See also: IRC log
<mscottm> hi oliver
<curoli> hi scott
timClark: Scientific Discourse:
doing 3 IG notes
... Paolo and Alex working on them
... on schedule for having something in early may
timClark: looking at swan, sioc,
myExperiment, we are missing the ontology piece
... is a big piece to attack, so starting with the
provenance
... starting with Sudeshna's microarray and lilly's @@1
ontology
... awaiting approval from lilly
carl: what's the scope of scientific discourse
timClark: google "swan
sioc"
... not a general view
... using pre-existing ontologies in the area
... integrating them - bottom-up approach
... working with specific goals in use cases
... you (carl) have a scientific discourse portal. we'd like to
integrate your ontology
carl: goes back to toni kasik's
appeal for scholarly discourse networks
... i guess your's is geared to concrete apps
... toki's use case was connecting researchers with
publishers
timClark: sioc relates statements
to inviduals
... in swan, there is a citation ontology
... many folks interested in e.g. disambiguating authors
carl: will read up and contribute
timClark: we'll read your [carl's] paper
susie: will scientific discourse have a break-out at the f2f?
timClark: there's a meeting on
linked biomedical web ontologies the day before
... can't do too much prep
<Susie> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
timClark: with dave derue, karen skinner, marian, i can come up with work material
<mscottm> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
<matthias_samwald> sorry for being late.
<scribe> ACTION: timClark to write break-out plans on http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F [recorded in http://www.w3.org/2009/03/19-hcls-minutes.html#action01]
susie: f2f is backed on to
timClark's meeting, a URI workshop, and BIO-IT
... feel free to drag along other folks who might be
interested/interesting
<mscottm> yes.
UNKNOWN_SPEAKER: focusing on BMC
informatics paper
... is basically an update from the C-SHALS meeting
... adrian paske is a co-organizer of this issue, they've
extended the deadline to 3 weeks from now
... need to move on this
... will discuss break-out goals with the task force
... working on Query Federation and ATAG
... will look at aida toolkit ( mscottm )
... interface is one of the goals of biordfd
<scribe> ACTION: kei to sketch break-out ideas in http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F [recorded in http://www.w3.org/2009/03/19-hcls-minutes.html#action02]
timClark: JohM will be at f2f.
wants to do a co-break-out
... if everyone meets with everyone, it's not a break-out
ericP: focused up AMIA submisison and finishing demo
<scribe> ACTION: ericP to talk to coi about break-outs at COI [recorded in http://www.w3.org/2009/03/19-hcls-minutes.html#action03]
Susie: we got a paper
accepted
... (at WWW)
... looks like either william sanchez or oktai will present at
WWW
... just met one accomplished. tidying up
mscottm: does that include managing URI synonyms?
Susie: yes (for identifiers).
field names as well
... fields sometimes at different or inconsistent levels of
aggregation
... adding links which we were tentative about
... working on rules to automate adding linkages in the
future
... so:
... .. cleaning up existing data
... .. considering new data sets (e.g. chemical structure --
concensus around gross structure)
<egonw> gross structure?
Susie: .. been using naive
@@2s
... many of the LOD folks are interested in pharma ontology
<johnM> Yes sorry, mute me if necessary. I can actually talk from here if called on.
Susie: see connections to scientific discourse as we
carl: is the prob with synonyms for chemical entity better in the non-healthcare chem industry?
<mscottm> johnM - can you give a Terminology update? If not, I can.
carl: or is chem industry better able to standardize?
susie: different strings used for the same chemical
<egonw> carl: no, unless you use something like InChI
susie: many names, but not exactly the same thing
<johnM> Scott could you do it? I can chime in briefly about OWLIM.
susie: e.g. active ingredients
vs. buffers vs...
... for chem structure, IInCHIs work
<egonw> for organic structures, yes
<egonw> like most drugs
mscottm: InCHIs can produce mutilple names for the same structure, depending on traversal
Susie: yes, and can be very long, but still fairly effective
<mscottm> johnM - sure, I'll do it.
Susie: id'd steps, dates and
actors
... want to work out ontology for translational medicine
... covering drugs to patients, genomics to medicine
... started by defining questions which players (pharmas,
payers, medical orgs) want to ask
... will then pick 2-3 translational medicine use cases
... then build an ontology for one use case, then an app tests
it
... expecting to drive better ontology development
<scribe> ACTION: Susie to check f2f logisitcs for Pharma Onotology Task Force [recorded in http://www.w3.org/2009/03/19-hcls-minutes.html#action04]
Carl: can contribute a radio@@3 ontology
mscottm: looking at side-effect similarity?
Susie: not yet. but side-effects are likely to be captured in the high-level template
<johnM> can you unumute me?
johnM: haven't done much on the
sesame server this week
... our main produce is a server which serves skos versions of
SNOMED, LOINC, and @@@4
... current snomed representation has no inferencing
... trying to do another interface with rdfs closures
... working out tech details with aida
... means that mappings to other ontologies can be done with a
few additional triples
... strugging with owlim to work with sesame2
... next goal is to federate with the repositories in berlin
and vienna
... expect that we have triples that other groups want to share
and expect others have triples that we want
... Simon Schenk has a federation add-in for sesame
... can be used across any sparql endpoint
mscottm: kolstas and
matthias_samwald got aida to talk to the galway deri
database
... re-coded some to talk to virtuoso
... allows you to take a term from a terminology and look for a
similar name in the deri installation
... to find e.g. GO term for dendrites
<matthias_samwald> it is located in ireland.
ACTIONL: johnM to update http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F with break-out ideas/goals
susie: folks from text mining,
ontology, NCI
... tim clark did an update on scidis
... nigam shah did an update on bio ontologies
... did a talk on pharma ont
... room was fool -- maybe 100 folkks