HCLSIG BioRDF Subgroup/Meetings/2011/03-21 Conference Call

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Conference Details

  • Date of Call: Monday, March 21, 2011

[NOTE: Daylight Savings Time in U.S. means calls are 1 hour earlier in Europe.]

  • Time of Call: 11:00 am Eastern Time, 3 pm UK, 4 pm CET
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)

[Note: limited access to European dial in numbers below]

  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.203.318.0479 (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: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
  • Duration: ~1 hour
  • Convener: M. Scott Marshall
  • Scribe: TBD


  • Vocabularies for describing HCLS KB named graphs - All
  • Setting up a federation endpoint to dispatch between DERI Galway (Virtuoso) and Berlin (Allegrograph) - All
  • Microarray RDF, Getting started on the W3C note - All
  • AOB


16:10  mscottm	http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/Meetings/2011/03-21_Conference_Call
16:12	Lena	http://ckan.net/package/hcls-knowledge-base
16:15	mscottm	http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph
16:17		*** jun quit (Quit: ChatZilla 0.9.86 [Firefox 3.5.17/20110121150727])
16:18		*** jun joined #hcls
16:25	Lena	http://labs.mondeca.com/sparqlEndpointsStatus/index.html
16:31		*** Zakim joined #hcls
16:31	ericP	Zakim, this is biordf
16:31	Zakim	ok, ericP; that matches SW_HCLS(BioRDF)11:00AM
16:31	ericP	Zakim, please dial ericP-office
16:31	Zakim	ok, ericP; the call is being made
16:32	Zakim	+EricP
16:33	ericP	Zakim, who is here?
16:33	Zakim	On the phone I see ??P5, +1.832.386.aaaa, ??P3, ??P7, +1.206.732.aabb, EricP
16:33	Zakim	On IRC I see jun, michael, mscottm, Lena, sudeshna, egonw_, ericP
16:34	ericP	michael, http://www.w3.org/2001/sw/hcls/#ie
16:36	mscottm	https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&hl=en#
16:45	ericP	jun, should we map the ontology in the gene lists workshop paper to OPM?
16:46	ericP	scribenick: ericP 
16:47	ericP	jun: recording provenence info isn't very bio-focused
16:47	ericP	... perhaps not in scope of this note
16:48	ericP	... OPMD talks about inputs and outputs and what genes were investigated
16:48	ericP	... PIs can be expressed as agents
16:48	ericP	... OPMD doesn't talk about e.g. samples
16:49	ericP	Lena: i think we could use OPMD for provenance in the note
16:49	ericP	... what can we use for more domain-specific stuff?
16:49	ericP	jun: i've been using NCBO search facilities and ending up with many ontologies
16:49	ericP	... MAGE doesn't cover many of them
16:50	michael	what does OPMD stand for?
16:50		*** matthias_samwald joined #hcls
16:50	ericP	... in the best practice doc, we talked about a medium ontology called CRO (Common Reference Ontology)
16:50	ericP	... we could use that here
16:51	ericP	michael, open provenance model D-something-or-other
16:51	michael	thanks
16:51	ericP	mscottm: RDF for gene expression atlas expected to be settled in coming weeks
16:52		*** matthias_samwald quit (Quit: Leaving.)
16:52	ericP	... we should present sudeshna's mappings
16:52	ericP	... did DEXI (SP?) come from wholes in OBI?
16:53	ericP	sudeshna: EFO is an app ontologies to express all of their database. predated a lot of OBI
16:53	ericP	... they discuss biomaterials (possibly not included in OBI)
16:54	ericP	... their motivation: instead of cobbling together 15 ontologies, let's have one and do a mapping
16:55	ericP	... although OBI has term coverage, it didn't have the structural coverage we needed
16:55	michael	NCI has some rich descriptions of biomaterial
16:55	ericP	... e.g. study 1 says {gene X  linked to autism} and study 2 says {gene X  not linked to autism} 
16:55	ericP	... OBI doens't give you the summary view of the experiment
16:57	ericP	Lena: we want to align our gene lists with their gene atlas's gene lists
16:57	ericP	mscottm: it's the manually curated subset of array express
16:58	ericP	... if we have their RDF available, we can dynamically create interfaces
16:59	jun	they also have some very useful restful services
17:00	Zakim	- +1.206.732.aabb
17:00	Zakim	-EricP
17:00	Zakim	-??P5
17:00		*** michael left #hcls
17:05		*** egonw_ quit (Ping timeout)
17:09	Lena	gotta go.. thanks for the dicussion  
17:10		*** sudeshna quit (Quit: http://www.mibbit.com ajax IRC Client)
17:11	Zakim	-??P7
17:11	Zakim	-??P3
17:11	Zakim	- +1.832.386.aaaa
17:11	Zakim	SW_HCLS(BioRDF)11:00AM has ended
17:11	Zakim	Attendees were +1.832.386.aaaa, +1.206.732.aabb, EricP