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