HCLSIG/PharmaOntology/Meetings/2009-09-03 Conference Call

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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

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