Introduction
See Service API Design for the rationale and design details for this api.
See Developer Bootstrap#DeveloperBootstrap-ServiceDevelopment for instructions on how to run a local instance of this service.
Encoding
The primary request and response encoding for the service is JSON. Here's a handy tool to make a blob of JSON more readable: http://jsonformatter.curiousconcept.com/
In responses from the service, dates are serialized as long integers expressing epoch time - the number of seconds elapsed since midnight Coordinated Universal Time (UTC) of January 1, 1970, not counting leap seconds. Here's a handy tool to convert from epoch time to human readable dates: http://www.epochconverter.com/
In requests to the service, dates can be serialized either as long integers expressing epoch time or human readable dates in http://www.ietf.org/rfc/rfc3339.txt format such as '2011-01-31' or '2011-01-31T22:00:00'
Security
Eventually these services will be HTTPS only and disallow HTTP. Users will pass something like ?access_token=... as a query parameter for every request to the service
Query API Examples
'Select *' Query
Right now only a subset of query functionality is supported
SELECT * FROM <data type> [LIMIT <#>] [OFFSET <#>]
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+limit+3+offset+1'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:33 GMT
Server: Apache-Coyote/1.1
Content-Length: 4269
Connection: keep-alive
{
"results": [
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"],
"dataset.Internal_Name": ["ACRG_gastric"],
"dataset.Number_of_Samples": [2000],
"dataset.Posting_Restriction": ["unspecified"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Stomach"],
"dataset.Type": ["GCD"],
"dataset.citation": ["This study is not yet published. "],
"dataset.creationDate": 1302043624000,
"dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)",
"dataset.description": "Eli Lilly and Company, Merck, and Pfizer Inc. have formed the Asian Cancer Research Group, Inc., (ACRG), an independent, not-for-profit company established to accelerate research and ultimately improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. Over the next two years ACRG have committed to create one of the most extensive pharmacogenomic cancer databases known to date. This database will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "741",
"dataset.last_modified": ["2010-11-05"],
"dataset.name": "Gastric Cancer ACRG",
"dataset.number_of_downloads": [55],
"dataset.number_of_followers": [79],
"dataset.pubmed_id": [20705566],
"dataset.releaseDate": 1215129600000,
"dataset.status": "Future",
"dataset.version": "1.0.0"
},
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"],
"dataset.Internal_Name": ["ACRG_lung"],
"dataset.Number_of_Samples": [2000],
"dataset.Posting_Restriction": ["unspecified"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Lung"],
"dataset.Type": ["GCD"],
"dataset.citation": ["This study is not yet published. "],
"dataset.creationDate": 1302043626000,
"dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)",
"dataset.description": "Eli Lilly and Company, Merck, and Pfizer Inc. have formed the Asian Cancer Research Group, Inc., (ACRG), an independent, not-for-profit company established to accelerate research and ultimately improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. Over the next two years ACRG have committed to create one of the most extensive pharmacogenomic cancer databases known to date. This database will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "742",
"dataset.last_modified": ["2011-10-25"],
"dataset.name": "Lung Cancer ACRG",
"dataset.number_of_downloads": [34],
"dataset.number_of_followers": [83],
"dataset.pubmed_id": [21821572],
"dataset.releaseDate": 1267660800000,
"dataset.status": "Future",
"dataset.version": "1.0.0"
},
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Fred Hutchinson Cancer Research Center /SKCCC at Johns Hopkins"],
"dataset.Internal_Name": ["AML-Ped_TARGET"],
"dataset.Number_of_Samples": [200],
"dataset.Posting_Restriction": ["Link to data source"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Blood"],
"dataset.Type": ["GCD"],
"dataset.citation": ["http://target.cancer.gov/ "],
"dataset.creationDate": 1302043627000,
"dataset.creator": "Soheil Meshinchi/ Bob Arceci",
"dataset.description": "http://target.cancer.gov/dataportal/about/ ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "743",
"dataset.last_modified": ["2011-10-24"],
"dataset.name": "Pediatric AML TARGET",
"dataset.number_of_downloads": [57],
"dataset.number_of_followers": [29],
"dataset.pubmed_id": [22914086],
"dataset.releaseDate": 1292630400000,
"dataset.status": "Pending",
"dataset.version": "1.0.0"
}
],
"totalNumberOfResults": 115
}
'Order By' Query
Right now only a subset of query functionality is supported
SELECT * FROM <data type> ORDER BY <field name> [ASC|DESC] [LIMIT <#>] [OFFSET #]
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+order+by+Number_of_Samples+DESC+limit+3+offset+1'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:35 GMT
Server: Apache-Coyote/1.1
Content-Length: 4808
Connection: keep-alive
{
"results": [
{
"dataset.Disease": ["Multiple"],
"dataset.Institution": ["NHLBI"],
"dataset.Internal_Name": ["Framingham"],
"dataset.Number_of_Samples": [5000],
"dataset.Posting_Restriction": ["Link to data source"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Blood"],
"dataset.Type": ["GCD"],
"dataset.citation": ["Genetics of the Framingham Heart Study population. Govindaraju DR, Cupples LA, Kannel WB, O'Donnell CJ, Atwood LD, D'Agostino RB Sr, Fox CS, Larson M, Levy D, Murabito J, Vasan RS, Splansky GL, Wolf PA, Benjamin EJ.Adv Genet. 2008;62:33-65. http://www.framinghamheartstudy.org/ "],
"dataset.creationDate": 1302043699000,
"dataset.creator": "Dan Levy",
"dataset.description": "The Framingham Heart Study comprises a longitudinal three-generation population study (n~15,000). Genotyping at 500K SNPs is available for ~9,500 individuals and gene expression for blood on 5,000-7,000. Phenotypes in the cohort include serum lipid/cholesterol, CRP, glucose levels, adiposity measures, hypertension, T2D, chronic kidney disease, imaging measures and heart disease outcomes (MI, failure) ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "771",
"dataset.last_modified": ["2009-07-06"],
"dataset.name": "Framingham Heart Study",
"dataset.number_of_downloads": [42],
"dataset.number_of_followers": [115],
"dataset.pubmed_id": [18201960],
"dataset.releaseDate": 1210032000000,
"dataset.status": "Future",
"dataset.version": "1.0.0"
},
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"],
"dataset.Internal_Name": ["ACRG_gastric"],
"dataset.Number_of_Samples": [2000],
"dataset.Posting_Restriction": ["unspecified"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Stomach"],
"dataset.Type": ["GCD"],
"dataset.citation": ["This study is not yet published. "],
"dataset.creationDate": 1302043624000,
"dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)",
