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Sep 16, 2020

WikiPathways: A Wikipedia for biological pathways

An overview of the collaboratively edited structured pathway encyclopedia.

Since its inception in 2008, WikiPathways, a wiki for biological pathways, has grown to include over 2,800 individual pathways. It currently has over 700 active users and boasts more than 500 citations in scientific literature.

What is WikiPathways?

WikiPathways is a structured knowledge base for biological pathways that is collaboratively edited by the scientific community. Like Wikipedia, it allows anyone to create or edit encyclopedia records which are all moderated and curated by other WikiPathways users.

Each WikiPathways entry combines genes, proteins, metabolites, and interactions involved in a single pathway or process. All elements of the pathway have links to corresponding entries in reference databases such as UniProt and PubChem, making WikiPathways an important crystallisation point for integrating knowledge about biological pathways.

Applications of WikiPathways

A large biological pathway database, WikiPathways is used for a variety of applications including omics and gene expression analyses.

The dataset can also be used to perform other types of data analysis, visualise research data in the context of pathways, and build pathway models. Moreover, the WikiPathways website itself is a useful resource for learning about pathways.

Accessing WikiPathways data

The primary way to access WikiPathways is via, the official website of the project. The data can also be accessed programmatically via the web service API.

WikiPathways entries are also referenced in Wikipedia, Wikidata, and other open datasets.

WikiPathways as linked data

Since 2016, the WikiPathways dataset has also been provided in the RDF (linked data) format. The data can be queried programmatically using the SPARQL endpoint which also provides a user-friendly SPARQL query editor.

The WikiPathways RDF dataset uses two core vocabularies and the standard set of identifiers for genes, proteins, and metabolites to support linking to other linked biological data sources. This enables users to utilise SPARQL federation to easily combine information from WikiPathways with other linked data sets.

The bottom line

The collaboratively edited WikiPathways encyclopedia was launched in 2008 as an "experiment", and today integrates the data for over 2,800 biological pathways and makes it easily accessible both via and programmatically as linked data.

The Wikipedia-like style of WikiPathways makes it stand out from other omics datasets. It actively promotes the collaborative approach to research and sharing of biological knowledge.

See also
AstraZeneca's knowledge graph: Drug discovery is a lot about connections
The biomedical knowledge graph built by AstraZeneca helps the company find new drugs and drug targets.
Scalable genomic alignment with Progressive Cactus
How progressive alignment makes it possible to efficiently align hundreds to thousands of large genomes.
The RDF model of the Gene Ontology, demystified
An outline of the structure of the Gene Ontology RDF graph and ways to query it.
The ambitious challenge of finishing the human genome
Generating a complete human genome sequence, chromosome by chromosome.
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