HCLSIG/Meetings/2010-03-04 Conference Call
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- Date of Call: Thursday March 4, 2010
- Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 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), Quick Start: Click on mibbit for instant IRC access.
- Duration: ~1h
- Convener: Scott
- Scribe: EricP
- Updates by BioRDF, Terminology, COI, LODD, Translational Medicine Ontology, Scientific Discourse - All
- Meetings: CSHALS, F2F, The Future of the Web for Collaborative Science WWW Workshop
- Grant opportunities
- W3C Standards update: SPARQL, OWL2, RDB2RDF, Provenance
04 Mar 2010 See also: IRC log Attendees Present Scott, Susie, Eric, Matthias, Bosse, Elgar, Julia, Anita, Tim Regrets Kei Chair Scott Scribe ericP Contents Topics updates C-SHALS f2f Summary of Action Items [IPcaller] <scribe> scribenick: ericP updates mscottm: [BioRDF] ... federation work in microarray use case and TCM (traditional chinese medicine) ... thread with mged folks thanks to Michael Miller (Chris Stoeckert, John Quackenbush, Aedin Culhane, Gavin Sherlock, Catherine Ball, Scott Marshall) ... discussion of how to disclose a genelist in e,g, magetab ... possibly ask journals to accept machine-readable gene lists ... HelenaDeus, ... have expressed microarray data in RDF ... Satya, kei, jun have addressed provenance issues in a BioRDF wiki page ... looking at using VoID to describe 200 named graphs in the KB matthias_samwald: (TCM work) [BioRDF/LODD] ... submitted an article to journal of chinese medicine ... using ethno-pharma data and TCM to inform modern drug design ... and find efficacy/safety of TCM ... use case: medication related to depression ... curated data by hand. michelD expressed pharma of depression work in ATAGs ... some sources were not available to us despite claims in papers to the contrary ... there is less data than you might expect [from papers] than you can link and make available mscottm; [Term] scribe: JohnM described bottom-up and top-down processes for coding documents ... talked about advantages of SKOS ... has expressed a sample doc in RDF ... will share the doc with us to see if we invent similar [compatible?] RDF ... trying to get folks to serve terms from sharable URIs ... discussion of mapping SNOMED-CT term to a purl ... looking for a SNOMED-annotated document susie: [LODD] ... egon has made ChemBl (EBI dataset of medicinal chemistry) available in RDF <mscottm> Yay! susie: oktie updating his clinicaltrials.gov to include coded inclusion/exclusion criteria ... data available in free text ... mapping databases to create linked data and support queries <mscottm> susie: lots of repeat usage of incl/exclusion criteria so LODD wants to encode them as URI's for use in queries <mscottm> ..also interested in creating a hierarchy of inclusion/exclusion criteria ericP: in COI Patient Recruitment, we coded inclusion/exclusion as SPARQL Susie: pharmas re-use these, so we want to assign them URIs and create a hierarchy ... would like work segmented by tasks rather than fractured across tasks ... we have lots of overlap between TMO and LODD. tempted to aggregate calls. feedback? Bosse: +1 ElgarPichler: while i prepared my [C-SHALS] talk, i learned of the stuff made available by michel in LODD ... drug ontology relevent to inclu/exclu criteria <mscottm> Elgar: many datasets in LODD and TMO are the same or of similar interest, also many provided by Michel ElgarPichler: looking at using RxNORM or UMLS ... happy to see a closer integration of LODD and TMO Susie: TMO copies, changes LODD data. likewise BioRDF matthias_samwald: loading LODD output into KB doesn't require work or discussion in the BioRDF calls ... not any real lost work here <mscottm> Scott: [interpreting and agreeing] All three task forces would ideally use the same tools to access the same data from the same place (in HCLS-created resources) matthias_samwald: TCM split between BioRDF and LODD could be more of a problem ... suggest that there is some fuzziness, and not try to fit things into one place ElgarPichler: [TMO] ... Bosse working on interface side ... (also of interest to other task forces) ... hvae a poster at AMIA ... don't know about JBI Susie: we're submitting a short paper about the TMO and design to ISMB ... longer paper not yet targeted mscottm: trish noted challenges around long author lists Susie: maybe we should exclude names, but reference TMO or HCLS ... OBI consortium does stuff like that Bosse: [TMO interface] ... we need to visualize the potential of using TMO ... will discuss proposals in the next hour mscottm: [SciDisc] ... noted at C-SHALS a shared interest in provenance about scientific experiments between BioRDF and SciDisc ... SciDisc is describing experiments in SWAN ... Gobel at al are describing "Research Objects" in a workflow ... David Shotton asked Jun to liaison between scidisc and biordf ... Tim Clark said that Sudeshna will look at this. also Dave Neuman Anita: looking at rhetorical structure ... paolo cicarase described SWAN ... tudor descibed his <mscottm> ..SALT, CITO, ABCDE structures (descriptions of) Anita: course-grained work: structure of portions of documents ... if we have a list of journals, how many will agree to structure ... Intro Results Discussion (InReD) ... other side is markup of hypothesis ... some existing tools. can we get them to talk to each other? ... paolo and tudor will look at that ... CYCLE being aligned with SWAN/SIOC ... investigation into bibliograph info ... PRISM is the most common publishing standard ... lots of standards both at libraries and for publishers TimClark: have four alignment tracks: ... .. Rhetorical Structure ... .. Bibliograph ontology's e.g. CITO ... .. SWAN + MyExperiment + Research Objects + Kei's work (Jun Zhao and Matt Gamble) <mscottm> ..and Sudeshna Das from Tim's group will work on it as well TimClark: .. Documet annotation model. we have proposals, but insufficient bandwidth mscottm: paolo said that stephane corlosque will provide RDF for SWAN through Drupal ericP: [COI] HelenChen and ericP pushing on access policies C-SHALS f2f mscottm: likely aggregations of HCLS-ers at BioIT and WWW ... can have small f2fs Susie: biggest value may be seeing each other f2f ... (we're used to working in a distributed environment), could just meet for dinner and drinks <mscottm> ack <Zakim> ericP, you wanted to say when we have reservations at Stata <mscott> Forgot to mention that Concept Web Alliance folks have been discussing how to represent claims/statements as triples and adopted SWAN/SIOC as their starting point!