SBOannotator: a Python tool for the automated assignment of systems biology ontology terms.

Journal: Bioinformatics (Oxford, England)
Published Date: Jul 1, 2023

Abstract

MOTIVATION: 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 is challenging. 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 controlled vocabularies named Systems Biology Ontology (SBO). The SBO terms enable modelers to explicitly define and describe model entities, including their roles and characteristics.

Authors

  • Nantia Leonidou
    Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, 72076 Tübingen, Germany.
  • Elisabeth Fritze
    Department of Computer Science, Eberhard Karl University of Tübingen, 72076 Tübingen, Germany.
  • Alina Renz
    Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, 72076 Tübingen, Germany.
  • Andreas Dräger
    Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.

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