Chem2Bio2RDF: a semantic resource for systems chemical biology and drug discovery - Open Source Software in Life Science Research - page 422

Table 18.2

Open source software used in Chem2Bio2RDF

Software Purpose Where to fi nd it

Virtuoso Open
Source Edition

RDF Triple Store http://www.openlinksw.com/wiki/

main/Main

D2R RDF interface to relational

database

http://www4.wiwiss.fu-berlin.de/
bizer/d2r-server/

Chemistry
Development
Kit (CDK)

Cheminformatics
functionality in SPARQL
search

http://sourceforge.net/projects/
cdk/

BioJava Bioinformatics functionality

in SPARQL search

http://biojava.org/wiki/
Main_Page

Jena ARQ Adding functionality to

SPARQL

http://jena.sourceforge.net/
ARQ/

Cytoscape Visualization of query

results

http://www.cytoscape.org/

Protégé Ontology Editing http://protege.stanford.edu/

SIMILE Data visualization in web

pages

http://www.simile-widgets.org/
exhibit/

￿ ￿ ￿ ￿ ￿

Tools and algorithms that employ Chem2Bio2RDF.
More details and access to the tools can be obtained
at http://djwild.info

Figure 18.2