HCLSIG BioRDF Subgroup/Meetings/2006-04-17 Conference Call

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Conference Details

  • Date of Call: Monday April 17, 2006
  • Time of Call: 11:00am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Participant Access Code: 246733 ("BIORDF")
  • IRC Channel: irc.w3.org port 6665 channel #BioRDF (see W3C IRC page for details)
  • Duration: ~1 hour
  • Convener: Susie Stephens
  • Scribe: John Barkley

Draft Agenda

  1. Review progress on task templates and tasks
      Alan Ruttenberg - Update on the reagents task
       http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Reagents/Status_Reports/2006-04-17
      Ora Lassila - Task interests, and overview of work on UniProt with OINK
       http://wiki.nrcc.noklab.com/SwapMe/OINK?action=AttachFile&do=get&target=oink-biordf.pdf
      Davide Zaccagnini - NLP and RDF Task update 
       http://www.landcglobal.com/articles/HCLSIG/free-text-to-RDF.ppt
  1. Next F2F - when and where?
  2. AOB

Meeting Minutes

Attendees: John Barkley, A.J. Chen, Tim Clark, Chiquito Crasto, Roger Cutler, Ora Lassila, Scott Marshall, Daniel Rubin, Alan Ruttenberg, Susie Stephens, Elizabeth Wu, Davide Zaccagnini

Review progress on task templates and tasks

Alan Ruttenberg - Update on the reagents task

Alan presented the information available on the Wiki at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Reagents/Status_Reports/2006-04-17

Questions/discussion included:

  1. It was noted that the knowledge base in antibody1.owl.gz did not load into Protege. Alan said that the knowledge base does load into SWOOP, and that he would look into the problem.
  2. It was pointed out that the information in the files: antibody-db-dump-2006-04-16.txt.gz, antibody1.owl.gz, and parsed-epitopes.txt, should be kept in the group. After some discussion, it was decided to remove the files from the web site until a release is obtained. In the meanwhile, those who want the files should send email to Alan.

Ora Lassila - Task interests, and overview of work on UniProt with OINK

Ora presented the slides available at: http://wiki.nrcc.noklab.com/SwapMe/OINK?action=AttachFile&do=get&target=oink-biordf.pdf

He noted these additional points:

  1. OINK makes heavy use of reasoning.
  2. A user can see the definitions of properties, as well as, their values. The green arrows indicates information in the triple store. The red arrows indicate results from the reasoner.
  3. Reasoning takes place on the fly as things are added.
  4. Ora is investigating how useful OINK will be for large databases like UniProt.
  5. OINK will be included in the Wilbur open source and will be available in a couple of weeks.

Davide Zaccagnini - NLP and RDF Task update

Davide presented the slides available at: http://www.landcglobal.com/articles/HCLSIG/free-text-to-RDF.ppt

As indicated on the slides, he emphasized the differences between natural language processing (NLP) and information extraction (IE).

Susie noted that the hour was past noon. She ask the presenters to update the Wiki for Thursday's HCLS call. She also noted that the plan is for data sources to be identified at the end of 3 months and that these are to be made available at the end of 6 months.

The scheduled part of the call concluded with discussion with the presenters continuing for those who could remain.