Pathway Commons

Pathway Commons
Name	Pathway Commons
Developer	The Institute for Systems Biology
Released	2010
Programming language	Java, Python
Platform	Web, RESTful APIs
License	Various

Pathway Commons is an integrated resource that aggregates biological pathway and interaction data to support computational analysis, modeling, and visualization for researchers in molecular biology and systems biology. It serves as a hub for curated and computationally inferred interactions drawn from multiple public repositories, enabling cross-referencing among databases maintained by institutions such as National Institutes of Health, European Bioinformatics Institute, University of California, San Francisco, Broad Institute, and Stanford University. Pathway Commons facilitates data reuse across platforms used by researchers at Harvard University, Massachusetts Institute of Technology, Johns Hopkins University, Cold Spring Harbor Laboratory, and Max Planck Society.

Overview

Pathway Commons consolidates pathway models, protein–protein interactions, signaling networks, and biochemical reactions originally hosted by sources including Reactome, KEGG, WikiPathways, BioGRID, IntAct, STRING, MINT, PhosphoSitePlus, Human Protein Atlas, Gene Ontology Consortium, UniProt, NCBI, and Ensembl. The resource supports interoperability with standards developed by HUPO PSI-MI, BioPAX, SBML, SIF, and PSI-MI XML, enabling use in analytic environments common at European Molecular Biology Laboratory, Wellcome Trust Sanger Institute, European Research Council, and National Center for Biotechnology Information. Pathway Commons underpins workflows used in projects at Dana-Farber Cancer Institute, Memorial Sloan Kettering Cancer Center, Salk Institute, Weill Cornell Medicine, and Cold Spring Harbor Laboratory Press.

Data Sources and Integration

Data integration in Pathway Commons draws from curated datasets contributed by repositories such as Reactome, WikiPathways, BioGRID, IntAct, MINT, STRING, PhosphoSitePlus, PathBank, and PID. Integration pipelines map identifiers across systems like UniProt, Ensembl, NCBI Gene, HGNC, RefSeq, KEGG Gene, ChEBI, and PubChem, and reconcile annotations from Gene Ontology Consortium, InterPro, Pfam, SMART, and SCOP. The project interoperates with ontologies and vocabularies maintained by OBO Foundry, NCBO BioPortal, Medical Subject Headings, Human Phenotype Ontology, and Disease Ontology. Data ingestion workflows parallel practices established at European Molecular Biology Laboratory-European Bioinformatics Institute, National Center for Biotechnology Information, and European Genome-phenome Archive.

Architecture and Access

Pathway Commons exposes data through RESTful APIs and bulk downloads compatible with formats promoted by BioPAX and SBML, and supports querying via technologies used by Apache Lucene, Neo4j, GraphQL, JSON-LD, and SPARQL endpoints akin to those hosted by Wikidata and EBI RDF. The architecture was developed by teams associated with Institute for Systems Biology, University of California, San Diego, University of Washington, Carnegie Mellon University, and University of Toronto, and follows software practices from projects such as Cytoscape, NDEx, Bioconductor, Galaxy Project, and Jupyter Project. Authentication and access patterns align with standards used by ORCID, ELIXIR, GA4GH, and Kubernetes deployments in research infrastructures at Lawrence Berkeley National Laboratory and Argonne National Laboratory.

Tools and Applications

Pathway Commons content is consumed by visualization and analysis tools including Cytoscape, Cytoscape.js, Gephi, NDEx, RStudio, Python, Bioconductor, GSEA, EnrichmentMap, ClusterProfiler, Metascape, Reactome Pathway Browser, and GenePattern. Use cases include pathway enrichment in studies from The Cancer Genome Atlas, ENCODE Project, 1000 Genomes Project, Cancer Cell Line Encyclopedia, and GTEx Project, and integrative analyses performed at Broad Institute, Scripps Research, Fred Hutchinson Cancer Center, Institut Pasteur, and Weizmann Institute of Science. Clinical and translational applications intersect with efforts at National Cancer Institute, European Medicines Agency, Food and Drug Administration, and pharmaceutical research at Pfizer, Novartis, Roche, and GlaxoSmithKline.

Community and Curation

Curation workflows combine manual expert review by curators affiliated with Reactome, WikiPathways, PhosphoSitePlus, and BioGRID with automated aggregation pipelines influenced by community resources such as Wikidata, Open Targets, ClinVar, COSMIC, and dbSNP. Community engagement leverages collaborations with consortia like ELIXIR, GA4GH, HUPO, ISCB, Global Alliance for Genomics and Health, and educational initiatives at EMBL-EBI Training. Outreach and contribution models echo practices from GitHub, Zenodo, Figshare, Dryad, and Zenodo Community hosting workflows used by Nature Publishing Group and PLOS.

History and Development

Development of Pathway Commons began as a collaborative initiative involving researchers at the Institute for Systems Biology, UC San Diego groups, curators from Reactome and BioGRID, and funding agencies such as the National Human Genome Research Institute and National Institutes of Health. The project evolved alongside milestone resources like Reactome, KEGG, and UniProt and adapted to community standards promoted by HUPO PSI-MI and BioPAX. Major software contributions came from teams with ties to Cytoscape Consortium, Broad Institute, Stanford University, Harvard Medical School, and EMBL-EBI, and the resource has been cited in studies conducted at Dana-Farber Cancer Institute, Broad Institute, Salk Institute, and Memorial Sloan Kettering Cancer Center.

Category:Bioinformatics