This help document answers the following questions:
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.
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:
|Home||Links to the MouseMine Home Page|
|Templates||Links 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.|
|Lists||The 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.|
|Viewer||Links 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|
|Data||Lists the general MouseMine data categories, the types of data in each category and the sources of data|
|API||Provides instructions for using Perl, Python, Ruby, and Java web service access to MouseMine|
|MyMine||When logged in, provides access to your saved Lists, Queries, favorite Templates and Account Details|
|MGI||Links to the Mouse Genome Informatics (MGI) Home Page.|
|Keywords||If 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.|
|Lists||If 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 (at the top right hand section of the web page) first. 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.
MouseMine is refreshed with new data from MGI and other sources weekly.
A. How can you find exon information for the Lrp4 gene in these 3 strains, C57BL/6J, 129S1/SvImJ and BALB/cJ?
Note: the MGP (Sanger Mouse Genomes Project) IDs can be decoded:
B. How can you find genotypes associated with emphysema (MP:0001958) and abnormal lung elastance (MP:0011043)?
This returns a list of genes and transgenes and genotypes associated with these phenotypes terms and their subterms. Now you can modify the query:
C. How can you search with a list of IDs or genes?
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.
The results will provide a list of all markers with a phenotype description, and will also provide a functional description for those markers.