Using the Mammalian Phenotype (MP) Browser
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The Mammalian Phenotype (MP) Ontology is a community effort to provide standard terms for annotating phenotypic data. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Links to summary annotated phenotype data at MGI are provided in Term Detail reports.

This help document answers the following questions about the MP Browser:

See also:

How is the Mammalian Phenotype Ontology organized?

The Mammalian Phenotype Ontology has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria.

What can I use the Mammalian Phenotype Browser to find?

Use the Browser to find vocabulary terms that may be used in annotations of phenotypic data. You can choose a term here to search, using the Phenotype/Disease box on the Phenotypes, Alleles, and Disease Models Query Form.

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What is the difference between and browsing and searching the vocabulary?

You can either browse or search from the MP Browser entry report. Browsing brings up Term Detail reports displaying the relevant information, including any synonyms associated with the phenotype term. Searching requires entering a text string or full MP accession number in the Query box and clicking Search. This brings up a Query Results report displaying all matches.

How do I browse the vocabulary?

To browse the vocabulary, click a category and navigate until you find the desired phenotypic term. You can copy term IDs into the Phenotypes box on the Phenotypes, Alleles, and Disease Models Query Form to search for data associated with this term.

How do I search the vocabulary?

The MP Browser query field accepts any text string and searches for all terms containing that string and any synonyms. For example, if you enter eye in the MP Browser, the search returns all terms which include "eye."

If you enter the MP accession number, the MP Browser searches the vocabulary by this identifier (ID) and returns only an exact match on it. Note: Do include the MP prefix and the colon but not the brackets when searching by ID, e.g. MP:0005378 and not [MP:0005378] or 0005378.

To search the MP Browser:

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What can I find on the query results report?

The Mammalian Phenotype Browser - Query Results report lists any matches found. Click the desired term from the query results list. The Field Description - Term Detail report appears.

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How do I interpret a Term Detail report?

Field Color Description
MP term, MP ID
Definition, Synonyms,
Number of paths to term
Yellow
Selected phenotype term, unique identifier for the term, definition of the term, any synonyms associated with the term, and number of paths to the term in the vocabulary structure. Some terms may also have Alternate IDs.
Unique identifierRedName of the phenotype term selected, followed by the a unique identifier. There is one identifier for each term in the MP Browser. This means that no matter how many times the term appears, the ID is always the same. This is also true if the term changes. For example, if "anophthalmia" becomes simply "absent eyes," the Mammalian Phenotype identifier does not change.
"Is-a" RelationshipGreenIndicates that the term is an instance or type of the more general term above it in the tree. For example, anophthalmia is a type of eye abnormality.
+BlueA plus sign (+) following a term indicates that the term has children. Click to see the additional paths to the term.
# genotypes
# annotations
BlueNumber of genotypes annotated to the term or a descendant of the term. Click this link to see the Mammalian Phenotype Ontology Annotation Query Results -- Summary.

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How do I interpret the Mammalian Phenotype Ontology Annotations Query Results?

The summary report presents a list of MGI genotypes annotated to a term or its descendents. You access this report by clicking the text displaying the number of genotypes and annotations for a featured term in the MP browser.

FieldDescription
Allelic Composition (Genetic Background)The genotype composed of the mutation, linked to the MGI Allele Detail report, and the mouse strain background.
Annotated TermSpecific MP term used to describe the given genotype, linked to its Mammalian Phenotype Ontology Term Detail report.
ReferenceA listing of the supporting MGI references, linked to the References Detail report containing the full citation.

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How can I contribute to the vocabulary?

Your input is welcome. Additional terms or revisions may be requested through our tracking system at Sourceforge. Please contact us with suggestions, additions, or questions about the Mammalian Phenotype Ontology.

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