FB2017_02, released April 18, 2017

A Database of Drosophila Genes & Genomes

Querying FlyBase using our pre-computed files or SQL

In addition to the web-based search tools on FlyBase, such as QuickSearch and QueryBuilder, FlyBase provides access to all our data through a series of pre-computed data files as well as direct access to a public read-only instance of the database that can be queried through SQL.

Our pre-computed files can be found in the Files menu in the navbar. This menu provides a number of options, including access to our FTP site (ftp://ftp.flybase.net/). At the FTP site, various cuts of the data are provided, ranging from GFF and FastA files to Chado XML data sliced into portions such as chromosomes, genes, intergenic regions and syntenic regions. These data are provided for the current genome release and all older releases for the 12 sequenced Drosophila genomes. The latest, most up-to-date D. melanogaster genome can be found in the Drosophila_melanogaster-current subdirectory.

In addition to our FTP site, we provide pre-computed cuts of the data for download direct from the FlyBase website. A description of the available data can be found in the Files Overview help document situated at the top of the Files menu. In brief, data relating to the current release of FlyBase data can be accessed via the ‘Current release’ option, with selected previous releases giving an overview of the data back to November 2004. Pre-computed downloads are available for many of the objects found in FlyBase, such as genes (e.g. Geneā€”GO association data), alleles (e.g. XML versions of all the data found on allele report pages) and stocks (e.g. a tab-separated file of all the stock records in FlyBase). In addition, we provide downloads of every Controlled Vocabulary used in FlyBase, tables of FlyBase references with their PubMed identifiers and tables of genomic coordinates with cytological location. If there is a slice of the data that you would like but you cannot find on our pre-computed file list, please email us and we will try to assist you.

If you are familiar with SQL, we allow direct searching of our Chado schema PSQL database (for more information on Chado see Mungall et al., 2007). Direct access for moderate usage requires a PostgreSQL client application installed on the user’s computer (see www.postgresql.org for PostgreSQL software and documentation). For extensive usage, we recommend that a copy of the FlyBase PostgreSQL Chado database be installed locally. The PostgreSQL dumps can be downloaded from ftp://ftp.flybase.net/releases/current/psql. See the README file for further information. Like any relational database, information in FlyBase is stored in fields that are arranged in tables. Understanding the relationship between these tables is key to the formulation of SQL to query the data. Example SQL queries that can be used to learn about the structure of the database can be found on the FlyBase forum. In addition, documentation, including the FlyBase field mapping tables, is available on the GMOD website.