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Publications and Presentations

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Author Type [ Year

]

2012

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.

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.

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.

R. Walls, Smith, B., Elser, J., and Goldfain, A., “A plant disease extension of the Infectious Disease Ontology”, in International Conference on Biomedical Ontology (ICBO-2012), Graz, Austria, 2012, vol. 897.

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.

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

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

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

K. Van Auken, Fey, P., Berardini, T. Z., Dodson, R., Cooper, L., Li, D., Chan, J., Li, Y., Basu, S., Muller, H. - M., Chisholm, R., Huala, E., and Sternberg, P. W., “Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR”, Database, vol. 2012, 2012.

E. Arnaud, Cooper, L., Shrestha, R., Menda, N., Nelson, R. T., Matteis, L., Skofic, M., Bastow, R., Jaiswal, P., Mueller, L., and McLaren, G., “Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotype”, in International Conference on Knowledge Discovery and Information Retrieval (IC3K2012), Barcelona, Spain, 2012.

2013

J. Preece, “AISO: Annotation of Image Segments using Ontologies”, Plant and Animal Genome XXI Conference. San Diego, CA, 2013.

N. T. V. Lingutla, “Annotation of image segments with ontologies (AISO)”, Oregon State University, Corvallis, 2013.

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

L. Cooper, “Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics”, Plant and Animal Genome XXI Conference. San Diego, CA, 2013.

C. N. Arighi, Carterette, B., Cohen, B. K., Krallinger, M., Wilbur, J. W., Fey, P., Dodson, R., Cooper, L., Van Slyke, C. E., Dahdul, W., Mabee, P., Li, D., Harris, B., Gillespie, M., Jimenez, S., Roberts, P., Matthews, L., Becker, K., Drabkin, H., Bello, S., Licata, L., Chatr-aryamontri, A., Schaeffer, M. L., Park, J., Haendel, M., Van Auken, K., Li, Y., Chan, J., Muller, H. - M., Cui, H., Balhoff, J. P., Chi-Yang Wu, J., Lu, Z., Wei, C. - H., Tudor, C. O., Raja, K., Subramani, S., Natarajan, J., Cejuela, J. M., Dubey, P., and Wu, C., “An overview of the BioCreative 2012 Workshop Track III: interactive text mining task”, Database, vol. 2013, 2013.

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

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.

P. Jaiswal, “A Resource for a Common Reference Ontology for Plants”, Plant and Animal Genome XXI Meeting. San Diego, CA, 2013.

E. Arnaud, “The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes”, Plant and Animal Genome XXI Conference. San Diego, CA, 2013.

2014

L. Cooper, “Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics”, Plant and Animal Genome XXII Meeting. San Diego, CA, 2014.

P. Jaiswal, “Plant Environmental Condition Ontology (EO)”, Fourth Annual Summit of the Phenotype Ontology Research Coordination Network. Phenotype Research Coordination Network, Biosphere2, Tucson, AZ, 2014.

L. Cooper, “The Plant Ontology and the Trait Ontology: Resources for Plant Genomics”, Workshop on Crop Ontology and Phenotyping Data Interoperability. Montpellier, France, 2014.

2015

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.

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