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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.
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.
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.
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.
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.
2017
B. Qu, Kumar, P., Zhang, E., Jaiswal, P., Cooper, L. D., Elser, J., and Zhang, Y., “Interactive design and visualization of N-ary relationships”, in SIGGRAPH Asia 2017 Symposium on Visualization, Bangkok, Thailand, 2017.
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
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.
S. Lennon, Cooper, L., Jaiswal, P., Ougham, H., and Stevenson, D. W., “New Phytologist and the Plant Ontology: Working Together to Enhance Journal Content”. 2015.
A. Oellrich, Walls, R. L., Cannon, E. K. S., Cannon, S. B., Cooper, L., Gardiner, J., Gkoutos, G. V., Harper, L., He, M., Hoehndorf, R., Jaiswal, P., Kalberer, S. R., Lloyd, J. P., Meinke, D., Menda, N., Moore, L., Nelson, R. T., Pujar, A., Lawrence, C. J., and Huala, E., “An ontology approach to comparative phenomics in plants.”, Plant methods, vol. 11, p. 10, 2015.
L. Cooper, “Planteome Overview- DivSeek 2015”. 2015.
2014
N. Lingutla, Preece, J., Todorovic, S., Cooper, L., Moore, L., and Jaiswal, P., “AISO: Annotation of Image Segments with Ontologies”, Journal of Biomedical Semantics, vol. 5, p. 50, 2014.
L. Cooper, “Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics”. San Diego, CA, 2014.
P. Jaiswal, “Plant Environmental Condition Ontology (EO)”. Phenotype Research Coordination Network, Biosphere2, Tucson, AZ, 2014.

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Planteome by http://planteome.org is licensed under a Creative Commons Attribution 4.0 International License.
Based on a work at planteome.org.

Planteome is an international collaborative effort and is supported by primary funding (IOS:1340112 award) from the National Science Foundation of USA.