14:55:25 <RRSAgent> RRSAgent has joined #hcls
14:55:25 <RRSAgent> logging to http://www.w3.org/2010/04/01-hcls-irc
14:55:33 <ericP> Zakim, this will be hcls
14:55:33 <Zakim> "hcls" matches SW_HCLS(TransMed)11:00AM, and SW_HCLS()11:00AM, ericP
14:55:38 <ericP> Zakim, this will be hcls()
14:55:38 <Zakim> ok, ericP; I see SW_HCLS()11:00AM scheduled to start in 5 minutes
14:55:44 <ericP> Zakim, please dial ericP-office
14:55:44 <Zakim> ok, ericP; the call is being made
14:55:45 <Zakim> SW_HCLS()11:00AM has now started
14:55:48 <Zakim> +EricP
14:55:56 <jun> jun has joined #hcls
14:57:47 <Susie> Susie has joined #hcls
15:00:16 <Zakim> + +1.610.651.aaaa
15:00:44 <bbalsa> bbalsa has joined #HCLS
15:00:45 <ericP> Zakim, +1.610.651.aaaa is Susie 
15:00:45 <Zakim> +Susie; got it
15:01:44 <Zakim> +??P8
15:01:50 <mscottm> mscottm has joined #hcls
15:01:52 <Zakim> + +1.503.488.aabb
15:01:55 <jun> zakim, ??P8 is jun
15:01:59 <ericP> Zakim, ??P8 is jun 
15:02:01 <Zakim> +jun; got it
15:02:03 <Zakim> I already had ??P8 as jun, ericP
15:02:05 <michel> michel has joined #HCLS
15:02:17 <ericP> Zakim, +1.503.488.aabb is EricMiller
15:02:21 <Zakim> +EricMiller; got it
15:02:36 <Zakim> +[IPcaller]
15:02:43 <Zakim> +mscottm
15:02:46 <Zakim> + +46.4.63.3.aacc
15:02:59 <ericP> Zakim, [IPcaller] is michel
15:03:00 <Zakim> +michel; got it
15:03:06 <ericP> Zakim, +46.4.63.3.aacc is bosse
15:03:10 <Zakim> +bosse; got it
15:03:21 <ericP> Zakim, who is here?
15:03:27 <Zakim> On the phone I see EricP, Susie, jun, EricMiller, michel, mscottm, bosse
15:03:33 <Zakim> On IRC I see michel, mscottm, bbalsa, Susie, jun, RRSAgent, Zakim, AlexPassant, trackbot, ericP
15:05:18 <ericP> meeting: HCLS
15:05:25 <ericP> topic: BioRDF update
15:05:31 <mscottm> Jun (BioRDF): trying to model gene lists in RDF
15:05:46 <ericP> jun: Lena is passing RDF modeling work to someone else
15:05:55 <ericP> ... Satya has created an OWL ontology
15:06:08 <ericP> ... describes genes:
15:06:12 <Zakim> -EricMiller
15:06:14 <ericP> ... .. organization
15:06:18 <ericP> ... .. signal values
15:06:30 <ericP> ... i [jun] will create RDF graphs
15:06:44 <ericP> ... we'll test this data against kei's queries
15:06:53 <ericP> ... will report next BioRDF
15:06:57 <Zakim> +EricMiller
15:07:21 <ericP> ... will allow us to compare with SciDisc (who also describe experiments and resulting data)
15:07:42 <ericP> scribenick: ericP 
15:07:52 <ericP> topic: Scientific Discourse
15:08:05 <ericP> mscottm: working on provenance:
15:08:17 <ericP> ... .. that from gene lists
15:08:32 <ericP> ... .. origins of claims (e.g. literature)
15:08:56 <ericP> ... working with sudeshna das's work on microarrays
15:09:48 <ericP> ... inspecting MGED, OBI, experimental factor (EBI)
15:10:06 <ericP> ... , swan ontology
15:10:26 <ericP> ... Concept Web Alliance selected SWAN as the unit of micro-assertions
15:10:49 <ericP> ... also working with Yolanda Gill on provenance
15:10:55 <ericP> ... sudeshna leading this
15:12:17 <ericP> topic: Terminology
15:12:47 <ericP> mscottm: want URI for e.g. SNOMED, LOINC, ... terms
15:13:07 <ericP> ... re: SNOMED policy, no restrictions on that if you're in a member country
15:13:46 <ericP> topic: Clinical Observations Interoperability
15:13:46 <ericP> ericP: development of SWObjects
15:13:54 <ericP> ... Helen chen working with waterloo stuff
15:14:09 <mscottm> s/folks/stuff/
15:14:33 <mscottm> ..Helen Chen has folks at Waterloo working on a JNI wrapper for SWObjects
15:15:19 <mscottm> ..and Matt Charion from digg is working on a SWIG version of SWObjects
15:15:36 <mscottm> ..he is working on policy and access control for that.
