HCLSIG/LODD/Meetings/2009-03-04 Conference Call

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Conference Details

  • Date of Call: Wednesday March 4, 2009
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 Greenwich Mean Time (GMT), 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: Susie
  • Scribe:

Agenda

  • News on the paper
  • Cleaning up existing data - Anja
  • Identifier rules - Susie
  • Capturing user input & how applications (e.g. LarKC) can add value - Bosse
  • Physician use case - Don
  • Patient use case - Jun & Kei
  • AOB

Minutes

  • Attendees: Oktie, Bosse, Kei, Anja, Chris, EricP, Egon, Jun, Susie
  • Apologies: Don
  • News on the paper
  • <Susie> Anja: The paper has been accepted!
  • <Susie> Anja: Need to respond to comments by March 9
  • <Susie> Anja: Will compile changes from anyone by March 5
  • <Susie> Susie: Try to include more references, e.g. nictonine paper, more references to LarKC
  • <Susie> Susie: Try to include screen snapshot of other browser
  • Cleaning up existing data - Anja
  • <Susie> Anja: Working to clean up data with Oktie
  • <Susie> Anja: New version of D2R
  • <Susie> Anja: Easier dereferencing of URIs across vocab.
  • <Susie> Anja: Could be interesting feature for this work
  • <Susie> Anja: Released a tool call Silk
  • <AnjaJentzsch> http://www4.wiwiss.fu-berlin.de/bizer/silk/
  • <Susie> Anja: It works against SPARQL endpoints
  • <Susie> Anja: Generates link sets
  • <Susie> Anja: Will be testing the tool
  • <Susie> Anja: If we provide rules, then we could try it out
  • <Susie> Anja: Could link companies from dailymed to dbpedia
  • <Susie> Anja: Could link diseases to dbpedia
  • Identifier rules - Susie
  • <Susie> Susie discussed chemical similarity with cheimists at Lilly
  • <Susie> Susie: Do regular similarity searches between local repository and PubChem
  • <Susie> Susie: Concerned as to how updates would be done
  • <Susie> Chris: Updates is more advanced work, start with rules
  • <Susie> Susie: Saw presentation at CSHALS by Tony Williams on Chemspider
  • <Susie> Susie: Prepared to share his data
  • <Susie> Susie: Might help us to determine chemical rules too
  • <egonw> please let me know how I can help as chemist
  • <egonw> in particular, what the immediate issues are... because I can likely work something out quickly regarding similarity with the CDK, which has means for calculating those...
  • <Susie> We want to create links between data sources that reference chemical structures
  • <Susie> Want to define rules that can help us to determine when different sources are talking about the same structure
  • <Susie> And rules that say when structures are similar
  • <egonw> good, as verification of owl:sameAs rules...
  • <egonw> rules -> links
  • <Susie> Do you know how chemists define similar compounds?
  • <egonw> this sounds more like 'identical' than 'similar'
  • <Susie> yes, rules would help create links with the right relationship
  • <egonw> yes, those are non-identical but which share a large chemical fragment
  • <Susie> we want both identical, and various degrees of similarity
  • <egonw> yes
  • <egonw> I think this nicely links to MarkW's suggestion...
  • <egonw> to have OWL relations be defined by services
  • <egonw> similarity matrices scale badly
  • <egonw> but might work for just the drug space
  • <egonw> there is the additional issue which similarity you actually want to focus on...
  • <egonw> so, there's that dimension too...
  • <egonw> Susie: please email me the context, and I can work out a demo
  • <egonw> (btw, sorry that I could not make the phone call itself)
  • Capturing user input & how applications (e.g. LarKC) can add value - Bosse
  • <SusieS> TimBL has done some work with Tabulator on editing work spaces
  • <SusieS> Can post edits into the data space
  • Patient use case - Jun & Kei
  • <SusieS> Kei: Been busy over the last couple of week's so haven't done so much
  • <SusieS> Kei: Looking at data sets in english that refer to herbs
  • <SusieS> Kei: One extracts data from biomedical literature
  • <SusieS> Kei: Cross reference from herbal db to other db
  • <SusieS> Kei: Good data sets for bridging herbs and drugs
  • <SusieS> Kei: Authors have agreed to let us have the data and convert to RDF
  • <SusieS> Kei: So we've done that and converted the data into RDF
  • <SusieS> Kei: On BioRDF wiki
  • <SusieS> Kei: And in HCLS KB in Berlin
  • <SusieS> Kei: Can now ask extra questions relating to AD
  • <SusieS> Kei: Interested if could link to existing LODD data sets
  • <SusieS> Kei: Still looking at Faviki and how it can be integrated with data sets
  • <egonw> kei: what info do you have on the drugs?
  • <SusieS> Kei: Chemical information on herbs is provided
  • <egonw> or, can I browse the RDF somewhere online?
  • <SusieS> Kei: that could be an interesting linkages points
  • <Jun> http://code.google.com/p/junsbriefcase/wiki/RDFTCMData
  • <SusieS> Kei: have disease gene herb associations
  • <egonw> kei: sounds rather interesting... the metabolomics community has shown a lot of interest in knowing which species a metabolite has been found in
  • <SusieS> Susie: Having more chemical information could result in good linkage points
  • <egonw> I'll explore...
  • <SusieS> Kei: Focus on linkage rather than conversion of more data sources just now
  • <SusieS> Kei: But will explore data sources to prioritise
  • egonw likes to see an overview of what RDF for chemicals is around right now (and link rdf.openmolecules.net to that)
  • <kei> that's great!
  • <egonw> (and see how I can help grow the net)
  • <Jun> I will check with my lab
  • AOB
  • <SusieS> Susie: The HCLS IG has a F2F meeting on April 30/May 1
  • <SusieS> Susie: Backs onto Bio-IT World, workshop on URIs, and Linked BioCommunities meeting
  • <SusieS> Susie: F2F includes 2 invited speakers, potential talk from CDISC, task overviews, task breakouts, discussion of outreach opportunities, and HCLS strategy discussion
  • <SusieS> Susie: Tasks may combine for the F2F
  • <SusieS> Susie: Please let me know if you can make it, as it'll influence which groups combine.
  • <SusieS> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
  • <egonw> sounds interesting, wish I could be there :(