Allen Brain Atlas API: RMA Grammar

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Connected Services and Pipes

Learn about Connected Services and Pipes with comprehensive guides and examples from Allen Institute for Brain Science.

service::dev_human_correlation

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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.

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Examples

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_correlation[set$eqrna_seq_genes][probes$eq1090294][structures$eq'CBC']
http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_correlation[set$eqrna_seq_exons][probes$eq279330730][structures$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$eqexon_microarray_genes][probes$eq9463][structures$eq'CBC']
http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_correlation[set$eqexon_microarray_exons][probes$eq280550735][structures$eq'CBC']

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service::dev_human_differential

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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.

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Examples

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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]

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service::dev_human_expression

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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.

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Examples

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_expression[set$eq'rna_seq_genes'][probes$eq1090294] 
http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_expression[set$eq'rna_seq_exons'][probes$eq279330730] 
http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_expression[set$eq'exon_microarray_genes'][probes$eq9463] 
http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_expression[set$eq'exon_microarray_exons'][probes$eq280550735]

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service::dev_human_microarray_correlation

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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.

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Example

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_microarray_correlation[probes$eq1048426][structures$eqSG]

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service::dev_human_microarray_differential

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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.

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Example

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::dev_human_microarray_differential[structures1$eqMZ][structures2$eqCP]

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service::dev_human_microarray_expression

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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.

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Example

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

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service::dev_mouse_agea

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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.

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Example

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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]

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service::dev_mouse_correlation

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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.

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Example

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

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service::gbm_correlation

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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.

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Example

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::gbm_correlation[probes$eq3551][structures$eqGBM]

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service::gbm_differential

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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.

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Example

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::gbm_differential[structures1$eqGBM][structures2$eqCTpan]

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service::gbm_expression

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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 gbm expression results.
structures	Integer (optional)	Comma delimited list of Structure.id to filter gbm expression results.

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Example

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::gbm_expression[probes$eq3551][donors$eq703393][structures$eqGBM]

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service::gbm_ish_differential

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Parameters

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.

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Examples

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::gbm_ish_differential[structures1$eqCTpnn][structures2$eqIT]

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service::gbm_ish_expression

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Parameters

structures	Array	Comma delimited list of Structure.id.
threshold	Array (optional)	Comma delimited Integer pair indicating thresholds.
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.

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Examples

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::gbm_ish_expression[structures$eqCTpnn][threshold$eq0,100000]

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service::human_microarray_correlation

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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.

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Example

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

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service::human_microarray_differential

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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.

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Examples

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

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service::human_microarray_expression

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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.

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Examples

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

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service::mouse_agea

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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 the coordinates of a point in 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.

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Example

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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]

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service::mouse_correlation

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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.

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Example

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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]

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service::mouse_differential

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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.

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Examples

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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]‍

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service::mouse_connectivity_correlation

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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.
injection_structures	Array (optional)	Comma delimited list of Integer Structure.id or String Structure.acronym.
primary_structure_only	String (optional)	‘true’ or ‘false’
sort_order	String (optional)	‘asc’ or ‘desc’. Defaults to ‘desc’.
product_ids	Array (optional)	Comma delimited list of Integer Product.ids.
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.

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Example

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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]

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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.

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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.
injection_structures	Array (optional)	Comma delimited list of Integer Structure.id or String Structure.acronym.
primary_structure_only	String (optional)	‘true’ or ‘false’
product_ids	Array (optional)	Comma delimited list of Integer Product.ids.
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.

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Example

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

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service::mouse_connectivity_injection_structure

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

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Parameters

injection_structures	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.
transgenic_lines	Array (optional)	Comma delimited list of Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.
injection_domain	Array (optional)	Comma delimited list of Integer Structure.id or String Structure.acronym.
primary_structure_only	String (optional)	‘true’ or ‘false’
product_ids	Array (optional)	Comma delimited list of Integer Product.ids.
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.

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Example

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

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service::mouse_connectivity_target_spatial

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.

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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.
injection_structures	Array (optional)	Comma delimited list of Integer Structure.id or String Structure.acronym.
primary_structure_only	String (optional)	‘true’ or ‘false’
product_ids	Array (optional)	Comma delimited list of Integer Product.ids.
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.

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Example

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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]

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service::nhp_lmd_microarray_correlation

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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.

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Example

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

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service::nhp_lmd_microarray_differential

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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.

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Example

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

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service::nhp_lmd_microarray_expression

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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.

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Example

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

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service::nhp_macro_microarray_correlation

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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.

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Example

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

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service::nhp_macro_microarray_differential

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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.

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Examples

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

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service::nhp_macro_microarray_expression

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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.

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Example

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

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service::tbi_correlation

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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.

