Tripal MegaSearch: a tool for interactive and customizable query and download of big data. (26th April 2021)

• Record Type: Journal Article
• Authors: Jung, Sook; Cheng, Chun-Huai; Buble, Katheryn; Lee, Taein; Humann, Jodi; Yu, Jing; Crabb, James; Hough, Heidi; Main, Dorrie
• Is Part Of: Database. Volume 2021(2021)
• Publication Date: 2021-04-26
• Subjects: Biology -- Databases -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1093/database/baab023
• Languages: English
• ISSNs: 1758-0463

Abstract

Abstract: 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/ .