The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Presenting and exploring biological pathways with PathVisio
Open accessAbstract
BACKGROUND: Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio is a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects. The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs. RESULTS: PathVisio can be combined with other bioinformatics tools to open up three possible uses: visual compilation of biological knowledge, interpretation of high-throughput expression datasets, and computational augmentation of pathways with interaction information. PathVisio is open source software and available at http://www.pathvisio.org. CONCLUSION: PathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.
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Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
WikiPathways: Pathway Editing for the People
Pico, A. R., Kelder, T., van Iersel, M. P., Hanspers, K., Conklin, B. R., & Evelo, C. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060184 · Cited by 701
Self-citationUsing process diagrams for the graphical representation of biological networks
Kitano, H., Funahashi, A., Matsuoka, Y., & Oda, K. (2005) · Nature Biotechnology · doi:10.1038/nbt1111 · Cited by 483
Pathway information for systems biology
Cary, M. P., Bader, G. D., & Sander, C. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.02.005 · Cited by 152
Cited by
Into the Eye of the Cytokine Storm
Tisoncik, J. R., Korth, M. J., Simmons, C. P., Farrar, J., Martin, T. R., & Katze, M. G. (2012) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.05015-11 · Cited by 1,940
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
Karp, P. D., Paley, S., & Romero, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s225 · Cited by 661
Time-Resolved and Tissue-Specific Systems Analysis of the Pathogenesis of Insulin Resistance
Kleemann, R., van Erk, M., Verschuren, L., van den Hoek, A. M., Koek, M., Wielinga, P. Y., Jie, A., Pellis, L., Bobeldijk-Pastorova, I., Kelder, T., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008817 · Cited by 146
Self-citationBictash, M., Ebbels, T. M., Chan, Q., Loo, R. L., Yap, I. K. S., Brown, I. J., de Iorio, M., Daviglus, M. L., Holmes, E., Stamler, J., et al. (2010) · Journal of Clinical Epidemiology · doi:10.1016/j.jclinepi.2009.10.001 · Cited by 140
Metadata
- Authors
- van Iersel, M. P., Kelder, T., Pico, A. R., Hanspers, K., Coort, S., Conklin, B. R., & Evelo, C.
- Venue
- BMC Bioinformatics
- Published
- 2008-09-25
- Volume
- 9
- Issue
- 1
- Pages
- 399-399
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1970594207
- Cited by
- 360
- References
- 5
- FWCI
- 8.56
- Type
- journal article
- Language
- en
- Open access
- gold
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- van Iersel, M. P., Kelder, T., Pico, A. R., Hanspers, K., Coort, S., Conklin, B. R., & Evelo, C. (2008). Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-9-399
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
