HCLSIG/Meetings/2012-07-03 Conference Call

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Meeting:       HCLS General Forum
Convener:      Michel Dumontier
Date:          July 3, 2012 @ 11am EDT
Frequency:     1st Tuesday of the month
Past Meetings: http://goo.gl/NFqPx
Dial-In #:     +1.617.761.6200 (Cambridge, MA)
VoIP address:  sip:zakim@voip.w3.org
Participant    Access Code: 4257 ("HCLS")
IRC Channel:   irc.w3.org port 6665 channel #HCLS
IRC Web:       http://goo.gl/A6WZn

Agenda

  • Bio2RDF - michel
  • HL7/FHIR - eric

Minutes

Bio2RDF datasets - https://docs.google.com/spreadsheet/ccc?key=0AnGgKfZdJasrdElfQzRWWWhKUFR0UnRpeG14NGZRS2c#gid=0
11:15	egonw	CTD is interesting!
11:15	matthias_samwald	does STITCH not cover most molecular interaction datasets now?
11:16	Zakim	On the phone I see Bob_Powers, Erich, Marc, +1.510.541.aaaa, ??P3, michel, +1.631.444.aabb, egonw__, ericP, matthias_samwald, Joanne_Luciano
11:16	Zakim	On IRC I see mscottm, JoanneLuciano, matthias_samwald, eBremer, Zakim, michel, Marc, egombocz, bobP, kalpana, achille_zappa, MacTed, egonw, ericP
11:17	ericP	topic: Bio2RDF maintenance
11:18	egonw	Q: chembl has been part of Bio2RDF too... why is it not listed?
11:18	ericP	michel: out of date, unmaintained (due to end of project) data sources leads to SPARQL endpoints and download endpoints being unavailable
11:18	ericP	... goal of Bio2RDF is to consolidate resoruces
11:19	michel	github repository - https://github.com/bio2rdf
11:19	ericP	... github repo includes converstion scripts and maps
11:19	ericP	... hope to take the HCLS data will be available in Bio2RDF
11:19	ericP	... making scripts available
11:20	michel	dataset statistics - https://docs.google.com/spreadsheet/ccc?key=0AnGgKfZdJasrdElfQzRWWWhKUFR0UnRpeG14NGZRS2c#gid=1
11:20	ericP	this should provide persistence for our data contributions
11:20	ericP	michel: the above stats includes predicates, counts, refs to other datasets
11:22	ericP	ericP: i advocate data examples which span the types
11:23	ericP	michel: at hackathon in Japan, we discussed which data we want to collect about a dataset
11:23	ericP	JoanneLuciano: what sort of metadata? 
11:24	ericP	michel: is everything types, what predicates, how many of what?
11:24	ericP	... we have a manuscript but haven't pushed forward for a while
11:25	ericP	... would like to make it an HCLS note
11:25	ericP	ericP: use case?
11:25	eBremer	http://vocab.deri.ie/void
11:26	ericP	... .. person has a biological question and the stats help him/her compose a federated query
11:26	michel	sindicetech - http://hcls.sindicetech.com/pivot-browser/#ff=Compound
11:26	ericP	... .. the stats maintain redundant endpoints and the system automagically routes you appropriate endpoints
11:27	ericP	michel: former is more compelling
11:27	michel	diagram - overview of the datasets & connectivity - http://hcls.sindicetech.com/explore/
11:27	ericP	-> diagram - overview of the datasets & connectivityhttp://hcls.sindicetech.com/explore/
11:28	ericP	michel, this diagram shows the types and connectivity and size
11:28	ericP	michel: this diagram shows the types and connectivity and size
11:28	ericP	... color for datasets
11:28	egonw	brb
11:29	ericP	michel: this allows a user to figure out how to construct a query
11:30	ericP	... produced by a spinoff of DERI called sindece
11:31	egonw	back
11:31	ericP	... we have sources like chem2bio2rdf
11:31	ericP	... but no coordination of scripts
11:32	JoanneLuciano	@ericP -- what happened with your hackathon idea?
11:33	ericP	... we talked with giovani about hosting at DERI
11:34	JoanneLuciano	when?
11:34	ericP	... we hope we can guide folks through the process of contributing to bio2rdf
11:35	ericP	ericP: so that's release engineering?
11:36	michel	topic: hl7/fhir
11:36	ericP	scribenick: michel 
11:37	michel	charlie: HL7 has worked on a comprehensive model for health data; 
11:37	michel	... messaging strategy not really working
11:38	michel	... FHIR is a new approach, radical; open; xml resources available through rest interfaces
11:38	michel	... freely available to everyone
11:39	michel	... not much semantic web technology in HL7
11:40	michel	... ericP went to an HL7 meeting;  produce RDF-compatible representations to RIM resources
11:40	michel	... multi layers - RDF + SPIN + SPIN
11:40	michel	... to check validity and consistency of data
11:41	michel	... opportunity to get semantic web technology into health care;  
11:41	ericP	q+ to talk about LDP
11:41		Zakim sees ericP on the speaker queue
11:42	ericP	-> http://www.w3.org/2012/04/FHIR/labreport-short.ttl FHIR lab report
11:44	michel	ericP: been doing it in XML because audience knows hows to sling XML around; 
11:44	michel	... by REST-y -> about having persistent identifiers for resources
11:45	michel	... bunch of named graphs -> one for lab report, etc
11:45	michel	... what should that graph look like? 
11:46	ericP	_bs1 bservation <obs1> ; :codingSystem <snomed> ; :code "12345-67" ; :value 140 ; :units  "mmHg" => <obs1> ystolicBP 140 .
11:46	ericP	_bs9 bservation <obs3> ; :codingSystem <snomed> ; :code "76543-21" ; :value 139 ; :units  "mmHg" => <obs3> ystolicBP 139 .
11:47	michel	... some observation; has a code from snomed; has a value, units
11:48	michel	... one organization (HL7) to provide the structure/framework; another organization for the terminology (SNOMED); 
11:48	michel	... fairly chaotic space wrt integration
11:49	michel	... harder to ask questions 
11:49	michel	... create a marketplace for apps to query the data; 
11:50	michel	... expose similarly shaped graphs
11:51	michel	... can't effectively curate all the biomedical codes into an enormous RDF graph tomorrow; gotta pick some pieces and derive  coherent graphs
11:51	michel	... FHIR is using the reified form in XML;  ericP's work on RDF is similar; 
11:53	michel	... extract out portions of interest for the use cases; rules that transform data into a desired form
11:54	michel	... build a RDF-backend for a  FHIR server
11:58	michel	charlie: how to interface michel's SPIN-managed use case to this?
11:58	michel	ericP: that can be accommodate using the proposed endpoint
11:58	JoanneLuciano	great update -- regrets have to leave for another meeting -- Happy 4th Everyone (and those not in US -- OK to virtually  celebrate (I'll be celebrating with some good UK friends). 
11:58	JoanneLuciano	@ericP -- lets catch up next week.
11:59	JoanneLuciano	@michel  great job. thank you.  When are you coming to visit RPI  
12:00	egombocz	excellent efforts! great work on the 2 SPIN layer concept
12:00	michel	Charlie: single biggest problem is governance / conformance of the resources
12:01	michel	... check that the bindings are legitimate & correct
12:01	egombocz	regrets, have to leave - really great approach to assure consistency
12:03	kalpana	@eric and @michel thanks great update
12:03	eBremer	yes tks