HCLSIG/PharmaOntology/Meetings/2010-04-15 Conference Call
Conference Details
* Date of Call: Thursday April 15 2010
* Time of Call: 12:00pm - 1:00pm 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 quick start: Click on mibbit for instant IRC access
* Duration: 1h
* Convener: Susie
Agenda
- TMO Ontology - Elgar, Michel, Trish
- Demo Data - Michel
- Interface - Bosse
- eMerge - Chris
- IO Informatics Data - Elgar
- Inclusion/Exclusion Criterion - Michel, Bosse
- Drug Ontology Update - Susie
- Linked eHR - Susie
- Outreach (BioOntologies, NRDD, IHI, UPenn Translational Medicine) - Michel, Colin, Chris
- Upcoming Gathering - Susie
- AOB
Minutes
Attendees: Chris, Bosse, Rajesh, Michel, Joanne, Elgar, Trish
<Susie> TMO <michel> http://translationalmedicineontology.googlecode.com/svn/trunk/ontology/tmo.owl
<epichler> http://code.google.com/p/translationalmedicineontology/
<Susie> Michel: Made a pile of changes
<Susie> Michel: Mainly to allow us to better align with the data
<Susie> Michel: Reorganized some stuff
<Susie> Michel: Organized informational entities
<Susie> Michel: Put them into categories called 'Measures'
<Susie> Michel: There are clinical measures, drug measures, etc
<Susie> Michel: Overcomes the problem of lots of orphan terms
<Susie> Michel: Needed to organize roles and material entities
<Susie> Michel: Mainly talking about material entities, e.g. molecular entities
<Susie> Michel: Needed these categories for material entities
<Susie> Michel: Better organized the roles
<Susie> Michel: Created categories for roles where needed
<Susie> Elgar: Did the imported ontologies also change?
<Susie> Michel: Ensured all URIs we were using were correct
<Susie> Michel: Refreshed TMO external file
<Susie> Elgar: If imported ontologies change then there can be problems
<Susie> Elgar: So have been reading up on MIREOT
<Susie> Elgar: There can be probelms when revisions change
<Susie> Michel: Want file for TMO external
<Susie> Elgar: Want to be able to compare external connections
<Susie> Michel: Sometimes using MIREOT, and sometimes using our own term
<Susie> Michel: So was being inconsistent
<epichler> http://obi-ontology.org/page/MIREOT
<Susie> Joanne: My bias is to do MIREOT
<Susie> Michel: Ontology only extends RO, BFO, IAO
<Susie> Michel: We define terms for everything else
<Susie> Trish: Why do it the way you did Michel?
<Susie> Michel: Do that for stability
<Susie> Michel: Easier to do mappings
<Susie> Joanne: End up using term rather than defining it
<Susie> Michel: Don't need to change our terms if an external ontology changes
<Susie> Michel: Good to spend time to think about the terms that we need
<Susie> Michel: We did a good job
<Susie> Michel: Use RDFS label and Dublin core for definition
<Susie> Michel: 223 between TMO classes and 40 other ontologies
<Susie> Elgar: Please send any feedback to the group
<Susie> Demo Data
<Susie> Michel: The data stayed the same
<Susie> Michel: Equivalent mapping means we can query the data with any term
<Susie> Elgar: Do you have query examples written up?
<michel> http://esw.w3.org/HCLSIG/PharmaOntology/TMKB
<Susie> Michel: Queries are on the hcls page
<michel> http://esw.w3.org/HCLSIG/PharmaOntology/Queries
<Susie> Michel: See question 2 relating to diagnostic criteria for AD
<Susie> Michel: The query using inferencing
<Susie> Michel: Inclusion/Exclusion criteria are tied to the diagnostic criteria
<Susie> Michel: So is an example of reasoning across the ontology
<Susie> Michel: Q3 - is Donepezil available through medicare d
<Susie> Michel: restrict query to data in medicare d
<Susie> Michel: this also using reasoning
<Susie> Michel: So examples of example of subclass and equivalence reasoning
<Susie> Michel: Patient data is the weakest area
<Susie> Michel: Patient queries rely on the labels
<Susie> Michel: As opposed to picking a particular node
<Susie> Michel: Using relations to query across the structure of the output document
<Susie> Michel: Basically doing XML querying in RDF
<Susie> Michel: So it'd be good to make that more semantic
<Susie> Elgar: Were you able to use my mappings for drugs
<Susie> Michel: Think we should address is when we do the work on the patient records
<Susie> Michel: RxNorm will be exceptionally useful
<Susie> Elgar: let me know when you are ready
<Susie> Elgar: EricP pointed me to the XSL files for converting XML to RDF
<Susie> Michel: Will take a little time and effort to map into our ontology
<Susie> Susie: Janos has created a linked version of RxNorm
<Susie> Susie: He has licensing questions
<Susie> Michel: We are licensed for RxNorm
<Susie> Michel: And should be OK because it's in our KB
<Susie> Elgar: RxNorm is freely available
<Susie> Elgar: May be questions about redistributing
<Susie> Susie: In LODD we notify data source providers to check wwe are OK with licensing, and to promote RDF
<Susie> BioOntologies Paper
<Susie> Michel: Sent out the latest version about 1 hour ago
<Susie> Michel: Final comments would be good
<Susie> Susie: Take Christi's name off for now
<Susie> Michel: Need comments by the end of today
<Susie> Susie: Good job with the paper!
<Susie> User Interface
<Susie> Chris: Had call with Marshfield last week
<Susie> Chris: Luke couldn't make it
<Susie> Chris: Put many TMO folks could
<Susie> Chris: Asked specific questions to Adam
<Susie> Chris: Level and type of query across data is very timely and related to genotype/phenotype queries
<Susie> Chris: Uses eHR as data source, which is the best option
<Susie> Chris: Main question is the ability to perform powerful queries
<Susie> Chris: Talked about i2b2 approach
<Susie> Chris: TAlked about confidentiality
<Susie> Chris: Less issues if they use our tools
<Susie> Chris: Then try to spread across other groups
<Susie> Chris: Waiting to hear from Luke regarding his hopes, and our quesitons
<Susie> Chris: Luke will then run a potential collaboration by his board
<Susie> Chris: Wanted to use simple approaches to narrow the focus down
<Susie> Chris: Conor recommends we make simple little recommendations, one step at a time
<Susie> Chris: Marshfield patients have clearly indicated if they are happy for their data to be used for research
<Susie> IO Informatics
<Susie> Elgar: Chased on April 8
<Susie> Elgar: Heard back on April 9 that everything looks good
<Susie> Elgar: And that they will get in touch over the next weeks
<Susie> Elgar: Should chase them weekly
<Susie> Susie: OK. Let's keep tracking
<Susie> Outreach
<Susie> Basically done for BioOntologies
<Susie> IHI is our next opportunity
<Susie> http://ihi2010.sighi.org/
<Susie> We'll need to think how we can extend our content for healthcare
<Susie> Could work on the eHR extensions proposed by Michel
<Susie> Outreach
<Susie> 2 Gathering planned