Gramene: a resource for comparative grass genomics. - Doreen Ware; Pankaj Jaiswal; Junjian Ni; Xiaokang Pan; Kuan Y. Chang; Kenneth Clark; Leonid Teytelman; Steven Schmidt; Wei Zhao 005; Samuel Cartinhour; Susan McCouch; Lincoln Stein (Nucleic Acids Res., 2002)

Gramene: a bird's eye view of cereal genomes. - Pankaj Jaiswal; Junjian Ni; Immanuel Yap; Doreen Ware; William Spooner; Ken Youens-Clark; Liya Ren; Chengzhi Liang; Wei Zhao 005; Kiran Ratnapu; Benjamin Faga; Payan Canaran; et al. (Nucleic Acids Res., 2006)

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

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

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

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

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

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

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

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

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)

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

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

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)

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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)

Ensembl Genomes 2020 - enabling non-vertebrate genomic research. - Kevin L. Howe; Bruno Contreras-Moreira; Nishadi De Silva; Gareth Maslen; Wasiu A. Akanni; James E. Allen; Jorge Álvarez-Jarreta; Matthieu Barba; Dan M. Bolser; Lahcen Cambell; Manuel Carbajo; Marc Chakiachvili; et al. (Nucleic Acids Res., 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 Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. - Elizabeth Arnaud; Marie-Angélique Laporte; Soonho Kim; Céline Aubert; Sabina Leonelli; Berta Miro; Laurel Cooper; Pankaj Jaiswal; Gideon Kruseman; Rosemary Shrestha; Pier Luigi Buttigieg; Christopher J. Mungall; et al. (Patterns, 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)

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