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Boolean Anatomy Search - Query Syntax Help

It is possible to build, modify or extend your Boolean Search by entering/editing the query string in the text box at the foot of the Boolean Anatomy Search page.

The format of the query string is explained in this help page.

We'll start with an example:

To search for genes with present (p) expression in the bladder from Theiler Stage (TS) 20 to 24 with graded pattern (pt) and distal location (lc).

The query string looks like this: GENE: p{in "bladder" TS20..TS24 pt=graded lc=distal}

In the example the items in bold italics are individual components of the query string. We'll go through each one in turn, explaining it's purpose, syntax and options.

Component 1 – What to search for
Options(2): GENE: and GUDMAP:

This specifies whether to search for ‘genes’ (GENE:) or ‘GUDMAP entries’ (GUDMAP:). The colon must be included and a blank space must come after it. If we wanted to search for GUDMAP entries instead of genes in our example the syntax would be:
GUDMAP: p{in "bladder" TS20..TS24 pt=graded lc=distal}

Component 2 – Expression selection
Options(3): p (present), nd (not detected) & u (uncertain)

GENE: p{in "bladder" TS20..TS24 pt=graded lc=distal}

This specifies what type of expression to search for. To use more than one of these separate with a comma.
e.g. for present OR uncertain, use
GENE: p,u{in "bladder" TS20..TS24 pt=graded lc=distal}


The next 4 sections – structure, stage, pattern and location all are contained within braces (curly brackets) with a blank space between each.

Component 3 - Anatomical Structure/Component
Open braces followed by ‘in’ then a space.
Now add the name of the structure you want to search for (e.g bladder, testis, ovary, renal vesicle etc.). The name of the structure must be enclosed in double-quotes. In our example we are using "bladder".

GENE: p{in "bladder" TS20..TS24 pt=graded lc=distal}

Component 4 - Stage
Options: Users can specify any stage range from TS17 to TS28
Use the TS abbreviation for Theiler Stage followed by the stage number.
Separate stages with two full-stops

GENE: p{in "bladder" TS20..TS24 pt=graded lc=distal}

Component 5 – Pattern (optional)
Options: graded, regional, restricted, single cell, spotted, ubiquitous.
Use the keyword ‘pt=’ to add pattern information followed by the pattern you want to include.
To search all patterns, omit the pattern section.

For graded
GENE: p{in "bladder" TS20..TS24 pt=graded}

For single cell
GENE: p{in "bladder" TS20..TS24 pt=single cell}

For all patterns
GENE: p{in "bladder" TS20..TS24}

Component 6 – Location (optional)
Options: caudal, deep, distal, dorsal, lateral, medial, proximal, radial, rostral, surface, ventral.
Use the keyword ‘lc=’ to add location information followed by the location you want to include.
To search all locations, omit the location section.

For distal
GENE: p{in "bladder" TS20..TS24 pt=graded lc=distal}

For ventral
GENE: p{in "bladder" TS20..TS24 pt=single cell lc=ventral}

For all location with graded pattern
GENE: p{in "bladder" TS20..TS24 pt=graded}


Adding in multiple structures.
What has been described so far is for one structure and constitutes one 'element' of the query
(e.g p{in "bladder" TS20..TS24 pt=graded} is considered an element of the query)

To add multiple structures to your query simply add in further elements. Separate elements by using your Boolean operator AND or OR.

Example: to find genes that have present expression in the "renal vesicle" AND "s-shaped body" from stages TS22 to TS27, use the following syntax.

GENE: p{in "renal vesicle" TS22..TS27} AND p{in "s-shaped body" TS22..TS27}

Note – the NOT operator cannot be applied as the equivalent of a Boolean ‘NOT’ can be obtained by selecting AND in conjunction with ‘not detected’.

Example: to find genes that have present expression in the "renal vesicle" and NOT in the "s-shaped body" from stages TS22 to TS27, use the following syntax.

GENE: p{in renal vesicle TS22..TS27} AND nd{in s-shaped body TS22..TS27}


Searching for multiple patterns and locations.
With each set of braces only one pattern and one location can be applied. To search for multiple patterns and locations enter a new element to the query.

Example: to find genes with present expression in the "renal vesicle" from Theiler Stage 20 to 24 that has either graded OR regional expression, use the following syntax:

GENE: p{in "renal vesicle" TS20..TS24 pt=graded} OR p{in "renal vesicle" TS20..TS24 pt=regional}