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. Organizing the phenotype terms as a Directed Acyclic Graph (DAG), i.e., in which a term can have more than one parent, allows presentation of phenotypes from multiple perspectives.

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 or MP ID here to improve your searches with the Phenotype/Disease box on the Phenotypes, Alleles, & Disease Models and Genes and Markers Query Forms as well as the appropriate fields on the Gene Expression Data Query and Human - Mouse: Disease Connection forms. Selected terms in the Phenotype Tree View link to a listing of all genotypes annotated to the term and it descendants.

You can either browse or search from the MP Browser. You can browse by clicking on terms in the Phenotype Tree View. This shows a term's place in the hierarchy, provides links to all genotypes annotated to a selected term, and updates the Phenotype Term Detail section of the page with the selected term's parent terms, ID, definition, and any synonyms associated with the phenotype term. Searching requires entering a text string in the Phenotype Search box. This brings up an autocomplete list displaying all matches.

How do I browse the vocabulary?

To browse the vocabulary, click a term in the Tree View or a parent term in the Term Detail section until you find the desired phenotypic term. A black triangle at the beginning of a term indicates the term has subterms. You can expand branches by clicking on a term or its preceding triangle. If you click on a term, this also updates the Phenotype Term Detail section. You can collapse branches by clicking on the downward-pointing black triangle. You can also click on the triangles to navigate the branches without updating the Term Detail section. You can copy term IDs into the Phenotypes/Disease box on the Phenotypes, Alleles, & Disease Models Query Form to search for data associated with this term.

How do I search the vocabulary?

The Phenotype Search field accepts any text string and searches for all terms containing that string and any synonyms. To do this:

Select a term in your search results to automatically update the Phenotype Term Detail and Phenotype Tree View sections on the right. Use the Clear button to start a new search.

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How do I interpret my results?

Phenotype Search The search finds all phenotype terms that contain all of your search terms and displays a ranked list of those terms. Click on a term to update the Phenotype Term Detail and Tree View sections of the page with the appropriate phenotypes and the selected term highlighted in blue.
Phenotype Term Detail
Term The selected term is highlighted in blue. If you accessed this page by clicking on a term on another page, the appropriate phenotype is highlighted. Otherwise, before you initiate a search or browse, the default term is mammalian phenotype.
Synonyms Alternative search terms for the selected term
Definition Official definition for the term
Parent TermsThe immediate parent terms for the selected phenotype. Because the Mammalian Phenotype Ontology is built on a DAG framework, a term may have more than one parent term. This means a term appears in multiple branches of the tree. For example, seizures is an abnormal behavior and an abnormal nervous system physiology phenotype. The term has an "is a" relationship to the parent term.
IDThe unique accession ID for the phenotype term
Other IDsAlternative IDs for the term, such as Fyler codes, a hierarchical classification of congenital heart disease.
Phenotype Tree View The main phenotype headings are shown beneath the section header. The number of genotypes/annotations to the selected term is shown. Child terms are shown beneath the selected term in the tree view. You can collapse or expand branches by clicking on a triangle. When you select a new term, it is highlighted in blue and the Term Detail section is updated.
Click on the number of genotypes/annotations for a listing of all the genotypes annotated to the term.
"Is-a" RelationshipIndicates 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.
Black TriangleA black triangle preceding a term in the Tree View indicates that the term has children. Click on the triangle to see the additional paths. You can collapse branches by clicking on the downward-pointing triangles. Unlike clicking on a term, clicking on a triangle does not update the selected term.
# genotypes,  # annotationsNumber of genotypes annotated to the term and its descendants, followed by the number of annotations to each term and its descendants. Click this label to see the Mammalian Phenotype Ontology Annotations Query Results.

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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 descendants. You access this report by clicking the text displaying the number of genotypes and annotations for a featured term in the MP browser or the number of phenotypes in the Mutations, Alleles, and Phenotypes section of a Gene Detail page. Depending upon how you reached the results, you may be offered the option of exporting the results in a spreadsheet format.

FieldDescription
Genotype/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, with links to the Journal (if available) and data curated from the reference.

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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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