{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T04:10:33Z","timestamp":1770523833166,"version":"3.49.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,2,12]],"date-time":"2025-02-12T00:00:00Z","timestamp":1739318400000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010251","name":"Washington State Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010251","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007588","name":"Washington State University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007588","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020811","name":"Northern Pulse Growers Association","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020811","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017073","name":"USA Dry Pea and Lentil Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017073","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2014-51181-2237 2014-51181-22378 2022-51181-38449 National Research Support Project 10"],"award-info":[{"award-number":["2014-51181-2237 2014-51181-22378 2022-51181-38449 National Research Support Project 10"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010251","name":"Washington State Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010251","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007588","name":"Washington State University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007588","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020811","name":"Northern Pulse Growers Association","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020811","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017073","name":"USA Dry Pea and Lentil Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017073","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2014-51181-2237 2014-51181-22378 2022-51181-38449 National Research Support Project 10"],"award-info":[{"award-number":["2014-51181-2237 2014-51181-22378 2022-51181-38449 National Research Support Project 10"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The unprecedented volume of big data being routinely generated for nonmodel crop species, coupled with advanced technology enabling the use of big data in breeding, gives further impetus for the need to have access to crop community databases, where all relevant data are curated and integrated. Funding for such databases is, however, insufficient and intermittent, resulting in the data being underutilized. While increased awareness of the importance of funding databases is important, it is practically necessary to find a more efficient way to build a community database. To meet the need for integrated database resources for various crop genomics, genetics, and breeding research communities, we have built five crop databases over the last decade using an open-source database platform and software. We describe the system and methods used for database construction, curation, and analysis protocols, and the data and tools that are available in these five crop databases.<\/jats:p>\n               <jats:p>Database URL: The Genome Database for Rosaceae (GDR, www.rosaceae.org), the Genome Database for Vaccinium (GDV, www.vaccinium.org), the Citrus Genome Database (CGD, www.citrusgenomedb.org), the Pulse Crop Database (PCD, www.pulsedb.org), and CottonGen (www.cottongen.org)<\/jats:p>","DOI":"10.1093\/database\/baaf005","type":"journal-article","created":{"date-parts":[[2025,1,17]],"date-time":"2025-01-17T15:16:26Z","timestamp":1737126986000},"source":"Crossref","is-referenced-by-count":3,"title":["Building resource-efficient community databases using open-source software"],"prefix":"10.1093","volume":"2025","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3968-2769","authenticated-orcid":false,"given":"Sook","family":"Jung","sequence":"first","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]},{"given":"Chun-Huai","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]},{"given":"Taein","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]},{"given":"Katheryn","family":"Buble","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]},{"given":"Jodi","family":"Humann","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]},{"given":"Ping","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]},{"given":"Jing","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]},{"given":"Dorrie","family":"Main","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University , 303c Plant Sciences Building, Pullman, WA 99164-6414,","place":["USA"]}]}],"member":"286","published-online":{"date-parts":[[2025,2,12]]},"reference":[{"key":"2025092510532589500_R1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-021-03173-5","article-title":"A pan-genomic approach to genome databases using maize as a model system","volume":"21","author":"Woodhouse","year":"2021","journal-title":"BMC Plant Biol"},{"key":"2025092510532589500_R2","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baac034","article-title":"GrainGenes: a data-rich repository for small grains genetics and genomics","volume":"2022","author":"Yao","year":"2022","journal-title":"Database"},{"key":"2025092510532589500_R3","doi-asserted-by":"publisher","first-page":"D1036","DOI":"10.1093\/nar\/gku1165","article-title":"The Sol Genomics Network (SGN)\u2014from genotype to phenotype to breeding","volume":"43","author":"Fernandez-Pozo","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025092510532589500_R4","doi-asserted-by":"publisher","first-page":"D1441","DOI":"10.1093\/nar\/gkaa1025","article-title":"SoyBase: a portal for soybean research","volume":"49","author":"Brown","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025092510532589500_R5","doi-asserted-by":"publisher","first-page":"D1137","DOI":"10.1093\/nar\/gky1030","article-title":"15 years of GDR: new data and functionality in the Genome Database for Rosaceae","volume":"47","author":"Jung","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025092510532589500_R6","doi-asserted-by":"publisher","DOI":"10.3390\/plants10122805","article-title":"CottonGen: the community database for cotton genomics, genetics, and breeding research","volume":"10","author":"Yu","year":"2021","journal-title":"Plants"},{"key":"2025092510532589500_R7","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab238","article-title":"Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases","volume":"22","author":"Staton","year":"2021","journal-title":"Brief Bioinform"},{"key":"2025092510532589500_R8","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baz077","article-title":"Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases","volume":"2019","author":"Spoor","year":"2019","journal-title":"Database"},{"key":"2025092510532589500_R9","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bar044","article-title":"Tripal: a construction toolkit for online genome