Connected Services and Pipes - Part I

[SvenOtto]

• service::dev_human_correlation
• service::dev_human_differential
• service::dev_human_expression
• service::dev_human_microarray_correlation
• service::dev_human_microarray_differential
• service::dev_human_microarray_expression
• service::dev_mouse_agea
• service::dev_mouse_correlation
• service::gbm_correlation
• service::gbm_differential
• service::gbm_expression
• service::gbm_ish_differential
• service::gbm_ish_expression
• service::human_microarray_correlation
• service::human_microarray_differential
• service::human_microarray_expression
• service::mouse_agea
• service::mouse_correlation
• service::mouse_differential
• service::mouse_connectivity_correlation
• service::mouse_connectivity_injection_coordinate
• service::mouse_connectivity_injection_structure
• service::mouse_connectivity_target_spatial
• service::nhp_lmd_microarray_correlation
• service::nhp_lmd_microarray_differential
• service::nhp_lmd_microarray_expression
• service::nhp_macro_microarray_correlation
• service::nhp_macro_microarray_differential
• service::nhp_macro_microarray_expression

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$eqrna_seq_genes][probes$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']

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$eq'rna_seq_genes'][probes$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]

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::gbm_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::gbm_correlation[probes$eq3551][structures$eqGBM]

service::gbm_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::gbm_differential[structures1$eqGBM][structures2$eqCTpan]

service::gbm_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 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::gbm_expression[probes$eq3551][donors$eq703393][structures$eqGBM]

service::gbm_ish_differential

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.

Examples

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

service::gbm_ish_expression

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.

Examples

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

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 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.

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::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.
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.

Example

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]

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 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.

Example

http://api.brain-map.org/api/v2/data/query.xml?criteria= service::mouse_connectivity_injection_coordinate[seed_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_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.

Example

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]

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.

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.

Example

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

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]