WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Author(s)
Denise N Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L Coort, Daniela Digles, Friederike Ehrhart, Pieter Giesbertz, Marianthi Kalafati, Marvin Martens, Ryan Miller, Kozo Nishida, Linda Rieswijk, Andra Waagmeester, Lars M T Eijssen, Chris T Evelo, Alexander R Pico, Egon L Willighagen
Abstract

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities.

Organisation(s)
Department of Pharmaceutical Chemistry
External organisation(s)
Maastricht University (UM), Gladstone Institutes, Technische Universität München, Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Suita, Osaka 565-0874, Japan., University of California, Berkeley, Micelio, Antwerp, Belgium.
Journal
Nucleic Acids Research
Volume
46
Pages
D661–D667
ISSN
0305-1048
DOI
https://doi.org/10.1093/nar/gkx1064
Publication date
11-2017
Peer reviewed
Yes
Austrian Fields of Science 2012
Bioinformatics
Keywords
Portal url
https://ucris.univie.ac.at/portal/en/publications/wikipathways-a-multifaceted-pathway-database-bridging-metabolomics-to-other-omics-research(a0b36227-6904-4cc6-8c2d-321e55873034).html