Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://www.wikipathways.org
Full name: WikiPathways
Description: WikiPathways is an open,public platform dedicated to the curation of biological pathways by and for the scientific community.
Year founded: 2011
Last update: 5/16/2015
Version: v1.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Netherlands
Data type:
Data object:
NA
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: Maastricht University
Address: Department of BioinformaticsÑBiGCaT,Maastricht University,Maastricht,The Netherlands
City: Maastricht
Province/State:
Country/Region: Netherlands
Contact name (PI/Team): Thomas Kelder
Contact email (PI/Helpdesk): thomaskelder@gmail.com

Publications

26481357
WikiPathways: capturing the full diversity of pathway knowledge. [PMID: 26481357]
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 (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies. We provide updates on extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio and Cytoscape, web applications and common programming environments. We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities. In addition to the latest milestones in our pathway collection and curation effort, we also highlight the latest means to access the content as publishable figures, as standard data files, and as linked data, including bulk and programmatic access. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 190 Citations (from Europe PMC, 2021-06-19)
27336457
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. [PMID: 27336457]
Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico AR.

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

PLoS Comput Biol. 2016:12(6) | 14 Citations (from Europe PMC, 2021-06-19)
22096230
WikiPathways: building research communities on biological pathways. [PMID: 22096230]
Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further.

Nucleic Acids Res. 2012:40(Database issue) | 269 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
183/5061 (96.404%)
Pathway:
11/349 (97.135%)
183
Total Rank
473
Citations
52.556
z-index

Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Record metadata

Created on: 2015-06-20
Curated by:
Shoaib Saleem [2019-11-13]
Lina Ma [2016-01-18]
lin liu [2016-01-17]
Hongyan Yin [2015-11-22]
Hongyan Yin [2015-06-26]