Abstract
BackgroundOntologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated. As more ontology based applications begin to emerge, tools are required that enable domain experts to contribute their knowledge to the growing pool of ontologies. There are many barriers that prevent domain experts engaging in the ontology development process and novel tools are needed to break down these barriers to engage a wider community of scientists.ResultsWe present Populous, a tool for gathering content with which to construct an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies. Populated tables are mapped to patterns that can then be used to automatically generate the ontology's content. These forms can be exported as spreadsheets, providing an interface that is much more familiar to many biologists.ConclusionsPopulous's contribution is in the knowledge gathering stage of ontology development; it separates knowledge gathering from the conceptualisation and axiomatisation, as well as separating the user from the standard ontology authoring environments. Populous is by no means a replacement for standard ontology editing tools, but instead provides a useful platform for engaging a wider community of scientists in the mass production of ontology content.
Highlights
Ontologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated
Populous’s contribution is in the knowledge gathering stage of ontology development; it separates knowledge gathering from the conceptualisation and axiomatisation, as well as separating the user from the standard ontology authoring environments
Populous is by no means a replacement for standard ontology editing tools, but instead provides a useful platform for engaging a wider community of scientists in the mass production of ontology content
Summary
Ontologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated. As more ontology based applications begin to emerge, tools are required that enable domain experts to contribute their knowledge to the growing pool of ontologies. The increasing quantity of bio-medical data being published in both the databases and the literature provides many challenges for bioinformatics analysis. Many bio-medical ontologies are under development to provide. There are many bio-medical ontologies that are well developed and in regular use across the discipline [1,4]. In this paper we present the Populous application that provides a framework within which domain experts can contribute their knowledge to a developing ontology. Populous uses a simple template based approach to ontology construction, but with semantic constraints that guide the filling of those templates; we exemplify its use in the development of an application ontology for the Kidney and Urinary Pathway (KUP) domain
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