HCLSIG BioRDF Subgroup/Meetings/2007-09-17 Conference Call

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Conference Details

  • Date of Call: Monday September 17, 2007
  • Time of Call: 11:00am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • 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: Elizabeth Wu


  • HCLS F2F (Agenda, Location, Registration, etc.) - EricP
  • SfN Poster Update - Don
  • URI note - Jonathan - see /UriNoteStatus
  • Demo extensions - Alan
  • Documentation of SenseLab conversion - Kei
  • AOB


EricP: F2F meeting associated with the tech plenary. [talk about details / schedule F2F not included in this log]

Alan: We could do an overview of the ontology/schema information in the demo – if participants are interested.

Alan: We should ask people via the mailing list if they plan on coming, so we can adapt the schedule of the F2F

Susie: We can offer a form where people can informally register themselves. There are people on the CLS mailing list that are not W3C members or invited experts. Can they attend (besides Vipul's open session)?

EricP: We can extend the open session to all of Tuesday. It is also possible to run the whole meeting as an open meeting.

Susie: I will send a mail to the HCLS mailing list.

  • ** SFN poster ***

Don: Virtuoso is now running, everything is installed. Thanks to Alan. The main problem with loading the data were directories with spaces – this took a long time to figure out.

Don: About the poster: I am now focusing on the content. Thinking about queries that neuroscientists are interested in. Not so much detail about technical background, the audience will be primarily interested in results. I will send something out within the next week. If you have suggestions, please contact me. I will get something of the poster out before the next BioRDF teleconference.

Matthias: How are queries represented? Maybe we should represent them as natural language.

Don agrees.

Alan: If you look at the Banff demo page, you can find some slides from John Wilbanks, containing comparisons of our Sparql-based demo with other, non-Semantic Web approaches. Something like that might be useful.

  • ** URI Note ***

Jonathan: I wrote a little bit about our use cases. This needs to be addressed in any demo we write. The messages Eric Neumann and Science Commons are different, and that is because they are talking to different audiences: Are you talking about navigation or a precise query? Is it consume immediately or should it be archived and used for a long time? Are we talking about 'quick and dirty' RDF that is easy to access for new comers, or are we talking about something more complicated? The taxonomic data working group wrote their own document. They chose to use LSIDs, but they do not have a detailed documentation, but at least it is something to start. You can have a look at that. About the 'The Meaning of a term' document: I only got feedback from David Booth.

Eric P: I want to see some candidate 'final text' where we can make some more detailed comments about.

Jonathan: I can work on something.

Susie: once we begin working on the final document, feedback will increase.

Jonathan: I will have something by October 1.

Jonathan: I will not use the word 'recommendations', because it has a special meaning in the W3C context.

  • ** HCLS 'demo' / knowledge base ***

Alan: Matthias Samwald and Holger Stenzhorn will be at DERI.

Matthias: I will work on getting the demo running at DERI during the first week of October.

Alan: Hal Abelson had to give a talk about science on the Semantic Web. He was looking through the HCLS KB and could not find some things.

Jonathan: I was looking for a triple that was a statement of scientific interest. I scanned over the data sources and most in there is descriptive. I wanted something that was not created by a 'curation factory' but by a scientific lab, the only thing I could find was SenseLab. Statements describe contents of articles, for example, but does not make real assertions.

Alan: I think you are misinterpreting something.

Matthias silently agrees with Alan while typing this log.

Jonathan: Falsifiability (and philosophy of science in general) in important.

Alan: 'If you cannot falsify it, why are you talking about it?'

Jonathan: I was trying to make an example with Brainpharm, but links to databases were missing. I added a link to Pubchem myself.

Kei: Brainpharm is still a prototype.

Kei: The wiki page about the conversion of SenseLab has been updated. The database dump will also be made available, but we still need to make sure that no 'private' data gets published. It will be made available through our new SVN repository.

  • ** HCLS questionnaire ***

EricP: 41 people filled out the form.

Susie will be sending out a mail to a list of people that might also be interested.

  • ** Other topics ***

Alan: I sent a list of SQL queries against GO that were sent to the HCLS mailing list by Chris Mungall. I want people to do SPARQL queries and compare.