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Connected Services and Pipes

service::dev_human_correlation
Parameters

set

String

Data set name: rna_seq_genes, rna_seq_exons, exon_microarray_genes or exon_microarray_exons

donors

Array (optional)

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

structures

Array

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

probes

Integer

Probe id to correlate against.

sort_order

String (optional)

'asc' for ascending order, or 'desc' for descending order. Defaults to descending.

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
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_correlation[set$eqrna_seq_genes][probes$eq1102244][structures$eq'CBC']

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_correlation[set$eqrna_seq_exons][probes$eq1102244][structures$eq'CBC']

Retrieve exon_microarray_genes correlation values for structure with the acronym, "CBC".

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_correlation[set$eqexon_microarray_genes][probes$eq81745][structures$eq'CBC']

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_correlation[set$eqexon_microarray_exons][probes$eq652249][structures$eq'CBC']
service::dev_human_differential
Parameters

set

String

Data set name: rna_seq_genes, rna_seq_exons, exon_microarray_genes or exon_microarray_exons

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.

Examples
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_differential[set$eq'rna_seq_genes'][structures1$eqDFC][structures2$eqMFC]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_differential[set$eq'rna_seq_genes'][structures1$eqDFC][structures2$eqMFC]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_differential[set$eq'exon_microarray_exons'][structures1$eqDFC][structures2$eqMFC]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_differential[set$eq'exon_microarray_genes'][structures1$eqDFC][structures2$eqMFC]
service::dev_human_expression
Parameters

set

String

Data set name: rna_seq_genes, rna_seq_exons, exon_microarray_genes or exon_microarray_exons

probes

Integer

Probe.id to correlate against

donors

Integer (optional)

Comma delimited list of Donor.id to filter expression results.

structures

Integer (optional)

Comma delimited list of Stucture.id to filter expression 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.

Examples
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_expression[set$eq'rna_seq_genes'][probes$eq1102244]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_expression[set$eq'rna_seq_exons'][probes$eq1014952]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_expression[set$eq'exon_microarray_genes'][probes$eq15]

http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_expression[set$eq'exon_microarray_exons'][probes$eq652249]
service::dev_human_microarray_correlation
Parameters

donors

Array (optional)

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

structures

Array

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

probes

Integer

Probe 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
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_microarray_correlation[probes$eq1048426][structures$eqSG]
service::dev_human_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
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_microarray_differential[structures1$eqMZ][structures2$eqCP]
service::dev_human_microarray_expression
Parameters

probes

Integer

Comma delimited list of Probe.id to filter microarray expression 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.

donors

Integer (optional)

Comma delimited list of Donor.id to filter microarray expression results.

structures

Integer (optional)

Comma delimited list of Structure.id to filter microarray expression results.

Example
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_human_microarray_expression[probes$eq1053223,1053224][donors$eq12566][structures$eq11587]
service::dev_mouse_agea
Parameters

seed_age

String

Age.id

map_age

String

Age.id

seed_point

Array

Comma delimited list of integers representing a point in the age's space.

seed_threshold

Array

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

map_threshold

Array

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

contrast_threshold

Array (optional)

Pair of integer values representing the contrast domain threshold.

target_threshold

Array (optional)

Pair of integer values representing the target domain threshold.

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
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_mouse_agea[seed_age$eq'E18.5'][map_age$eq'E15.5'][seed_point$eq4200,2380,2360]
[map_threshold$eq0.467,0.657][seed_threshold$eq0.811,0.924]
service::dev_mouse_correlation
Parameters

row

Integer

DataSet.id or Gene.id to correlate against.

structures

Array (optional)

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

ages

Array (optional)

Comma delimited list of Age.name.

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
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::dev_mouse_correlation[row$eq13267][structures$eq'NP'][ages$eq'P14','P28']
service::human_microarray_correlation
Parameters

donors

Array (optional)

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

structures

Array

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

probes

Integer

Probe.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
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::human_microarray_correlation[probes$eq1048426][structures$eq'FL']
service::human_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

'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
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::human_microarray_differential[structures1$eq4005][structures2$eq4006]
service::human_microarray_expression
Parameters

probes

Integer

Comma delimited list of Probe.id to filter microarray expression results.

donors

Integer (optional)

Comma delimited list of Donor.id to filter microarray expression results.

structures

Integer (optional)

Comma delimited list of Stucture.id to filter microarray expression 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.

Examples
http://api.brain-map.org/api/v2/data/query.xml?criteria=
service::human_microarray_expression[probes$eq1014952][donors$eq9861,10021][structures$eq4079]
service::mouse_agea
Parameters

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 a point in the data set 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.

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

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.

Response

A comma separated list made up of the values found according to the path is assigned to the variable. More than one variable may be assigned in a single list pipe.

Notes

A pipe may not be used at the beginning or end of a query pipeline. Pipe::list may be used between model and service stages in any combination. The scope of a variable in a pipe::list stage is from the pipe to the end of the pipeline. Prefix a pipe list variable with a dollar sign ($) to reference it. Use the $in operator when referencing a pipeline variable set by pipe::list because the output is a list.

Fragment
pipe::list[gene_ids$eq'id'][probe_ids$eq'probes/probe/id']
Example
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]
pipe::replace
Input

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.

Response

A string with the substitutions applied is assigned to the output variable.

Fragment
pipe::replace[pattern$eq'a'][replacement$eq'b'][input$in'abcd'][output$eqexample]
Example
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]
pipe::split
Input

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.

Response

An comma-separated list of input string split where the pattern matched.

Fragment
pipe::split[pattern$eq'x'][input$in'axbxcxd'][output$eqexample]
Example
http://api.brain-map.org/api/v2/data/query.json?criteria=
model::Structure[acronym$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]
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