HCLSIG/LODD/Meetings/2009-02-18 Conference Call

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Conference Details

  • Date of Call: Wednesday February 18, 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 #: + (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: Anja


  • Update on the paper
  • Triplification challenge
  • What's next?
    • Follow up on the issues identified in the outlook section (browser performance and functionality, identifier ambiguity, platform for reasoning).
    • Adding new data sources as proposed (SWAN hypothesis, epidemiology, companies, Medpedia).
    • Address the need to capture user input
    • Explore how applications like LLD (LarKC) can add value into the Linked Data cloud.
    • Links to similar compounds
  • Improve quality of the data sets
  • AOB


Attendees: Oktie, Jun, Chris, Don, Kei, Anja, Susie

Apologies: Matthias, Bosse

<kei> Agenda

<kei> susie: 1. update on paper

<kei> susie 2. what's next

<kei> susie: paper was submitted

<kei> susie: thank to everyone's hard work

<kei> susie: when will we hear

<kei> chris: 30+ submissions

<kei> chris: notification date -- March 1st

<kei> susie: need to get permission to be a co-author on the paper -- it was approved

<kei> chris: matthias sent email about an interface to the lodd datasets?

<kei> chris: crawl the datasets and put them in triplestore

<kei> chris: marble too slow

<AnjaJentzsch> Matthias Mail: "... The linked data generated by the LODD task has been crawled and is now available for faceted browsing at http://visinav.deri.org/hcls/

<AnjaJentzsch> Example query: http://visinav.deri.org/hcls/list?keyword=varenicline "

<kei> susie: share with scientists -- asking them to test and validate and for feedback

<kei> chris: a lot of info displayed for drugs

<kei> chris: need more provenance info. but a nice interface

<kei> susie: people should play with the interface and give feedback ...

<kei> don: where is the data from?

<kei> Anja: sparql endpoints

<kei> susie: main home for the data sources should be accessed more obviously

<kei> Susie: can Anja take care of this?

<kei> Anja: Andreas became aware of LODD data sets through Richard.

<kei> susie: next step

<kei> susie: one next step is to make sure data connections are good

<kei> susie: google doc was written about this

<kei> susie: ask people in Lilly to address the data connection issue

<kei> susie: Don knows anything about how to connect generic drugs vs. specific drugs

<kei> Don: can look into it (e.g., pdb contains information about binding sites)

<kei> susie: give Don access to google doc

<Donald_Doherty> donald.doherty@brainstage.com

<kei> chris: need someone who knows more about the data and how to use the data to guide us

<kei> chris: devise rules for linking data sets

<kei> chris: some example rules based on similar names, similar properties, etc

<kei> susie: Lilly people are excited about using this approach to find out more about compounds (developed internally and externally)

<kei> susie: how rules help to identify similarity/difference between internally developed compounds and externally developed ones?

<kei> susie: need to work with domain experts in developing the appropriate rules ...

<kei> anja: bio2rdf focuses on chemical compound related data -- could be a good resource

<kei> chris: link to bio2rdf instances -- so no need to store such instances locally

<kei> susie: chemical compounds exist in public repositories or lab-specific databases

<kei> susie: tighten up the links ...

<kei> susie: better develop the rules ...

<Susie> Triplify challenge: http://www.i-semantics.tugraz.at/triplification_challenge

<kei> oktie: semantic conference in austria -- submissions about using linked data

<kei> oktie: our application is a nice demonstration of this challenge

<kei> oktie: deadline for submission to the conference is May 30

<kei> susie: is this a conference paper?

<kei> oktie: it's only a 2-page report on challenge.

<kei> chris: it's appropriate

<kei> susie: also think it's appropriate

<kei> oktie: we may need to think more about ontologies

<kei> oktie: coming from data management background, would be nice if someone with strong ontology background can participate ...

<kei> susie: how ontology helps in aggregation of linked data?

<kei> chris: put all data out as first step, next step people starts exploring data, ontology mapping and the like ...

<kei> chris: we are near the end of the 1st phase

<kei> chris: might use ontology to help browsing/mapping

<kei> oktie: two clouds: data cloud and class-level interlinking cloud

<OktieH> http://umbel.org/images/lod_constellation.html

<kei> susie: can more information about this new cloud be available?

<kei> oktie: schema of data

<kei> chris: can find high level information but not more detailed info...

<kei> susie: may make sense to take advantage of ontologies ...

<kei> chris: don't need to agree on global ontology

<kei> chris: simple/light-weight one may make more sense ...

<kei> susie: pharma-ontology work may help ..

<kei> susie: disease and patient centric not drug related in this case ...

<kei> susie: lodd might be a potential use case for pharma ontology

<kei> susie: good to see deliverables in the pharm ontology group

<kei> susie: update the web site to mention the challenge for the conference

<kei> susie: other things to discuss

<kei> susie: outlook section -- identify ambuguities, etc ...

<kei> susie: build up a robust platform for reasoning

<kei> susie: capture user input -- adding more content to the cloud.

<kei> susie: exploring datasets to add to the cloud ...

<kei> susie: hypothesis data

<kei> susie: ask elizabeth wu and tim clark

<kei> susie: adding more data regarding epidemiology ...

<kei> susie: more wiki related resource just started ...

<Susie> http://wiki.medpedia.com/Special:ListAllArticles

<kei> susie: data source contributed by experts ...

<kei> Susie: ask Don to present in 2 weeks

<kei> Susie: ask Jun and Kei to present in 2 weeks

<Susie> Jun: presented on void during BioRDF call

<Susie> Jun: Looking for community feedback

<Susie> Jun: Not many tools yet

<Susie> Jun: Very early to be using void

<Jun> http://rdfs.org/ns/void-guide

<Susie> Susie: I'll be giving a brief presentation on LODD to CSHALS next week