ALLEN BRAIN ATLAS API
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The NIH Blueprint Non-Human Primate (NHP) Atlas consists of a suite of gene expression data, neuroanatomical data and informatics tools for exploring the cellular and molecular architecture of the developing rhesus macaque brain. Data includes:
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Download expression values for all 48 mo donors in structure "V1-1" for all probes associated with gene MET.
Find Donor ID for all 48 mo donors (id = 9878,11196,11272)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,age[name$eq'48 mo'],organism[name$eq'Macaca mulatta'], products[name$eq'Non-Human Primate LMD Microarray'], rma::options[only$eq'donors.id']Find Structure ID for "V1-1" (id = 10027)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[acronym$il'V1-1'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$eq'structures.id']Find AffymetrixMacaqueProbeset IDs associated with gene MET (id = 12414,29851,29853,29854,49439 )
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AffymetrixMacaqueProbeset, rma::criteria,gene_association(gene[acronym$eq'MET']), rma::options[only$eq'affymetrix_macaque_probesets.id'][order$eq'affymetrix_macaque_probesets.id']Use Donor, Structure and AffymetrixMacaqueProbeset IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.json?criteria= service::nhp_lmd_microarray_expression[structures$eq10027] [probes$eq12414,29851,29853,29854,49439][donors$eq9878,11196,11272]
The output of the service is two top level ordered arrays "probes" and "samples". For example:
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"probes":[
{"id":12414,
"name":"MmugDNA.19034.1.S1_at",
"gene-id":183127,
"gene-symbol":"MET",
"gene-name":"met proto-oncogene (hepatocyte growth factor receptor)",
"entrez-id":704562,"chromosome":"3","start-position":"n/a","end-position":"n/a",
"expression_level":["4.3598","4.4762","4.4883"],
"z-score":["-0.3668","0.2633","0.3287"]},
{"id":29851,
"name":"MmugDNA.34584.1.S1_at",
"gene-id":183127,
"gene-symbol":"MET",
"gene-name":"met proto-oncogene (hepatocyte growth factor receptor)",
"entrez-id":704562,"chromosome":"3","start-position":"n/a","end-position":"n/a",
"expression_level":["4.2801","4.1808","4.0958"],
"z-score":["0.0110","-0.2272","-0.4310"]}, ...
],
"samples":[
{"donor":{"id":11272,"name":"MMU36322","age":"48 mo","color":"333333"},
"structure":{"id":10027,"name":"layer I of V1","abbreviation":"V1-1","color":"EDC9C0"},
"top_level_structure":{"id":4004,"name":"occipital cortex","abbreviation":"Ocx","color":"E7ACA1"}},
{"donor":{"id":11196,"name":"MMU36358","age":"48 mo","color":"333333"},
"structure":{"id":10027,"name":"layer I of V1","abbreviation":"V1-1","color":"EDC9C0"},
"top_level_structure":{"id":4004,"name":"occipital cortex","abbreviation":"Ocx","color":"E7ACA1"}},
{"donor":{"id":9878,"name":"MMU36468","age":"48 mo","color":"333333"},
"structure":{"id":10027,"name":"layer I of V1","abbreviation":"V1-1","color":"EDC9C0"},
"top_level_structure":{"id":4004,"name":"occipital cortex","abbreviation":"Ocx","color":"E7ACA1"}}
]
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Example:
Differential search for genes with higher expression in "basal ganglia" than in the "neocortex"
Find Structure ID for "basal ganglia" (id = 4001)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'*basal ganglia*'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$eq'structures.id']Find Structure ID for "neocortex" (id = 294021746)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'neocortex'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$eq'structures.id']Use Structure IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=service::nhp_lmd_microarray_differential [structures1$eq294021746][structures2$eq4001][sort_by$eq'fold-change']- Visualize the same search result in the Web application
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Example:
Differential search for genes with higher expression at 0 months than at 3 months
Find Donor ID for all 0 mo donors (id = 12149,3786,9321,12143)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,age[name$eq'0 mo'],organism[name$eq'Macaca mulatta'], products[name$eq'Non-Human Primate LMD Microarray'], rma::options[only$eq'donors.id']Find Donor ID for all 3 mo donors (id = 9479,2554,11197,12185)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,age[name$eq'3 mo'],organism[name$eq'Macaca mulatta'], products[name$eq'Non-Human Primate LMD Microarray'], rma::options[only$eq'donors.id']Use Donor IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=service::nhp_lmd_microarray_differential [donors1$eq9479,2554,11197,12185][donors2$eq12149,3786,9321,12143][sort_by$eq'fold-change']- Visualize the same search result in the Web application
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Example:
Correlative search for probes with similar expression to NTNG1 probe MmuSTS.4647.1.S1_at over the cerebral cortex
Find AffymetrixMacaqueProbeset ID for probe "MmuSTS.4647.1.S1_at" (id = 51317)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AffymetrixMacaqueProbeset, rma::criteria,[displayable_id_from_affymetrix$eq'MmuSTS.4647.1.S1_at'], rma::options[only$eq'affymetrix_macaque_probesets.id']Find Structure ID for "cerebral cortex" (id = 128011354)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'cerebral cortex'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$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::nhp_lmd_microarray_correlation [probes$eq51317][structures$eq128011354]
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Download expression values for all 48 months donors in structure "neocortex" for all probes associated with gene MET.
