HCLSIG BioRDF Subgroup/Meetings/2006-08-28 Conference Call

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Conference Details

  • Date of Call: Monday August 28, 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, or see Web IRC)
  • Duration: ~1 hour
  • Convener: Susie Stephens
  • Scribe: Davide Zaccagnini



Attendees: Susie Stevens, Satya Sahoo, Olivier Bodenreider, John Barkley, Davide Zaccagnini, ......

Introducing Satya’s work on converting NCBI resources into RDF, experience on Entrez Gene. 

Satya’s presentation is available at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Entrez_Gene_to_RDF


- Q: How did you manage synonyms?
  A: there were no synonyms in the database analyzed 
- Q: how much of Entrez Gene did you convert?
  A: 9000 triplets resulted from the conversion. The original 5 gigas resulted in 35 gigas of RDF data.
- Q: any other database you plan to convert, OMIN for instance?
  A: OMIN has many free text fields, it may be too complicated. We are looking at terminological data bases, such as UMLS. These can support interesting applications for knowledge discovery. 

Mesh might be used as a diseases ontology for translational research. We could convert Mesh into RDF and than integrate it with Enrtez Gene to perform queries on both. There is manual work to be done, but that’s our direction.

- Q: can we have the data?
  A: yes, data are public and will be accessible.  We are going to work on them in the next few months, it may be advisable to wait, but they are also available now.
- Q: how are you going to share the data?
  A: not defined jet, open to suggestions
- Q: we could ask Google to find ways of sharing data
- Q: could we make it available as odbc?
  A: that might raise security issues. The final goal is to share all data publicly, not only Entrez Gene

General discussion

- Q: should we establish weekly calls to finalize the discussion on  URIs y or keep the BIORDF call every two weeks and set a separate call on URIs?
  A: BIORDF biweekly and separate call for URIs