Managers 29Nov06

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GO Managers Meeting Minutes 29 November 2006

Participants: Michael Ashburner, Midori Harris, David Hill, Rex, Chris Mungall, Jane Lomax, Eurie Hong, Mike Cherry, Judy Blake


Specific items:

A. Can we form a working group to evaluate OBO-Edit vs. Protege? (John suggested this during the Nov. 16 OBO-Edit chat).

  • CM: A direct comparison between OBO-edit and Protege is not the way to go. Probably should discuss more in the future.
  • MH: Need to be sure this issue is on the radar screen. Will likely be discussed at the Consortium meeting
  • DH: OBO-edits internal development allows real change to occur rapidly to address the users needs
  • CM: OBO Edit working group cycle for improvements is definitely an advantage
  • DH: low learning curve is also a benefit.


B. Crediting contributors (relevant to operations/procedures and maybe software): see Chris' email from Nov. 22.

  • MH: the way credit is given needs to be reviewed. Currently it is hidden in the ontology in the DBXref field.
  • Jane: Maybe it should be separate from DBXref.
  • CM: Maybe we should highlight the credits in amigo in a more visible way?
  • JL: How about putting it in a contributions field
  • All: general agreement to concept of a contributions field
  • CM: This should be able to handle external references
  • DH: For efforts such as the immunology revisions we could create short abstracts with authors that describe the contribution. Links to the abstract could then go into the contributions field.
  • ALL: general agreement with this idea
  • EH: all terms tagged with that abstract also provide a means for identifying terms resulting from that effort.

Action items:

MH will email abstract link (go/doc/GO.references in CVS, ftp).

CM will explore introduction of a contributions field.

C. Web conference options: Jen won't be able to join the call, but she sent a summary to the managers' list.

  • Jen Clark provided a summary. There was no further discussion


D. Ontology Development and Reference Genome Annotation interface.

  • MH: The goal has been to turn around requests from the reference genome annotators quickly so as to leverage everyone’s attention. This works well with small changes, but concerns have been raised about times when ontologies need more extensive revision. How do we not slow down reference genome annotation
  • RC: We can simply flag genes requiring major ontology revisions as “defer”. That let’s annotators know to skip that gene and that flag can be used to help us refocus annotator attention when the appropriate changes are made to the ontology.


The usual topics:

1. Review Action Items from previous meeting

New Nov. 8:

  • a. Jane to merge go/scratch/IsaComplete.obo with live GO. [on hold while obo edit merge is implemented]
  • b. David to send is_a complete GO to Jonathan Liu—[done]
  • c. January meeting agenda suggestions must be on wiki by first week December—[many additions have been made in the past two weeks]
  • d. GO editors to tell refgen annotators to choose "reference genome" group & put "rg" in summary. [done]
  • e. David and Suzi to work on list of experts for heart dev content meeting—[DH: some people contacted. Looking to Wisconsin group to identify a partner to work with David in the same way Doug Howe did for the CNS development content group]
  • f. David to put higher-level function issue on meeting agendas. [done]
  • g. Michael to look at sex determination terms and questions about them from is_a complete work (David to remind him).
    • [DH: Michael Ashburner to look at sex determination terms, MH: will email sex determination questions to Ashburner]
  • h. Suzi & Chris to send new definition of "flagellum" (SF item).—[pending]
  • i. GO-tops to discuss tech writer possibility; budget considerations.— [MA: budget unlikely—idea tabled]
  • j. Jane & Eurie to go ahead with including public wiki in AmiGO/web presence wg remit. [In process.]

Carried over from Oct. 25

  • k. Conference call with ChEBI; also including Chris. [CM: chatted with someone a ChEBI regarding REX, but currently awaiting a web enabled tool.]
  • l. Chris to look at J. Liu/MIT material.—[defered to ontology development group]
  • m. The advocacy group will look into some type of calendar to keep track of which meetings are being attended by GOC members. [EH: found something to put on the wiki that would track these activities, but needs time to implement]
  • n. Judy will send a copy of the instance paper to Chris and Michael—[done]

2. Individual Manager reports

a. Ontology Development

report on is_a complete (http://gocwiki.geneontology.org/index.php/Isa-complete_BP)

  • DH: “is_a complete” revisions is major focus now. Now exists as an is_a complete draft. Every term has a term to root, but still reorganizing. Progress notes available at above address. Hoping to have it done by GOC meeting in January.
  • CM: Has developed a cron job that adds cross product definitions. These defined terms can than be imported into obo edit which will then reason to insert IS_A relationships and needed terms. Next step is to put definitions in the obo file itself rather than holding as a separate file.
  • DH: more material from Jonathan Liu at MIT identifying terms as being too specific or too general has been provided. Analysis of too specific terms typically identifies a problem in the graph
  • RC: too general terms may be needed for graph structure, but too specific need to be reviewed as they may be wrong


b. Outreach

  • defered Jen at conference

c. Software

  • CM: added to the API a way to assess enrichment of terms in a collection of gene products. Works directly on the database—based on Gavin Sherlock’s GO TERM finder. This should be a valuable tool that can eventually be integrated with AmiGO
  • CM: met with SGD regarding database loading efficiency issues. Have identified areas that could be improved.
  • JL: Reminded about the discussion to remove underscores from term names due to problems for software.
  • CM: plan remains to be to remove, however we need to warn people that namespaces might now be different from term name.
  • MC: this is likely to break software, so definitely need to put out a warning and see what kind of response is obtained.

d. Reference Genomes

  • RC: the addition of a Refgenome tag to sourceforge ontology changes has been working well. Changes are generally made in a timely fashion and the tags also provide a useful way of monitoring how many changes have resulted from the reference genome effort.
  • RC: By popular demand there will be no additional genes added to the reference genome target list for December. Instead annotators will use this month to “catch up”. The hope is to review this process in a conference call of the reference genome annotators in early January just before the GO consortium meeting. Another topic for discussion at that phone conference will be the value of establishing a separate file or interface that allows viewing/visualization of the fruits of the reference genome annotation effort.

e. User Advocacy

  • JL: the new, improved AmiGO is almost ready. Trying to finish testing early in Dec. Plan is for it to be out by Jan. meeting. Amigo working group already starting to think about next version.
  • JL: The December Issue of the Newsletter out.

3. Meetings

  • PATO meeting Friday
  • Consortium meeting in Jan.

4. Collaborations and Interactions, active and new

  • JL: Developing viral terms for bacteriophages. There is much work to be done next year regarding this

5. Operations and Procedures.

  • no issues.

6. Staffing and Personnel.

  • no issues.

7. Budget issues.

  • JB: Meeting with budget officer. May be roll-over funds available. Think about supply/instrument needs.

8. Publications.

  • Instance paper in revision.
  • Reviews back on obo-edit applications note submitted to bioinformatics. There are concerns that the reviewers are too focused on an OBO-Edit/protégé comparison.
  • Applications Note on improvements in immunology is preparation

9. Other Current Topics and Concerns. None