HCLSIG BioRDF Subgroup/Meetings/2006-05-01 Conference Call

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Conference Details

  • Date of Call: Monday May 1, 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:


Attendees: Davide Davide Zaccagnini, Olivier Bodenreider, Joanne Lucianno, Ora Lassila, Kei Cheung, John Barkley, Scott Marshall, Susie Stephens, Alan Ruttenberg, Brian Gilman, Karen Skinner, Eric Prud’hommeaux

1. Scott Marshall – Progress in hosting an instance of the Oracle RDF Data Model

An instance of Oracle RDF Data Model is now available at the SARA supercomputing centre. People can access the instance by tunnelling with ssh.

If people are interested in using it, then Scott can share security information.

To date, has just been reading the Oracle documentation, and researching how to convert data from RDF/XML to NTRIPLE, so that the Oracle batch loader can be used.

Kei is interested in using the hosted instance. Would be interested in using the Sesame Web interface with the RDF Data Model. Susie to research whether this is possible.

Should be possible to also use Java Server Pages for loading data.

Ora plans to integrate OINK with the Oracle RDF Data Model, and OINK has a Web based method for loading data. You just need to provide the URL of the RDF document that you want to load. There isn’t a date yet for the completion of the integration work.

Kei wanted to know if the Oracle RDF Data Model is integrated with Protégé or Razer. Susie said that there is already an RDF Data Model plugin for Protégé. Oracle is also considering supporting a DIG interface to allow reasoners to be plugged in. Alan, John, and Joanne all thought that a DIG interface would be useful.

Joanne would be interested in loaded BioPAX into the RDF Data Model instance at SARA.

Susie would be interested in loading the RDF data that was generated with Joanne and Siderean. It consists of subsets of a dozen different bioinformatics data sets.

2. Kei Cheung - Human Brain Project Meeting Update

Kei attended the Human Brain Project meeting, and was successful in getting to meet Bill Bug. Bill is passionate about the use of RDF for neuroscience.

Kei has posted slides that outline the meeting at: (http://twiki.med.yale.edu/kei_web/sw_group/hbp2006_meeting_uupdate_hclsig.ppt )

The 3 themes of the meeting were collaborate, integration and communities.

Kei attended the Ontology Working Group session which was hosted by Perry Miller (Yale). Issues, needs, and problems were identified during the meeting. For example, it was established that there is a need for ontologies to work together, and also a need for education. There is also a need for the relevance of exisiting ontology to be reviewed in the context of neuroscience.

Many people gave presentations. Bill Bug presented on the differences between XML and RDF, and how the Semantic Web can be applied to neuroscience. Many people hadn’t even heard of RDF, so more education is needed. Kei presented on OWL-based integration of 2 different neuroscience databases (neurodb and cocodata).

Kei made the attendees aware of BioRDF and BIONT, and W3C’s willingness to educate people.

There was a mix of people at the meeting. Many people are pure researchers, and therefore don’t have a focus on any particular disease. Not aware of many clinical people attending. There were also neuroinformatics people in attendance, rather than data gatherers. Don Doherty was at the meeting, as was Karen Skinner.

There is going to be a pilot exploration of Semantic Web technology. HBP and BioRDF form a strong bridge across communities. Kei would like to form the link between the two groups.

More information on the Human Brain Project can be seen at: http://ycmi-hbp.med.yale.edu/hbpdb/ http://ycmi-hbp.med.yale.edu/hbpdb/eavObList.asp?c=65

3. Brian Gilman - Overview of experiences with Ruby on Rails

There has been lots of hype around Ruby on Rails. He decided to buy a book to learn more, so that he could build an application. It turns out that it’s not just hype, and that it really works, and that it works well. It integrates with Oracle and MySQL, and other databases. You can put a few lines of code into a template file, integrate with a Web Server, and then start to browse the schema. You can run scripts that generate code to navigate the database. You can automatically connect a database to a framework, and you get all CRUD operations for free. You can then start to hack all of the operations that they’ve generated for you.

It’s an object-oriented language, like Python and Smalltalk, so it makes a lot of sense for people with that background.

Connecting using a frame and then connecting to RDF would be a good idea, and is what has happened with ActiveRDF. It would effectively be like putting the Semantic Web on Rails.

In Brian’s proteomics application it took him 50% less lines of code to develop. You can abstract away from the details of RDF. The examples on the Web page work well, but it is lacking in some features. For example, connecting with the RDF store and browsing the store – so there are no Rails available. You also can’t do the CRUD operations (e.g. add, delete, search) over N-triple as nicely as you can with Rails. It’s actively being developed at the moment.

Brian hasn’t posted any code yet, as he’s still actively working on it. He’d be happy to share the alpha code with anyone who’s interested.

Brian provided a series of useful URLs: ROR main link: www.rubyonrails.com ActiveRDF link: http://activerdf.org/ eyaloren.org/pubs/sfsw2006.pdf http://morenews.blogspot.com/ W3C Links: http://www.w3.org/TR/2006/NOTE-sw-oosd-primer-20060309/ BioRuby: http://bioruby.org/

The W3C site contains a lot of information on scripting. It helped Brian to get up to speed on layering and utilizing OWL. Sections 3.2 and 4 were especially useful.

Jena documentation is also very good for people who want to program.

Dieter Fensel is using RDF and ROR, but he’s lacking a use case, so there’s a possible opportunity for a collaboration. Steffen Decker is also another candidate for collaboration. Ted Slater is also a big Ruby guy. The BioRuby package is very good, and supports genomic stuff.

Eric Prud’hommeaux has been hacking a SPARQL parser into MySQL, and will be presenting this at XTECH. He’s currently using GO.

Possibly connect ActiveRDF to the Oracle RDF Data Model using ODBC.