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Example

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http://api.brain-map.org/api/v2/data/query.xml?criteria= service::tbi_correlation[structures$eqHIP][probes$eq499304660]

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service::tbi_differential

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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.

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Example

‍

http://api.brain-map.org/api/v2/data/query.xml?criteria= service::tbi_differential[structures1$eqFWM][structures2$eqTCx]

‍

service::tbi_expression

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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 gbm expression results.
structures	Integer (optional)	Comma delimited list of Structure.id to filter gbm expression results.

Example

‍

http://api.brain-map.org/api/v2/data/query.xml?criteria= service::tbi_expression[donors$eq309335438][structures$eqPCx][probes$eq499304660]

‍

service::text_search

‍

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]

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pipe::list

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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]

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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]

‍

SectionDataSet

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API

Restful Model Access RMA

Learn about Restful Model Access RMA with comprehensive guides and examples from Allen Institute for Brain Science.

RESTful Model Access (RMA) is an HTTP service designed along RESTful principles to allow access to data in the Allen Institute API. Data model queries support JSON, XML and CSV formats. They can include join, filter, sort, page and eager loading of associations. RMA can also pipe results to perform compound queries and connect to data services. RMA services support JSON and XML formats. The API utility, RMA Query Builder, can be used to compose RMA queries.

‍

RESTful Resources

The path to the RMA service is /api/v2/data. Other models may be substituted for Organism, such as Gene, Chromosome, or Structure. Model names are always capitalized and singular. The number following the model is a resource id. Valid result formats include JSON (.json), XML (.xml) and CSV (.csv)

‍

Prototype

‍

http://api.brain-map.org/api/v2/data/[Model]/[Model.id].[json|xml|csv]

‍

Examples

Use a browser or other HTTP client to access:

‍

http://api.brain-map.org/api/v2/data/Organism/1.xml 
http://api.brain-map.org/api/v2/data/Gene/15.xml 
http://api.brain-map.org/api/v2/data/Chromosome/12.json 
http://api.brain-map.org/api/v2/data/Structure/4005.xml

‍

Use the keyword query rather than an id to search across all resources in a model.

‍

http://api.brain-map.org/api/v2/data/Organism/query.xml

‍

Use the keyword describe to retrieve information about the available associations for a model. .json format is also available.

‍

http://api.brain-map.org/api/v2/data/Gene/describe.xml

‍

Use the keyword enumerate to retrieve information about all available models and associations. .json format is also available.

‍

http://api.brain-map.org/api/v2/data/enumerate.xml

‍

Use the keyword query without a model or id if the needed information is specified elsewhere in the url. The part after the question mark is explained throughout this document.

‍

http://api.brain-map.org/api/v2/data/query.xml?include=model::Gene[id$eq15]

‍

Response

JSON, XML and CSV formats are supported. For example:

‍

<Response success="true" id="0" start_row="0" num_rows="1" total_rows="1"> 
  <organisms> 
    <organism>
     <id>1</id>
     <name>Homo Sapiens</name> 
     <ncbitaxonomyid>9606</ncbitaxonomyid>
    </organism>
  </organisms>
</Response>

‍

Include

Resources in the models are associated with other resources. Display this additional information using the include= parameter:

‍

Example

Retrieve details for the Chromosome with ID=12 and include its associated organism:

‍

http://api.brain-map.org/api/v2/data/Chromosome/12.xml?include=organism

‍

Response

The associated information will be nested in the response:

‍

<Response success="true" id="0" start_row="0" num_rows="1" total_rows="1">
  <chromosomes>
    <chromosome>
      <id>15</id> 
      <name>21</name>
      <organism-id>1</organism-id> 
      <organism> 
        <id>1</id>
        <name>Homo Sapiens</name>
        <ncbitaxonomyid>9606</ncbitaxonomyid>
      </organism>
    </chromosome>
  </chromosomes>
</Response>

‍

The include= parameter is discussed in more detail in the RMA Path Syntax section.

‍

Criteria

Use the criteria parameter to refine the query.

‍

Example

The following criteria will find chromosome resources from the organism with NCBI taxonomy id 9606 (which happens to be Homo Sapiens).

‍

http://api.brain-map.org/api/v2/data/Chromosome/query.xml?criteria=organism[ncbitaxonomyid$eq9606]

‍

The criteria= parameter is discussed in more detail in the RMA Path Syntax section.

‍

Only, Except And Tabular

Use the only= or except= parameters to restrict the attributes returned in the response. By default the results include all literal attributes of the resource. These options can be applied to model stages, but not service or pipe stages.

