mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data. - Martin Larralde; Thomas N. Lawson; Ralf J. M. Weber; Pablo A. Moreno; Kenneth Haug; Philippe Rocca-Serra; Mark R. Viant; Christoph Steinbeck; Reza M. Salek (Bioinform., 2017)

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (Database J. Biol. Databases Curation, 2022)

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (CoRR, 2022)

Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. - Martin Larralde (J. Open Source Softw., 2022)

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. - Anthony Fullam; Ivica Letunic; Thomas S. B. Schmidt; Quinten R. Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn 004; Martin Larralde; Oleksandr M. Maistrenko; Lukas Malfertheiner; Alessio Milanese; João F. Matias Rodrigues; et al. (Nucleic Acids Res., 2023)

PyHMMER: a Python library binding to HMMER for efficient sequence analysis. - Martin Larralde; Georg Zeller (Bioinform., 2023)

Horned-OWL: Flying Further and Faster with Ontologies. - Phillip Lord; Björn Gehrke; Martin Larralde; Janna Hastings; Filippo De Bortoli; James A. Overton; James P. Balhoff; Jennifer D. Warrender (TGDK, 2024)

Horned-OWL. - Phillip Lord; Björn Gehrke; Martin Larralde; Janna Hastings; Filippo De Bortoli; James A. Overton; James P. Balhoff; Jennifer D. Warrender (DROPS Artifacts, 2024)