HCLSIG/Meetings/2010-03-04 Conference Call

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Conference Details

  • 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 #: + (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



04 Mar 2010

See also: IRC log


Present Scott, Susie, Eric, Matthias, Bosse, Elgar, Julia, Anita, Tim
Regrets Kei
Chair Scott
Scribe ericP

Summary of Action Items
<scribe> scribenick: ericP

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


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!