15:16:09 <ericP> mscottm: last week: Eli Cohen demo'd caMatch
15:16:19 <ericP> ... lots of functional overlap with the COI demo
15:17:01 <ericP> ... code is carefully constructed tool to give fine-grained selectors for breast-cancer trials
15:17:19 <ericP> ... they've given us their sample data
15:18:08 <ericP> ... caMatch data structures are data objects where COI data are managed in RDF.
15:18:34 <ericP> ... want to generalize this using the COI approach
15:18:50 <ericP> topic: LODD
15:19:17 <ericP> Susie: matthias converting FDA safety data to RDF
15:19:28 <ericP> ... egon converting ChemBL to RDF
15:20:08 <ericP> ... matthias submitted a paper to a special issue that kei is organizing
15:20:43 <ericP> ... ericP will present to ACS
15:21:09 <ericP> ... we're interested in best practices in matching e.g. drug data to RDF
15:21:39 <ericP> ... and harder scenarios like longitudinal patient study data
15:22:06 <ericP> ... these increase complexity of model
15:23:05 <ericP> ... j&j is feeding data to rdb2rdf, hoping to get RDB2RDF them to meet our needs
15:23:18 <ericP> topic: Translational Medicine Ontology
15:23:40 <ericP> Susie: moved to a weekly schedule to maintain momentum
15:23:54 <ericP> ... michel's tidying the demo
15:24:14 <Zakim> -bosse
15:24:14 <ericP> ... ensuring that the TMO is cleaned up and posted at bioportal
15:24:33 <ericP> ... J&J looking at TMO for internal use
15:24:55 <Zakim> +bosse
15:25:07 <ericP> ... Bosse, chrisD and others working with clinical sources via "emerge" group
15:25:21 <ericP> ... Bosse looking at physician interface
15:25:34 <ericP> ... michel submitting to ISMB
15:25:57 <ericP> ... ChrisD presenting TMO at drug industry conference (DC, Oct)
15:26:34 <mscottm> s/SIGONT at ISMB/ISMB/
15:26:41 <ericP> ... still want an ontology for collaboration with e.g. compounds
15:27:23 <mscottm> Zakim, who is here?
15:27:23 <Zakim> On the phone I see EricP, Susie, jun, michel, mscottm, EricMiller, bosse
15:27:26 <Zakim> On IRC I see michel, mscottm, bbalsa, Susie, jun, RRSAgent, Zakim, AlexPassant, trackbot, ericP
15:27:26 <ericP> ... met Eric Bonebieu, who's persuing this
15:27:36 <matthias_samwald> matthias_samwald has joined #hcls
15:27:50 <ericP> michel: [re demo]
15:28:03 <ericP> ... there were terms in the data that weren't mapped to the ontology
15:28:16 <ericP> ... the demo queries didn't use the TMO
15:28:48 <Zakim> +??P13
15:29:13 <matthias_samwald> zakim, ??P13 is matthias_samwald
15:29:13 <Zakim> +matthias_samwald; got it
15:29:27 <michel> http://esw.w3.org/HCLSIG/PharmaOntology/TMKB
15:30:17 <ericP> mscottm: tx to W3 for migrating to media wiki
15:30:41 <ericP> topic: Image database at Stanford
15:31:08 <ericP> mscottm: ericP set up a SPARQL interface to this DB (using SWObjects)
15:31:18 <ericP> ... relates to semantic annotaiton of images
15:31:45 <emillerpdx> emillerpdx has joined #hcls
15:32:06 <ericP> topic: Future of the Web for Collaborative Science
15:32:08 <mscottm> http://esw.w3.org/topic/HCLS/WWW2010/Workshop
15:32:23 <ericP> jun: workshop program online, papers ready
15:32:38 <ericP> ... confirmed keynote. confirming panelists
15:33:13 <ericP> ... it will be an exciting workshop, want to see hcls folks
15:33:23 <ericP> mscottm: re: f2f issue
15:33:33 <ericP> topic: f2f issues
15:34:05 <ericP> mscottm: folks want to go to BioIT (Boston) and WWW (Raleigh) , but not both
15:34:44 <Zakim> -matthias_samwald
15:35:02 <ericP> ... setting up two dinners, drinks, and discussion meetings
15:35:08 <mscottm> Zakim, who is here?
