How to Search for JAX® Mice
With information on several thousand strains of laboratory mice, the JAX® Mice website provides direct access to comprehensive information resources on laboratory mouse biology and genetics. The following two search options are available:
For help with The Jackson Laboratory's site-wide search tool, please see the website search help page.
NEW SEARCH TOOLS:
Strain search by phenotype or relationship to human disease
Strains can now be found using the Mammalian Phenotype Ontology (Smith, et al (2005).
PLEASE NOTE that curation is in progress, and not all strains have been annotated. However, we are curating all new strains and reducing the backlog as quickly as possible.
Smith, C. L., Goldsmith, C. A., and Eppig, J. T. (2005). The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6, R7.
Finding a Strain by Phenotype
Facts about the phenotype search function:
- You can select a phenotype term by searching the mammalian phenotype ontology or by browsing the terms.
- The term search uses synonyms built into the vocabulary, so that a search for fat will find the term adipose tissue phenotype.
- You can go directly to a list of related JAX® Mice Strains at any time during a search, or you can add phenotype terms to the Quick Query Form and refine your search from there.
- The default is set to search or browse only for terms associated with related JAX® Mice Strains. To search for all terms, deselect "Only display terms with JAX® Mice Strains" when you search or browse.
To search for a specific phenotype
| Step 1 | Result |
| From the Quick Query Form or the Advanced Search Query Form, click the "Add Phenotype Terms" button. |
The system displays the "Search for strains by phenotype using Mammalian Phenotype Ontology" form. Phenotype ontology terms are listed on the left. The quantities of related JAX® strains are listed on the right.
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| Step 2 | Result |
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Type the phenotype term in the search box and click the "Search" button. (To also include results that do not have related JAX® Mice strains, deselect "Only display terms with JAX® Mice strains.")
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The system displays a list of matching Mammalian Phenotype terms and the quantities of JAX® Mice Strains related to each term |
| Step 3 | Result |
| To go directly to the list of JAX® Mice strains, click the number of strains in the JAX® Mice Strains column. | The system displays the list of strains. |
| OR | |
| To query on search options in addition to Mammalian Phenotype terms, select one or more terms and click the "Add Selected Terms to Query" button. | The system displays the Quick Query Form, with your selected Mammalian Phenotype terms in the Phenotype of Interest area. |
To browse for a specific phenotype
| Step 1 | Result |
| From the Quick Query Form or the Advanced Search Query Form, click the "Add Phenotype Terms" button. |
The "Search for strains by phenotype using Mammalian Phenotype Ontology" page appears. Phenotype ontology terms are listed on the left. The numbers of related JAX® strains are listed on the right.
|
| Step 2 | Result |
| Click through the hierarchy in the Phenotype Ontology list. (To restrict terms to those with related JAX® mice strains, select "Only display terms with JAX® mice strains.") |
The "Mammalian Phenotype Browse" page, including the MP id, MP Name, Definition (optional), Synonyms (optional) for the terms, and the numbers of related JAX® Mice strains.
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| Step 3 | Result |
| To go directly to the list of related strains for a phenotype, click the quantity of JAX® Mice strains link in the right column. | The list of strains. |
| OR | |
| To query on search options in addition to the displayed MP term, click the "Add Term to Query" button. | The Quick Query Form, with your selected MP term in the Phenotype of Interest field. |
Finding a Strain by Relationship to Human Disease
Facts about the disease search function:
- You can select a disease term by searching the mammalian phenotype ontology or browsing the terms.
- The term search uses synonyms built into the vocabulary, so that a search for diabetes will find the term Lipodystrophy, Congenital Generalized, Type 2; CGL2.
- You can go directly to a list of related JAX® Mice Strains at any time during a search, or you can add disease terms to the Quick Query Form and refine your search from there.
- The OMIM ID provides a link to the OMIM disease page.
- The default is to search or browse only for terms associated with related JAX® Mice Strains. To search for all terms, deselect "Only display terms with JAX® Mice Strains" when you search or browse.
