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Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_agea[set$eqmouse_coronal][seed_age$eqP56][map_age$eqP56][seed_point$eq6800,4200,5600]
[correlation_threshold1$eq0.84][correlation_threshold2$eq0.93]

service::mouse_correlation

Parameters

set

String

Data set name: mouse or mouse_coronal.

structures

Array (optional)

Comma delimited list of Structure.id or Structure.acronym.

row

Integer

DataSet.id to correlate against.

sort_order

String (optional)

'asc' or 'desc'. Defaults to 'desc'.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_correlation[set$eqmouse][row$eq68918934]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_correlation[set$eqmouse_coronal][row$eq357096]

service::mouse_differential

Parameters

set

String

Data set name: mouse or mouse_coronal.

structures1

Array

Comma delimited list of Structure.id.

structures2

Array

Comma delimited list of Structure.id.

threshold1

Array (optional)

Comma delimited Integer pair indicating thresholds for domain 1.

threshold2

Array (optional)

Comma delimited Integer pair indicating thresholds for domain 2.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Examples

Code Block

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_differential[set$eq'mouse'][structures1$eq8][structures2$eq315]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_differential[set$eq'mouse_coronal'][structures1$eq8][structures2$eq315]

service::mouse_connectivity_correlation

Parameters

row

Integer

SectionDataSet.id to correlate against.

structures

Array (optional)

Comma delimited list of Integer Structure.id or String Structure.acronym.

hemisphere

String (optional)

Structure’s hemisphere. Use 'Right' or 'Left'. Defaults to both hemispheres.

transgenic_lines

Array (optional)

Comma delimited list of Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

sort_order

String (optional)

'asc' or 'desc'. Defaults to 'desc'.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_connectivity_correlation[row$eq112162251][structures$eqTH][hemisphere$eqright][num_rows$eq100][transgenic_lines$eq0,177838259]

...

Search for injection sites near a set of 3-D coordinates, ranking the results by their distance from the coordinates.

Parameters

seed_point

Array

A comma delimited triple indicating the coordinates of a point in 3-D space.

transgenic_lines

Array (optional)

Comma delimited list of Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_connectivity_injection_coordinate[seed_point$eq6600,5400,4800][transgenic_lines$eq0]

...

Search by injection structures, ranking the results the results by signal in the target structures.

Parameters

injection_domain

Array

Comma delimited list of Integer Structure.id or String Structure.acronym.

target_domain

Array (optional)

Comma delimited list of Integer Structure.id or String Structure.acronym.

injection_hemisphere

String (optional)

'Right' or 'Left'. Defaults to both hemispheres.

target_hemisphere

String (optional)

'Right' or 'Left'. Defaults to both hemispheres.

injection_threshold

Array (optional)

Pair of floating point values representing the correlation seed age threshold.

target_threshold

Array (optional)

Pair of floating point values representing the correlation seed age threshold.

transgenic_lines

Array (optional)

Comma delimited list of Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_connectivity_injection_structure[injection_domain$eqTH][injection_hemisphere$eqRight][target_domain$eqVIS][target_hemisphere$eqRight][transgenic_lines$eq0]

...

Displays all SectionDataSets with projection signal density >= 0.1 at the seed point. This service also returns the path along the most dense pixels from the seed point to the center of each injection site.

Parameters

seed_point

Array

A comma delimited triple indicating the coordinates of a point in 3-D SectionDataSet space.

transgenic_lines

Array (optional)

Comma delimited list of Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

section_data_set

Integer (optional)

SectionDataSet.id to filter the results.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_connectivity_target_spatial[seed_point$eq6600,5400,4800][start_row$eq25][num_rows$eq50]

service::nhp_lmd_microarray_correlation

Parameters

donors

Array (optional)

comma separated list of integers Donor ids. Defaults to all donors.

structures

Array

Comma delimited list of Structure.id.

probes

Integer

Probe.id to correlate against.

sort_order

String (optional)

'asc' or 'desc'. Defaults to 'asc'.

start_row

Integer (optional)

starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::nhp_lmd_microarray_correlation[probes$eq30357][structures$eqBN]

service::nhp_lmd_microarray_differential

Parameters

donors1

Array (optional)

