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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  
Tripal is a mature, open source platform built to meet this need.  ...  least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data.  ...  Data availability statement Tripal is open source software provided under the GNU General Public License v2.0 and can be found at https://githu b.com/tripal/tripal. .  ... 
doi:10.1093/bib/bbab238 pmid:34251419 pmcid:PMC8574961 fatcat:khqsm7dedrgupeu7h5iyaoi7wi

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  
The organism databases of today are no longer simply catalogs or containers of genetic information.  ...  These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments.  ...  The databases described here are leveraging larger open-source projects as their base framework and sharing web-based applications for common functionality, such as genome browsing and sequence similarity  ... 
doi:10.3389/fpls.2019.00813 pmid:31293610 pmcid:PMC6603172 fatcat:vpbwpe3sg5f3hmnzboiwaxanga

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

2019 Database: The Journal of Biological Databases and Curation  
The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases.  ...  These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades.  ...  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

Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family

Sudhansu Dash, Jacqueline D. Campbell, Ethalinda K.S. Cannon, Alan M. Cleary, Wei Huang, Scott R. Kalberer, Vijay Karingula, Alex G. Rice, Jugpreet Singh, Pooja E. Umale, Nathan T. Weeks, Andrew P. Wilkey (+2 others)
2015 Nucleic Acids Research  
LIS provides access to genetic and genomic information for major crop and model legumes.  ...  To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by  ...  ACKNOWLEDGEMENTS We would like to thank the many developers of GMOD components used at LIS, particularly including Stephen Ficklin, Lacey Sanderson and Dorrie Main for Tripal, and developers of the Legume  ... 
doi:10.1093/nar/gkv1159 pmid:26546515 pmcid:PMC4702835 fatcat:2cxwekkuu5dxfn6sylkfb75z7i

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  
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  ...  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  ...  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

Wheatgene: a genomics database for common wheat and its related species

Diego F. Garcia, Zhengyu Wang, Jiantao Guan, Lingjie Yin, Shuaifeng Geng, Aili Li, Long Mao
2021 Crop Journal  
Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries.  ...  Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information  ...  Acknowledgments Appendix A. Supplementary data Supplementary data for this article can be found online at http://doi.org/10.1016/j.cj.2020.xx.xxx.  ... 
doi:10.1016/j.cj.2021.04.011 fatcat:vldc7glrmbdtviscpafkdcgx2e

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics

Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei (+2 others)
2020 Horticulture Research  
Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.  ...  To efficiently store, analyze, integrate, and disseminate these large-scale datasets to the research community, we constructed the Kiwifruit Genome Database (KGD; http://kiwifruitgenome.org/).  ...  Acknowledgements This study was supported by grants from the National Natural Science Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1038/s41438-020-0338-9 pmid:32821400 pmcid:PMC7395147 fatcat:hrkefpgi2vdgdpv233fuqse75q

ZEAMAP, a comprehensive database adapted to the maize multi-omics era

Songtao Gui, Linfeng Yang, Jianbo Li, Jingyun Luo, Xiaokai Xu, Jianyu Yuan, Lu Chen, Wenqiang Li, Xin Yang, Shenshen Wu, Shuyan Li, Yuebin Wang (+4 others)
2020 iScience  
To this end, we constructed ZEAMAP, a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions, chromatin interactions,  ...  With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte.  ...  DISCUSSION We have created ZEAMAP, a database for maize research and breeding that collects multi-dimensional omics information, including genome assemblies, comparative genomics, transcriptomes, open  ... 
doi:10.1016/j.isci.2020.101241 pmid:32629608 pmcid:PMC7306594 fatcat:6j5ihsfuf5c2hkfoave3cgrcci

The Banana Genome Hub

Gaëtan Droc, Delphine Larivière, Valentin Guignon, Nabila Yahiaoui, Dominique This, Olivier Garsmeur, Alexis Dereeper, Chantal Hamelin, Xavier Argout, Jean-François Dufayard, Juliette Lengelle, Franc-Christophe Baurens (+6 others)
2013 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank all those who applied their expertise for the gene and transposable annotation and contributed to the improvement of the quality of the banana reference sequence: Eva  ...  However, few such plant information hubs have the following complete integrated functionalities: (i) A Chado-based (10, 11) community annotation system (CAS) (ii) Connectivity to a mainstream genome annotation  ...  But to generate a larger volume of high-quality genomic annotations within a dispersed heterogeneous community, an operational high-quality and user-friendly 'crowd sourcing' on-line annotation system  ... 
doi:10.1093/database/bat035 pmid:23707967 pmcid:PMC3662865 fatcat:jvjzcmd2qba4fdrbbbbghrp36y

