16:04:48 <RRSAgent> RRSAgent has joined #hcls2
16:04:48 <RRSAgent> logging to http://www.w3.org/2010/09/30-hcls2-irc
16:04:53 <ericP> Zakim, this is tmo
16:04:53 <Zakim> ok, ericP; that matches SW_HCLS(TMO)11:00AM
16:05:01 <ericP> Zakim, please dial ericP-office
16:05:01 <Zakim> ok, ericP; the call is being made
16:05:02 <Zakim> +EricP
16:05:07 <Bob> Link is for both the paper and the review
16:07:04 <mscottm> mscottm has joined #hcls2
16:07:28 <ericP> Zakim, who is here?
16:07:28 <Zakim> On the phone I see Bob_Powers, [IPcaller], ??P18, ??P25, Chimezie_Ogbuji, EricP
16:07:30 <Zakim> On IRC I see mscottm, RRSAgent, Zakim, Bob, matthias_samwald, michel, ericP
16:08:32 <ericP> http://www.w3.org/2010/09/30-hcls2-irc
16:08:40 <ericP> http://esw.w3.org/HCLSIG/PharmaOntology/Publications
16:09:42 <Bob> Michel: Cover Matthias bigOWLim, then Eric/Chime, then paper comments
16:09:54 <ericP> topic: bigOWLim
16:09:58 <michel> Agenda (revised)  TMO+LOD consistency checking - Matthias Patient data representation and reasoning - EricP and Chime Reconciliation of workshop paper with reviewer comments - paper & reviews - all next steps
16:10:19 <Bob> Matthias: Uncovering inconsistency in ont, mappings or LODD data
16:10:51 <Bob> ... loaded data into TMO imports into bigOWLim repository
16:11:17 <Bob> ... reasoning rules, then queries, looking at subsumption issues
16:11:41 <Bob> ... happy to report that there are no inconsistencies so far!
16:12:00 <Bob> ... also need to find out about more soph. consistency checking rules
16:12:40 <Bob> ... looking into how to do more subtle checking
16:13:15 <Bob> ... default rules are called OWL max, mostly OWL Lite plus stuff, also a little RL
16:13:49 <Bob> ... Yes, loaded the mapping files from the wiki page
16:14:13 <Bob> ... but had to fix a few small inconsistencies there; should be an ongoing effort
16:14:41 <Bob> Scott: Contacted OntoText?
16:15:03 <Bob> Matthias: Yes, they would be glad to help w. consistency checking
16:16:02 <Bob> Scott: There is a main OWLim programmer, ping Lucille
16:16:56 <Bob> ... Do other people on the list understand this agenda: importing into one repository, then run the reasoner
16:17:04 <Bob> Matthias: Yes
16:17:39 <Bob> ... Wiki page from Matthias coming up...
16:17:41 <matthias_samwald> http://esw.w3.org/HCLSIG/LODD_TMO_consistency_checking
16:17:56 <mscottm> Scott tells Bob that Lucille is actually Vassil Momtchev :)
16:18:28 <Bob> Michel: Does this include Silk mapping?
16:19:01 <Bob> Matthias: Not sure about exactly which mappings
16:19:27 <Bob> Michel: We have an LODD equivalence file that I will load in
16:19:46 <Bob> ... gives difference among provenance of source for drug data
16:20:50 <ericP> agenda+ TMO+LOD consistency checking - Matthias
16:21:02 <ericP> agenda+ Patient data representation and reasoning - EricP and Chime
16:21:10 <ericP> agenda+ Reconciliation of workshop paper with reviewer comments - paper & reviews - all
16:21:15 <ericP> agenda+ next steps
16:21:24 <ericP> Zakim, take up agendum 1
16:21:25 <Zakim> agendum 1. "TMO+LOD consistency checking - Matthias" taken up [from ericP]
16:21:55 <ericP> Zakim, take up next agendum
16:21:55 <Zakim> agendum 1 was just opened, ericP
16:22:00 <Bob> Michel: Patient data representation
16:22:03 <ericP> Zakim, close this agendum
16:22:03 <Zakim> agendum 1 closed
16:22:04 <Zakim> I see 3 items remaining on the agenda; the next one is
16:22:05 <Zakim> 2. Patient data representation and reasoning - EricP and Chime [from ericP]
16:22:07 <ericP> Zakim, take up next agendum
16:22:07 <Zakim> agendum 2. "Patient data representation and reasoning - EricP and Chime" taken up [from ericP]
16:22:29 <ericP> https://dvcs.w3.org/hg/TMO-Indivo/rev/74371f75a6d3
16:22:32 <Bob> Eric: Focus on mechanics, no fun this week
16:22:44 <Bob> ... recently committed change shows some files
16:22:58 <ericP> https://dvcs.w3.org/hg/TMO-Indivo/rev/74371f75a6d3#l2.2
16:23:12 <Bob> ... tweaked xslt and started Indivo --> turtle xslt in link
16:23:45 <mscottm> SSL connection error.