Comma delimited list of Donor.id. Defaults to all donors.

structures1

Array

Comma delimited list of Structure.id.

donors2

Array (optional)

Comma delimited list of Donor.id. Defaults to all donors.

structures2

Array

Comma delimited list of Structure.id.

sort_by

String (optional)

'p-value' or 'fold-change'. Defaults to 'p-value'.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::nhp_lmd_microarray_differential[structures1$eqHF][structures2$eqBN]

service::nhp_lmd_microarray_expression

Parameters

probes

Integer

Probe.id to correlate against.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::nhp_lmd_microarray_expression[probes$eq15815]

service::nhp_macro_microarray_correlation

Parameters

donors

Array (optional)

Donor.id. Defaults to all donors.

structures

Array

Comma delimited list of Structure.id.

probes

Integer

Probe.id to correlate against.

sort_order

String (optional)

'asc' or 'desc'. Defaults to 'asc'.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::nhp_macro_microarray_correlation[probes$eq49067][structures$eqBN]

service::nhp_macro_microarray_differential

Parameters

donors1

Array (optional)

Donor.id. Defaults to all donors.

structures1

Array

Comma delimited list of Structure.id.

donors2

Array (optional)

Donor.id. Defaults to all donors.

structures2

Array

Comma delimited list of Structure.id.

sort_by

String (optional)

'p-value' or 'fold-change'. Defaults to 'p-value'.

start_row

Integer (optional)

starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Examples

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::nhp_macro_microarray_differential[structures1$eqHF][structures2$eqBN]

service::nhp_macro_microarray_expression

Parameters

probes

Integer

Probe.id to correlate against.

start_row

Integer (optional)

Starting row of data for paging purposes. Defaults to 0.

num_rows

Integer (optional)

Number of rows of data for paging purposes. Defaults to 2000.

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::nhp_macro_microarray_expression[probes$eq15815]

Parameters

query_string

String

String to search for (* is a wildcard)

k

String

The model that is the type of object to search for (i.e. Gene)

Example

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::text_search[query_string$eq'abat'][k$eqGene]

...

The output from the previous pipeline stage in json format.

Parameters

(left hand side of parameter)

The variable id to be set in the pipeline namespace.

(right hand side of parameter)

A string using simple path syntax.

...

Code Block
pipe::list[gene_ids$eq'id'][probe_ids$eq'probes/probe/id']

Example

Code Block
http://api.brain-map.org/api/v2/data/query.json?criteria=
model::Organism[name$il'*sapiens'],
pipe::list[xorganism_id$eq'id'],
model::Gene[organism_id$in$xorganism_id]

...

The constant string or variable passed into the input parameter

Parameters

pattern

Regular expression pattern to match against

replacement

String to replace the strings in input that match pattern.

input

Variable obtained from pipe::list or a constant string.

output

Name of a variable to assign the results to.

...

Code Block
pipe::replace[pattern$eq'a'][replacement$eq'b'][input$in'abcd'][output$eqexample]

Example

Code Block
http://api.brain-map.org/api/v2/data/query.json?criteria=
model::Structure[acronym$eq'HiF'][ontology_id$eq7],
pipe::list[path$eq'structure_id_path'],
pipe::replace[pattern$eq'$'][replacement$eq'*'][input$in$path][output$eq'descendents'],
model::Structure[structure_id_path$il$descendents][ontology_id$eq7]

...

The constant string or variable passed into the input parameter

Parameters

pattern

A regular expression pattern to match against.

input

A variable obtained from pipe::list or a constant string.

output

The name of a variable to assign the results to.

...

Code Block
pipe::split[pattern$eq'x'][input$in'axbxcxd'][output$eqexample]

Example

Code Block
http://api.brain-map.org/api/v2/data/query.json?criteria=
model::Structure[acronym$eq'HiF'][ontology_id$eq7],pipe::list[path$eq'structure_id_path'],
pipe::replace[pattern$eq'(^\/)|(\/$)'][replacement$eq''][input$in$path][output$eq'path'],
pipe::split[pattern$eq'/'][input$in$path][output$eq'ancestors'],model::Structure[id$in$ancestors][ontology_id$eq7]

...