Managers 16Jan08

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GO Managers, Weds. Jan. 16, 2008 8a.m. PST, 9a.m. MST, 10a.m. CST, 11a.m. EST, 4p.m. GMT

Agenda/chair: Midori

Minutes: Pascale

Present: Midori, Pascale, Jen, Chris.

Review Action Items from previous meeting

  1. All: review document on regulation wiki page
  2. Chris: Draft proposal for GO slim maintenance. [in progress will send email to managers with the different options by the next meeting]
  3. Pascale, Jim et al.: Continue discussing wiki-based annotation tool.
  4. Jen: Organize conf call on gohelp technology. [Done; problem went away magically]
  5. Pascale (and rest of annotators): Continue improving annotation SOPs.
  6. Judy: Contact sea urchin db about doing GO annotation. Mike had contact with the Sea Urchin group and they are not ready to annotate yet. They are still assembling the genome. We should contact them again maybe in April or March.

[to revisit]

  1. See if we can collaborate with journals to obtain annotations from users. Responsible groups: managers, software group and annotators?: Test various methods of accepting user submissions for annotation; converge on best solution, and seek journal buy-in.
  2. Tanya and managers: Schedule Webex/call for Tanya to present her annotation-acquisition talk.
  3. Midori: Follow up on fungal terms with Val and Maria for sensu work: [Done]
  4. Chris: Ask the wider group whether the ontology development wiki should be public. Maybe also there are better ways to link the two wikis?

Individual Manager reports

Ontology Development


many relationship fixes; ready to deploy 'regulates' relationship; draft announcement email on wiki:

  • Chris: summary of achievements: repositioned many of the is_a relationships so that they are more accurate, ie structure of the graph is improved. This allows better statistical analyses using the GO. Would be nice to quantify this, for example by taking papers that used GO and repeat analyses and see if results are better. Added >900 relationships.
  • See wiki for all details

In progress

Transport, electron transport

Next priorities

Function- process links?

Outreach/User Advocacy


Avian annotation workshop

Fiona McCarthy is organizing an Avian annotation workshop (Miss. St University), May 19-20, 2008


Fiona is giving a GO tutorial at the ISAFG - International Symposium on Animal Functional Genomics.



  • Set up an instance of AmiGO at Berkeley running with all the IEAs to test what problems are in moving on with this
  • Annotation cross products: (extra column in annotation file): Evelyn sent some examples

see Chris would like some more examples

Reference Genomes


  • At the last conference call there was a big discussion about how should Interpro2 GO and other GO mappings be used (IEAs, or can they be 'upgraded' to ISS). The annotation guidelines clearly state that ISS can be used for domain analysis, but different databases have different practices.
  • One issue (related to Pascale's two action items) is that we need to figure out how to deal with annotation practices, SOPs, Quality Control, etc. It can be in the context of the reference genome group (as this involves or should involve all the GOC curators), but we need to set up dedicated meetings or means of communication for this.


  • Avian annotation workshop May 19-20, 2008
  • Jen gives a tutorial in Belgium (funded by EBI) Feb
  • Midori will give a talk at the London School of economics in march

Collaborations and Interactions, active and new

  1. Report from Larry Hunter on Jan 11th meeting re NLP & ontology QA

Several people met in person and by webex/skype. Larry presented ways to use Natural Language Processing to use with ontology quality control. Jen thought it was helpful and would like more discussion. Chris suggest starting with a wiki page. Should this be on the public wiki ?

Operations and Procedures


Staffing and Personnel

Amina has accepted the OBO-Edit developer position :)

Budget issues



  • Erika and Jen wrote a paper about the muscle meeting; asked one journal if they'd consider such a paper. Awaiting reply.
  • Pascale sent a draft of reference genome paper to some people for help.
  • Erika Feltrin is writing her PhD thesis, which describes the muscle and cns content meetings, and her work on central nervous system annotation and ontology content. It also covers her work on the disease ontology.

Other Current Topics and Concerns

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