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]
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]
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]