2023
Thessen, A. E., Cooper, L., Swetnam, T. L., Hegde, H., Reese, J., Elser, J., & Jaiswal, P. (2023). Using knowledge graphs to infer gene expression in plants. Frontiers In Artificial Intelligence, 6, 1201002. https://doi.org/10.3389/frai.2023.1201002 (Original work published 2023)
Cooper, L., Elser, J., Laporte, M. -A., Arnaud, E., & Jaiswal, P. (2023). Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad1028 (Original work published 2023 Dec 06 C.E.)
Consortium, G. O., Aleksander, S. A., Balhoff, J., Carbon, S., Cherry, M., Drabkin, H. J., et al. (2023). The Gene Ontology knowledgebase in 2023. Genetics, 224(1). https://doi.org/10.1093/genetics/iyad031 (Original work published 2023 May 04 C.E.)
2022
Arnaud, E., Hazekamp, T., Laporte, M. -A., Antezana, E., Hernandez, A., Pot, D., et al. (2022). Crop Ontology Governance and Stewardship Framework. Retrieved de https://hdl.handle.net/10568/118001
2021
Consortium, T. G. O. (2021). The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research, 49(D1), D325 - D334. Retrieved de https://doi.org/10.1093/nar/gkaa1113 (Original work published 0 B.C.E.)
2020
Arnaud, E., Laporte, M. -A., Auber, C., Leonelli, S., Miro, B., Cooper, L., et al. (2020). The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. Patterns, 1(7). https://doi.org/10.1016/j.patter.2020.100105 (Original work published 2020)
Cooper, L., Laporte, M. -A., Elser, J. L., Blake, V. C., Sen, T. Z., Mungall, C., et al. (2020). The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics. ICBO 2020. Presented at the. Virtual: CEUR-WS.org. Retrieved de http://ceur-ws.org/Vol-2807/abstractT.pdf (Original work published 2020)
2019
Walls*, R. L., Cooper*, L. D., Elser, J. L., Gandolfo, M. A., Mungall, C. J., Smith, B., et al. (2019). The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. Frontiers In Plant Science, 10. https://doi.org/doi:10.3389/fpls.2019.00631 (Original work published In Press)
2018
Endara, L., Burleigh, G., Cooper, L., Jaiswal, P., Laporte, M. -A., & Cui, H. (2018). A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a Focus on Flagellate Plants. ICBO 2018. Presented at the. Corvallis, OR: CEUR. Retrieved de http://ceur-ws.org/Vol-2285/ICBO_2018_paper_50.pdf (Original work published 2018)
Meier, A., Laporte, M. -A., Elser, J., Cooper, L., Preece, J., Jaiswal, P., & Poelen, J. (2018). OOPS: The Ontology of Plant Stress, A semi-automated standardization methodology. ICBO 2018. Presented at the. Corvallis, OR: CEUR. Retrieved de http://ceur-ws.org/Vol-2285/ (Original work published 2018)
Stevenson, D., & -Cardona, Z. (2018). Plant Ontology to Gene Ontology and back. Current Plant Biology, 14. https://doi.org/10.1016/j.cpb.2018.09.009 (Original work published 2018)
Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., et al. (2018). AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture. Database, 2018(1). https://doi.org/https://doi.org/10.1093/database/bay088
Matentzoglu, N., Balhoff, J. P., Bello, S. M., Boerkoel, C., Bradford, Y. M., Carmody, L. C., et al. (2018). Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. In Zenodo. https://doi.org/ 10.5281/zenodo.2382757 (Original work published 2018)
Cooper, L., Meier, A., Laporte, M. -A., Elser, J. L., Mungall, C., Sinn, B. T., et al. (2018). The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx1152 (Original work published 11-2017 C.E.)
Stevenson, D. W., Li, N., Stevenson, D. W., & Griffith, P. (2018). Spines and Prickles. In Memoirs of The New York Botanical Garden (Vol. 117, pp. 54-65). NYBG Press. https://doi.org/ http://dx.doi.org/10.21135/893275389.005
Braun, I., Balhoff, J., Berardini, T. Z., Cooper, L. D., Gkoutos, G., Harper, L., et al. (2018). 'Computable' phenotypes enable comparative and predictive phenomics among plant species across domains of life. In Application of Semantic Technologies in Biodiversity Science (Vol. 33, pp. 187-205). Berlin: OS Press/AKA Verlag. https://doi.org/10.3233/978-1-61499-854-9-187
Trigkakis, D., Preece, J., Meier, A., Elser, J., Kvilekval, K., Fedorov, D., et al. (2018). Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks. 9th International Conference on Biological Ontology (ICBO 2018) . Presented at the. Corvallis, OR: CEUR-ws. Retrieved de http://ceur-ws.org/Vol-2285/ICBO_2018_paper_11.pdf (Original work published 2018)
2017
Meier, A., & Jaiswal, P. (2017). internal GO annotation.
