15:14:17 <RRSAgent> RRSAgent has joined #HCLS
15:14:17 <RRSAgent> logging to http://www.w3.org/2013/03/06-HCLS-irc
15:14:38 <michel> michel has changed the topic to: #hcls  W3C HCLS – Clinical Pharmacogenomics
15:14:42 <michel> Meeting: W3C HCLS – Clinical Pharmacogenomics
15:14:48 <michel> Chair: michel
15:14:59 <michel> zakim, who is here?
15:14:59 <Zakim> sorry, michel, I don't know what conference this is
15:15:01 <Zakim> On IRC I see RRSAgent, Zakim, agray, jhajagos, michel, egonw_, ericP
15:15:06 <ericP> Zakim, this is hcls
15:15:06 <Zakim> ok, ericP; that matches SW_HCLS(LODD)10:15AM
15:15:11 <ericP> Zakim, who is here?
15:15:12 <Zakim> On the phone I see michel, +1.919.681.aaaa
15:15:13 <Zakim> On IRC I see RRSAgent, Zakim, agray, jhajagos, michel, egonw_, ericP
15:15:13 <Zakim> + +1.631.642.aabb
15:15:19 <egombocz> egombocz has joined #hcls
15:15:47 <Zakim> +??P9
15:15:54 <Zakim> + +1.510.705.aacc
15:16:07 <michel> zakim, ??P9 is alistair
15:16:07 <Zakim> +alistair; got it
15:16:20 <Sal> Sal has joined #HCLS
15:16:32 <michel> zakim, aacc is erich
15:16:32 <Zakim> +erich; got it
15:16:41 <egombocz> 510-705 is me, egombocz
15:18:11 <Zakim> +[IPcaller]
15:18:31 <michel> zakim, IPcaller is matthias
15:18:31 <Zakim> +matthias; got it
15:19:36 <matthias_samwald> matthias_samwald has joined #hcls
15:20:13 <michel> janos: started rxnorm project as part of lodd in 2010
15:20:34 <michel> ... rxnorm is an NLM project, need to sign UMLS license agreement to download and work with it
15:20:50 <michel> ... contains proprietary sources, but ways to filter out
15:20:55 <michel> ... and get only the public domain content
15:21:25 <michel> ... Susie Stephens had contacted Olivier Bodenreider - anything at level 0 is public
15:21:57 <michel> ... never released the entire dump of files - part in license that you can make the whole thing available at once
15:22:04 <michel> ... created a front end to it
15:22:13 <michel> ... last update in 2011
15:22:26 <BobF> BobF has joined #HCLS
15:22:31 <Zakim> +Tony
15:22:41 <michel> ... NLM has released a subset of RxNorm - called current prescribable content
15:22:44 <BobF> Zakim, Tony is BobF
15:22:44 <Zakim> +BobF; got it
15:22:51 <jhajagos> http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html
15:23:22 <jhajagos> http://www.w3.org/wiki/HCLSIG/LODD/Data
15:23:42 <jhajagos> http://link.informatics.stonybrook.edu/rxnorm/
15:24:18 <michel> janos: without license agreement required to be signed - easy to generate RDF
15:24:50 <michel> ... wants to update the toolchain
15:25:39 <jhajagos> http://link.informatics.stonybrook.edu/rxnorm/RXAUI/2994963
15:25:40 <michel> michel: can we explore the data a bit
15:27:50 <jhajagos> http://link.informatics.stonybrook.edu/rxnorm/RXCUI/153892
15:28:38 <matthias_samwald> michel: URIs could be replaced with labels where available
15:28:51 <matthias_samwald> michel: i also notice that some of the links do not have labels at all
15:29:52 <matthias_samwald> janos: right now it is quite close to the original data
15:30:09 <matthias_samwald> michel: RXnorm has formulation, ingredients -- are there other relationships?
15:30:28 <matthias_samwald> janos: ingredients, product labels, trade names, a hierarchy of types
15:30:36 <matthias_samwald> michel: any information regarding the function?
15:30:40 <matthias_samwald> zakim, who is talking?
15:30:51 <Zakim> matthias_samwald, listening for 10 seconds I heard sound from the following: michel (60%), +1.631.642.aabb (35%), alistair (81%)
15:32:07 <matthias_samwald> janos: they link to the VA drug file, and this has information on indications and contraindications
15:32:16 <matthias_samwald> janos: that data might not be in the public domain
15:32:37 <matthias_samwald> michel: i think the therapeutic application areas are what we would be most interested in.
15:33:25 <michel> http://bio2rdf.org/ndc:54569-4605-0
15:33:30 <matthias_samwald> janos: for some of the drugs with links to DrugBank, that could give such information
15:34:04 <matthias_samwald> michel: in the latest Bio2RDF release we included NDCs, this could be used for linking RxNorm.
15:34:34 <matthias_samwald> (NDC = National Drug Code)
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15:35:57 <jhajagos> http://link.informatics.stonybrook.edu/sparql/
15:36:49 <jhajagos> http://nlm.nih.gov/research/umls/rxnorm/
15:37:27 <matthias_samwald> janos: first link is the SPARQL endpoint, second link is the name of the graph in the endpoint containing RxNorm data.
