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.



  • 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.


  • 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


  • 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.