"dataset.description": "Eli Lilly and Company, Merck, and Pfizer Inc. have formed the Asian Cancer Research Group, Inc., (ACRG), an independent, not-for-profit company established to accelerate research and ultimately improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. Over the next two years ACRG have committed to create one of the most extensive pharmacogenomic cancer databases known to date. This database will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "741",
"dataset.last_modified": ["2010-11-05"],
"dataset.name": "Gastric Cancer ACRG",
"dataset.number_of_downloads": [55],
"dataset.number_of_followers": [79],
"dataset.pubmed_id": [20705566],
"dataset.releaseDate": 1215129600000,
"dataset.status": "Future",
"dataset.version": "1.0.0"
},
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"],
"dataset.Internal_Name": ["ACRG_lung"],
"dataset.Number_of_Samples": [2000],
"dataset.Posting_Restriction": ["unspecified"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Lung"],
"dataset.Type": ["GCD"],
"dataset.citation": ["This study is not yet published. "],
"dataset.creationDate": 1302043626000,
"dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)",
"dataset.description": "Eli Lilly and Company, Merck, and Pfizer Inc. have formed the Asian Cancer Research Group, Inc., (ACRG), an independent, not-for-profit company established to accelerate research and ultimately improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. Over the next two years ACRG have committed to create one of the most extensive pharmacogenomic cancer databases known to date. This database will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "742",
"dataset.last_modified": ["2011-10-25"],
"dataset.name": "Lung Cancer ACRG",
"dataset.number_of_downloads": [34],
"dataset.number_of_followers": [83],
"dataset.pubmed_id": [21821572],
"dataset.releaseDate": 1267660800000,
"dataset.status": "Future",
"dataset.version": "1.0.0"
}
],
"totalNumberOfResults": 115
}
'Where Equal To' Query
Right now only a subset of query functionality is supported
SELECT * FROM <data type> WHERE <field name> == "<value>" [LIMIT <#>] [OFFSET #]
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+where+name+==+%22MSKCC+Prostate+Cancer%22'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:36 GMT
Server: Apache-Coyote/1.1
Content-Length: 2095
Connection: keep-alive
{
"results": [{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Memorial Sloan Kettering Cancer Center"],
"dataset.Internal_Name": ["Prostate cancer-MSKCC"],
"dataset.Number_of_Samples": [218],
"dataset.Posting_Restriction": ["unspecified"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Prostate"],
"dataset.Type": ["GCD"],
"dataset.citation": ["Integrative genomic profiling of human prostate cancer. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Cancer Cell. 2010 Jul 13;18(1):11-22. "],
"dataset.creationDate": 1302043815000,
"dataset.creator": "Charles Sawyers",
"dataset.description": "Genetic and epigenetic alterations have been identified that lead to transcriptional Annotation of prostate cancer genomes provides a foundation for discoveries that can impact disease understanding and treatment. Concordant assessment of DNA copy number, mRNA expression, and focused exon resequencing in the 218 prostate cancer tumors represented in this dataset haveidentified the nuclear receptor coactivator NCOA2 as an oncogene in approximately 11% of tumors. Additionally, the androgen-driven TMPRSS2-ERG fusion was associated with a previously unrecognized, prostate-specific deletion at chromosome 3p14 that implicates FOXP1, RYBP, and SHQ1 as potential cooperative tumor suppressors. DNA copy-number data from primary tumors revealed that copy-number alterations robustly define clusters of low- and high-risk disease beyond that achieved by Gleason score. ",
"dataset.hasClinicalData": true,
"dataset.hasExpressionData": true,
"dataset.hasGeneticData": true,
"dataset.id": "828",
"dataset.last_modified": ["2009-03-06"],
"dataset.name": "MSKCC Prostate Cancer",
"dataset.number_of_downloads": [32],
"dataset.number_of_followers": [7],
"dataset.pubmed_id": [20579941],
"dataset.releaseDate": 1221350400000,
"dataset.status": "Current",
"dataset.version": "1.0.0"
}],
"totalNumberOfResults": 1
}
'Where Equal To' Query with a Limit
Right now only a subset of query functionality is supported
SELECT * FROM <data type> WHERE <field name> == "<value>" [LIMIT <#>] [OFFSET #]
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+where+Species+==+%22Human%22+limit+3+offset+1'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:38 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"],
"dataset.Internal_Name": ["ACRG_gastric"],
"dataset.Number_of_Samples": [2000],
"dataset.Posting_Restriction": ["unspecified"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Stomach"],
"dataset.Type": ["GCD"],
"dataset.citation": ["This study is not yet published. "],
"dataset.creationDate": 1302043624000,
"dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)",
"dataset.description": "Eli Lilly and Company, Merck, and Pfizer Inc. have formed the Asian Cancer Research Group, Inc., (ACRG), an independent, not-for-profit company established to accelerate research and ultimately improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. Over the next two years ACRG have committed to create one of the most extensive pharmacogenomic cancer databases known to date. This database will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "741",
"dataset.last_modified": ["2010-11-05"],
"dataset.name": "Gastric Cancer ACRG",
"dataset.number_of_downloads": [55],
"dataset.number_of_followers": [79],
"dataset.pubmed_id": [20705566],
"dataset.releaseDate": 1215129600000,
"dataset.status": "Future",
"dataset.version": "1.0.0"
},
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"],
"dataset.Internal_Name": ["ACRG_lung"],
"dataset.Number_of_Samples": [2000],
"dataset.Posting_Restriction": ["unspecified"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Lung"],
"dataset.Type": ["GCD"],
"dataset.citation": ["This study is not yet published. "],
"dataset.creationDate": 1302043626000,
"dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)",
"dataset.description": "Eli Lilly and Company, Merck, and Pfizer Inc. have formed the Asian Cancer Research Group, Inc., (ACRG), an independent, not-for-profit company established to accelerate research and ultimately improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. Over the next two years ACRG have committed to create one of the most extensive pharmacogenomic cancer databases known to date. This database will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "742",
"dataset.last_modified": ["2011-10-25"],
"dataset.name": "Lung Cancer ACRG",
"dataset.number_of_downloads": [34],
"dataset.number_of_followers": [83],
"dataset.pubmed_id": [21821572],
"dataset.releaseDate": 1267660800000,
"dataset.status": "Future",
"dataset.version": "1.0.0"
},
{
"dataset.Disease": ["Cancer"],
