15:00:52 <RRSAgent> RRSAgent has joined #hcls
15:00:52 <RRSAgent> logging to http://www.w3.org/2012/07/19-hcls-irc
15:00:55 <michel> zakim, this is hcls
15:01:04 <Zakim> ok, michel; that matches SW_HCLS()11:00AM
15:01:13 <michel> Chair: michel
15:01:17 <michel> zakim, who is here?
15:01:24 <Zakim> On the phone I see Erich
15:01:29 <Zakim> On IRC I see RRSAgent, Zakim, michel, egombocz, achille_z, MacTed, ericP
15:02:30 <Zakim> +michel
15:03:18 <Zakim> + +1.412.624.aaaa
15:03:26 <matthias_samwald> matthias_samwald has joined #hcls
15:03:35 <boycer> boycer has joined #hcls
15:03:40 <Zakim> +??P31
15:03:46 <mscottm> mscottm has joined #hcls
15:03:50 <Zakim> +[IPcaller]
15:03:59 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
15:03:59 <Zakim> +matthias_samwald; got it
15:05:00 <iker> iker has joined #hcls
15:05:03 <Zakim> + +1.215.239.aabb
15:05:57 <iker> iker has joined #hcls
15:08:54 <mscottm> Michel: About revision of OMIM in RDF via Bio2RDF
15:09:14 <mscottm> ..occasional revision is necessary due to changes
15:09:46 <mscottm> ..so Michel picked OMIM for a revision because it seemed pretty out of date
15:12:33 <michel> omim entry - http://www.omim.org/entry/608547
15:12:45 <mscottm> ..plan to talk to Johns Hopkins University School of Medicine to offer RDF dump for their web page.
15:13:10 <mscottm> Scott: Possibly offer SPARQL endpoint that they could link to..?
15:13:38 <mscottm> Michel: Yes, this is a general question for data sources. Area of exploration.
15:14:14 <michel> omim api - http://www.omim.org/api
15:15:10 <michel> http://omim.org/help/api#1.4
15:17:04 <mscottm> Michel: API is *much* better and more complete than the data dump!
15:17:41 <mscottm> ..Example: allelicVariantList isn't available in the downloadable data dump but is available via API (see Entry section of help URL above).
15:20:19 <mscottm> ..update is in process, downloading now.
15:20:41 <mscottm> Scott: General question about SPARQL to SQL vs. SPARQL to set of APIs
15:21:24 <Zakim> +Tony
15:21:29 <mscottm> Michel: Bio2RDF started out with an approach of dynamically calling e-Utils and converting on the fly.
15:21:33 <bobf> bobf has joined #hcls
15:22:17 <mscottm> ..Since then, we've started downloading data wholesale and converting it to RDF.
15:24:23 <mscottm> Scott: Ever consider a procedural attachment to SPARQL query (ala SADI) and converting the results?
15:24:50 <mscottm> Michel: Yes, we've done things like that in SADI/SHARE but you can take a performance hit.
15:25:59 <mscottm> Scott: Where specifically do you take the performance hit?
15:26:39 <mscottm> Michel: If you have a large scan of 10,000 rows, it could translate to 10,000 API calls.
15:27:09 <mscottm> ..For example, OMIM can translate into 10 entries per request.
15:28:35 <mscottm> Michel: If there are no questions, we'll move on to Richard's work.
15:29:28 <mscottm> http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083378.htm
15:29:52 <michel> rich discussing FDA PGx biomarkers
15:29:52 <boycer> http://swat-4-med-safety.googlecode.com/svn/trunk/linkedSPLs/FDA-pharmacogenetic-info-mapping/
15:31:40 <mscottm> Richard: http://swat-4-med-safety.googlecode.com/svn/trunk/linkedSPLs/FDA-pharmacogenetic-info-mapping/FDAPharmgxTable.csv is the manually edited version of the table extracted from the link that Scott posted above.
15:32:32 <mscottm> ..fda-active-moiety-string-name-rxnorm-mapping.csv was made using the NCBO Annotator
15:34:02 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/directory/FDAPharmgxTable
15:35:00 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/page/FDAPharmgxTable/1
15:36:59 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/structuredProductLabelMetadata/9b32f5a4-d0f7-486b-b699-8dc9202b6869
15:37:57 <boycer> Regardless of HLA-B*5701 status, permanently discontinue TRIZIVIR if hypersensitivity cannot be ruled out. (5.1)                                                                                       Following a hypersensitivity reaction to abacavir,
15:39:25 <mscottm> Scott: What kind of server? (it's a little slow, a few seconds to respond)
15:42:24 <mscottm> Richard: Using D2R server. Have resorted to dumping RDF and loading into Virtuoso for speed (see e-mail for link to Virtuoso server).
15:43:38 <boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/
15:43:52 <boycer>  Known Issues (July 2012)
15:44:50 <Zakim> - +1.215.239.aabb
15:46:11 <egonw> egonw has joined #HCLS
15:47:10 <michel> topic - pharmgkb genotype phenotype association 
15:47:12 <michel> https://docs.google.com/spreadsheet/ccc?key=0Aoy0zfdRviKsdGFJR0ZwQWs4TE9ZUVhuSGpFSWFOQXc
16:03:34 <michel> will be working to i) do mappings and ii) normalize phenotypes
16:05:33 <bobf> apologies - I need to drop off
16:05:37 <Zakim> -Tony
16:06:12 <boycer> http://www.cdc.gov/genomics/gtesting/EGAPP/recommend/
16:06:51 <Zakim> - +1.412.624.aaaa
16:06:54 <Zakim> -Erich
16:07:04 <Zakim> -matthias_samwald
16:10:10 <michel> https://github.com/alisoncallahan/bio2rdf-lucene-searcher
16:10:36 <michel> http://sindicetech.com/
16:15:22 <michel> Chair: michel
16:15:30 <Zakim> -??P31
16:15:32 <Zakim> -michel
16:15:34 <Zakim> SW_HCLS()11:00AM has ended
16:15:34 <Zakim> Attendees were Erich, michel, +1.412.624.aaaa, matthias_samwald, +1.215.239.aabb, Tony
16:15:48 <michel> rrsagent, draft minutes
16:15:48 <RRSAgent> I have made the request to generate http://www.w3.org/2012/07/19-hcls-minutes.html michel
16:15:56 <michel> rrsagent, make log world-visible
17:09:49 <mscottm> mscottm has joined #hcls
17:25:05 <Zakim> Zakim has left #hcls
18:00:42 <MacTed> MacTed has joined #hcls
18:22:26 <matthias_samwald> matthias_samwald has joined #hcls
18:35:06 <matthias_samwald1> matthias_samwald1 has joined #hcls
18:44:33 <matthias_samwald> matthias_samwald has joined #hcls
20:28:12 <mscottm> mscottm has joined #hcls