This help document answers the following questions:
The traditional way to describe space within the embryo is to use anatomical terms. The Mouse Anatomical Dictionary provides a standardized nomenclature for these anatomical terms.Back to top
For each developmental stage (using the staging system defined by Theiler), the Anatomical Dictionary organizes the terms hierarchically from body region or system to tissue 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. The Mouse Anatomical Dictionary Browser lets you navigate the extensive dictionary hierarchies for the different developmental stages, locate specific anatomical structures within those hierarchies, and see the expression results associated with those structures.Back to top
You can either browse or search from the Mouse Anatomical Dictionary Browser entry page. Browsing brings up a Term Detail page displaying the highest level terms in the hierarchy at that stage, providing a starting point for navigating the ontology to locate specific anatomical structures. Clicking an individual term on a Term Detail page displays the specified anatomical structure, together with its parents (superstructures), siblings (structures at the same level), and children (substructures).
Searching by entering a text string in the Query field and selecting a developmental stage brings up a Query Results page displaying all structures that match the query.Back to top
You can search by term to determine where a particular structure exists in the Anatomical Dictionary and whether there is any gene expression data associated with the structure. To do this:
To select two or more stages, do the following:
|Text: Bold, black||Number of entries found per Theiler Stage(s) (TS). For example, 5 Theiler stage 16 means there are five anatomical structures that match or include your query term at TS 16. If you select more than one stage or ALL, the stages with terms matching your query appear in chronological order.|
|Links: Blue||A list of structures that match or include the term queried.|
Click the desired structure from the query results list to get its AD Browser-term detail page. The table below describes the fields on the AD Browser-term detail page.Back to top
To examine the hierarchy of anatomical structures at each stage and to determine which structures have gene expression results attached to them, click on one of the Theiler stages highlighted in blue on the AD Browser page. The search returns an AD Browser-term detail page; the table below describes the information on that page. Click on structures to navigate progressively through the hierarchy to locate specific anatomical terms.Back to top
|Name of the selected anatomical structure and its synonyms.|
|Selected structure||Red||The selected anatomical structure appears, highlighted in red. If there are any gene expression results associated with this structure, the number appears in parentheses following this term. To see a summary listing of the results, click show all.|
|Links||Blue||List of all paths to the term. Click on the desired link to bring up the detail page for that term. The AD Browser displays terms in a hierarchy to indicate the parents (superstructures), siblings (structures at the same level), and children (substructures) of the selected structure.