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  • All donors in the Product
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/Donor/query.xml?include=age&criteria=products[id$eq24]
    
  • All samples in the Product
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Specimen,
    rma::criteria,donor(products[id$eq24]),
    well_known_files(well_known_file_type[name$eqRNASeqSummarizedToGenes]),
    rma::include,donor(age)
    
  • All prenatal donors in the Product
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[id$eq24],rma::include,age[embryonic$eqtrue]
    
  • All postnatal donors in the Product
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[id$eq24],rma::include,age[embryonic$eqfalse]
    
  • All surveyed structures
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,structure_sets[name$eq'Developing Human - Transcriptome'],
    rma::options[only$eq'structures.id,structures.acronym,structures.name,structures.color_hex_triplet']
    

...

  • Find Donor ID for "H376.VI.52" (id = 12890)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H376.VI.52'],
    rma::options[only$eq'donors.id']
    
  • Find Gene ID associated with gene CARTPT (id = 1098278)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Gene,
    rma::criteria,[acronym$eq'CARTPT'][type$eq'EnsemblGene'],organism[name$eq'Homo Sapiens'],
    rma::options[only$eq'genes.id']
    
  • Use set = rna_seq_genes, Gene ("probe") and Donor IDs as parameter to the service::dev_human_expression
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.json?criteria=service::dev_human_expression
    [set$eq'rna_seq_genes'][probes$eq1098278][donors$eq12890]
    

The output of the service is two top level ordered arrays "probes" and "samples". For example:

Code Blocknoformat
"probes":[
    {"id":1098278,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT","gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":"n/a","end-position":"n/a",
    "expression_level":["5.5566","4.9466","5.6331",...]}
    ],
"samples":[
    {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10173,"name":"dorsolateral prefrontal cortex","abbreviation":"DFC","color":"D4B235"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10185,"name":"ventrolateral prefrontal cortex","abbreviation":"VFC","color":"C2A335"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
     ],

...

  • Find Donor ID for "H376.VI.52" (id = 12890)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H376.VI.52'],
    rma::options[only$eq'donors.id']
    
  • Find GoExons ID associated with gene CARTPT (id = 279330730,279330740,279330735)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::GoExon,
    rma::criteria,gene_association(gene[acronym$eq'CARTPT']),
    rma::options[only$eq'go_exons.id']
    
  • Use set = rna_seq_exons, GoExon ("probe") and Donor IDs as parameter to the service::dev_human_expression
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.json?criteria=service::dev_human_expression
    [set$eq'rna_seq_exons'][probes$eq279330730,279330740,2793307356][donors$eq12890]
    

The output of the service is two top level ordered arrays "probes" and "samples". For example:

Code Blocknoformat
"probes":[
    {"id":279330730,
    "name":"ENSG00000164326",
    "gene-id":1098278,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71014989,"end-position":71015279,
    "expression_level":["5.7282","4.8102","5.7152", ... ]},
    {"id":279330735,
    "name":"ENSG00000164326",
    "gene-id":1098278,"gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71015405,"end-position":71015790,
    "expression_level":["4.4128","3.8230","4.3135", ... ]},
    {"id":279330740,
    "name":"ENSG00000164326",
    "gene-id":1098278,"gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71016334,"end-position":71016875,
    "expression_level":["5.9593","5.4664","6.1137", ... ]}
    ],
"samples":[
    {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10173,"name":"dorsolateral prefrontal cortex","abbreviation":"DFC","color":"D4B235"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10185,"name":"ventrolateral prefrontal cortex","abbreviation":"VFC","color":"C2A335"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
     {"donor":{"id":12890,"name":"H376.VI.52","age":"4 mos","color":"76EB76"},
     "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
     "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
     ],

...

  • Find Donor ID for "H376.VI.50" (id = 12296)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H376.VI.50'],
    rma::options[only$eq'donors.id']
    
  • Find Gene ID associated with gene CARTPT (id = 9463)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Gene,
    rma::criteria,[acronym$eq'CARTPT'][type$eq'NcbiGene'],organism[name$eq'Homo Sapiens'],
    rma::options[only$eq'genes.id']
    
  • Use set = exon_microarray_genes, Gene ("probe") and Donor IDs as parameter to the service::dev_human_expression
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.json?criteria=service::dev_human_expression
    [set$eq'exon_microarray_genes'][probes$eq9463][donors$eq12296]
    

The output of the service is two top level ordered arrays "probes" and "samples". For example:

