Pathguide: a Pathway Resource List

By Gary D. Bader, Michael P. Cary, Christopher Sander. Nucleic Acids Res., 2005

461 citations recorded by the source corpus.

Pathguide: the Pathway Resource List () 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.

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Citations in the corpus

OmniPath: guidelines and gateway for literature-curated signaling pathway resources (2016, background): “Nucleic Acids Research 39: D793–D799 (Database 1, 2011). 25. Fazekas D., Koltai M., Türei D., Módos D., Pálfy M., Dúl Z., Zsákai L., Szalay-Bekő M., Lenti K., Farkas I. J., Vellai T., Csermely P. and Korcsmáros T. SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. BMC”
NetPath: a public resource of curated signal transduction pathways (2010, methodology): “To avoid this, data standards are adopted by many of the pathway databases [12,46].”
iRefIndex: A consolidated protein interaction database with provenance (2008, background): “The potential for new IMEx members is enormous: one recent compilation of protein-protein interaction resources listed over 90 databases [11].”
The ConsensusPathDB interaction database: 2013 update (2012, background): “Thus, hundreds of thousands of interactions have already been detected, reported in the literature and assembled in interaction databases (2); however, these databases are often complementary and tend to focus on one or a few types of interactions while in reality all the different interaction types”
ConsensusPathDB—a database for integrating human functional interaction networks (2008, background): “Even worse, the existing knowledge on human functional interactions is dispersed in over 200 interaction databases, each of which has a speciﬁc data format, focus and bias (8).”
Bridging semantics and syntax with graph algorithms —state-of-the-art of extracting biomedical relations (2015, methodology): “To keep up with the exponential growth of the literature, automated methods have been applied to mining protein-protein interactions [15,16], gene-phenotype associations [17,18], gene ontology [19], and pathway information [20], which we collectively call biomolecular information extraction.”
The IntAct molecular interaction database in 2010 (2009, background): “As a result, many resources (28), including IntAct, aim to capture molecular interaction data from the scientific literature, through direct data deposition, expert curation, automated approaches like literature mining (29), or a combination of these (30); acting in isolation, or in coordination, fo”
BioPAX – A community standard for pathway data sharing (2010, unknown): “17 ).”
Data Mining Techniques for the Life Sciences (2010, methodology): “Databases containing sequences and structure annotations for the signal recognition particle RNA (SRPDB, (31)), RNAse P (32), tmRNA (tmRNAdb, (33)) group I (GISSD, (34)) and group II introns (35) are available as well.”
Bridging semantics and syntax with graph algorithms - state-of-the-art of extracting biomedical relations (2017, methodology): “To keep up with the exponential growth of the literature, automated methods have been applied to mining protein–protein interactions (PPIs) [20, 21], gene–phenotype associations [22, 23], gene ontology [24] and pathway information [25], which we collectively call biomolecular information extraction.”
WikiPathways: Pathway Editing for the People (2008, background): “A number of groups have taken on the challenge of curating and archiving biological pathways [8].”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “A list of several other pathway databases can be found at PathGuide (http://pathguide.org; Bader et al., 2006).”
The NCBI BioSystems database (2009, background): “Fortunately, a considerable number of resources have been created to address this issue: the Pathguide (1) resource lists nearly 300 pathway resources alone, including KEGG (2), Reactome (3), PID (4), PharmGKB (5), GenMAPP (6), Biocyc (7) and many others.”
Pathway Commons, a web resource for biological pathway data (2010, background): “Unfortunately, this information is currently highly fragmented among many databases, making it difficult for individual researchers to access a complete pathway data set (4).”