Qu, B., Kumar, P., Zhang, E., Jaiswal, P., Cooper, L. D., Elser, J., & Zhang, Y. (2017). Interactive design and visualization of N-ary relationships. SIGGRAPH Asia 2017 Symposium on Visualization. Presented at the. Bangkok, Thailand: ACM digital. https://doi.org/10.1145/3139295.3139314 (Original work published 11-2017 C.E.)
Yeumo, E. D., Alaux, M., Arnaud, E., Aubin, S., Baumann, U., Buche, P., et al. (2017). Developing data interoperability using standards: A wheat community use case. F1000 Research, 6. Retrieved de https://f1000research.com/articles/6-1843/v1 (Original work published 2017)
2016
Laporte, M. -A., Valette, L., Cooper, L., Mungall, C., Meier, A., Jaiswal, P., & Arnaud, E. (2016). Comparison of ontology mapping techniques to map plant trait ontologies. ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion. Presented at the. Corvallis, Oregon, USA: CEUR Workshop Proceedings (CEUR-WS.org). Retrieved de http://ceur-ws.org/Vol-1747/IP17_ICBO2016.pdf (Original work published 2016ICBO-BioC C.E.)
Meier, A., Cooper, L., Laporte, M. -A., Elser, J., & Jaiswal, P. (2016). Annotating germplasm to Planteome reference ontologies. ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion. Presented at the. Corvallis, Oregon, USA: CEUR Workshop Proceedings (CEUR-WS.org). Retrieved de http://ceur-ws.org/Vol-1747/IT407_ICBO2016.pdf (Original work published 2016)
Qu, B., Diefenbaugh, J., Elser, J., Carbon, S., Mungall, C., Zhang, E., & Jaiswal, P. (2016). Planteome Gene Annotation Enrichment Analysis. ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion. Presented at the. Corvallis, Oregon, USA: CEUR Workshop Proceedings (CEUR-WS.org). Retrieved de http://ceur-ws.org/Vol-1747/IP31_ICBO2016.pdf (Original work published 2016)
Cooper, L., Meier, A., Elser, J. L., Laporte, M. -A., Preece, J., Carbon, S., et al. (2016). The Planteome Project. ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion. Presented at the. Corvallis, OR: CEUR Workshop Proceedings (CEUR-WS.org). Retrieved de http://ceur-ws.org/Vol-1747/IT406-IP35_ICBO2016.pdf (Original work published 2016)
Cooper, L. D., Jaiswal, P., & Edwards, D. (2016). The Plant Ontology: A Tool for Plant Genomics. In Plant Bioinformatics: Methods and Protocols (Vol. 1374). Retrieved de http://link.springer.com/protocol/10.1007/978-1-4939-3167-5_5
2015
Thessen, A. E., Bunker, D. E., Buttigieg, P. L., Cooper, L. D., Dahdul, W. M., Domisch, S., et al. (2015). Emerging semantics to link phenotype and environment. Peerj, 3(e1470). Retrieved de https://peerj.com/manuscripts/5750/ (Original work published 2015)
Oellrich, A., Walls, R. L., Cannon, E. K. S., Cannon, S. B., Cooper, L., Gardiner, J., et al. (2015). An ontology approach to comparative phenomics in plants. Plant Methods, 11, 10. https://doi.org/10.1186/s13007-015-0053-y (Original work published 2015)
Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., et al. (2015). Finding Our Way through Phenotypes. Plos Biol, 13, e1002033. https://doi.org/10.1371/journal.pbio.1002033 (Original work published 01 C.E.)
2014
Lingutla, N., Preece, J., Todorovic, S., Cooper, L., Moore, L., & Jaiswal, P. (2014). AISO: Annotation of Image Segments with Ontologies. Journal Of Biomedical Semantics, 5, 50. https://doi.org/10.1186/2041-1480-5-50
2013
Lingutla, N. T. V. (2013). Annotation of image segments with ontologies (AISO) (Oregon State University). Oregon State University, Corvallis. Retrieved de http://hdl.handle.net/1957/42883
Arighi, C. N., Carterette, B., Cohen, B., Krallinger, M., Wilbur, J., Fey, P., et al. (2013). An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database, 2013. Retrieved de http://database.oxfordjournals.org/content/2013/bas056.abstract (Original work published 2013)
Cooper, L., Walls, R. L., Elser, J., Gandolfo, M. A., Stevenson, D. W., Smith, B., et al. (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant & Cell Physiology, 54, 1-23. https://doi.org/10.1093/pcp/pcs163 (Original work published 2013 Feb C.E.)
