Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns

Journal of Biomedical Semantics

Yongqun He²  Yu Lin²  Jie Zheng¹  Zuoshuang Xiang² 

[1] University of Pennsylvania, Philadelphia, PA, USA;University of Michigan, Ann Arbor, MI, USA

关键词: Ontology development;    QTT;    Quick term templates;    ODP;    Ontology design pattern;    Ontorat;   

Others  :  1133342
DOI  :  10.1186/2041-1480-6-4

 received in 2014-10-20, accepted in 2014-12-25,  发布年份 2015

【 摘 要 】

Background

It 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.

Results

Inspired 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.

Conclusions

With 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/ webcite

【 授权许可】

   
2015 Xiang et al.; licensee BioMed Central.

【 图 表 】

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