See also: IRC log
<mscottm> Jun (BioRDF): trying to model gene lists in RDF
jun: Lena is passing RDF modeling
work to someone else
... Satya has created an OWL ontology
... describes genes:
... .. organization
... .. signal values
... i [jun] will create RDF graphs
... we'll test this data against kei's queries
... will report next BioRDF
... will allow us to compare with SciDisc (who also describe
experiments and resulting data)
<scribe> scribenick: ericP
mscottm: working on
provenance:
... .. that from gene lists
... .. origins of claims (e.g. literature)
... working with sudeshna das's work on microarrays
... inspecting MGED, OBI, experimental factor (EBI)
... , swan ontology
... Concept Web Alliance selected SWAN as the unit of
micro-assertions
... also working with Yolanda Gill on provenance
... sudeshna leading this
mscottm: want URI for e.g.
SNOMED, LOINC, ... terms
... re: SNOMED policy, no restrictions on that if you're in a
member country
ericP: development of
SWObjects
... Helen chen working with waterloo stuff
<mscottm> s/folks/stuff/
<mscottm> ..Helen Chen has folks at Waterloo working on a JNI wrapper for SWObjects
<mscottm> ..and Matt Charion from digg is working on a SWIG version of SWObjects
<mscottm> ..he is working on policy and access control for that.
mscottm: last week: Eli Cohen
demo'd caMatch
... lots of functional overlap with the COI demo
... code is carefully constructed tool to give fine-grained
selectors for breast-cancer trials
... they've given us their sample data
... caMatch data structures are data objects where COI data are
managed in RDF.
... want to generalize this using the COI approach
Susie: matthias converting FDA
safety data to RDF
... egon converting ChemBL to RDF
... matthias submitted a paper to a special issue that kei is
organizing
... ericP will present to ACS
... we're interested in best practices in matching e.g. drug
data to RDF
... and harder scenarios like longitudinal patient study
data
... these increase complexity of model
... j&j is feeding data to rdb2rdf, hoping to get RDB2RDF
them to meet our needs
Susie: moved to a weekly schedule
to maintain momentum
... michel's tidying the demo
... ensuring that the TMO is cleaned up and posted at
bioportal
... J&J looking at TMO for internal use
... Bosse, chrisD and others working with clinical sources via
"emerge" group
... Bosse looking at physician interface
... michel submitting to ISMB
... ChrisD presenting TMO at drug industry conference (DC,
Oct)
<mscottm> s/SIGONT at ISMB/ISMB/
Susie: still want an ontology for
collaboration with e.g. compounds
... met Eric Bonebieu, who's persuing this
michel: [re demo]
... there were terms in the data that weren't mapped to the
ontology
... the demo queries didn't use the TMO
<michel> http://esw.w3.org/HCLSIG/PharmaOntology/TMKB
mscottm: tx to W3 for migrating to media wiki
mscottm: ericP set up a SPARQL
interface to this DB (using SWObjects)
... relates to semantic annotaiton of images
<mscottm> http://esw.w3.org/topic/HCLS/WWW2010/Workshop
jun: workshop program online,
papers ready
... confirmed keynote. confirming panelists
... it will be an exciting workshop, want to see hcls folks
mscottm: re: f2f issue
mscottm: folks want to go to
BioIT (Boston) and WWW (Raleigh) , but not both
... setting up two dinners, drinks, and discussion
meetings
... susie to set up BOS, Kei to set up Raleigh
ericP will be at both
BOS: ericP Susie mscottm (tentative)
DRU: ericP Susie Jun
EricMiller
... ericP Jun EricMiller
Susie: next W3C TPAC meeting 1-5
Nov Lyon
... last f2f was in CA, US. both gatherings in US.
... + an opportunity for europeans
... - perhaps not many hcls folks will be at TPAC
Lyon: Jun Susie at risk: mscottm Bosse matthias
Susie: looks iffy, maybe should look at SWAT4LS
mscottm: SWAT4LS organizers intrested in such a meeting
mscottm: submitted proposal for
coordinating omics for neurodegenerative diseases
... had michel, christine, kei, ... ellen parkinson (EBI)
... innovative medicine initiative grants in knowledge
management (funding by interested pharmas)
... barend mons/CWA won an IMI as well as a couple teams from
leiden
ericP: this calibrates us re: competitiveness
mscottm: would be a good idea to see how CWA packaged their stuff
<mscottm> Eric (Standards): RIF (Rule Interchange Format) just moved to PR (Proposed Rec)
<mscottm> ..SPARQL: 'minus' and 'not exists' made it into SPARQL
<mscottm> ..EricP submitted a SPARQL Federated Query extensions
<mscottm> ..maybe just in time to make it into the document (yes!)
<mscottm> RDB2RDF: Seems to be dominated by SQL people at the moment, I am interested in grounding things more in use cases.
<mscottm> ..RDB2RDF: Seems to be dominated by SQL people at the moment, I am interested in grounding things more in use cases.
<mscottm> ..<discussion about how to bring the RDF concerns of HCLS to RDB2RDF>
-> http://www.w3.org/2010/01/Turtle/#⋈ Turtle Spec
-> http://www.w3.org/2009/sparql/docs/fed/service SPARQL extensions for federated query
This is scribe.perl Revision: 1.135 of Date: 2009/03/02 03:52:20 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) FAILED: s/folks/stuff/ FAILED: s/SIGONT at ISMB/ISMB/ Found ScribeNick: ericP Inferring Scribes: ericP WARNING: No "Present: ... " found! Possibly Present: AlexPassant BOS DRU EricMiller IPcaller Lyon P11 P13 P8 RDB2RDF Susie aaaa aabb aacc bbalsa bosse emillerpdx ericP jun matthias_samwald michel mscottm scribenick trackbot You can indicate people for the Present list like this: <dbooth> Present: dbooth jonathan mary <dbooth> Present+ amy WARNING: No meeting chair found! You should specify the meeting chair like this: <dbooth> Chair: dbooth Got date from IRC log name: 01 Apr 2010 Guessing minutes URL: http://www.w3.org/2010/04/01-hcls-minutes.html People with action items:[End of scribe.perl diagnostic output]