HCLSIG/PharmaOntology/Meetings/2009-09-10 Conference Call
Conference Details
- Date of Call: Thursday September 10 2009
- Time of Call: 11:00am - 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: 2h
- Convener: Susie
Agenda
- Refinement of Classes and Class Definitions
- Use case polishing - Chris
- F2F meeting - Susie
- Progress on time line - Susie
Minutes
Attendees: Colin, Anja, Julia, Bosse, Christi, Trish, Elgar, Michel, Chris, Eric, Susie
Apologies: Elgar
<Susie> Susie: F2F
<Susie> Trish - likely to attend
<Susie> Christi - very unlikely to attend in person
<Susie> Bosse - Maybe able to attend
<Susie> Julia - Maybe able to attend
<Susie> Julia - Elgar may be able to attend
<Susie> Colin - Very unlikely I can attend in person
<Susie> Susie: Focus on next steps after the paper
<Susie> Susie: Everything is open, even wrapping up the task
<Susie> Colin: Ontologies need caring for, so unlikely we could wrap up the task
<Susie> Susie: Made comment to be somewhat provocative
<Susie> Joanne: It's likely the deadline for papers will be extended, so we may want to work on the paper during the F2F
<Susie> Susie: very good point. So let's have a flexible agenda, so we can easily work on the paper if the deadline is extended
<Susie> Susie: Use Cases
<Susie> Susie: Chris has worked to enhance the Chemogenomics and Pharmacogenomics Use Cases
<Susie> Susie: Susie will post onto wiki while Chris works out his login information
<Susie> Susie: Let's select 6 or so use cases during next weeks call to map to the ontology
<Susie> Trish: Want more than one ontology to make sure that we don't overfit it to a use case
<Susie> Susie: Let's also identify the one use case we want to pursue
<Susie> Julia: That would make Elgar happy
<Susie> Julia: Elgar also wants us to identify the data
<Susie> Colin: Seems like we're close to the point where we are going in circles with class definitions, so more of a focus on use cases would be good
<Susie> Susie: Will create a time line that we should work towards in order to make sure that we don't miss the deadline
<Susie> Susie: Classes
<Susie> Colin: Filled in class information
<Susie> Colin: Do we need 'ClinicalGuideline'
<Susie> Susie: Would be happy to just have 'ClinialProtocol'
<Susie> Joanne: Depends on use cases
<Susie> Susie: Use cases don't drill into these details a lot
<Susie> Christi: We should delete
<Susie> Colin: What about 'Clinician'
<Susie> Susie: Don't think we need it
<Susie> Christi: Maybe need specialities
<Susie> Christi: need role
<Susie> Colin: Like the idea of 'Expert'
<Susie> Chris: Isn't there something that lists all experts
<Susie> Susie: We're only looking for a minimal set of 30, so loose Clinicians
<Susie> Colin: Lets keep 'Expert' for now
<Susie> Colin: Company
<Susie> Susie: No
<Susie> Joanne: No
<Susie> Trish: Like company, but OK to go with concensus
<Susie> Colin: ConnectionTable
<Susie> Susie: Think it's too detailed
<Susie> Miche: Lots of in silico work
<Susie> Colin: Instinct is to keep it
<Susie> Colin: CostBenefitAnalysis
<Susie> Chris: anyone involved in this
<Susie> Christi: Something pharma looks at
<Susie> Chris: Rather important from clinical view
<Susie> Colin: Is this something we have data for
<Susie> Susie: Pharma interested in comparative effectiveness, disease population, patents
<Susie> Chris: Important in determining treatment
<Susie> Susie: Lets defer to Chime and Vipul
<Susie> Colin: Dosage
<Susie> Susie: Too detailed
<Susie> Christi: Too detailed
<Susie> Chris: CYP influences warfarin dosage
<Susie> Susie: Happy to cover dosage under ClinicalProtocol
<Susie> Michel: Don't think it should be under ClinicalProtocol
<Susie> Christi: See it as part of the treatment regiment
<Susie> Christi: Rather than ClinicalProtocol per se
<Susie> Colin: There isn't another ontology to defer 'Dosage' to
<Susie> Colin: Keep but specify as non-core
<Susie> Colin: Drug
<Susie> Colin: Covered by active ingredient, and pharma product
<Susie> Christi: Actually need as pharma product could be an insulin pen
<Susie> Colin: Effector
<Susie> Christi: Isn't a major piece, but is needed
<Susie> Colin: Shall we call it 'yes, but non-core'
<Susie> Colin: Finding
<Susie> Colin: Let's defer to OBI
<Susie> Susie: Need to include high level terms, but it seems too generic
<Susie> Chris: We've already compartmentalized everything, e.g. side effect, observation
- ** mib_2ah7oezt is now known as AnjaJentzsch
<Susie> Chris: What would blood test go into
<Susie> Colin: Isn't it a sign, as it's something that's discovered by a physician
<Susie> Colin: Can't we use 'BiologicalMeasure'
<Susie> Colin: Generic
<Susie> Colin: Were going to refer to Elgar's hierarchy
