16:02:00 <RRSAgent> RRSAgent has joined #hcls2
16:02:00 <RRSAgent> logging to http://www.w3.org/2011/10/27-hcls2-irc
16:02:06 <michel> rrsagent, make logs public
16:02:35 <michel> michel has changed the topic to: #hcls2 W3C HCLSIG - Translational Medicine group (michel)
16:02:42 <mscottm2> mscottm2 has joined #hcls2
16:02:44 <simona> simona has joined #HCLS2
16:03:00 <michel> Chair: michel
16:03:46 <mscottm2> Zakim, this is TMO
16:03:46 <Zakim> ok, mscottm2; that matches SW_HCLS(TMO)11:00AM
16:04:02 <Zakim> +??P13
16:04:04 <Zakim> +??P14
16:04:10 <mscottm2> Zakim, who is here?
16:04:10 <Zakim> On the phone I see Scott_Bauer, Bob_Powers, Scott_Bauer.a, Scott_Bauer.aa, [IPcaller], +1.215.239.aaaa, ??P1, mscottm, [IPcaller.a], ??P13, ??P14
16:04:12 <Zakim> On IRC I see simona, mscottm2, RRSAgent, sivaram, Zakim, matthias_samwald, xorcon, iker, BobF, bobP, rkiefer, michel, Lena, ericP
16:04:24 <michel> zakim, who is making noise?
16:04:35 <Zakim> michel, listening for 10 seconds I heard sound from the following: mscottm (36%), +1.215.239.aaaa (4%), ??P13 (75%), Scott_Bauer.a (25%)
16:04:52 <michel> http://informatics.mayo.edu/LCD/images/c/c6/LCDatHCLS.ppt
16:04:56 <sivaram> Hi This is Sivaram Arabandi and Alan Yagoda from Elsevier
16:05:01 <bobP> http://informatics.mayo.edu/LCD/index.php/Main_Page
16:06:30 <bobP> Jyotishman Pathak: The Linked Clincal Data Project, from Mayo Clinic
16:06:45 <bobP> scribenick bobP
16:07:53 <mscottm2> Zakim, ??P13 is JyotishmanPathak
16:07:54 <Zakim> +JyotishmanPathak; got it
16:08:11 <bobP> Jyotishman: Have been involved in HCLS, Clinical interoperability
16:08:33 <bobP> ... started last fall, up and running since early this year
16:09:28 <bobP> ... Mayo has patient data since 1907
16:10:02 <bobP> ... focussing on chronic diseases, but also risk for carviovascular diseases as well
16:12:04 <bobP> ... LCD architecture using Virtuoso
16:12:54 <bobP> ... MCLSS endpoint, exposed and made queryable
16:13:19 <bobP> ... private sparql endpoint will stay within Mayo firewall
16:13:35 <Zakim> + +1.781.431.aabb
16:14:01 <bobP> ... Virtuoso commercial edition, discussion
16:14:56 <bobP> ... have used the TMO! plus added a few things, from a cancer ontology
16:15:18 <bobP> ... drugs, diagnosis info, lab measurements, demo info
16:16:37 <bobP> ... queried sider at Stonybrook, created federated query
16:17:02 <bobP> ... an early proof-of-concept w real clinical data, learning experience
16:17:24 <bobP> ... starting to look at linked-data api
16:17:49 <bobP> ... IT likes idea of leveraging linked data, but not going to write sparql
16:18:03 <bobP> ... need more user-friendly graph UI
16:18:53 <Lena> sounds interesting, looking forward to hearing the rest :)
16:19:04 <bobP> Matthias: Use of federated query, conformant?
16:19:12 <iker> q+
16:20:05 <mscottm2> q+
16:20:05 <bobP> Jyotishman: Also looked at topbraid and twinkle(?)
16:20:50 <bobP> ... audience mostly clinical investigators; Don't quite get it yet
16:21:15 <sivaram> q+
16:21:19 <bobP> ... needed to convince people
16:21:45 <bobP> (?Elsevier): Are endpoints stable?
16:22:19 <bobP> Jyotishman: Have played around w sider and Stonybrook.
16:22:47 <bobP> ... mixed results. Endpoints are up and down, so considered put everything local
16:22:47 <matthias_samwald> ?Elsevier = Alan Yagoda
16:22:48 <Zakim> -JyotishmanPathak
16:23:00 <simona> simona has left #HCLS2
16:23:06 <bobP> ... but still want to make public, w institutional challenges
16:23:25 <bobP> ... also struggle to find endpoints; 3 endpoints for RxNorm
16:23:26 <Lena> q+
16:24:04 <bobP> ... 3rd issue, data may be old in public endpoints
16:24:23 <bobP> ... have not figured it all out yet, re endpoints.
