• Please join to be notified of any changes to the mechanisms listed here.

• Batch Query

Input a list of IDs or gene symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO, expression data).

• Gene Expression Batch Search

Input a list of IDs or gene symbols and retrieve associated gene expression assay data. Search results include a tissue-by-gene matrix view to enable the comparison of expression patterns between genes.

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

• 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 backups are available from our ftp site at: http://www.informatics.jax.org/downloads/database_backups/
• Backups are available for MySQL 5.0.67 and PostgreSQL 9.3.5.
• 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.

• 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.
• The Quick Search, as well as these query forms, offer tab-delimited outputs:
• 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.
• Phenotypes, Alleles & Disease Models Query
  Search for mutations or QTL based on phenotype, human disease, mutation type, gene, or genome location.
• Human—Mouse: Disease Connection
  Search for phenotype and disease associations by human and mouse genes and genome regions.
• Gene Expression Data Query
  Search for detailed gene expression assay results.
• References
  Search curated references by author, journal or text. The output to this form provides the text export option
• Mouse SNP Query Form
  Search for SNPS by strain(s), SNP attributes, genomic position, or associated genes

• 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
• RefSeq transcript sequences for their human, rat, and zebrafish homologs
• Protein sequences for human, rat, and zebrafish homologs.

• The MouseMine web services API offers robust and comprehensive programmatic access to MGI data. For assistance using MouseMine web services, see:
  • InterMine Web Services Documentation
  • MGI API Documentation
  • Or Contact User Support.

• 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 (https://squirrel-sql.sourceforge.io).
• 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.