<Susie> Chris: Would like to keep, as several pharma drugs become a generic
<Susie> Colin: Don't think it's our job to keep track of names
<Susie> Susie: Delete
<Susie> Joanne: Delete
<Susie> Colin: HealthOutcome
<Susie> Colin: Do we need 'healthoutcome' and 'outcome'
<Susie> Colin: Delete healthoutcome
<Susie> Colin: Hypothesis
<Susie> Susie: Keep
<Susie> Christi:
<Susie> yes
<Susie> colin: Institution
<Susie> Colin: keep
<Susie> Colin: Lead
<Susie> Susie: Lead is very similar to compound
<Susie> Colin: Do we want to differentiate between compounds we're pursuing and not
<Susie> Colin: Isn't the ontology only going to be used on public data
<Susie> Susie: No, internal too
<Susie> Christi: Want to use it internally too, and likely extend
<Susie> Colin: Delete
<Susie> Colin: Medical History
<Susie> Colin: This is of interest
<Susie> Colin: Molecular function
<Susie> Colin: Already have 'pathway' and 'moa'
<Susie> Susie: 'MolecularFunction' is more fine grained that pathway or moa
<Susie> Susie: Want as much biological detail as possible
<Susie> Susie: Would prefer 'MolecularFunction' to 'Effector'
<Susie> Colin: Could hand of Effector to Chebi or GO
<Susie> Colin: 3DMolecularStructure
<Susie> Michel:How does this differ to ConnectionTable
<Susie> Colin: ConnectionTable is 2D only
<Susie> colin: Rename ConnectionTable to MolecularStructure
<Susie> Colin: Then say no to 3DMolecularStructure
<Susie> Colin: Molecule
<Susie> Colin: Don't need in addition to compound
<Susie> Colin: Patient
<Susie> Chris: may want to broaden to animal studies
<Susie> Susie: individual may not be sick
<Susie> Colin: re-name to subject
<Susie> Joane: not convinced
<Susie> Joanne: Maybe we should have more of a focus on defintions
<Susie> Colin: Absolutely need definitions, and more important than names
<Susie> Colin: Prognosis and PatientPrognosis
<Susie> Christi: Looked at this as part of costbenefitpiece
<Susie> Colin: Prognosis is an outcome that may or maynot happen
<Susie> Colin: that's a yes
<Susie> Colin: Receptor
<Susie> Colin: That's very specific
<Susie> Susie: Delete
<Susie> Colin: Regulator
<Susie> Colin: is this the biological process, or the organization
<Susie> Colin: can't be both
<Susie> Christi: Have RegulatoryAuthority below
<Susie> Colin: Too detailed as a biological process
<Susie> Colin: Repressor
<Susie> Chris: Have we included the compound that can extend the life of an active ingredient and/or making it work
<Susie> Chris: Drugs are used synergistically more often these days
<Susie> Colin: Added 'ActiveIngredientStabilityRegulator'
<Susie> Chris: Works for me
<Susie> Colin: Repressor
<Susie> Susie: Delete
<Susie> Susie: ResponseBySubjectToDrug
<michel> i had previously suggested 'excipient' for the supporting material of a formulation. this covers the cases we discussed
<Susie> Colin: Have side effect and outcome
<Susie> Chris: Scratch
<Susie> Colin: Risk
<Susie> Susie: Could be risk of developing drugs
<Susie> Susie: Have lists of factors that make targets good or bad
<Susie> Susie: Likely we wouldn't share the list externally
<Susie> Chris: Could be patient risk
<Susie> Susie: subject risk is covered by side effects, prognosis, outcome
<Susie> Susie: Risk of drug discovery and development isn't covered
<Susie> Susie: But not sure it's needed
<Susie> Susie: Delete
<Susie> Colin: Safety
<Susie> Colin: Does it show up in the data
<Susie> chris: Safety is becoming more individualized
<Susie> Susie: Largely covered by outcome, prognosis, side-effect
<Susie> Christi: Safety is largely tied ot outcomes
<Susie> Colin: Let's keep for now
<Susie> Colin: Re-name 'Stratification' to 'SubsetofPopulation'
<Susie> Susie: Could encompass geography, e.g. phenotype, genetic, life style
<Susie> Colin: Yes
<Susie> Colin: Study
<Susie> Christi: Why did we say maybe
<Susie> Susie: Did compare study and experiment
<Susie> Susie: Let's keep
<Susie> Colin: Syndrome
<Susie> Susie: It was my term
<Susie> Susie: A catch all for diseases that aren't fully defined yet
<Susie> Chris: Sometimes a collection of diseases is a syndrome
<Susie> Colin: TherapyCostBenefit
<Susie> Susie: similar to costbenefitanalysis
<Susie> Colin: delete
<Susie> Colin: We have 1 maybe, roughly 30 no, and roughly 60 yes
<Susie> Colin: Should make the ontology the size it needs to be
<Susie> Colin: Will create figure of the ontology
<Susie> Colin: Will create in Protege in OWL
<Susie> Susie: Should we include Time
<ericP> http://www.w3.org/TR/2006/WD-owl-time-20060927/
<Susie> Susie: Time relates to patient stage, patent duration, etc
<Susie> Anja: Recommend connect to higher level representation
<Susie> Chris: Interesting seminar coming up in PA
<Susie> chris: Will send details