Leonidou, N.; Fritze, E.; Renz, A.; Dräger, A. SBOannotator: A Python Tool for the Automated Assignment of Systems Biology Ontology Terms. Bioinformatics 2023, doi:10.1093/bioinformatics/btad437.
Leonidou, N.; Fritze, E.; Renz, A.; Dräger, A. SBOannotator: A Python Tool for the Automated Assignment of Systems Biology Ontology Terms. Bioinformatics 2023, doi:10.1093/bioinformatics/btad437.
Leonidou, N.; Fritze, E.; Renz, A.; Dräger, A. SBOannotator: A Python Tool for the Automated Assignment of Systems Biology Ontology Terms. Bioinformatics 2023, doi:10.1093/bioinformatics/btad437.
Leonidou, N.; Fritze, E.; Renz, A.; Dräger, A. SBOannotator: A Python Tool for the Automated Assignment of Systems Biology Ontology Terms. Bioinformatics 2023, doi:10.1093/bioinformatics/btad437.
Abstract
The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and reproducible manner ischallenging. Using precisely defined ontologies enables the encoding of field-specific knowledge and the association of disparate data types. In computational modeling, the medium for representing domain knowledge is the set of orthogonal structured controlledvocabularies named Systems Biology Ontology (SBO). TheSBOterms enable modelers to explicitly define and unambiguously describe model entities, including their roles and characteristics. Here, we present the first standalone tool that automatically assignsSBOterms to multiple entities of a given SBML model, named the SBOannotator. The main focus lies on the reactions, as the correct assignment of preciseSBOannotations requires their extensive classification. Our implementation does not consider onlytop-level terms but examines the functionality of the underlying enzymes to allocate precise and highly specific ontology terms to biochemical reactions. Transport reactions are examined separately and are classified based on the mechanism of molecule transport.Pseudo-reactions that serve modeling purposes are given reasonable terms to distinguish between biomass production and the import or export of metabolites. Finally, other model entities, such as metabolites and genes, are annotated with appropriate terms.Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks.Availability:The open-source project SBOannotator is freely available under the terms ofLGPLversion 3.0 fromhttps://github.com/draeger-lab/SBOannotator/.
Computer Science and Mathematics, Computer Science
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
