HCLSIG/PharmaOntology/Meetings/2010-05-20 Conference Call

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Conference Details

* Date of Call: Thursday May 20 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: Elgar
* Scribe: Bob, Elgar


Agenda

  • CPR Presentation- Chime
  • TMO Updates - Michel, Elgar
  • OGMS Review - Bob
  • Patient Mapping - Michel, Chime, EricP
  • Sources of Patient Data - Scott
  • Provenance Requirements - Joanne
  • Interface/eMerge - Bosse, Chris
  • Outreach (IHI, UPenn Translational Medicine) - Michel, Susie
  • AOB


Minutes

Attendees: Bob, Bosse, Chris, Elgar, Julia, Matthias, Paul, Scott, Trish

Apologies: Chime, Susie

12:03 <mscottm>  Zakim, this is transmed
12:03 <Zakim>    ok, mscottm; that matches SW_HCLS(TransMed)11:00AM
12:03 <mscottm>  Zakim, who is here?
12:03 <Zakim>    On the phone I see Bob_Powers, +0151709aaaa, +1.781.431.aabb, ??P17, +1.781.839.aacc, mscottm, +46.4.63.3.aadd
12:03 <Zakim>    On IRC I see Julia, Bob, RRSAgent, Zakim, mscottm, epichler, matthias_samwald, ericP

CPR Presentation        
      <epichler> skipping this item since Chime is not on call

TMO Updates
      <epichler> Elgar: still working on drug part of ontology
      <epichler> don't know if Michel has made any additions
12:04 <Bob>      Elgar using rxNorm for drug ontology
12:05 <Zakim>    + +1.302.598.aaee
12:05            *** bbalsa joined #HCLS2
12:05 <Bob>      Trish: TMO is uploaded into Bioportal
12:06 <Zakim>    + +1.215.628.aaff
12:06 <Bob>      Trish: need to get the automatic updates going
12:06 <Zakim>    - +1.302.598.aaee
12:06            *** pkonstant joined #HCLS2
12:06 <epichler> have problems with audio 

OGMS Review

12:02 <Bob>      OGMS Ontology of General Medical Science
12:02 <Bob>      OGMS Google group http://groups.google.com/group/ogms-discuss
12:03 <Bob>      OGMS Google code http://code.google.com/p/ogms/
12:07 <epichler> Bob: OGMS (ont. of general medical science) review
12:08 <Zakim>    + +1.302.598.aagg
12:08 <epichler> Bob: sign, symptom possibly classified incorrectly in TMO, talked to Michel about that; will be changed
12:08 <Zakim>    + +1.603.868.aahh
12:08 <epichler> Bob: only classes, no properties in OGMS
12:09 <epichler> Bob: discussion of "risk factors"
12:10 <epichler> Bob: classification of diseases based on etiology (see Bjorn Peters, @La Hoya)
12:11 <epichler> Bob: have talked with Michel about signs and symptoms
12:11 <epichler> Bob: Michel also following this discussion; as is Barry Smith
12:12 <epichler> Bob: TMO seems more advanced in this respect, also with respect to mappings
12:13 <epichler> Bob: not clear how OGMS will relate to TMO: direct integration like IAO or via mappings ...
12:14 <epichler> Bob: future alignment discussions between these ontologies would be useful: strategies not yet discussed or agreed upon
12:16 <epichler> Bob: will contact Chime and Michel re OGMS, TMO, CPR (Chime's version of patient record ontology) alignments
12:19 <Zakim>    - +1.603.868.aahh
12:19 <epichler> Scott: want OGMS for disease?; a few years back used OMIM;
12:20 <epichler> Elgar: TMO has disease mappings to other vocabularies, but good ontological treatment of disease, symptoms, etc. still
                   needs to be worked out
12:23 <Zakim>    - +1.302.598.aagg
12:24 <epichler> Scott: for many disease no objective measure for classification; but still need to be able to talk about disease ...;
                   curious about handling of this in CPR
12:25 <epichler> Bosse: if def of disease not clear, then include term list for symptoms => this list more important than naming a disease
12:27 <epichler> Chris: need to consider both: pathology, list of signs and symptoms, ...
12:29 <epichler> Scott: agreed; also will have to change definitions for diseases as we learn more about them ...

