Using the Adult Mouse Anatomy Browser
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The Anatomy Ontology for the Adult Mouse was developed and is being refined to provide standardized nomenclature for anatomical structures in the postnatal mouse (Theiler stage 28).

Use the Adult Mouse Anatomy Browser to view the anatomical terms and their relationships in a hierarchical display.

This help document answers the following questions about the Browser:

See also:

How is the Adult Mouse Anatomy Ontology organized?

The Anatomy Ontology for the Adult Mouse is organized spatially and functionally, using "is a" and "part of" relationships. Anatomical terms are arranged as a hierarchy from body region or organ system to tissue substructure.

Modeling the anatomy hierarchically makes it possible to record expression results from assays with differing spatial resolution in a consistent and integrated manner. Organizing the anatomical terms as a Directed Acyclic Graph (DAG), i.e., in which a term can have more than one parent, allows presentation of the anatomy from multiple perspectives.

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What can I use the Browser to find?

Use the Browser to find standardized vocabulary terms for anatomical structures present in the postnatal mouse (Theiler stage 28).

You can either browse or search from the Adult Mouse Anatomy Browser entry page.

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How do I browse the vocabulary?

To browse the vocabulary, click Adult Mouse Anatomy Ontology on the Adult Mouse Anatomy Browser page. A Term Detail page appears displaying the highest level terms in the hierarchy. Click on structures to navigate progressively through the ontology in order to locate specific anatomical terms.

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How do I search the vocabulary?

The Query field accepts any text string and searches for all terms containing that string plus any synonyms. For example, entering cranium returns all terms containing the word cranium, such as chondrocranium, viserocranium, chondrocranium bone and viserocranium bone, as well as, for example, neurocranium, which is a synonym for chondrocranium.

Entering the MA accession identifier in the Query field returns only an exact match on the number.

To search the Adult Mouse Anatomy Browser:

  1. Type either a text string or an MA accession number in the Query box.
  2. Click Submit Query. The search returns a Query Results page that displays all matching terms in the vocabulary.
  3. Click the desired term to view its Term Detail page.

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What can I find on the Query Results page?

The Query Results page lists all matching anatomical terms in the vocabulary. Click the desired term to view its Term Detail page.

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How do I interpret the Term Detail page?

The Term Detail page provides the following information.

FieldColorDescription
MA term,
MA ID,
Synonyms,
Number of paths to term
Yellow The selected anatomical term, the unique identifier (accession number) for the term, any synonyms associated with the term (if available), and the number of paths to the term within the ontology.
Name, Unique identifierRedName of the anatomical term selected, followed by its unique identifier. There is one identifier for each term in the Adult Mouse Anatomy Ontology. This means that the ID is always the same regardless of how many times the term is displayed as part of a specific path to that term. The unique identifier for a given structure remains the same even if its name changes.
LinksBlueList of all paths to the term. Click the desired link to bring up a detail page for that term.
 "Is-a" Relationship Purple Indicates that the term is an instance or type of the more general term (parent or superstructure) above it in the hierarchy.
 "Part-of" Relationship BlueIndicates that the term is a component of the more general term (parent or superstructure) above it in the hierarchy.
+ BlueA plus sign (+) following a term indicates that the term has children (substructures) within the vocabulary. Click on the term to see the additional paths.

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How can I contribute to the vocabulary?

Your input is welcome. Please contact us with suggestions, additions, or questions about the Adult Mouse Anatomy Ontology.

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Terry Hayamizu, Mary Mangan, John Corradi, and Martin Ringwald developed the Adult Mouse Anatomy Ontology as part of the Gene Expression Database (GXD) project. GXD is funded by NIH grant HD062499. Postdoctoral fellowships F32 HD08435-01 and F32 HG00215-01 supported M.M. and J.C.