FAQ

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About MouseMine

  1. What is MouseMine?
    MouseMine is an instance of the InterMine data warehouse system populated with mouse data from MGI. The MouseMine project is part of the InterMOD project, funded under a grant from NHGRI (HG004834).
  2. How can I cite MouseMine in a paper?
    Motenko, et.al., 2015 (PMID:26092688)
  3. Who is MouseMine for?
    MouseMine is for anyone interested in mouse data from MGI, but is especially suited for those needing more power (and less comfort) than the MGI interface provides. Interactive users are able to save query results in lists, chain their querying steps (feed the results from one query into the next), choose from a large set of precanned queries (aka templates) and modify/customize those queries as they see fit, and more. In addition, a comprehensive web services interface API supports programmatic access, and multiple language bindings are available.
  4. Does MouseMine contain all the data from MGI?
    No. Not yet, anyway. Currently MouseMine focusses on the MGI core objects (genome features, alleles, strains, genotypes, publications), curated annotations (GO, MP, OMIM), plus database cross references, orthology relationships, and a few other things.  We plan to incorporate more of MGI over time. Examples include mouse gene models and mouse expression data.
  5. Does MouseMine contain any data not from MGI?
    Yes, there are several examples. (1) MouseMine (like all instances of InterMine) loads the Sequence Ontology (SO), and all sequence features in the database refer to their corresponding SO term. (2) MouseMine loads orthology and paralogy relationships directly from Homologene. MGI is currently doing a project to do the same thing, but that will not be released until the end of May. (3) MGI uses the (flat) OMIM vocabulary for disease annotations. MouseMine uses MEDIC, developed by the Comparative ToxicoGenomics Database (CTD), which effectively merges OMIM terms into the MeSH disease hierarchy. Disease annotations from MGI are mapped to their corresponding MEDIC terms while loading MouseMine.
  6. How often, and when, is MouseMine updated?
    Currently, on Saturdays, between 5 and 6 am eastern time. MouseMine’s build process is triggered when a data update is detected in MGI, and build times can vary. So the actual time of MouseMine’s update may vary.
  7. What is the difference between www.mousemine.org and beta.mousemine.org?
    The first (www) is the stable public site. It is refreshed weekly, and only contains “released” software. The second (beta) is rebuilt every day, and shows our latest software and data developments.
  8. Where can I learn more about how to use MouseMine?
    Look at our help page. It has MouseMine tutorials and links to tutorials for other mines.

Searching

  1. At MGI, if I do a quicksearch for “Hox” if get 54 matches, most of which are genes, but in MouseMine, I only get 2 genes. Why?
    (1) In MouseMine, you have to use a wildcard (*) character. (2) In general, MouseMine (being an instance of InterMine) implements very different search indexing and processing than does MGI. The same search string will not necessarily match the same objects in both systems.
  2. I added an output field to my query, and the number of results went down. Why?
    Queries in InterMine (the system that MouseMine is built on) are based on the concept of paths, where a path is a sequence (actually a tree) of connected objects in the database. A query specifies a pattern; running a query finds all paths that match the pattern, and returns the fields you specify from the objects along the path. When you add an output field in the query builder, if that field is part of the existing path/pattern, then it should have no effect on the number of output rows. But if the output field opens up a new branch in the path (or extends it), then there is a new implied constraint that the path exists.

Results Tables

  1. How do I change the order of columns in a table?
    Click the “Manage Columns” button at the top of the table. You will see a popup with the columns listed. Drag the columns up/down to rearrange the order. Then click “Apply”.
  2. How do I remove a column from a table?
    Mouse over the column header. You will see additional tool icons appear. Click on the circled “x”.

Templates

  1. How do I find a template that does what I want? (Also, what’s up with their ordering?)
    Templates are listed on the home page, under the various tabs (“Genome”, “Function”, …) and on the Templates page. They are ordered by “popularity”, which basically means how often they’ve been executed. 
  2. What if I can’t find a template that does what I want?
    There are several options, depending on circumstance. If you can find one that almost does what you want, you can customize if by clicking the “Edit” button. And if you are logged in, you can then save your customized template permanently. Alternatively, you can execute the template, and then add/remove columns and filters on the results table. In some cases, you can obtain your results by running several separate templates and combining their results or feeding the results of one template into the next.
  3. How do I “feed the results” of one template into another?
    This is best shown by an example. Question: what phenotypes are associated with homeostasis genes? (1) Go to the template “Functions (GO terms and children)  –>  Mouse features“, enter “homeostatic process”, and execute. (2) From the results table, save the list of genes. (3) Go to the template “Mouse features –> Mammalian phenotypes (MP terms)“. Click the checkbox “constrain to be in saved list”. Select your saved list from the dropdown and execute.
  4. Why doesn’t my saved list show up in the dowpdown on a template form?
    The type of your list may be incompatible with the type required by the template. Another possibility if you are not logged in is that your session expired, and the list was removed. (Saved lists and queries are only temporary if you are not logged in.)

Miscellaneous

  1. The “Oops” message. I did a query/clicked a link/other, and I get an error message / a bunch of error messages that say “Oops – blah blah blah.” What’s up with that?
    One reason: expired session. If you come back to a browser window that’s open to a MouseMine page and has been sitting a long time, you’ll see this message. You’ll have to rerun your query / reload your report page, etc.