Managers 14Feb07

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MINUTES, Managers conference call 14th February, 2007 (Happy Valentine's Day!)

Present: Jen Clark, Midori Harris, David Hill, Suzi Lewis, Eurie Hong, Judy Blake, Chris Mungall, Michael Ashburner, Mike Cherry

Minutes: Midori

something about penguins from Judy ...

Action items from last call(s)

  • Midori & Alex: Add references for immunology content meeting.
A mechanism in place for creating and using GO_REF entries for content meetings.
There was some discussion, including some questions and answers. A brief summary:
We envision one GO_REF for each content meeting in which several experts participate, and large changes are made. The GO_REF will be cited in a structured comment associated with each term created or substantially modified (e.g. parentage or definition) during the meeting.
For smaller-scale changes (e.g. one or a few additions, such as those done for SourceForge requests), we use definition dbxrefs to document contributions from individual curators, annotators, or community experts. We may use a dbxref representing the SF item submitter, the GO curator, or both, depending on who contributed to the definition. We know that we're shoehorning some history tracking into the definition dbxrefs. Another limitation is that there's no date associated with curator dbxrefs, except ones referring to content meetings.
Note: the dbxref order is meaningless.
New action item: associate a date (more precise than year) to GO_REFs, especially those for meetings. [all curators; ongoing]
  • Jane and Suzi will sit in on conference call with OBI group to coordinate how groups give credit for developments.
  • Google calendar - everyone to fill in their meetings.
Ongoing
We decided to include conference calls, both phone line and Skype. This will help us stay informed about what's going on; the former will also let us see when the phone line will be is use.
  • WebEx - funds available for 6 months (@ 500/month) from MGI. Need several passwords (one per institution) - Hinxton, Bar Harbor, Denver, Berkeley, Chicago. Judy to purchase.
Judy requested a purchase order before she left; MGI "got Webex" but there was a delay due to Judy's absence. Now that she's back, Webex should be available very soon. We have a 6-month contract, at $300/month.
  • David to send MIT meeting spreadsheet round to this group [It was originally sent to GO-top, David, Jane, Chris and Midori. If you would like to see it, please let David know]
David reiterates that anyone who wants it should ask him to email it.
Meeting is on for March 16th. Participants from GO: David, Midori, Jane, Chris, Judy.
Action item: Judy will figure out which funding pot to use.
Action item: At least a week before the meeting (i.e. by March 9th), look at the spreadsheet and manuscript from Jonathan again. Schedule conference call to firm up our position.
Action item: David will book rooms at the MIT hotel. All participants, please email arrival and departure dates to David.
  • Need a way to prioritize meetings that GOC members will attend (Jane and Eurie)
See advocacy report.
  • Jen to request gocvs access for Erika
Done.
  • Jane will work on IMG mapping.
Jane not present.

8. Gene of the quarter? CLN3. Susan to lead. David will send note about the status of the spreadsheets on this gene.

Emails going around to get CLN3 blurb finished. Rest of newsletter is ready.

Individual Manager reports

Ontology Development

  • The big thing now is renaming "sensu" terms. Terms will now be named based on what the things they represent really are, and what features distinguish them from the parent(s) and sibling(s).
Doing cellular component terms first, because many biological process terms refer directly to component terms.
There are only about a dozen component terms remaining to do.
Calling experts for specific organisms or taxa as needed, eg. Val, Becky, Tanya, Michelle.
Work has just started on process terms; ther eare about 300, of which about 100 refer to insects. Becky is helping a lot.
Committing changes in 'live' GO as they're agreed upon (different from is_a-complete procedure).
An observation: past laziness in definition-writing is biting us -- many 'sensu' terms definitions are just the parent definition plus 'as in ...' so we have to ferret out the real distinguishing features now.
Suzi: This is fabulous.
  • Jennifer Clark, Val Wood and Michelle Gwinn have started working on transporters, using webex & conference calls.
  • Jane is working on resolving violations of disjointness among multicellular organismal process, cellular process and multi-organism process.
  • Using the 'regulates' relationship and cross-products
Chris generates a list of 'regulation of [process]' terms, where the process term doesn't exist. David is about to start resolving these.
We hope we'll soon get to the point where there's just one 'switch' to create 'regulates' relationships.
Chris autogenerates a file, go/scratch/gene_ontology_xp.obo, that contains 'regulates' relationships and intersection_of tags
We must decide whether to simply accept all those changes, and put them in the live file.
The autogenerated file doesn't remove part_of relationships unless they're redundant with 'regulates' relationships. Chris' procedure figures out what the correct decomposition is; OBO-Edit finds the correct place in graph, and removes part_of relationships that have been made redundant.
David (and the rest of us) can't think of any cases where regulation of a process is really part_of the process.
We will have to announce this several months before it goes live. We should send out notification when the work is close enough to being done that we have an accurate estimate of when it will be complete.
  • Function-process links
We plan to hold a conference call with Chris, Amelia, David and Midori to get started.
The first thing we need is the relationship; we'll consider the possibility of using a temporary relationship for a while, just to get the biological/biochemical side of the work up and running.
We also have to decide whether the links wil go into the gene_ontology_edit.obo file or a separate file.

