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:

http://localhost:8080/pipes/bio2rdf_subject_object_slicing/namespace=keywords/identifier=11

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.

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.

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 ?

Tabulator and Bio2RDF sparql point a new integrated way to surf genomic knowledge

Try the Tabulator generic data browser to surf the 2 billions triples from Bio2RDF sparql points network. Install the FireFox plugin and strart from here :

http://bio2rdf.org/demo

Semantic Web Challenge 2008 participation

The Bio2RDF team is presenting a demo at the Semantic Web Challenge 2008.

http://challenge.semanticweb.org/

Good luck to Marc-Alexandre, Michel and Peter and all the others team member.

The paper is available here.

Bio2RDF Network Of Linked Data

Bio2RDF OWL ontology finaly available

This is the new OWL ontology file description of Bio2RDF project. It is a rough description of most types and predicates in the new Bio2RDF network of sparql graph.

http://bio2rdf.org/bio2rdf-2008.owl

A nice way to discover it is by using Protege tool and the Ontoviz plugin.

Here is what 2 billions triples from 40 datasources looks like :

2,3 Billions triples made available by Bio2RDF 27 SPARQL endpoints

27 public SPARQL endpoints build with a Virtuoso server are made available to the scientific community. Enjoy.

The list of databases is available here :

http://www.freebase.com/view/user/bio2rdf/public/sparql

For example the followings SPARQL endpoints offer a complete copy of the corresponding databases :

http://biocyc.bio2rdf.org/sparql
http://kegg.bio2rdf.org/sparql
http://geneid.bio2rdf.org/sparql
http://go.bio2rdf.org/sparql
http://iproclass.bio2rdf.org/sparql
http://mesh.bio2rdf.org/sparql
http://obo.bio2rdf.org/sparql
http://reactome.bio2rdf.org/sparql
http://uniprot.bio2rdf.org/sparql