W3C HCLS – General Meeting -- 11 Sep 2012

Introductions, Charting directions for the next year

<mary> this is mary, for some reason i do not get the email from HCLS for this meeting. mary@knoesis.org

Michel: Charting directions for the next year
... First, past HCLS meetings had introductions by email; send an email to the list w interests and task forces

<SimonLin> is there a list of the current task forces?

<michel> task forces: http://www.w3.org/wiki/HCLSIG

Michel: ericP and Charlie Mead have been working on clinical interoperability

Scott: What we could do to pick up when John Madden had to step down.
... Daniel and I are still interested in continuing

<michel> scribenick: bobP

Reports from task forces

scribe: Reports from task forces;

Scott: Linked Life Data. Richard Boyce has been in final edit
... article tutorial style on different approaches to RDF and sparql for life science data
... also, an article came out last year of translating standards to practice
... navigating thru datasets using sparql on-the-fly
... we went to make a more tutorial style article; ongoing process, but has stalled out
... essentially: We are poised for the final re-structure and rewrite for target audience
... people who have microarray data and want to go to semweb
... also, we want to reinforce representations in RDF
... also, discussed moving forward w Data discovery platform for linked data
... Biohackathon 2011, there is interest in expression-RDF, interest in continuing on federated discovery
... this comes from two different groups, now consolidating
... most interesting is federating across cliinical data
... connecting up both life science and clinical, like radiology
... these all have practical applications, like Eureka(?) that I'm working on
... also EHR4CR from Kersten
... all related to FHIR that ericP and Charlie are working on
... can easily connect information for datamining in your clinic

<ericP> LLoyd is now able to represent most of HL7's RIM in OWL.

Scott: semweb representation for patient info; Ex: my clinic has already used

<ericP> we're using that to define FHIR resources

<ericP> has the cool effect that anything in FHIR has a defined RDF representation

Scott: potential path to the future for that group.
... couple of people are also interested in expression RDF;

Michel: There was pretty cool work at the Biohackathon in Japan

<ericP> also can combine with OWL for SNOMED to discover equivalence between observations using a single pre-coordinated SNOMED term vs. the parameters in that term sprinkled throughout multiple observations and structural elements

Michel: they used jBrowse to do sparql queries
... showed how to scan through the genome pretty fast

<ericP> this allows one to e.g. be (more) complete when querying for patient facets

Scott: sparql to access(?)

<ericP> i'm now in a SMART Platforms meeting. hoping to unify SMART with TMO...

<mscottm> SPARQL to access tracks in Genome Browser

<ericP> (Indivo already unified with SMART)

Michel: Worked with a simple ontology to query a resource that already exists

<mscottm> EURECA project http://eurecaproject.eu/

<ericP> (so that job is done)

<mscottm> Ratnesh mentioned http://www.linked2safety-project.eu

Michel: we have genomic info, not just microarray data; plus all of the other typical data
... need to show how to get from a certain kind of data and integrate

Scott: Excited about the genome browser; have been talking about for years

<michel> http://2012.biohackathon.org

Michel: link to wiki has details

<mscottm> SPARQL-enabled Genome Browser - Yes!

<mscottm> http://www.ehr4cr.eu/

Michel: Biohackathon contribution from Andrea(?)

<mscottm> http://www.hl7.org/implement/standards/fhir/introduction.htm

Michel: other major issue is adoption for URIs
... all of this has to be consolidated, canonical URIs

<mscottm> identifiers.org

Michel: tried to map to canonical URIs; would like to push this out in HCLS
... to normalize namespaces and URI patterns

<mscottm> Andrea Splendiani

Michel: Scientific Discouse no longer to continue(?)

Scott: I was always interested in having a sparql interface to a discussion forum
... Alzheimer's Forum is an example

Joanne and Michel discussing Sci Discourse

<mary> Would you please send the link for different project at HCLS

Joanne: Drug label enhancement came out of this
... had served its purpose

<mscottm> mary - does this help? http://www.w3.org/wiki/HCLSIG

<mary> thanks

Joanne: Mining treatment outcomes on hold

Michel: Would go under clinical decision support when starts again
... Systems Biology for Drug Discovery
... working with a variety of biopax data; using G fusion tables
... protein complex evolution, to map out metabolics

Scott: wrote an email about this
... can use G refine to clean data; export to RDF etc

Michel: Pathways Commons now has sqarql endpoint!
... using Fuzeki(?)
... using identiifiers.org
... identifiers.org
... Xfefs for proteins in interactions; they intend to make this a strong recommendation for data producers
... we can all use identifiers.org URIs
... there is a whole discussion around this; Uniprot would try to go to source first, then go to identifiers.org (have this correct?)
... HCLS: what should data providers do?
... happy to discuss this in a linked life data call

<mary> Did she make federated query from gene to pathway? or from gene to biological process? and does she use biopax?

Joanne; Also invite them to call and put in note

Michel: Long discussion w Uniprot. They are moving toward significantly less restrictive licensing
... we are in position to provide guidance on how to deal with licenses, when going to LOD
... show people how to do this; Should be on the table for Linked Life Data

Joanne: Just came back from Wolfram conference
... some people were not convinced about sharing data; Surprising
... So Linked Life Data has a huge mandate right now
... take over the slot for Discourse?

Michel: Scott has to do more multi-tasking? :)

Scott: Can still work some of this into the emerging practice note
... some people just don't get why to use a URI that is not from the authoritative issuer
... hard to get over this cultural old fashioned way
... we need to change this.

Michel: After Biohackathon, I'm confident that we can do this job

Joanne: Q about Emerging practice doc

Scott: Clocking down to a few weeks

Michel: Matthias couldn't come for PGx task force
... dealing w sources of data of genetic variation
... strategy to dbSNP to RDF to endpoint
... Matthias and I and other have been working on snp-to-haplotype, looks good
... genetic variation for pharmacogenomic sensitivity; all being done in Clinical Decision Support
... safetycode.org can provide decision support
... check back in the archives for Matthias' websites
... Richard Boyce has been working on structured product labels

<mary> for the project was involved in itegration data from NCBI, OMIM,... I did this work in last summer at NIH. who is working in this project?

Michel: rxNorm, curating evidence and linking to clincial studies
... need to regularize the knowledge representation, to help support personal health lens(?)

Mary: HCLS summer school

<michel> http://www.w3.org/wiki/HCLSHackathon2012

Mary: we went through SADI and other tools
... it was very good.

<mscottm> http://swat4ls.blogspot.nl/2012/09/swat4ls-2012-keynotes.html

Scott: I have asked ericP to organized swat4ls in Paris

<michel> http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/

Michel: We will be hosting in Montreal next year; three conferences back-to-back
... all in first week of July 2013; hoping to organize a hackathon in Montreal
... Principle issues, update the wiki to show all the work

<mscottm> I asked Eric if he would help with the SWAT4LS hackathon along with Toshiaki Katayama in Paris in November. Parallel hackathon and tutorial for 2 days (wed, thu) followed by plenary session on friday.

Mary: I already integrated OMIM etc at NIH

Michel: BioRDF has about 50 datasets being managed
... BIo2RDF release in mid-Sept(?)

<mscottm> +1 on archiving/sharing RDF conversion scripts for reference

<mscottm> http://www.w3.org/blog/hcls/

<mscottm> Thanks to Bob for scribing!!

<dbooth> Scribe: Bob Powers

- DRAFT -

W3C HCLS – General Meeting

11 Sep 2012

Attendees

Contents

Introductions, Charting directions for the next year

Reports from task forces

Summary of Action Items

Scribe.perl diagnostic output