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Conference Paper

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.

Conference Poster

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.

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

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.

J. L. Elser, “Plant Ontology: Databases And Applications”, Plant & Animal Genomes XVIII Conference. San Diego, CA, 2010.

Conference Presentation

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. 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: A Database for Plant Genomics”, Plant Biology 2010. Quebec, Montreal, Canada, 2010.

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

J. L. Elser, “Plant Ontology: Databases And Applications”, Plant & Animal Genomes XVIII Conference. San Diego, CA, 2010.

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.

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.

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

Journal Article

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, 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.

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.

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.

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.