HCLSIG/PharmaOntology/Meetings/2010-06-10 Conference Call

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Conference Details

* Date of Call: Thursday June 10 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 Updates - Michel, Elgar
  • Patient Mapping - Michel, Chime, EricP
  • Interface/eMerge - Bosse, Chris
  • Outreach (UPenn Translational Medicine) - All
  • AOB


Minutes

* Attendees: Chris, Joanne, Jim, Bob, Matthias, Christi, Janos, Michel, Scott, EricP, Susie
* <Bob> Agenda: updates to TMO, patient mapping, interface, outreach
* <Bob> TMO updates
* <Bob> Michel: working closely w. Chime on CPR ontology, to get happy with it
* <Bob> Michel: after CPR then we can do patient mapping, and will be aligned w. TMO world view
* <Bob> Susie: email to Ben and Ken to join us about Indivo
* <michel> chime's changes, comments, etc are on the CPR mailing list
* <michel> http://groups.google.com/group/cpr-ontology
* <Bob> Susie: hopefully we will hear from them about this, important to get clarified
* <Bob> Susie: is Chime best person to ask about Indivo?
* <Bob> Susie: hoping to work on updating patient data in Indivo, hoping to get Ben
* <Bob> Scott: Q Indivo is to id people?
* <Bob> Susie: Indivo is schema for personally controlled health record from Harvard, plus Dossia
* <michel> http://wiki.chip.org/indivo/index.php/Indivo
* <Bob> Scott: Q chosen a schema yet?
* <Bob> Susie: We would like to use Indivo b/c pubicly available, more comprehensive than traditional EHRs
* <michel> http://wiki.chip.org/indivo/index.php/Schemas
* <Bob> Susie: Maybe can captured more for clinical trials, etc
* <mscottm> Tolven - open source EHR used by I-Spy, Laura Esserman, Ken Butew (caBIG)
* <Bob> Susie: If something better than Indivo comes, then we'll certainly look.
* <Bob> Susie: Saw 18month ago paper about Tolven
* <Bob> Scott: Q connection to VistaA?
* <Bob> Susie: VistA may miss some significant categories of med, not nec as comprehensive as traditional EHR
* <mscottm> Epoch from NCBO
* <Bob> Scott: Epoch treats records as propietary, not open source
* <janos> http://indivo.org/vocab/xml/
* <Bob> Susie: Indivo is open, using RDF, Ben was one of the RDFa authors
* <Bob> Susie: Wonder if we should look into Tolven?
* <michel> indivo presentation at user group meeting: http://www.slideshare.net/benadida/2010-0415indivooverview
* <mscottm> http://collabrx.com/
* <Bob> Susie: If caBIG is using Tolven, then this might be a good path into FDA, etc
* <Bob> Scott: Have contacts w. CollabRx
* <Bob> Scott: CollabRx has taken linked open data, Mike Traverse(?) 
* <Bob> Scott: Clinical trials, drug bank etc all in there.
* <Bob> Scott: Might be good for longitudial record on patient
* <Bob> Scott: CollabRx is focussing initially on capture as first use case.
* <Bob> Susie: microarray, SNP etc., using w clinical trial data
* <Bob> Scott: They have appointed editors for wiki pages to view patient data against models.
* <Bob> Scott: They are interested in HCLS
* <Bob> Susie: Q how much is CollabRx done?
* <Bob> Susie: 1 1/2 yr ago was still early, but sounds like they have built out a lot
* <Bob> Scott: CollabRx has talked about releasing code very soon, may intend to put out on web
* <Bob> Scott: Saw some very nice integrated demos yesterday.  Mike Traverse has done work w. Science Commons
* <Bob> Scott: They are riding on their own steam now.  Have internalized their own data.
* <Bob> Scott: They are interested in collaborating.  Might be able to create demo when they go public
* <Bob> Scott: Entry form for patient data is already pretty much done.
* <Bob> Scott: They are sparql-aware.
* <Bob> Susie: Use their schema?
* <Bob> Scott: We might use bits of their code plus data as well; they have a KB
* <Bob> Scott: Would be a nice link to SNP analysis
* <Bob> Scott: Scenario: work w them and build part of demo w them, or take components and put them in our own
* <Bob> Susie: Q environment is open?
* <Bob> Scott: Yes. Only reason so far, "Not quite ready yet."
* <Bob> Scott: Sense is that a month or two for putting stuff out.
* <Bob> Susie: Phases alternate between exploration, then work.
* <Bob> Susie: Hope that we get to patient record work soon; don't want to wait 2 months
* <Bob> Susie: Tolven is interesting, but Indivo already has RDF for patient record and is open
* <Bob> Susie: Plus Harvard Indivo people are rock stars.
* <Bob> Susie: Would like to make a decision about Tolven in a week or so.
* <Bob> Scott: Another possibility: get CollabRx to demo to us
* <Bob> Scott: Struck me as a nice example of working semweb, as we like. Wants definitely to look at it
* <Bob> Susie: Q can you do high level review of open part?
* <Bob> Scott: Will try to dig up something on it for a heads-up...
* <Bob> Susie: CollabRx, reach out for this call? Scott: Will do
* <Bob> Susie: Interface.
* <Bob> Chris: Conor is real busy, but he's been coordinating w. Luke
* <Bob> Chris: This part is not yet in my purvue yet, but we will get there!
* <Bob> Susie: Let's keep Conor in mind.
* <Bob> Outreach.
* <mscottm> Zakim, who is making noise?
* <Bob> Susie/Joanne discussion of upcoming conferences
* <Bob> Susie: Planning to go to bioontologies
* <Bob> Susie: Michel, can to to biopathways?
* <mscottm> https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2010en
* <Bob> Joanne and Michel will coordinate about biopathways
* <Bob> Scott: Sep 9-10 Mannheim, 2-4 pages July 1
* <Bob> Scott: Will present split presentation at semtech
* <Bob> Scott: My talk is June 24 Thu