Managers 21June06

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GO Managers call 21 June 2006

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

Meeting agenda

  1. Review previous Action Items (Pasted at bottom of page)
  2. Individual Manger reports: Overall Project Priorities & Progress & Deliverables status reports (on _existing_ tasks)
  3. Upcoming talks, papers, and meetings (e.g. are we going to submit anything to Genome Informatics?)
  4. Collaborations and Interactions, active and new
  5. Operations and Procedures(e.g. tcons)
  6. Staffing and Personnel (i.e. new hires, departures, leave, vacations...)
  7. Budget issues
  8. Other Current Topics and Concerns:
    1. a. report on the neuro-dev content meeting last week.
    2. b. OBO-Edit paper
    3. c. Annotation tool(s)
    4. d. GO associate status

Action items from previous meeting

  1. Status of GO wiki and who will do what.
  2. Action items for Mike, Chris, Eurie and possibly Amelia. (Below)

    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.


Production URL: http://wiki.geneontology.org/

We will go ahead and start using the Wiki for internal documentation without password protecting it or requiring users to have an account. In addition, additional features and extensions will be added in the future. Stanford sysadmin group is shorthanded currently. New features will be added in the near future.

If it turns out that pages are inappropriately being editing, the pages can be restricted.

Chris also brought up that the GO FAQ can be put in as a wiki. All the questions will need to be manually entered though - cannot easily transfer the text. We do not want public and internal wikis to be the same. So we will start with the internal-only wiki first.

New action item: Eurie and Amelia will send out structure of navigation and organization to the group and proceed.


  • Status of St Croix minutes, and posting on GO.
  • Action items: i) Judy to send text to complete minutes. ii) Minutes to be sent to Amelia to be put on website. (Kimberley)

    Judy will send text to Kimberly.


  • Discussion of CASP7 proposal
  • 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.

    There was discussion about several aspects of this involvement: What is the source of the structures used in the challenge? Who picked these genes? Could the GOC provide a list of genes that already have been annotated? Is there experimental evidence associated with these structures? or is there just ISS information?

    What should the GOC role be in this? Do we need to devote additional curator time to annotating the genes that are chosen for CASP? There was some agreement that the GOC could be involved in reviewing the completeness of the annotations but not committing to review all the results.

    Tim Hubbard, at Sanger, has been involved with CASP.

    New action item: Midori (or another member of the GO editorial office) will contact Tim and gather information about the set of structures (source, associated information, etc). Depending on the information, GO tops will have a conference call with Alfonso.


  • Proposed Web Group
  • Action: i) All decision making on this devolved to Advocacy group. Jane and Eurie to take forward.


  • Next GO Consortium meeting. Who?
  • Action: i)GO-top will approach possible organisers in order: a) GOA b) GOA + Val Wood c) GOA + GO Editorial Office d) GO Editorial Office.

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

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


    Meeting will begin with dinner on Jan 7th and end with lunch on Jan 10th. Any working groups can meet before dinner on Jan 7th. Tentative location is Jesus College.


  • Do we need a PubMed id for a GO annotation?
  • Action: Implement this policy: i)We cannot restrict just to PubMed ids. ii)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).

  • Reference genomes and ISS checks.
  • Action: i) Implement policy that if the source annotation for an ISS is found to be wrong then the ISS must be rechecked. ii) 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. iii) 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. iv) 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. v) Reference Genome group to work out standards for ISS.


    David has sent Rex MGI's strategy for making rat and human annotations.


  • Ensuring all emails to gohelp are being answered
  • Action: i) People volunteer to be on rota, one week each. Put calendar on wiki. (Advocacy group to co-ordinate.)


    Jane and Eurie will add this to the Wiki once the organization has been finalized. Compliments to Jane is answering the emails!


  • Users meeting (Seattle, Sept. '06) update
  • Action: i) Midori will open abstract submission (with technical help from Amelia and Mike), and will review and select abstracts. ii) Midori is to document how she sets up the user meeting so that others can do it next year. iii) Try to avoid having gaps between adjacent meetings and overlaps with other meetings in future. iv) Midori to contact Judy with MGED9 contact info.


    All GOC members need to register and pay the $75 fee.


  • Revised proposal for Ontology Working Group.
  • Action: i) 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. ii) Jen to set up voice recording on laptop for neurogenesis meeting.


  • New E. coli Collaboration
  • Action: i) 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.

    Rex has sent this information to Jen.

    Individual Manager reports

    1. Reference Genome
    2. Rex is getting ready for the Annotation Camp so that reference genome annotation strategy can be tackled as a group. Annotation Consistency is starting: originally began with 2 curators from 5 groups. Has expanded to include 5 additional groups. The same papers will be used for the training portion of the Annotation Camp.

