They have a section for functional annotation under Alfonso Valencia.
      2. Relates to the function annotation, IEA method discussion.
      3. They have different computational methods.
      4. We can leverage some of the CASP organisation.

      Reasons against:

      1. They want manual annotation done for 100 genes and may want to choose the genes. This could be very time consuming and take us away from our priority genes.

      Conclusion:

      1. We should try to have some control over which genes are annotated. Preferably some that are prioritised by the reference genomes group.

      Action items:

      1. Rex + Evelyn + GO-Top to take the discussion forward.
    7. Proposed Web Group
    8. Q/ Should we have a web presence working group?

      Q/ Should web presence be devolved to the Advocacy Group ?

      Conclusion: All decisions relating to this have been devolved to the Advocacy group.

      Action: Jane and Eurie to take forward.


    9. Next GO meeting.
    10. Q/Where?

      Action: Ask if we can get lucy cavendish.

      Q/When?

      January 2007 preferred

      Avoid:

      PAG 13-17 January
      PSB 3-7 January
      University term time (16th onwards).

      Meeting should be 3 days.

      Action: Meeting set for 7th-10th January.

      Q/Who to organize?

      Ask people in this order:

      1. GOA
      2. GOA + Val Wood
      3. GOA + GO Editorial Office
      4. GO Editorial Office.

      ACTION: GO-top will approach Evelyn.


    11. Reference Genomes Working group question:
    12. Q/Is it a problem for the "gold standard" annotation metric to limit annotations to just those that have a PubMed ID?

      Some discussion leads to a clarification of the question:

      Q/ If a large scale experiment is carried out and produces a huge amount of data e.g. as images showing gene products localisation, can this data been used for annotation even though it is not being published?

      Gold standard annotation criteria:

      1. The reference id has to point to an experiment. This need not necessarily be via a literature publication.
      2. We greatly prefer peer reviewed experimental data.
        1. Need details of how the experiment was done.
        2. Need an expert to check experiment was meaningful.

        3)The data must be permanently stored so it doesn't disappear.

      One solution:
      If the database e.g. MGI takes the data and curates it then it has been manual checked and GO would be happy with it.

      Problem:
      MGI does not have the resources to take the data and manually curate it immediately.

      Solution:
      MGI could take the data and archive it for curation later.

      Conclusion:

      1. We cannot restrict just to PubMed ids.
      2. If data from a large scale experiment is taken into a database like MGI and manually curated then we would accept that as equivalent to publication.
    13. Reference genomes and ISS checks.
    14. Problem: If an annotation has been made manually with an experimental evidence code then another annotation can be inferred by ISS. However, if the initial annotation is then found to contain an error then the ISS annotation is also wrong.

      Q/ In this situation should we make a requirement and a system for checking of ISS annotation?

      A/ Yes to both of these.

      David described here what he does in the MGI system when he makes an ISS annotation (particularly with regard to the structured notes field), and he also described how he sends annotation to GOA via the ftp site.

      Action: David is to write a one paragraph description of this.

      Q/ Can we improve how other databases send data to GOA? Daniel Barrel says the easiest way is to send gene_association files.

      Action: David + Rex to make a proposal to present before the annotation camp. Action: Mike and Chris to make a script to check ISS annotation for corrections to the annotation from which ISS was inferred. Action: Reference Genome group to work out standards for ISS (relates to CASP7 proposal).


    15. Ensuring all emails to gohelp are being answered
    16. A proposal has previously been sent to the list. 15 people on gohelp list right now.

      Thoughts:

      i) Most mails are already being answered and the isse is to make sure that someone is responsible for making sure that unanswered mails are claimed by someone.

      ii) Technically: We can track mails manually. Just use your own inbox. Only delete mail when answered.

      iii) Not all on management list have time to do this so we will ask for volunteers.

      iv) Make list of experts on each type of question.

      v) Questions should be in faq so we can reuse answers.

      vi) More formal way to track maybe? (Not yet, wait to see how it goes.)

      vii) Maybe wiki could have form letter to send.

      Action: People volunteer to be on rota, one week each. Put calendar on wiki. (Advocacy group to co-ordinate.)


    17. Users meeting (Seattle, Sept. '06) update
    18. User meeting is Sept 10 2006. $75 registration fee for all (including GO people).

      Registration is open.

      Q/ We are doing abstracts. Can we open submission now? Q/ Who reviews abstracts? Q/ If we get enough to have to select who does the selection? (Midori volunteers.)

      Response:

      1. This is within the remit of the advocacy group.
      2. Advocacy group delegates all these jobs to Midori. Midori agrees.

      Action: Midori will open abstract submission, and will review and select abstracts. Action: Midori is to document how she sets up the user meeting so that others can do it next year.

      Rex mentions that it is inconvenient how MGED is sandwiched between and overlapping with the user meeting and the external advisory board meeting. Response is that this was just a consequence of too many meetings at the same time. Action: Try to avoid this in future.

      Q. How do we get rooms for the advisory board meeting? Action: Midori will forward contact details for her. (done)


    19. . Revised proposal for Ontology Working Group.
    20. The proposal has been sent round. Comments were received from Judy. The document has been modified accordingly.

      Q/Should there be a mailing list or over GO list.

      Points:

      1. Sourceforge is good for term requests.
      2. Might be good to have internal mailing list for main group to discuss proposals that can then be sent to the mail list.
      3. Maybe succession of little ad hoc groups forming and unforming as needed.
      4. Maybe use main mailing list for all discussions?

      Action: I think we decided on (iii)

      Purpose of Ontology Working Group.

      1. biological rigour.
      2. Find biologists to help ensure biological rigour or working group will ensure biological rigour by own efforts.
      3. Get changes implemented and to fit logically in graph.

      Points: i) In discussions people should only ne included if their research background fits. No sense sending e-coli stuff to doug. Just write straight to michelle.

      Q/ How do we archive?

      Thoughts:

      1. Have discussions and then minute in sourceforge or on list?
      2. Use wiki?

      Q/ How do we communicate?

      1. Use chat? (It produces transcripts so no need for minutes?)
      2. Record discussion at content meeting for archiving. (Try using microphone on laptop.)

      Action (implied): Jen will try to get this working for the content meeting.

      Current plans:

      Neurobiology meeting: To talk about biological issues with experts then send the generated graph to all. Examine from ontology point of view. Are terms and definitions consistent?

      Progress so far: From a small region of neurobiology they now have nearly 500 terms (expressions of astonishment!) This many terms are needed to annotate literature. Graph has been sent out.


    21. New E. coli Collaboration
    22. Rex announces that he has had contact with Jim Hoo of Texas A&M.(Head of an E. coli database) They have agreed to be actively involved in GO annotation and are coming to the annotation camp. Barry Water probably also coming. Good for reference genome group as they are keen to get in as reference genome. Big breakthrough.

      Action: Rex to send more details (name spellings, database name and e-mail address) to Jennifer to go in the anntotation-outreach records.


    23. Next Call
    24. 21st June 8 am Pacific, 11 noon Eastern, 10 am Central, 4 pm UK.

      Action: Jennifer to compile agenda.

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