HCLSIG/LODD/Meetings/2010-01-06 Conference Call

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Conference Details

  • Date of Call: Wednesday January 6, 2010
  • 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 #: + (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


  • Open data follow up - all
  • Data update - Anja, Jun, Matthias, Egon
  • ESWC Paper - Matthias, Jun
  • TCM special issue - Matthias, Jun
  • Bio-Ontologies SIG - Susie
  • AOB


Attendees: Oktie, Richard, Susie, Anja, Bosse, Elgar, Egon

Apologies: Matthias, Kei

<Susie> Open Data

<Susie> Anja: Drugbank is free for non commercial use

<Susie> Anja: Dailymed is free

<Susie> Anja: Diseasome is free

<Susie> Anja: STITCH is cc

<Susie> Anja: SIDER is cc

<Susie> Anja: Should still send mails to content providers

<Susie> Anja: Will draft the email and share

<Susie> Anja: Focus mail on publishing rather than interlinking

<Susie> Anja: Describe some of advantages

<Susie> Anja: Will draft by end of week in GoogleDoc

<Susie> Oktie: ClinicalTrials.gov has some terms and conditions

<Susie> Oktie: For example, keeping data up to date

<Susie> Oktie: Don't think there are any licensing problems

<Susie> Oktie: Should have updated version by the end of the week

<Susie> Oktie: Haven't reached out to LinkedCT, but maybe could do that

<Susie> Oktie: Will look at their t&c again, and may send mail

<Susie> Egon: Reached out to Bio2RDF about licensing

<Susie> Egon: Bio2RDF haven't typically contacted the data providers

<Susie> Egon: Do include licensing conditions

<Susie> Egon: Keep the data sources apart

<Susie> Egon: Which helps mitigate the linking problem

<Susie> Egon: Occassionally they have contact with data providers

<Susie> Egon: Mark Alexander may have more details on some of the data sets

<Susie> Egon: Some are published with cc licenses

<Susie> Egon: People typically want data to be shared

<Susie> Susie: Seems that we are good shape in terms of licensing

<Susie> Egon: In some cases universities are actually considered commercial entities

<Susie> Bosse: In order to persuade our companies to use linked data we need to be sure it's OK

<Susie> Bosse: could impact adoption of the technology

<Susie> Data Update

<Susie> Anja: Talis nodality from Aug/Sep. 2009 has an article on some of the licensing problems, etc.

<Susie> Anja: Matthias has made a new version of STITCH available

<Susie> Anja: Matthias said that the format and schema has changed so may take a week or 2 to look into it

<Susie> Oktie: New version of LinkedCT by the end of the week

<egonw> http://www.ebi.ac.uk/chembldb/index.php

<Susie> Egon: Will work on an RDF version of ChEMBL either this week or next

<Susie> Egon: ChEMBL has cc license

<Susie> Egon: Has chemistry data - from patents - small and large molecules

<Susie> Egon: 500,000 bioactive compounds

<Susie> Egon: Also includes activity data

<Susie> Egon: Suprised it's not already in RDF

<Susie> Oktie: HAven't heard from colleague about FDA related data sety

<Susie> Oktie: Believe data is available, but want to make sure the quality is good enough to make publicly available

<Susie> Susie: Ideas for other data sources

<Susie> Susie: Susie discusses drug ontology interest and possible alignment of ChEMBL

<Susie> Elgar: Definitely interest

<Susie> Susie: Colin Batchelor also interested in a drug ontology

<Susie> Outreach

<Susie> Susie: Matthias said missed deadline for ESWC

<Susie> Susie: But continuing to work on the TCM papwr

<Susie> Susie: Bio-Ontologies SIG has been accepted

<Susie> Susie: Still good opportunity for us

<Susie> Egon: ACS in August

<Susie> Egon: Set up mini conference semantic web in cheminformatics and life sciences

<Susie> Egon: Could be intersting venue for others to submit papers too

<Susie> Egon: It's in Boston in August

<Susie> Egon: Will send more details when available

<Susie> Richard: Should consider the AMIA fall meeting

<Susie> Richard: Submission date in March (ish)

<Susie> Richard: Discussion and interest in drug ontology in AMIA community

<egonw> http://www.myexperiment.org/search?type=workflows&query=kind:SPARQL

<Susie> Egon: Availability of SPARQL queries over linked data

<Susie> Egon: Will have students focusd on queries over ChEMBL and other linked data source

<Susie> Egon: Cheminformatics people don't know about RDF and SPARQL

<Susie> Egon: Need to guide people how to use these technologies

<Susie> Egon: Especially like SPARQL queries

<Susie> Susie: Let's focus on the queries after we've done work on chEMBl and the Drug Ontology