HCLSIG/Meetings/2009-04-02 Conference Call

Conference Details

Date of Call: Thursday April 2, 2009
Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
Dial-In #: +1.617.761.6200 (Cambridge, MA)
Dial-In #: +33.4.89.06.34.99 (Nice, France)
Dial-In #: +44.117.370.6152 (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)
Duration: ~1h
Convener: Scott, Susie

Agenda

News Updates by BioRDF, COI, LODD, Pharma Ontology, Scientific Discourse, Terminology - All
F2F Planning - Scott
AOB

Minutes

Attendees: John, Jamie, Scott, Bosse, Kevin, Michel, EricP, Stefan, Jun, Egon, Oliver, Marco, Matthias, Susie
Apologies: Kei
<ericP> topic: task force updates
<ericP> topic: BioRDF [ScottM]
<ericP> mscottm: working on a BMC Bioinformatics paper (due monday)
<ericP> ... topics included ATAGS, Aida use of HCLS DERI KB
<ericP> ... (same interface used to browse JohnM's SKOS)
<ericP> ... discussion of merging jun's herbal DB with LODD datasets
<ericP> ... will load those into the KB
<ericP> jun: discussed traditional chinese datasets with Anja
<ericP> ... dataset comes from text mining, so proceeding cautiously
<ericP> ... re f2f: confirmations from John Breslin, Michel Dumontier
<ericP> jun: talked about demo of AIDA access to deri hcls kb
<mscottm> http://ws.adaptivedisclosure.org/search/
<mscottm> http://tarski.duhs.org:8080/openrdf-sesame
<mscottm> In Server Details: enter tarski link
<mscottm> click on Repositories
<mscottm> http://adaptivedisclosure.org
<ericP> michel: am working with Bio2RDF group to expand the dataset and make the data more meaningful
<ericP> ... tying to ontologies and unifying terms
<ericP> johnM: is @@1 using quads?
<ericP> mscottm: when you click on instances, you see the named graphs
<ericP> ... many named graphs, and you can't guess what's in them
<ericP> ... in general, federation requires named descriptions of repositories *and* named graphs
<ericP> topic: LODD
<ericP> Susie: working on LODD paper for WWW
<ericP> ... thinking about what we not to do next
<ericP> ... goal: submit a paper to the iTriplification challenge (due May 30)
<ericP> ... working on connecting to other datasets, e.g. dbpedia's large corpus of company data
<ericP> ... looking at traditional chinese datasets
<ericP> ... looing at pharma ontologies role questions to pick the 3 most interesting
<ericP> ... will help us choose a couple more datasets to add to the cloud
<ericP> ... (at a lower priorty) looking for more consistancy in mappings so using pharma onts
<ericP> ... want a hybrid interface for not only browsing, but querying
mscottm provides details that didn't flow during the task force update: The resources that we are querying in BioRDF paper are: the KBs, SenseLab, aTags, Faviki, IUPHAR
<ericP> ... .. adding template queries e.g. what do you know about this gene?
<ericP> ... LODD will not meet at f2f as many europeans won't make it
<ericP> ... pharma ont will meet and will be working on onts useful to LODD
<ericP> topic: pharma ont
<ericP> Susie: goal: create a template ontology for plugging in existing/upcoming onts
<ericP> ... so we can generate queries which span covered areas
<ericP> ... working on what questions folks need to ask and what roles they imply
<ericP> ... expect to finalize the roles and their questions in the next call (35 mins)
<ericP> ... expect ~ 40 entities in ontology
<ericP> ... given entities and use cases, we'll build out the ontology in that area and build a tool to use it
<ericP> ... submitting abstact biomedical ontologies and @@2 at ISMB
<ericP> ... encouraing companies to share their internal ontologies
<ericP> ... these (e.g. lilly's) are developed in isolation so looking at adopting e.g. BFO practices
<ericP> topic: COI
<ericP> HelenC: ericP produced SWtransformer and Holger and I worked on an interface
<ericP> ... we submitted to AMIA conference
<ericP> ... will look at a more tech opportunity e.g. WWW or ISWC
<ericP> ... will be at the f2f to examine query federation
<ericP> ... canadian research consulate (member of W3C?) has a large group working in semweb
<ericP> ... talking with them

<ericP> ... next week will discuss ops for new collaboration <ericP> ... looking for use cases and data of clinical relevence

ericP tx HelenC!
<ericP> topic: Terminology
<ericP> johnM: we have a couple repos on the server working with AIDA
<ericP> ... want a 2nd ont with RDFS turned on so we can do on-the-fly terminologies
<ericP> ... last time we had the repo up, but AIDA was having probs accessing repo. will have a webcon to debug
<ericP> ... we're using the native sesame RDFS inferencer
<ericP> ... trying to use OWLIM, but it's difficult to get it to talk to sesame
<ericP> ... federation is still on my plate
<ericP> ... we got Simon Schenk and his lightweight federation gear
<ericP> ... we have all these terminologies, but we need data
<ericP> ... have been using scott's text data
<ericP> ... but want SNOMED-encoded data
<ericP> ... just spoke to a collegue at Duke who has to large repos set of RDBs
<ericP> ... 1: Duke tissue bank
<ericP> ... 2: anotomoical? DB
<ericP> ... both are up on web-accessible RDBs
<ericP> ... will ask him to install d2r server
<ericP> ... style of annotating medical records is flat (no S P O triples)
<ericP> ... basically same as the needs driving the pharma ont
<ericP> ... haven't worked with Chime's [CPR] patient ontology yet. will look at it and associated use cases
<ericP> ... two deadlines ~ Sept:
<ericP> ... .. 1 will be platform speakers at AMIA/APIII
<ericP> ... .. .. will talk about semantic extraction (using GRDDL)
<ericP> ... .. .. can use a the patient ontology
<ericP> ... hope to wow audience with a soup-to-nuts semweb application
<ericP> topic: f2f
<ericP> mscottm: anybody here who isn't going to f2f?
<ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F HCLS F2F
<ericP> Susie: a bunch of folks at onto tf: Elgar Pichler, Bosse, and christi dialing in
<ericP> mscottm: BioRDF plans to spend a couple hours to geek with johnM about HC terminolgies
<ericP> [Susie reviews agenda]
<ericP> R&D open 'till 10pm
<ericP> Susie: please add your names to the attendance list, and inidicate if you will be calling in
<mscottm> http://www.slideshare.net/micheldumontier/accurate-biochemical-knowledge-starting-with-precise-structurebased-criteria-f...
<ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F#attend attendance list
<ericP> topic: michel's preso to NCBO
<ericP> mscottm: this is a structure-based approach to chemical identificationh
<jun> i was there. it was a really good talk:)
<ericP> topic: misc
<ericP> Susie: sometimes we drill into a particular task during the general HCLS calls (thursdays) or invite presenters
<ericP> ... if you have suggestions or requests, please mail the chairs list team-hcls-chairs so we can try to please everyone
<ericP> marco: Concept Web Alliance is working on a large hcls use case
<ericP> mscottm: a bit in parallel with hcls
<ericP> [susie and marco will represent hcls use cases]
<ericP> mscottm: is similar in goals to this group
<mscottm> CWA = Concept Web Alliance = HCLS IG in another flavor
<ericP> Susie: could be synergistic with hcls
<ericP> ... if they get a wide group thinking about what they want from an eScience environment, hcls can help fill in missing pieces