With the growth of ontologies used in diverse application areas, the need for module extraction and modularisation techniques has risen. The notion of the modular structure of an ontology, which comprises a suitable set of base modules together with their logical dependencies, has the potential to help users and developers in comprehending, sharing, and maintaining an ontology. We have developed a new modular structure, called atomic decomposition (AD), which is based on modules that provide strong logical properties, such as locality-based modules. In this article, we present the theoretical foundations of AD, review its logical and computational properties, discuss its suitability as a modular structure, and report on an experimental evaluation of AD. In addition, we discuss the concept of a modular structure in ontology engineering and provide a survey of existing decomposition approaches.

An ontology is a machine processable artifact that captures knowledge about some domain of interest. Ontologies are used in various domains including healthcare, science, and commerce. In this paper we examine the ontology bootstrapping problem. Specifically, we look at an approach that uses both competency questions and knowledge source reuse via recommendations to address the "cold start problem" that is, the task of creating an ontology from scratch. We describe this approach, an implementation of it, and we present an evaluation in the form of a controlled user study. We find that the approach leads users into creating significantly more detailed initial ontologies that have a greater domain coverage than ontologies produced without this support. Furthermore, in spite of a more involved workflow, the usability and user satisfaction of the bootstrapping approach is as good as a state-of-the-art ontology editor with no additional support.

We present a domain specific ontology editor for viewing, updating and managing a clinical documentation knowledge base. The editor is designed to allow clinical content specialists, who do not have a working knowledge of OWL, Semantic Web technologies or knowledge engineering, to quickly generate ontologies that describe clinical documentation templates along with rich bi-directional mappings between these documentation template ontologies and biomedical domain ontologies. While the editor has been designed and implemented for a specific use-case, many of the novel design choices are applicable to more traditional ontology editing environments. Furthermore, we believe that the workflow that is promoted by the editing environment and the partitioning and arrangement of the ontologies that are compiled by the editor are applicable to more general scenarios where two sets of ontologies corresponding to different application sub-domains need to be edited side-by-side and mapped between using a set of binding ontologies.

UNLABELLED: WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtégé also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtégé itself by configuring the project as an OBO project. AVAILABILITY AND IMPLEMENTATION: WebProtégé is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtégé is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege.

SUMMARY The increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in semantic data annotation and in the constriction of terminologies and ontologies used for annotation. The BioSharing community are developing standards and terminologies for annotation, which have been adopted across bioinformatics, but the real challenge is to make these standards accessible to laboratory scientists. Widespread adoption requires the provision of tools to assist scientists whilst reducing the complexities of working with semantics. This paper describes unobtrusive ‘stealthy’ methods for collecting standards compliant, semantically annotated data and for contributing to ontologies used for those annotations. Spreadsheets are ubiquitous in laboratory data management. Our spreadsheet‐based RightField tool enables scientists to structure information and select ontology terms for annotation within spreadsheets, producing high quality, consistent data without changing common working practices. Furthermore, our Populous spreadsheet tool proves effective for gathering domain knowledge in the form of Web Ontology Language (OWL) ontologies. Such a corpus of structured and semantically enriched knowledge can be extracted in Resource Description Framework (RDF), providing further means for searching across the content and contributing to Open Linked Data ( http://linkeddata.org/ ). Copyright © 2012 John Wiley & Sons, Ltd.

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. 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. We 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. 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.

MOTIVATION: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation. RESULTS: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is 'semantic annotation by stealth', with an annotation process that is less error-prone, more efficient, and more consistent with community standards. AVAILABILITY AND IMPLEMENTATION: RightField is open source under a BSD license and freely available from http://www.rightfield.org.uk