Open Access Research

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms

Priti P Parikh1*, Jie Zheng2, Flora Logan-Klumpler34, Christian J Stoeckert2, Christos Louis5, Pantelis Topalis5, Anna V Protasio3, Amit P Sheth1, Mark Carrington4, Matthew Berriman3 and Satya S Sahoo16

Author Affiliations

1 The Kno.e.sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA

2 Center for Bioinformatics, Department of Genetics, University of Pennsylvania, 1420 Blockley Hall, 423 Guardian Drive, Philadelphia, Pennsylvania, 19104, USA

3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 ISA, UK

4 Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK

5 Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, and Dept. of Biology, University of Crete, 700 13, Heraklion, Crete, Greece

6 Division of Medical Informatics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA

For all author emails, please log on.

Journal of Biomedical Semantics 2012, 3:5  doi:10.1186/2041-1480-3-5

Published: 23 May 2012

Abstract

Background

Genome sequencing of many eukaryotic pathogens and the volume of data available on public resources have created a clear requirement for a consistent vocabulary to describe the range of developmental forms of parasites. Consistent labeling of experimental data and external data, in databases and the literature, is essential for integration, cross database comparison, and knowledge discovery. The primary objective of this work was to develop a dynamic and controlled vocabulary that can be used for various parasites. The paper describes the Ontology for Parasite Lifecycle (OPL) and discusses its application in parasite research.

Results

The OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. The first version of the OPL models complex life cycle stage details of a range of parasites, such as Trypanosoma sp., Leishmaniasp., Plasmodium sp., and Shicstosoma sp. In addition, the ontology also models necessary contextual details, such as host information, vector information, and anatomical locations. OPL is primarily designed to serve as a reference ontology for parasite life cycle stages that can be used for database annotation purposes and in the lab for data integration or information retrieval as exemplified in the application section below.

Conclusion

OPL is freely available at http://purl.obolibrary.org/obo/opl.owl webcite and has been submitted to the BioPortal site of NCBO and to the OBO Foundry. We believe that database and phenotype annotations using OPL will help run fundamental queries on databases to know more about gene functions and to find intervention targets for various parasites. The OPL is under continuous development and new parasites and/or terms are being added.