2012
Consortium, G. O. (2012). The Gene Ontology: enhancements for 2011. Nucleic Acids Research, 40(Database issue), D559-64. https://doi.org/10.1093/nar/gkr1028 (Original work published 2012 Jan C.E.)
Walls, R., Smith, B., Elser, J., & Goldfain, A. (2012). A plant disease extension of the Infectious Disease Ontology. International Conference on Biomedical Ontology (ICBO-2012), 897. Graz, Austria: CEUR Workshop Proceedings. Retrieved de http://ceur-ws.org/Vol-897/ (Original work published July 2012)
Arnaud, E., Cooper, L., Shrestha, R., Menda, N., Nelson, R. T., Matteis, L., et al. (2012). Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotype. International Conference on Knowledge Discovery and Information Retrieval (IC3K2012). Presented at the. Barcelona, Spain. (Original work published 2012)
Lens, F., Cooper, L., Gandolfo, M. A., Groover, P., Jaiswal, P., Lachenbruch, R., et al. (2012). An extension of the Plant Ontology project supporting wood anatomy and development research. Iawa Journal, 33, 113-117. Retrieved de http://www.researchgate.net/publication/232271560_An_extension_of_the_Plant_Ontology_project_supporting_wood_anatomy_and_development_research
Walls, R. L., Cornet, R., Steven, R., Cooper, L. D., Macklin, J. A., Cui, H., et al. (2012). Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources. 3rd International Conference on Biomedical Ontology (ICBO 2012). Presented at the. Graz, Austria: KR-MED Series. Retrieved de http://ceur-ws.org/Vol-897/ (Original work published 2012)
Walls, R. L., Athreya, B., Cooper, L., Elser, J., Gandolfo, M. A., Jaiswal, P., et al. (2012). Ontologies as Integrative Tools for Plant Science. American Journal Of Botany, 99(8), 1263-75. https://doi.org/10.3732/ajb.1200222 (Original work published 2012 Aug C.E.)
Van Auken, K., Fey, P., Berardini, T. Z., Dodson, R., Cooper, L., Li, D., et al. (2012). Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database, 2012. Retrieved de http://database.oxfordjournals.org/content/2012/bas040.abstract (Original work published 2012)
2011
Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., et al. (2011). The genome of woodland strawberry (Fragaria vesca). Nat Genet, 43, 109 - 116. Retrieved de http://dx.doi.org/10.1038/ng.740 (Original work published 2011)
Preece, J., Elser, J., & Jaiswal, P. (2011). Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes. 4th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2011), 96-97. London, UK: ACM New York, NY. https://doi.org/10.1145/2166896.2166921 (Original work published Dec 7-9, 2011)
2010
Preece, J., Elser, J., & Jaiswal, P. (2010). A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species. NETTAB 2010 conference on Biological Wikis, 109-112. Naples, Italy: Aracne. Retrieved de http://www.nettab.org/2010/ (Original work published 2010)
2008
Ilic, K., Rhee, S. Y., Kellogg, E. A., Stevens, P. F., Burger, A., Davidson, D., & Baldock, R. (2008). Plant Structure Ontology (PSO) - A Morphological and Anatomical Ontology of Flowering Plants. In Anatomy Ontologies for Bioinformatics (Vol. 6, pp. 27-42). London: Springer. https://doi.org/10.1007/978-1-84628-885-2_2
Avraham, S., Tung, C. -W., Ilic, K., Jaiswal, P., Kellogg, E. A., McCouch, S., et al. (2008). The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research, 36, D449-54. https://doi.org/10.1093/nar/gkm908 (Original work published 2008 Jan C.E.)
2007
Ilic, K., Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent, L. P., et al. (2007). The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology, 143, 587-99. https://doi.org/10.1104/pp.106.092825 (Original work published 2007 Feb C.E.)
2006
Pujar, A., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, S., et al. (2006). Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology, 142, 414-28. https://doi.org/10.1104/pp.106.085720 (Original work published 2006 Oct C.E.)
2005
Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E. A., McCouch, S., Pujar, A., et al. (2005). Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comparative And Functional Genomics, 6, 388-97. https://doi.org/10.1002/cfg.496 (Original work published 2005)
2002
Consortium, P. O. (2002). The Plant Ontology™ Consortium and Plant Ontologies. Comparative And Functional Genomics, 3, 137-142. https://doi.org/10.1002 / cfg.154