15:35:08 <Zakim> On the phone I see EricP, Susie, jun, michel, mscottm, EricMiller, bosse
15:35:10 <Zakim> On IRC I see emillerpdx, matthias_samwald, michel, mscottm, bbalsa, Susie, jun, RRSAgent, Zakim, AlexPassant, trackbot, ericP
15:35:21 <ericP> ... susie to set up BOS, Kei to set up Raleigh
15:35:26 <Zakim> +??P11
15:35:33 <ericP> ericP will be at both
15:35:39 <matthias_samwald> zakim, ??P11 is matthias_samwald
15:35:41 <Zakim> +matthias_samwald; got it
15:36:41 <mscottm> Zakim, who is here?
15:36:41 <Zakim> On the phone I see EricP, Susie, jun, michel, mscottm, EricMiller, bosse, matthias_samwald
15:36:44 <Zakim> On IRC I see emillerpdx, matthias_samwald, michel, mscottm, bbalsa, Susie, jun, RRSAgent, Zakim, AlexPassant, trackbot, ericP
15:37:03 <ericP> BOS: ericP Susie mscottm (tentative)
15:37:04 <ericP> DRU: ericP Susie Jun EricMiller
15:37:14 <ericP> DRU: ericP Jun EricMiller
15:38:41 <ericP> Susie: next W3C TPAC meeting 1-5 Nov Lyon
15:39:23 <ericP> ... last f2f was in CA, US. both gatherings in US.
15:39:39 <ericP> ... + an opportunity for europeans
15:40:03 <ericP> ... - perhaps not many hcls folks will be at TPAC
15:41:10 <ericP> Lyon: Jun Susie at risk: mscottm Bosse matthias
15:41:33 <ericP> Susie: looks iffy, maybe should look at SWAT4LS
15:41:56 <ericP> mscottm: SWAT4LS organizers intrested in such a meeting
15:42:07 <ericP> topic: Grant Opportunities
15:42:50 <ericP> mscottm: submitted proposal for coordinating omics for neurodegenerative diseases
15:43:19 <ericP> ... had michel, christine, kei, ... ellen parkinson (EBI)
15:44:12 <ericP> ... innovative medicine initiative grants in knowledge management (funding by interested pharmas)
15:44:53 <ericP> ... barend mons/CWA won an IMI as well as a couple teams from leiden
15:45:32 <ericP> ericP: this calibrates us re: competitiveness
15:45:47 <ericP> mscottm: would be a good idea to see how CWA packaged their stuff
15:46:02 <ericP> topic: web standards
15:46:58 <mscottm> Eric (Standards): RIF (Rule Interchange Format) just moved to PR (Proposed Rec)
15:47:45 <mscottm> ..SPARQL: 'minus' and 'not exists' made it into SPARQL
15:48:12 <mscottm> ..EricP submitted a SPARQL Federated Query extensions
15:49:12 <mscottm> ..maybe just in time to make it into the document (yes!)
15:49:53 <mscottm> RDB2RDF: Seems to be dominated by SQL people at the moment, I am interested in grounding things more in use cases.
15:50:04 <mscottm> ..RDB2RDF: Seems to be dominated by SQL people at the moment, I am interested in grounding things more in use cases.
15:56:30 <mscottm> ..<discussion about how to bring the RDF concerns of HCLS to RDB2RDF>
15:59:36 <ericP> -> http://www.w3.org/2010/01/Turtle/#⋈ Turtle Spec
16:00:12 <Zakim> -Susie
16:00:14 <Zakim> -bosse
16:00:19 <Zakim> -michel
16:00:25 <Zakim> -EricMiller
16:00:40 <michel> michel has left #HCLS
16:00:44 <Zakim> -matthias_samwald
16:01:18 <ericP> -> http://www.w3.org/2009/sparql/docs/fed/service SPARQL extensions for federated query
16:01:27 <ericP> RRSAgent, please draft minutes
16:01:27 <RRSAgent> I have made the request to generate http://www.w3.org/2010/04/01-hcls-minutes.html ericP
16:01:34 <ericP> RRSAgent, please make log world-visible
16:03:10 <Zakim> -EricP
16:03:11 <Zakim> -jun
16:03:12 <Zakim> SW_HCLS()11:00AM has ended
16:03:14 <Zakim> Attendees were EricP, Susie, jun, EricMiller, mscottm, michel, bosse, matthias_samwald
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