WikiPathways: connecting communities

By Marvin Martens, A. Ammar, Anders Riutta, A. Waagmeester, D. Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, E. N. Lopes, F. Ehrhart and 7 more. Nucleic Acids Res., 2020

690 citations recorded by the source corpus.

Abstract WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/6a591983e1607035ac6da77367bb39ab1d861acf

How researchers see this paper

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In Molecular Biology

1. Li Zhan
2. Meijun Chen
3. Wenli Tang
4. Tianzhi Wu
5. Erqiang Hu
6. Zehan Dai
7. Shuangbing Xu
8. Tingze Feng

Citations in the corpus

• g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update) (2023, neutral): “…is further coupled with Human Phenotype Ontology ( 4 ), known annotations from pathway databases of KEGG ( 17 ), Re-actome ( 2 ) and WikiPathways ( 18 ), protein expression across tissues from Human Protein Atlas ( 19 ), CORUM ( 3 ) pr otein–pr otein interactions, and pr edicted r egulatory r…”
• Using clusterProfiler to characterize multiomics data (2024, neutral): “Notably, NCG focuses on gene-cancer associations, making it useful for researching gene roles in cancer development and progression • WikiPathways delivers manually curated information on biological pathways, making it ideal for studying gene functions in particular pathways or fields • Reactome Pat”
• clusterProfiler 4.0: A universal enrichment tool for interpreting omics data (2021, background): “27 There is an urgent need for integration and support of these databases.”