wikipathways

is a Data Source.

It is part of the BER collection.

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. The database contains 1,913 human-curated pathways across 27 species with 36,334 gene products and 7,052 metabolites, supporting multiple data formats (GPML, GMT, RDF) and programmatic access via SPARQL endpoints and web APIs. Community-driven curation with version control and CI/CD infrastructure enables rapid pathway annotation and knowledge sharing in an open science framework.

Domains

pathways, genomics, biomedical

License

CC0 (Creative Commons Zero)

Homepage

wikipathways

Repository

GitHub

Infores ID

infores:wikipathways

FAIRsharing ID

FAIRsharing.1x53qk

Product Summary

Products

From this Resource
ID Name URL Category Format Description
wikipathways.gpml WikiPathways GPML gpml Product xml Pathways in Graphical Pathway Markup ...
wikipathways.gmt WikiPathways GMT gmt Product tsv Pathways in Gene Matrix Transposed (G...
wikipathways.rdf WikiPathways RDF rdf Product ttl Pathways in RDF (Resource Description...
wikipathways.sparql WikiPathways SPARQL Endpoint sparql.wikipathways.org ProgrammingInterface ❔ SPARQL endpoint for querying WikiPath...
wikipathways.web WikiPathways Web Interface www.wikipathways.org GraphicalInterface ❔ The main web interface for browsing, ...
From other Resources
ID Name URL Category Format Description
spoke.graph SPOKE Graph ❔ GraphProduct ❔ The SPOKE knowledge graph containing ...
ubkg.neo4j UBKG Neo4j Docker Distribution ubkg-downloads.xconsortia.org GraphProduct ❔ Turnkey neo4j distributions that depl...
ubkg.csv UBKG Ontology CSV Files ubkg-downloads.xconsortia.org GraphProduct csv Ontology CSV files that can be import...
alzkb.browser AlzKB Graph Database Browser login GraphicalInterface http A browser interface for a knowledge g...
alzkb.data AlzKB Data Release (Version 2.0.0) v2.0.0 GraphProduct ❔ Memgraph data release for AlzKB.
indra.cogex.code INDRA CoGEx Build Code indra_cogex ProcessProduct ❔ INDRA CoGEx is a graph database integ...
rna-kg.kg.neo4j RNA-KG Neo4j Dump rnakgv20.dump (3.7 GB) GraphProduct neo4j RNA-KG as a Neo4j Dump
rna-kg.kg.nodes RNA-KG Nodes nodes.csv (4.1 GB) GraphProduct csv RNA-KG Nodes in CSV format
rna-kg.kg.edges RNA-KG Edges edges.csv (17.1 GB) GraphProduct csv RNA-KG Edges in CSV format
genecards.pathway.data ⚠ GeneCards Pathway Data www.genecards.org Product http Pathway information integrated from R...
ttd.wiki-pathways Target WikiPathways P4-06-Target_wikipathway.txt Product txt WikiPathways data for all targets
rampdb.database RaMP-DB Integrated Database rampdb.nih.gov DatabaseProduct ❔ Multi-sourced relational database int...
string.protein.links STRING Protein Links protein.links.v12.0.txt.gz (128.7 GB) GraphProduct txt protein network data (full network, s...
string.protein.links.detailed STRING Protein Links Detailed protein.links.detailed.v12.0.txt.gz (189.6 GB) GraphProduct txt protein network data (full network, i...
string.protein.links.full STRING Protein Links Full protein.links.full.v12.0.txt.gz (199.6 GB) GraphProduct txt protein network data (full network, i...
string.protein.physical.links STRING Protein Physical Links protein.physical.links.v12.0.txt.gz (11.1 GB) GraphProduct txt protein network data (physical subnet...
string.protein.physical.links.detailed STRING Protein Physical Links Detailed protein.physical.links.detailed.v12.0.txt.gz (13.8 GB) GraphProduct txt protein network data (physical subnet...
string.protein.physical.links.full STRING Protein Physical Links Full protein.physical.links.full.v12.0.txt.gz (14.5 GB) GraphProduct txt protein network data (physical subnet...
string.cog.links STRING COG Links COG.links.v12.0.txt.gz (176.8 MB) GraphProduct txt association scores between orthologou...
string.cog.links.detailed STRING COG Links Detailed COG.links.detailed.v12.0.txt.gz (238.7 MB) GraphProduct txt association scores (incl. subscores p...
string.database STRING Database Network Schema network_schema.v12.0.sql.gz (262.2 GB) GraphProduct ❔ full database, part II: the networks ...
obo-db-ingest.wikipathways.tsv wikipathways Nodes TSV wikipathways.tsv (32.8 KB) Product tsv wikipathways Nodes TSV

Details

WikiPathways

WikiPathways is an open, collaborative platform dedicated to the curation and dissemination of biological pathways. Established to facilitate community contribution and maintenance of pathway knowledge, WikiPathways provides researchers with a user-friendly web interface and comprehensive toolkit for discovering, visualizing, analyzing, and sharing biological pathway information across 27 organisms.