"dataset.Institution": ["Fred Hutchinson Cancer Research Center /SKCCC at Johns Hopkins"],
"dataset.Internal_Name": ["AML-Ped_TARGET"],
"dataset.Number_of_Samples": [200],
"dataset.Posting_Restriction": ["Link to data source"],
"dataset.Species": ["Human"],
"dataset.Tissue_Tumor": ["Blood"],
"dataset.Type": ["GCD"],
"dataset.citation": ["http://target.cancer.gov/ "],
"dataset.creationDate": 1302043627000,
"dataset.creator": "Soheil Meshinchi/ Bob Arceci",
"dataset.description": "http://target.cancer.gov/dataportal/about/ ",
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "743",
"dataset.last_modified": ["2011-10-24"],
"dataset.name": "Pediatric AML TARGET",
"dataset.number_of_downloads": [57],
"dataset.number_of_followers": [29],
"dataset.pubmed_id": [22914086],
"dataset.releaseDate": 1292630400000,
"dataset.status": "Pending",
"dataset.version": "1.0.0"
}
],
"totalNumberOfResults": 92
}
'Select *' Query for the Layers of a Dataset
Right now only a subset of query functionality is supported
SELECT * FROM layer WHERE dataset.id == <datasetId> [LIMIT <#>] [OFFSET <#>]
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+layer+where+dataset.id+==+%22828%22'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:40 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"layer.creationDate": 1302043868000,
"layer.description": null,
"layer.id": "67",
"layer.locations": null,
"layer.name": "phenotypes",
"layer.platform": "",
"layer.preview": null,
"layer.processingFacility": "",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "C",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043870000,
"layer.description": null,
"layer.id": "68",
"layer.locations": null,
"layer.name": "sequencing",
"layer.platform": "iPLEX Sequenom ",
"layer.preview": null,
"layer.processingFacility": "iPLEX Sequenom ",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "G",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043872000,
"layer.description": null,
"layer.id": "69",
"layer.locations": null,
"layer.name": "CNV",
"layer.platform": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"layer.preview": null,
"layer.processingFacility": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "G",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043875000,
"layer.description": null,
"layer.id": "70",
"layer.locations": null,
"layer.name": "miRNA expression",
"layer.platform": "Agilent microRNA V2 arrays",
"layer.preview": null,
"layer.processingFacility": "Agilent microRNA V2 arrays",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "E",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043877000,
"layer.description": null,
"layer.id": "71",
"layer.locations": null,
"layer.name": "exon expression",
"layer.platform": "Affymetrix Human Exon 1.0 ST array",
"layer.preview": null,
"layer.processingFacility": "Affymetrix Human Exon 1.0 ST array",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "E",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043879000,
"layer.description": null,
"layer.id": "72",
"layer.locations": null,
"layer.name": "phenotypes",
"layer.platform": "",
"layer.preview": null,
"layer.processingFacility": "",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "C",
"layer.version": "1.0.0"
}
],
"totalNumberOfResults": 6
}
'Order By' Query for the Layers of a Dataset
Right now only a subset of query functionality is supported
SELECT * FROM layer WHERE dataset.id == <datasetId> ORDER BY <field name> [ASC|DESC] [LIMIT <#>] [OFFSET <#>]
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+layer+where+dataset.id+==+%22828%22+ORDER+BY+type'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:43 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"layer.creationDate": 1302043868000,
"layer.description": null,
"layer.id": "67",
"layer.locations": null,
"layer.name": "phenotypes",
"layer.platform": "",
"layer.preview": null,
"layer.processingFacility": "",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "C",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043879000,
"layer.description": null,
"layer.id": "72",
"layer.locations": null,
"layer.name": "phenotypes",
"layer.platform": "",
"layer.preview": null,
"layer.processingFacility": "",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "C",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043875000,
"layer.description": null,
"layer.id": "70",
"layer.locations": null,
"layer.name": "miRNA expression",
"layer.platform": "Agilent microRNA V2 arrays",
"layer.preview": null,
"layer.processingFacility": "Agilent microRNA V2 arrays",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "E",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043877000,
"layer.description": null,
"layer.id": "71",
"layer.locations": null,
"layer.name": "exon expression",
"layer.platform": "Affymetrix Human Exon 1.0 ST array",
"layer.preview": null,
"layer.processingFacility": "Affymetrix Human Exon 1.0 ST array",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "E",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043870000,
"layer.description": null,
"layer.id": "68",
"layer.locations": null,
"layer.name": "sequencing",
"layer.platform": "iPLEX Sequenom ",
"layer.preview": null,
"layer.processingFacility": "iPLEX Sequenom ",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "G",
"layer.version": "1.0.0"
},
{
"layer.creationDate": 1302043872000,
"layer.description": null,
"layer.id": "69",
"layer.locations": null,
"layer.name": "CNV",
"layer.platform": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"layer.preview": null,
"layer.processingFacility": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"layer.publicationDate": null,
"layer.qcBy": null,
"layer.qcDate": null,
"layer.releaseNotes": null,
"layer.tissueType": null,
"layer.type": "G",
"layer.version": "1.0.0"
}
],
"totalNumberOfResults": 6
}
REST API Examples (Read Only)
Sanity check request
This is just a 'hello world' type request that you can make to ensure that the service is running.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/test'
Response
HTTP/1.1 200 OK
Cache-Control: no-cache, no-store, max-age=0
Content-Language: en-US
Content-Type: application/json;charset=UTF-8
Date: Wed, 06 Apr 2011 01:59:43 GMT
Expires: Thu, 01 Jan 1970 00:00:00 GMT
Pragma: no-cache
Server: Apache-Coyote/1.1
Content-Length: 35
Connection: keep-alive
{"hello": "REST for Datasets rocks"}
Get All Datasets
Optional Parameters
- offset - integer - 1-based pagination offset
- limit - integer - maximum number of results to return
- sort - string - the name of the field upon which to sort
- ascending - boolean - whether or not to sort ascending
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset?sort=name&limit=3'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:43 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"paging": {"next": "/repo/v1/dataset?offset=4&limit=3&sort=name&ascending=true"},
"results": [
{
"annotations": "/repo/v1/dataset/814/annotations",
"creationDate": 1302043790000,
"creator": "Stephen Friend",
