ALLEN BRAIN ATLAS API
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The Allen Human Brain Atlas is a multimodal atlas of the human brain that integrates anatomic and microarray-based gene expression information. Microarray sampling sites (~400-1000 sites per brain) were identified by expert anatomists using cytoarchitectural information from multiple histological stains. Sampling site delineations in the high resolution histological images were subsequently mapped into each individual's MR image space to provide 3-D anatomical context. All brains were also registered to MNI space to enable cross-individual comparisons.
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Download expression values for donor "H0351.1015" in structure "locus ceruleus" for all probes associated with gene SLC6A.
Find Donor ID for "H0351.1015" (id = 15496)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,[name$eq'H0351.1015'], rma::options[only$eq'donors.id']Find Structure ID for "locus ceruleus" (id = 9148)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'locus ceruleus'],ontology[name$eq'Human Brain Atlas'], rma::options[only$eq'structures.id']Find Probes associated with gene SLC6A2 (id = 1023146,1023147 )
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Probe, rma::criteria,[probe_type$eq'DNA'],products[abbreviation$eq'HumanMA'],gene[acronym$eq'SLC6A2'], rma::options[only$eq'probes.id']Use Donor, Structure and Probe IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.json?criteria= service::human_microarray_expression[probes$eq1023146,1023147][donors$eq15496][structures$eq9148]
The output of the service is two top level ordered arrays "probes" and "samples". For example:
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"probes":[{
"id":1023146,
"name":"A_23_P358345",
"gene-id":6494,
"gene-symbol":"SLC6A2",
"gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
"entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
"expression_level":["13.2802","13.9603","13.9650"],
"z-score":["9.3381","9.8663","9.8700"]},
{
"id":1023147,
"name":"CUST_16472_PI416261804",
"gene-id":6494,
"gene-symbol":"SLC6A2",
"gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
"entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
"expression_level":["8.1878","8.5644","8.2310"],
"z-score":["9.3201","9.8326","9.3790"]}
],
"samples":[
{"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
"sample":
{"well":148955246,"polygon":127107914,"mri":[95,121,126]},
"structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
"top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}},
{"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
"sample":
{"well":148955204,"polygon":126786164,"mri":[97,151,131]},
"structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
"top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}},
{"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
"sample":
{"well":156435966,"polygon":126789834,"mri":[96,159,134]},
"structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
"top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}}
]
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Example:
Differential search for genes with higher expression in thalamus than the cerebral cortex
Find Structure ID for "thalamus" (id = 4392)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'thalamus'],ontology[name$eq'Human Brain Atlas'], rma::options[only$eq'structures.id']Find Structure ID for "cerebral cortex" (id = 4008)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'cerebral cortex'],ontology[name$eq'Human Brain Atlas'], rma::options[only$eq'structures.id']Use Structure IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=service::human_microarray_differential [structures1$eq4008][structures2$eq4392][sort_by$eq'fold-change']- Visualize the same search result in the Web application
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Example:
Correlative search for probes with similar expression to PVALB probe CUST_11451_PI416261804 over the whole Brain
Find Probe ID for probe "CUST_11451_PI416261804" (id = 1052410)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Probe, rma::criteria,[name$eq'CUST_11451_PI416261804'], rma::options[only$eq'probes.id']Find Structure ID for "Brain" (id = 4005)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'brain'],ontology[name$eq'Human Brain Atlas'], rma::options[only$eq'structures.id']Use Probe and Structure IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=service::human_microarray_correlation [probes$eq1052410][structures$eq4005]- Visualize the same search result in the Web application
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All T1 images were registered to MNI space. FreeSurfer's affine registration was used for the in cranio scans. For ex cranio brains, the T1 was first rigidly aligned using FSL (Jenkinson, et. al, 2002) and then non-rigidly aligned using ANTS (Avants, et. al., 2011). The 3-D affine transform from a location in the MR volume to MNI space is encapsulated in the Alignment3d model.
Examples queries:
Download links for all MR and DTI data available
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,products[abbreviation$in'HumanMA','HumanSZ','HumanCtx','HumanSubCtx'],organism[name$il'Homo Sapiens'], rma::include,specimens(well_known_files(well_known_file_type[name$in'T1-MRI','T2-MRI','DTI-MRI'])), rma::options[only$eq'donors.name,products.name,well_known_files.download_link,specimens.id']Download TI MR scan for donor 'H0351.2002'
No Format http://human.brain-map.org/api/v2/well_known_file_download/157723301Download the MR to MNI transform parameters
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,products[abbreviation$eq'HumanMA'], rma::include,specimens[parent_id$eqnull](alignment3d), rma::options[only$eq'donors.id,donors.name,specimens.id']
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