16:24:35 <Lena> rxnorm has a Java API: we should instead of converting to RDF, place a SPARQL endpoint on top of that
16:24:48 <Lena> how doable would that be? (similar discussion for other SPARQL endpoints)
16:25:02 <bobP> ... local solution, personal OP does not really leverage open linked data
16:25:40 <mscottm2> Zakim, who is talking?
16:25:42 <bobP> Alan Yagoda: Lots of endpoints are stale, not reliable. Have started to pull some data in
16:25:52 <Zakim> mscottm2, listening for 10 seconds I heard sound from the following: Scott_Bauer.a (83%)
16:26:11 <iker> +1 Alan opinion, SPARQL endpoint are not reliable
16:26:18 <bobP> Jyotishman: Also need to deal w issues of latest update of RxNorm
16:26:46 <mscottm2> Relevant links: http://labs.mondeca.com/sparqlEndpointsStatus/index.html
16:26:54 <mscottm2> http://thedatahub.org/
16:26:56 <iker> Please see the speaker queue
16:27:13 <bobP> Matthias: Important also is to have ways to convert legacy data; Alan +1
16:27:36 <bobP> Iker: Q
16:27:39 <matthias_samwald> (sorry for ignoring the queue!)
16:27:49 <epichler> epichler has joined #HCLS2
16:28:14 <mscottm2> no prob
16:28:18 <bobP> Jyotishman: Project in google code, so API is going public, do not want to rebuild what others have done
16:28:19 <Zakim> + +1.302.598.aacc
16:28:29 <xorcon> http://code.google.com/p/linked-data-api/
16:30:07 <Lena> (don't agree with RDF-izing... we should be talking about drinking from the source!)
16:30:19 <bobP> Iker: (Should create your own custom scripts)
16:30:43 <mscottm2> q-
16:30:49 <bobP> ... commercial environment, you are responsible for quality of data!
16:31:16 <bobP> Jyotishman: RxNorm weekly update, we pull a virtual RDF graph
16:31:34 <iker> q-
16:32:00 <bobP> Scott: Q Federating endpoints. Virtuoso, need to use select-as structure
16:32:26 <iker> I must attend another meeting and will leave now, Jyotishman really great project!!! congratulations!!!
16:32:26 <bobP> Jyotishman: Using service keywords, problems.
16:32:41 <trish_whetzel> trish_whetzel has joined #hcls2
16:33:03 <mscottm2> Sorry Bob - that was hard to scribe - it was a comment about Virtuoso not supporting 'BIND' from SPARQL 1.1 - probably doesn't apply to the problem they were having
16:33:35 <trish_whetzel> is there a use case for translating and adding the weekly rxnorm updates as RDF to a sparql endpoint?
16:33:36 <bobP> (?): (details re Virtuoso tech here)
16:34:04 <bobP> Scott: Fed queries and reliability: have been hearing this for quite a long time
16:34:18 <bobP> ... pharma has found sparql going down all the time
16:34:36 <bobP> ... LinkedCT improved, updated nightly
16:35:16 <bobP> ... NLP -> linked data not quite good, going out of semweb
16:35:42 <bobP> ... make a local copy (in real-time) when the public sources goes down
16:35:46 <Zakim> -??P14
16:36:04 <bobP> ... notion that there is one unique copy is going to change
16:36:23 <bobP> ... different copies have different styles of RDF
16:37:24 <bobP> ... culture *will* change, publish your own copy if you like it
16:37:43 <bobP> Jyotishman: Yes, this may be the approach we should take
16:38:21 <bobP> ... BobF here are Mayo, have been looking at SNPedia
16:38:48 <mscottm2> q
16:40:10 <bobP> ... Goals: navigate EMR w OMIM and dbSNP, look at co-morbidities
16:42:11 <bobP> ... did not find a good dbSNP endpoint
16:42:42 <bobP> ... did dump of dbSNP; BobF wrote script to filter out;
16:43:56 <bobP> ... took brute force approach to download, etc
16:45:09 <matthias_samwald> q+
16:45:25 <Lena> we can host dbSNP here at DERI
16:45:47 <michel> Bio2RDF can host as well
16:47:03 <matthias_samwald> ack sivaram
16:47:05 <xorcon> paper on PhewAS: http://www.ncbi.nlm.nih.gov/pubmed/20335276
16:47:12 <bobP> Sivaram from Elsevier: Q How are you actually linked the terms?
16:47:43 <mscottm2> Your voice fell out for me?
