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The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L Elser, Chris Mungall, Brandon T Sinn, Dario Cavaliere, Seth Carbon, Nathan A Dunn, Barry Smith, Botong Qu, Justin Preece (+7 others)
2017 Nucleic Acids Research  
Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data.  ...  The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes.  ...  ACKNOWLEDGEMENTS We would like to thank all the collaborating databases and projects (listed in Tables 4 and 5 ) who contributed annotated data to the Planteome database and all the projects and genomics  ... 
doi:10.1093/nar/gkx1152 pmid:29186578 pmcid:PMC5753347 fatcat:7hbnerl4uvf47c6ikf2m3sm6se

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 (+5 others)
2016 International Conference on Biomedical Ontology  
The Planteome project (www.planteome.org) develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data.  ...  The project database and the online resources provide researchers tools to search and browse and access remotely via APIs for semantic integration in annotation tools and data repositories providing resources  ...  ACKNOWLEDGMENT Funding for the Planteome project is provided by the National Science Foundation award IOS #1340112  ... 
dblp:conf/icbo/CooperMEPXKQZTJ16 fatcat:nurcyvvylbaalod6qjjjtglf7m

Plant Molecular Biology Databases

Zubir Awan
2019 Highlights in BioScience  
We are here targeting to review and rank some of the plant databases according to their use and feature.  ...  Many of plant biological database comprises data from study fields including metabolomics, proteomics, genomics, microarray gene expression, and phylogenetic.  ...  Ontologies act as popular norms for the semantic integration of a wide and increasing body of plant phenomics, genomics, and genetic data.  ... 
doi:10.36462/h.biosci.20191 fatcat:56ptwcsu7ngqljfstdfgcrvu6i

Growing and cultivating the forest genomics database, TreeGenes

Taylor Falk, Nic Herndon, Emily Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M Baker, Risharde Ramnath, Stephen Ficklin, Margaret Staton, Frank A Feltus, Sook Jung (+2 others)
2018 Database: The Journal of Biological Databases and Curation  
The database provides a curated archive for high-throughput genomics, including reference genomes, transcriptomes, genetic maps and variant data.  ...  : Hardwood Genomics Web, Genome Database for Rosaceae, and the Citrus Genome Database.  ...  Acknowledgements We would like to thank the Computational Biology Core within the Institute of Systems Genomics at the University of Connecticut and The High Performance Computing Facility at the UConn  ... 
doi:10.1093/database/bay084 pmid:30239664 pmcid:PMC6146132 fatcat:o5a5wj5ylvdkdncttoebsk3ni4

Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment

Jill L. Wegrzyn, Margaret A. Staton, Nathaniel R. Street, Dorrie Main, Emily Grau, Nic Herndon, Sean Buehler, Taylor Falk, Sumaira Zaman, Risharde Ramnath, Peter Richter, Lang Sun (+6 others)
2019 Frontiers in Plant Science  
These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services.  ...  Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing  ...  All of these databases are also seeking stronger connections to more broadly plant focused repositories, such as Phytozome, PLAZA, and Planteome, that provide genetic and ontological resources that improve  ... 
doi:10.3389/fpls.2019.00813 pmid:31293610 pmcid:PMC6603172 fatcat:vpbwpe3sg5f3hmnzboiwaxanga

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
2018 Database: The Journal of Biological Databases and Curation  
Database URL: https://www.agbiodata.org CMO http://obofoundry.org/ontology/cmo.html Crop Ontology a collection of vocabularies that describe breeders' traits for agriculturally important plants: banana  ...  As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
doi:10.1093/database/bay088 pmid:30239679 pmcid:PMC6146126 fatcat:spcxmd66qrgdnos4larqfvf6ai

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees

Jill L Wegrzyn, Taylor Falk, Emily Grau, Sean Buehler, Risharde Ramnath, Nic Herndon
2019 Evolutionary Applications  
Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non-model plant species.  ...  These data contribute to forest tree biology, but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomic platforms  ...  Recent efforts, focused on high-throughout phenotyping, include GnpIS, which serves as a FAIR, international information resource for integrating phenomic, genomic, and metadata for plants and plant  ... 
doi:10.1111/eva.12860 pmid:31892954 pmcid:PMC6935593 fatcat:r2zcwfc7irdgdln4faunycp3ui

RTO, An Specific Crop Ontology for Rice Trait Concepts

Xinzhi Yao, Yun Liu, Qidong Deng, Yusha Liu, Xinchen Ma, Yufei Shen, Qianqian Peng, Zaiwen Feng, Jingbo Xia
2022 Zenodo  
Unfortunately, a standardization of rice trait ontology has been lacking, and make it challenging to normalize the description of lab results.  ...  To make it easier for concept query, a user-friendly web service is released via the link, http://lit-evi.hzau.edu.cn/RiceTraitOntology.  ...  ACKNOWLEDGEMENTS The authors expressed their gratitude for many instructive discussions with Dr. Claire Nédellec and Dr. Pierre Larmande.  ... 
doi:10.5281/zenodo.6950749 fatcat:t7wbu4s33zfizdqvixksvgeopi

