D506 Nucleic Acids Research, 2006, Vol. 34, Database issue as many high-quality links as possible for network analysis requires well organized and convenient pathway database access. Databases that are freely accessible (open-access) and support standard languages facilitate their distribution and use. To encourage this, databases are highlighted if they are ‘Free to all users’ and can be downloaded in a standard format, such as the Proteomics Standards Initiative Molecular Interaction (2) and BioPAX (www.biopax.org) pathway data exchange standards and the Systems Biology Markup Language (SBML) (3) and CellML (4) pathway simulation model exchange standards. Biologists looking for data that can be analyzed in tools supporting these standards and compu- tational biologists wishing to integrate available pathway data for global analyses may ﬁnd this helpful. IMPLEMENTATION Pathguide is curated by the authors and regularly updated. Generation of web pages (HTML) is implemented using the scripting language PHP with a relational database (MySQL) backend, which stores all information in a structured manner. The Google ranking for a particular database is updated using a Perl script to query the Google SOAP Application Program- ming Interface for pages anywhere on the Internet that link to the database homepage address (URL), not counting links from the database site itself. We have designed Pathguide to facilitate research on biological pathways and to be com- plementary to existing database link resources, such as Michael Galperin’s Molecular Biology Database Collection (5) and the UBiC Bioinformatics Links Directory (http:// bioinformatics.ubc.ca/ resources/links_directory). FUTURE DEVELOPMENT Future plans include adding search features (e.g. show me all databases with human protein–protein interaction information), automatically updated database content statistics (where available), graphical Pathguide content summaries, improved links to PubMed, differentiating primary (original content) and secondary (derived or predicted content) data- bases, automatic URL validation, homepage uptime statistics, an RSS feed to track updates and to include a section on pathway tools, a commonly requested feature. Comments, questions and information about missing pathway resources are most welcome. ACKNOWLEDGEMENTS Thanks to Robert Hoffmann for input on the Google ranking, Emek Demir for manuscript comments, users who have sub- mitted new pathway resources and the editors of Nucleic Acids Research for supporting open-access publications. Funding to pay the Open Access publication charges for this article was provided by Memorial Sloan-Kettering Cancer Center. Conflict of interest statement. None declared. REFERENCES 1. Cary,M.P., Bader,G.D. and Sander,C. (2005) Pathway information for systems biology. FEBS Lett., 579, 1815–1820. 2. Hermjakob,H., Montecchi-Palazzi,L., Bader,G., Wojcik,J., Salwinski,L., Ceol,A., Moore,S., Orchard,S., Sarkans,U., von Mering,C. et al. (2004) The HUPO PSI’s molecular interaction format—a community standard for the representation of protein interaction data. Nat. Biotechnol., 22, 177–183. 3. Hucka,M., Finney,A., Sauro,H.M., Bolouri,H., Doyle,J.C., Kitano,H., Arkin,A.P., Bornstein,B.J., Bray,D., Cornish-Bowden,A. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524–531. 4. Lloyd,C.M., Halstead,M.D. and Nielsen,P.F. (2004) CellML: its future, present and past. Prog. Biophys. Mol. Biol., 85, 433–450. 5. Galperin,M.Y. (2005) The Molecular Biology Database Collection: 2005 update. Nucleic Acids Res., 33, D5–D24.