databases","volume":"2011","author":"Ficklin","year":"2011","journal-title":"Database"},{"key":"2025092510532589500_R10","doi-asserted-by":"publisher","first-page":"i337","DOI":"10.1093\/bioinformatics\/btm189","article-title":"A Chado case study: an ontology-based modular schema for representing genome-associated biological information","volume":"23","author":"Mungall","year":"2007","journal-title":"Bioinformatics"},{"key":"2025092510532589500_R11","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci Data"},{"key":"2025092510532589500_R12","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baab023","article-title":"Tripal MegaSearch: a tool for interactive and customizable query and download of big data","volume":"2021","author":"Jung","year":"2021","journal-title":"Database"},{"key":"2025092510532589500_R13","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baz100","article-title":"Tripal MapViewer: a tool for interactive visualization and comparison of genetic maps","volume":"2019","author":"Buble","year":"2019","journal-title":"Database"},{"key":"2025092510532589500_R14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/database\/bax052","article-title":"New extension software modules to enhance searching and display of transcriptome data in Tripal databases","volume":"2017","author":"Chen","year":"2017","journal-title":"Database"},{"key":"2025092510532589500_R15","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baab054","article-title":"The Breeding Information Management System (BIMS): an online resource for crop breeding","volume":"2021","author":"Jung","year":"2021","journal-title":"Database"},{"key":"2025092510532589500_R16","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bax092","article-title":"Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases","volume":"2017","author":"Jung","journal-title":"Database"},{"key":"2025092510532589500_R17","doi-asserted-by":"publisher","DOI":"10.3390\/plants8090333","article-title":"CottonGen: a database of cotton genetics and genomics","volume":"8","author":"Yu","year":"2019","journal-title":"Plants"},{"key":"2025092510532589500_R18","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol"},{"key":"2025092510532589500_R19","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf"},{"key":"2025092510532589500_R20","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1093\/bib\/bbz104","article-title":"Pathway Tools version 23.0 update: software for pathway\/genome informatics and systems biology","volume":"22","author":"Karp","year":"2021","journal-title":"Brief Bioinform"},{"key":"2025092510532589500_R21","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bar051","article-title":"The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data","volume":"2011","author":"Jung","year":"2011","journal-title":"Database"},{"key":"2025092510532589500_R22","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baw010","article-title":"Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado","volume":"2016","author":"Jung","year":"2016","journal-title":"Database"},{"key":"2025092510532589500_R23","article-title":"Tripal\/Tripal_jBrowse: Tripal JBrowse 3.0","author":"Sanderson","year":"2019","journal-title":"Zenodo"},{"key":"2025092510532589500_R24","doi-asserted-by":"publisher","first-page":"D418","DOI":"10.1093\/nar\/gkac993","article-title":"InterPro in 2022","volume":"51","author":"Paysan-Lafosse","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025092510532589500_R25","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyad031","article-title":"The Gene Ontology knowledgebase in 2023","volume":"224","author":"The Gene Ontology Consortium","year":"2023","journal-title":"Genetics"},{"key":"2025092510532589500_R26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025092510532589500_R27","doi-asserted-by":"publisher","first-page":"13996","DOI":"10.1073\/pnas.1821905116","article-title":"Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers","volume":"116","author":"Ryu","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025092510532589500_R28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-0716-2067-0_1","article-title":"Using GenBank and SRA","volume":"2443","author":"Sayers","year":"2022","journal-title":"Methods Mol Biol"},{"key":"2025092510532589500_R29","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2025092510532589500_R30","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"key":"2025092510532589500_R31","doi-asserted-by":"publisher","first-page":"2936","DOI":"10.1093\/bioinformatics\/btt515","article-title":"Consed: a graphical editor for next-generation sequencing","volume":"29","author":"Gordon","year":"2013","journal-title":"Bioinformatics"},{"key":"2025092510532589500_R32","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2025092510532589500_R33","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1101\/gr.9.9.868","article-title":"CAP3: a DNA sequence assembly program","volume":"9","author":"Huang","year":"1999","journal-title":"Genome Res"},{"key":"2025092510532589500_R34","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"2025092510532589500_R35","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2025092510532589500_R36","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0410-6","article-title":"Corset: enabling differential gene expression analysis for de novo assembled transcriptomes","volume":"15","author":"Davidson","year":"2014","journal-title":"Genome Biol"},{"key":"2025092510532589500_R37","doi-asserted-by":"publisher","first-page":"D1237","DOI":"10.1093\/nar\/gkt1096","article-title":"The Genome Database for Rosaceae (GDR): year 10 update","volume":"42","author":"Jung","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2025092510532589500_R38","doi-asserted-by":"publisher","first-page":"D1548","DOI":"10.1093\/nar\/gkad1028","article-title":"Planteome 2024 update: reference ontologies and knowledgebase for plant biology","volume":"52","author":"Cooper","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025092510532589500_R39","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1002\/humu.24141","article-title":"GRIN database: a unified and manually curated repertoire of GRIN variants","volume":"42","author":"Garc\u00eda-Recio","year":"2021","journal-title":"Hum Mutat"},{"key":"2025092510532589500_R40","doi-asserted-by":"publisher","first-page":"1433","DOI":"10.21273\/HORTSCI17676-23","article-title":"A Blueberry (Vaccinium L.) Crop Ontology to Enable Standardized Phenotyping for Blueberry Breeding and Research","volume":"59","author":"Hislop","journal-title":"horts"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaf005\/61862601\/baaf005.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaf005\/61862601\/baaf005.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:53:36Z","timestamp":1758812016000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaf005\/8010488"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":40,"URL":"https:\/\/doi.org\/10.1093\/database\/baaf005","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"baaf005"}}