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Join the MGI Developer's Forum Mailing List
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- Please join to be notified of any changes to the mechanisms listed here.
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Batch Queries
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- • 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
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Creating Web Links to MGI
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Data Files for Download
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Public Reports via FTP
Database Dumps via FTP
- 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.
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.
- 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
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
- RefSeq transcript sequences for their human, rat, and zebrafish homologs
- Protein sequences for human, rat, and zebrafish homologs.
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MGI Web Service
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- The MouseMine web services API offers robust and comprehensive programmatic access to MGI data. For assistance using MouseMine web services, see:
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Direct SQL Account
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NOTICE
Due to funding cutbacks for model organism databases that affect MGI, our public database server (mgi-adhoc.jax.org), which hosts a small number of SQL accounts, will be retired as of June 1st, 2025. The last update of mgi-adhoc data was 12/24/24. No further updates will be made on mgi-adhoc before the termination date. We apologize for any inconvenience this action may cause. Current versions of the mgd database dump file will continue to be accessible at (https://www.informatics.jax.org/downloads/database_backups/mgd.postgres.dump). To use this dump file, your system will need to have Postgres 17 installed. MGI data are also accessible from public reports, which can be found on the MGI Data and Statistical Reports page (https://www.informatics.jax.org/downloads/reports/index.html), organized by data type. Increasingly, MGI data are also available through the Alliance of Genome Resources (https://www.alliancegenome.org/), which ultimately will be one of the primary sources of function, phenotype, and disease model data for the mouse. If you experience difficultly obtaining the data you need from these other resources, please contact [email protected] or [email protected] for assistance.
- 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
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Analysis Tools