Pathguide: a pathway resource list

Abstract

Pathguide: the Pathway Resource List (http://pathguide.org) is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic pathways, signaling pathways, transcription factor targets, gene regulatory networks, genetic interactions, protein-compound interactions, and protein-protein interactions. The listed databases are maintained by diverse groups in different locations and the information in them is derived either from the scientific literature or from systematic experiments. Pathguide is useful as a starting point for biological pathway analysis and for content aggregation in integrated biological information systems.

Figure 1

The 40 largest databases in Pathguide. Pathway databases are diverse, both in volume of data (Database size, vertical) and in the attention they appear to generate (Popularity Estimate, horizontal). Database size is the sum of interaction and pathway records (where available; some database statistics may be incomplete). Popularity Estimate is taken to be the number of web pages in Google that mention the database homepage URL. Five main database categories (see symbol legend) out of eight are represented in the top 40. Databases in multiple categories are only represented in one (arbitrarily chosen) category. See the Pathguide website for expanded database names.