HCLSIG BioRDF Subgroup/Meetings/2011/03-21 Conference Call
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 #: +33.4.26.46.79.03 (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
Agenda
- 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
Minutes
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