Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies

• Published in: Artificial intelligence in medicine Vol. 80; pp. 11 - 28
• Main Author: Lamy, Jean-Baptiste
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.07.2017; Elsevier
• Subjects: Artificial Intelligence; Automatic classification; Biological Ontologies; Biomedical ontology; Computer Science; Gene Ontology; Humans; Life Sciences; Local closed world reasoning; Ontology-oriented programming; OWL; Programming Languages; Santé publique et épidémiologie; Semantic web; Software; Semantic web; Automatic classification; Biomedical ontology; Local closed world reasoning; OWL; Ontology-oriented programming
• ISSN: 0933-3657; 1873-2860; 1873-2860
• DOI: 10.1016/j.artmed.2017.07.002

•OwlReady is an ontology-oriented programming module for Python.•It provides automatic classification and high level constructs inspired by medical ontologies.•It has a specific syntax for manipulating classes and role-filler constructs.•It supports some form of local closed world reasoning.•These features have been useful for reasoning on drug contraindications. Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated “role-filler” constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation.