WikiPathways: capturing the full diversity of pathway knowledge.
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.
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands martina.kutmon@maastrichtuniversity.nl.
Martina
M
Kutmon
Gladstone Institutes, San Francisco, California, CA 94158, USA.
Anders
http://orcid.org/0000-0002-4693-0591
A
Riutta
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Nuno
N
Nunes
Gladstone Institutes, San Francisco, California, CA 94158, USA.
Kristina
K
Hanspers
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Egon L
http://orcid.org/0000-0001-7542-0286
EL
Willighagen
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Anwesha
http://orcid.org/0000-0001-7073-5852
A
Bohler
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Jonathan
http://orcid.org/0000-0001-8624-2972
J
Mélius
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands Micelio, Antwerp, 2180 Antwerp, Belgium.
Andra
http://orcid.org/0000-0001-9773-4008
A
Waagmeester
Keshav Memorial Institute of Technology, Hyderabad, Telangana 500029, India.
Sravanthi R
http://orcid.org/0000-0002-4503-0401
SR
Sinha
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Ryan
http://orcid.org/0000-0003-3477-7443
R
Miller
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Susan L
http://orcid.org/0000-0003-1224-9690
SL
Coort
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Elisa
http://orcid.org/0000-0002-0241-7833
E
Cirillo
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Bart
http://orcid.org/0000-0001-6370-6965
B
Smeets
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands.
Chris T
CT
Evelo
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands apico@gladstone.ucsf.edu.
Alexander R
AR
Pico
D062126:Databases, Chemical; D020869:Gene Expression Profiling; D005796:Genes; D006801:Humans; D055432:Metabolomics; D008954:Models, Biological