• 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.

• MouseMine currently contains genetic, genomic and annotation data (function, phenotype, disease) from MGI
• offers many useful "canned" queries, plus point-and-click query editing
• supports links to any object's detail page or to any query results page
• allows any query result to be downloaded (text, xml, json) or forwarded to Galaxy
• supports uploading and manipulating lists of objects
• provides web service access to all of the above functions

• 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.

• 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 Fridays between 6:00am and 7:00am 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.

• 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:
• 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
• MGI BioMart
  Query MGI's mouse genetic, genomic and expression data; compare and integrate results from other databases
• References
  Search curated references by author, journal or text. The output to this form provides the text export option

• 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

• The MGI Web Service provides programmatic access to select portions of the database by uploading a set of identifiers (e.g. EntrezGene, GenBank, mouse gene symbol.).
• The service accepts SOAP 1.1 and 1.2 requests. See MGI Web Service for details and examples.

• 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

• Contact User Support for custom SQL queries if you prefer not to write them yourself.