Parikh Priti P, Zheng Jie, Logan-Klumpler Flora, Stoeckert Christian J, Louis Christos, Topalis Pantelis, Protasio Anna V, Sheth Amit P, Carrington Mark, Berriman Matthew, Sahoo Satya S
The Kno,e,sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA.
J Biomed Semantics. 2012 May 23;3(1):5. doi: 10.1186/2041-1480-3-5.
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.
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.
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.
许多真核病原体的基因组测序以及公共资源上可用的数据量，明确要求有一个一致的词汇表来描述寄生虫发育形式的范围。在数据库和文献中，对实验数据和外部数据进行一致的标注，对于数据整合、跨数据库比较和知识发现至关重要。这项工作的主要目标是开发一个可用于各种寄生虫的动态且可控的词汇表。本文描述了寄生虫生命周期本体（OPL）并讨论了其在寄生虫研究中的应用。
OPL基于基础形式本体（BFO）并遵循OBO铸造厂联盟设定的规则。OPL的第一个版本对一系列寄生虫的复杂生命周期阶段细节进行了建模，如锥虫属、利什曼原虫属、疟原虫属和血吸虫属。此外，该本体还对必要的背景细节进行了建模，如宿主信息、媒介信息和解剖位置。OPL主要设计用作寄生虫生命周期阶段的参考本体，可用于数据库注释目的，以及在实验室中用于数据整合或信息检索，如下文应用部分所示。
