HCLSIG/PharmaOntology/Meetings/2010-10-14 Conference Call/minutes 141010
Zakim ok, michel; that matches SW_HCLS(TMO)11:00AM
12:09 Bob Michel: Consistency checking.
12:09 Bob Matthias: Have not gotten to yet.
12:10 Bob ... does provide a sparql endpoint, not up and running yet, just on laptop
12:11 Bob ...you can host it like a normal java servlet
12:12 Zakim On the phone I see Bob_Powers, mscottm, michel, Joanne, matthias_samwald, Chimezie_Ogbuji
12:12 Bob Scott: John Madden has OWLim running now
12:12 Bob ...Big, also 3.3, has been playing around w. reasoning
12:13 Bob ...he'd be happy to host TMO on his machine
12:13 mscottm John Madden's machine: http://tarski.duhs.org:8080/openrdf-sesame
12:14 Bob Matthias: Before we go public, we should make sure we have the resources to make stable.
12:14 Bob Joanne: RPI will be around for a while!
12:16 Bob Michel: We should have a go at installing simultaneously.
12:16 Bob ...can John host the data?
12:16 Bob Scott: Will ask John re hosting, etc.
12:18 michel matthias - have to check that bigowlim is as best configured as possible
12:18 michel ... searching through log file is not the best way
12:18 michel ... to find inconsistencies
12:18 michel ... has been performing SPARQL queries over kb
12:22 michel chime working on diagrams for the publication
12:22 michel ericP has made his results available to the w3 repository
12:22 ericP http://dvcs.w3.org/hg/TMO-Indivo/file/adb31ffd0258/syntheticPatients/AD_PCHR_1-tmo.trig
12:23 michel ericp - where is the relationship between a patient record and a patient
12:24 michel ericp - can run unit testing to compare the results of the queries
12:25 ericP http://dvcs.w3.org/hg/TMO-Indivo/file/adb31ffd0258/syntheticPatients/tests
12:29 bobP Michel and Eric discussing xslt
12:30 michel we need to rdfize ndc codes and link this to ndc dataset
12:32 michel michel need people to inspect the NDC codes and get the correct ones
12:33 bobP What about having a server for NDC codes, rather than pulling them out of hats?
12:34 bobP Eric: We could set up a persistent server for NDC codes
12:35 bobP Michel: Integration with CPR
12:36 bobP Eric: going forward, recognizing terms
12:36 ericP http://dvcs.w3.org/hg/TMO- Indivo/file/adb31ffd0258/syntheticPatients/Indivo2Trig.xsl
12:37 michel we want to replace "trans:" to "cpr:"
12:37 bobP Eric: link to Indivo-to-Trig
12:37 bobP Eric: This will pay off in the first 30 mins of work
12:38 ericP hg clone https://eric:cleartxt@dvcs.w3.org/hg/TMO-Indivo
12:38 bobP Chime: Will follow up w. Eric
12:39 ericP chimezie, note the .dmg in https://sourceforge.net/projects/swobjects/files/
12:39 bobP Michel: Have a lot of text descriptions, "atrial defib", etc
12:39 bobP ...which ontologies can we refer to and use for these to augment our descriptions?
12:39 ericP you will have to fiddle with your path to put e.g. /Applications/Sparql.app/Contents/MacOS/Sparql in your path or add it to the Makefile
12:40 ericP -> Makefile http://dvcs.w3.org/hg/TMO-Indivo/file/adb31ffd0258/syntheticPatients/Makefile
12:40 bobP ...we have drug codes, tests, like lipid panel etc
12:40 bobP Chime: Check snomed first
12:41 bobP ...NCI thesaurus would be next
12:41 ericP Lipid Panel: 80061
12:41 bobP Michel: Want to use standard vocabs, to show value of electronic patient records
12:42 ericP .. LOINC: 12919-2
12:42 bobP Chime: Use of standard URIs are fine. Formulate some URIs w/o violatiing license?
12:42 michel chime can we use SNOMED-CT terms in public rdf
12:43 bobP Michel: Serve the terms behind purl
12:43 michel that's scott talking
12:43 bobP Scott: ...then that is centrally served
12:43 bobP ...then the consumer has to worry about license issues
12:44 bobP Scott: Preferable to use purls as URIs
12:45 bobP Chime: Have a script for discovering these.
12:48 bobP Michel: Add the URIs back into the EPR
12:50 bobP Joanne, Chime talking about this job
12:51 bobP Michel: Use BioPortal if not an exact string match.
12:53 bobP Scott: Can get in touch w. service that builds up a lexicon of URIs
12:53 bobP ...might be interesting to compare w. BioPortal
12:54 bobP ...would be happy to have customers. Concept Web Alliance uses this tech
12:54 bobP List needs to be extracted from patient recors
12:55 bobP Scott: Run lucene index?
12:55 bobP Michel: Can pull out w sparql
12:56 bobP Matthias: Paper?
12:57 bobP Eric: Move from trig to turtle?
12:58 Zakim SW_HCLS(TMO)11:00AM has ended
12:58 Zakim Attendees were Bob_Powers, michel, mscottm, Joanne, EricP, matthias_samwald, Chimezie_Ogbuji