HCLSIG/PharmaOntology/Meetings/2009-06-25 Conference Call

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Conference Details

  • Date of Call: Thursday June 25, 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, Michel
  • Material for ICBO/DILS A0 poster at International Conference on BioMedical Ontology - Colin and Holger
  • AOB

Minutes

  • Attendees: Julia, Elgar, Jun, Bosse, Susie
  • Apologies: Michel, Christi, Colin, Joanne
  • <Susie> Susie: Reviews action items
  • <Susie> Elgar: Provides background on identified classes
  • <Susie> Elgar: Homework for everyone to go through the classes and point out ones that look relevant, and those that don't
  • <Susie> Elgar: Rows in red are ones that someone thinks should be deleted
  • <Susie> Elgar: We should review this further
  • <Susie> Elgar: Michel added 10 or so additional classes of interest
  • <Susie> Elgar: I've done something similar
  • <Susie> Elgar: I recommended ones for addition, and ones for removal
  • <Susie> Elgar: Christi has done the same
  • <bosse> Can link to the document be added to irc?
  • <Susie> http://spreadsheets.google.com/ccc?key=raxNP5J7F6eeypM3nQN5p0A&hl=en
  • <Susie> Elgar: Have copied Michel's comments into the spreadsheet
  • <Susie> Elgar: People had views on compound
  • <Susie> Elgar: Chemical, drug and compound are all similar
  • <Susie> Susie: Could start with drug for now
  • <Susie> Susie: If needed later we could drill down into small and large molecules
  • <Susie> Susie: Would drug refer to only active ingredient, or active ingredient and packaging
  • <Susie> Elgar: Should different isomers be classed differently too
  • <Susie> Elgar: I have the beginnings of an ontology that I could share
  • <Susie> Susie: Wonderful!
  • <Susie> Susie: Samson Tu has developed a Drug Ontology" that might be useful
  • <Susie> Elgar: I'll follow up on that
  • <Susie> Elgar: All agree that concepts such as cheminformatics and bioinformatics shouldn't be included
  • <Susie> Elgar: One definition was for 'cost benefit'
  • <Susie> Elgar: have gone through several defininitions
  • <Susie> Elgar: They get split up, and should strive to tie them together through properties and/or relations
  • <Susie> Susie: Hard to disagree with without concrete examples
  • <Susie> Elgar: We have many potential subclasses for chemicals
  • <Susie> Elgar: Based on that is chemical similarity
  • <Susie> Elgar: Whole thing on relationship between chemicals and drugs
  • <Susie> Elgar: Have many things under 'pharma'
  • <Susie> Elgar: Needs to be a clean out there
  • <Susie> Elgar: Polypharmacology could be removed
  • <Susie> Elgar: Don't know if we need all of these concepts
  • <Susie> Susie: Happy to use others ontologies where it makes sense
  • <Susie> Bosse: Observations and symptoms are both included
  • <Susie> Elgar: Those 2 terms haven't been put together yet
  • <Susie> Elgar: This isn't written in stone
  • <Susie> Elgar: First attempt to whittle it down
  • <Susie> Elgar: In area of observation of symptom also have terms such as patient prognosis
  • <Susie> Elgar: Could replace with 'diagnosis'
  • <Susie> Elgar: Diagnosis could be based on observations or symptoms
  • <Susie> Susie: Also need to consider concept of 'sign'
  • <Susie> Susie: Patients report 'symptoms' and physicians measure 'signs'
  • <Susie> Elgar: I don't actually like sign, symptom, or observation
  • <Susie> Elgar: I prefer phenotype
  • <Susie> Elgar: I think it's more neutral
  • <Susie> Susie: Sounds good to me
  • <Susie> Bosse: Phenotype is something very different to me
  • <Susie> Bosse: Interesting that we have different definitions
  • <Susie> Elgar: Phenotype might not be well understood by others and that would be a problem
  • <Susie> Elgar: Wanted to throw out industrial terms such as competitor
  • <Susie> Elgar: Michel want to throw out industrial terms such as competitor
  • <Susie> Elgar: But these things do matter to companies
  • <Susie> Elgar: If look at business analyst use case we will need these terms
  • <Susie> Elgar: May need streamlining
  • <Susie> Susie: Nice to keep something along the lines of 'organization' to reflect collaboration
  • <Susie> Elgar: Could be time to move to a different format
  • <Susie> Elgar: Still make comments in the spreadsheet
  • <Susie> Susie: Identify 3 or 4 areas to focus on for the next call
  • <Susie> Susie: Then add them to a strawman ontology
  • <Susie> Elgar: Sounds good
  • <Susie> Susie: What would be the best areas to focus on
  • <Susie> Jun: Impressed by how much is covered by the translational medicine ontology
  • <Susie> Jun: Look at LODD data sets to see if any concepts are missing
  • <Susie> Jun: Working through existing data would help make sure we are grounded
  • <Susie> Susie: Next week work more on classes
  • <ElgarPichler> http://esw.w3.org/topic/TMO_Review_MD
  • <Susie> Susie: the call after that look at the LODD data sets
  • <Susie> Elgar: look at link for other concepts which we may want to include
  • <Susie> Elgar: look to see if we are happy with that kind of structuring