15:04:27 <RRSAgent> RRSAgent has joined #hcls
15:04:27 <RRSAgent> logging to http://www.w3.org/2012/07/26-hcls-irc
15:04:30 <michel> zakim, this is hcls
15:04:30 <Zakim> ok, michel; that matches SW_HCLS()11:00AM
15:06:52 <BobF> BobF has joined #hcls
15:09:04 <matthias_samwald> matthias_samwald has joined #hcls
15:09:37 <matthias_samwald> scribenick: matthias
15:12:09 <JoanneLuciano> Matthias: done with prototype, wants to move to clinical decision support application
15:12:39 <JoanneLuciano> BobF: working on domain model for guidelines
15:12:51 <matthias_samwald> scribenick: JoanneLuciano
15:12:57 <JoanneLuciano> moving towards thinking about implementation
15:13:00 <matthias_samwald> (thanks Joanne)
15:13:17 <JoanneLuciano> and linking to a CDS repository 
15:13:28 <JoanneLuciano> (clinical decision support)
15:14:04 <JoanneLuciano> currently focused on guidlines that are not computable -- to make to a structured format and link to a standardized representation for a DS report rule that would help the clinical guideline
15:15:07 <JoanneLuciano> has been looking at CDS but got sidetracked to look at provenance, which will be important for the instutions to track (for status and for tracking)
15:15:37 <JoanneLuciano> looking into w3c provenance working group
15:16:13 <JoanneLuciano> Matthias reports some overlap with HCLSIG, Joanne reports RPI expertise in the area and activity in the group.
15:16:40 <JoanneLuciano> Bob - how to addopt the prov model to support clinical descion support rules
15:16:48 <JoanneLuciano> evidence or provenance only.
15:17:39 <JoanneLuciano> BF wasn't going to try to model evidence at this point  -- currenlty looking at two types of guidlines on PharmGKB:  
15:17:50 <BobF> CPIC - clinical pharmacogenetics implementation consortium
15:17:57 <BobF> dutch pgx working group
15:18:46 <JoanneLuciano> aiming to standardize into a common model - representing content of the guidelines
15:21:25 <JoanneLuciano> Joanne: possibly overlap and opportunity for dovetailing with Drug Product Label and Drug Drug Interaction task group
15:22:21 <JoanneLuciano> Matthias: Spoke with Anita de Warrd re: work with Philips - looking to come up with a prototype for EHR where clinicans are shown relevant snipits 
15:22:40 <BobF> zakim, who is here?
15:22:40 <Zakim> On the phone I see no one
15:22:41 <Zakim> On IRC I see matthias_samwald, BobF, RRSAgent, Zakim, michel, JoanneLuciano, achille_zappa, MacTed, egonw, ericP
15:23:49 <JoanneLuciano> MS - voices concern re: scope if we get too far into provenance and evidence 
15:24:01 <JoanneLuciano> how will info be entered and maintained
15:24:36 <JoanneLuciano> spreadsheets are a good way to collaborate with those users who are not computer experts
15:25:12 <JoanneLuciano> Bob - finish up model and take one or two guidelines, put in XML-schema that matches model and..
