Making Sense of Biological Pathways

Over the last several years, the amount of information regarding protein–protein interactions has grown exponentially. In order to accommodate all of that information, hundreds of databases have been created which reside in numerous places throughout the internet. While the existence of disparate databases has been helpful in memorializing the hard work of protein scientists, finding and subsequently mining those databases has become akin to navigating a complicated maze of information.

Thanks to the hard work of Thomas Klingström and Dariusz Plewczynski a valuable tool has been created to help reduce the time necessary to gain a broad overview of protein-protein-interaction-databases. Recently published in Briefings in Bioinformatics, the Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources. These include links to databases on protein-protein interactions, metabolic and signaling pathways, Transcription Factors / Gene Regulatory Networks, Protein-Compound Interactions, Genetic Interaction Networks, Protein Sequences and Pathway Diagrams.

In addition to the hyperlinked list of databases, Klingström and Plewczynski created a network diagram showing the links among many databases in Pathguide with with linkouts to database details and to the database itself. The network diagram is organized by database name and category and has a legend that includes Interactions, Pathways, Predictive interactions, Metamining, Exchange format language, Unifying efforts, and a few uncategorized databases.

You can checkout the pathguide at

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