"description": "Clinical outcomes with responder/non-responder status for standard of care therapies. Partial retrospective, partial prospective. Patient-driven. Minimum full exome sequencing. ",
"etag": "378679746",
"hasClinicalData": false,
"hasExpressionData": false,
"hasGeneticData": false,
"id": "814",
"layer": "/repo/v1/dataset/814/layer",
"name": "AML Nonresponders Cohort",
"releaseDate": 1301270400000,
"status": "Future",
"uri": "/repo/v1/dataset/814",
"version": "1.0.0"
},
{
"annotations": "/repo/v1/dataset/836/annotations",
"creationDate": 1302043828000,
"creator": "TCGA",
"description": "The Cancer Genome Atlas is generating multiple levels of genomic information on a panel of 500 AML tumor samples. For more information, go to: http://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp ",
"etag": "-789629581",
"hasClinicalData": false,
"hasExpressionData": false,
"hasGeneticData": false,
"id": "836",
"layer": "/repo/v1/dataset/836/layer",
"name": "AML TCGA",
"releaseDate": 1258243200000,
"status": "Future",
"uri": "/repo/v1/dataset/836",
"version": "1.0.0"
},
{
"annotations": "/repo/v1/dataset/765/annotations",
"creationDate": 1302043662000,
"creator": "Cookson",
"description": "We have created a global map of the effects of polymorphism on gene expression in 400 children from families recruited through a proband with asthma. We genotyped 408,273 SNPs and identified expression quantitative trait loci from measurements of 54,675 transcripts representing 20,599 genes in Epstein-Barr virus-transformed lymphoblastoid cell lines. We found that 15,084 transcripts (28%) representing 6,660 genes had narrow-sense heritabilities (H2) > 0.3. We executed genome-wide association scans for these traits and found peak lod scores between 3.68 and 59.1. The most highly heritable traits were markedly enriched in Gene Ontology descriptors for response to unfolded protein (chaperonins and heat shock proteins), regulation of progression through the cell cycle, RNA processing, DNA repair, immune responses and apoptosis. SNPs that regulate expression of these genes are candidates in the study of degenerative diseases, malignancy, infection and inflammation. We have created a downloadable database to facilitate use of our findings in the mapping of complex disease loci. ",
"etag": "264262187",
"hasClinicalData": false,
"hasExpressionData": false,
"hasGeneticData": false,
"id": "765",
"layer": "/repo/v1/dataset/765/layer",
"name": "Asthma Human Lymphoblastoid Cell Lines",
"releaseDate": 1241395200000,
"status": "Future",
"uri": "/repo/v1/dataset/765",
"version": "1.0.0"
}
],
"totalNumberOfResults": 115
}
Get a Dataset
This returns the primary fields of a dataset and links to get additional info.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:44 GMT
ETag: -433162931
Server: Apache-Coyote/1.1
Content-Length: 1255
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/828/annotations",
"creationDate": 1302043815000,
"creator": "Charles Sawyers",
"description": "Genetic and epigenetic alterations have been identified that lead to transcriptional Annotation of prostate cancer genomes provides a foundation for discoveries that can impact disease understanding and treatment. Concordant assessment of DNA copy number, mRNA expression, and focused exon resequencing in the 218 prostate cancer tumors represented in this dataset haveidentified the nuclear receptor coactivator NCOA2 as an oncogene in approximately 11% of tumors. Additionally, the androgen-driven TMPRSS2-ERG fusion was associated with a previously unrecognized, prostate-specific deletion at chromosome 3p14 that implicates FOXP1, RYBP, and SHQ1 as potential cooperative tumor suppressors. DNA copy-number data from primary tumors revealed that copy-number alterations robustly define clusters of low- and high-risk disease beyond that achieved by Gleason score. ",
"etag": "-433162931",
"hasClinicalData": true,
"hasExpressionData": true,
"hasGeneticData": true,
"id": "828",
"layer": "/repo/v1/dataset/828/layer",
"name": "MSKCC Prostate Cancer",
"releaseDate": 1221350400000,
"status": "Current",
"uri": "/repo/v1/dataset/828",
"version": "1.0.0"
}
Get Annotations for a Dataset
This returns the annotations for a dataset.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:44 GMT
ETag: 622666294
Server: Apache-Coyote/1.1
Content-Length: 922
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "622666294",
"id": "828",
"longAnnotations": {
"Number_of_Samples": [218],
"number_of_downloads": [32],
"number_of_followers": [7],
"pubmed_id": [20579941]
},
"stringAnnotations": {
"Disease": ["Cancer"],
"Institution": ["Memorial Sloan Kettering Cancer Center"],
"Internal_Name": ["Prostate cancer-MSKCC"],
"Posting_Restriction": ["unspecified"],
"Species": ["Human"],
"Tissue_Tumor": ["Prostate"],
"Type": ["GCD"],
"citation": ["Integrative genomic profiling of human prostate cancer. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Cancer Cell. 2010 Jul 13;18(1):11-22. "],
"last_modified": ["2009-03-06"]
},
"uri": "/repo/v1/dataset/828/annotations"
}
Get all the Layers for a Dataset
This returns the primary fields for all the layers of a dataset.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:46 GMT
Server: Apache-Coyote/1.1
Content-Length: 3629
Connection: keep-alive
{
"paging": {},
"results": [
{
"annotations": "/repo/v1/dataset/828/layer/71/annotations",
"creationDate": 1302043877000,
"description": null,
"etag": "1551208644",
"id": "71",
"locations": [
"/repo/v1/dataset/828/layer/71/awsS3Location",
"/repo/v1/dataset/828/layer/71/sageLocation",
"/repo/v1/dataset/828/layer/71/locations"
],
"name": "exon expression",
"platform": "Affymetrix Human Exon 1.0 ST array",
"preview": "/repo/v1/dataset/828/layer/71/preview",
"processingFacility": "Affymetrix Human Exon 1.0 ST array",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "E",
"uri": "/repo/v1/dataset/828/layer/71",
"version": "1.0.0"
},
{
"annotations": "/repo/v1/dataset/828/layer/72/annotations",
"creationDate": 1302043879000,
"description": null,
"etag": "-524449647",
"id": "72",
"locations": [
"/repo/v1/dataset/828/layer/72/locations",
"/repo/v1/dataset/828/layer/72/sageLocation",
"/repo/v1/dataset/828/layer/72/awsS3Location"
],
"name": "phenotypes",
"platform": "",
"preview": "/repo/v1/dataset/828/layer/72/preview",
"processingFacility": "",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "C",
"uri": "/repo/v1/dataset/828/layer/72",
"version": "1.0.0"
},
{
"annotations": "/repo/v1/dataset/828/layer/69/annotations",
"creationDate": 1302043872000,
"description": null,
"etag": "-1684328331",
"id": "69",
"locations": [
"/repo/v1/dataset/828/layer/69/locations",
"/repo/v1/dataset/828/layer/69/sageLocation",
"/repo/v1/dataset/828/layer/69/awsS3Location"
],
"name": "CNV",
"platform": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"preview": "/repo/v1/dataset/828/layer/69/preview",
"processingFacility": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "G",
"uri": "/repo/v1/dataset/828/layer/69",
"version": "1.0.0"
},
{
"annotations": "/repo/v1/dataset/828/layer/70/annotations",
