HCLSIG/Meetings/2009-01-08 Conference Call

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Conference Details

  • Date of Call: Thursday January 8, 2009
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 Greenwich Mean Time (GMT), 17:00 Central European Time (CET)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: +33.4.89.06.34.99 (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 4257 ("HCLS").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC)
  • Duration: ~1h
  • Convener: Scott, Susie
  • Scribe: Tim Clark

Agenda

Minutes

<Susie> Attendees: Scott, Rob, Don, JohnM, EricP, Kei, Jun, Bosse, Oliver, Matthias, Susie, ChrisB, TimC, Rinke, Banderss, Helen

<Susie> BioRDF Update

<Tim> Kei: Email from Adrian - additional HCLS KB set up at Free Uni Berlin, in addition to the one at DERI -we are exploring query federation - including federating dbpedia - explore how to issue distributed queries against multiple sources and integrate results highlights issues on semweb data integration - goal is to come up with a demo - adrian also interested in rule-based system - could we apply a rule scenario in integration? Want do work on a demo.

<Susie> Kei: Matthias proposing interesting project.

<Tim> Kei: Matthias proposal interesting, agree with Tim that it should be coordinated with Sci Discourse - need to make sure what he is doing is synergistic and complementary to SWANSIOC - we have a general consensus - need more tech detail from Matthias - Kei will request tech overview of his proposed method.

<Tim> Matthias: i want to build a prototype - just to go ahead - see how it can interlink - why is there so much skepticism about generating data? I don't understand? of course I'm eager to keep things aligned - no need to be concerned -

<Tim> Susie: no-one thinks you will damage, just want to keep aligned.

<Susie> Tim: Don't want to limit your creativity, just fully benefit from it.

<Susie> CDISC Update

<Tim> EricP: CDISC call - people more receptive to the RDF message than I was expecting despite their current investment in XML - CDISC want more concrete technical examples of how this would work - trying to figure out how to educate them about RDF without scaring them away :-) - they are meeting in Feb in MD so they have to be well-informed before the meeting - Call with CDISC on Dec. 19.

<ericP> http://www.w3.org/2008/Talks/1219-CDISC/#(30)

<Susie> TimC: Was Rich Ferranti involved?

<Susie> EricP: Not that I'm aware of.

<Susie> TimC: He could be a good person to liaise with.

<Susie> EricP: Has he worked on extending ontologies in Protege?

<Susie> TimC: Maybe, but not how I know him.

<Susie> TimC: Done lots of work on cheminformatics, and software architectures in life science.

<Susie> ACTION: TimC send EricP Rich Ferranti's email address.

<Susie> COI Update

<Susie> Susie: COI doesn't appear to have had a call recently.

<Susie> Linking Open Drug Data Update

<Tim> Chris: started in Oct - make datasets on drugs that are freely available eg clin trials, publish on web and integrate, answer questions that can't be answered if they are separate- we have started to investigate the identifiers commonly used that can be used to link - we have published info on 60K clin trials, about 10M triples, interlinked with DBpedia and other things such as Bio2RDF version of PubMed.

<Susie> Chris: Aiming to publish paper by February, so work is accelerating.

<Susie> Scientific Discourse Update

<Susie> TimC: 2 threads in Scientifc Discourse.

<Susie> TimC: Technical work on integrating SWAN and SIOC is done.

<Susie> TimC: Will write an IG Note that describes SWAN, SIOC and integration.

<Susie> TimC: Planning on doing a demonstration project that will query across web communities using this model.

<Susie> TimC: Think the demonstration work is important.

<Susie> TimC: 2nd thread focuses on integrating SWAN with MyExperiment.

<Susie> TimC: MyExperiment is about computational analysis of experiements, rather than experiments themselves.

<Susie> TimC: This is challenging. How to do this without boiling the ocean.

<Susie> TimC: Will discuss this more tomorrow. 2 approaches.

<Susie> TimC: Start with well characterized experiments, e.g. microarrays and brain imaging.

<Susie> TimC: Have identified partners.

<Susie> Terminology Update

<Tim> John: thread one is a SKOS mapping for SNOMED - has been on hiatus - but we'll be taking this up again tomorrow - lots of discussion on SNOMED bb on OWL implementation of SNOMED - I think it's very naive - SKOS is better - lots of people in snomed however are getting excited so that;s good - my server is up again too thread two - clin medicine use case - very document oriented - how do you extract metadata from documents? - and in that regard - there is a Google code site project with College american pathology and maybe also radiology society North America - framework for describing synoptic reports - framework is a document schema and a set of rules - should be able to extract owl from them - thread three - OASIS open doc metadata - writing standard to attach metadata to open docs - like PDFs - they can assoc any number of RDF docs with word prcessing docs - wonderful - there is an alternate way using RDFa.

<johnM> http://code.google.com/p/synoptic-report/

<johnM> http://wiki.oasis-open.org/office/Metadata

<Susie> ACTION: John to send mail to list about about the upcoming terminology call.

<Susie> Susie: Describe the potential pharma ontology task.

<Susie> http://esw.w3.org/topic/HCLSIG/PharmaOntology

<Susie> Susie: Wiki describes goals, deliverables, and scope.

<Susie> Susie: First call scheduled for Jan. 22 at noon ET.

<Susie> Rob: Presents on CCR-to-NCI Thesaurus and Pathways Explorer.

<RobFrost> note: to see live demo, go to https://www2.gotomeeting.com/register/204170405 for webinar.

<RobFrost> if you hit a problem with that, the slides and screen shots are at: http://esw.w3.org/topic/HCLSIG/Meetings/2000-01-08_Conference_Call

<Susie> TimC: Nice demo. We should think about RDF enabled SOA.

<mscottm> 1+

<Susie> TimC: When relational databases came out people throught they'd solve all probles, but a middle layer was needed, same could be the case here.

<Susie> Kei: Agree with Tim. Want to come up with this kind of layer in BioRDF.

<johnM> Rob - great demo! I have lots of questions, but will ask tomorrow on Terminology call.

<Susie> Kei: Like pathway demo, could expand query input by allowing people to enter gene symbol, and things GO, rather than just pathway name.

<Susie> Susie: Lilly is interested in combining RDF & SOA.

<Susie> Rob: Company founded early 2008, just a couple of people, and working on getting customers.

<Susie> Scott: F2F Update

<Tim> Scott: plans for next f2f - back to back with BioIT World <http://www.bio-itworldexpo.com/> are there any objections? - would like to do strategy talks and breakouts and demos - ideas for invited talks solicited - there may be a URI workshop organized by Mark Musen - esp aimed at data providers - want to make it very important event. Plan is to back F2F onto Bio-IT World.

<Susie> Scott: Plans would be to hold the meeting on April 29, 30, & May 1.

<Susie> Scott: Looking for sponsors for food.

<Susie> Scott: Will be held at the Stata Center, MIT.

<Susie> Susie: Next call in 2 weeks.