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Querying by Anatomy (Tree View and Facet View) | GUDMAP
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Querying by Anatomy (Tree View and Facet View)

On this page:

Finding anatomy search options

From the menu navigation, go to BROWSE DATA > Anatomy Terms Search and choose either Anatomy Facet Search or Anatomy Tree View.

Navigating to the Anatomy searches via the menu

Using the Anatomy Tree

This option provides a tree structure view of anatomical terms that conforms to the GUDMAP Ontology. You can use this visualization to understand the hierarchy of anatomical regions and see any data in GUDMAP related to that region.

Start by typing an anatomical region in the search field. You may also use the dropdown button to specify a Theiler stage to indicate the age.

As a result, the tree will highlight corresponding term(s).

In the example below, we’re typing “proximal tubule” and using Theiler stage TS23 (15dpc):

Animation of typing prostate into the search field and seeing results

Click a term to go to its Anatomy record page.

In the following screenshot, we are seeing the resulting record for “early proximal tubule EMAPA:28003” (the ID corresponds to the GUDMAP Ontology identifier.)

Navigating to the Anatomy searches via the menu

Choosing Anatomy Terms Search takes you directly to the Anatomy section of the Data Browser.

From here you can use use the filtering sidebar or the free text search to find anatomy records by Name or ontology IDs (ie, EMAPA:18976).

Click the “View” icon of the row you’re interested in to view the corresponding Anatomy record page (see below).

Screenshot of the Anatomy faceted search

Elements of the Anatomy record page

Let’s search for “cortical renal tubule” from the anatomy faceted search:

Example of searching for cortical renal tubule

Here is the resulting Anatomy record page:

Screenshot of the Anatomy faceted search

On the Sections sidebar to the left side of the page, you’ll see a list of available data including:

Section Description
Part of Indicates “parent” regions to this anatomical region. For example, pelvic urethra is part of urethra.
Includes Indicates “children” regions to this anatomical region. For example, pelvic urethra includes epithelium of pelvic urethra.
Specimen Expression Rollup TODO
Anchor Gene Rollup TODO
Marker Gene Rollup TODO
Gene List Rollup TODO
Mouse Allele Expression TODO