Managers 12March08

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GO Managers, Weds. March. 12th, 2008 8a.m. PDT, 9a.m. MDT, 10a.m. CDT, 11a.m. EDT, 3p.m. GMT

Agenda/chair: Jennifer

Minutes: Midori

Present: Jennifer, Judy, Midori, Chris, David, Pascale

Action Items

Review Action Items from previous meeting

Action Item: Software group to implement new ontology filenames and directory structure. Proposal available at

Proposed reorganization would not break any scripts, links, etc., so we should announce our plan, but we don't need several weeks' lead time. We can continue to make files available at old locations indefinitely.
New action item: Forge ahead with adding new files; curators switch to editing gene_ontology_write on date to be announced.

Action Item: Judy will contact sea urchin db in March or April.

Communication now established; sea urchin community has to decide who is responsible for annotation.

Action Item: Reference Genomes: Decide whether to do QC review for every single gene every single time.

David provides background (also see Ref Gen call notes). Mainly a RG issue; not yet resolved by RG group.

Action Item: Decide how to keep track of function-process links in electron transport; options include spreadsheet, Phenote or OBO-Edit.

Subsequent discussion of advantages and disadvantages of different approaches has reaffirmed choice of Google spreadsheet. Chris has convinced Suzi as well. Spreadsheet features that won the day:
  • Biologists get to use a familiar tool
  • Curators can make notes on specific links
  • Can automate conversion to OBO representation

Outreach/User Advocacy

Jen - EBI training "roadshow" in Ghent; demos of current and new (beta) AmiGO well received. Audience with general interest in bioinformatics resources.


OBO-Edit: Still waiting for Amina's entry clearance. Nomi still working on OBO-Edit, not quite ready for release. OBO mapper - part of OBO-Edit codebase; supports more options.

AmiGO: almost ready to release; sorting out consistent icons for AMiGO and OBO-Edit.

Ref Gen: some progress on tracking tool; should have demo soon. Seth moving Mary's graph visualization software to AmiGO codebase; can query genes by homology sets.

Ontology Development

David and Tanya still working on implementing regulates relationship; have finished going through Chris' report of missing or mismatched process and regulation term names; will send samples to Larry Hunter.

Now working on QC report on graph consistency between regulated-process and regulation "trees". Some possible false positives in cases where regulation of a function involved in process.

Demo yesterday of creating regulation terms using regulates relationships.

Chris will continue to generate QC reports, and David and Tanya will go through them.

Longer-term plan: when OBO-Edit 2.0 is live, use reasoner to find errors.

Ref Gen curators reminded to create Curator Requests tracker items for content questions that arise from QC work.

Electron transport function-process links - one hour for one MF-BP pair! Discussion of when you know that a process always has a constituent function, or when a function is always part of a process. Harold also more confident of has_part than part_of MF_BP links in glycolysis. Also, what counts as "canonical" or "normal".

Jen going over signal transduction at textbook level.

Chris working with Michelle on Column 16 use cases - Michelle has some pathogenesis use cases. Can use col. 16 to include specifics rather than adding very specific new terms.

Reference Genome

Conf call yesterday; minutes available at

Kara - PPOD running; secondary UniProt ID issue

Orthology sets - feedback from curators to cluster analysis

How much ISS should MODs inherit? David suspects misunderstanding; all should be checked, but only those that make sense would be added. Discuss protocol at SLC meeting.

Pascale in Geneva - general annotation point: several Swiss-Prot mapping-derived annotations could use ISM rather than IEA.


No agenda for relationship meeting yet (Larry Hunter, Colorado). Many relationships that could be discussed are very relevant to GO and biology, so if they'll be covered at the meeting some GO people (e.g. David, Tanya) might want to attend. Also see the OBO_REL tracker

Collaborations and Interactions

Operations and Procedures

Questions about UniProt -> UniProtKB change, and communication worries. Everyone should switch to using UniProtKB.

Try WebEx "raise hand" feature for next Ref Gen calls.

Staffing and Personnel

Jane is back (part time)!

Budget issues


Erika and Jen redrafting paper on muscle content meeting to submit to BMC Medical Genomics.

David working on blood pressure regulation paper.


Pascale asks about a visualization tool that Judy sent around a while ago; David, Pascale will look for the email and forward it if they find it.

Next call

March 26, 2008, 8 AM PDT/11 AM EDT/3 PM GMT

Agenda: Midori; Minutes: Pascale

Summary of Action items

All: Check list of database contacts and make any additions needed. Chris to email GO List.

Chris and ontology development group: Forge ahead with adding new files; curators switch to editing gene_ontology_write.obo on date to be announced.

Reference Genome group: Decide on QC procedures, frequency, etc.

Reference Genome group: Determine protocol for making ISS annotations.

Reference Genome group: Try WebEx "raise hand" feature for next conf call.

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