Abstract
BackgroundIt is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format.ResultsInspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s). The inputs of an Ontorat execution include axiom expression settings, an input data file, ID generation settings, and a target ontology (optional). The axiom expression settings can be saved as a predesigned Ontorat setting format text file for reuse. The input data file is generated based on a template file created by a specific ODP (text or Excel format). Ontorat is an efficient tool for ontology expansion. Different use cases are described. For example, Ontorat was applied to automatically generate over 1,000 Japan RIKEN cell line cell terms with both logical axioms and rich annotation axioms in the Cell Line Ontology (CLO). Approximately 800 licensed animal vaccines were represented and annotated in the Vaccine Ontology (VO) by Ontorat. The OBI team used Ontorat to add assay and device terms required by ENCODE project. Ontorat was also used to add missing annotations to all existing Biobank specific terms in the Biobank Ontology. A collection of ODPs and templates with examples are provided on the Ontorat website and can be reused to facilitate ontology development.ConclusionsWith ever increasing ontology development and applications, Ontorat provides a timely platform for generating and annotating a large number of ontology terms by following design patterns.Availability: http://ontorat.hegroup.org/
Highlights
It is time-consuming to build an ontology with many terms and axioms
Inspired by the Ontology Design Patterns (ODPs) theories and Ontology for Biomedical Investigations (OBI) project Quick Term Templates (QTTs) operation, we developed Ontorat, a web application with the aim to automatically generate a large number of new ontology classes or add additional axioms to existing classes for a specific target ontology
Overall design Based on the ODP concept and the Quick Term Templates (QTT) procedure, we developed an overall strategy of applying these mechanisms to ontology expansion (Figure 1)
Summary
It is time-consuming to build an ontology with many terms and axioms. it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format. Ontology development and updating in OWL format is often time consuming and requires specialized knowledge of ontology tools as well as specific scientific domains. An OWL format ontology includes a set of axioms that provides explicit logical assertions about three types of entities - classes, individuals and properties. As with software design patterns for software engineering, an Ontology Design Pattern (ODP) represents a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. ODPs can be represented using ontological axioms or graphic diagrams
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