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Publications and Presentations

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Author [ Type(Desc)] Year
Conference Presentation
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: an updated tool for all plant biologists, International Botanical Congress (IBC2011). Melbourne, Australia, 2011.
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.
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.
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.
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.
V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. C., Celton, J. - M., Rees, J. D. G., Williams, K. P., Holt, S. H., Rojas, J. J. R., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. L., Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., The genome of woodland strawberry (Fragaria vesca), Nat Genet, vol. 43, pp. 109 - 116, 2011.
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.
S. Avraham, Tung, C. - W., Ilic, K., Jaiswal, P., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Zapata, F., and Ware, D., The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations, Nucleic Acids Research, vol. 36, pp. D449-54, 2008.
P. Jaiswal, Avraham, S., Ilic, K., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Ware, D., and Zapata, F., Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages, Comparative and Functional Genomics, vol. 6, no. 7-8, pp. 388-97, 2005.
P. O. Consortium, The Plant Ontology™ Consortium and Plant Ontologies, Comparative and Functional Genomics, vol. 3, no. 2, pp. 137-142, 2002.
K. Ilic, Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent, L. P., Avraham, S., Reiser, L., Pujar, A., Sachs, M. M., Whitman, N. T., McCouch, S. R., Schaeffer, M. L., Ware, D. H., Stein, L. D., and Rhee, S. Y., The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant, Plant Physiology, vol. 143, no. 2, pp. 587-99, 2007.
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.
A. Pujar, Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, S., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Ware, D., and McCouch, S., Whole-plant growth stage ontology for angiosperms and its application in plant biology, Plant Physiology, vol. 142, no. 2, pp. 414-28, 2006.

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