15:38:08 <michel> types and labels : http://sparqlbin.com/#ed8e6610c703076a944e3bf3ace1c712
15:38:28 <michel> y	label http://link.informatics.stonybrook.edu/rxnorm/RXCUI	RXCUI: is a unique concept identifier http://link.informatics.stonybrook.edu/rxnorm/SAB	SAB is the source vocabulary http://link.informatics.stonybrook.edu/rxnorm/TTY	TTY (term type) http://link.informatics.stonybrook.edu/rxnorm/RXAUI	RXAUI: identifies a string down to its source
15:39:15 <matthias_samwald> michel: i would have expected types (classes, property types)
15:39:33 <matthias_samwald> janos: they are typed, in the UMLS way -- typing is done in a specific vocabulary
15:42:41 <matthias_samwald> michel: i would like to have some feedback on this approach to RDFizing
15:43:38 <matthias_samwald> michel: we are also facing this decision in Bio2RDF a lot -- either reflecting source data as unaltered as possible, or re-interpreting the data to make it more useful to the RDF world (e.g., restructuring, adding classes)
15:43:55 <matthias_samwald> janos: i would be afraid of misinterpreting something.
15:45:16 <michel> matthias: the problem of reinterpreting the data is that you could get things wrong, and it could be more difficult to keep those data updated - mappings might need to be revisited
15:45:52 <michel> ... maybe some middle ground; janos could maintain this generic representation, and perhaps add some more content with some simple rules
15:46:37 <michel> ... rdfs:label, dc:title, simple class typing
15:46:43 <michel> ... opt for both options to some degree
15:47:54 <michel> janos: maybe maintain each in different graphs?
15:49:01 <Zakim> -BobF
15:49:17 <matthias_samwald> michel: i think it is an opportunity for us -- not multiple values -- it is possible to translate one graph to another graph
15:49:32 <Zakim> -matthias
15:50:07 <Zakim> +??P14
15:50:27 <matthias_samwald> (back on the call)
15:51:17 <michel> michel: sparql construct of rxnorm into "linked data + rdfs reasoning" friendly
15:51:38 <michel> ... dealing semantic relationships in umls
15:52:18 <matthias_samwald> michel: had conversation with BioPortal team, who have RxNorm -- they refuse to add any semantics, i think you cannot even navigate the tree well
15:53:12 <matthias_samwald> michel: RxNorm is part of a family of datasets, representation-wise
15:53:38 <matthias_samwald> michel: seeing how to better reflect that in RDF is interesting
15:53:42 <egombocz> Agree with this; BioPortal's version is also from 3/7/2011 so it's old too. We really should get this into a more useful representation
15:54:24 <matthias_samwald> erich: BioPortal version is a pain indeed. It is also out of date.
15:54:52 <matthias_samwald> erich: that is not just issue of RxNorm, we have interconnectivity issues in lots of UMLS-based environments.
15:56:27 <matthias_samwald> alistair: janos, do you plan on using VoiD for dataset metadata? i sugget using it.
15:56:37 <matthias_samwald> janos: yes, i will look into it.
15:56:52 <matthias_samwald> alistair: i also suggest the PAD vocabulary for provenance
15:57:01 <agray> PAV: provenance versioning and authoring ontology http://purl.org/pav/
15:57:20 <matthias_samwald> s/PAD/PAV/
15:58:31 <matthias_samwald> michel: okay, we need a workplan
15:58:40 <matthias_samwald> janos: i can make N3 files available
15:59:05 <matthias_samwald> janos: about representation and publishing, we need to discuss as a group. in which namespace should result be published?
15:59:12 <matthias_samwald> janos: Bio2RDF namespace?
15:59:43 <matthias_samwald> michel: we use Bio2RDF namespace for the datasets we convert.
16:00:30 <matthias_samwald> michel: generally, URIs are generated based on specific rules we defined
16:00:51 <michel> http://www.slideshare.net/micheldumontier/bio2rdf-release-2-improved-coverage-interoperability-and-provenance-of-linked-data-for-the-life-sciences
16:01:13 <matthias_samwald> michel: details are shown in these slides
16:02:47 <matthias_samwald> janos: original files are in RRF format. then the data is important into SQL database, then scripts are doing transformations based on the SQL database
16:03:07 <matthias_samwald> janos: i plan to rewrite scripts so they run without SQL server
16:04:11 <matthias_samwald> janos: scripts are in Python
16:05:36 <matthias_samwald> michel: ideally for Bio2RDF would be PHP, but other languages are also okay if they are well-commented
16:05:45 <Zakim> - +1.919.681.aaaa
16:08:18 <matthias_samwald> janos: i plan to have this updated by April 1.
16:11:34 <matthias_samwald> michel: we will consolidate our provenance models (see bio2rdf wiki)
16:12:11 <matthias_samwald> michel: in April we will know better about which provenance representation would be best.
16:13:00 <Zakim> -erich
16:13:03 <Zakim> - +1.631.642.aabb
16:13:04 <Zakim> -michel
16:13:11 <agray> It is the open phacts and bio2rdf provenacne models which are being consolidated
16:13:21 <matthias_samwald> RRSagent, please draft logs
16:13:21 <RRSAgent> I'm logging. I don't understand 'please draft logs', matthias_samwald.  Try /msg RRSAgent help
16:13:28 <michel> rrsagent, draft minutes
16:13:28 <RRSAgent> I have made the request to generate http://www.w3.org/2013/03/06-HCLS-minutes.html michel
16:13:31 <Zakim> -alistair
16:13:38 <michel> rrsagent, make log world-visible
16:14:06 <matthias_samwald> Michel, I guess you send out the e-mail with the minutes?
16:14:11 <matthias_samwald> or should I?
16:14:39 <Zakim> -??P14
16:14:40 <Zakim> SW_HCLS(LODD)10:15AM has ended
16:14:40 <Zakim> Attendees were michel, +1.919.681.aaaa, +1.631.642.aabb, +1.510.705.aacc, alistair, erich, matthias, BobF
17:56:59 <Zakim> Zakim has left #hcls
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