Managers 23May07

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Participants: Michael Ashburner, Judy Blake, Mike Cherry, David Hill, Eurie Hong, Suzi Lewis, Chris Mungall.
Agenda/Chair: Chris Mungall
Minutes: Eurie Hong

Review Action Items from previous meeting

Chris: Send document about versioning

Still an action item for Chris.

Rex: Unify approaches to orthology.

Most of the groups have put their methods used for determining orthology on the wiki. As previously mentioned, there will be a meeting in October for reference genomes. In preparation for this meeting, there will be discussion on how the orthology calls are made. There is also a suggestion for inviting an expert who understands the pitfalls and caveats and strengths of the algorithms used for makng orthology calls.

Action item for everyone: Suggest experts who could attend the Reference Genome meeting.

Suzi: Send update of PharmGKB meeting about sequence variation.

During the meeting, Suzi forwarded an email with the minutes and action items from the PharmGKB meeting. In response, Mike suggested that other groups, namely Lincoln Stein, who deal with SNP data should be included in this discussion.

Chris: Update the cross-products between GO and Cell

This is still pending. The new beta version of OBO-Edit will be able to make this easier. David recently added additional terms that could be cross-products. He would like to say during the advisory board meeting that we have made cross-products with Cell Ontology.

Action item for Chris: Get John to release the next beta version of OBO-Edit.
Action item for David: Use this version of OBO-edit to go through the cross-products file in the scratch directory.


Individual Manager reports

Ontology Development

  • Recently been focusing on cleaning up SourceForge items.
  • Fixing the last few problems with disjointedness between "multicellular" and "organismal" processes. These items have been put into SourceForge.
  • The cardiovascular meeting is progress. There is a current proposal in the scratch directory that adds about 50 terms to the ontology. The organization is based on physiology but can't really capture "major/minor" influences. In order to address this way of viewing the biology, links will be made to SIMAP which takes a more physiological view of the process.
  • Muscle meeting appears to be on track for July.
  • Suzi said there will be a SO meeting in June with an emphasis on immunology. Alex will be attending to help describe the biology.

Outreach

  • The group is still working on a flowchart for documentation.
  • Minutes from last week's call is available on the wiki

Software

  • Chris has a teleconference with Sohel and Mary to discuss the prototype for the reference genome database. It will be sent out to the reference genome list soon.
  • go-dev documentation has been improved and moved to the main geneontology.org website. It's not linked up to anything but will need to be before it's released to the public. THen the godatabase.org pages can be retired.
  • support for the "replace" and "consider" tags has been added to go-perl.

Reference Genomes

  • Rex is traveling today.

User Advocacy

  • Newsletter: Jane will send version to the GOC mailing list for final proofing. Will be emailed out by the end of the month.
Action item: The go-dev documentation to other geneontology.org website pages before newsletter 
sent out to announce the EBI mirror.
  • We had a webex to train new members of the gohelp team (David Hill, Tanya Berardini, Kimberly Van Auken, Amelia Ireland) how to navigate through gohelp.
  • Stefan Goetz emailed gofriends to start a discussion about tools. Many of the types of metadata he listed are similar to the types of information we were considering putting on the GOC tools pags. Jane had compiled a list of tool standards to use in evaulating the tools.

We should touch base with Stefan to see where his efforts intersect with our and see if he's interested in working with us. Then participate in the gofriends discussion about having this information available on the GOC website.

Action Item: Chris will send email to Stefan Goetz to touch base with him about working with the 
GOC in compiling this information.

Meetings

  • Suzi is leaving this afternoon for the American Society of Microbioogy meeting
  • David is attending the Society of Dev Bio meeting
  • Judy will be attending a PubMed Plus meeting, discussing issues of metadata (annotations, etc.) and supplementary data associated with publications.
  • Chris reported that the attendees at a Clinical Trials meeting in Bethesada were supportive of GO.

Collaborations and Interactions, active and new

  • The MIT collaboration has resulted in a publication which is currently being edited by Chris, Judy, David.

Operations and Procedures

Staffing and Personnel

Budget issues

Publications

  • A paper submitted by David, Barry, and Judy to the Bio-ontology SIG about "What is a GO annotation" has been accepted. It is unclear whether it will be published outside the context of the meeting.
  • Seth has a draft of an AmiGO paper
  • Michael and Judy pointed out there are several publications addressing OBO and OWL. And the community in Manchester is strongly encouraging biologists to use OWL instead. But for bench scientists, they just want the data and the annotations. The purpose and goals are different. Michael suggested GO write a joint paper with the Machester group in order to discourage "religious wars" that can flare up over this issue.

This does bring up the issue that many times our documentation can be misleading or confusing and not provide adequte information for members of the community to understand what we do.

Chris clarified that you can go from OBO v1.2 to OWL 1.0 without loss of information so the issue of people who want to use GO in the OWL format is moot.

Other Current Topics and Concerns

  • Judy suggested a web-based journal club to review relevant publications about GO. This was met with much enthusiasm.

Summary of Action items

  • Chris: Send document about versioning
  • Everyone: Suggest experts in orthology algorithms who could attend the Reference Genome meeting.
  • Chris and David: Get GO and Cell Ontology cross-products. Chris gets John to release the next beta version of OBO-Edit. David to use this beta version of OBO-edit to go through the GO and Cell Ontology cross-products file in the scratch directory.
  • Chris and website group: The go-dev documentation to other geneontology.org website pages before newsletter sent out to announce the EBI mirror.
  • Chris will send email to Stefan Goetz to touch base with him about working with the GOC in compiling information about GO Tools.