"creationDate": 1302043875000,
"description": null,
"etag": "622767659",
"id": "70",
"locations": [
"/repo/v1/dataset/828/layer/70/locations",
"/repo/v1/dataset/828/layer/70/awsS3Location",
"/repo/v1/dataset/828/layer/70/sageLocation"
],
"name": "miRNA expression",
"platform": "Agilent microRNA V2 arrays",
"preview": "/repo/v1/dataset/828/layer/70/preview",
"processingFacility": "Agilent microRNA V2 arrays",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "E",
"uri": "/repo/v1/dataset/828/layer/70",
"version": "1.0.0"
},
{
"annotations": "/repo/v1/dataset/828/layer/67/annotations",
"creationDate": 1302043868000,
"description": null,
"etag": "1927937721",
"id": "67",
"locations": [
"/repo/v1/dataset/828/layer/67/locations",
"/repo/v1/dataset/828/layer/67/awsS3Location",
"/repo/v1/dataset/828/layer/67/sageLocation"
],
"name": "phenotypes",
"platform": "",
"preview": "/repo/v1/dataset/828/layer/67/preview",
"processingFacility": "",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "C",
"uri": "/repo/v1/dataset/828/layer/67",
"version": "1.0.0"
},
{
"annotations": "/repo/v1/dataset/828/layer/68/annotations",
"creationDate": 1302043870000,
"description": null,
"etag": "-1498813326",
"id": "68",
"locations": [
"/repo/v1/dataset/828/layer/68/awsS3Location",
"/repo/v1/dataset/828/layer/68/sageLocation",
"/repo/v1/dataset/828/layer/68/locations"
],
"name": "sequencing",
"platform": "iPLEX Sequenom ",
"preview": "/repo/v1/dataset/828/layer/68/preview",
"processingFacility": "iPLEX Sequenom ",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "G",
"uri": "/repo/v1/dataset/828/layer/68",
"version": "1.0.0"
}
],
"totalNumberOfResults": 6
}
Get a Expression Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/71'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:46 GMT
ETag: 1551208644
Server: Apache-Coyote/1.1
Content-Length: 619
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/828/layer/71/annotations",
"creationDate": 1302043877000,
"description": null,
"etag": "1551208644",
"id": "71",
"locations": [
"/repo/v1/dataset/828/layer/71/awsS3Location",
"/repo/v1/dataset/828/layer/71/sageLocation",
"/repo/v1/dataset/828/layer/71/locations"
],
"name": "exon expression",
"platform": "Affymetrix Human Exon 1.0 ST array",
"preview": "/repo/v1/dataset/828/layer/71/preview",
"processingFacility": "Affymetrix Human Exon 1.0 ST array",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "E",
"uri": "/repo/v1/dataset/828/layer/71",
"version": "1.0.0"
}
Get Annotations for a Expression Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/71/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:46 GMT
ETag: 923521
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "71",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/828/layer/71/annotations"
}
Get preview data for a Expression Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/71/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:47 GMT
ETag: -919955460
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "-919955460",
"id": "71",
"preview": 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t246\t122\t241\t218\t323\t211\t190\t213\t123\t80\t124\t103\t69\t313\t130\t175\t235\t67\t153\t136\t191\t177\t168\t80\t143\t183\t110\t141\t107\t166\t131\t103\t168\t166\t123\t166\t207\t154\t250\t84\t314\t241\t147\t172\t110\t205\t232\t76\t271\t294\t106\t211\t103\t178\t123\t248\t152\t322\t55\t82\t125\t132\t80\t157\t147\t80\t269\t244\t267\t150\t195\t147\t142\t127\t86\t83\t172\t112\t144\t168\t140\t157\t245\t276\t174\t145\t165\t108\t113\t122\t181\t88\t188\t98\t79\t162\t147\n11\t562\t614\t627\t726\t633\t378\t842\t463\t813\t534\t572\t671\t432\t1144\t416\t959\t1444\t683\t1562\t1008\t1982\t1810\t387\t685\t349\t2145\t818\t650\t436\t540\t1387\t367\t317\t1941\t2276\t651\t1462\t1559\t1869\t457\t1150\t864\t1105\t1054\t1408\t562\t541\t795\t745\t1069\t1362\t695\t1028\t1404\t213\t802\t1138\t2297\t894\t1038\t999\t810\t935\t1011\t939\t1125\t1361\t1049\t934\t931\t668\t959\t1761\t1393\t1608\t1123\t1024\t1599\t1415\t2386\t1590\t1814\t2778\t1571\t1986\t1771\t1910\t1804\t1525\t1563\t2106\t2477\t2792\t612\t978\t546\t557\t760\t559\t450\t1208\t623\t898\t795\t239\t822\t392\t1067\t651\t958\t616\t499\t1166\t645\t1475\t730\t575\t643\t596\t722\t881\t578\t1053\t957\t998\t2485\t490\t2174\t2979\t2390\t1463\t786\t752\t1049\t324\t1970\t1392\t433\t2027\t1340\t1401\t1679\t980\t1692\t4384\t122\t259\t963\t1323\t320\t1023\t1892\t285\t1569\t1452\t720\t1126\t1307\t1253\t1619\t1202\t746\t891\t804\t1038\t600\t955\t768\t1509\t1148\t1487\t546\t517\t459\t442\t500\t453\t753\t801\t615\t404\t358\t807\t952\n",
"uri": "/repo/v1/dataset/828/layer/71/preview"
}
Get preview data as a map for a Expression Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/71/previewAsMap'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:47 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"DU145": "608",
"LNCaP": "918",
"LNCaP104S": "145",
"PAN0095": "1094",
"PAN0107": "872",
"PAN0109": "826",
"PAN0110": "763",
"PAN0112": "1049",
"PAN0113": "868",
"PAN0114": "775",
"PAN0115": "586",
"PAN0117": "920",
"PAN0120": "1064",
"PAN0122": "702",
"PAN0125": "966",
"PAN0127": "785",
"PAN0128": "738",
"PAN0129": "1348",
"PAN0134": "1238",
"PAN0135": "351",
"PAN0136": "238",
"PAN0144": "220",
"PAN0147": "239",
"PAN0151": "204",
"PAN0157": "179",
"PAN0162": "296",
"PAN0164": "371",
"PAN0167": "285",
"PAN0169": "229",
"PAN0171": "154",
"PAN0172": "181",
"PAN0174": "388",
"PC3": "1012",
"PCA0001": "331",
"PCA0002": "349",
"PCA0003": "308",
"PCA0005": "330",
"PCA0007": "363",
"PCA0008": "601",
"PCA0009": "453",
"PCA0010": "334",
"PCA0011": "734",
"PCA0012": "385",
"PCA0013": "519",
"PCA0014": "391",
"PCA0015": "239",
"PCA0017": "1279",
"PCA0018": "189",
"PCA0020": "529",
"PCA0021": "966",
"PCA0022": "523",
"PCA0024": "586",
"PCA0025": "555",
"PCA0026": "1110",
"PCA0027": "873",
"PCA0028": "201",
"PCA0029": "343",
"PCA0030": "403",
"PCA0031": "3019",
"PCA0032": "484",
"PCA0033": "150",
"PCA0034": "252",
"PCA0035": "264",
"PCA0036": "996",
"PCA0037": "171",
"PCA0038": "200",
"PCA0040": "1074",
"PCA0050": "1440",
"PCA0052": "243",
"PCA0054": "583",
"PCA0056": "574",
"PCA0057": "617",
"PCA0058": "187",
"PCA0062": "536",
"PCA0063": "457",
"PCA0064": "544",
"PCA0065": "489",
"PCA0066": "692",
"PCA0068": "127",
"PCA0073": "372",
"PCA0074": "706",
"PCA0075": "424",
"PCA0077": "591",
"PCA0080": "784",
"PCA0081": "271",
"PCA0082": "543",
"PCA0083": "618",
"PCA0084": "174",
"PCA0086": "463",
"PCA0087": "519",
"PCA0089": "1725",
"PCA0090": "577",
"PCA0092": "353",
"PCA0093": "512",
"PCA0094": "575",
"PCA0095": "461",
"PCA0096": "577",
"PCA0097": "530",
"PCA0099": "461",
"PCA0100": "822",
"PCA0101": "654",
"PCA0103": "429",
"PCA0104": "404",
"PCA0105": "382",
"PCA0107": "594",
"PCA0108": "757",
"PCA0109": "853",
"PCA0110": "753",
"PCA0111": "493",
"PCA0112": "553",
"PCA0113": "806",
"PCA0114": "748",
"PCA0115": "1187",
"PCA0117": "1004",
"PCA0118": "685",
"PCA0119": "1892",
"PCA0120": "847",
"PCA0122": "1229",
"PCA0123": "1007",
"PCA0124": "853",
"PCA0125": "618",
"PCA0126": "530",
