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EXAMPLE QUERIES FOR EXPERIMENT METADATA

Table of Contents
minLevel2
maxLevel3
stylenone
classtoc-style

The following query examples demonstrate how to use RESTful Model Access (RMA) to retrieve metadata for experiments.

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

No Format
http://api.brain-map.org/api/v2/status/query.xml

Mouse Brain

All Mouse Brain ISH experiments

No Format
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

No 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

No Format
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

No Format
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

No 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

No Format
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

No 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

No Format
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

No 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

No Format
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

No Format
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:

No Format
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

No Format
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

No Format
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

No Format
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

No Format
http://api.brain-map.org/api/v2/data/SectionDataSet/query.xml?id=73931410&include=structure_unionizes(structure)

Developing Human Brain Prenatal LMD Microarray experiments

No Format
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

No Format
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)