Author:
Fisher Malcolm E.,Segerdell Erik,Matentzoglu Nicolas,Nenni Mardi J.,Fortriede Joshua D.,Chu Stanley,Pells Troy J.,Osumi-Sutherland David,Chaturvedi Praneet,James-Zorn Christina,Sundararaj Nivitha,Lotay Vaneet S.,Ponferrada Virgilio,Wang Dong Zhuo,Kim Eugene,Agalakov Sergei,Arshinoff Bradley I.,Karimi Kamran,Vize Peter D.,Zorn Aaron M.
Abstract
Abstract
Background
Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease.
Results
Here we present the Xenopus phenotype ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated.
Conclusions
The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype–phenotype data that can be directly related to other uPheno compliant resources.
Funder
Eunice Kennedy Shriver National Institute of Child Health and Human Development
National Human Genome Research Institute
Publisher
Springer Science and Business Media LLC
Subject
Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology
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