"PCA0127": "932",
"PCA0128": "1115",
"PCA0129": "1777",
"PCA0130": "2036",
"PCA0132": "235",
"PCA0133": "1318",
"PCA0134": "207",
"PCA0135": "143",
"PCA0136": "288",
"PCA0141": "273",
"PCA0144": "231",
"PCA0145": "768",
"PCA0146": "273",
"PCA0147": "294",
"PCA0149": "685",
"PCA0150": "163",
"PCA0151": "576",
"PCA0155": "198",
"PCA0156": "409",
"PCA0157": "464",
"PCA0158": "432",
"PCA0159": "206",
"PCA0160": "127",
"PCA0161": "513",
"PCA0162": "486",
"PCA0163": "746",
"PCA0164": "398",
"PCA0165": "465",
"PCA0167": "257",
"PCA0168": "183",
"PCA0169": "354",
"PCA0170": "493",
"PCA0171": "210",
"PCA0172": "596",
"PCA0173": "494",
"PCA0174": "565",
"PCA0175": "1322",
"PCA0176": "190",
"PCA0178": "1176",
"PCA0179": "1268",
"PCA0180": "1101",
"PCA0181": "1119",
"PCA0182": "234",
"PCA0184": "715",
"PCA0187": "782",
"PCA0188": "132",
"PCA0189": "777",
"PCA0190": "626",
"PCA0193": "249",
"PCA0194": "1046",
"PCA0199": "840",
"PCA0200": "825",
"PCA0201": "903",
"PCA0206": "568",
"PCA0207": "813",
"PCA0208": "4710",
"PCA0209": "68",
"PCA0210": "165",
"PCA0211": "313",
"PCA0213": "898",
"PCA0215": "184",
"Vcap": "818",
"feature_id": "6"
},
{
"DU145": "241",
"LNCaP": "545",
"LNCaP104S": "186",
"PAN0095": "723",
"PAN0107": "328",
"PAN0109": "258",
"PAN0110": "299",
"PAN0112": "265",
"PAN0113": "86",
"PAN0114": "245",
"PAN0115": "313",
"PAN0117": "202",
"PAN0120": "311",
"PAN0122": "144",
"PAN0125": "106",
"PAN0127": "340",
"PAN0128": "329",
"PAN0129": "308",
"PAN0134": "324",
"PAN0135": "290",
"PAN0136": "176",
"PAN0144": "138",
"PAN0147": "162",
"PAN0151": "152",
"PAN0157": "103",
"PAN0162": "243",
"PAN0164": "239",
"PAN0167": "235",
"PAN0169": "145",
"PAN0171": "125",
"PAN0172": "146",
"PAN0174": "222",
"PC3": "463",
"PCA0001": "232",
"PCA0002": "183",
"PCA0003": "209",
"PCA0005": "253",
"PCA0007": "114",
"PCA0008": "140",
"PCA0009": "287",
"PCA0010": "229",
"PCA0011": "170",
"PCA0012": "179",
"PCA0013": "224",
"PCA0014": "190",
"PCA0015": "241",
"PCA0017": "605",
"PCA0018": "205",
"PCA0020": "266",
"PCA0021": "405",
"PCA0022": "181",
"PCA0024": "350",
"PCA0025": "168",
"PCA0026": "373",
"PCA0027": "256",
"PCA0028": "219",
"PCA0029": "268",
"PCA0030": "212",
"PCA0031": "528",
"PCA0032": "276",
"PCA0033": "100",
"PCA0034": "195",
"PCA0035": "273",
"PCA0036": "235",
"PCA0037": "157",
"PCA0038": "62",
"PCA0040": "349",
"PCA0050": "488",
"PCA0052": "128",
"PCA0054": "289",
"PCA0056": "273",
"PCA0057": "368",
"PCA0058": "116",
"PCA0062": "187",
"PCA0063": "318",
"PCA0064": "435",
"PCA0065": "317",
"PCA0066": "417",
"PCA0068": "125",
"PCA0073": "180",
"PCA0074": "211",
"PCA0075": "107",
"PCA0077": "220",
"PCA0080": "285",
"PCA0081": "128",
"PCA0082": "286",
"PCA0083": "347",
"PCA0084": "101",
"PCA0086": "179",
"PCA0087": "212",
"PCA0089": "845",
"PCA0090": "297",
"PCA0092": "188",
"PCA0093": "233",
"PCA0094": "241",
"PCA0095": "162",
"PCA0096": "186",
"PCA0097": "252",
"PCA0099": "241",
"PCA0100": "457",
"PCA0101": "248",
"PCA0103": "189",
"PCA0104": "326",
"PCA0105": "189",
"PCA0107": "346",
"PCA0108": "324",
"PCA0109": "232",
"PCA0110": "220",
"PCA0111": "286",
"PCA0112": "195",
"PCA0113": "302",
"PCA0114": "316",
"PCA0115": "636",
"PCA0117": "247",
"PCA0118": "330",
"PCA0119": "360",
"PCA0120": "262",
"PCA0122": "304",
"PCA0123": "300",
"PCA0124": "329",
"PCA0125": "216",
"PCA0126": "217",
"PCA0127": "345",
"PCA0128": "216",
"PCA0129": "383",
"PCA0130": "363",
"PCA0132": "171",
"PCA0133": "322",
"PCA0134": "256",
"PCA0135": "124",
"PCA0136": "142",
"PCA0141": "263",
"PCA0144": "152",
"PCA0145": "490",
"PCA0146": "129",
"PCA0147": "132",
"PCA0149": "441",
"PCA0150": "78",
"PCA0151": "216",
"PCA0155": "110",
"PCA0156": "233",
"PCA0157": "226",
"PCA0158": "145",
"PCA0159": "184",
"PCA0160": "103",
"PCA0161": "232",
"PCA0162": "298",
"PCA0163": "418",
"PCA0164": "272",
"PCA0165": "197",
"PCA0167": "261",
"PCA0168": "147",
"PCA0169": "126",
"PCA0170": "167",
"PCA0171": "147",
"PCA0172": "314",
"PCA0173": "255",
"PCA0174": "319",
"PCA0175": "383",
"PCA0176": "154",
"PCA0178": "374",
"PCA0179": "395",
"PCA0180": "361",
"PCA0181": "333",
"PCA0182": "150",
"PCA0184": "279",
"PCA0187": "290",
"PCA0188": "209",
"PCA0189": "470",
"PCA0190": "286",
"PCA0193": "296",
"PCA0194": "318",
"PCA0199": "305",
"PCA0200": "308",
"PCA0201": "347",
"PCA0206": "259",
"PCA0207": "242",
"PCA0208": "1728",
"PCA0209": "48",
"PCA0210": "83",
"PCA0211": "75",
"PCA0213": "271",
"PCA0215": "121",
"Vcap": "606",
"feature_id": "7"
},
{
"DU145": "974",
"LNCaP": "1732",
"LNCaP104S": "548",
"PAN0095": "1301",
"PAN0107": "1071",
"PAN0109": "1612",
"PAN0110": "1239",
"PAN0112": "1380",
"PAN0113": "978",
"PAN0114": "773",
"PAN0115": "742",
"PAN0117": "767",
"PAN0120": "799",
"PAN0122": "605",
"PAN0125": "615",
"PAN0127": "987",
"PAN0128": "1148",
"PAN0129": "1170",
"PAN0134": "1493",
"PAN0135": "845",
"PAN0136": "767",
"PAN0144": "594",
"PAN0147": "539",
"PAN0151": "924",
"PAN0157": "608",
"PAN0162": "724",
"PAN0164": "804",
"PAN0167": "1002",
"PAN0169": "735",
"PAN0171": "545",
"PAN0172": "823",
"PAN0174": "1032",
"PC3": "1771",
"PCA0001": "1293",
"PCA0002": "785",
"PCA0003": "1152",
"PCA0005": "2045",
"PCA0007": "1173",
"PCA0008": "401",
"PCA0009": "1400",
"PCA0010": "1105",
"PCA0011": "752",
"PCA0012": "1325",
"PCA0013": "604",
"PCA0014": "971",
"PCA0015": "694",
"PCA0017": "1197",
"PCA0018": "453",
"PCA0020": "907",
"PCA0021": "1369",
"PCA0022": "839",
"PCA0024": "1775",
"PCA0025": "1196",
"PCA0026": "2772",
"PCA0027": "3238",
"PCA0028": "541",
"PCA0029": "2095",
"PCA0030": "662",
"PCA0031": "2309",
"PCA0032": "651",
"PCA0033": "1544",
"PCA0034": "670",
"PCA0035": "593",
"PCA0036": "1635",
"PCA0037": "855",
"PCA0038": "385",
"PCA0040": "2172",
"PCA0050": "2399",
"PCA0052": "738",
"PCA0054": "1496",
"PCA0056": "1555",
"PCA0057": "1954",
"PCA0058": "527",
"PCA0062": "1522",
"PCA0063": "1192",
"PCA0064": "1544",
"PCA0065": "1708",
"PCA0066": "1588",
"PCA0068": "592",
"PCA0073": "585",
"PCA0074": "812",
"PCA0075": "709",
"PCA0077": "1032",
"PCA0080": "1198",
"PCA0081": "536",
"PCA0082": "1560",
"PCA0083": "1569",
"PCA0084": "288",
"PCA0086": "1252",
"PCA0087": "1749",
"PCA0089": "3578",
"PCA0090": "1319",
"PCA0092": "1678",
"PCA0093": "1282",
"PCA0094": "731",
"PCA0095": "1355",
"PCA0096": "1490",
"PCA0097": "931",
"PCA0099": "2245",
"PCA0100": "1643",
"PCA0101": "1658",
"PCA0103": "1307",
"PCA0104": "1787",
"PCA0105": "1346",
"PCA0107": "1941",
"PCA0108": "2501",
"PCA0109": "2552",
"PCA0110": "1922",
"PCA0111": "1357",
"PCA0112": "1081",
"PCA0113": "2092",
"PCA0114": "1895",
"PCA0115": "3795",
"PCA0117": "2200",
"PCA0118": "2740",
"PCA0119": "3757",
"PCA0120": "2254",
"PCA0122": "2817",
"PCA0123": "2844",
"PCA0124": "3171",
"PCA0125": "2931",
"PCA0126": "2165",
"PCA0127": "2310",
"PCA0128": "2785",
"PCA0129": "3335",
"PCA0130": "5936",
"PCA0132": "1226",
"PCA0133": "1373",
"PCA0134": "1192",
"PCA0135": "1038",
"PCA0136": "1678",
"PCA0141": "1340",
"PCA0144": "1090",
"PCA0145": "2006",
"PCA0146": "1125",
"PCA0147": "1305",
"PCA0149": "1311",
"PCA0150": "208",
"PCA0151": "1043",