Code Blocknoformat
"probes":[
       {"id":9463,
       "name":"ENSG00000164326",
       "gene-id":9463,
       "gene-symbol":"CARTPT",
       "gene-name":"CART prepropeptide",
       "entrez-id":9607,"chromosome":"5","start-position":"n/a","end-position":"n/a",
       "expression_level":["8.1073","5.9564","6.3102","7.0532","9.6157","7.1290","5.1168","4.4212","4.2779"],
       "z-score":["1.3547","0.0538","0.2678","0.7172","2.2670","0.7630","-0.4541","-0.8748","-0.9615"]}
    ],
"samples":[
       {"donor":{"id":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
       "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
       "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
       {"donor":{"id":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
       "structure":{"id":10243,"name":"posterior (caudal) superior temporal cortex (area 22c)","abbreviation":"STC","color":"D670A0"},
       "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
    ]

...

  • Find Donor ID for "H376.VI.50" (id = 12296)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H376.VI.50'],
    rma::options[only$eq'donors.id']
    
  • Find AffymetrixProbeset ID associated with gene CARTPT (id = 280550735,280550750,280550740,280550730,280550745)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AffymetrixProbeset,
    rma::criteria,gene_association(gene[acronym$eq'CARTPT'](organism[name$eq'Homo Sapiens'])),
    rma::options[only$eq'affymetrix_probesets.id']
    
  • Use set = exon_microarray_exons, AffymetrixProbeset ("probe") and Donor IDs as parameter to the service::dev_human_expression
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.json?criteria=service::dev_human_expression
    [set$eq'exon_microarray_exons'][probes$eq280550735,280550750,280550740,280550730,280550745][donors$eq12296]
    

The output of the service is two top level ordered arrays "probes" and "samples". For example:

Code Blocknoformat
"probes":[
    {"id":280550735,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71015125,"end-position":71015265,
    "expression_level":["8.1073","6.4681","6.3102","7.0532","9.4350","7.1290","5.1560","5.0550","4.9879"],
    "z-score":["1.4783","0.0367","-0.1021","0.5513","2.6458","0.6179","-1.1171","-1.2059","-1.2649"]},
    {"id":280550750,
    "name":"ENSG00000164326",
    "gene-id":9463,
    "gene-symbol":"CARTPT",
    "gene-name":"CART prepropeptide",
    "entrez-id":9607,"chromosome":"5","start-position":71016613,"end-position":71016799,
    "expression_level":["10.1951","8.8021","7.7846","9.4317","11.8110","10.0210","6.1850","5.6075","4.5526"],
    "z-score":["1.2342","0.6566","0.2348","0.9177","1.9041","1.1620","-0.4284","-0.6678","-1.1052"]},
    ],
"samples":[
    {"donor":{"id":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
    "structure":{"id":10278,"name":"anterior (rostral) cingulate (medial prefrontal) cortex","abbreviation":"MFC","color":"E26880"},
    "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}},
    {"donor":{"id":12296,"name":"H376.VI.50","age":"4 mos","color":"80FF80"},
    "structure":{"id":10243,"name":"posterior (caudal) superior temporal cortex (area 22c)","abbreviation":"STC","color":"D670A0"},
    "top_level_structure":{"id":10153,"name":"neural plate","abbreviation":"NP","color":"D7D8D8"}}, ...
    ]

...

  • Find Structure ID for "striatum" (id = 10333 )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'striatum'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Structure ID for "neural plate" (id = 10153)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'neural plate'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Differential search for gene-level RNA-Seq data (set = rna_seq_genes)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'rna_seq_genes'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    
  • Differential search for exon-level RNA-Seq data (set = rna_seq_exons )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'rna_seq_exons'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    
  • Differential search for gene-level exon microarray data (set = exon_microarray_genes )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'exon_microarray_genes'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    
  • Differential search for probeset-level exon microarray data (set = exon_microarray_exons )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'exon_microarray_exons'][structures1$eq10153][structures2$eq10333][sort_by$eq'fold-change']
    
  • Visualize the gene-level RNA-Seq differential search result in the Web application

...