Patient Mapping
12:31 <Bob>      Patient mapping: moving past [since Michel, Chime & Eric are not on call]

Sources of Patient Data
12:32 <Bob>      Scott: Patient data. Number of leads. John Madden has some data working to understand in current relational form
12:33 <Bob>      Scott: unclear how much we want to access, assuming that we can
12:33 <Bob>      Scott: Daniel Rubin(?) has done caBIG project for annotation of images
12:33 <Bob>      Scott: He has a liver database.
12:34 <mscottm>  http://caties.cabig.upmc.edu/
12:34 <Bob>      Scott: Wendy Chapman U of Pgh know Rebecca Crowley
12:34 <mscottm>  http://www.dbmi.pitt.edu/faculty/crowley.html
12:35 <Bob>      Initial contect w. Rebecca, well to get access you need to have official res. project
12:35 <Bob>      Might need NIH cert program, exists a course on-line to get certified
12:36 <mscottm>  http://nlp.dbmi.pitt.edu/report_repository.html
12:36 <Bob>      Scott: Another set: 1000s or reports in XML, needs Wendy Chapman's tools to connect names to ontologies
12:37 <Bob>      Scott: similar hoops must be jumped thru, but may be easier
12:37 <Bob>      Scott: EHR scenario, to package up for non-semweb
12:38 <Bob>      Scott: EHR scenario: clinician alert, eligibility for clinical trial, using TMO to link up
12:39 <Bob>      Scott: Could be recognized as an EHR
12:39 <Bob>      Scott: will continue to look into sources of patient data; all help welcome
12:40 <Bob>      Elgar: Q are you looking at getting access to Chapman data. Not yet
12:40 <Bob>      Elgar: Chapman data look like great data
12:41 <Bob>      Scott: Have already done some NLP for mapping
12:41 <Bob>      Scott: Maybe map to Chime's CPR.
12:42 <Bob>      Scott: Mark Wilkinson NCBO ontology for patient privacy, describe level of disclosure, opt-in
12:42 <Bob>      Scott: Is deidentification enough?
12:43 <Bob>      Scott: w/o privacy ontology would have to describe post-facto about what was found
12:43 <Bob>      eMerge had discussion on this privacy issue; will ask Luke next week
12:44 <Bob>      Conor is trying to help them w. de-identified data
12:44 <Bob>      This was Chris talking about eMerge

Interface/eMerge
12:45 <Bob>      Scott/Chris: Conor still engaged, trying to help Luke at Marshfield
12:46 <Bob>      Chis: Bruce and I have use cases
12:46 <Bob>      Chris: Marshfield has data back to the 60s
12:47 <Bob>      Chris: Putting together a very basic question or two
12:48 <Bob>      Chris: Conor helping Luke to show; Marshfield is member of eMerge
12:49 <Bob>      Chris: Tried to make it simple, usable by clinician
12:49 <epichler> would be nice to have an eMerge usecase for IHI for http://ihi2010.sighi.org/
12:49 <Bob>      Elgar: Q timeline for eMerge/Marshfield/Conor?
12:50 <Bob>      Chris: realistically, next week defining questions we want to ask of the data
12:51 <Bob>      Chris: Will meet w Conor early next week
12:51 <Bob>      Chris: Maybe by EO month, can get one query through, wind up with sparql endpoint, get feedback
12:51 <Bob>      Chris: Question is, does it help Luke to interact w. eMerge better?

Outreach
12:52 <Bob>      Elgar: IHI agenda, June 4 may be too close
12:53 <Bob>      Elgar: abstract submission for IHI Int'l Health Informatics, Arlington VA
12:54 <Bob>      Elgar: IHI would be an interesting conference for us, may be too soon
12:55 <Bob>      UPenn translational, Oct conference, invitation only!
12:55 <Bob>      Chris Stockert involved @UPenn
12:56 <Bob>      Chris: another meeting not yet planned w. Luke
12:56 <Zakim>    - +1.215.628.aaff

Provenance
12:57 <Bob>      Elgar: Joanne was looking at provenance relevance for TMO for a workshop/conference paper, postpone further discussion
                   for next week since Joanne not on call
12:57 <mscottm>  http://tw.rpi.edu/portal/IPAW2010
12:57 <Bob>      Elgar: IHI abstract next week, but paper submission is June 4 according to web page
12:58 <Bob>      Scott: provenance work in BioRDF and also in Scientific Discourse
12:59 <Bob>      provenance work in SWAN
12:59 <Bob>      HLCS is trying to unify provenance work
13:00 <Bob>      Elgar has talked w. Joanne about provenance
13:00 <mscottm>  Sudeshna Das (Harvard) is currently chairing the combined HCLS provenance subtask telcons

13:00 <Zakim>    - +1.781.839.aacc
13:00 <Zakim>    - +46.4.63.3.aadd
13:00 <Zakim>    -Bob_Powers
13:00 <Zakim>    -mscottm
13:00 <Zakim>    - +0151709aaaa
13:00 <matthias_samwald> bye!