    3. Ontology Development
    4. There is the ongoing basal level of work. The merged document from Midori and David has been sent around and needs a couple of edits. There appears that there will be a trend towards large-scale ontology development work and not just term-by-term additions.

      Michael A. mentioned that he has encouraged the mosquito group to be involved with PAMGO. Suzi mentioned Bruce Conklin from UCSF has expressed interest in being involved in cardio development. Simon Twigger is working with an expert in blood pressure who is happy with the recent development and is interested in being involved in future development.

      Jane and Amelia are attending the PAMGO jamboree at TIGR. Erika expressed interested in working on the "response to drug" branch.

    5. Software
    6. New hire at Berkeley: Seth Carbon, who will be taking over most of Shu's responsibilities with AmiGO. He will need to be involved with the AmiGO working group.

      OBO-edit was released!

    7. Outreach
    8. GSK is interested in making annotations. The group recently had an IRC chat and discussed many projects. Now, they need to prioritize the projects.

    9. Advocacy
    10. Already discussed Wiki and GO help. The newsletter will be sent out in August.

      Jane and Eurie asked Rex if the members of the reference genome group could be good candidates because they will be able to provide feedback from their user communities. Rex expressed concern about spreading people too thin. It was also suggested that we need to involve the general biologists and make sure the web site is informative without being too overwhelming.

      New action item: Rex will forward Eurie and Jane's request to the reference genome group.

    Upcoming talks, papers, and meetings

    1. Genome Informatics
    2. Who should represent GO? MGI is thinking of presenting a poster on the intersection of ontology development and functional annotation.

    3. Judy, Michael A., and Suzi will be attending the SwissProt anniversary meeting
    4. Judy will be giving a talk on GO at a BISTI meeting.
    5. SGD curators (Jodi and Stacia) will be giving posters talking about how GO tools could be useful for bench biologists: presenting the poster with questions that would be relevant to those members in a lab will encounter.
    6. Alex will be attending an Immunology meeting in the fall and trying to give a GO tutorial.
    7. MGI is writing an inference paper about annotations. Running into journals are requesting payment for copyright permission to reproduce figures. It was suggested that they contact authors directly for an equivalent figure.
    8. Jane is finishing a book chapter on using GO for parasitology.
    9. Midori is finishing a chapter on developing ontologies for Methods in Molecular Biology.
    10. Michael A. has been asked to write an Annual Review chapter on GO. He will discuss this further with the GO tops.

    New action item: Put these into the Wiki. The Wiki page should be restricted.


    Collaborations and Interactions, active and new

    1. Collaboration with MeSH to create a mesh2go.
    2. Jane has been involved with creating this mapping. NLM has a proprietary tool that requires a subscription. Using this tool increases the efficiency of creating these mappings since they are often not 1:1. David suggested correlating from MeSH - PMID - GO but NLM will do a first pass based on the UMLS.

      Jane will continue with this collaboration and EBI will pay for the subscription to the tool.

    3. Neurobiology development content meeting
    4. Many experts were involved in a 1.5 day meting. In preparation for the meeting, a graph was sent out to the participants. Several comments were provided which then prompted a new version of the graph to be sent a week before the meeting.

      The first day covered what GO is, how GO meshes and works with other ontologies, etc. During the meeting, there were two projectors: one that just projected OBO-edit and showed the editing real time. During the course of the meeting, many new terms were added and definitions were modified and structure of the ontology was edited. There will be 500 BP terms added and > 1000 changes to the graph. The is_a complete paths still need to be made.

      One of the key outcomes of this meeting was that GO cannot ignore anatomy since this is how many users are searching for terms. They don't know the processes necessarily.

      Aside about FMA: a subset is in OBO format. There has been a request to put a browser on the OBO site so that all the ontologies can be browsed on the web.

      New action item: Rex will need to ensure that there is a representative from each reference genome at the September meeting to further discuss anatomy development related terms.

    Operations and Procedures

    Next phone call: July 5 8 am Pacific, 11 noon Eastern, 10 am Central, 4 pm UK.

    Schedule for agendas and minutes


    Staffing and Personnel

    New hire: Seth Carbon at Berkeley

    Budget issues

    We do have a small rollover from this current fiscal year. There was enthusiasm for using it for more ontology development meetings.

    Other Current Topics and Concerns

    1. Report on the neuro-dev content meeting last week
    2. See above.

    3. OBO-Edit paper
    4. It is in the works.

    5. Annotation tool(s)
    6. Mike C. will send the text from the grant that addresses this issue. Suzi and the reference genome group will need to involved in this.

    7. GO associate status
    8. It is important that the groups be committed and involved in the submission of gene_association files and development of the ontologies. In addition, groups should be well trained in annotations before trying to train new groups. It is completely appropriate for Jen to pass on contacts to the GO tops in order to work out details of the interactions. Phrase of the morning - "You hook 'em, we'll reel 'em in".


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