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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  
AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development  ...  Each section describes challenges and opportunities for these topics, along with recommendations and best practices.  ...  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

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P Ficklin, Ksenija Gasic, Kristin Scott, Morgan Frank, Sushan Ru (+11 others)
2018 Nucleic Acids Research  
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining  ...  Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView.  ...  and sharing Tripal modules and code, the AgBioData Consortium and US Land Grant Universities for support.  ... 
doi:10.1093/nar/gky1000 pmid:30357347 pmcid:PMC6324069 fatcat:mwwos4ljmnekvl4u6penvw2joa

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski (+8 others)
2021 Briefings in Bioinformatics  
least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data.  ...  databases, and support for implementing FAIR principles.  ...  of Agriculture.  ... 
doi:10.1093/bib/bbab238 pmid:34251419 pmcid:PMC8574961 fatcat:khqsm7dedrgupeu7h5iyaoi7wi

MaizeGDB 2018: the maize multi-genome genetics and genomics database

John L Portwood, Margaret R Woodhouse, Ethalinda K Cannon, Jack M Gardiner, Lisa C Harper, Mary L Schaeffer, Jesse R Walsh, Taner Z Sen, Kyoung Tak Cho, David A Schott, Bremen L Braun, Miranda Dietze (+9 others)
2018 Nucleic Acids Research  
Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly.  ...  Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding.  ...  We would like to give a special thank you to Ed Coe as not only the founder of the original Maize Genetics Database and continued contributor to the database, but also for his contribution to the generation  ... 
doi:10.1093/nar/gky1046 pmid:30407532 fatcat:4kigm7hldzfxpmy6zpwwxsqki4

CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, J. Todd Campbell, Josh Udall (+1 others)
2021 Plants  
Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools.  ...  CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community.  ...  AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database 2018, 2018, bay088. [CrossRef] [PubMed]  ... 
doi:10.3390/plants10122805 pmid:34961276 pmcid:PMC8705096 fatcat:52aawyzzavgvbfrvwfy54jlhyq

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  
We offer a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation  ...  Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications.  ...  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

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases

2019 Database: The Journal of Biological Databases and Curation  
These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades.  ...  Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement.  ...  Funding Tripal is developed by an international group of researchers and programmers. Conflict of interest. None declared.  ... 
doi:10.1093/database/baz077 pmid:31328773 pmcid:PMC6643302 fatcat:ybq2vbsqsngotlu4tubpqhjhem

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  
Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes.  ...  as the genomic data sampled for each individual.  ...  Related to species of agricultural interest, the AgBioData consortium, formed in 2015, represents more than 25 genetic, genomic, and breeding databases hosted in a range of platforms.  ... 
doi:10.1111/eva.12860 pmid:31892954 pmcid:PMC6935593 fatcat:r2zcwfc7irdgdln4faunycp3ui

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR)  ...  It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model  ...  Plant genome browser.  ... 
doi:10.1093/nar/gkz996 pmid:31680153 pmcid:PMC7145600 fatcat:ykzfjhf4hvgs7keopndswr5req

D1.11- Annual work plan for the fourth year [article]

ANSES
2021 Zenodo  
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database 1-32  Janssens D, Arahal DR, Bizet C et al (2010).  ...  We will follow recommendations established by the scientific community such as for instance the US AgBiodata consortium ( .  ... 
doi:10.5281/zenodo.4897080 fatcat:sle543ekvrhp5fitnkygqerg64

D1.15 Annual Work Plan for the fifth year

ANSES
2022 Zenodo  
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database 1-32  Janssens D, Arahal DR, Bizet C et al (2010).  ...  Mine databases of sequenced genomes for the occurrence of this transfer the genetic construct among clinically isolated Enterobacteriacea (with focus on E. coli, K. pneumoniae and S. enterica), and determine  ...  This task is for organising the hands-on in-silico workshops and liaising with task 1 for event planning and organisation.  ... 
doi:10.5281/zenodo.5906869 fatcat:uwpfsvsqazfqtim3ogffmdmvcu

Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database

Judi Walters, Kate Light, Nathan Robinson
2021 F1000Research  
This has given rise to an urgent need for robust metadata.  ...  Results: Our analyses showed that (i) OFT Trial Project metadata can be used as a dataset to detect trends in sowing date; and (ii) cropping research trials are being sown earlier in Victoria and Western  ...  Acknowledgements Online Farm Trials is a collaboration between the Grains Research and Development Corporation (GRDC) and the Centre for eResearch and Digital Innovation (CeRDI) at Federation University  ... 
doi:10.12688/f1000research.26903.2 fatcat:3brkbznuczfuzeq2iea6uxnmwq

Referee report. For: Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS) [version 1; peer review: 1 approved with reservations]

Runxuan Zhang
2020
In this paper, we present our experience, the challenges we faced, and the answer we brought for establishing an international research community to build an informational infrastructure.  ...  Our hope is that our experience with building wheatis.org will guide current and future research communities to facilitate institutional and international challenges to create global tools and resources  ...  We thank the Wheat Initiative led by Hélène Lucas, Peter Langridge and Frank Ordon that created a remarkable umbrella organization for WheatIS to thrive.  ... 
doi:10.5256/f1000research.25960.r64353 fatcat:u673jzfgtrbdpge2moitdm636e

Referee report. For: Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS) [version 1; peer review: 1 approved, 1 approved with reservations]

Stavros Makrodimitris
2021
In this paper, we present our experience, the challenges we faced, and the answer we brought for establishing an international research community to build an informational infrastructure.  ...  Our hope is that our experience with building wheatis.org will guide current and future research communities to facilitate institutional and international challenges to create global tools and resources  ...  We thank the Wheat Initiative led by Hélène Lucas, Peter Langridge and Frank Ordon that created a remarkable umbrella organization for WheatIS to thrive.  ... 
doi:10.5256/f1000research.25960.r79260 fatcat:x3pgklvutvfwrltq54jwxcrnku