The reactome pathway knowledgebase 2022

By M. Gillespie, B. Jassal, Ralf Stephan, Marija Milacic, K. Rothfels, A. Senff-Ribeiro, J. Griss, Cristoffer Sevilla, L. Matthews, Chuqiao Gong and 25 more. Nucleic Acids Res., 2021

1,546 citations recorded by the source corpus.

Abstract The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes. The processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Recent curation work has expanded our annotations of normal and disease-associated signaling processes and of the drugs that target them, in particular infections caused by the SARS-CoV-1 and SARS-CoV-2 coronaviruses and the host response to infection. New tools support better simultaneous analysis of high-throughput data from multiple sources and the placement of understudied (‘dark’) proteins from analyzed datasets in the context of Reactome’s manually curated pathways.

Subfields: Computational Theory and Mathematics, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/dfc3df1eea66af990cd1731bb21111f2c2088467

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Citations in the corpus

The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest (2022, background): “The granularity of what constitutes a ‘common function’ is not formally defined; it should not be understood too broadly, however, and operationally it roughly corresponds to the specificity of pathways ‘maps’ or ‘diagrams’ in knowledgebases such as KEGG (31) or Reactome (32).”
JBrowse 2: a modular genome browser with views of synteny and structural variation (2022, background): “Examples of third-party plugins that can be installed include a multiple sequence alignment viewer, an ideogram viewer with Reactome [36] pathway visualization (Fig.”
Comparative Toxicogenomics Database (CTD): update 2023 (2022, background): “External integration of CTD content with imported annotations from the Gene Ontology (GO) (9), KEGG (10), Reactome (11) and BioGRID (12) produces an additional 13 million inferences.”
Best practices for single-cell analysis across modalities (2023, neutral): “3).”