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set

String

Data set name: mouse_coronal.

seed_age

String

An age identifier. P56.

map_age

String

An age identifier. P56.

seed_point

Array

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

correlation_threshold1

Float (optional)

Correlation threshold for domain 1.

correlation_threshold2

Float (optional)

Correlation threshold for domain 2.

threshold1

Array (optional)

Comma delimited Integer pair defining the threshold for domain 1.

threshold2

Array (optional)

Comma delimited Integer pair defining the threshold 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.

...

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' (not case sensitive). Defaults to both hemispheres.

transgenic_lines

Array (optional)

Comma delimited list of Integer TransgenicLinesTransgenicLine.id . Use ID 0 for wild typeor String TransgenicLine.name. Specify ID 0 to include 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.

...

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_connectivity_correlation[section_data_set$eq112162251row$eq112162251][structures$eqTH][hemisphere$eqright][num_rows$eq100][transgenic_lines$eq0,177838259]

service::mouse_connectivity_injection_coordinate

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 the data set 3-D space.

transgenic_lines

Array (optional)

Comma delimited list of Integer TransgenicLine.id . Use ID 0 for wild typeor String TransgenicLine.name. Specify ID 0 to include 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.

...

Code Block
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::mouse_connectivity_injection_coordinate[coordinates$eq6600seed_point$eq6600,5400,4800][transgenic_lines$eq0]

service::mouse_connectivity_injection_structure

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' (not case sensitive). Defaults to both hemispheres.

target_hemisphere

String (optional)

'Right' or 'Left' (not case sensitive). 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 TransgenicLinesTransgenicLine.id . Use ID 0 for wild typeor String TransgenicLine.name. Specify ID 0 to include 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.

...

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]

service::mouse_connectivity_target_spatial

Parameters

...

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 . Use ID 0 for wild typeor String TransgenicLine.name. Specify ID 0 to include 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[coordinates$eq6600seed_point$eq6600,5400,4800][start_row$eq25][num_rows$eq50]

...

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]

...

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]

...

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]

...

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]

...

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]

...

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]

...

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]

...

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]

...

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]

...

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]

SectionDataSet