An ontology approach to comparative phenomics in plants Public Deposited

http://ir.library.oregonstate.edu/concern/articles/jm214q64q

To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central Ltd. The published article can be found at:  http://www.plantmethods.com/. Supporting information can be found at:  http://www.plantmethods.com/content/11/1/10/additional.

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  • 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 Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes. CONCLUSIONS: The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics that enhances the utility of model genetic organisms and can be readily applied to species with fewer genetic resources and less well-characterized genomes. In addition, these tools should enhance future efforts to explore the relationships among phenotypic similarity, gene function, and sequence similarity in plants, and to make genotype-to-phenotype predictions relevant to plant biology, crop improvement, and potentially even human health.
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  • Oellrich, A., Walls, R. L., Cannon, E. K. S., Cannon, S. B., Cooper, L., Gardiner, J., ... & Huala, E. (2015). An ontology approach to comparative phenomics in plants. Plant Methods, 11, 10. doi:10.1186/s13007-015-0053-y
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  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2015-04-16T22:10:29Z No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) CooperLaurelBotanyPlantPathologyOntologyApproachComparative.pdf: 2155759 bytes, checksum: cd91fc44444d0803275199fe1d60e40d (MD5)
  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2015-04-16T22:10:43Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) CooperLaurelBotanyPlantPathologyOntologyApproachComparative.pdf: 2155759 bytes, checksum: cd91fc44444d0803275199fe1d60e40d (MD5)
  • description.provenance : Made available in DSpace on 2015-04-16T22:10:43Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) CooperLaurelBotanyPlantPathologyOntologyApproachComparative.pdf: 2155759 bytes, checksum: cd91fc44444d0803275199fe1d60e40d (MD5) Previous issue date: 2015-02-25

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