Overview and Mission

WikiPathways operates on open science principles with a mission to democratize pathway knowledge curation by leveraging the expertise of the global research community. The platform reduces barriers to participation through intuitive web-based tools while maintaining rigorous quality standards through peer review and modern software development practices including version control and continuous integration testing.

Database Content and Scale

Pathway Coverage

Current Content (2024):

  • 1,913 curated pathways across 27 species
  • 866 human pathways (approximately 45% of total)
  • 36,334 gene products integrated across all pathways
  • 7,052 metabolites represented in pathway models
  • 85,647 molecular interactions documented
  • 201 pathway authors with contributions over the past three years
  • 10,873 edits in the past three years reflecting active community engagement

Species Coverage

WikiPathways provides comprehensive pathway information for:

  • Human (primary focus with 866 curated pathways)
  • Model organisms with automatic homology-based translations:
    • Mouse
    • Rat
    • Zebrafish
    • Fruit fly (Drosophila melanogaster)
    • Caenorhabditis elegans
    • Yeast (Saccharomyces cerevisiae)
    • Arabidopsis thaliana
    • And 4 additional vertebrate organisms

Pathway Types and Coverage

WikiPathways covers diverse biological processes including:

  • Signal transduction pathways - Cell signaling and communication
  • Metabolic pathways - Biochemical transformations and energy production
  • Gene regulatory networks - Transcriptional control and expression
  • Disease pathways - Mechanisms underlying specific diseases
  • Drug response pathways - Pharmacological interactions and responses
  • Developmental pathways - Organism growth and differentiation
  • Immune response pathways - Immunological mechanisms
  • Cross-kingdom interactions - Plant-pathogen, host-microbe interactions

Data Access Methods

Web Interface

Main Portal: https://www.wikipathways.org/

The redesigned WikiPathways website (2024 update) offers:

  • Interactive pathway browsing with expandable pathway trees and hierarchical organization
  • Full-text search across pathway names, descriptions, and molecular components
  • Pathway pages displaying current diagrams, descriptions, authors, references, citations, annotations
  • Community features for connecting with authors, viewing edit history, and learning contribution guidelines
  • Pathway editing interface with integrated collaboration tools
  • Version history tracking via Git-backed version control
  • Export capabilities in multiple formats directly from the web interface

Programmatic Interfaces

SPARQL Endpoint: https://sparql.wikipathways.org/

  • Full W3C SPARQL 1.1 protocol support
  • Query WikiPathways RDF data using semantic graph patterns
  • Complex federated queries for cross-database integration
  • Result formats: JSON, XML, CSV, TSV, N-Triples

R Package - rWikiPathways:

  • CRAN package for R environments
  • Programmatic queries from R/Bioconductor
  • Integrates with pathway analysis workflows
  • Available at: https://cran.r-project.org/web/packages/rWikiPathways/

Python Package - pywikipathways:

  • Python interface to WikiPathways API
  • Integration with scientific Python stack
  • Supports data analysis and visualization workflows

Data Download Services

Download Portal: https://data.wikipathways.org/

Available in multiple formats:

  • GPML (Graphical Pathway Markup Language) - Native WikiPathways XML format
  • GMT (Gene Matrix Transposed) - Gene set format for pathway enrichment analysis
  • RDF (Resource Description Framework) - Semantic web format
  • SVG and PNG - Image formats for visualization and publication
  • TSV - Tab-separated tabular data

Organized by:

  • Species-specific exports
  • Individual pathway downloads
  • Batch downloads with compressed archives
  • Versioned releases for reproducibility

Data Standards and Technical Infrastructure

Biological Data Representation

GPML (Graphical Pathway Markup Language):

  • Custom XML format purpose-built for pathway diagrams
  • Supports visualization of nodes (genes, proteins, metabolites) and interactions
  • Compatible with pathway visualization tools (PathVisio, Cytoscape)
  • Preserves layout, styling, and annotation information

Gene Matrix Transposed (GMT):

  • Standard format for pathway enrichment analysis
  • Compatible with GSEA (Gene Set Enrichment Analysis) and similar tools
  • Lists genes/proteins per pathway for statistical testing

RDF and Semantic Web:

  • Triple-based knowledge representation for linked data
  • Enables integration with biomedical ontologies and cross-database queries
  • Semantic reasoning over implicit pathway relationships
  • Interoperability with other linked data resources

Curation Infrastructure

Community-Driven Curation Process:

  • Version control via Git for all pathway content
  • Pull request workflow for quality control
  • Automated testing of pathway structure and data integrity
  • Continuous integration ensuring only valid pathways are published
  • Distinction between automated and human-reviewed merges
  • Focus on human expertise for biologically significant changes

