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Peer-reviewedCC BY 4.0Nucleic Acids Research

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

  • Maddox J Mendieta1
  • Robert J Dodson2
  • Siddhartha Basu2
  • Rex L Chisholm2
  • K Matthew Scaglione1,3
  1. 1Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, NC 27710 ,
  2. 2Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University , Chicago, IL 60611 ,
  3. 3Department of Cell Biology, Duke University School of Medicine , Durham, NC 27710 ,
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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.

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Cite

BibTeXRIS
BibTeX
@article{mendieta2026dictybase,
  title = {{dictyBase 2026: a reimplementation of the Dictyostelium model organism database on minimal infrastructure}},
  author = {Maddox J Mendieta and Robert J Dodson and Siddhartha Basu and Rex L Chisholm and K Matthew Scaglione},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1077},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1077/9005081},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - dictyBase 2026: a reimplementation of the Dictyostelium model organism database on minimal infrastructure
AU  - Maddox J Mendieta
AU  - Robert J Dodson
AU  - Siddhartha Basu
AU  - Rex L Chisholm
AU  - K Matthew Scaglione
PY  - 2026
DA  - 2026/10/30
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1077
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1077/9005081
AB  - 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.
SN  - 0305-1048
SN  - 1362-4962
ER  -