{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T02:44:49Z","timestamp":1770518689758,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T00:00:00Z","timestamp":1619395200000},"content-version":"vor","delay-in-days":115,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Mcintire Stennis","award":["WNP00009"],"award-info":[{"award-number":["WNP00009"]}]},{"name":"USDA Hatch project","award":["1014919"],"award-info":[{"award-number":["1014919"]}]},{"name":"USDA NIFA National Research Support Project 10","award":["NRSP10"],"award-info":[{"award-number":["NRSP10"]}]},{"name":"National Science Foundation Plant Genome Research Program","award":["#444573"],"award-info":[{"award-number":["#444573"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Tripal MegaSearch is a Tripal module for querying and downloading biological data stored in Chado. This module allows site users to select data types, restrict the dataset by applying various filters and then customizing fields to view and download through a single interface. Set by site administrators, example data types include gene, germplasm, marker, map, QTL, genotype, phenotype and expression data. When querying for genes, users can restrict the gene dataset using various filters such as name, chromosome position and functional annotation. They can then customize fields to download, such as name, organism, type, chromosome position, various functional annotations such as BLAST, KEGG, InterPro and GO term. FASTA files can also be downloaded for the sequence data. Site administrators can choose from two different data sources to serve data: Tripal MegaSearch materialized views or Chado tables. If neither data source is desired, administrators may also create their own materialized views and serve them through the flexible dynamic Tripal MegaSearch query form. Tripal MegaSearch is currently implemented in several databases including the Genome Database for Rosaceae www.rosaceae.org and TreeGenes www.https:\/\/treegenesdb.org\/.<\/jats:p>","DOI":"10.1093\/database\/baab023","type":"journal-article","created":{"date-parts":[[2021,4,17]],"date-time":"2021-04-17T00:49:18Z","timestamp":1618620558000},"source":"Crossref","is-referenced-by-count":13,"title":["Tripal MegaSearch: a tool for interactive and customizable query and download of big data"],"prefix":"10.1093","volume":"2021","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, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"Chun-Huai","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"Katheryn","family":"Buble","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"Taein","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"Jodi","family":"Humann","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"Jing","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"James","family":"Crabb","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"Heidi","family":"Hough","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]},{"given":"Dorrie","family":"Main","sequence":"additional","affiliation":[{"name":"Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,4,26]]},"reference":[{"key":"2021070818440860700_R1","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bat075","article-title":"Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases","volume":"2013","author":"Sanderson","year":"2013","journal-title":"Database"},{"key":"2021070818440860700_R2","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":"2021070818440860700_R3","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","year":"2017","journal-title":"Database"},{"key":"2021070818440860700_R4","doi-asserted-by":"publisher","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":"2021070818440860700_R5","doi-asserted-by":"publisher","first-page":"W589","DOI":"10.1093\/nar\/gkv350","article-title":"The BioMart community portal: an innovative alternative to large, centralized data repositories","volume":"43","author":"Smedley","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2021070818440860700_R6","doi-asserted-by":"publisher","first-page":"D1137","DOI":"10.1093\/nar\/gky1000","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":"2021070818440860700_R7","doi-asserted-by":"publisher","first-page":"D1229","DOI":"10.1093\/nar\/gkt1064","article-title":"CottonGen: a genomics, genetics and breeding database for cotton research","volume":"42","author":"Yu","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2021070818440860700_R8","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2019.00813","article-title":"Cyberinfrastructure to improve forest health and productivity: the role of tree databases in connecting genomes, phenomes, and the environment","volume":"10","author":"Wegrzyn","year":"2019","journal-title":"Front. 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