An ontology approach to comparative phenomics in plants

作者：Anika Oellrich, Ramona Walls, Ethalinda K. S. Cannon, Steven B. Cannon, Laurel Cooper, Jack M. Gardiner, Georgios V. Gkoutos, Lisa Harper, Mingze He, Robert Hoehndorf, Pankaj Jaiswal, Scott R. Kalberer, John P. Lloyd, David W. Meinke, Naama Menda, Laura Moore, Rex T. Nelson, Anuradha Pujar, Carolyn J. Lawrence, Eva Huala · 发表于：Plant Methods · 年份：2015 · DOI：10.1186/s13007-015-0053-y · 被引用次数：67 · 研究领域：Biomedical Text Mining and Ontologies、Bioinformatics and Genomic Networks、Semantic Web and Ontologies

BACKGROUND: Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. RESULTS: We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait On...