16:23:47 <Bob> ... 2 steps: reasonable coding in Indivo, then make sure turtle OK
16:23:52 <mscottm> me2
16:23:56 <matthias_samwald> me2
16:24:21 <chimezie> chimezie has joined #hcls2
16:24:28 <Bob> Eric: We have a problem w this link
16:25:17 <Bob> ... challenge is in Indivo, b/c xml extensibility problem, some of our tests are for SNPs
16:25:30 <Bob> ... have nothing to do w Indivo model
16:25:52 <Bob> ... trying to draw relationship between SNP and, say, BP test
16:26:28 <Bob> Scott: SNP is like microarray data, also different from BP
16:26:53 <Bob> Eric: Difficulty w XML extension for this stuff
16:27:08 <Bob> Scott: Important to look at how SNPs are represented in RDF
16:27:18 <Bob> ... we should be partly prepared
16:27:45 <Bob> Eric: Got it into RDF, hacked. Easy to do adequately, not too hard to do well
16:27:51 <ericP> http://esw.w3.org/HCLSIG/PharmaOntology/Queries#Q6._Are_there_any_AD_patients_without_the_APOE4_allele_as_these_would_be_good_candidates_for_the_clinical_trial_involving_Bapineuzumab.3F
16:28:00 <Bob> ... it's the XML where the problem is, not RDF
16:28:27 <Bob> ... Look at this query 6
16:28:52 <Bob> Scott: Should we try to harmonize w RDF for microarrays?
16:28:55 <ericP>       <Test>
16:28:56 <ericP>         <dateMeasured>2009-07-15</dateMeasured>
16:28:56 <ericP>         <name>ADmark Alzheimer's Evaluation</name>
16:28:56 <ericP>         <SNPresult>
16:28:56 <ericP>           <LabTest>
16:28:58 <ericP>             <variant_Synonyms>APOE4, NG_007084.2:g.7903T&gt;C</variant_Synonyms>
16:29:00 <ericP>           </LabTest>
16:29:03 <ericP>         </SNPresult>
16:29:05 <ericP>         <status>@@@</status>
16:29:08 <ericP>       </Test>
16:29:11 <Bob> Eric: Depends on conventions for representing
16:29:28 <Bob> Chime: Trying to extend XML to accommodate?
16:29:34 <ericP> Genotyping SNPs
16:30:24 <Bob> Eric: Any medical record system taking these kinds of properties
16:30:52 <Bob> ... caBIG, i2b2, Indivo, another Harvard system are all medical systems
16:31:03 <Bob> Anybody representing biomarkers in RDF?
16:31:38 <Bob> Eric: We may be far ahead in attempting to do this
16:32:11 <Bob> HL7, RIM, openEHR
16:32:35 <mscottm> Scott: Anybody representing biomarkers in RDF? There must be somebody.
16:32:41 <mscottm> Michel: Yes, we've done some work on it.
16:33:13 <Bob> Eric: What is my mandate here? Started w Indivo.
16:33:29 <Bob> ... other piece is re-working the RDF side
16:33:57 <Bob> ... (discussing pipeline)
16:34:30 <Bob> Scott: Let's not forget certain inform. needs will come up for provenance
16:34:45 <Bob> ... Ex, SNP from GWAS
16:35:04 <Bob> ... James Malone software ontology, may be useful here
16:35:19 <Bob> ... may be worth feeding back to Indivo folks
16:35:51 <Bob> Eric: None of provenance in in Indivo originally
16:36:29 <Bob> ... but move provenance into RDF, hard-coded
16:36:45 <Bob> ... or leave provenance path for later?
16:37:42 <Bob> Scott: Provenance could be by default according to which hospital or institute?
16:37:58 <Bob> Eric: Still have to make something up here
16:38:15 <Bob> Scott: As long as it creates the type of structure that we want
16:38:32 <Bob> ... extra bit of fantasy on RDF, might not be a real problem
16:38:53 <Bob> ... Can we ask the original people?
16:39:50 <Bob> Eric: Chris gave us most of the medical perspective, probably had some institution in mind
16:40:04 <Bob> ... this would be the most realistic thing to represent
16:40:43 <Bob> Scott: Clinician may by chance know the origin
16:41:02 <Bob> More discussion of origins of data...
16:41:25 <Bob> Scott: Will check out
16:41:46 <Bob> Michel: XML --> RDF, etc, What more is there to do?
16:42:15 <Bob> Eric: Looking for stuff appropriate for both us and Terminology
16:42:50 <matthias_samwald> (need to leave now, bye!)
16:42:54 <Zakim> -[IPcaller]
16:42:54 <michel> bye!
16:43:16 <matthias_samwald> (by the way, i added an issue to the TMO issue tracker -- does anyone still look at that?)
16:43:17 <ericP> https://dvcs.w3.org/hg/
16:43:34 <ericP> https://dvcs.w3.org/hg/TMO-Indivo/
16:43:52 <Bob> Eric: Everybody has access to this link
16:44:33 <Bob> ... but I have to push harder and harder to see updated changes...
