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Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

Lacey-Anne Sanderson, Stephen P. Ficklin, Chun-Huai Cheng, Sook Jung, Frank A. Feltus, Kirstin E. Bett, Dorrie Main
2013 Database: The Journal of Biological Databases and Curation  
Here a site developer can change the viewable name for a field, the table on which a field can join and set sort, field and filter handlers.  ...  Conflict of interest. None declared. Page 17 of 18  ...  Tripal is an open-source, freely available, standards-based toolkit for storage, integration and dissemination of biological data.  ... 
doi:10.1093/database/bat075 pmid:24163125 pmcid:PMC3808541 fatcat:khwlk7dc6zadpntbze5xskz7um

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  
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  ...  WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological 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

The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine [article]

Tavis K Anderson, Blake K Inderski, Diego G Diel, Benjamin M Hause, Elizabeth Porter, Travis Clement, Eric A Nelson, Jianfa Bai, Jane Christopher-Hennings, Phillip C Gauger, Jianqiang Zhang, Karen M Harmon (+3 others)
2021 bioRxiv   pre-print
We implemented the Tripal toolkit, using the open source Drupal content management system and the Chado database schema.  ...  Users can download annotated genomic sequences from the database using a customized search interface that incorporates data mined from published literature; search for similar sequences using BLAST-based  ...  Mol Biol Evol, 37, , L.A., Ficklin, S.P., Cheng, C.H., Jung, S., Feltus, F.A., Bett, K.E. and 544 Main, D. (2013) Tripal v1.1: a standards-based toolkit for construction of online 545 genetic and genomic  ... 
doi:10.1101/2021.04.16.439882 fatcat:4rqkegysqbc2jm5ydkzni2yacq

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  ...  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  ...  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