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

Njobvu-AI: An open-source tool for collaborative image labeling and implementation of computer vision models. - Koning, Jonathan S.; Subramanian, Ashwin; Alotaibi, Mazen; Appel, Cara L.; Sullivan, Christopher M.; Chao, Thon; Truong, Lisa; Tanguay, Robyn L.; Jaiswal, Pankaj; Levi, Taal; Lesmeister, Damon B. (CoRR, 2023)

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

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

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

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

Ensembl Genomes 2020 - enabling non-vertebrate genomic research. - Howe, Kevin L.; Contreras-Moreira, Bruno; Silva, Nishadi De; Maslen, Gareth; Akanni, Wasiu A.; Allen, James E.; Álvarez-Jarreta, Jorge; Barba, Matthieu; Bolser, Dan M.; Cambell, Lahcen; Carbajo, Manuel; Chakiachvili, Marc; et al. (Nucleic Acids Res., 2020)

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. - Arnaud, Elizabeth; Laporte, Marie-Angélique; Kim, Soonho; Aubert, Céline; Leonelli, Sabina; Miro, Berta; Cooper, Laurel; Jaiswal, Pankaj; Kruseman, Gideon; Shrestha, Rosemary; Buttigieg, Pier Luigi; Mungall, Christopher J.; et al. (Patterns, 2020)

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

Involving community in genes and pathway curation. - Naithani, Sushma; Gupta, Parul; Preece, Justin; Garg, Priyanka; Fraser, Valerie; Padgitt-Cobb, Lillian K.; Martin, Matthew; Vining, Kelly; Jaiswal, Pankaj (Database J. Biol. Databases Curation, 2019)

Improving Publication Pipeline with Automated Biological Entity Detection and Validation Service. - Xu, Weijia; Gupta, Amit; Jaiswal, Pankaj; Taylor, Crispin; Lockhart, Patti; Regala, Jennifer (Data Inf. Manag., 2019)

Classification of Smart City Research - a Descriptive Literature Review and Future Research Agenda. - Gupta, Parul; Chauhan, Sumedha; Jaiswal, Pankaj (Inf. Syst. Frontiers, 2019)

Extracting Domain Information using Deep Learning. - Gupta, Amit; Xu, Weijia; Jaiswal, Pankaj; Taylor, Crispin; Regala, Jennifer (2019)

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. - Harper, Lisa C.; Campbell, Jacqueline D.; Cannon, Ethalinda K. S.; Jung, Sook; Poelchau, Monica; Walls, Ramona L.; Andorf, Carson M.; Arnaud, Elizabeth; Berardini, Tanya Z.; Birkett, Clayton L.; Cannon, Steven B.; Carson, James D.; et al. (Database J. Biol. Databases Curation, 2018)

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

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

Expression Atlas: gene and protein expression across multiple studies and organisms. - Papatheodorou, Irene; Fonseca, Nuno A.; Keays, Maria; Tang, Y. Amy; Barrera, Elisabet; Bazant, Wojciech; Burke, Melissa L.; Füllgrabe, Anja; Fuentes, Alfonso Muñoz-Pomer; George, Nancy; Huerta, Laura; Koskinen, Satu; et al. (Nucleic Acids Res., 2018)

A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate Plants. - Endara, Lorena; Burleigh, J. Gordon; Cooper, Laurel; Jaiswal, Pankaj; Laporte, Marie-Angélique; Cui, Hong (2018)

Domain Informational Vocabulary Extraction Experiences with Publication Pipeline Integration and Ontology Curation. - Gupta, Amit; Xu, Weijia; Jaiswal, Pankaj; Taylor, Crispin; Regala, Jennifer (2018)

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

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

'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of Life. - Braun, Ian; Balhoff, James P.; Berardini, Tanya Z.; Cooper, Laurel; Gkoutos, Georgios V.; Harper, Lisa C.; Huala, Eva; Jaiswal, Pankaj; Kazic, Toni; Lapp, Hilmar; Macklin, James A.; Specht, Chelsea D.; et al. (2018)

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA, August 7-10, 2018. (CEUR-WS.org, 2018)

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

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

Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. - Petryszak, Robert; Keays, Maria; Tang, Y. Amy; Fonseca, Nuno A.; Barrera, Elisabet; Burdett, Tony; Füllgrabe, Anja; Fuentes, Alfonso Muñoz-Pomer; Jupp, Simon; Koskinen, Satu; Mannion, Oliver; Huerta, Laura; et al. (Nucleic Acids Res., 2016)

