KNIT: Ontology reusability through knowledge graph exploration

Abstract

Ontologies have become a standard for knowledge representation across several domains. In Life Sciences, numerous ontologies have been introduced to represent human knowledge, often providing overlapping or conflicting perspectives. These ontologies are usually published as OWL or OBO, and are often registered in open repositories, e.g., BioPortal. However, the task of finding the concepts (classes and their properties) defined in the existing ontologies and the relationships between these concepts across different ontologies – for example, for developing a new ontology aligned with the existing ones – requires a great deal of manual effort in searching through the public repositories for candidate ontologies and their entities. In this work, we develop a new tool, KNIT, to automatically explore open repositories to help users fetch the previously designed concepts using keywords. User-specified keywords are then used to retrieve matching names of classes or properties. KNIT then creates a draft knowledge graph populated with the concepts and relationships retrieved from the existing ontologies. Furthermore, following the process of ontology learning, our tool refines this first draft of an ontology. We present three BioPortal-specific use cases for our tool. These use cases outline the development of new knowledge graphs and ontologies in the sub-domains of biology: genes and diseases, virome and drugs.