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Software Developer Tools
Creating Web Links to MGI
Data Files for Download
Public Reports via FTP
  • Over 75 data files are generated nightly and available for download.
  • See MGI Data and Statistical Reports for the list of reports and their field descriptions.
Tab Delimited Output from our Web Interface
  • User-defined results for gene, SNP, and sequence 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, Protein Superfamilies, or Orthologies.
  • 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
  • Use these query forms to generate reports with the FASTA format option available:
Direct SQL Account
  • The MGI Public Ad Hoc SQL Server is available for running custom SQL queries against the MGI database.
  • MGI uses Sybase relational databases to store information.
  • You must install client software that can connect to a Sybase data 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/).
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 MGI User Support to request an SQL account. You will receive you a login and password.
  • Configure requirements:
    1. A database connection client such as JDBC, ODBC, SQuirrel-SQL, etc.
    2. Application to query the database; such as: isql, ODBC client, jdbc client, etc.
    3. Sybase Interface Entry
      Server Entry Version 1
    4. Server Name ADHOC_MGI
      Server Service SQL Server
      Server Status 4 Unknown
      Server Address TCP-gondor.informatics.jax.org.4025
Custom SQL Reports from MGI
  • Contact MGI User Support for custom SQL queries if you prefer not to write them yourself.

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
05/13/2008
MGI_4.01
Web browser compatibility
The Jackson Laboratory