service::dev_human_correlation

‍

Parameters

‍

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']

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service::dev_human_differential

‍

Parameters

‍

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]

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service::dev_human_expression

‍

Parameters

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

Example

‍

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

‍

service::gbm_differential

‍

Parameters

‍

Example

‍

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

‍

service::gbm_expression

‍

Parameters

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

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

‍

Example

‍

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

‍

service::tbi_correlation

‍

Parameters

‍

Example

‍

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

‍

service::tbi_differential

‍

Parameters

‍

Example

‍

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

‍

service::tbi_expression

‍

Parameters

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

‍

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

‍

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

‍

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

‍

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

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

‍

Response

‍

ActiveRecord Query and Serialization

RMA uses the ActiveRecord Query Interface.

‍

Parameters

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.

‍

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.

‍