16:44:38 <ericP> https://dvcs.w3.org/hg/TMO-Indivo/rev/74371f75a6d3#l2.2
16:45:08 <Bob> ... here is stuff from trig generator, skeleton of what I'll add to
16:45:42 <Bob> Michel: Q use of blank nodes(?) for patient; Needed to change this when loading
16:45:50 <ericP> <>
16:46:41 <Bob> Eric: There was an 'empty url' problem instead: blank nodes should now be easier
16:47:03 <Bob> Michel: Q is there inverse functional information here?
16:47:35 <Bob> Eric: No. No national health code ID for linking patients
16:48:19 <Bob> ... they do a heuristic name search, etc. Don't need this quite yet?
16:48:52 <Bob> Scott: This could be a real valuable feature!
16:49:16 <Bob> Eric: But dangerous to put a stake in the ground here b/c HIPAA
16:49:36 <Bob> Scott: Use something that could be used internally in clinic
16:49:58 <Bob> Eric: We might endanger adoption of ontology if it relied on this
16:50:25 <mscottm> good
16:50:43 <michel> http://esw.w3.org/HCLSIG/PharmaOntology/Publications
16:50:59 <Bob> Michel: Here is the link to the paper and the reviews
16:51:05 <mscottm> good < referring to notion of reviewing paper not endangering adoption of ontologies! >
16:51:49 <Bob> ... 1st review is happy, wants another figure
16:52:27 <Bob> ... figure would show patient --> drug --> experiment or test results
16:53:19 <Bob> ... make sure that upper level entities are represented, major types and relations
16:53:22 <michel> http://esw.w3.org/HCLSIG/PharmaOntology/Queries
16:53:43 <Bob> ... Here is sparql query, want a graph to show the major classes
16:54:43 <Bob> ... how the data are interconnected, give a visual representation to sparql query
16:55:57 <Bob> Michel: review #2, wanted more detail about TMO function, put in one sentence about process
16:56:14 <Bob> ... but we did a good job about design process
16:56:50 <Bob> ... what is the coverage of the ontology? We did queries, and we answered all the questions!
16:57:22 <Bob> Chime: Generally representative coverage
16:57:53 <Bob> Michel: Took use cases etc, but would be nice to show a query that we actually could not answer
16:58:11 <Bob> ... Ex, doing regex queries
16:58:25 <Bob> ... highlighting this as an issue
16:58:46 <Bob> Eric: TMO is intended as a connective tissue, not end-game
16:58:55 <Bob> ... but have had to move to clinical space
16:59:14 <Bob> ... that's the area where we will have insufficient coverage
16:59:19 <Zakim> -Chimezie_Ogbuji
16:59:44 <Bob> ... somebody who knows this space, need more feedback from these people
17:00:13 <Bob> Michel: query #4 we already have a patient record aspect, using terms in other vocabularies
17:00:56 <Bob> Eric: We may have pretty good coverage already
17:01:37 <Bob> ... clinical questions should cover standard stuff, plus test results
17:01:53 <matthias_samwald> matthias_samwald has joined #hcls2
17:02:01 <Bob> Michel: We did not show query to icd-9
17:02:35 <Bob> Eric: snomed has some subsumption, we can show specializations with such queries
17:03:20 <Bob> ... does icd-9 have subsumption of any relations?
17:03:43 <Bob> Michel: Tiimeline is good question!
17:04:03 <Bob> ... want to get all results by next week, so we can focus on the paper
17:04:04 <mscottm> Thanks Eric for the XSLT (i.e. gruelling) work!
17:04:41 <michel> Final Paper due November 16th
17:06:00 <Zakim> -EricP
17:06:01 <Zakim> -Bob_Powers
17:06:02 <Zakim> -??P25
17:06:08 <Zakim> -??P18
17:06:09 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:06:11 <Zakim> Attendees were Bob_Powers, [IPcaller], Chimezie_Ogbuji, EricP
17:06:13 <michel> Zakim, ??P25 is michel
17:06:13 <Zakim> I already had ??P25 as ??P25, michel
17:06:46 <michel> RRSAgent, please draft minutes
17:06:46 <RRSAgent> I have made the request to generate http://www.w3.org/2010/09/30-hcls2-minutes.html michel
17:06:50 <mscottm> Zakim, ??P25 is michel
17:06:50 <Zakim> I already had ??P25 as ??P25, mscottm
17:06:50 <michel> RRSAgent, please make log world-visible
17:06:58 <mscottm> huh?
17:10:15 <ericP> mscottm, still here?
17:10:23 <mscottm> yup#
17:10:37 <mscottm> call you at the office? Just tried that and the mobile
17:10:37 <ericP> Zakim, please dial ericP-office
17:10:37 <Zakim> sorry, ericP, I don't know what conference this is
17:10:53 <ericP> mscottm, can you hang up and i'll create an ad-hoc meeting?
17:10:58 <ericP> or i can call you directly
17:11:01 <mscottm> I already hung up
17:11:22 <mscottm> I just tried to call you directly. Call me? See ericP window