06 Oct 2011

See also: IRC log


+62427aaaa, Bob_Powers, +, Tony


scribenick bobP

Michel: Look at use case template, think of task to perform
... this group can champion what we want to do with the KB
... Agenda: Matthias, develop use cases, and research

Matthias: Thanks everybody for great collaboration

<adrien> thank you Matthias for submitting it!

Matthias: one of difficulties was that we did two things at once
... report on how semantics implemented, also design choices etc on the other hand
... another paper will be research article in biomed semantics
... Special Report short paper, turned out to be longer, so wrote a proper review article
... produced a very interesting and useful piece of scientific literature
... can use as a basis to communicate

Michel: Hit the level that we wanted; broad scope of utility
... readers will get the gist. Tech platform for what we are doing

BobF: Thank you very much for driving this manuscript

Matthias: Now that this is done, other paper should be easier
... can really focus on tech. Pgx in OWL will be very interesting
... pgx data and related data, at the end will be very interesting

Michel: Would really like to see a list of design patterns for expressing data
... in line w. new interest group. More on the vocab side
... not much yet from w3c about representational patterns
... how to represent snp data, relation to pgx. Patterns, should be possible to marshal
... going to try to push this, beyond just strict RDF, but a bit more (disciplined)

BobF: Absolutely.

<mscottm> 1+


Michel: bio2rdf, need patterns for representation, not yet well developed
... we have always used obo ontologies in my research
... have a whole list of design patterns, then becomes like a recipe
... go the W3C and get the pattern.
... Next step. Use case template, would like to...

<michel2> https://docs.google.com/document/d/1I9xyVKhO9wG7My2fWu9S-wMwWZxG6PkRc98kOxUqH-o/edit?hl=en_US

BobF: dbSNP last correspondence, mentioned that working here too
... development has been fairly good. We have a local copy, have stripped out immediate utility data
... can share by email. Plan is to load local DB here.
... how to expose for the rest of the group?

Matthias: Problem may be larger? Ensure the scalability of the data

Michel: Agree, going to make a note of this.

BobF: Institutional guidlines are strict on external servers.
... approval to stand up an instance here

Michel: You can load it at Carleton
... SWObjects, expose sparql endpoint?

Scott: Iker has down exploratory work w d2r
... idea was to take specific data w dbSNP and access via sql mapped in swobjects
... not trying to expose everything
... Iker found that infra was the problem

(I think he found that it was too big etc)

Iker: Did mapping w d2r, swobjects. Used a subset, here is the link

<iker> https://cgsmd.isi.edu/dbsnpq/

Iker: first we should generate a subset of dbSNP that we will use. Huge

Michel: BobF has done this part.

BobF: Pulled out only those fields that are relevant. Excluded historical groupings of the RFs themselves
... contig mappings omitted. Just took SNPs, genes, classification etc
... four different tables, but can extend from there.

<iker> SNP table at https://cgsmd.isi.edu/dbsnpq/downloads.php

Michel: No contigs?

<iker> this table collects more or less the information Bob is talking about

BobF: Yes, no contigs. Each build has its own mappings
... pulling in contig maps would imply pulling in the build data too
... but we can associate RS numbers w chromosomes
... also there will be some ambiguity in some
... not QC, just pulled data
... snp, chrome, validation info, locus id, proximity info, etc
... gene symbol with local ID

Michel: (asking...)
... rewrite DB relations to swobjects forms

Matthias: SWObjects in addition?

Michel: (implement to graph pattern - didn't quite get)

Iker and Michel talking DB exchange

Iker: ...Is ethnicity a requirement?

Michel: Depends...longer term thing is to predict, related to pop genetics

ScottScott: Scenario, have SNP for a particular patient
... might hapmap to see freq on pop. Pre-warfarin biomarker research
... warfarin, you already know whether patient has SNP or not.

<iker> could you provide a link to the wiki page of this work?

Michel: Get trimmed down version of dbSNP up and running.
... Matthias' scalability issue. Would like to collaborate on a framework

<mscottm> @iker: we discussed that for initial versions of the paper so there is a wiki page and a few relevant google docs such as an article draft.

Scott: Sustainability for HCLS, should have agree to have common method of methods, scripts, versions

(that was Michel!)

<iker> @Scott, I am talking about the wiki page where we added the SPARQL queries of dbSNP I cannot find it

Michel: Resources need to be kept up to date

<mscottm> for iker (in case you haven't seen this): http://www.w3.org/wiki/HCLSIG/TranslationalMedicine/pharmacogenomics

Matthias: Miriam, identifiers.org, etc

(that was Michel again!)

<iker> @Scott, maybe I am wrong but I think there was another wiki page with the SPARQL queries, I will check, thanks anyway

Michel: Will try to take the medicine, on representation of pgx data.

<mscottm> @iker: maybe one of the google docs? Not this one (the modeling): https://docs.google.com/drawings/d/1OaqlmiTbIAkgHM6kCV-4xbRddHJiN1YZkCWdNHvwiGI/edit?authkey=CIT4rcwM&hl=en_US&authkey=CIT4rcwM

<matthias_samwald> maybe you meant http://www.w3.org/wiki/HCLSIG/pharmacogenomics_2011 ?

<adrien> I wish you all a very good day.

Scott: One of Bob's Mayo people has project, sounds uncannily similar

<mscottm> http://informatics.mayo.edu/LCD/

Scott: Project talks about LD, linking clinical records etc
... sent questions to LOD group, so contacted him
... can Mayo take advantage, and we can take advantage to get use cases and data

BobF: Some of the work is what is offerring here

Summary of Action Items

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