28 Jun 2012

See also: IRC log


michel, +1.518.276.aaaa, +1.510.705.aabb, joanne_luciano, Erich, ram, ericP, SimonLin_Marshfie


<egombocz> cannot get on the conference line. Anything changed?

<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

Ram, Metaome -

<Joanne_Luciano> Clinical Decision Support for Personalized Medicine http://www.w3.org/wiki/HCLSIG/CDS

<Joanne_Luciano> Last week Michel Made progress on converting dbSNP

<matthias_samwald> joanne, could you keep scribing?

<Joanne_Luciano> If Michel talks a little slower :-)

<Joanne_Luciano> I wasn't there last week or for a few works.

<matthias_samwald> (Thanks, Joanne)

<Joanne_Luciano> using the list annotated SNPs from PharmGKB

<matthias_samwald> eUtils web service

<Joanne_Luciano> queries eUtils gets back XML record, from them parses (RDF)

<Joanne_Luciano> fields of intrest were discussed last week

<Joanne_Luciano> looked at SNP record last week (See notes from last week)

<Joanne_Luciano> then generated from 1300 from dbSNP and loaded them into endpoints from email

<michel> one example: http://bio2rdf.semanticscience.org:8007/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fdbsnp%3Ars59421388

<michel> ncbi entry: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=59421388

<Joanne_Luciano> I can't tell what he is referring to.

<michel> the XML record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&retmode=xml&id=rs59421388

i can also help with the scribing

maps to can reference several assemblies such as celera genome

<Joanne_Luciano> for example: <Assembly dbSnpBuild="137" genomeBuild="37.3" groupLabel="GRCh37.p5" current="true" reference="true">

<Joanne_Luciano> Assemblies vary by project

MapLoc element refers to the interesting part i.e the variations

has variations based on the mRNA/protein form that it references

in the each FxnSet

<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"/>

<Joanne_Luciano> Genomic, Contig, mRNA, protein /// 4 different identifers

<matthias_samwald> http://translationalmedicineontology.googlecode.com/svn/trunk/ontology/extensions/core_pharmacogenomics.ttl

M samwald created a whole scale rdf version using the batch export with a limited set of properties

from dbDNP

has an identifier for the exact combination for alleles which is useful, also has xref to bio2rdf (albeit a slightly older version)

this is a new derivative dataset (the bio2rdf conversion could have enough information to derive this)

Next topic: TMO

- Translational Medicine Ontology

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

The challenge with Schema.org may not be complete, e.g SNP may be present, will fine grained information be there?

Use as much of schema.org as possible and create own ontology

the approach in bio2rdf has been to create in its own namespace and then refer to them and then define equivalences

M Dumontier: 2 reasons why it is a problem (went too fast, did'nt catch that)

<ericP> matthias_samwald, were you hoping to have the subset of data which is expressible in schema.org be indexed by google

<ericP> ?

<michel> i. BFO and RO are insufficient to accurately capture the semantics of data in HCLS

<michel> matthias: substantial overlap between TMO and schema.org

<matthias_samwald> http://schema.org/

<michel> extensions: http://schema.org/docs/extension.html

would be good to ask schema.org (google) to ask them to include subclass/sub property

Consensus: Extend Schema.org, switch over to SIO from TMO or some middle ground (correct if this wrong!)

<michel> dataset - https://docs.google.com/spreadsheet/ccc?key=0AnGgKfZdJasrdElfQzRWWWhKUFR0UnRpeG14NGZRS2c#gid=0

<michel> statistics - https://docs.google.com/spreadsheet/ccc?key=0AnGgKfZdJasrdElfQzRWWWhKUFR0UnRpeG14NGZRS2c#gid=1

gid is different

<matthias_samwald> https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit#

<Joanne_Luciano> Matthias re: paper -- bioinformats journal or medical informatics? (leaning towards medical informatics now)

<Joanne_Luciano> Michel: missing from paper - what are the results we will present as an interesting finding?

<egombocz> apologies - need to logoff, another meeting

<Joanne_Luciano> Mathias - presenting RDF utility is not enough (agreeing)

<Joanne_Luciano> Michel - GWAS linked to Pharmacogenomic -- how big of a problem is it to not be genogyped?

<Joanne_Luciano> idea is from the frequency of a specific allele and outcome - can get an idea of the impact.


interesting call

Summary of Action Items

[End of minutes]

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