To search for a specific disease
| Step 1 | Result |
|
From the Quick Query Form or the Advanced Search Query Form, click the "Add Disease Terms" button. |
The "Search for strains by phenotype using Mammalian Phenotype Ontology" page appears.
|
| Step 2 | Result |
|
Type the phenotype term in the search box and click the "Search" button. (To also include results that do not have related JAX® Mice strains, deselect "Only display terms with JAX® Mice strains.") |
The system displays a list of matching OMIM terms with the quantities of JAX® Mice Strains related to each term and a link to the OMIM disease page.
|
| Step 3 | Result |
|
To go directly to the list of related strains for a disease, click the quantity of JAX® Mice strains link. |
The list of strains. |
| OR | |
| To query on search options in addition to OMIM term(s), select one or more terms by checking the "add term to strain search" and then click the "Add Selected Terms to Query" button. | The Quick Query Form, with your selected MP term in the Phenotype of Interest field. |
To browse for a specific disease
| Step 1 | Result |
|
From the Quick Query Form or the Advanced Search Query Form, click the "Add Disease Terms" button.
|
The "Search for strains by phenotype using Mammalian Phenotype Ontology" page appears. |
| Step 2 | Result |
|
Click through the terms in the alphabetical list. (To restrict terms to those with related JAX® mice strains, select "Only display terms with JAX® mice strains.")
|
The system displays a list of disease terms with the numbers of related JAX® Mice strains, OMIM term, and a link to the OMIM disease page. |
| Step 3 | Result |
|
To go directly to the list of related strains for a phenotype, click the quantity of JAX® Mice strains link in the right column. |
The list of strains. |
| OR | |
| To query on search options in addition to OMIM term(s), select one or more terms by checking the "Add term to strain search" and then click the "Add Selected Terms to Query" button. | The Quick Query Form, with your selected MP term in the Phenotype of Interest field. |
Other Ways to Search
Research areas
These categories are more general than the phenotype and disease vocabularies and have been more comprehensively curated, so searches by research area will generally bring back a larger set of strains. For example, someone interested in Parkinson's disease may be interested in a strain that expresses a reporter gene specifically in the substantia nigra, or a mouse that is resistant to toxin-induced Parkinson's disease. These strains would not be found searching for Parkinson's disease or by phenotype, but would be found by a research area search.
To find strains relevant to a specific scientific topic, use the Research Area pull-down on either the simple or advanced search. Note that Research Area can be searched using any of the three levels, enabling either a broad ("Cancer Research") or specific ("Cancer Research/Increased Tumor Incidence/Prostate Tumors") search.
Alternatively, go to the "Mouse Model Lists" link at the bottom of the page, then select the research area of interest. Note that pdf versions will not be as up-to-date as database-generated lists.
Gene/Allele Symbol or Strain Name/Common Name
Default settings are "contains" for most fields.
For gene and allele symbols, the default is "begins".
"equals" will define your search to look for an exact match to what you have entered in the search field.
"contains" will define your search to look for all instances of what you have entered in the search field (i.e.: searching for "a" under symbol will bring up all symbols with the letter "a" in it)
"begins" will define your search to look only at the beginning of the field being searched.
Advanced Search Form
Chromosome
Select a chromosome in the pulldown list to find strains carrying a mutation on a chromosome of interest.
MT: mitochondrial
UN: unknown
XY: pseudoautosomal
Promoter
Select a gene in the promoter pulldown list to find transgenic mice where transgenic expression is driven by your gene of interest.
Reference
If you know an author, title or reference of the paper describing the characterization of a strain, there are multiple ways in the advanced search query form to search for the strains linked to that paper:
- enter the journal name, year, volume, page number or last name of the 1st author in the Reference or 1st author field using begins or contains.
- enter author last name (not specific to 1st Author) in the Author(s) field using begins or contains.
- enter word(s) from the title in the Title field using equals, begins or contains.
General Search Information
Search forms are not case sensitive.
Multiple search criteria can be used once, e.g. you can find strains related to apoptosis AND that are spontaneous mutations AND that are available as live mice.
If you still cannot find what you need, fill out the Express Technical Support Form and our Techncial Information staff will respond in 1-2 business days. This form can also be used to suggest a new strain that we do not currently provide.