"PCA0155": "902",
"PCA0156": "1620",
"PCA0157": "807",
"PCA0158": "1249",
"PCA0159": "1008",
"PCA0160": "896",
"PCA0161": "1401",
"PCA0162": "871",
"PCA0163": "1575",
"PCA0164": "879",
"PCA0165": "936",
"PCA0167": "1145",
"PCA0168": "1081",
"PCA0169": "1567",
"PCA0170": "953",
"PCA0171": "1012",
"PCA0172": "1319",
"PCA0173": "1395",
"PCA0174": "1518",
"PCA0175": "2264",
"PCA0176": "428",
"PCA0178": "2441",
"PCA0179": "2035",
"PCA0180": "1988",
"PCA0181": "1542",
"PCA0182": "496",
"PCA0184": "1040",
"PCA0187": "1309",
"PCA0188": "438",
"PCA0189": "1711",
"PCA0190": "1819",
"PCA0193": "566",
"PCA0194": "1737",
"PCA0199": "666",
"PCA0200": "1694",
"PCA0201": "2021",
"PCA0206": "1202",
"PCA0207": "2154",
"PCA0208": "5235",
"PCA0209": "202",
"PCA0210": "305",
"PCA0211": "975",
"PCA0213": "1187",
"PCA0215": "466",
"Vcap": "1508",
"feature_id": "9"
},
{
"DU145": "157",
"LNCaP": "147",
"LNCaP104S": "80",
"PAN0095": "267",
"PAN0107": "150",
"PAN0109": "195",
"PAN0110": "147",
"PAN0112": "142",
"PAN0113": "127",
"PAN0114": "86",
"PAN0115": "83",
"PAN0117": "172",
"PAN0120": "112",
"PAN0122": "144",
"PAN0125": "168",
"PAN0127": "140",
"PAN0128": "157",
"PAN0129": "245",
"PAN0134": "276",
"PAN0135": "174",
"PAN0136": "145",
"PAN0144": "165",
"PAN0147": "108",
"PAN0151": "113",
"PAN0157": "122",
"PAN0162": "181",
"PAN0164": "88",
"PAN0167": "188",
"PAN0169": "98",
"PAN0171": "79",
"PAN0172": "162",
"PAN0174": "147",
"PC3": "269",
"PCA0001": "180",
"PCA0002": "80",
"PCA0003": "179",
"PCA0005": "227",
"PCA0007": "154",
"PCA0008": "110",
"PCA0009": "255",
"PCA0010": "141",
"PCA0011": "96",
"PCA0012": "164",
"PCA0013": "173",
"PCA0014": "108",
"PCA0015": "123",
"PCA0017": "270",
"PCA0018": "119",
"PCA0020": "120",
"PCA0021": "216",
"PCA0022": "96",
"PCA0024": "182",
"PCA0025": "204",
"PCA0026": "344",
"PCA0027": "381",
"PCA0028": "118",
"PCA0029": "196",
"PCA0030": "140",
"PCA0031": "270",
"PCA0032": "142",
"PCA0033": "183",
"PCA0034": "143",
"PCA0035": "140",
"PCA0036": "261",
"PCA0037": "124",
"PCA0038": "69",
"PCA0040": "292",
"PCA0050": "241",
"PCA0052": "89",
"PCA0054": "138",
"PCA0056": "260",
"PCA0057": "318",
"PCA0058": "64",
"PCA0062": "167",
"PCA0063": "194",
"PCA0064": "239",
"PCA0065": "161",
"PCA0066": "209",
"PCA0068": "81",
"PCA0073": "175",
"PCA0074": "111",
"PCA0075": "81",
"PCA0077": "155",
"PCA0080": "191",
"PCA0081": "145",
"PCA0082": "204",
"PCA0083": "304",
"PCA0084": "51",
"PCA0086": "127",
"PCA0087": "156",
"PCA0089": "353",
"PCA0090": "186",
"PCA0092": "172",
"PCA0093": "197",
"PCA0094": "187",
"PCA0095": "128",
"PCA0096": "120",
"PCA0097": "176",
"PCA0099": "198",
"PCA0100": "247",
"PCA0101": "218",
"PCA0103": "202",
"PCA0104": "277",
"PCA0105": "136",
"PCA0107": "192",
"PCA0108": "235",
"PCA0109": "212",
"PCA0110": "183",
"PCA0111": "208",
"PCA0112": "150",
"PCA0113": "337",
"PCA0114": "240",
"PCA0115": "379",
"PCA0117": "197",
"PCA0118": "230",
"PCA0119": "203",
"PCA0120": "181",
"PCA0122": "180",
"PCA0123": "218",
"PCA0124": "245",
"PCA0125": "246",
"PCA0126": "122",
"PCA0127": "241",
"PCA0128": "218",
"PCA0129": "323",
"PCA0130": "211",
"PCA0132": "190",
"PCA0133": "213",
"PCA0134": "123",
"PCA0135": "80",
"PCA0136": "124",
"PCA0141": "103",
"PCA0144": "69",
"PCA0145": "313",
"PCA0146": "130",
"PCA0147": "175",
"PCA0149": "235",
"PCA0150": "67",
"PCA0151": "153",
"PCA0155": "136",
"PCA0156": "191",
"PCA0157": "177",
"PCA0158": "168",
"PCA0159": "80",
"PCA0160": "143",
"PCA0161": "183",
"PCA0162": "110",
"PCA0163": "141",
"PCA0164": "107",
"PCA0165": "166",
"PCA0167": "131",
"PCA0168": "103",
"PCA0169": "168",
"PCA0170": "166",
"PCA0171": "123",
"PCA0172": "166",
"PCA0173": "207",
"PCA0174": "154",
"PCA0175": "250",
"PCA0176": "84",
"PCA0178": "314",
"PCA0179": "241",
"PCA0180": "147",
"PCA0181": "172",
"PCA0182": "110",
"PCA0184": "205",
"PCA0187": "232",
"PCA0188": "76",
"PCA0189": "271",
"PCA0190": "294",
"PCA0193": "106",
"PCA0194": "211",
"PCA0199": "103",
"PCA0200": "178",
"PCA0201": "123",
"PCA0206": "248",
"PCA0207": "152",
"PCA0208": "322",
"PCA0209": "55",
"PCA0210": "82",
"PCA0211": "125",
"PCA0213": "132",
"PCA0215": "80",
"Vcap": "244",
"feature_id": "10"
},
{
"DU145": "1023",
"LNCaP": "1892",
"LNCaP104S": "285",
"PAN0095": "720",
"PAN0107": "1126",
"PAN0109": "1307",
"PAN0110": "1253",
"PAN0112": "1619",
"PAN0113": "1202",
"PAN0114": "746",
"PAN0115": "891",
"PAN0117": "804",
"PAN0120": "1038",
"PAN0122": "600",
"PAN0125": "955",
"PAN0127": "768",
"PAN0128": "1509",
"PAN0129": "1148",
"PAN0134": "1487",
"PAN0135": "546",
"PAN0136": "517",
"PAN0144": "459",
"PAN0147": "442",
"PAN0151": "500",
"PAN0157": "453",
"PAN0162": "753",
"PAN0164": "801",
"PAN0167": "615",
"PAN0169": "404",
"PAN0171": "358",
"PAN0172": "807",
"PAN0174": "952",
"PC3": "1569",
"PCA0001": "562",
"PCA0002": "614",
"PCA0003": "627",
"PCA0005": "726",
"PCA0007": "633",
"PCA0008": "378",
"PCA0009": "842",
"PCA0010": "463",
"PCA0011": "813",
"PCA0012": "534",
"PCA0013": "572",
"PCA0014": "671",
"PCA0015": "432",
"PCA0017": "1144",
"PCA0018": "416",
"PCA0020": "959",
"PCA0021": "1444",
"PCA0022": "683",
"PCA0024": "1562",
"PCA0025": "1008",
"PCA0026": "1982",
"PCA0027": "1810",
"PCA0028": "387",
"PCA0029": "685",
"PCA0030": "349",
"PCA0031": "2145",
"PCA0032": "818",
"PCA0033": "650",
"PCA0034": "436",
"PCA0035": "540",
"PCA0036": "1387",
"PCA0037": "367",
"PCA0038": "317",
"PCA0040": "1941",
"PCA0050": "2276",
"PCA0052": "651",
"PCA0054": "1462",
"PCA0056": "1559",
"PCA0057": "1869",
"PCA0058": "457",
"PCA0062": "1150",
"PCA0063": "864",
"PCA0064": "1105",
"PCA0065": "1054",
"PCA0066": "1408",
"PCA0068": "562",
"PCA0073": "541",
"PCA0074": "795",
"PCA0075": "745",
"PCA0077": "1069",
"PCA0080": "1362",
"PCA0081": "695",
"PCA0082": "1028",
"PCA0083": "1404",
"PCA0084": "213",
"PCA0086": "802",
"PCA0087": "1138",
"PCA0089": "2297",
"PCA0090": "894",
"PCA0092": "1038",
"PCA0093": "999",
"PCA0094": "810",
"PCA0095": "935",
"PCA0096": "1011",
"PCA0097": "939",
"PCA0099": "1125",
"PCA0100": "1361",
"PCA0101": "1049",
"PCA0103": "934",
"PCA0104": "931",
"PCA0105": "668",
"PCA0107": "959",
"PCA0108": "1761",
"PCA0109": "1393",
"PCA0110": "1608",
"PCA0111": "1123",
"PCA0112": "1024",
"PCA0113": "1599",
"PCA0114": "1415",
"PCA0115": "2386",
"PCA0117": "1590",
"PCA0118": "1814",
"PCA0119": "2778",
"PCA0120": "1571",
"PCA0122": "1986",
"PCA0123": "1771",
"PCA0124": "1910",
"PCA0125": "1804",
"PCA0126": "1525",
"PCA0127": "1563",
"PCA0128": "2106",
"PCA0129": "2477",
"PCA0130": "2792",
"PCA0132": "612",
"PCA0133": "978",
"PCA0134": "546",
"PCA0135": "557",
"PCA0136": "760",
"PCA0141": "559",
"PCA0144": "450",
"PCA0145": "1208",
"PCA0146": "623",
"PCA0147": "898",
"PCA0149": "795",
"PCA0150": "239",
"PCA0151": "822",
"PCA0155": "392",
"PCA0156": "1067",
"PCA0157": "651",
"PCA0158": "958",
"PCA0159": "616",
"PCA0160": "499",
"PCA0161": "1166",
"PCA0162": "645",
"PCA0163": "1475",
"PCA0164": "730",
"PCA0165": "575",
"PCA0167": "643",
"PCA0168": "596",
"PCA0169": "722",
"PCA0170": "881",
"PCA0171": "578",
"PCA0172": "1053",
"PCA0173": "957",
"PCA0174": "998",
