HCLSIG/Meetings/2012-07-03 Conference Call
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 why is it not listed? 11:18 ericP michel: out of date, unmaintained (due to end of project) data sources leads to SPARQL endpoints and download endpoints being unavailable 11:18 ericP ...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