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Publications and Presentations

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Journal Article

L. Cooper, Walls, R. L., Elser, J., Gandolfo, M. A., Stevenson, D. W., Smith, B., Preece, J., Athreya, B., Mungall, C. J., Rensing, S., Hiss, M., Lang, D., Reski, R., Berardini, T. Z., Li, D., Huala, E., Schaeffer, M., Menda, N., Arnaud, E., Shrestha, R., Yamazaki, Y., and Jaiswal, P., “The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses”, Plant & Cell Physiology, vol. 54, no. 2, pp. 1-23, 2013.

R. L. Walls, Athreya, B., Cooper, L., Elser, J., Gandolfo, M. A., Jaiswal, P., Mungall, C. J., Preece, J., Rensing, S., Smith, B., and Stevenson, D. W., “Ontologies as Integrative Tools for Plant Science”, American Journal of Botany, vol. 99, no. 8, pp. 1263-75, 2012.

A. R. Deans, Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, G. J., Chanet, B., Cooper, L. D., Courtot, M., Csösz, S., Cui, H., Dahdul, W., Das, S., Dececchi, A. T., Dettai, A., Diogo, R., Druzinsky, R. E., Dumontier, M., Franz, N. M., Friedrich, F., Gkoutos, G. V., Haendel, M., Harmon, L. J., Hayamizu, T. F., He, Y., Hines, H. M., Ibrahim, N., Jackson, L. M., Jaiswal, P., James-Zorn, C., Köhler, S., Lecointre, G., Lapp, H., Lawrence, C. J., Le Novère, N., Lundberg, J. G., Macklin, J., Mast, A. R., Midford, P. E., Mikó, I., Mungall, C. J., Oellrich, A., Osumi-Sutherland, D., Parkinson, H., Ramírez, M. J., Richter, S., Robinson, P. N., Ruttenberg, A., Schulz, K. S., Segerdell, E., Seltmann, K. C., Sharkey, M. J., Smith, A. D., Smith, B., Specht, C. D., Squires, B. R., Thacker, R. W., Thessen, A., Fernandez-Triana, J., Vihinen, M., Vize, P. D., Vogt, L., Wall, C. E., Walls, R. L., Westerfeld, M., Wharton, R. A., Wirkner, C. S., Woolley, J. B., Yoder, M. J., Zorn, A. M., and Mabee, P., “Finding Our Way through Phenotypes”, PLoS Biol, vol. 13, p. e1002033, 2015.

F. Lens, Cooper, L., Gandolfo, M. A., Groover, P., Jaiswal, P., Lachenbruch, R., Spicer, R., Staton, D., Stevenson, D. W., Walls, R. L., and Wegrzyn, J., “An extension of the Plant Ontology project supporting wood anatomy and development research”, IAWA Journal, vol. 33, pp. 113-117, 2012.

Conference Presentation

R. L. Walls, “Using the Plant Ontology to Link Anatomical Structures to Gene Annotations in Physcomitrella patens”, Moss 2011. Black Forest, Germany, 2011.

R. L. Walls, “Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets”, Plant Genomes & Biotechnology: from Genes to Networks. Cold Spring Harbor Laboratory, New York, 2011.

L. D. Cooper, “The Plant Ontology: Linking Genomic and Phenomic Data Across Plant Taxa”, Plant and Animal Genome XX Conference. San Diego, CA, 2012.

R. L. Walls, “The Plant Ontology: an updated tool for all plant biologists”, International Botanical Congress (IBC2011). Melbourne, Australia, 2011.

R. L. Walls, “The Plant Ontology: a tool for structural, developmental, and molecular plant biologists”, Botany 2010. Providence, RI, 2010.

R. L. Walls, “The Plant Ontology: A Common Reference Ontology for Plants”, Bio-Ontologies 2010: Semantic Applications in Life Sciences. Boston, MA, 2010.

L. D. Cooper, “Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa”, Plant and Animal Genome XX Conference. San Diego, CA, 2012.

P. Jaiswal, “Annotating the Maize B73 Gene Expression Atlas in the Plant Ontology- A Tool for Plant Genomics.”, 54th Annual Maize Genetics Conference. Portland, OR, 2012.

L. D. Cooper, “Annotating Gene Expression in Physcomitrella patens using the Plant Ontology: Facilitating Cross-Taxa Comparisons”, Plant and Animal Genome XX Conference. San Diego, CA, 2012.

Conference Poster

L. Cooper, “The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa”, Plant Biology 2012. Austin, Tx, 2012.

J. Preece, “The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa”, Genome Informatics 2012. Robinson College, Cambridge, UK, 2012.

B. Atkinson, “Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines”, Botany 2013. New Orleans, LA, 2013.

E. Huala, “Development of a Unified Phenotype Dataset for Plants”, Plant and Animal Genome 2013. San Diego, CA, 2013.

L. D. Cooper, “Annotating the Maize B73 Gene Expression Atlas – A Plant Ontology Use Case for Genomics Data Curation”, Biocuration 2012. Washington DC, USA, 2012.

Conference Paper

R. L. Walls, “Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources”, in 3rd International Conference on Biomedical Ontology (ICBO 2012), Graz, Austria, 2012.