Pathguide: a Pathway Resource List
Open accessAbstract
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.
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The number of pathway and molecular interaction related online resources grew from 190 in 2006 to 325 in 2010, a 70% increase.
“The number of pathway and molecular interaction related online resources has grown from 190 in 2006 to 325 in 2010, a 70% increase17.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [17]
Over 300 pathway or molecular interaction related data resources and many visualization and analysis software tools have been developed.
“Over 300 pathway or molecular interaction related data resources17 and many visualization and analysis software tools3,20-22 have been developed.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [17]
Current fragmentation of pathway information across many databases with incompatible formats creates barriers to effective use.
“However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [17]
The total volume of pathway data mapped by biologists and stored in databases has entered a rapid growth phase.
“The total volume of pathway data mapped by biologists and stored in databases has entered a rapid growth phase17, similar to the rapid expansion of biological sequence data after the introduction of automated sequencing technology.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [17]
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Self-citationCellML: its future, present and past
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Pathway information for systems biology
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Self-citationThe Molecular Biology Database Collection: 2007 update
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- Authors
- Bader, G. D.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Corresponding author
- Bader, G. D.
- ORCID
- Bader, G. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-01
- Volume
- 34
- Issue
- 90001
- Pages
- D504-D506
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1347488
- OpenAlex
- W2143969914
- Cited by
- 435
- References
- 7
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 8 · 2023: 12 · 2022: 8 · 2021: 15 · 2020: 11 · 2019: 18 · 2018: 21 · 2017: 19 · 2016: 21 · 2015: 39 · 2014: 33 · 2013: 30 · 2012: 44
- FWCI
- 6.67
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Memorial Sloan-Kettering Cancer Center
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- biological pathway databases, metabolic pathways, signaling pathways, transcription factor targets, gene regulatory networks, genetic interactions, protein-protein interaction, metadata database
- MeSH terms
- Gene Expression Regulation, Metabolism, Proteins, Transcription Factors, User-Computer Interface, Signal Transduction, Systems Integration, Internet, Databases, Genetic
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