HCLSIG/PharmaOntology/Meetings/2010-04-08 Conference Call

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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

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