HCLSIG/Meetings/2010-02-04 Conference Call

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Conference Details

  • Date of Call: Thursday February 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: Susie
  • Regrets: Scott (on a plane)
  • Scribe: TBD

Agenda

Minutes

<Zakim> Attendees were EricP, Kei_Cheung, Bosse, Susie, AllenHobbs, elgar, Joanne_Luciano

<ericP> topic: BioRDF

<ericP> kei: exploring query federation scenarios

<ericP> ... grabbing gene lists from several neuroscience experiments

<ericP> ... gene lists are in excell

<ericP> ... includes samples of gene lists content and structure

<ericP> ... lena deus working out how to express in RDF

<ericP> ... hope for a strawman structure to share with the group soon

<ericP> ... will solicit feedback from public-semweb-lifesci

<ericP> ... could provide use cases to RDB2RDF group (after excel loaded into an RDB)

<ericP> ... mscottm looking at using these gene ids as a shared names use case

<ericP> ... sridhar and jun will connect these gene lists larger structure representing exeriments and their data sets

<ericP> ... looking a using don doherty's iPhone app to connect this data to other data sets

<ericP> ... open to other apps and use cases

<ericP> ... collaborating with LODD on paper

<ericP> Susie: need to look at terms and conditions for using the ADNI data

<ericP> ... might just learn from the data

<Susie> COI

<Susie> Joshua Phillips working on cabig

<Susie> Have application called camatch

<Susie> Similar to the COI demo

<Susie> So interested in extending and using COI code with camatch

<Susie> Waiting for them to share some data with us

<Susie> The data covers fake patient records in XML

<Susie> Will be coverting to RDF and trying to align to TMO

<ericP> topic: LODD

<ericP> Susie: matthias working on a TCM paper (traditional chinese medicine)

<ericP> ... data sets are proprietary, workin on terms of use

<ericP> ... easy to map e.g. drug bank to RDF. a reasonable graph structure is fairly clear

<ericP> ... harder to represent experimental data

<ericP> ... e.g. results from a particular machine analyzed by a particular algorithm

<ericP> ... LODD working on a best practices paper and allignment with [existing] ontologies

<ericP> topic: TMO

<ericP> Susie: refining TMO work:

<ericP> ... .. extending to include e.g. biomarker. how does our data support the biomarker idea?

<ericP> ... .. strengthening alignment with Translational medicine ont. e.g. LODD ont wasn't aligned with TMO

<ericP> ... .. representing inclusion/exclusion criteria in an ontology of phenotypes. allow CRO to see how many patients match

<ericP> ... .. interface for TMO

<ericP> ... we saw a dearth of e.g. drug ontologies

<ericP> ... pharmas don't have a standard way to share e.g. compounds in drugs

<ericP> ... in 37 mins, we have Janna presenting KEBBI and Rich VA NDFRT (perhaps FDA stipulates pharmas use)

<ericP> ElgarPichler: hard to consolidate all the ontology efforts in the drug/compound space

<ericP> ... will attempt mapping via RXnorm

<ericP> ... linkCT, MEDRA, etc.

<ericP> Bosse: will have UI plans in two weeks

<ericP> kei: how are inclusion/exclusion represented? (rules, ontology, query?)

<ericP> Susie: currently pharmas look for previous reps of similar trial protocols

<ericP> ... we're competing against piles of paper

<ericP> ... we think inclusion/exclusion criteria should include phenotypes

<ericP> ... michel dumontier has been looking into this

<ericP> ericP: in COI demo, we represented incl/excl as queries. person in this age ranging taking X and not taking Y

<ericP> ... didn't get as far as what you would call phenotytpes

<ericP> topic: Meetings

<ericP> Susie: LeeF will introduce SemWeb standards

<ericP> ... Elgar will cover standards in pharma industry

<ericP> ... Vipul will talk about apps in health care

<ericP> ... Tim Clark will talk about Scientific Publishing apps

<ericP> ... Kei will give tech talk about federated query work

<ericP> ... JohnM will give tech talk on terminologies

<ericP> topic: F2F

<ericP> Susie: BioIT is 3rd week of April

<ericP> ... HCLS f2f will be in 22,23 in the Stata Center

<ericP> ... soliciting agenda suggestions

<ericP> Bosse: i like the combo of break-outs. still lots to do in TMO

<ericP> ... also appreciated invited talks

<ericP> ... and networking time

<ericP> Susie: could get updates from other W3C folks

<ericP> kei: +1 to break-outs

<ericP> ... at TPAC we enjoyed the visit from the SPARQL folks

<ericP> ... would like RDB2RDF talk

<Zakim> +Joanne_Luciano

  • ** jluciano [ad30d086@128.30.52.43] has joined #hcls

<ericP> Allen: want to move back into BioRDF group

<ericP> ... research at Kaiser Permanente and NIH

<ericP> ... working with extremely large datasets

<ericP> ElgarPichler: +1 to break-outs, presentations

<ericP> ... would like dedicated slot for encountered problems

<ericP> ... "couldn't do X, ran into limitations with tool set Y"

<ericP> ... could come from task forces, or a critical outside presenter

<ericP> Susie: could get feedback from the folks in the room which satisfies questioner, or discussion suggesting future work

<ericP> topic: Future of the Web for Collaborative Science

<ericP> -> http://esw.w3.org/topic/HCLS/WWW2010/Workshop Future of the Web for Collaborative Science Homepage

<ericP> Susie: submission deadline 15 Feb. please submit

<ericP> topic: grants

<ericP> Susie: submitting grants will give us more HCLS resources

<ericP> ... JohnM was talking about the required short turn-around for ARAA grants

<ericP> ... JohnM was suggesting about a corpus of bios and projects

<ericP> alan: SHARP grants have 2 week turn-around

<ericP> ... expect others coming

<ericP> ericP: ARAA are ~ 40 pages. are SHARP as well?

<ericP> Allen: i expect so

<Allen> ONC site:http://healthit.hhs.gov/portal/server.pt?open=512&objID=1310&parentname=CommunityPage&parentid=8&...

<ericP> Allen: HL7 is offering funding ops

<ericP> ... John Glen (CTO of HL7) is interested in reaching out to w3c

<ericP> ... Bob Dole is chair of HL7

<ericP> ... overlap: moving towards semantic ontologies for use in RIM

<Susie> RIF is at CR

<Susie> RIF is waiting for more implementations

<Susie> Federated query is at risk in SPARQL

<Susie> Been writing Turtle spec so it can be included in specs

<Allen> John Quinn...CTO HL7

<Susie> So Turtle will become more official soon

<Susie> RDB2RDF is trying to figure out use cases and what they should do

<ericP> http://esw.w3.org/topic/HCLSIG/RDB2RDF_Use_Cases

<Susie> Started use case doc for us to submit to them

<Allen> Chuck Jaffe ...CEO HL7

<Susie> Should help them to understand scale

<Susie> And use cases

<Susie> OWL2 is at rec

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