Planteome annotation wiki: a semantic application for the community curation of plant genotypes and phenotypes. - Justin Preece; Justin Elser; Pankaj Jaiswal (SWAT4LS, 2011)

A plant disease extension of the Infectious Disease Ontology. - Ramona L. Walls; Barry Smith 001; Justin Elser; Albert Goldfain; Dennis W. Stevenson; Pankaj Jaiswal (ICBO, 2012)

The Planteome Project. - Laurel Cooper; Austin Meier; Justin Elser; Justin Preece; Xu Xu; Ryan Kitchen; Botong Qu; Eugene Zhang; Sinisa Todorovic; Pankaj Jaiswal; Marie-Angélique Laporte; Elizabeth Arnaud; et al. (ICBO/BioCreative, 2016)

Annotating Germplasm to Planteome Reference Ontologies. - Austin Meier; Laurel Cooper; Justin Elser; Pankaj Jaiswal; Marie-Angélique Laporte (ICBO/BioCreative, 2016)

Plant Image Segmentation and Annotation with Ontologies in BisQue. - Justin Preece; Justin Elser; Pankaj Jaiswal; Kristian Kvilekval; Dmitry V. Fedorov; B. S. Manjunath; Ryan Kitchen; Xu Xu; Dmitrios Trigkakis; Sinisa Todorovic; Seth Carbon (ICBO/BioCreative, 2016)

Planteome Gene Annotation Enrichment Analysis. - Botong Qu; Jaden Diefenbaugh; Eugene Zhang; Justin Elser; Pankaj Jaiswal; Seth Carbon; Christopher J. Mungall (ICBO/BioCreative, 2016)

Gramene 2016: comparative plant genomics and pathway resources. - Marcela K. Tello-Ruiz; Joshua C. Stein; Sharon Wei; Justin Preece; Andrew Olson; Sushma Naithani; Vindhya Amarasinghe; Palitha Dharmawardhana; Yinping Jiao; Joseph Mulvaney; Sunita Kumari; Kapeel Chougule; et al. (Nucleic Acids Res., 2016)

Interactive design and visualization of N-ary relationships. - Botong Qu; Prashant Kumar; Eugene Zhang; Pankaj Jaiswal; Laurel Cooper; Justin Elser; Yue Zhang 009 (SIGGRAPH Asia Symposium on Visualization, 2017)

Plant Reactome: a resource for plant pathways and comparative analysis. - Sushma Naithani; Justin Preece; Peter D'Eustachio; Parul Gupta; Vindhya Amarasinghe; Palitha Dharmawardhana; Guanming Wu; Antonio Fabregat; Justin Elser; Joel Weiser; Maria Keays; Alfonso Muñoz-Pomer Fuentes; et al. (Nucleic Acids Res., 2017)

OOPS: The Ontology of Plant Stress, A Semi-Automated Standardization Methodology. - Austin Meier; Marie-Angélique Laporte; Justin Elser; Laurel Cooper; Justin Preece; Pankaj Jaiswal; Jorrit H. Poelen (ICBO, 2018)

Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks. - Dimitrios Trigkakis; Justin Preece; Austin Meier; Justin Elser; Kristian Kvilekval; Dmitry V. Fedorov; B. S. Manjunath; Pankaj Jaiswal; Sinisa Todorovic (ICBO, 2018)

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. - Laurel Cooper; Austin Meier; Marie-Angélique Laporte; Justin Elser; Chris Mungall; Brandon T. Sinn; Dario Cavaliere; Seth Carbon; Nathan A. Dunn; Barry Smith 001; Botong Qu; Justin Preece; et al. (Nucleic Acids Res., 2018)

Gramene 2018: unifying comparative genomics and pathway resources for plant research. - Marcela K. Tello-Ruiz; Sushma Naithani; Joshua C. Stein; Parul Gupta; Michael Campbell; Andrew Olson; Sharon Wei; Justin Preece; Matthew J. Geniza; Yinping Jiao; Young Koung Lee; Bo Wang 117; et al. (Nucleic Acids Res., 2018)

The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper). - Laurel Cooper; Marie-Angélique Laporte; Justin Elser; Victoria Carollo Blake; Taner Z. Sen; Chris Mungall; Elizabeth Arnaud; Pankaj Jaiswal (ICBO/ODLS, 2020)

Plant Reactome: a knowledgebase and resource for comparative pathway analysis. - Sushma Naithani; Parul Gupta; Justin Preece; Peter D'Eustachio; Justin Elser; Priyanka Garg; Daemon A. Dikeman; Jason Kiff; Justin Cook; Andrew Olson; Sharon Wei; Marcela K. Tello-Ruiz; et al. (Nucleic Acids Res., 2020)

The Gene Ontology resource: enriching a GOld mine. - Seth Carbon; Eric Douglass; Benjamin M. Good; Deepak R. Unni; Nomi L. Harris; Christopher J. Mungall; Siddartha Basu; Rex L. Chisholm; Robert J. Dodson; Eric Hartline; Petra Fey; Paul D. Thomas; et al. (Nucleic Acids Res., 2021)

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. - Marcela K. Tello-Ruiz; Sushma Naithani; Parul Gupta; Andrew Olson; Sharon Wei; Justin Preece; Yinping Jiao; Bo Wang 117; Kapeel Chougule; Priyanka Garg; Justin Elser; Sunita Kumari; et al. (Nucleic Acids Res., 2021)

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. - Andrew D. Yates; James E. Allen; M. Ridwan Amode; Andrey G. Azov; Matthieu Barba; Andrés Becerra; Jyothish Bhai; Lahcen I. Campbell; Manuel Carbajo Martinez; Marc Chakiachvili; Kapeel Chougule; Mikkel B. Christensen; et al. (Nucleic Acids Res., 2022)

Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. - Jennifer L. Clarke; Laurel D. Cooper; Monica F. Poelchau; Tanya Z. Berardini; Justin Elser; Andrew D. Farmer; Stephen P. Ficklin; Sunita Kumari; Marie-Angélique Laporte; Rex T. Nelson; Rie Sadohara; Peter Selby; et al. (Database J. Biol. Databases Curation, 2023)

Using knowledge graphs to infer gene expression in plants. - Anne E. Thessen; Laurel Cooper; Tyson L. Swetnam; Harshad Hegde; Justin T. Reese; Justin Elser; Pankaj Jaiswal (Frontiers Artif. Intell., 2023)