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15:01:24 <matthias_samwald> zakim, this is hcls
15:01:35 <Zakim> ok, matthias_samwald; that matches SW_HCLS()11:00AM
15:03:42 <Zakim> +michel
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15:04:44 <Zakim> + +1.518.276.aaaa
15:05:10 <egombocz> cannot get on the conference line. Anything changed?
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15:05:50 <Zakim> + +1.510.705.aabb
15:06:11 <michel> zakim, aaaa is joanne_luciano
15:06:11 <Zakim> +joanne_luciano; got it
15:06:23 <Zakim> +??P0
15:06:32 <michel> zakim, aabb is Erich
15:06:32 <Zakim> +Erich; got it
15:06:48 <Joanne_Luciano> Agenda Continue discussions from last Thursday (dbSNP etc.) Deciding on extensions of the Translational Medicine Ontology (TMO) - what should be covered in the TMO and what should be left to ad-hoc schemas based on source data? Revisiting the plans for a journal submission 
15:06:58 <michel> zakim, ??P0 is ram
15:06:58 <Zakim> +ram; got it
15:07:00 <ram> Ram, Metaome - 
15:07:06 <Joanne_Luciano> Clinical Decision Support for Personalized Medicine http://www.w3.org/wiki/HCLSIG/CDS
15:07:36 <Zakim> +??P52
15:08:22 <Joanne_Luciano> Last week Michel Made progress on converting dbSNP
15:08:38 <matthias_samwald> joanne, could you keep scribing?
15:08:48 <Joanne_Luciano> If Michel talks a little slower :-)
15:09:03 <Joanne_Luciano> I wasn't there last week or for a few works.
15:09:34 <matthias_samwald> (Thanks, Joanne)
15:10:00 <Joanne_Luciano> using the list annotated SNPs from PharmGKB
15:10:16 <matthias_samwald> eUtils web service
15:10:52 <Joanne_Luciano> queries eUtils gets back XML record, from them parses (RDF)
15:11:04 <Joanne_Luciano> fields of intrest were discussed last week 
15:11:38 <Joanne_Luciano> looked at SNP record last week (See notes from last week)
15:12:00 <Joanne_Luciano> then generated from 1300 from dbSNP and loaded them into endpoints from email
15:12:06 <michel> one example: http://bio2rdf.semanticscience.org:8007/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fdbsnp%3Ars59421388
15:12:18 <michel> ncbi entry: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=59421388
15:14:07 <Joanne_Luciano> I can't tell what he is referring to.
15:17:55 <michel> the XML record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&retmode=xml&id=rs59421388
15:18:43 <Zakim> +ericP
15:19:15 <ram> i can also help with the scribing
15:20:19 <ram> maps to can reference several assemblies such as celera genome
15:20:27 <Joanne_Luciano> for example: <Assembly dbSnpBuild="137" genomeBuild="37.3" groupLabel="GRCh37.p5" current="true" reference="true">
15:20:58 <Joanne_Luciano> Assemblies vary by project
15:21:31 <ram> MapLoc element refers to the interesting part i.e the variations 
15:22:05 <Zakim> -ericP
15:22:18 <Zakim> -??P52
15:23:08 <ram> has variations based on the mRNA/protein form that it references
15:23:27 <ram> in the each FxnSet
15:23:29 <Joanne_Luciano> Function Set: FxnSet geneId="1565" symbol="CYP2D6" mrnaAcc="NM_001025161" mrnaVer="1" protAcc="NP_001020332" protVer="1" fxnClass="missense" readingFrame="1" allele="A" residue="M" aaPosition="286"/>
15:24:04 <Joanne_Luciano> Genomic, Contig, mRNA, protein /// 4 different identifers
15:25:25 <matthias_samwald> http://translationalmedicineontology.googlecode.com/svn/trunk/ontology/extensions/core_pharmacogenomics.ttl
15:26:45 <ram> M samwald created a whole scale rdf version using the batch export with a limited set of properties
15:27:04 <ram> from dbDNP
15:27:39 <Zakim> +ericP
15:29:20 <ram> has an identifier for the exact combination for alleles which is useful, also has xref to bio2rdf (albeit a slightly older version)
15:32:34 <ram> this is a new derivative dataset (the bio2rdf conversion could have enough information to derive this)
15:33:29 <ram> Next topic: TMO
15:33:47 <ram> - Translational Medicine Ontology
15:34:03 <Zakim> +SimonLin_Marshfie
15:35:25 <ericP> Zakim, unmute SimonLin_Marshfie
15:35:25 <Zakim> SimonLin_Marshfie should no longer be muted
15:37:36 <ram> Should we continue with TMO or move to something like CIO, or have a higher level ontology (M Samwald's thought) or the option of Schema.org
15:38:48 <ram> The challenge with Schema.org may not be complete, e.g SNP may be present, will fine grained information be there?