  • Find Structure ID for "neural plate" (id = 10153)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'neural plate'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Donor IDs for donors within age 8-9 pcw (id = 12833,13058)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[name$eq'Developing Human Transcriptome'],age[embryonic$eqtrue][days$ge56][days$le63],
    rma::options[only$eq'donors.id']
    
  • Find Donor IDs for donors within age 10-12 pcw (id = 12835,12960,13060)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[name$eq'Developing Human Transcriptome'],age[embryonic$eqtrue][days$ge70][days$le84],
    rma::options[only$eq'donors.id']
    
  • Differential search for gene-level RNA-Seq data (set = rna_seq_genes)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'rna_seq_genes'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
    [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    
  • Differential search for exon-level RNA-Seq data (set = rna_seq_exons )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'rna_seq_exons'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
    [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    
  • Differential search for gene-level exon microarray data (set = exon_microarray_genes )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'exon_microarray_genes'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
    [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    
  • Differential search for probeset-level exon microarray data (set = exon_microarray_exons )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_differential
    [set$eq'exon_microarray_exons'][donors1$eq12835,12960,13060][donors2$eq12833,13058]
    [structures1$eq10153][structures2$eq10153][sort_by$eq'fold-change']
    

...

  • Correlative search for gene-level RNA-Seq data  ( seed Ensembl Gene id = 1089164, set = rna_seq_genes )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    service::dev_human_correlation[set$eqrna_seq_genes][probes$eq1089164][structures$eq10153]
    
  • Correlative search for exon-level RNA-Seq data  ( seed GoExon id = 278724739, set = rna_seq_exons )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    service::dev_human_correlation[set$eqrna_seq_exons][probes$eq278724739][structures$eq10153]
    
  • Correlative search for gene-level exon microarray data (seed NCBI Gene id = 5784, set = exon_microarray_genes )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    service::dev_human_correlation[set$eqexon_microarray_genes][probes$eq5784][structures$eq10153]
    
  • Correlative search for probeset-level exon microarray data ( seed AffymetrixProbeset id = 281337753, set = exon_microarray_exons )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    service::dev_human_correlation[set$eqexon_microarray_exons][probes$eq281337753][structures$eq10153]
    

...

  • Find Donor ID for "H376.IIIA.02" (id = 12840)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H376.IIIA.02'],
    rma::options[only$eq'donors.id']
    
  • Find Structure ID for "cerebellar cortex" (id = 10657)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'cerebellar cortex'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Probes associated with gene SLC6A2(id = 1023146,1023147 )
    Code Blocknoformat
    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
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.json?criteria=
    service::dev_human_microarray_expression[probes$eq1023146,1023147][donors$eq12840][structures$eq10657]
    

The output of the service is two top level ordered arrays "probes" and "samples". For example:

Code Blocknoformat
"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":["5.6462","5.9486","3.1022"],
    "z-score":["2.4164","2.6249","0.6624"]},
    {"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":["2.8149","1.2956","1.7658"],
    "z-score":["0.8169","-0.9788","-0.4231"]}
    ],
"samples":[
    {"donor":{"id":12840,"name":"H376.IIIA.02","age":"15 pcw","color":"0080FF"},
    "structure":{"id":10658,"name":"cerebellar vermis","abbreviation":"CBV","color":"76A2D5"},
    "top_level_structure":{"id":10657,"name":"cerebellar cortex","abbreviation":"CBC","color":"89ADDB"}},
    {"donor":{"id":12840,"name":"H376.IIIA.02","age":"15 pcw","color":"0080FF"},
    "structure":{"id":12384,"name":"paravermis of cerebellum","abbreviation":"CBPV","color":"4A8ECC"},
    "top_level_structure":{"id":10657,"name":"cerebellar cortex","abbreviation":"CBC","color":"89ADDB"}},
    {"donor":{"id":12840,"name":"H376.IIIA.02","age":"15 pcw","color":"0080FF"},
    "structure":{"id":12390,"name":"lateral hemisphere of cerebellum","abbreviation":"CBL","color":"4A8ECC"},
    "top_level_structure":{"id":10657,"name":"cerebellar cortex","abbreviation":"CBC","color":"89ADDB"}}
    ]

...

  • Find Structure ID for "thalamus" (id = 10390)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'thalamus'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Structure ID for "transient structures of forebrain" (id = 10506)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'transient structures of forebrain'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Structure IDs as parameters to the connected service
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_microarray_differential
    [structures1$eq10506][structures2$eq10390][sort_by$eq'fold-change']
    
  • Visualize the same search result in the Web application 

...

  • Find Probe ID for probe "CUST_11451_PI416261804" (id = 1052410)
    Code Blocknoformat
    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 "neural plate" (id = 10153)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'neural plate'],ontology[name$eq'Developing Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Probe and Structure IDs as parameters to the connected service
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::dev_human_microarray_correlation
    [probes$eq1052410][structures$eq10153]
    
  • Visualize the same search result in the Web application

...