You are here

Publications

Found 77 results
2018
L. Harper, Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C. G., Farmer, A., Ficklin, S. P., Grant, D., Grau, E., Herndon, N., Hu, Z. - L., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M. - A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C. J., Munoz-Torres, M. C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L. - A., Sen, T. Z., Staton, M., Subramaniam, S., Tello-Ruiz, M. K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J., and Main, D., AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture, Database, vol. 2018, no. 1, 2018.
I. Braun, Balhoff, J., Berardini, T. Z., Cooper, L. D., Gkoutos, G., Harper, L., Huala, E., Jaiswal, P., Kazic, T., Lapp, H., Macklin, J. A., Specht, C. D., Vision, T. J., Walls, R. L., and Lawerence-Dill, C. J., 'Computable' phenotypes enable comparative and predictive phenomics among plant species across domains of life, in Application of Semantic Technologies in Biodiversity Science, vol. 33, A. E. Thessen, Ed. Berlin: OS Press/AKA Verlag, 2018, pp. 187-205.
L. Endara, Burleigh, G., Cooper, L., Jaiswal, P., Laporte, M. - A., and Cui, H., A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a Focus on Flagellate Plants, in ICBO 2018, Corvallis, OR, 2018.
A. Meier, Laporte, M. - A., Elser, J., Cooper, L., Preece, J., Jaiswal, P., and Poelen, J., OOPS: The Ontology of Plant Stress, A semi-automated standardization methodology, in ICBO 2018, Corvallis, OR, 2018.
N. Matentzoglu, Balhoff, J. P., Bello, S. M., Boerkoel, C., Bradford, Y. M., Carmody, L. C., Cooper, L. D., Grove, C. A., Harris, N. L., Köhler, S., Laporte, M. - A., Laulederkind, S. L. F., Lee, R., Mazandu, G. K., McMurry, J. A., Mungall, C., Osumi-Sutherland, D., Pilgrim, C., Rageth, K., Robb, S. M. C., Robinson, P. N., Segerdell, E., Thessen, A., Vasilevsky, N., Zhang, X. A., and Haendel, M. A., Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species, 2018.
D. Stevenson and Zumajo-Cardona, Plant Ontology to Gene Ontology and back, Current Plant Biology, vol. 14, 2018.
D. Trigkakis, Preece, J., Meier, A., Elser, J., Kvilekval, K., Fedorov, D., Manjunath, B. S., Jaiswal, P., and Todorovic, S., Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks, in 9th International Conference on Biological Ontology (ICBO 2018) , Corvallis, OR, 2018.
L. Cooper, Meier, A., Laporte, M. - A., Elser, J. L., Mungall, C., Sinn, B. T., Cavaliere, D., Dunn, N. A., Smith, B., Qu, B., Preece, J., Zhang, E., Todorovic, S., Gkoutos, G., Doonan, J., Stevenson, D. W., Arnaud, E., and Jaiswal, P., The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics, Nucleic Acids Research, 2018.
L. Cooper and Jaiswal, P., The Planteome Project- Reference Ontologies for Data Integration. 2018.
D. W. Stevenson, Spines and Prickles, in Memoirs of The New York Botanical Garden, vol. 117, N. Li, Stevenson, D. W., and Griffith, P. M., Eds. NYBG Press, 2018, pp. 54-65.
2016
A. Meier, Cooper, L., Laporte, M. A. -, Elser, J., and Jaiswal, P., Annotating germplasm to Planteome reference ontologies, in ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion, Corvallis, Oregon, USA, 2016.
M. - A. Laporte, Valette, Léo, Cooper, L., Mungall, C., Meier, A., Jaiswal, P., and Arnaud, E., Comparison of ontology mapping techniques to map plant trait ontologies, in ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion, Corvallis, Oregon, USA, 2016.
L. D. Cooper and Jaiswal, P., The Plant Ontology: A Tool for Plant Genomics, in Plant Bioinformatics: Methods and Protocols, vol. 1374, D. Edwards, Ed. 2016.
P. Jaiswal, Cooper, L., Elser, J., Meier, A., and et al, Planteome: A Resource for Common Reference Ontologies and Applications for Plant Biology. 2016.
B. Qu, Diefenbaugh, J., Elser, J., Carbon, S., Mungall, C., Zhang, E., and Jaiswal, P., Planteome Gene Annotation Enrichment Analysis, in ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion, Corvallis, Oregon, USA, 2016.
L. Cooper, Meier, A., Elser, J. L., Laporte, M. - A., Preece, J., Carbon, S., Xu, X., Kitchen, R. S., Qu, B., Zhang, E., Todorovic, S., Smith, B., Gkoutos, G., Doonan, J., Stevenson, D. W., Arnaud, E., Mungall, C., and Jaiswal, P., The Planteome Project, in ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion, Corvallis, OR, 2016.
2015
L. D. Cooper, Curating Maize Diversity: Plant Trait Ontology Annotations for GWAS and QTL Data. 2015.
A. E. Thessen, Bunker, D. E., Buttigieg, P. L., Cooper, L. D., Dahdul, W. M., Domisch, S., Franz, N. M., Jaiswal, P., Lawrence-Dill, C. J., Midford, P. E., Mungall, C. J., Ramírez, M. J., Specht, C. D., Vogt, L., Vos, R. A., Walls, R. L., White, J. W., Zhang, G., Deans, A. R., Huala, E., Lewis, S. E., and Mabee, P. M., Emerging semantics to link phenotype and environment, PeerJ, vol. 3, no. e1470, 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.

Pages