MODOMICS is a comprehensive database for systems biology of RNA modification, integrating information on the chemical structure of modified nucleosides, their localization in RNA sequences, biosynthesis pathways, and the enzymes involved. The database includes literature references and links to other resources, with a focus on Escherichia coli and Saccharomyces cerevisiae. It offers querying options by nucleoside type, RNA type, reaction type, and enzyme name or sequence. Data presentation includes pathway graphs, multiple sequence alignments, and tabular forms. MODOMICS is accessible via the web at http://genesilico.pl/modomics/ and can be used for research purposes. The authors acknowledge contributions from various databases and funding sources.MODOMICS is a comprehensive database for systems biology of RNA modification, integrating information on the chemical structure of modified nucleosides, their localization in RNA sequences, biosynthesis pathways, and the enzymes involved. The database includes literature references and links to other resources, with a focus on Escherichia coli and Saccharomyces cerevisiae. It offers querying options by nucleoside type, RNA type, reaction type, and enzyme name or sequence. Data presentation includes pathway graphs, multiple sequence alignments, and tabular forms. MODOMICS is accessible via the web at http://genesilico.pl/modomics/ and can be used for research purposes. The authors acknowledge contributions from various databases and funding sources.