Find Donor ID for all 48 mo donors (id = 9353,9481,9480)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,age[name$eq'48 mo'],organism[name$eq'Macaca mulatta'], products[name$eq'Non-Human Primate Macro Microarray'], rma::options[only$eq'donors.id']Find Structure ID for "neocortex" (id = 294021746)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'neocortex'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$eq'structures.id']Find AffymetrixMacaqueProbeset IDs associated with gene MET (id = 12414,29851,29853,29854,49439 )
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AffymetrixMacaqueProbeset, rma::criteria,gene_association(gene[acronym$eq'MET']), rma::options[only$eq'affymetrix_macaque_probesets.id'][order$eq'affymetrix_macaque_probesets.id']Use Donor, Structure and AffymetrixMacaqueProbeset IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.json?criteria= service::nhp_macro_microarray_expression[structures$eq294021746] [probes$eq12414,29851,29853,29854,49439][donors$eq9353,9481,9480]
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Example:
Differential search for genes with higher expression in "basal ganglia" than the "neocortex"
Find Structure ID for "basal ganglia" (id = 4001)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'*basal ganglia*'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$eq'structures.id']Find Structure ID for "neocortex" (id = 294021746)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'neocortex'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$eq'structures.id']Use Structure IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=service::nhp_macro_microarray_differential [structures1$eq294021746][structures2$eq4001][sort_by$eq'fold-change']
Example:
Differential search for genes with higher expression at 0 mo than 3 mo
Find Donor ID for all 0 mo donors (id = 148141688,9590,9425)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,age[name$eq'0 mo'],organism[name$eq'Macaca mulatta'], products[name$eq'Non-Human Primate Macro Microarray'], rma::options[only$eq'donors.id']Find Donor ID for all 3 mo donors (id = 148141705,9639,9630)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor, rma::criteria,age[name$eq'3 mo'],organism[name$eq'Macaca mulatta'], products[name$eq'Non-Human Primate Macro Microarray'], rma::options[only$eq'donors.id']Use Donor IDs as parameters to the connected service
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=service::nhp_macro_microarray_differential [donors1$eq148141705,9639,9630][donors2$eq148141688,9590,9425][sort_by$eq'fold-change']
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Example:
Correlative search for probes with similar expression to NTNG1 probe MmuSTS.4647.1.S1_at over the cerebral cortex
Find AffymetrixMacaqueProbeset ID for probe "MmuSTS.4647.1.S1_at" (id = 51317)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AffymetrixMacaqueProbeset, rma::criteria,[displayable_id_from_affymetrix$eq'MmuSTS.4647.1.S1_at'], rma::options[only$eq'affymetrix_macaque_probesets.id']Find Structure ID for "cerebral cortex" (id = 128011354)
No Format http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure, rma::criteria,[name$il'cerebral cortex'],ontology[name$eq'Non-Human Primate Brain Atlas'], rma::options[only$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::nhp_macro_microarray_correlation [probes$eq51317][structures$eq128011354]