EXAMPLE QUERIES FOR EXPERIMENT METADATA

Allen Brain Atlas API > Example Queries for Experiment Metadata > rma.png The following query examples demonstrate how to use RESTful Model Access (RMA) to retrieve metadata for experiments.

RMA Query Builder, an API utility, can be used to compose RMA queries.
SectionImage Download Service can be used to download images.
WellKnownFile Download Service can be used to download a file.

Please note that multiple line example RMA queries on this page represent spaces enclosed in quotation marks with the "+" character to make the examples compatible with some browsers.

Allen Brain Atlas API Status

Date Updated

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

Mouse Brain

All Mouse Brain ISH experiments

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'Mouse'],treatments[name$eq'ISH'],
rma::include,genes,specimen(donor(age)),plane_of_section
&num_rows=50&start_row=0

All Mouse Brain ISH experiments in comma delimited format

http://api.brain-map.org/api/v2/data/query.csv?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'Mouse'],treatments[name$eq'ISH'],genes,plane_of_section,
rma::options,
[tabular$eq'plane_of_sections.name+as+plane','genes.acronym+as+gene','data_sets.id+as+section_data_set_id'],
[order$eq'plane_of_sections.name,genes.acronym,data_sets.id']
&num_rows=50&start_row=0

Sagittal Mouse Brain ISH experiments for Adora2a

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eq'false'],products[abbreviation$eq'Mouse'],plane_of_section[name$eq'sagittal'],genes[acronym$eq'Adora2a']

Images for sagittal Mouse Brain ISH Adora2a experiment 70813257

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionImage,
rma::criteria,[data_set_id$eq70813257]

Mouse Brain coronal images for Adora2a in comma delimited format

http://api.brain-map.org/api/v2/data/query.csv?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'Mouse'],treatments[name$eq'ISH'],genes[acronym$eq'Adora2a'],plane_of_section,section_images,
rma::options,
[tabular$eq'plane_of_sections.name+as+plane','genes.acronym+as+gene','data_sets.id+as+section_data_set_id','sub_images.id+as+section_image_id'],
[order$eq'plane_of_sections.name,genes.acronym,data_sets.id,sub_images.id']
&num_rows=50&start_row=0

Expression summary for coronal Adora2a experiment 72109410

http://api.brain-map.org/api/v2/data/SectionDataSet/query.xml?id=72109410&include=structure_unionizes(structure)

Mouse Connectivity

Projection summary for Mouse Connectivity experiment 183282970 in comma delimited format

http://api.brain-map.org/api/v2/data/query.csv?criteria=
model::ProjectionStructureUnionize,
rma::criteria,[is_injection$eq'f'],hemisphere,structure,section_data_set[id$eq183282970](specimen(stereotaxic_injections(primary_injection_structure,stereotaxic_injection_coordinates))),rma::include,section_data_set(specimen(stereotaxic_injections(primary_injection_structure))),
rma::options[tabular$eq'distinct+specimens.name+as+specimen_name,stereotaxic_injection_coordinates.coordinates_ap,stereotaxic_injection_coordinates.coordinates_dv,stereotaxic_injection_coordinates.coordinates_ml,data_sets.id+as+data_set_id,stereotaxic_injections.primary_injection_structure_id,structures.acronym+as+target_structure,hemispheres.symbol+as+hemisphere,projection_structure_unionizes.is_injection,projection_structure_unionizes.sum_pixels,projection_structure_unionizes.sum_projection_pixels,projection_structure_unionizes.sum_pixel_intensity,projection_structure_unionizes.sum_projection_pixel_intensity,projection_structure_unionizes.projection_density,projection_structure_unionizes.projection_intensity,projection_structure_unionizes.projection_energy,projection_structure_unionizes.volume,projection_structure_unionizes.projection_volume,projection_structure_unionizes.normalized_projection_volume,projection_structure_unionizes.max_voxel_density,projection_structure_unionizes.max_voxel_x,projection_structure_unionizes.max_voxel_y,projection_structure_unionizes.max_voxel_z'][start_row$eq0][num_rows$eq3000]

Developing Mouse Brain

All Developing Mouse Brain ISH experiments with images

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'DevMouse'],treatments[name$eq'ISH'],
rma::include,genes,specimen(donor(age)),plane_of_section,section_images
&num_rows=10&start_row=0

All Developing Mouse Brain Genes in comma delimited format

http://api.brain-map.org/api/v2/data/query.csv?criteria=
model::Gene,
rma::criteria,products[abbreviation$eq'DevMouse'],
rma::options,[tabular$eq'genes.id','genes.acronym+as+gene_symbol','genes.name+as+gene_name','genes.entrez_id+as+entrez_gene_id','genes.homologene_id+as+homologene_group_id'],
[order$eq'genes.acronym']
&num_rows=all&start_row=0

P28 Developing Mouse Brain ISH experiments for Gad1

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eq'false'],products[abbreviation$eq'DevMouse'],specimen(donor(age[name$eq'P28']))

Developing Mouse Brain P28 ISH images for Gad1

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eq'false'],
rma::include,genes[acronym$eq'Gad1'],section_images,specimen(donor(age[name$eq'P28']))

Sleep Study

Sleep Study ISH experiments with images, including the experimental condition:

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'Sleep'],treatments[name$eq'ISH'],
rma::include,probes(gene),plane_of_section,specimen(donor(disease_categories,medical_conditions)),section_images
&num_rows=10

Human Brain

Human Brain ISH Autism Study experiments with images, including the donor's conditions

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'HumanASD'],treatments[name$eq'ISH'],
rma::include,probes(gene),specimen(donor(age,disease_categories,medical_conditions)),section_images
&num_rows=10

Human Brain Microarray experiments

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::MicroarraySlide,
rma::criteria,microarray_data_sets[failed$eqfalse](products[abbreviation$eq'HumanMA']),
rma::include,structures,well_known_files,microarray_data_sets(specimen(donor(age)))

Developing Human Brain

Developing Human Brain ISH experiments with images

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'DevHumanISH'],treatments[name$eq'ISH'],
rma::include,probes(gene),specimen(donor(age,disease_categories,medical_conditions)),section_images
&num_rows=10

Expression summary for GAD1 Developing Human Brain ISH

http://api.brain-map.org/api/v2/data/SectionDataSet/query.xml?id=73931410&include=structure_unionizes(structure)

Developing Human Brain Prenatal LMD Microarray experiments

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::MicroarraySlide,
rma::criteria,microarray_data_sets[failed$eqfalse](products[abbreviation$eq'DevHumanMA']),
rma::include,structures,well_known_files,microarray_data_sets(specimen(donor(age)))

Developing Human Brain Transcriptome experiments

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Specimen,
rma::criteria,data_sets(products[abbreviation$eq'DevHumanTrans']),
rma::include,structure,donor,well_known_files(well_known_file_type)