15:26:44 <JoanneLuciano> Bob exploring representations, for example, GEM - formalizing clinical guidelines / maybe able to be reused / how to represent and serialize the guildelines and get in position to seek funding. possibly thru a repository 
15:27:47 <JoanneLuciano> Matthias: skeptical about using GEM and others because they are not easy to use and overly complex
15:29:19 <JoanneLuciano> {an asside ... this just out:  We are very pleased to announce Last Call on 3 documents that define the core of the PROV family of specifications. These 3 documents focus on how to model provenance information for the purposes of interchange.  - PROV-DM is a data model for provenance interchange - PROV-O is an OWL2 ontology mapping of PROV-DM to RDF - PROV-N 
15:30:12 <JoanneLuciano> bottom line - something based on a spreadsheet would be useful; BF - will think about, interesting perspective
15:30:30 <matthias_samwald> http://www.snpedia.com/index.php/Criteria_syntax
15:30:56 <matthias_samwald> SNPedia criteria syntax
15:32:19 <michel> HGNC nomenclature : http://www.hgvs.org/mutnomen/recs.html#general
15:35:19 <JoanneLuciano> http://www.w3.org/wiki/HCLSIG/CDS
15:38:03 <JoanneLuciano> CONTEXT: currently this discussion is focusing on the use cases described on the HCLSIG CDS web page, specifically: formalize (use case 1) and integrate (use case 2)
15:39:08 <michel> star allele nomenclature described here - http://www.nature.com/clpt/journal/v82/n3/full/6100284a.html
15:39:53 <JoanneLuciano> most guidelines use a combination of ways to specify criteria (e.g. *1 or *2) other guidelines will specify "if one variant allele) - which then indicates which guideline to reference
15:39:58 <matthias_samwald> https://docs.google.com/spreadsheet/ccc?key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&hl=en_US&pli=1#gid=3
15:42:49 <JoanneLuciano> the data will evolve... and the interpretation of phenotypes are subjective (intermediate metabolized, poor metab) based on distrib of activity that overlap
15:43:57 <JoanneLuciano> phenotype based classification of rules is problematic, so unless doing an enzymatic test, you're going to be starting with genotype info, so BF thinking of ways to support he phenotype based, which are being used all the time, so wants to support with genotype based.
15:44:23 <JoanneLuciano> want more precise guidelines
15:45:56 <JoanneLuciano> objectives - easily maintainable by non-computer experts
15:46:17 <JoanneLuciano> Michel - adventures with OMI (?)
15:46:21 <matthias_samwald> OMIM
15:47:22 <JoanneLuciano> Michel wrote a parser for OMIM - use OMIM API to retireve OMIM records (better structured than download) - turned to RDF and can get access to SNP entries (all diseases that have links to DBSnp)
15:47:29 <michel> one example : http://bio2rdf.semanticscience.org:8009/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fomim_resource%3A608547_allele_1
15:49:04 <JoanneLuciano> MS: how many of those entries are relevant for Pharmacogenomics? 
15:49:23 <JoanneLuciano> Michel is composing a SPARQL query in real time to answer :-)  (Michel is awesome)
15:49:45 <JoanneLuciano> And the answer is......
15:50:46 <JoanneLuciano> genes, phenotypes, of genes or phenotypes, predicate is variant in OMIM vocab. all variants that have a  DBSnp entry and count them.
15:50:57 <JoanneLuciano> 1767 have entries
15:50:58 <michel> query: SELECT count(distinct ?a) WHERE {  ?a <http://bio2rdf.org/omim_vocabulary:variant> ?b .  ?b <http://bio2rdf.org/omim_vocabulary:dbsnp> ?y . }
15:51:45 <JoanneLuciano> out of 23,000 (approx)
15:52:25 <JoanneLuciano> about 9 % coverage (roughly)
15:53:34 <JoanneLuciano> But the clinical reference can only be determined by PharmGKB and to see if there is an impact in pharmocogenomic or pharmocodynamic (free text in PharmGKB), can possibly annotate ourselves(?)
15:55:44 <JoanneLuciano> Drugbank, PharmGKB, OMIM need to be integrated to answer the questions
15:56:38 <JoanneLuciano> recently upgraded machine to: 192 GB  RAM, so should be enough for now
16:00:03 <matthias_samwald> RRSagent, please draft minutes
16:00:03 <RRSAgent> I have made the request to generate http://www.w3.org/2012/07/26-hcls-minutes.html matthias_samwald
16:00:06 <michel> hope to have some numbers as to the overlap between omim and pharmgkb; we'll need to examine the differences in detail -
16:00:35 <matthias_samwald> RRSAgent, please make log world-readable
16:02:45 <Zakim> SW_HCLS()11:00AM has ended
16:02:47 <Zakim> Attendees were 
16:03:55 <matthias_samwald> Joanne, it seems you are not online in Skype?
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