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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.
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.
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.
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
E. D. Yeumo, Alaux, M., Arnaud, E., Aubin, S., Baumann, U., Buche, P., Cooper, L., Ćwiek-Kupczyńska, H., Davey, R. P., Fulss, R. A., Jonquet, C., Laporte, M. - A., Larmande, P., Pommier, C., Protonotarios, V., Reverte, C., Shrestha, R., Subirats, I., Venkatesan, A., Whan, A., and Quesneville, H., “Developing data interoperability using standards: A wheat community use case”, F1000 Research, vol. 6, 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.
P. Jaiswal, Cooper, L., Elser, J., Meier, A., and et al, “Planteome: A Resource for Common Reference Ontologies and Applications for Plant Biology”. 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
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.
L. Harper, Oellrich, A., Walls, R., Cannon, E., Cannon, S. B., Cooper, L., Gardiner, J., Gkoutos, G., He, M., Hoehndorf, R., and et al, “An Ontology Approach to Comparative Phenomics in Plants”. 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.
L. Cooper, “The Plant Ontology and the Trait Ontology: Resources for Plant Genomics”. Montpellier, France, 2014.
2013
E. Huala, “Development of a Unified Phenotype Dataset for Plants”. San Diego, CA, 2013.
L. Cooper, “Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics”. San Diego, CA, 2013.
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.
B. Atkinson, “Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines”, Botany 2013. New Orleans, LA, 2013.
L. Cooper and Walls, R. L., “The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses”, Plant & Cell Physiology, vol. 54, pp. 1-23, 2013.

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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.