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

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

Comparison of Ontology Mapping Techniques to Map Plant Trait Ontologies. - Laporte, Marie-Angélique; Valette, Léo; Cooper, Laurel; Mungall, Chris; Meier, Austin; Jaiswal, Pankaj; Arnaud, Elizabeth (2016)

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

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

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

Enhancing Information Accessibility of Publications with Text Mining and Ontology. - Xu, Weijia; Gupta, Amit; Jaiswal, Pankaj; Taylor, Crispin; Lockhart, Patti (2016)

A Web Application for Extracting Key Domain Information for Scientific Publications Using Ontology. - Xu, Weijia; Gupta, Amit; Jaiswal, Pankaj; Taylor, Crispin; Lockhart, Patti (2016)

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016. (CEUR-WS.org, 2016)

AISO: Annotation of Image Segments with Ontologies. - Lingutla, Nikhil; Preece, Justin; Todorovic, Sinisa; Cooper, Laurel; Moore, Laura; Jaiswal, Pankaj (J. Biomed. Semant., 2014)

Gramene 2013: comparative plant genomics resources. - Monaco, Marcela K.; Stein, Joshua C.; Naithani, Sushma; Wei, Sharon; Dharmawardhana, Palitha; Kumari, Sunita; Amarasinghe, Vindhya; Youens-Clark, Ken; Thomason, James; Preece, Justin; Pasternak, Shiran; Olson, Andrew; et al. (Nucleic Acids Res., 2014)

Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotypes. - Arnaud, Elizabeth; Cooper, Laurel; Shrestha, Rosemary; Menda, Naama; Nelson, Rex T.; Matteis, Luca; Skofic, Milko; Bastow, Ruth; Jaiswal, Pankaj; Mueller, Lukas A.; McLaren, Graham (2012)

Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources. - Walls, Ramona L.; Cui, Hong; Macklin, James A.; Mungall, Chris; Cooper, Laurel; Stevenson, Dennis W.; Jaiswal, Pankaj (2012)

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

QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. - Smita, Shuchi; Lenka, Sangram Keshari; Katiyar, Amit; Jaiswal, Pankaj; Preece, Justin; Bansal, Kailash Chander (Database J. Biol. Databases Curation, 2011)

Gramene database in 2010: updates and extensions. - Youens-Clark, Ken; Buckler, Edward S.; Casstevens, Terry M.; Chen, Charles; DeClerck, Genevieve; Derwent, Paul S.; Dharmawardhana, Palitha; Jaiswal, Pankaj; Kersey, Paul J.; Karthikeyan, A. S.; Lu, Jerry; McCouch, Susan; et al. (Nucleic Acids Res., 2011)

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

Gramene QTL database: development, content and applications. - Ni, Junjian; Pujar, Anuradha; Youens-Clark, Ken; Yap, Immanuel; Jaiswal, Pankaj; Tecle, Isaak Y.; Tung, Chih-Wei; Ren, Liya; Spooner, William; Wei, Xuehong; Avraham, Shuly; Ware, Doreen; et al. (Database J. Biol. Databases Curation, 2009)

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. - Avraham, Shulamit; Tung, Chih-Wei; Ilic, Katica; Jaiswal, Pankaj; Kellogg, Elizabeth A.; McCouch, Susan; Pujar, Anuradha; Reiser, Leonore; Rhee, Seung Yon; Sachs, Martin M.; Schaeffer, Mary L.; Stein, Lincoln; et al. (Nucleic Acids Res., 2008)

Gramene: a growing plant comparative genomics resource. - Liang, Chengzhi; Jaiswal, Pankaj; Hebbard, Claire; Avraham, Shuly; Buckler, Edward S.; Casstevens, Terry M.; Hurwitz, Bonnie L.; McCouch, Susan; Ni, Junjian; Pujar, Anuradha; Ravenscroft, Dean; Ren, Liya; et al. (Nucleic Acids Res., 2008)

Gramene: a bird's eye view of cereal genomes. - Jaiswal, Pankaj; Ni, Junjian; Yap, Immanuel; Ware, Doreen; Spooner, William; Youens-Clark, Ken; Ren, Liya; Liang, Chengzhi; Zhao, Wei; Ratnapu, Kiran; Faga, Benjamin; Canaran, Payan; et al. (Nucleic Acids Res., 2006)

Gramene: a resource for comparative grass genomics. - Ware, Doreen; Jaiswal, Pankaj; Ni, Junjian; Pan, Xiaokang; Chang, Kuan Y.; Clark, Kenneth; Teytelman, Leonid; Schmidt, Steven; Zhao, Wei; Cartinhour, Samuel; McCouch, Susan; Stein, Lincoln (Nucleic Acids Res., 2002)