WikiPathways
WikiPathways provides an open-access, community-curated database of biological pathways for pathway visualization, annotation, and integrative analysis of experimental omics data.
Key Features:
- Community-curated pathway database: A repository of biological pathway models contributed and curated by the scientific community.
- Tool integration: Pathway models integrate with PathVisio and Cytoscape for pathway analysis and visualization.
- Programmatic access and web services: Offers web applications and programmatic access via SOAP web services with OpenAPI-documented endpoints.
- Data formats and outputs: Provides publishable figures, standard data files, and linked data formats for downstream analysis and interoperability.
- Metabolite annotation and metabolic pathway curation: Curations associate previously unmapped metabolites with database identifiers and expand interaction annotations, increasing annotated metabolite nodes.
- Interoperability and FAIR compliance: Emphasizes FAIR principles and links pathway content to external resources such as Wikidata to improve findability and reuse.
Scientific Applications:
- Omics data integration: Map and visualize omics data onto curated pathways for integrative analysis.
- Metabolomics and metabolic pathway analysis: Improve identification and interpretation of metabolite nodes and metabolic interactions through enhanced metabolite annotation.
- Pathway development and prioritization: Support prioritization in pathway development using curated models, published figures, and recognition technologies.
- Linked-data integration: Connect pathway knowledge to external databases and linked data resources, including Wikidata, to support integrative analyses.
Methodology:
Provides web applications and programmatic access via SOAP web services (OpenAPI-documented), integrates with PathVisio and Cytoscape, exports publishable figures, standard data files and linked data formats, and curates metabolites by mapping unmapped metabolites to database identifiers and expanding interaction annotations.
Topics
Collections
Details
- License:
- Apache-2.0
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- api, web application
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- JavaScript
- Added:
- 7/20/2017
- Last Updated:
- 11/24/2024
Operations
Publications
Kutmon M, Riutta A, Nunes N, Hanspers K, Willighagen EL, Bohler A, Mélius J, Waagmeester A, Sinha SR, Miller R, Coort SL, Cirillo E, Smeets B, Evelo CT, Pico AR. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Research. 2015;44(D1):D488-D494. doi:10.1093/nar/gkv1024. PMID:26481357. PMCID:PMC4702772.
Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. Mining Biological Pathways Using WikiPathways Web Services. PLoS ONE. 2009;4(7):e6447. doi:10.1371/journal.pone.0006447. PMID:19649250. PMCID:PMC2714472.
Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, A. Miller R, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M. WikiPathways: connecting communities. Nucleic Acids Research. 2020;49(D1):D613-D621. doi:10.1093/nar/gkaa1024. PMID:33211851. PMCID:PMC7779061.
Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research. 2017;46(D1):D661-D667. doi:10.1093/nar/gkx1064. PMID:29136241. PMCID:PMC5753270.