dictyBase 2026: a reimplementation of the Dictyostelium model organism database on minimal infrastructure

Dictyostelium discoideum is a model organism used to investigate a wide array of biological processes including chemotaxis, cell motility, phagocytosis, multicellular development, and autophagy. Many of its genes have human orthologs implicated in disease, making it a useful model organism for studying conditions ranging from cancer to neurodegeneration. dictyBase has served this community for two decades as a home for genomic data, protocols, a stock center, and community news. Here we describe a complete reimplementation of dictyBase as a self-contained service that uses static data files rather than a database server. Each gene record gathers curated function, human-disease context, developmental expression, and protein structure in a single webpage. The site also provides tools for sequence search, genome browsing, enrichment analysis, and experimental design. The complete Dicty Stock Center catalog of 7055 strains and 1265 plasmids is included, and both can be ordered from the site. New literature is curated by an author-in-the-loop pipeline. A language model drafts the annotations, the authors of the paper correct them, and a curator approves them. Analyses can be run on curator-approved annotations alone or extended to include those still awaiting review. dictyBase is freely available at https://dicty.org.

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Publication Details

Journal
Nucleic Acids Research
Published
2026-10-30
DOI
https://doi.org/10.1093/nar/gkag1077
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
0.00

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article

dictyBase 2026: a reimplementation of the Dictyostelium model organism database on minimal infrastructure

Rex L. Chisholm, Kenneth Matthew Scaglione, Siddhartha Basu, Robert J. Dodson et al.
Nucleic Acids Research
Genomics and Phylogenetic Studies
article

dictyBase 2026: a reimplementation of the Dictyostelium model organism database on minimal infrastructure

Rex L. Chisholm, Kenneth Matthew Scaglione, Siddhartha Basu, Robert J. Dodson, Maddox Mendieta
article en

Abstract

Dictyostelium discoideum is a model organism used to investigate a wide array of biological processes including chemotaxis, cell motility, phagocytosis, multicellular development, and autophagy. Many of its genes have human orthologs implicated in disease, making it a useful model organism for studying conditions ranging from cancer to neurodegeneration. dictyBase has served this community for two decades as a home for genomic data, protocols, a stock center, and community news. Here we describe a complete reimplementation of dictyBase as a self-contained service that uses static data files rather than a database server. Each gene record gathers curated function, human-disease context, developmental expression, and protein structure in a single webpage. The site also provides tools for sequence search, genome browsing, enrichment analysis, and experimental design. The complete Dicty Stock Center catalog of 7055 strains and 1265 plasmids is included, and both can be ordered from the site. New literature is curated by an author-in-the-loop pipeline. A language model drafts the annotations, the authors of the paper correct them, and a curator approves them. Analyses can be run on curator-approved annotations alone or extended to include those still awaiting review. dictyBase is freely available at https://dicty.org.

Nucleic Acids Research
Northwestern University (US), Duke University (US), Duke Medical Center (US), Northwestern Medicine (US)
National Institutes of Health, National Institute of General Medical Sciences
Openalex Percentile: Top 41%
Genomics and Phylogenetic Studies
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