ZEAMAP, a comprehensive database adapted to the maize multi-omics era [article]

Songtao Gui, Linfeng Yang, Jianbo Li, Jingyun Luo, Xiaokai Xu, Jianyu Yuan, Lu Chen, Wenqiang Li, Xin Yang, Shenshen Wu, Shuyan Li, Yuebin Wang (+4 others)
2020 bioRxiv   pre-print
To this end, we constructed ZEAMAP (http://www.zeamap.com), a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions,  ...  With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte.  ...  ACKNOWLEDGEMENTS The authors would like to thank Dr Qing Li and Ms Jing Xu (National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University) for providing the DNA methylation data  ... 
doi:10.1101/2020.01.04.894626 fatcat:f7rzhmwb6ffxdglnkzvfyksacy

An integrated approach for increasing breeding efficiency in apple and peach in Europe

Francois Laurens, Maria José Aranzana, Pere Arus, Daniele Bassi, Marco Bink, Joan Bonany, Andrea Caprera, Luca Corelli-Grappadelli, Evelyne Costes, Charles-Eric Durel, Jehan-Baptiste Mauroux, Hélène Muranty (+10 others)
2018 Horticulture Research  
Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding.  ...  FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.  ...  The authors would like to thank sincerely Vincent Troillard (INRA Transfert) who managed all the administrative and financial tasks of the project and all the participants.  ... 
doi:10.1038/s41438-018-0016-3 pmid:29507735 pmcid:PMC5830435 fatcat:zuvjvdfwovhivb4gbudjoszjgu

Apple whole genome sequences: recent advances and new prospects

Cameron P. Peace, Luca Bianco, Michela Troggio, Eric van de Weg, Nicholas P. Howard, Amandine Cornille, Charles-Eric Durel, Sean Myles, Zoë Migicovsky, Robert J. Schaffer, Evelyne Costes, Gennaro Fazio (+15 others)
2019 Horticulture Research  
Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees.  ...  Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple  ...  10 "Database resources for crop genomics, genetics and breeding research", the IDEEV, Laboratoire d'Excellence BASC, and the Inserm ATIP-Avenir program.  ... 
doi:10.1038/s41438-019-0141-7 pmid:30962944 pmcid:PMC6450873 fatcat:wfubttiirbgv5jov3dl43oekau

Safeguarding and using global banana diversity: a holistic approach

Ines Van den houwe, Rachel Chase, Julie Sardos, Max Ruas, Els Kempenaers, Valentin Guignon, Sebastien Massart, Sebastien Carpentier, Bart Panis, Mathieu Rouard, Nicolas Roux
2020 CABI Agriculture and Bioscience  
By implementing the 10-year workplan set out in the Global Strategy for the Conservation and Use of Musa Genetic Resources, the network MusaNet supports Musa researchers and stakeholders, including the  ...  Genomic and bioinformatic studies of several banana wild relatives greatly enhance our understanding of Musa genetic diversity, links to important phenotypic traits and bring new methods for management  ...  , L'Institut de recherche pour le développement, and Botanic Garden of Meise.  ... 
doi:10.1186/s43170-020-00015-6 fatcat:pmxlggopnffmdncsawkbmisj3u

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
2021 Zenodo  
the National Research Agency, and a strong commitment of our supporting institutions to open permanent positions.  ...  genomic surveillance.  ...  >> Detailed report of the survey  ... 
doi:10.5281/zenodo.5324333 fatcat:py5xp6q7ungkdevdqx25zxfwmq

Breeding Climate-Resilient Bananas [chapter]

Allan Brown, Sebastien C. Carpentier, Rony Swennen
2020 Genomic Designing of Climate-Smart Fruit Crops  
Acknowledgements This study has been supported by Grants Nº 19308/PI/14 and Nº 19879/GERM/15 of the Seneca Foundation of the Region of Murcia and the Apricot Breeding project Converse (1987) , Tzanetakis  ...  (2010) , Petrzik et al. (1998), Thompson and Jelkman (2003) , , Tzanetakis et al. (2007) , Yoshikawa et al. (1986) , Yoshikawa and Inouye (1988) , Ratti et al. (2006) Nematode Jones and Wood  ...  It enables cross-database communication and connection based on the Tripal Gateway.  ... 
doi:10.1007/978-3-319-97946-5_4 fatcat:cqzcfw6fnfcjtbnsw2bchzkx3q
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