Quality Assurance:

  • Peer review by domain experts
  • Cross-reference validation (genes, proteins, metabolites)
  • Consistency checking across species homologs
  • Automated identifier validation and standardization

Use Cases and Applications

Pathway Analysis and Discovery

  • Gene Set Enrichment Analysis (GSEA) - Using GMT-formatted pathways for statistical significance testing
  • Network analysis - Visualizing interaction networks and identifying functional modules
  • Pathway visualization - Creating publication-quality pathway diagrams
  • Cross-species comparison - Leveraging homology mappings for comparative pathway analysis

Systems Biology and Modeling

  • Systems-level understanding - Integrating multi-omics data with pathway context
  • Hypothesis generation - Identifying novel pathway interactions and cross-talk
  • Computational modeling - Using pathway diagrams as templates for mathematical models
  • Integrated pathway analysis - Combining multiple pathways into larger biological systems

Drug Discovery and Development

  • Target identification - Identifying potential drug targets within pathways
  • Drug response pathways - Understanding how drugs interact with biological systems
  • Adverse effect prediction - Mapping potential side effects through pathway mechanisms
  • Polypharmacology - Identifying off-target drug interactions

Educational Applications

  • Pathway biology learning - Educational resources for understanding biological mechanisms
  • Bioinformatics training - Examples for computational biology education
  • Collaborative learning - Community-driven knowledge building in research groups

Integration with Other Tools and Databases

WikiPathways integrates with diverse analysis platforms:

  • Cytoscape plugins - Direct pathway visualization in Cytoscape
  • PathVisio - Pathway editing and analysis
  • Enrichment Map - GSEA pathway enrichment visualization
  • BioGRID, STRING - Protein interaction network overlays
  • Systems biology tools - Including Reactome and KEGG integration

Organizational Structure and Leadership

Leadership Team

Martina Kutmon (Maastricht University)

  • Pathway curator and database manager
  • Contact: martina.kutmon@maastrichtuniversity.nl
  • Expertise in pathway curation, network approaches, and knowledge management

Egon Willighagen (Maastricht University)

  • Pathway curator and database manager
  • Contact: egon.willighagen@maastrichtuniversity.nl
  • Expertise in pathway curation, chemistry, and knowledge management

Host and Partner Institutions

Primary Affiliation:

  • Maastricht University
  • Provides infrastructure, funding, and institutional support

Community Model

  • Open-source development with transparent governance
  • Community curation leveraging global pathway expertise
  • Public Git repository for source code and database content
  • Distributed development with contributions from 201+ authors
  • Ongoing maintenance with active community engagement

Funding and Sustainability

Primary Support:

  • Institutional funding from Maastricht University and partner institutions
  • NIH and EU research funding for specific projects
  • Community volunteer contributions
  • OpenStack community infrastructure support
  • ELIXIR Europe Service

Status:

  • Actively maintained with regular database releases
  • Continuous improvements to infrastructure and tools
  • Growing pathway collection with average of 84 new pathways per year

Standards Compliance and Interoperability

  • Open Science Standards - CC0 public domain licensing
  • Semantic Web Standards - RDF, SPARQL, OWL compatibility
  • Biological Data Standards - Integration with Gene Ontology, ChEBI, UniProt identifiers
  • Interoperability - Support for pathway exchange formats and cross-database queries
  • FAIR Principles - Findable, Accessible, Interoperable, Reusable data

Citation and Usage

WikiPathways data and services are freely accessible with CC0 (public domain) licensing. All pathway content is available for unrestricted use with optional attribution to the original authors.

For WikiPathways general use: “WikiPathways. Available at: https://www.wikipathways.org/”

For research using WikiPathways data, cite the latest update: “Agrawal A, et al. (2024) WikiPathways 2024: next generation pathway database. Nucleic Acids Research. 52(D1):D679-D685. https://doi.org/10.1093/nar/gkad960”

For previous versions, see full publication record below.

Additional Resources

  • Main Website: https://www.wikipathways.org/
  • SPARQL Endpoint: https://sparql.wikipathways.org/
  • Data Downloads: https://data.wikipathways.org/
  • GitHub Repository: https://github.com/wikipathways/wikipathways-database
  • R Package (rWikiPathways): https://cran.r-project.org/web/packages/rWikiPathways/
  • Python Package: https://github.com/wikipathways/pywikipathways
  • Pathway Editing Guide: https://www.wikipathways.org/index.php/Help:EditPathway
  • API Documentation: https://webservice.wikipathways.org/
  • GitHub Organization: https://github.com/wikipathways

WikiPathways continues to serve as the premier open-source pathway database, enabling researchers worldwide to discover biological knowledge, share pathway expertise, and integrate pathway information into systems biology research through modern collaborative tools and open science practices.

Is this information incorrect or incomplete? Request an update.

Created: June 05, 2025 | Last modified: December 20, 2025