16:47:48 <matthias_samwald> it works for me
16:47:50 <bobP> Jyotishman: Queries w sider and RxNorm, have been using Rx terms
16:47:51 <michel> works for me
16:48:28 <michel> check identifiers.org
16:48:34 <bobP> ... point is good re vocabulary
16:48:35 <Zakim> -mscottm
16:48:35 <trish_whetzel> are the needed mappings stored in bioportal?
16:49:14 <bobP> Sivaram: Connecting genomic data to EMR, quite a wide domain
16:49:52 <bobP> Jyotishman: Some data already have the snomed, but not exosed yet by endpoints
16:50:18 <bobP> ... starting to run queries in earnest just now
16:50:23 <Zakim> + +62427aadd
16:50:46 <bobP> Matthias: Q snpedia, using rdf version?
16:50:59 <Zakim> - +62427aadd
16:51:02 <Zakim> + +20416aaee
16:51:31 <bobP> Jyotishman: They will not give us access. Not an endpoint yet for snpedia
16:51:42 <mscottm2> mscottm2 has joined #hcls2
16:52:02 <bobP> ... Matthias: SNPedia producing only part of info that you will need
16:52:56 <bobP> Matthias: There are other datasets, I can point you
16:53:36 <bobP> ... Q expanding TMO; collaborate on TMO development?
16:54:26 <bobP> Jyotishman: Yes. Extended only of necessity. Definitely interested in pursuing collaboration
16:54:32 <michel> q?
16:54:34 <trish_whetzel> 	is there a use case for translating and adding the weekly rxnorm updates as RDF to a sparql endpoint?
16:54:41 <michel> ack matthias_samwald
16:54:43 <trish_whetzel> are the needed mappings stored in bioportal?
16:55:13 <bobP> Lena: Should focus on pushing providers to give either sparql or sql endpoints, at the source
16:55:37 <mscottm2> See also NCBO's upcoming SPARQL endpoint: http://alphasparql.bioontology.org/
16:55:39 <bobP> ... danger is lack of funding; data may not be in synch
16:55:59 <bobP> ... ask sources to build the endpoints
16:56:40 <bobP> Jyotishman: Example Sider, OMIM endpoints would be fantastic
16:56:59 <bobP> ... +1
16:57:22 <bobP> Scott: Republish w metadata *about* your local copy
16:57:57 <bobP> Lena: Semweb 10 yrs. Most providers may actually be willing to do so
16:58:00 <michel> ack Lena
16:58:39 <bobP> Jyotishman: A about BioPortal/RxNorm. BioPortal does not map Sider/RxNorm
16:58:53 <matthias_samwald> RxNorm is in BioPortal: http://bioportal.bioontology.org/ontologies/1423 
16:58:56 <trish_whetzel> thanks - was referring to term mappings. 
16:58:56 <matthias_samwald> (via UMLS)
16:59:26 <trish_whetzel> bioportal does include rxnorm via the mayo lex backend architecture
17:01:19 <bobP> Jyotishman: Thank you on behalf of Rick and BobF here at Mayo.
17:01:51 <Lena> RXnorm in bioportal does not seem to have instance data, is that right?
17:02:00 <bobP> Michel: Interested in dbSNP here, maybe discuss about putting into public domain
17:02:00 <sivaram> Thanks Jyoti - on behalf of Sivaram and Alan
17:02:14 <mscottm2> Thanks Jyoti!
17:02:18 <Zakim> - +1.215.239.aaaa
17:02:20 <Zakim> -Scott_Bauer.aa
17:02:20 <Zakim> -Scott_Bauer.a
17:02:21 <Zakim> -Scott_Bauer
17:02:22 <Zakim> - +1.302.598.aacc
17:02:22 <Zakim> -[IPcaller.a]
17:02:25 <Zakim> -Bob_Powers
17:02:33 <michel> rrsagent, draft minutes
17:02:33 <RRSAgent> I have made the request to generate http://www.w3.org/2011/10/27-hcls2-minutes.html michel
17:02:34 <Zakim> - +20416aaee
17:02:35 <Zakim> - +1.781.431.aabb
17:02:35 <Zakim> -[IPcaller]
17:02:41 <michel> rrsagent, make log world-visible
17:07:35 <Zakim> disconnecting the lone participant, ??P1, in SW_HCLS(TMO)11:00AM
17:07:38 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:07:39 <Zakim> Attendees were Scott_Bauer, Bob_Powers, [IPcaller], +1.215.239.aaaa, mscottm, JyotishmanPathak, +1.781.431.aabb, +1.302.598.aacc, +62427aadd, +20416aaee
18:46:51 <matthias_samwald> matthias_samwald has joined #hcls2
19:16:09 <Zakim> Zakim has left #hcls2
20:23:23 <matthias_samwald> matthias_samwald has joined #hcls2