Managers 16Aug06

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GO Managers call 16 August 2006

Calling in: Michael Ashburner, Judy Blake, Rex Chisholm, Jennifer Clark, Jane Lomax, Midori Harris, David Hill, Eurie Hong, Suzi Lewis, Chris Mungall

Minutes: Midori/Rex

some preliminary chat about traveling to Hinxton ...

David - plans for is_a complete paths in biological process

timing - some during MGED9 in Seattle
actual paths
need 'developmental process' as is_a parent (and sib of development)

David does agenda on the fly ...

Action items from last call

  • Jane will document is_a complete CC
not up yet, but ready to go
  • Jim Hu's GO wiki - David to send address
  • split annotation camp into computational vs. manual
based on experience with latest camp; they were duly warned that emphasis was on literature curation
mainly for Mike C/SGD
So will there be a 'computational-annotation' camp?
Judy - Mike C did say something about organizing it, maybe Sept/Oct; idea is we would promote SOPs
  • Will we use RCA for InterPro2go, TMHMM, etc?
wanted to try, but MGI ran into some difficulties
annotation camp recommendations for GOC
many at camp thought the policies were being set then & there
campers did think some should go to GOC
need input from Michelle Gwinn on proposed RCA usage
  • Eurie to start next newsletter
well under way; Kimberly will send it out
includes all items on list from previous call

Reference Genome progress

  • Rex has sent first gene list
too time-consuming for Rex to provide orthologs; MODs etc. to look up; seems to be working so far
will send UniProt IDs where available, otherwise Entrez Gene IDs
protein seq most useful for orthology determination
also consider connection between OMIM and UniProt
David - please use HGNC-approved standard name
another problem - in some cases, there's an enormous amount of literature; may have to refine understanding of 'complete annotation'
does 'complete annotation' for now mean using a set of recent + key refs, rather than all available?
David - risk of missing original basic biology
mouse has only 10-20 papers (cf S. pombe 80)
these genes very well studied in other species
Rex - issue is how to balance; different studies, different genes, different organisms
intentionally picked fundamental biology for first set, so most or all spp have orthologs; maybe alternate with genes where, say, mouse has lots of the experimentation
David - maybe put whole list somewhere for dbs to tackle at own pace (with tracker), rather than distribute piecemeal? MGI will have to pick & choose papers for some genes
Rex envisions people annotating, and annotations flowing into CVS by normal route; will assume a week's genes are done unless he hears otherwise (but note WB flow, with curation and testing on 4-6 week cycle)
hard to know when tasks are accomplished; want to minimize differenCes from dbs' usual procedures
David - tracker would only need to address Ref Genomes list; chart with genes and each db's progress; put on wiki
Judy - someone can fill in UniProt IDs & HGNC names; db reps can fill in their IDs
Rex - ask for ID and percent of literature annotated per gene
  • Action item: Rex (with help as needed) to put spreadsheet on wiki as table, with new columns as requested for UniProt, HGNC, etc. Run draft by GO managers; notify Reference Genomes list when it's ready.
  • Rex welcomes input on points from longer ref genome email
  • Rex will continue sending emails to both reference-genome and GO managers

User Advocacy progress

  • Newsletter
  • Group priorities on wiki

Annotation Outreach progress

  • Waiting to hear from PIs on priority list

Ontology Development progress

  • CNS development additions committed
  • progress on immunology (Alex)
  • PAMGO content meeting - about 150 new terms (Jane, Amelia, PAMGO cuRators)
  • New tracker wish list (David & Midori)
  • Action item: Midori to put wish list on wiki
  • Many people want quick way to get new terms in
David - allow people to submit OBO stanza
Suzi - need faster initial response
Suzi - three issues: ease of submission; ranking ease of implementation; response turnaround time
Jen - gets faster response phoning (or Skype) than SF comments or email
aside on Skype
David - we have a list of MOD curators who are ontology development group members; don't hesitate to ask them about requests in their area
Suzi - may be able to do better than SourceForge now

Software group

  • AmiGO progress
Seth visited SGD to gather requirements, etc.
want to do something more 'with-it'; go in new directions with AmiGO
AmiGO working group IRC tomorrow? (there was one yesterday)
Suzi & Chris to join next AmiGO chat, whenever it is
Eurie - waiting for Ben Hitz to return from vacation
TAIR switched to RefSeq IDs for sequences, which has slowed loading (4-fold!!!); updates no longer 3x/week at the moment
some discussion of technical aspects and possible fixes; SGD programmers are looking into it
considering using Chado as underlying db, with bridge layer to be interoperable with existing schema
a few technical points; stay in touch with Gail Binkley (SGD DBA) as this progresses
  • John's history toolkit proposal
is the managers list the best place to discuss that sort of thing?
several people say yes
also good to include software people for technical aspects
trial would be feasible, using obodiff; use as basis for future development

Advisory Board Meeting

  • Any comments on the agenda?
Judy - working with Peter Tarczy-Harnach (advisor); he's found a room
PIs will send out CD to participants, with material from StX meeting, research portion of grant, study section reviews and our response, etc.
Suzi - basic time frame settled, e.g. presentations from 8 AM - 1 PM
please add comments to wiki; also any other material to put on CD
Judy - could try to get presentation drafts beforehand - in time for next managers call
David & Midori to tag-team on biological aspects of content
Judy - logistics; 20 people listed; suggestions for additional people (e.g. Monte)
Craig Neville-Manning can't come this time
Judy will plan for 25
  • Action item: advisory board meeting presenters to prepare talk drafts in time for Aug 30 call


  • Rex - table on wiki (for people who joined late; see above)
wiki table setup is ugly; may not work for 20-25 columns -- and hundreds of genes -- we'd need; is there any other technology we could use?
try Google spreadsheets
  • Ontology stuff from Swiss-Prot meeting (Suzi)
round table of people interested in disease ontology; want to collaborate but also have to get on with own projects
Rex - we've put in tons of work so far
have an outline (tho not one that Barry would like)
has multiple parentage
may be good enough to start with, tho horribly flawed
will fix problems, but have to ignore much of what Barry & Anand recommend
Suzi - we now have a window; prospective users can't wait
Rex - many problems easily fixable, e.g. incorrect parents, incomplete paths
Owen White, Win Hide and others can try to use it, and give feedback
Rex - file is 25 MB
put on ftp site?
reason not on public web yet is that it includes cross-refs to SNOMED
Suzi - might be fine; only has xref, nothing more, and xref can be ignored
Michael - would SNOMED object to the xrefs?
Rex - that's the worry
Michael - if you use only the SNOMED ID, there's no proprietary info ...
Rex - there's also a version With the SNOMED xrefs stripped out
Michael - Yves Lussier is on SNOMED board; Rex has talked to him; MA will 'put pressure' on Yves
make it available one way or another, then make sure others (e.g. Owen, Win) can map to their systems
latest isn't on OBO site yet (v3beta30)
organized using FMA and GO biological process
  • Action item: Rex to make file available to GO managers by Aug. 23rd

Next call

August 30, 8 AM PDT, 10 AM CDT, 11 AM EDT, 4 PM BST

agenda: Midori

minutes: Jen

(from the rota)

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