HCLSIG/PharmaOntology/Meetings/2009-09-03 Conference Call
Conference Details
- Date of Call: Thursday September 3 2009
- Time of Call: 12:00pm - 1pm ET
- 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
- Refinement of Classes and Class Definitions
Minutes
Attendees:Susie, Colin, Elgar, Chris, Julia, Bosse, Trish, Christi, Joanne, Scott
Apologies: Michel
<Susie> Susie: Goal to refine terms
<Susie> Susie: Did action items of including definitions
<Susie> Susie: Elgar did action of re-organizing the spreadsheet
<Susie> Colin: Moved definite drops onto another tab
<Susie> Elgar: Didn't delete any lines
<Susie> Elgar: Changed 'keep status'
<Susie> Elgar: Changed how 'keep status' is represented
<Susie> Elgar: Added column call 'class_type'
<Susie> Elgar: Could be used to represent where a class is biological, chemical etc.
<Susie> Colin: I'd like to work on this
<Susie> Elgar: Great
<Susie> Elgar: Added column for 'External Reference'
<Susie> Elgar: this would be an xref
<Susie> Eglar: column is sparse at the moment
<Susie> Elgar: Added another column called 'sameas/comparedto'
<Susie> Elgar: Lots of comments like 'is equivalent to', 'think about replacing with', 'is synonym for'
<Susie> Elgar: added those to this new column
<Susie> Trish: Can 'sameas' refer to another term in our list
<Susie> Elgar: It usually is, but not always
<Susie> Trish: 'sameas/comparedto' sounds like formal ontological relations
<Susie> Elgar: They aren't meant to be formal terms
<Susie> Colin: It could also relate to a subclass
<Susie> Chris: Terms we want to make sure they are accounted for, but will likely scratch at the end
<Susie> Elgar: 2 or 3 terms mentioned multiple times
<Susie> Elgar: Have collapsed into one record
<jluciano> scott - i added you. did you get the link (in your email)?
<Susie> Elgar: Except for 'diagnosis', which has 2 distinct definitions
<Susie> Elgar: Ended up with 55 terms that we definitely want to keep, and 50 maybes
<jluciano> i see scott on the spreadheet sharing. good!
<Susie> Colin: Sub-classified 'diagnosis'
<Susie> Elgar: Also cleaned up words, e.g. all capitals
<Susie> Colin: Don't see Susie's definitions
<Susie> Susie: Didn't complete the 'curator' column
<Susie> Susie: Should we work our way down the spreadsheet
<Susie> Colin: Couldn't we start by removing the ones we'd agreed not to keep
<Susie> Elgar: Was keeping them at the bottom of the spreadsheet one last time
<Susie> Christi: Are there comments for the terms we decided not to keep
<Susie> Elgar: There are comments
<Susie> Elgar: I won't be here in 2 weeks, so have 2 suggestions
<Susie> Elgar: Colin agreed to add the class type
<Susie> Elgar: Useful if we add the external references
<Susie> Joanne: Is it OK for me to edit the spreadsheet, e.g. add definitions
<Susie> Elgar: Sometimes as a group we have multiple definitions for a term
<Susie> Elgar: Am trying to make it clear who said what
<Susie> Christi: Please do just contribute
<Susie> Elgar: Good to include the URI to the definition source
<Susie> Joanne: Definition source is important
<Susie> Christi: We capture in column I
<Susie> Elgar: Please fill any gaps
<mscottm> http://code.google.com/p/ontology-of-clinical-research/
<Susie> Susie: Calls are weekly
<Susie> Susie: Next call runs from 11am - 1pm ET
<Susie> Scott: 2 ontologies of interest
<Susie> Scott: Have we contacted Samson about Drug Ontology
<Susie> Trish: Drug Ontology isn't published yet
<Susie> Scott: Interest in OCR?
<Susie> Trish: We have mentioned OCR, but not recently
<Susie> Trish: It may have some relevant terms
<Susie> Trish: Need to discuss similarity in the paper
<Susie> Colin: Am adding content to the paper as things come to mind
<Susie> Susie: Colin agrees to drive for a bit
<Susie> Joanne: Do the terms meet our use case requirement?
<Susie> Susie: Create first draft of the ontology
<Susie> Susie: Refine use cases
<Susie> Susie: Then check ontology meets our use case needs
<Susie> Joanne: The ontology and the use case should be aligned
<Susie> Trish: Doing work in waves
<Susie> Trish: Started with use cases, then went over to the terms, and will go back to the use cases
<Susie> Colin: Do we need animal and clinical trials
<Susie> Chris: They should stay separate
<Susie> Chris: At times you might want to focus on either the animal area or the human area
<Susie> Elgar: Study wouldn't preclude whether it's an animal or a human
<Susie> Chris: Atul Butte does differentiate between human and animal
<Susie> Christi: Would be happy for study to break down to human and animal
<Susie> Colin: Do we want antibody to be a drug or a target
<Susie> Chris: Have antibodies that are both drug and target
<Susie> Colin: Will it be subclass of a drug and target
<Susie> Scott: Can't it be a role?
<Susie> Scott: Might come across new drugs
<Susie> Colin: Under drug we shouldn't be looking to copy the SO
<Susie> Colin: For this reason, we should define antibody under drug and target
<Susie> Susie: Happy for antibody to be a subclass of drug and target
<Susie> Colin: Why such interest in antobodies
<Susie> Susie: Increasingly used in drug discovery, and different drug discovery process
<Susie> Colin: Will add a note stating interest
<Susie> Trish: May also want to mention safety related concerns
<Susie> colin: chemical Substance
<Susie> Colin: not single molecule, but portion of stuff
<Susie> Colin: seems implicit to me
<Susie> Chris: Sometimes a second substance that is active too, but isn't the active ingredient in the drug
<Susie> Scott: Touching upon active ingredience, etc.
<Susie> Chris: Have many things that need to be accounted for
<Susie> Colin: can be a separate molecule to represent the other thing
<Susie> Bosse: You had a model for drug names
<Susie> Bosse: Is it important that all these things are included
<Susie> Elgar: We did agree with a slight variation
<Susie> Elgar: compound, drug, pharmaceutical product, brand
<Susie> Elgar: we have compound
<Susie> Elgar: some discussion about drug, and replacing with active ingredient
<Susie> Elgar: agreed on pharmaceutical product, and brand
<Susie> Elgar: Also have inactive ingredient
<Susie> Elgar: which makes active ingredient
<Susie> a more useful term
<Susie> Elgar: still questions with drug
<Susie> Elgar: Thompson Reuters mash all terms up in one bag for their pharma product
<Susie> Elgar: We should do better than that
<Susie> Elgar: happy with what we have
<Susie> Colin: People think they have careful definitions for drug, but they are all different