15:39:48 <ram> Use as much of schema.org as possible and create own ontology
15:40:27 <ram> the approach in bio2rdf has been to create in its own namespace and then refer to them and then define equivalences
15:42:25 <ram> M Dumontier: 2 reasons why it is a problem (went too fast, did'nt catch that)
15:42:46 <ericP> matthias_samwald, were you hoping to have the subset of data which is expressible in schema.org be indexed by google
15:42:49 <ericP> ?
15:43:03 <michel> i. BFO and RO are insufficient to accurately capture the semantics of data in HCLS
15:43:37 <michel> matthias: substantial overlap between TMO and schema.org
15:43:49 <matthias_samwald> http://schema.org/
15:46:38 <michel> extensions: http://schema.org/docs/extension.html
15:46:54 <ram> would be good to ask schema.org (google) to ask them to include subclass/sub property
15:49:17 <ram> Consensus: Extend Schema.org, switch over to SIO from TMO or some middle ground (correct if this wrong!)
15:50:28 <michel> dataset - https://docs.google.com/spreadsheet/ccc?key=0AnGgKfZdJasrdElfQzRWWWhKUFR0UnRpeG14NGZRS2c#gid=0
15:50:54 <michel> statistics - https://docs.google.com/spreadsheet/ccc?key=0AnGgKfZdJasrdElfQzRWWWhKUFR0UnRpeG14NGZRS2c#gid=1
15:52:11 <ram> gid is different
15:56:30 <matthias_samwald> https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit#
15:59:01 <Joanne_Luciano> Matthias re: paper -- bioinformats journal or medical informatics? (leaning towards medical informatics now)
15:59:33 <Joanne_Luciano> Michel:  missing from paper - what are the results we will present as an interesting finding?
15:59:49 <egombocz> apologies - need to logoff, another meeting
16:00:06 <Zakim> -Erich
16:00:16 <Joanne_Luciano> Mathias - presenting RDF utility is not enough (agreeing) 
16:00:58 <Joanne_Luciano> Michel - GWAS linked to Pharmacogenomic -- how big of a problem is it to not be genogyped?
16:01:50 <Joanne_Luciano> idea is from the frequency of a specific allele and outcome - can get an idea of the impact.
16:14:26 <ram> thanks
16:14:29 <Zakim> -SimonLin_Marshfie
16:14:31 <ram> interesting call
16:14:32 <Zakim> -michel
16:14:35 <Zakim> -joanne_luciano
16:14:46 <Zakim> -ram
16:14:57 <Zakim> -ericP
16:15:03 <Zakim> -??P17
16:15:05 <Zakim> SW_HCLS()11:00AM has ended
16:15:05 <Zakim> Attendees were michel, +1.518.276.aaaa, +1.510.705.aabb, joanne_luciano, Erich, ram, ericP, SimonLin_Marshfie
16:15:19 <ram> ram has left #hcls
16:15:45 <matthias_samwald> RRSAgent, please make log world-readable
16:16:19 <matthias_samwald> RRSAgent, please draft minutes
16:16:19 <RRSAgent> I have made the request to generate http://www.w3.org/2012/06/28-hcls-minutes.html matthias_samwald
16:16:33 <matthias_samwald> RRSAgent, please make log world-readable
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