D504–D506 Nucleic Acids Research, 2006, Vol. 34, Database issue doi:10.1093/nar/gkj126 Pathguide: a Pathway Resource List Gary D. Bader, Michael P. Cary and Chris Sander* Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10021, USA Received October 20, 2005; Accepted October 21, 2005 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 data- bases on metabolic pathways, signaling pathways, transcription factor targets, gene regulatory net- works, genetic interactions, protein–compound inter- actions, and protein–protein interactions. The listed databases are maintained by diverse groups in differ- ent locations and the information in them is derived either from the scientific literature or from syste- matic experiments. Pathguide is useful as a starting point for biological pathway analysis and for content aggregation in integrated biological information systems. MOTIVATION Databases and methods for computational analysis and data mining are an increasingly integral part of biological research because they provide easy access to a wealth of biological information, which biologists require to support analyses and effectively answer research questions. While individual databases cover important information in certain areas of bio- logical knowledge, integrated and reasonably comprehensive use of biological pathway and network datasets is severely hampered by the large number and fragmentation of available databases (1). CREATING THE PATHWAY RESOURCE LIST As a step toward effective navigation and selective pathway data integration, we have collected information on over 190 published online cellular pathway and network databases in Pathguide. By providing this community resource we aim to promote the development of an integrated view of the cell (the ‘cell map’) (1). While much cell map data are only found in the literature, the databases in the list already repre- sent a signiﬁcant amount of relatively well-organized pathway data at varying levels of accessibility that can eventually be integrated and comprehensively accessed. TYPES OF DATA AND DATABASE CATEGORIES Databases in the list are grouped into eight major categories based on the type of data made available, the data format and the biological focus (Table 1). The categories are approxi- mate and a database can be in multiple categories if it contains multiple data types. Protein–protein interaction databases mainly store pairwise interactions or complexes between proteins and sometimes other molecular interaction types. Metabolic pathway databases generally store a series of bio- chemical reactions in pathways involved in metabolite con- versions. Signaling pathway databases generally collect sets of molecular interactions and chemical modiﬁcations (such as post-translational protein modiﬁcations) as regulatory path- ways. Gene regulation network databases capture transcription factors and the genes they regulate. Genetic pathway databases are composed of genetic interactions, such as epistasis and synthetic lethality, which occur when two mutations have a combined phenotypic effect that is not simply the sum of the effects caused by either mutation alone. Pathway diagram databases generally store hyperlinked pathway images; while it is difﬁcult to extract computable information from these images, they are very useful for biologists as educational Table 1. Pathguide statistics Category Protein–protein interactions Metabolic pathways Signaling pathways Pathway diagrams Transcription factors/gene regulatory networks Protein–compound interactions Genetic interaction networks Protein sequence focused Other Unique total Number of databases 79 43 41 22 20 14 5 12 11 196 The number of pathway databases in each Path-guide database category is listed. Uncategorized databases are listed in ‘‘Other’’. Databases can be in more than one category, so the unique total number of databases is shown. *To whom correspondence should be addressed. Tel: +1 646 735 8079; Fax: +1 646 735 0021; Email: pathguide@cbio.mskcc.org The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org