Querying the GUDMAP Data Browser
This section describes various ways you can query GUDMAP/RBK data by gene, anatomy and data attributes.
- Query by Gene
- Faceting Sidebar
- Querying multiple genes (Batch Query)
- Query by Anatomy
- Boolean Anatomy Search
Query by Gene
Enter a gene symbol/name (or synonym) in the search box on the homepage (https://www.gudmap.org) or by using the menu navigation (Search > Genes).
The results include GUDMAP records that contain information about the expression of the gene or genes of interest and any available related data in our repository.
Columns indicate the presence of Expression Scoring, Array Data or Imaging data from specimen (in situ, etc). The Imaging column includes representative thumbnails of the imaging data.
The GUDMAP Data Browser implements a “faceting sidebar” to narrow your search results by various data attributes and metadata. The facets available are adapted for the type of GUDMAP records you are searching (Gene, Specimen, Anatomy, etc.)
For the gene search, in the left sidebar of the results, you may filter results further by these categories:
- NCBI Symbol
- MGI Symbol
- Any Data (present, not present)
- Imaging Data (present, not present)
- Array Data (present, not present)
- Scored Expression Data (present, not present)
- Scored Expression Region
- Assay Type
- Anchor Gene Anatomy
- Marker Gene Anatomy
- Antibody Tests
Each facet is in its own panel and displays up to 10 attributes, ranked by number of records associated with the attribute.
You can use the search field in the panel to narrow down your choices before selecting attributes.
In this example, we’ve cleared the previous search by clicking the Clear All button. Now we are narrowing down the NCBI symbol list using
sox2. Then we can select the
Sox2 attribute, which will avoid the results including
Since the facet panel can only display up to 10 attributes, you can click Show More to open up a window that displays all of the attributes (up to 25 attributes appear at a time; to view more, click the pagination arrows at the bottom of the window).
All will select all checkboxes that appear on the page. Clicking
None will de-select all checkboxes. You can also use the search field to narrow down your choices by typing in free text.
The search automatically assumes a ‘wildcard’ at the end of the search string; therefore, typing in ‘uro’ will search for words/symbols beginning with ‘uro’, e.g. urothelium, urogenital, uroplakin, etc.
Querying multiple genes (Batch Query)
To search for multiple genes, use the search method described above but enter multiple genes separated with a pipe character (
| ) with no spaces in between. This list may contain a mixture of different terms (e.g. MGI accession IDs and MCBI Gene Symbols).
For example, specifying:
in the main search box will returns all the records that have either the sub-string
Six2 associated with any metadata as the result.
- There should be no spaces between
|and individual search strings.
- The search string is not case sensitive.
- Hover over the seach icon (magnifying glass icon next to the search box) to get the tooltip of the search syntax.
Convert a column of gene symbols in a spreadsheet to a search string
If you already have a column of interesting gene symbols in a local spreadsheet, here’s how you can turn that into a query in GUDMAP.
Most spreadsheet applications support the concatenation or the text join on a range of cells. For Open Office and Google Spreadsheet, use the following formula to create the search string.
TEXTJOIN(delimiter, ignore_empty, text1, [text2, ...]) Where - delimiter: A string, possibly empty, or a reference to a valid string. If empty, text will be simply concatenated. - ignore_empty: A boolean; if TRUE, empty cells selected in the text arguments won't be included in the result. - text1 - Any text item. This could be a string, or an array of strings in a range. - text2, ... [OPTIONAL] - Additional text item(s). Sample Usage: TEXTJOIN(“|“, TRUE, “ATP6”, “COX1”) TEXTJOIN(“|”, TRUE, A2:A101) Where A2:A101 is the cell range containing gene symbols
Query by Anatomy
From the menu navigation, go to Search > Anatomy Terms and choose either Anatomy Tree or Faceted Search.
This option provides a tree structure view of anatomical terms that conform to the GUDMAP Ontology.
Start typing an anatomical region in the search field. In the example below, we’re typing “prostate”. You may also use the dropdown button to specify a Theiler stage:
…and the tree will highlight corresponding term(s). In the following screenshot you’ll see part of the tree with all terms related to “prostate”.
Click a term to go to the corresponding Anatomy records page (see further down the page).
This option takes you directly to the Anatomy section of the Data Browser where you may use the faceting sidebar to choose or search for anatomy regions by Name or ontology IDs (ie,
EMAPA:18976). Click the eye icon of the row you’re interested in to view the corresponding Anatomy record page (see below).
Anatomy record page
Let’s search for “cortical renal tubule” from the anatomy faceted search:
We click on the eye icon in the first row to display the following Anatomy record page.
On the Contents sidebar to the right side of the page, you’ll see a list of available data including the following types:
- Part of (indicates ‘parent’ anatomical regions)
- Includes (indicates ‘children’ anatomical regions)
- Specimen Expression Rollup
- Anchor Gene Rollup
- Marker Gene Rollup
- Gene List Rollup
- Mouse Allele Expression
The numbers to the right of the names indicate how many instances of these types of data are available.
Boolean Anatomy Search
The Boolean Anatomy Search allows complex queries to be constructed to search for gene expression based on selected anatomical structures.
The search allows combinations of structures and developmental stages and different combinations of expression found to be present, not detected and uncertain. The search can be applied to a combination of structures or just to one structure. For example, you can search for only genes expressed in a structure, or to compare expression in the same structure at different stages.
For more details, please go to the Boolean Anatomy Search help page.