Monday, September 14, 2009

Linking Open Drug Data wins the Triplify challenge

Congratulations to Kei's group and their Linking Open Drug Data (LODD) project for winning the Triplify challenge.

It is a new contribution to the LOD cloud and they have linked those new datasets to Bio2RDF and DBpedia URIs. That is the right way to do it !

Monday, July 20, 2009

The story so far of Linked Data, Bio2RDF is part of it !

In the latest publication of Tim Berner-Lee, he tells the recent story of emerging Linked Data, Bio2RDF is mentioned as an important Biology contributor. This paper is a must for anyone interested in this fantastic new approach.

In this map of Linked Data, Bio2RDF contribution is shown in purple. The corresponding SPARQL endpoints are available here :

Wednesday, July 01, 2009

Bio2RDF is now using Virtuoso 6 and its new facet browser

Bio2RDF is moving from Virtuoso 5 to Virtuoso 6 server. The new software support facet browsing in real time.

We invite you to explore our graph with a full text search query for hexokinase. Once the results list is shown try the options in the right menu. Enjoy the discovery experience.

Try the 2009 version of "Atlas about Human and Mouse" :

the graph can also be queried in sparql :

The list of the Bio2RDF converted graph will be published and updated here :

The facet browsers list :
The sparql endpoints list :

Bio2RDF visit at HCLS annual meeting

Bio2RDF team members Marc-Alexande Nolin, Michel Dumontier and Francois Belleau, have been invited to present actual state of the Bio2RDF project at the annual face to face meeting of the HCLS community. Here is a link to the presentation :

Thanks to the organizers of the event.

Tuesday, April 21, 2009

2,4 billions triples of Bioinformatics RAW DATA NOW

In his recent talk at TED, Tim Berner Lee invited the data provider to make available data in RDF format to help the building process of linked data web. He asked them to offer RAW DATA NOW.

We totally share this approach in the Bio2RDF community, our goal is to make public datasets from the bioinformatics community available in RDF format via standard SPARQL endpoints (Virtuoso server is used for that). We strongly believe in the semantic web approach to solve science problem but we do not want to wait for data provider to do the RAW DATA conversion job. Converting data to RDF is not fun, we did a lot of this dirty job, and here are the results for actual Bio2RDF release of 34 data sources.

Our current datasets in N3 format are available here :

We invite semantic search engine provider to index these files.

The way we produce them is documented in our Wiki at SourceForge in the Cookbook section :

The actual list of SPARQL endpoints in the linked data cloud is hosted here :

Bio2RDF 2,4 billions triples graph of linked data represents 51 % of the actual global linked data graph size.

Finally, this is what this highly connected knowledge world look like.

I would take this occasion to thanks all the enthusiast biologist and researcher who invest themselves by annotating article, protein and gene product. Without this essential work of connecting documents and concepts together, this project would not have been possible.

For the 20th anniversary of the web, I would also want to thanks Tim Berner Lee for his inspiring vision. Bio2RDF may not be the awaited killer app of the life science to demonstrate the semantic web potential, but let's say that it is only the beginning of the linked data cloud build by and for scientists.

The WWW2009 workshop Linked Data on the Web (LDOW2009) was held today, I would like to say how important the work of this community is. Finally a last word to congratulate Virtuoso team and especially Orri Erling for his fantastic work with the new Virtuoso 6.0 server soon to be released. I cannot wait to see Bio2RDF data into this amazing engine.

Bio2RDF's map new graphic representation

This word net represents the actual namespace connection between Bio2RDF SPARQL endpoints. RDF datasets which were analyzed comes from Bio2RDF's download page. These representations are generated with Many Eyes visualization tools.

Static version.

This graph represent connections between namespaces of Bio2RDF's network graph of SPARQL endpoints, highlighted orange dots corresponds to Bio2RDF rdfised database.

Static version.

Monday, March 30, 2009

Bio2RDF and Semantic Web Pipes

The Bio2RDF Servlet has been packaged with Semantic Web Pipes. It provides runtime support for pipes, without the designer. Pipes you design at either the public pipes website, or your own pipes webapp, will run inside your Bio2RDF server, providing another method for scripting your queries.

Once you download and install the Servlet you will be able to access the pipes functionality using URL's which look like the following:


Each of the Parameter's in the pipe are entered using "name=value" combinations and put together using "/".

Download the latest Bio2RDF Servlet to experiment.

Saturday, March 21, 2009

Bio2RDF's contribution to the GGG is on the map

I am very pleased to see that Bio2RDF contribution is now on the GGG map of linked data. A big thanks to all the data provider and the active members of the Bio2RDF group. All the SPARQL endpoints we provides are not there yet but it is a great beginning.

Thursday, February 05, 2009

When Bio2RDF meets Taverna

Try this Taverna workflow to explore the possibilities of building a mashup on the fly from Bio2RDF's sparql endpoints.

What is known about HIV using Bio2RDF's SPARQL endpoints ?