WikiPathways 2024: Next Generation Pathway Database

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2023 Nov 9

PMID 37941138

Authors

Ayushi Agrawal

Hasan Balci

Kristina Hanspers

Susan L Coort

Marvin Martens

Denise N Slenter

Friederike Ehrhart

Daniela Digles

Andra Waagmeester

Isabel Wassink

Tooba Abbassi-Daloii

Elisson N Lopes

Aishwarya Iyer

Javier Millan Acosta

Lars G Willighagen

Kozo Nishida

Anders Riutta

Helena Basaric

Chris T Evelo

Egon L Willighagen

Martina Kutmon

Alexander R Pico

Affiliations

Soon will be listed here.

Abstract

WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight the continuing efforts supporting WikiPathways, content growth and collaboration among pathway researchers. As an evolving database, there is a growing need for WikiPathways to address and overcome technical challenges. In this direction, WikiPathways has undergone major restructuring, enabling a renewed approach for sharing and curating pathway knowledge, thus providing stability for the future of community pathway curation. The website has been redesigned to improve and enhance user experience. This next generation of WikiPathways continues to support existing features while improving maintainability of the database and facilitating community input by providing new functionality and leveraging automation.

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References

Martens M, Kreidl F, Ehrhart F, Jean D, Mei M, Mortensen H . A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. Front Oncol. 2022; 12:849640. PMC: 9088009. DOI: 10.3389/fonc.2022.849640. View

Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z . clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2021; 2(3):100141. PMC: 8454663. DOI: 10.1016/j.xinn.2021.100141. View

Jiang W, Peng Y, Yang K . Cellular signaling pathways regulating β-cell proliferation as a promising therapeutic target in the treatment of diabetes. Exp Ther Med. 2018; 16(4):3275-3285. PMC: 6143874. DOI: 10.3892/etm.2018.6603. View

Fang Z, Liu X, Peltz G . GSEApy: a comprehensive package for performing gene set enrichment analysis in Python. Bioinformatics. 2022; 39(1). PMC: 9805564. DOI: 10.1093/bioinformatics/btac757. View

Kutmon M, van Iersel M, Bohler A, Kelder T, Nunes N, Pico A . PathVisio 3: an extendable pathway analysis toolbox. PLoS Comput Biol. 2015; 11(2):e1004085. PMC: 4338111. DOI: 10.1371/journal.pcbi.1004085. View

Pillich R, Chen J, Churas C, Fong D, Gyori B, Ideker T . NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinformatics. 2023; 39(3). PMC: 10023220. DOI: 10.1093/bioinformatics/btad118. View

Maier A, Hartung M, Abovsky M, Adamowicz K, Bader G, Baier S . Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing. Nucleic Acids Res. 2024; 52(W1):W481-W488. PMC: 11223884. DOI: 10.1093/nar/gkae388. View

Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S . The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. Curr Protoc Bioinformatics. 2016; 54:1.30.1-1.30.33. DOI: 10.1002/cpbi.5. View

Kelder T, van Iersel M, Hanspers K, Kutmon M, Conklin B, Evelo C . WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2011; 40(Database issue):D1301-7. PMC: 3245032. DOI: 10.1093/nar/gkr1074. View

10.

Hanspers K, Riutta A, Summer-Kutmon M, Pico A . Pathway information extracted from 25 years of pathway figures. Genome Biol. 2020; 21(1):273. PMC: 7649569. DOI: 10.1186/s13059-020-02181-2. View

11.

Pillich R, Chen J, Rynkov V, Welker D, Pratt D . NDEx: A Community Resource for Sharing and Publishing of Biological Networks. Methods Mol Biol. 2017; 1558:271-301. DOI: 10.1007/978-1-4939-6783-4_13. View

12.

Rezwani M, Pourfathollah A, Noorbakhsh F . rbioapi: user-friendly R interface to biologic web services' API. Bioinformatics. 2022; 38(10):2952-2953. DOI: 10.1093/bioinformatics/btac172. View

13.

Kutmon M, Lotia S, Evelo C, Pico A . WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Res. 2014; 3:152. PMC: 4168754. DOI: 10.12688/f1000research.4254.2. View

14.

Pico A, Kelder T, van Iersel M, Hanspers K, Conklin B, Evelo C . WikiPathways: pathway editing for the people. PLoS Biol. 2008; 6(7):e184. PMC: 2475545. DOI: 10.1371/journal.pbio.0060184. View

15.

Braisted J, Patt A, Tindall C, Sheils T, Neyra J, Spencer K . RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes. Bioinformatics. 2022; 39(1). PMC: 9825745. DOI: 10.1093/bioinformatics/btac726. View

16.

Martens M, Ammar A, Riutta A, Waagmeester A, Slenter D, Hanspers K . WikiPathways: connecting communities. Nucleic Acids Res. 2020; 49(D1):D613-D621. PMC: 7779061. DOI: 10.1093/nar/gkaa1024. View

17.

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

18.

van Iersel M, Pico A, Kelder T, Gao J, Ho I, Hanspers K . The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics. 2010; 11:5. PMC: 2824678. DOI: 10.1186/1471-2105-11-5. View

19.

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A . COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021; 17(12):e10851. PMC: 8696085. DOI: 10.15252/msb.202110851. View

20.

Kuleshov M, Jones M, Rouillard A, Fernandez N, Duan Q, Wang Z . Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016; 44(W1):W90-7. PMC: 4987924. DOI: 10.1093/nar/gkw377. View