Outreach

  • Conference calls now held regularly (7am Pacific time).
Preparing procedures, flowcharts
Have identified several promising conferences; Jen has a list.
Email from Folker Meyer, at The SEED with Ross Overbeek; they are mapping their manual annotations to GO.

Action item: Jen to put Folker in touch with Jane because The SEED is closely related to FIG.

Software

  • Ben is working on database loading, with a view to making it faster.
This is partly driven by need to display IEAs in AmiGO
Mike asked how many people need or want IEAs in AmiGO. David noted that for ontology development we often need to know whether a term is used for *any* annotations (or external2go mappings), but if we were to do a cost-benefit analysis, it may turn out not to be worth doing for such a small group of users.
  • John is temporarily redirected to NCBO work while we're waiting to hear about GO funding.
  • Chris and John have started thinking about OBO format 1.3.
This time it should be a smooth transition, backwards compatible
Seeking feature suggestions from the OBO-Edit working group and the wider community
  • Mirrors of go-full will be set up in a couple of places, including EBI
Allows direct mysql queries

Reference Genomes

Rex not present

User Advocacy

  • AmiGO
    • Meeting with AmiGO group to plan for next release, in June
    • New servers next week; will improve speed
    • Working group testing autocomplete and other new features
  • Newsletter waiting for Reference Genome (CLN3) article
  • Prioritizing meetings where someone should represent GO
Overlaps with annotation outreach
Rama has suggested two - one at JGI, and the next rice meeting in Japan
Mike noted that rice can be political ...
A bit of discussion, leading to general agreement that our immediate need is for a list of meetings; clever use of the calendar is a lower priority.
Action item: Eurie to put list of meetings to consider on wiki. Use calendar? Maybe; most important thing is just to have a list. Also, include which group(s) should send someone to a given meeting.
Action item: Jen, Jane, Eurie to confer about wiki pages, etc. to manage conference attendance.
  • GO Tools
Jen, Jane, and Eurie started going through the GO Tools page last week.
Looking at which features tools use, e.g. evidence, qualifier, etc. Judy suggests adding relatinoship types (e.g. will they adopt 'regulates' when we make it live?).
They will send a set of questions to tool developers; if there's no response, assume the tool no longer actively maintained, and remove it.
David volunteers to help.
Jen noted that tool developers all (should be) on go-friends.

Meetings

  • MIT meeting March 16th (see above)
  • David is going to the Society for Developmental Biology meeting in June; he'll have a poster on how GO represents developmental processes and how we coordinate with external ontologies to describe cell type and anatomy; it will also discuss structured annotations at MGI.
  • David will chair a workshop at the Biocurator meeting in San Jose (Oct. 2007) on good practices in ontology development
    • David will talk about rules for term requests, guidelines for developing one's own ontology. etc.
    • Chris will talk on ontology alignment, advantages, tools, etc.
    • One talk to be selected from abstracts

Collaborations and Interactions, active and new

  • Fritz Roth at Harvard is evaluating a tool to predict GO annotations for different genes; several different prediction mechanisms are used by different researchers there. David (mouse genes) and Julie Part (SGD; yeast genes) review the predicted annotations and note which are true (can find supporting evidence), likely true (but can't find evidence), or likely false.
  • David mentioned an intra-GO collaboration involving himself, Tanya, and Eurie; they're doing study of mitochondria-localized proteins. They are going to compare orthologs from the three organisms and see what the concordance is of mitochondria localization. They will also compare IEAs with large-scale experiments.

Operations and Procedures

Staffing and Personnel

Budget issues

We have no notice of award yet, but Judy has sent a letter to Chris Davis [name correct?], who will be managing the award. Meetings have been held; and the award amount has probably been settled (though of course we don't know what it is); estimating about 15% cut.

The Jax grants office has requested, and received, additional info from subcontractors; things are moving as well as they can. Judy will make sure we all know about the award letter as soon as it comes.

Publications

  • Alex's paper on ontology development for immunology is out as an epub (and in the GO Bibliography).

Other Current Topics and Concerns

Next call

February 28, usual time. Agenda: Midori; Minutes: Rex.

Action Items

  • New this time:
    • Action item: associate a date (more precise than year) to GO_REFs, especially those for meetings. [all curators; ongoing]
    • Action item: Judy will figure out which funding pot to use for the March MIT meeting.
    • Action item: At least a week before the meeting (i.e. by March 9th), look at the spreadsheet and manuscript from Jonathan again. Schedule conference call to firm up our position.
    • Action item: David will book rooms at the MIT hotel. All participants, please email arrival and departure dates to David.
    • Action item: Eurie to put list of meetings to consider on wiki. Use calendar? Maybe; most important thing is just to have a list. Also, include which group(s) should send someone to a given meeting.
    • Action item: Jen, Jane, Eurie to confer about wiki pages, etc. to manage conference attendance.
  • Carried over from earlier:
    • Action item: Google calendar - everyone to fill in their meetings.
    • Action item: Webex - complete purchase, issue passwords.
    • Action item: IMG mapping (Jane)


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