Using the MouseMine Data Warehouse
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This help document answers the following questions:

What is the purpose of the MouseMine data warehouse?

MouseMine is a data warehouse for accessing integrated mouse data from Mouse Genome Informatics (MGI) and other web resources. MouseMine is a member of an extensive community of online data resources based on the InterMine software framework. It provides multiple, diverse, query templates and supports custom and iterative querying. MouseMine gives you the ability to upload and manipulate lists of features, save and combine results from different queries, and its web services API offers robust and comprehensive programmatic access to MGI data.

See also: Motenko H, Neuhauser SB, O'Keefe M, Richardson JE. 2015. MouseMine: a new data warehouse for MGI. Mamm Genome. 2015 Aug;26(7):325-30. PubMed

How do I access the different MouseMine tools?

At the top right hand section of the web page are links to Log In, and to this help document. Create a Log In account to save lists and queries beyond one browser session.

Beneath the MouseMine logo are several tabs:

HomeLinks to the MouseMine Home Page
TemplatesLinks to a listing of all the templates. Templates are predefined queries that have a simple input type and return a defined table of results. Examples are Diseases --> Mouse models (returns mouse models of specified human diseases) and Genes/Features --> Phenotypes (MP terms) (returns the Mammalian Phenotype (MP) terms associated with the specified genes or other features). You can filter the list of templates by keyword or data category. In the center section of MouseMine Home Page, the templates are pre-sorted by category. Though the template table of results is pre-determined, you can easily remove, sort and filter columns, and add additional columns.
ListsThe Lists tab provides the ability to create and manage lists of objects, such as lists of genes, alleles, GO terms, or publications. When you create a list, a series of pre-defined queries (templates) and enrichments are run.
QueryBuilder   A flexible query interface allows advanced users to construct their own queries. The QueryBuilder lets you view the data model, apply constraints and select output. You can also export queries to share them with others. See example D.
ViewerLinks to the Multiple Genome Viewer (MGV). MGV allows you to explore and compare chromosomal regions and synteny blocks between the C57BL/6J reference genome and 18 other mouse inbred strains. See Using the Multiple Genome Viewer
DataLists the general MouseMine data categories, the types of data in each category and the sources of data
APIProvides instructions for using Perl, Python, Ruby, and Java web service access to MouseMine
MyMineWhen logged in, provides access to your saved Lists, Queries, favorite Templates and Account Details
MGILinks to the Mouse Genome Informatics (MGI) Home Page.

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How do I get started with MouseMine?

KeywordsIf you are interested a particular gene or gene family, or want to perform a keyword search, such as for a phenotype or disease, you can use the Search field in the black banner at the top of the page, or the identical Search field in the upper left hand section of the Home Page. The Search field supports the asterisk (*) as a wild-card. These searches can return a broad range of results, including genes, ontology terms, and publications. See example A.
Templates   For more specific results, use one of the predefined query templates. In the center section of the Home Page, these are organized by category (e.g., GENOME, EXPRESSION, PHENOTYPE). You can view all the templates by clicking on the Templates tab at the top of the page. If none of the templates seems to meet your needs, choose one that comes close and then modify it. See example B.
ListsIf you already have a list of items of interest (e.g., genes, alleles, ontology terms, publications), use the Lists tab to get additional information on those items. To save your list to use another time, create a Log In account first (at the top right hand section of the web page). See example C.
Note that MGI generates several weekly reports of MGI data and many of its query forms provide export options so you can create your own custom reports and use these to input in MouseMine to get additional information. See: http://www.informatics.jax.org/software.shtml#data.

How often are data updated?

MouseMine is refreshed with new data from MGI and other sources weekly.

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What are some examples of queries?

A.  How can you find exon information for the Lrp4 gene in these 3 strains, C57BL/6J, 129S1/SvImJ and BALB/cJ?

  1. On a MouseMine page, enter Lrp4 in the Search field and hit your return/enter key.
  2. Click on MGI:2442252 | Lrp4 to access the mouse data.
  3. Scroll down and click on Canonical gene --> Exons in specific strains.
  4. This will show you information on the exons for multiple transcripts for 19 mouse inbred strains. Click on the last icon in the Strain Name column header, the graph icon, and filter for the 3 strains.
  5. You can use the Export button to get all the exons, but for now, just get the first exon for the first 129S1/SvImJ transcript by clicking MGP_129S1SvImJ_E0056125_1 in the Exon Primary Identifier column.

Note: the MGP (Sanger Mouse Genomes Project) IDs can be decoded:

  1. Click the FASTA button to get the sequence.

B.  How can you find genotypes associated with emphysema (MP:0001958) and abnormal lung elastance (MP:0011043)?

  1. Click on the Templates tab near the top of the MouseMine page.
  2. Click on Mammalian phenotypes (MP terms) --> Mouse genes and models.
  3. Enter MP:0001958, MP:0011043 in the LOOKUP field and click the Show Results button.
  4. Toggle the 25 results so you can see all the results.

This returns a list of genes and transgenes and genotypes associated with these phenotypes terms and their subterms. Now you can modify the query:

  1. Click on the Manage Columns button and then click on Add a Column.
  2. Click on MGI Type the first time it is listed (under Subject).
  3. Click Add 1 new column.
  4. Click Apply Changes.
  5. This adds the gene feature types to the table. Now you can remove columns you don't want to see by clicking the X in the column heading and you can filter by clicking the last icon in a column heading, the graph icon.
  6. Click the Export button to select your formatting options.

C.  How can you search with a list of IDs or genes?

  1. Click on the Lists tab at the top of a MouseMine page.
  2. For this example, click click to see an example just above the identifiers field. This will populate the field with a few IDs and gene symbols.
  3. Click the Create List button.
  4. Save the list.
  5. This will also run some automatic queries (templates) and enrichments. Scroll down to see them and click on any that interest you.

D. How can you get a list of genes with their phenotype summaries?

For many mouse genes with phenotype data for mutant alleles, MGI curators have created a brief statement that summarizes those phenotypes. This example uses the QueryBuilder to generate a list of genes and their phenotype summaries.

  1. Click on the QueryBuilder tab near the top of the MouseMine page.
  2. Click on Gene and then the Select button to Select a Data Type to Begin a Query.
  4. In the Model browser section, under Gene, click on SHOW after MGI Type, Name, Primary Identifier, and Symbol to add these fields to your results.
  5. After Description, click on SHOW, then CONSTRAIN.
  6. In the pop-up window, toggle = to CONTAINS, and enter phenotype in the field. This will limit your results to those genes with a phenotype description.
  7. Click the Add to query button.
  8. In the bottom section of the page, Fields selected for output, drag the field boxes in the order you want them.
  9. Click the Show results button.

The results will provide a list of all markers with a phenotype description, and will also provide a functional description for those markers.

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