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• Find Donor ID for "H0351.1015" (id = 15496)

  Code Blocknoformat
  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)

  Code Blocknoformat
  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 )

  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::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:

"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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• Find Structure ID for "thalamus" (id = 4392)

  Code Blocknoformat
  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)

  Code Blocknoformat
  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

  Code Blocknoformat
  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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• 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 "Brain" (id = 4005)

  Code Blocknoformat
  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

  Code Blocknoformat
  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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• Download links for all MR and DTI data available

  Code Blocknoformat
  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'

  Code Blocknoformat
  http://human.brain-map.org/api/v2/well_known_file_download/157723301

• Download the MR to MNI transform parameters

  Code Blocknoformat
  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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