A Highly Literate Approach to Ontology Building

TL;DR

This paper introduces a literate programming-inspired environment for ontology development, enabling simultaneous creation of textual descriptions and ontological structures, demonstrated through the Karyotype Ontology for human chromosomes.

Contribution

It presents a novel environment that integrates text and ontology development, improving expressivity and documentation in bio-medicine.

Findings

Enhanced expressivity of ontologies with rich textual descriptions

Successful documentation of the Karyotype Ontology

Discussion of advantages and challenges of the approach

Abstract

Ontologies present an attractive technology for describing bio-medicine, because they can be shared, and have rich computational properties. However, they lack the rich expressivity of English and fit poorly with the current scientific "publish or perish" model. While, there have been attempts to combine free text and ontologies, most of these perform \textit{post-hoc} annotation of text. In this paper, we introduce our new environment which borrows from literate programming, to allow an author to co-develop both text and ontological description. We are currently using this environment to document the Karyotype Ontology which allows rich descriptions of the chromosomal complement in humans. We explore some of the advantages and difficulties of this form of ontology development.