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Publications

Found 82 results
2023
S. A. Aleksander, Balhoff, J., Carbon, S., J Cherry, M., Drabkin, H. J., Ebert, D., Feuermann, M., Gaudet, P., Harris, N. L., Hill, D. P., Lee, R., Mi, H., Moxon, S., Mungall, C. J., Muruganugan, A., Mushayahama, T., Sternberg, P. W., Thomas, P. D., Van Auken, K., Ramsey, J., Siegele, D. A., Chisholm, R. L., Fey, P., Aspromonte, M. Cristina, Nugnes, M. Victoria, Quaglia, F., Tosatto, S., Giglio, M., Nadendla, S., Antonazzo, G., Attrill, H., Santos, G. Dos, Marygold, S., Strelets, V., Tabone, C. J., Thurmond, J., Zhou, P., Ahmed, S. H., Asanitthong, P., Buitrago, D. Luna, Erdol, M. N., Gage, M. C., Kadhum, M. Ali, Li, K. Yan Chloe, Long, M., Michalak, A., Pesala, A., Pritazahra, A., Saverimuttu, S. C. C., Su, R., Thurlow, K. E., Lovering, R. C., Logie, C., Oliferenko, S., Blake, J., Christie, K., Corbani, L., Dolan, M. E., Drabkin, H. J., Hill, D. P., Ni, L., Sitnikov, D., Smith, C., Cuzick, A., Seager, J., Cooper, L., Elser, J., Jaiswal, P., Gupta, P., Jaiswal, P., Naithani, S., Lera-Ramirez, M., Rutherford, K., Wood, V., De Pons, J. L., Dwinell, M. R., G Hayman, T., Kaldunski, M. L., Kwitek, A. E., Laulederkind, S. J. F., Tutaj, M. A., Vedi, M., Wang, S. - J., D'Eustachio, P., Aimo, L., Axelsen, K., Bridge, A., Hyka-Nouspikel, N., Morgat, A., Aleksander, S. A., J Cherry, M., Engel, S. R., Karra, K., Miyasato, S. R., Nash, R. S., Skrzypek, M. S., Weng, S., Wong, E. D., Bakker, E., Berardini, T. Z., Reiser, L., Auchincloss, A., Axelsen, K., Argoud-Puy, G., Blatter, M. - C., Boutet, E., Breuza, L., Bridge, A., Casals-Casas, C., Coudert, E., Estreicher, A., Famiglietti, M. Livia, Feuermann, M., Gos, A., Gruaz-Gumowski, N., Hulo, C., Hyka-Nouspikel, N., Jungo, F., Le Mercier, P., Lieberherr, D., Masson, P., Morgat, A., Pedruzzi, I., Pourcel, L., Poux, S., Rivoire, C., Sundaram, S., Bateman, A., Bowler-Barnett, E., Bye-A-Jee, H., Denny, P., Ignatchenko, A., Ishtiaq, R., Lock, A., Lussi, Y., Magrane, M., Martin, M. J., Orchard, S., Raposo, P., Speretta, E., Tyagi, N., Warner, K., Zaru, R., Diehl, A. D., Lee, R., Chan, J., Diamantakis, S., Raciti, D., Zarowiecki, M., Fisher, M., James-Zorn, C., Ponferrada, V., Zorn, A., Ramachandran, S., Ruzicka, L., and Westerfield, M., The Gene Ontology knowledgebase in 2023., Genetics, vol. 224, no. 1, 2023.
L. Cooper, Elser, J., Laporte, M. - A., Arnaud, E., and Jaiswal, P., Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology, Nucleic Acids Research, 2023.
A. E. Thessen, Cooper, L., Swetnam, T. L., Hegde, H., Reese, J., Elser, J., and Jaiswal, P., Using knowledge graphs to infer gene expression in plants, Frontiers in Artificial Intelligence, vol. 6, p. 1201002, 2023.
2021
The Gene Ontology Consortium, The Gene Ontology resource: enriching a GOld mine, Nucleic Acids Research, vol. 49, no. D1, pp. D325 - D334, 2021.
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.

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