W3C HCLS – Life Sciences Forum

14 Feb 2012

See also: IRC log




<Helena> http://www.w3.org/2011/prov/wiki/Main_Page

<mscottm2> Have been trying to dialin but keep getting "This passcode is not valid."

<matthias_samwald> "hcls" passcode worked for me

<matthias_samwald> oh, you made it by now.

<mscottm2> Yeah, 4x a charm. :)

<mscottm2> http://www.w3.org/TR/2012/WD-prov-primer-20120110/

lena: can use provenance model on tcga dataset

<mscottm2> From Richard Boyce: For the SciDisc Use Case, we have created a set of web pages that show a very basic demo of one way that a drug package insert might be flagged to claims present in the other knowledge sources on the semantic web.

<mscottm2> http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/outfiles/

<mscottm2> Each web page shows DailyMed Structured Product Label sections (posted on the new linkedSPL endpoint <http://tinyurl.com/7b5rtpk>) that have been linked to 1) claims present in the linked data version of the Drug Interaction Knowledge Base (http://dbmi-icode-01.dbmi.pitt.edu:2020/) and 2) published results from studies involving the drug's active ingredient that have been registered in clinicaltrials.gov (via LinkedCT). I will discuss the use case and demo at



<jun> that link works fine for me. just tested it

mscottm2: biordf group - expression rdf w3c note
... gives guidelines for producing rdf on differentially expressed genes, experimental conditions
... getting people around the table fged, arrayexpress, more confidence in rdf created
... workshop article shows show to interconvert between representations
... tutorial aspect needs to be developed in the note - R script from jim mccusker to generate the rdf; python scripts from io informatics; other tools
... rdf representation + how to use it with other tools to perform analysis; take the results and do something with it
... looking at putting a SPARQL interface to synapse (API from sage bionetworks)
... includes snp data, patient data

matthias: seems that main access is now api, no file download

mscottm2: are they interested in linked open data? further discussion required
... focus on network biology
... goals are close; should be possible to work together
... stephen friend has raised some $16M in a years time, sage bionetworks have many partners in pharma

<mscottm2> i did get a chance to talk with mike about synapse and the semantic web.

<mscottm2> if i understood him right, currently he doesn't believe there really is a

<mscottm2> good use case to making the data available as a sparql end point. i kind

<mscottm2> of agree that HCLS hasn't made a compelling case for this yet. but, on

<mscottm2> the other hand, mike is working with NCBO in developing an ontology that

<mscottm2> describes and drives how synapse works, which will be published via

<mscottm2> bioportal. this concept is like what i worked on with mike at teranode,

<mscottm2> where our customers (who, sadly, never came to be) would describe their

<mscottm2> business process (how the drug pipeline worked, who reported to who,...)

<mscottm2> and that would drive the UI and what options users had.

<mscottm2> http://synapse.sagebase.org/#DatasetsHome:0

<mscottm2> http://sagebase.org/research/Synapse1.php

<mscottm2> re:eric's comments - I was hoping for a database connector (as usual :) )

<ericP> naturally

mscottm2: lodd
... paper in journal of web semantics - should be published soon
... w3c note derived from this without the use cases
... solicited comments, got a few
... pretty close to being done
... more comments welcome
... next discussion will be about future work
... and approval

<iker> @scott, could you send the link to the note please?


<iker> thanks

mscottm2: biohackathon 2011 got some people together to come up with a vocabulary to describe datasets (beyond void, etc)

<Helena> (i think the document is ready for publication as a working draft or something of the sort )

<Helena> (that would actually push us to finalize it, I think :) )


<mscottm2> https://docs.google.com/document/d/1qVSZ1n334fTTchCWS2tOaEL6z-H12pcqty98jQIg6nw/edit

<Helena> (never mind, was going to mention void, but now i saw it there in the document :) )

lena: signaling pathway leads to death; take list of proteins, go in tcga by exposing the data as rdf, snps/expression. idea is to look at what is happening in the pathway at several layers of biological info, see if the changes are localized
... gene, protein, snps, epigenetics
... patterns were previously uncovered; 1st layer epigenetics, 2nd layer snps, 3rd layer gene expression
... 4th layer protein expression
... lots of data (terabytes?), better to target specific data

<Helena> https://sites.google.com/site/simsciencesnuig/project-ssg--004

<iker> IMO sounds really interesting!!

<iker> @michel, do you have a couple of minutes after the call?

<mscottm2> Persons who discover new tools relevant to the HCLSIG can Tweet it using the hashtag #hclstool and I will periodically aggregate tweets with that hashtag and add these tools to the HCLSIG wiki <http://www.w3.org/wiki/HCLSIG/Tools>.

ericP: biohackathon in Boston in June?

<Helena> Yes!

<jun> Will try if I can get the visa for another meeting in June in USA

<iker> @ericP could you send a link to the Biohackathon website?

<jun> How about having one in Europe too?:)

<mscottm2> Ideas for experts: Paul Groth - http://www.youtube.com/OpenPHACTS

<mscottm2> Lee Harland (Pistoia, OpenPHACTS tech lead)

<mscottm2> http://www.ebusiness-unibw.org/tools/goodrelations-annotator/

Summary of Action Items

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