Transforming the study of organisms: Phenomic data models and knowledge bases

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel (+1 others)
2020 PLoS Computational Biology  
The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their  ...  We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.  ...  Acknowledgments The authors would like to acknowledge the organizers and sponsors of the 2019 US2TS Conference held at Duke University who created space for this discussion.  ... 
doi:10.1371/journal.pcbi.1008376 pmid:33232313 pmcid:PMC7685442 fatcat:d36yhdezgnbblbj4sy62jiqw3m

Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS

C. Pommier, C. Michotey, G. Cornut, P. Roumet, E. Duchêne, R. Flores, A. Lebreton, M. Alaux, S. Durand, E. Kimmel, T. Letellier, G. Merceron (+8 others)
2019 Plant Phenomics  
It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying.  ...  GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures.  ...  We are grateful to the other members of the Phenome-Emphasis.fr information system team, including V. Negre, A. Tireau, and in particular P. Neveu, for continuous fruitful discussions.  ... 
doi:10.34133/2019/1671403 pmid:33313522 pmcid:PMC7718628 fatcat:rbvmsk4pa5ffbf2igc5b6x6gxu

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

Ramona L. Walls, Laurel Cooper, Justin Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Barry Smith, Dennis W. Stevenson, Pankaj Jaiswal
2019 Frontiers in Plant Science  
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of  ...  annotations from genomic and phenomic studies.  ...  ACKNOWLEDGMENTS We would like to thank all the collaborating databases and projects that have contributed annotated data to the Planteome database and all the genomics platforms that have adopted the Plant  ... 
doi:10.3389/fpls.2019.00631 pmid:31214208 pmcid:PMC6558174 fatcat:66ha5uhgunh4bl666zq7sniwqa

Improving Publication Pipeline with Automated Biological Entity Detection and Validation Service

Weijia Xu, Amit Gupta, Pankaj Jaiswal, Crispin Taylor, Patti Lockhart, Jennifer Regala
2019 Data and Information Management  
These extracted entities are then stored in a database and made accessible through an interactive web application for curation and evaluation by authors.  ...  In a pilot program, we have deployed the first phase of development as a service integrated with the journals Plant Physiology and The Plant cell published by the American Society of Plant Biologists (  ...  Acknowledgements: This research is partially supported by CyVerse (NSF awards DBI-0735191 and DBI-1265383) and Gramene, a comparative plant genomics database (NSF award IOS-1127112).  ... 
doi:10.2478/dim-2019-0003 fatcat:w4swautdkbefti3gfy4scsle5u

Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use

Gayle M. Volk, Patrick F. Byrne, Clarice J. Coyne, Sherry Flint-Garcia, Patrick A. Reeves, Chris Richards
2021 Plants  
Citing specific examples, we describe how well-documented genomic and phenomic data have met or could meet the needs of plant genetic resource managers and users.  ...  Technological advances have made it possible to collect phenomic and genomic data for genebank collections, which, with the appropriate analytical tools, can directly inform breeding programs.  ...  USDA is an equal opportunity provider and employer.  ... 
doi:10.3390/plants10112260 pmid:34834625 pmcid:PMC8619436 fatcat:egeuklfgkvdcva7f6msecn4zqu

WTO, an ontology for wheat traits and phenotypes in scientific publications

Claire Nédellec, Liliana Ibanescu, Robert Bossy, Pierre Sourdille
2020 Genomics & Informatics  
In this paper we propose the Wheat Trait Ontology (WTO) that is suitable for the extraction and management of scientific information from scientific papers, and its combination with data from genomic and  ...  The need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison.  ...  The author work at the 6th Biomedical Linked Annotation Hackathon (BLAH6) was supported by the Database Center for Life Science (DBCLS).  ... 
doi:10.5808/gi.2020.18.2.e14 pmid:32634868 fatcat:kccvjrbqwnetfcfj6irx54gipq

AgroPortal: A vocabulary and ontology repository for agronomy

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
2018 Computers and Electronics in Agriculture  
By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain.  ...  The AgroPortal project re-uses the biomedical domain's semantic tools and insights to serve agronomy, but also food, plant, and biodiversity sciences.  ...  We also thank the National Center for Biomedical Ontologies for their help and time spent with us in deploying the AgroPortal.  ... 
doi:10.1016/j.compag.2017.10.012 fatcat:tsvou7l42bg5hn6cw43ogtj2je
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