Showing papers by "Matthew Horridge published in 2011"
TL;DR: The OWL API is a high level Application Programming Interface (API) for working with OWL ontologies that supports parsing and rendering in the syntaxes defined in the W3C specification; manipulation of ontological structures; and the use of reasoning engines.
Abstract: We present the OWL API, a high level Application Programming Interface (API) for working with OWL ontologies. The OWL API is closely aligned with the OWL 2 structural specification. It supports parsing and rendering in the syntaxes defined in the W3C specification (Functional Syntax, RDF/XML, OWL/XML and the Manchester OWL Syntax); manipulation of ontological structures; and the use of reasoning engines. The reference implementation of the OWL API, written in Java, includes validators for the various OWL 2 profiles - OWL 2 QL, OWL 2 EL and OWL 2 RL. The OWL API has widespread usage in a variety of tools and applications.
792 citations
TL;DR: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets, enabling scientists to consistently annotate their data with 'semantic annotation by stealth'.
Abstract: 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
97 citations
TL;DR: 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.
Abstract: Background
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.
58 citations
23 Oct 2011
TL;DR: A simple cognitive complexity model is introduced and the results of validating that model via experiments involving OWL users are presented, based on test data derived from a large and diverse corpus of naturally occurring justifications.
Abstract: In this paper, we present an approach to determining the cognitive complexity of justifications for entailments of OWL ontologies. We introduce a simple cognitive complexity model and present the results of validating that model via experiments involving OWL users. The validation is based on test data derived from a large and diverse corpus of naturally occurring justifications. Our contributions include validation for the cognitive complexity model, new insights into justification complexity, a significant corpus with novel analyses of justifications suitable for experimentation, and an experimental protocol suitable for model validation and refinement.
52 citations
23 Oct 2011
TL;DR: The majority of ontologies contain multiple justifications, while also exhibiting structural features which can be exploited in order to reduce user effort in the ontology engineering process.
Abstract: Current ontology development tools offer debugging support by presenting justifications for entailments of OWL ontologies. While these minimal subsets have been shown to support debugging and understanding tasks, the occurrence of multiple justifications presents a significant cognitive challenge to users. In many cases even a single entailment may have many distinct justifications, and justifications for distinct entailments may be critically related. However, it is currently unknown how prevalent significant numbers of multiple justifications per entailment are in the field. To address this lack, we examine the justifications from an independently motivated corpus of actively used biomedical ontologies from the NCBO BioPortal. We find that the majority of ontologies contain multiple justifications, while also exhibiting structural features (such as patterns) which can be exploited in order to reduce user effort in the ontology engineering process.
22 citations
01 Jan 2011
TL;DR: Populous presents authors with a table-based form where columns are tied to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity.
Abstract: We present Populous, an open source application for gathering content for an ontology and populating that ontology en masse. Populous presents authors with a table-based form where columns are tied to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity. Populated tables are fed into templates that can then be used to generate the ontology’s axioms. Populous separates knowledge gathering from the conceptualisation; it also removes users from the usual ontology authoring tools. Availability: Download, source and video via http://www.e-lico.eu/ populous. Ontology building environments such as Protege and OBOEdit offer facilities for the manual authoring of axioms. Such tools are vital for capturing an ontology’s form. Many ontologies are, however, large with considerable portions formed of repetitions of the same pattern of axioms, varying only in the fillers within that pattern. To avoid the tedium and potential errors of doing this manually, templates can be filled and the axioms for the pattern generated, avoiding the manual authoring of many axioms. Populous [1] does this by presenting a familiar form-filling table-based user interface for any ontology authors to populate ontology patterns or templates. Rows are tied to the entities being described; columns are tied to properties and the cells constrained to take values from particular ontologies or fragments of an ontology. As an author fills out the template, he or she is guided to place appropriate values within the template. The content of this table can then be transformed into the axioms of the target ontology with an OWL scripting language. Populous is an extension of RightField,1 which is used for creating Excel documents that contain ontology based restrictions on a spreadsheet’s content. RightField is primarily designed for generating spreadsheet templates for data annotation; Populous extends RightField to support knowledge gathering and ontology generation. Populous and RightField are both open source, cross platform Java applications released under the BSD licence. They use the Apache-POI 2 for interacting with Microsoft documents and manipulating Excel spreadsheets. 1 http://www.rightfield.org.uk 2 http://poi.apache.org Both OWL and OBO ontologies can be uploaded into Populous. Users can also browse and load ontologies directly from BioPortal. Once the ontologies are loaded they are classified by a reasoner and the basic class hierarchy can be inspected. Terms can be selected from the ontology to create validation sets for values that are permitted for a particular selection of cells in the table. Labels from an ontology’s entities can be used within a cell, not just URI or URI fragments. Populous allows the addition of free text, even if the cell has an associated validation range; these values are highlighted in red and can act as placeholders for new or suggested terms when no suitable candidate can be found in the validation set. Populous supports the use of the Ontology Pre-Processor Language 3 (OPPL) patterns in order to generate new OWL axioms from the populated template. OPPL is an extension of Manchester OWL Syntax to select, add and remove axioms and it has an interpreter for scripts that manipulate the ontology. Variables from the OPPL pattern are mapped to columns from the table using the column name through the Populous pattern Wizard. We have used Populous with biologists to populate large portions of a kidney and urinary pathway ontology [2]. Populous is another piece in the ‘jigsaw’ of tools that support the ontology authoring process. It starts to fill the gap between the term request system and the manual axiom authoring systems by providing a mechanism for ‘filling out’ templates in such a way that they can be validated against the ontologies with which the ontology is being composed. We see Populous as a means for engaging domain experts who are not ontology experts in the authoring process and any ontology author to more effectively populate their ontology’s content. Acknowledgements: We acknowledge Mikel Egana Aranguren for his advice, requirements and testing of Populous. This work was funded by the e-LICO project— EU/FP7/ICT-2007.4.4 and by SysMO-DB BBSRC grant BBG0102181.
4 citations