Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Open accessAbstract
MOTIVATION: Biological systems function through dynamic interactions among genes and their products, regulatory circuits and metabolic networks. Our development of the Pathway Tools software was motivated by the need to construct biological knowledge resources that combine these many types of data, and that enable users to find and comprehend data of interest as quickly as possible through query and visualization tools. Further, we sought to support the development of metabolic flux models from pathway databases, and to use pathway information to leverage the interpretation of high-throughput data sets. RESULTS: In the past 4 years we have enhanced the already extensive Pathway Tools software in several respects. It can now support metabolic-model execution through the Web, it provides a more accurate gap filler for metabolic models; it supports development of models for organism communities distributed across a spatial grid; and model results may be visualized graphically. Pathway Tools supports several new omics-data analysis tools including the Omics Dashboard, multi-pathway diagrams called pathway collages, a pathway-covering algorithm for metabolomics data analysis and an algorithm for generating mechanistic explanations of multi-omics data. We have also improved the core pathway/genome databases management capabilities of the software, providing new multi-organism search tools for organism communities, improved graphics rendering, faster performance and re-designed gene and metabolite pages. AVAILABILITY: The software is free for academic use; a fee is required for commercial use. See http://pathwaytools.com. CONTACT: pkarp@ai.sri.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Briefings in Bioinformatics online.
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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 [21]
Pathway Tools software and CellDesigner pathway editor are developing support for BioPAX-based data exchange.
“The Pathway Tools software21 and CellDesigner pathway editor54 are developing support for BioPAX-based data exchange.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [21]
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Adapting EcoCyc for use on the World Wide Web
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Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
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Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
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“Mirny [1,4,5]”
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“One reconstruction schema that supports extensive annotation and provenance tracking has been defined as part of the Pathway Tools software [28], but this schema has not yet been adopted more widely or supported by other software implementations, nor has this schema yet been extended to support ME models or reconstruc…”
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- Authors
- Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., Altman, T., Paulsen, I., Keseler, I. M., & Caspi, R.
- Affiliations
- SRI International (US)
- Monash University (AU)
- ORCID
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-12-02
- Volume
- 11
- Issue
- 1
- Pages
- 40-79
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- PMC
- PMC2810111
- OpenAlex
- W2168465568
- Cited by
- 694
- References
- 113
- Citations by year
- 2026: 6 · 2025: 21 · 2024: 38 · 2023: 43 · 2022: 39 · 2021: 42 · 2020: 49 · 2019: 38 · 2018: 36 · 2017: 63 · 2016: 53 · 2015: 52 · 2014: 47 · 2013: 61 · 2012: 52
- FWCI
- 14.24
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Briefings in Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM080746, GM077678, GM75742, R01GM080746, R01GM077678, U24GM077678, R01GM075742)
- U.S. National Library of Medicine (LM009651, R01LM009651)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- Pathway Tools, pathway/genome databases, multi-omics data analysis, metabolomics, pathway visualization
- MeSH terms
- Software, Genome, Computational Biology, Internet, Systems Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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