HCLSIG/PharmaOntology/Meetings/2009-06-11 Conference Call

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Conference Details

  • Date of Call: Thursday June 11, 2009
  • Time of Call: 12:00pm Eastern Daylight Time (EDT), 17:00 British Summer Time (BST)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: +33.4.89.06.34.99 (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 42572 ("HCLS2").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for details, or see Web IRC)
  • Mibbit instructions: go to http://www.mibbit.com/chat and click the server link. Enter irc.w3.org:6665 into that box, enter a nickname, and enter #HCLS2 for the channel
  • Duration: ~1h
  • Convener: Susie

Agenda

  • Review Actions
  • Review of Classes and Class Definitions - Colin, Christi, Elgar, Trish, Bosse
  • Review of Use Cases - Colin, Susie, Christi
  • Material for poster at International Conference on BioMedical Ontology - Colin and Holger
  • DILS abstract submissions - Christi
  • Review roadmap dates - Susie
  • AOB

Minutes

Attendees: Colin (Co), Elgar (E; scribe), Christi (Ch), Michel (M), EricN, Susie (S)

Apologies: Julia, Trish

  • 12:08 action items
  • 12:08 ElgarPichler S: review of action items
  • 12:08 ElgarPichler S: need to add details to use cases
  • 12:09 ElgarPichler Ch: created use case - wants feedback
  • 12:10 ElgarPichler -> Ch to iterate on initial use case
  • 12:10 ElgarPichler Co: still working on assignment, maybe done in 2w
  • 12:11 ElgarPichler Ch: Helen wanted to look at SK2 - no update from her
  • 12:13 ElgarPichler S: will upload ICBO poster, had problems with upload; changed ontology name on abstract
  • 12:13 ElgarPichler S: have identified logos (W3C, SemWeb) that we can use for posters
  • 12:16 *** michel joined #HCLS2
  • 12:16 ElgarPichler E: had problems with access to first Google doc - is resolved now
  • 12:17 ElgarPichler Ch: ontology name also changed for DILS poster
  • 12:17 class definitions
  • 12:18 ElgarPichler Co: no useful ontology for assigned chem concepts
  • 12:19 ElgarPichler Co: all except Julia submitted defs
  • 12:20 ElgarPichler E: Julia can't make it today, but was working on it, will upload her contributions as soon as possible
  • 12:23 ElgarPichler S: shall we go over list of concepts - decide which ones to keep
  • 12:23 ElgarPichler E: maybe do this as homework
  • 12:24 ElgarPichler Co: added column for that on spreadsheet
  • 12:24 ElgarPichler S: who should we consult on ontology
  • 12:26 ElgarPichler S: call to Larissa
  • 12:26 *** eneumann joined #HCLS2
  • 12:27 ElgarPichler M: will look over TMO too
  • 12:28 ElgarPichler E: any problems with approach of looking up classes in OBO, Wikipedia, etc.
  • 12:28 ElgarPichler Co: just with chemical concepts, not well covered there
  • 12:28 use cases
  • 12:30 ElgarPichler Ch: reviewed Alzheimers UC
  • 12:31 ElgarPichler Ch: with animal UC: problems: which animals to use; how to compare to human data ...
  • 12:32 ElgarPichler S: how common are transitions between various animal models
  • 12:33 michel Macaca mulatta = rhesus monkey
  • 12:33 ElgarPichler Ch: mostly do 4 animal models: mouse, monkey, rat, dog; question: are these enough?
  • 12:34 ElgarPichler Co: which monkey
  • 12:34 michel genome view: http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9544
  • 12:34 ElgarPichler Ch: not sure, but thinks only one species mostly used
  • 12:36 michel Rhesus macaque is an important animal model for many human diseases including AIDS
  • 12:36 ElgarPichler M: important concept: how to translate from simple system to human
  • 12:36 michel but we should be general
  • 12:36 michel that we capture the idea of animal models
  • 12:36 michel but it would be useful to have a specific one
  • 12:36 ElgarPichler Ch: on wiki doesn't want to go into details on experiments for animal models
  • 12:38 ElgarPichler M: suggest to document specific animal UC
  • 12:38 ElgarPichler Ch: don't have a specific case now - would also have to check if such data could be released
  • 12:40 ElgarPichler M: thinking of mice model to investigate stroke conditions - research done locally ...
  • 12:41 ElgarPichler S: would be interesting to use this for UC
  • 12:42 ElgarPichler S: UC on pharmaco/chemogenomics?
  • 12:42 ElgarPichler S: could have tie-in to integrative genomics UC
  • 12:43 ElgarPichler M: interested in UC, where specific drugs are given to patients with specific genomic makeup, considering dosing regimen, etc.
  • 12:44 ElgarPichler M: will try to prepare this UC for discussion at next TC
  • 12:44 posters
  • 12:45 ElgarPichler Co: still have upload problem - will check if uploading works
  • 12:46 ElgarPichler Co: working through abbrevs. on S's drug pipeline chart
  • 12:49 ElgarPichler Co & S: discussion of pipeline representation for poster (critical path picture, ...)
  • 12:49 ElgarPichler S & Co: will upload poster before starting vacation
  • 12:51 ElgarPichler Ch S: discussion of poster printing logistics, poster size, ...
  • 12:52 ElgarPichler Co: best to email Barry for poster dimensions
  • 12:55 ElgarPichler S: can we use same poster for ICBO & DILS
  • 12:55 ElgarPichler Co: think that would be OK
  • 12:56 ElgarPichler S: actual paper will only be published by ICBO
  • 12:57 roadmap
  • 12:57 ElgarPichler S: initially allocated time for project: middle of March to November
  • 12:58 ElgarPichler S: still working on UC - finalize by end of July
  • 12:59 ElgarPichler S: identify 30 classes and linkage point - push deadline also to end of July
  • 12:59 eneumann q: Is anyone planning on being at ISMB in a few weeks?
  • 13:00 ElgarPichler S: decide on UC in early August
  • 13:01 eneumann Note: there will be a SW BOF at ISMB, where we plan to have a discussion on ontology work
  • 13:01 ElgarPichler S: push out component build for ontology to October and light-weight application build to December deadline
  • 13:01 colin Hi eneumann, i'm coming to ismb.
  • 13:02 michel i'll be at ISMB also
  • 13:02 eneumann Great-- we should coordinate a bit for that
  • 13:02 michel sounds good
  • 13:02 michel do you have a day in mind
  • 13:03 eneumann Either Tues or Wed, will post on the mailing list
  • 13:03 michel k - let me know what i can do to help

Action Items

  • Julia to upload definitions to Google doc
  • all to rank TMO classes by importance (keep|discard for next iteration)
  • Christi to iterate on initial use case and animal use case, check on availability of data
  • Michel to check on availability of data for mouse model / stroke conditions use case
  • Colin to upload poster before going on vacation
  • Christi to check on dimensions for posters
  • [anything I missed?]
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