Managers 10Oct07

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GO Managers, Weds. Oct. 10 8 AM PDT / 10 AM CDT / 11 AM EDT / 4 PM BST

Agenda/chair: Midori
Minutes: Pascale
Present: Chris, Midori, Jen, Pascale, Judy, David, Suzi

Review Action Items from previous meeting

  • Display replaced_by & consider tags in AmiGO (Chris/swug)

DONE, Chris: you can see this in AmiGO already although the way it's done needs to be cleaned

  • Finish & submit NAR update (Midori)

DONE, accepted

  • Several meeting preparation tasks - reports, wiki additions, etc. (all managers)

DONE, obviously

Individual Manager reports

Ontology Development

  • Jen and David are cleaning the muscle and cardio file and will send out an announcement within the next week or so
  • Lung development is next: new file should be committed in November in the scratch directory; there will be a contents meeting about this in December in Boston
  • regulates: David is updating the live file, correcting terms that 'regulates' a process that does not exist. He's done about 1/10th of it. Then it will be possible to run tests to implement the regulates relationship
  • few term of transport need to be fixed
  • Suzi: what about using 'biologically friendly terms'? David: I think we agreed at the GOC meeting to use them; Jen: We use biologist-friendly names except in cases where the same name would be used twice, in which case we put the biologist-friendly name in the synonym field and a more precise name in the term name field.

Outreach / User Advocacy

  • Jen: Outreach has now been dropped as we were not getting many new groups. I am just taking care of advocacy now. I am checking that go-help gets answered and that the next newsletter is happening. This is going well.
  • Edinburgh farm animal meeting: should she attend?
  • Judy: I think we may skip that one since you already know those people and they are waiting for funding for annotation; let's wait for them to get funding.

Software

Chris

  • Amelia is in Berkeley working with Seth on AmiGO
  • Worked on ref genome reports Reference_Genome_Database_Reports
  • ready to load the google spreadsheets in a temporary database, so they will be able to put the information in a public database (will not solve curation problems)
  • John leaving! several people are familiar with the OBO-edit code and we are working on documenting the code.
  • Jen: I would like to request some documentation on how to do batch processing of ontology files using the existing OBO-Edit classes.
  • Chris: Yes that is a good idea, please enter it in the feature request tracker in the new 'documentation' category that Midori will make.

[ACTION ITEM] Midori- will create a new category in the Feature requests SF tracker

Reference Genomes

Pascale We had the first reference genome meeting after the GOC meeting, see Reference_Genome_minutes We got about 15 action items out of the meeting. We are nicely moving towards communicating more when annotating. We plan to meet again next year.

Meetings

  • Judy: Mammalian Genome meeting Tokyo (October)
  • Biocurator: San Jose, CA (end of Oct)
  • Midori and Emily, Erika are going to EU Network of excellence (Italy)
  • December: Karen, Barry, Judy, maybe Suzi: GO, MGI, PIR/protein ontology
  • May: Fiona setting up a chicken annotation workshop: Judy, Harold, others
  • GO annotation camp: we talked about doing it in Stanford

Collaborations and Interactions, active and new

nothing reported

Operations and Procedures

nothing reported

Staffing and Personnel

John has been Googled!!

Budget issues

nothing reported

Publications

  • NAR manuscript accepted!
  • Current Protocols in Bioinformatics article update (Judy & Midori)

Other Current Topics and Concerns

Annotation: Do we want to encourage submission of annotations of alternate spliceforms?

Judy summaries: the ref genome group is aware that the annotation of multiple splice forms can pose problems: - we need to know which product we are annotating and we need to know which gene this gene product belongs to.

- Do we need another column?

- Chris: at the RefG meeting we talked about using a mapping, similar to the gp2protein file, which can have a one-to-many relationship

- Chris: can I have a feel for how many groups do it? MGI (structured notes), rat, who?

- Suzi: would everyone NEED to to it?

- Judy, no

- Chris: there are two ways of doing it: for eg, if MGI has two splice variants, they use the gene ID, and if they know the splice variant, they include that in the structured note; the other way is like UniProt, which maps all back to the 'parent' gene. UniProt also uses s suffix (people don't really like to encode information in the ID)

- two options: (1)add splice variant ID in gene_id column or (2) in new column

- Suzi prefers the first option because it seems 'cleaner'; annotate to the actual product having activity; however several issues with that (which product used is not always specified, etc), so generally option 2 is favored

- Suzi: does that also include non-gene things like ESTs?

-David: that rises an interesting point: if there is an unpublished variant

[ACTION ITEM]: Chris will write a proposal for how to deal with this (including adding a new column?)

MicroRNA annotations

- Chris: Is it possible to allow more granular annotation so that someone can find all miRNAs, for example (GO help question earlier this week)?

- Pascale: isn't that dealt with in column 12 or so? and use SO terms there

- Yes but everyone has 'gene' there

- Should we not be annotating to gene products? yes, but most people do not do it yet

- Midori: we hadn't decided which part of SO we can use

-Suzi: I thought all SO terms were allowed (that made sense in that context)

- Suzi: back to microRNAs: there is the gene, the transcript, and the gene product (processed transcript)

- David: how does the SO treat the miRNAs?

- All gene products are grouped by functional categories; for mRNAs, is the SO talking about the pre-miRNA or the processed miRNA?

- Chris: I think they are both represented. If the SO needs to be fixed we'll do it.

- David: also, the miRNA field is changing really fast [ACTION ITEM]: (Think about) updating documentation to state that all terms from SO are accepted. Chris: we need to do this with/after dealing with the splice variants.