HCLSIG/PharmaOntology/Meetings/2010-04-08 Conference Call
Conference Details
* Date of Call: Thursday April 8 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
- Data - Michel - Ontology - Elgar, Colin - Interface - Bosse - eMerge/ IO Informatics - Chris, Bosse, Elgar - Outreach (BioOntologies, NRDD, IHI - Michel, Colin, Chris
- eHR/FDA, etc Outreach discussion - All
- Inclusion/Exclusion Criterion - Michel, Bosse
- Drug Ontology Update - Susie
- Other Outreach
- UPenn Translational Medicine (ITMIT) - Chris - Upcoming F2F - Susie * AOB
Minutes
Attendees: Bosse, Chris, Janos, Jim, Elgar, Michel, Trish, Susie
Apologies: Colin
<Susie> TMO Data
<Susie> Michel: Been preparing paper for BioOntologies submission
<Susie> Michel: When do we decide to include terms and when don't we?
<Susie> Michel: I'm not sure how we're deciding when to import terms and when not to
<Susie> Elgar assessed terms one by one
<Susie> Elgar: depending upon what other terms existed in ontologies
<Susie> Elgar: I never wanted canonical mappings
<Susie> Elgar: I want to leave the user to decide which ones to map to
<Susie> Elgar: Should decide how we can make the mapping more dynamic
<Susie> Michel: For ontology we can identify equivalent types as an annotation
<Susie> Michel: Could also map the formal equivalence statements
<Susie> Michel: These statements are useful for integration
<Susie> Michel: I'm happy to do that work
<Susie> Michel: Will check that our mappings are good
<Susie> Michel: And that they are used in the knowledgebase
<Susie> Trish: We could use SKOS properties
<Susie> Michel: Does SKOS have annotation properties?
<Susie> Michel: Want to make sure that we don't mix types
<Susie> Trish: I'd need to check into this, but it would be unfortunate if we can't use SKOS
<Susie> Michel: It's just that the SKOS terms couldn't be included in an OWL ontology
<Susie> Michel: Do you stick it an ontology as an annotation property
<Susie> Michel: Or do you have a separate document that includes the terms
<Susie> Michel: I'll arrange an offline call with Trish to discuss more
<Susie> Michel: Had to do syntactic mappings from ontology to database
<Susie> Michel: These need to be updated
<Susie> Michel: Need to include mappings to fake patient records
<Susie> Janos: What is the drug identifier?
<Susie> Susie: We used NDC
<Susie> Michel: I RDFized the NDC codes, but it didn't link to anything
<Susie> Janos: there are a few NDC codes, but the best ones are the 10 digit ones
<Susie> Janos: RxNorm records are better, and may help with the mapping
<Susie> Elgar: Will create the RxNorm data set
<Susie> Elgar: Will do this weekend
<Susie> Michel: Will work out how to exchange the data
<Susie> Janos: RxNorm maps to SNOMED, and other ontologies
<Susie> Michel: Was underwhelmed by NDC work
<Susie> Michel: Using RegEx matching against data set labels
<Susie> Michel: So needed queries that matched syntactically
<Susie> Michel: Will have version of paper for people to review by early next week
<Susie> Michel: The deadline for submission is next Friday
<Susie> Susie: Colin has decided that he doesn't want to lead the IHI paper
<Susie> Susie: Shout out if you'd like to take the lead
<Susie> Michel: Paper looks well positioned for IHI as their CFP includes references to Semantic Web
<Susie> Michel: Continue focus on patient records, and what other people are doing, then we can have some nice stuff for the IHI paper
<michel> http://ihi2010.sighi.org/
<Susie> Chris: Want to give an update on eMERGE
<Susie> Chris: Having follow up calls with Luke at Marshfield
<Susie> Chris: Sounds like they are getting data and dumping it into access
<Susie> Chris: Connor will participate tomorrow
<Susie> Chris: Few opportunities
<Susie> Chris: Use of ontology itself
<Susie> Chris: Unity of data across network
<Susie> Chris: User interface
<Susie> Chris: Have put some minutes online
<Susie> Chris: Also putting notes into a GoogleDoc
<Susie> Chris: What are 1 or 2 steps we could do that Luke could do with the data
<Susie> Chris: And thereby show the utility of what we can contribute
<Susie> Chris: This depends upon Luke's goals
<Susie> Chris: Could relate to query, storage, or linkability
<Susie> Chris: We should think of 1 clear thing to do that others could apply
<Susie> Chris: Lots of interest
<Susie> Chris: And they've just received another 15 million from the government
<Susie> Elgar: Approached by IO Informatics about supplying clinical data sets
<Susie> Elgar: Have exchanged emails
<Susie> Elgar: They are still interested
<Susie> Elgar: But are very busy
<Susie> Elgar: They say that they'll make it happen
<Susie> Elgar: Don't know how big the data set is, or the focus of the data
<Susie> Elgar: Very cautious as it's real patient data
<Susie> Susie: Need to be very wary of government regulations, and secondary reuse of patient data
<Susie> Chris: Need to demo without over stepping bounds
<Susie> Chris: Maybe a good way is to advise other organizations rather than doing it ourselves
<Susie> Chris: So we would just be giving them the tool
<Susie> Susie: Maybe we should just use fake patient data for our demos
<Susie> Susie: And advise others
<Susie> Susie: And take learnings and apply to our demos
<Susie> Elgar: Will present on TMO at Bio-IT World
<Susie> Inclusion/Exclusion Criteria
<Susie> Michel: Nothing new
<Susie> Chris: Waiting to finish my paper before approaching UPenn Translational Medicine
<Susie> Trish: TMO is listed in BioPortal
<Susie> Trish: Need contact point
<Susie> Susie: Will use new group email for contact
<Susie> Michel: Will invite lead developers to be on the email address
<michel> created a new TMO administration mailing address: tmo-administration@googlegroups.com
<Susie> Susie: Will name group TMO task in W3C's HCLS IG
<Susie> Trish: I have loaded TMO into webprotege
<michel> http://bmir-webprotege1.stanford.edu