title: The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.
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.
  
  
  CONCLUSIONS
  OPL is freely available at http://purl.obolibrary.org/obo/opl.owl 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.
authors.affiliation: The Kno,e,sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA. priti@knoesis.org.
authors.forename: Priti P
authors.initials: PP
authors.lastname: Parikh
authors.forename: Jie
authors.initials: J
authors.lastname: Zheng
authors.forename: Flora
authors.initials: F
authors.lastname: Logan-Klumpler
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
authors.forename: Christos
authors.initials: C
authors.lastname: Louis
authors.forename: Pantelis
authors.initials: P
authors.lastname: Topalis
authors.forename: Anna V
authors.initials: AV
authors.lastname: Protasio
authors.forename: Amit P
authors.initials: AP
authors.lastname: Sheth
authors.forename: Mark
authors.initials: M
authors.lastname: Carrington
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.forename: Satya S
authors.initials: SS
authors.lastname: Sahoo