Spotlight: WikiPathways

This week, we’re pleased to profile WikiPathways in our weekly Spotlight series. WikiPathways is our eight-most popular plugin in BioGPS, and of course we love the community intelligence model that also underlies the Gene Wiki. Check out the profile below…


1. In one tweet or less, introduce us to your website.
WikiPathways is a resource for biological pathway information where the biology community can share and collaboratively curate pathways.

2. Why is your database unique and special?
The content on WikiPathways is free, open and contributed and continuously maintained by the biology research community. We aim to make it easier to collect the growing amount of biological knowledge so it can be used to help interpreting large experimental datasets generated by transcriptomics, proteomics or metabolomics techniques. WikiPathways provides a platform for bringing experts in specific fields of biology together to form communities that share, discuss and curate pathway information and can use these pathways directly in popular data analysis tools like Cytoscape and GenMAPP.

3. What improvements are coming in the future?
We are continuously working on improving tools for curation and usability of the pathways, such as interoperability with data analysis tools such as Cytoscape and pathway data standards like BioPAX. One notable upcoming feature is the ability to organize and filter the continuously growing amount of pathway information by allowing users to annotate pathways with ontology terms to provide a context. For example, when a pathway is annotated to be specific for the liver, it can easily be excluded from an analysis of an experiment in muscle. Ontology annotation also provides the possibility to hierarchically organize pathways, allowing the users to view biology from different levels of detail and for example analyze their dataset from very global (e.g. considering the whole metabolic state) to more detailed (e.g. considering only fatty acid metabolism).

4. Who is the team behind your website?
The most important contributors to the WikiPathways project are the researchers from the biology community who create and maintain pathway content, including groups of experts on a specific topic that provide and curate a subset of specialized pathways, such as the micronutrient community (http://micronutrients.wikipathways.org).

The code development of WikiPathways is done by members of Bruce Conklin’s lab at the UC San Francisco and Chris Evelo’s lab at Maastricht University. Since we work on an open-source basis, there are several other code contributors including Pankaj Jaiswal’s group from Oregon State University and several Google Summer of Code students.

Thanks to the WikiPathways team for registering their site as a BioGPS plugin, and for participating in our Spotlight series.


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