NIF Data Spotlight: WikiPathways

There are tens of thousands of different biological pathways and each pathway involves complex sets of protein-protein interactions, small molecules, protein complexes, enzymes, regulators and reactions. These pathways are represented in published papers, databases and scientists heads; however now they can also be found on WikiPathways: an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. WikiPathways is a wiki so it is possible to access and contribute biological pathway information easily.

NIF’s federated search engine searches some information in WikiPathways such as pathway name, gene name, gene symbol, or organism. For example, we can search for Wnt signaling pathway in zebrafish (Wnt proteins are part of basic developmental processes, such as cell-fate specification, cell proliferation and asymmetric cell division) using the search syntax "Zebrafish Wnt signaling pathway".



Categories returned, as mentioned above, are pathway name, gene symbol, gene name, and organism. Clicking on the pathway name will take the users to WikiPathways page for more details on the pathway.



Information on Wikipathways page includes the current diagram, description, references, download options, version history, and component gene and protein lists.

For more thorough instructions on how to use Wikipathways, please visit NIF's Wikipathways tutorial.

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The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.