• MGI supports external links to our Web Interface using Accession IDs.
• See Creating Web Links to MGI for instructions and examples.
• Public reports generated nightly are available for obtaining Accession IDs. See MGI Data and Statistical Reports for an index of the reports available.

• 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.

• 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:
• MGI Batch Query
  Download gene/marker data for a batch of IDs or symbols
• Genes and Markers Query Form
  Search by symbol, location, gene ontology classification, or phenotype.
• Mouse SNP Query Form
  Search for SNPS by strain(s), SNP attributes, genomic position, or associated genes
• Mouse Sequence Query Form
  Search for mouse sequences by sequence attributes, sources, and/or properties of associated genes and markers in MGI

• 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:
• Mouse Sequence Query Form
• Protein Superfamily Browser
• Mammalian Orthology Query Form

• 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
   
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.