Software
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
-
* Corresponding author: Martijn P van Iersel martijn.vaniersel@bigcat.unimaas.nl
1 Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands
2 Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
3 Department of Computer Science, University of Missouri, Columbia, MO 65201, USA
4 Departments of Medicine and Cellular and Molecular Pharmacology, University of California San Francisco CA 94143, USA
BMC Bioinformatics 2010, 11:5 doi:10.1186/1471-2105-11-5
Published: 4 January 2010Additional files
Additional file 1:
BridgeDb example in Java. This is a simple example script that demonstrates how the BridgeDb library can be used to map an identifier using two different mapping services.
Format: JAVA Size: 2KB Download file
Additional file 2:
Counter-example not using BridgeDb. This is a counter-example that does the same as additional file 1, without using BridgeDb. Because specialized code has to be written for each webservice, this script is more complex and less flexible.
Format: JAVA Size: 3KB Download file
Additional file 3:
Raw results of the comparison of four different webservices. The script used to extract this data is included in additional file 4.
Format: XLS Size: 254KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 4:
Source code of the BridgeDb java library version 0.9. For the latest version we recommend to use our subversion repository at http://svn.bigcat.unimaas.nl/bridgedb webcite.
Format: GZ Size: 13.3MB Download file