Ramona Lynn Walls, Laurel Cooper, Justin Lee Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Barry Smith, Dennis William Stevenson & Pankaj Jaiswal
Frontiers in Plant Science 10 (2019)
AbstractThe Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
Similar books and articles
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith & Others - 2013 - Plant and Cell Physiology 54 (2):1-23..
Ontologies as Integrative Tools for Plant Science.Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson - 2012 - American Journal of Botany 99 (8):1263–1275.
The Planteome Database: An Integrated Resource for Reference Ontologies, Plant Genomics and Phenomics.Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L. Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud & Pankaj Jaiswal - 2018 - Nucleic Acids Research 46 (D1):D1168–D1180.
The Plant Ontology: A Common Reference Ontology for Plants.L. Walls Ramona, D. Cooper Laurel, Elser Justin, W. Stevenson Dennis, Barry Smith, Mungall Chris, A. Gandolfo Maria & Jaiswal Pankaj - 2010 - In Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010.
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Cooper Laurel, Walls Ramona, L. Elser, Justin Gandolfo, A. Maria, Stevenson Dennis, W. Smith, Barry Preece, Justin Athreya, Balaji Mungall, J. Christopher, Rensing Stefan & Others - 2012 - Plant and Cell Physiology.
A Plant Disease Extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert & W. Stevenson Dennis - 2012 - In Proceedings of the Third International Conference on Biomedical Ontology (CEUR 897). pp. 1-5.
The Philosophy of Plant Neurobiology: A Manifesto.Paco Calvo - 2016 - Synthese 193 (5):1323-1343.
The Philosophy of Plant Neurobiology: A Manifesto.Paco Calvo - 2016 - Synthese 193 (5).
Genomics and the Intrinsic Value of Plants.Bart Gremmen - 2005 - Genomics, Society and Policy 1 (3):1-7.
Plant Succession and Tree Architecture: An Attempt at Reconciling Two Scales of Analysis of Vegetation Dynamics.Jeanne Millet, André Bouchard & Claude Édelin - 1998 - Acta Biotheoretica 46 (1):1-22.
The History of the Plant Embryo. Terminology and Visualization From Ancient Until Modern Times.Hans Werner Ingensiep - 2004 - History and Philosophy of the Life Sciences 26 (3/4):309 - 331.
'All Is Leaf'. Goethe's Plant Philosophy and Poetry.Ina Goy - 2019 - In Cécilia Bognon-Küss & Charles T. Wolfe (eds.), Philosophy of Biology Before Biology. Abingdon: Routledge. pp. 146-169.
An Herbiary of Plant Individuality.Sophie Gerber - 2018 - Philosophy, Theory, and Practice in Biology 10 (5):1-5.
On the Evolution of Egg Placement and Gregariousness of Caterpillars in the Lepidoptera.Allen M. Young - 1983 - Acta Biotheoretica 32 (1):43-60.
Added to PP
Historical graph of downloads