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Bulk Data Access, APIs and Linking to MGI
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Batch Queries
Batch Query
Input a list of IDs or gene symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO, expression data).
MouseMine
Powered by InterMine, MouseMine offers flexible querying, numerous predefined query templates, iterative refinement of results, and linking to other model organism Mines. MouseMine:
  • offers many useful "canned" queries, plus point-and-click query editing
  • supports uploading and manipulating lists of objects
  • allows any query result to be downloaded (text, xml, json) or forwarded to Galaxy
MGI BioMart
Access MGI's mouse genetic, genomic and expression data using BioMart.
Creating Web Links to MGI
Data Files for Download
Public Reports via FTP
  • Over 65 data files are generated weekly and available for download.
  • See MGI Data and Statistical Reports for the list of reports and their field descriptions.
Database Dumps via FTP
  • Database backups are available from our ftp site at: ftp://ftp.informatics.jax.org/pub/database_backups/
    • Backups are available for MySQL 5.0.67 and PostgreSQL 9.0.2.
    • These backups assume you have a compatible version of MySQL or PostgreSQL installed, that you have created a database, and that you have adequate user permissions to load that database.
    • Backups are updated on Mondays between 12:30 AM and 1:30 AM EST, so please avoid downloading the files during that time, or your file may not download successfully.
  • To load the MySQL backup:
    • First, uncompress it: gunzip mgd.mysql.dump.gz
    • Then load it: mysql -e "mgd.mysql.dump" databaseName
  • To load the PostgreSQL backup:
    • Load it: pg_restore -c -d databaseName -j jobCount -O -h host -U user mgd.postgres.dump.Fc
    • jobCount should be an integer, representing the number of subprocesses. If you have a multiprocessor machine, using a jobCount between 2 and 4 will likely speed your restore significantly.
Tab Delimited Output from our Web Interface
  • User-defined results for references, gene and SNP data are available in tab delimited format.
  • You can modify the output format on the query form from Web to Tab-delimited.
  • Query Forms with the tab-delimited option available are:
FASTA Output from our Web Interface
  • The FASTA format is available on reports where sequences are returned for a specific gene or when querying sequences.
  • Click on the checkboxes next to each sequence to select it for FASTA download and click GO.
  • From a gene detail page, FASTA is available for:
    • Representative genomic, transcript, and polypeptide sequences
    • All mouse sequences
    • Human and rat orthologs
    • Mouse, human, and rat protein sequences for superfamily members
MGI Web Service
  • The old MGI Web Service interface has been replaced by MouseMine, which offers much more robust and comprehensive programmatic access to MGI data. For assistance using MouseMine web services, see:
Direct SQL Account
  • The MGI Public Ad Hoc SQL Server is available for running custom SQL queries against the MGI database.
  • MGI uses PostgreSQL relational databases to store information.
  • You must install client software that can connect to a PostgreSQL server in order to query the database. You can use free clients such as JDBC (Java), ODBC (Windows) or SQuirreL SQL (http://squirrel-sql.sourceforge.net/).
  • See our example JDBC Client. You can also use this to verify that your SQL account is active.
Schema Browser
  • In order to write your own custom SQL query, you must be familiar with SQL and the MGI database schema.
  • For help with the database schema, use the Schema Browser available in the Web Interface.
Login & Configuration
  • Contact User Support to request an SQL account. You will receive a login, password and connection parameters.
Custom SQL Reports from MGI

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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Send questions and comments to User Support.
last database update
11/18/2014
MGI 5.20
The Jackson Laboratory