Managers 25Oct06

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MINUTES: Oct 25 2006

Minute taker: Chris (first half) & David (2nd half)

Review previous Action Items from previous meeting

David, Judy, Suzi, Jane and Chris to report back to managers about meeting with Jonathan Liu


Chris will take a closer look at this

Mike to send list of people with cvs write-access


Jane and Jen to feedback OE issues to OE WG

This is from the RSC workshop


Jane and Eurie to send out proposal for users meeting before next meeting

new proposal for Users meetings (

done. on wiki.

Synopsis: No longer have single users meeting. User base is broad: annotators, data miners, text miners, bench biologists, etc. Instead the plan is to go to biology focused meetings; also larger society meetings, eg mitochondrial localisations. 3rd type of workshop like PAG. Also emerging fields - eg interation networks.

Judy: in addition, target meetings that we're not integrated with. keeep note all the mtgs we're going to.

David suggest a shared calendar? even a rough one.

Some discussion about how booths are expensive (purchase, shipping); Judy & Rex like posters. David suggests workshops.

Everyone to add agaenda items for Jan meeting to wiki

ACTION: everyone

Jane to feed this back to ChEBI, see where they want to go next


Jane to write a message template to say managers meeting minutes available, and send around


Jen, Midori and John to look into web conference options more fully and report back

Jen vanishes mysteriously

David & tanya have been using webex + skype, 4 people at once. Buggy but works. Voice poor. Will do another trial with Jen. Has worked well for isa completion so far. Michael mentions Skype beta (video)

Suzi to find out whether BaseCamp has shared task manager/calendar

website (

ACTION: suzi

Individual Manger reports

Ontology Development

report on is_a complete (

Those with no is_a parents tend to have no aristotelian definitions

Going through alphabetically: currently on "P"s

posted on wiki, scratch directory in cvs

Some discussion on aligning with ChEBI with response to drug terms.

ACTION: set up conf call with CHEBI?? Chris interested in partaking


My notes say:

ASP Copenhagen



Reference Genomes

 1. We have been doing 22 genes a month. Most are up to date. We want
    to have a graphical representation of the progress.
 2. Karen Eibeck is starting to help with visualization tools and metrics
       1. We will use SO to define categories for the metric of the
          number of genes (protein coding, etc).
       2. Have defined 8-10 types of “genes” for which we want to have
          information. Genome databases will be responsible for
          identifying these in their organisms. Eventually we will
          need a FASTA file for protein sequences and RNA sequences.
          There is some concern that there will be duplication of
          proteome sets from the same organism.

ACTION ITEM: Eurie will add Karen to the manager’s mailing list

User Advocacy

1. Held the first meeting of the AMIGO HUB group. The final release of AMIGO will be almost entirely an interface change. Mock-ups are almost finished and there is a target release date of mid-November.


1. Looking into data structures for doing cross-products during annotation

2. Mary Dolan is now part of the group

ACTION ITEM: Chris will look at the files provided by Jonathan Liu and the MIT group.


We need to start better organizing submeetings that are evolving around main meetings or other meetings where many GOC members will be.


1. Rex is collaborating with Peter Hornick (SP?) to compare our annotations with annotations made by his text-mining tool, biomediator.

2. Aspergillus has approached Jen about providing annotations.

Operations and Procedures:

ACTION ITEM: The advocacy group will look into some type of calendar to keep track of which meetings are being attended by GOC members.

Staffing and Personnel

1. Jen and Rex will be away for the next management call.

Budget Issues

1. The EBI folks are finally getting new computers!


1. OBO-Edit paper has been submitted to Bioinformatics

2. The ‘Instance’ paper has been submitted to PLOS-Computational Biology

ACTION ITEM: Judy will send a copy of the instance paper to Chris and Michael.

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