‍

Example

‍

http://api.brain-map.org/api/v2/data/Organism/1.xml?only=name

‍

Response

‍

<Response success="true" id="0" start_row="0" num_rows="1" total_rows="1">
  <organisms>
    <organism>
      <name>Homo Sapiens</name>
    </organism>
  </organisms>
</Response>

‍

Use tabular= to restrict the attributes and also return them in a tabular format. Use ‘as’ to alias an attribute name or ‘distinct’ to eliminate duplicate rows. This option is recommended for accessing data in applications where sorting and paging are used in a tabular, spreadsheet-like display. This option can be applied to model stages, but not service or pipe stages. The csv format is required to be tabular and it defaults to displaying all attributes of the model. If associated models are referenced in the tabular= option, they should be present in a criteria= option as well. The tabular= option masks include= for serialization purposes.

‍

Example

‍

http://api.brain-map.org/api/v2/data/Gene/15.xml?criteria=probes&tabular=distinct%20genes.name%20as%20gene_name,probes.name%20as%20probe_name

‍

Response

‍

<Response success="true" id="0" start_row="0" num_rows="15" total_rows="15">
  <hash>
    <gene-name>4-aminobutyrate aminotransferase</gene-name>
    <probe-name>RP_100125_04_D02</probe-name>
  </hash> 
  .....
</Response>

‍

Sorting And Paging

Limit the number of results by using the start_row=, num_rows= and order= URL parameters. Use num_rows=all to retrieve all records (not recommended for large queries). The response body contains information about the progress of paging. Use count=false if you do not want paging information returned in the response.

‍

Prototype

‍

http://api.brain-map.org/api/v2/data/[Model]/query.xml?num_rows=[#]&start_row=[#]&order=[...]

‍

Example

Request the first Product by specifying start_row=0:

‍

http://api.brain-map.org/api/v2/data/Product/query.xml?start_row=0&num_rows=1

‍

Request 10 Products beginning with the 20th row, and order by the Products’ names:

‍

http://api.brain-map.org/api/v2/data/Product/query.xml?num_rows=10&start_row=20&order=products.name

‍

Parameters

num_rows	Integer (optional)	Requested page size. The default is 50.
start_row	Integer (optional)	First row number requested. This is zero-based.
order	String (optional)	The value of order= is an attribute name which may be qualified with a lowercase plural table name (i.e. organisms.name). Use a comma-separated list in the order= parameter to sort on multiple attributes. Sort in reverse order by adding +desc to the order= parameter.

‍

Response

num_rows	Number of rows returned.
start_row	First row number requested. This is zero-based.
total_rows	The total number of rows that met the search criteria.

‍

ActiveRecord Query and Serialization

RMA uses the ActiveRecord Query Interface.

‍

Parameters

criteria	Associations are treated like an AR Query joins() argument and can be thought of as a series of SQL inner joins.
include	Associations are treated like an AR Query includes() argument and are used to drive eager loading of the associated resources. They can be thought of as a series of SQL outer joins.
start_row	Generates an offset() AR Query argument and is similar to an SQL OFFSET clause.
num_rows	Generates a limit() AR Query argument and is similar to an SQL ORDER BY clause.
order	Generates an order() AR Query argument and is similar to an SQL ORDER BY clause.
debug	Includes debugging information in the response such as equivalent ActiveRecord and SQL queries when set to ‘true’.

The filter clauses in both the criteria= parameter and the includes= parameter are treated as an AR Query where() argument. They can be thought of as an SQL where clause combined with the boolean ‘and’ operation.

Models are similar to SQL tables, attributes correspond to literal SQL columns and associations can be thought of as SQL foreign keys.

‍

Learn more

API

Quantified Data By Structures

Learn about Quantified Data By Structures with comprehensive guides and examples from Allen Institute for Brain Science.

Data from our large scale gene expression and connectivity products is processed through an informatics data analysis pipeline to obtain spatially mapped quantified expression/projection information.

Reference Atlases

Quantified data is available for the following:

The output of the pipeline are quantified values at a grid voxel level. Quantified values can be computed for each structure delineated in the associated reference atlas by combining or unionizing grid voxels with the same 3-D structural label. While the reference atlas is typically annotated at the lowest level of the ontology tree, statistics at upper level structures can be obtained by combining measurements of the hierarchical children to obtain statistics for the parent structure.

Expression statistics are encapsulated as a StructureUnionize object associated with one Structure and one SectionDataSet.

Projection statistics are encapsulated as a ProjectionStructureUnionize object associated with one Structure, either left, right or both Hemispheres and one SectionDataSet.

StructureUnionize and ProjectionStructureUnionize data can be downloaded via RMA and are used in the web application to display expression summary bar graphs for a set of coarse structures. Its usage is also demonstrated in the “structure networks” example application.

Refer to the atlas API pages for further details.

**Figure:** Bar plot of projection values by structure for an injection into the primary visual area.

‍

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