BioPAX – A community standard for pathway data sharing

By Emek Demir, Michael P. Cary, Suzanne M. Paley, Ken Fukuda, C. Lemer, Imre Vastrik, Guanming Wu, P. D’Eustachio, C. Schaefer, Joanne S. Luciano and 79 more. Nature Biotechnology, 2010

695 citations recorded by the source corpus.

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

Subfields: Molecular Biology

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Citations in the corpus

The IntAct molecular interaction database in 2012 (2011, methodology): “In addition to the original PSI-MI XML and PSI-MITAB standard formats, we have added the possibility of exporting to BioPAX (13) levels 2 and 3 formats which is an RDF-based format widely used for the exchange of biological pathway data.”
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) (2010, neutral): “RegulonDB is also accessible in BioPAX format, as we have contributed also in the expansion of this pathway exchange format (13).”
The Reactome pathway knowledgebase (2013, methodology): “Reactome is open-source and open-data, and we have continuously supported the major open-data standards in the domain, including BioPAX levels 2 and 3 (24), PSI MITAB (18), Protégé (http://protege.”
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015 (2014, background): “The appeal and utility of structured notations are evident nowadays with the emergence of other bio-languages, such as BioPax (15) and BEL (http: //www.”
A travel guide to Cytoscape plugins (2012, background): “Cytoscape imports interaction data in various generic tabular formats including CSV (comma-separated values), TSV (tab-separated values) and Excel, along with network-specific formats such as SIF (simple interaction file, originally developed for Cytoscape), XGMML (Extensible Graph Markup and Modeli”
WikiPathways: capturing the full diversity of pathway knowledge (2015, methodology): “One of the best ways to access our BioPAX content is via Pathway Commons (14), which validates and compiles pathway models from many resources.”
Reactome: a database of reactions, pathways and biological processes (2010, background): “Reactome is part of the BioPAX Consortium to develop a data-exchange language to describe pathways, reactions and interactions (29).”
Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “Second, the PANTHER pathway supports community standards, and all pathways are available in SBML (systems biology markup language 26 , BioPAX (biological pathway exchange format) 27 and SBGN 25 formats.”
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse (2015, methodology): “The users can employ some tools such as Sig2BioPax (43) to convert the regulations into the BioPAX Level 3 format (44).”
PharmGKB: The Pharmacogenomics Knowledge Base (2013, methodology): “This information is captured in the database in a Biopax [20] compatible format that can be downloaded and used in pathway analysis packages.”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “14 We joined in the effort to create the BioPAX standard for sharing annotated pathway information, 15 and have made PANTHER Pathways available in this format since that time.”
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016, background): “…set libraries from HumanCyc (15), a Nucleic Acids Research, 2016, Vol. 44, Web Server issue W91 metabolic pathway resource stored in BioPAX format (16); gene and small-molecule perturbations from the LINCS L1000 data set; NCI-Nature pathways (17); protein complexes from the NURSA project (18);…”
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation (2010, methodology): “Future work will include incorporating molecular interaction network and pathway information [47,48] into gene-set analysis methods, as has successfully been done for gene expression analysis [49,50,51,52,53].”
The ConsensusPathDB interaction database: 2013 update (2012, methodology): “BioPAX Level 3 export Networks viewed with the interaction visualization tool can now be exported in BioPAX Level 3 (4) format.”
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees (2012, methodology): “This service is used by the tool that generates BioPAX data.”
Maize Metabolic Network Construction and Transcriptome Analysis (2013, methodology): “For advanced users working on network modeling, we provide pathway data dumps in the standardized BioPax levels 2 and 3 (Demir et al., 2010) and systems biology markup language (SBML) (Hucka et al., 2003) formats.”