"PCA0175": "2485",
"PCA0176": "490",
"PCA0178": "2174",
"PCA0179": "2979",
"PCA0180": "2390",
"PCA0181": "1463",
"PCA0182": "786",
"PCA0184": "752",
"PCA0187": "1049",
"PCA0188": "324",
"PCA0189": "1970",
"PCA0190": "1392",
"PCA0193": "433",
"PCA0194": "2027",
"PCA0199": "1340",
"PCA0200": "1401",
"PCA0201": "1679",
"PCA0206": "980",
"PCA0207": "1692",
"PCA0208": "4384",
"PCA0209": "122",
"PCA0210": "259",
"PCA0211": "963",
"PCA0213": "1323",
"PCA0215": "320",
"Vcap": "1452",
"feature_id": "11"
}
],
"totalNumberOfResults": 5
}
Get the locations for a Expression Dataset Layer
This returns all the locations metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/71/locations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:47 GMT
ETag: -335671559
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "-335671559",
"id": "71",
"locations": [
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
},
{
"path": "mskcc_prostate_cancer.expression.zip",
"type": "awss3"
}
],
"uri": "/repo/v1/dataset/828/layer/71/locations"
}
Get the awsS3Location for a Expression Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/71/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:49 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/mskcc_prostate_cancer.expression.zip?Expires=1302055789&AWSAccessKeyId=AKIAI3BTGJG752CCJUVA&Signature=PmeouZZBHn8%2BHbug0x85QdSymrM%3D",
"type": "awss3"
}
Get the sageLocation for a Expression Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/71/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:49 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
}
Get a Clinical Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/72'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:50 GMT
ETag: -524449647
Server: Apache-Coyote/1.1
Content-Length: 546
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/828/layer/72/annotations",
"creationDate": 1302043879000,
"description": null,
"etag": "-524449647",
"id": "72",
"locations": [
"/repo/v1/dataset/828/layer/72/locations",
"/repo/v1/dataset/828/layer/72/sageLocation",
"/repo/v1/dataset/828/layer/72/awsS3Location"
],
"name": "phenotypes",
"platform": "",
"preview": "/repo/v1/dataset/828/layer/72/preview",
"processingFacility": "",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "C",
"uri": "/repo/v1/dataset/828/layer/72",
"version": "1.0.0"
}
Get Annotations for a Clinical Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/72/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:50 GMT
ETag: 923521
Server: Apache-Coyote/1.1
Content-Length: 185
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "72",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/828/layer/72/annotations"
}
Get preview data for a Clinical Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/72/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:50 GMT
ETag: 1782170291
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "1782170291",
"id": "72",
"preview": "phenotype_id\tsample_type\tmetastatic_site\tethnicity\tpredxbxpsa\tage\tclinical_primary_gleason\tclinical_secondary_gleason\tclinical_gleason_score\tpre_treatment_psa\tclinical_tnm_stage_t\tneoadjradtx\tchemotx\thormtx\tradtxtype\trp_type\tsms\textra_capsular_extension\tseminal_vesicle_invasion\ttnm_stage_n\tnumber_nodes_removed\tnumber_nodes_positive\tpathologic_tnm_stage_t\tpathologic_primary_gleason\tpathologic_secondary_gleason\tpathologic_gleason_score\tbcr_freetime\tbcr_event\tmetsevent\tsurvtime\tevent\tnomogram_pfp_postrp\tnomogram_nomopred_extra_capsular_extension\tnomogram_nomopred_lni\tnomogram_nomopred_ocd\tnomogram_nomopred_seminal_vesicle_invasion\tcopy_number_cluster\texpression_array_tissue_source\r\nPCA0004\tPRIMARY\tNA\tWhite Non Hispanic\t27.5\t68.93\t3\t2\t5\t11.8\tT2B\tNA\tNA\tNA\tNA\tRP\tNegative\tESTABLISHED\tNegative\tNormal_N0\t13\t0\tT3A\t3\t4\t7\t152.55\tNO\tNO\t152.55\tNO\tNA\t37.937846\t3.593974\t55.082939\tNA\t1\tNA\r\nPCA0006\tPRIMARY\tNA\tWhite Non Hispanic\t15.7\t56.64\t3\t3\t6\t8.2\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t4\t0\tT2C\t3\t3\t6\t160.96\tNO\tNO\t160.96\tNO\tNA\tNA\tNA\tNA\tNA\t4\tNA\r\nPCA0016\tPRIMARY\tNA\tWhite Non Hispanic\t12\t67.36\t3\t3\t6\t12\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t4\t8\t74.22\tNO\tNO\t74.22\tNO\t99\tNA\tNA\tNA\t97.11015465\t2\tNA\r\nPCA0019\tPRIMARY\tNA\tWhite Non Hispanic\t6.6\t68.12\t3\t4\t7\t6.6\tT1C\tNA\tNA\tNA\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t1\t0\tT2C\t3\t3\t6\t110.33\tBCR_Algorithm\tNO\t123.67\tNO\tNA\tNA\tNA\tNA\t79.85545652\t2\tNA\r\nPCA0023\tPRIMARY\tNA\tBlack Non Hispanic\t4.3\t60.57\t4\t3\t7\t3.88\tT1C\tNA\tNA\tPostHORM\tNA\tRP\tPositive\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t5\t9\t10.61\tBCR_Algorithm\tNO\t72.84\tDEATH FROM OTHER CANCER\t79.85546\t19.190208\t2.138938\t77.240045\t99\t4\tNA\r\n",
"uri": "/repo/v1/dataset/828/layer/72/preview"
}
Get preview data as a map for a Clinical Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/72/previewAsMap'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:50 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"age": "68.93",
"bcr_event": "NO",
"bcr_freetime": "152.55",
"chemotx": "NA",
"clinical_gleason_score": "5",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "2",
"clinical_tnm_stage_t": "T2B",
"copy_number_cluster": "1",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "ESTABLISHED",
"hormtx": "NA",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "37.937846",
"nomogram_nomopred_lni": "3.593974",
"nomogram_nomopred_ocd": "55.082939",
"nomogram_nomopred_seminal_vesicle_invasion": "NA",
"nomogram_pfp_postrp": "NA",
"number_nodes_positive": "0",
"number_nodes_removed": "13",
"pathologic_gleason_score": "7",
"pathologic_primary_gleason": "3",
"pathologic_secondary_gleason": "4",
"pathologic_tnm_stage_t": "T3A",
"phenotype_id": "PCA0004",
"pre_treatment_psa": "11.8",
"predxbxpsa": "27.5",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "152.55",
"tnm_stage_n": "Normal_N0"
},
{
"age": "56.64",
"bcr_event": "NO",
"bcr_freetime": "160.96",
"chemotx": "NA",
"clinical_gleason_score": "6",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "3",
"clinical_tnm_stage_t": "T2B",
"copy_number_cluster": "4",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "Neoadjuvant HORM",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "NA",
"nomogram_nomopred_lni": "NA",
"nomogram_nomopred_ocd": "NA",
"nomogram_nomopred_seminal_vesicle_invasion": "NA",
"nomogram_pfp_postrp": "NA",
"number_nodes_positive": "0",
"number_nodes_removed": "4",
"pathologic_gleason_score": "6",
"pathologic_primary_gleason": "3",
"pathologic_secondary_gleason": "3",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0006",
"pre_treatment_psa": "8.2",
"predxbxpsa": "15.7",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "160.96",
"tnm_stage_n": "Normal_N0"
},
{
"age": "67.36",
"bcr_event": "NO",
"bcr_freetime": "74.22",
"chemotx": "NA",
"clinical_gleason_score": "6",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "3",
"clinical_tnm_stage_t": "T2B",
"copy_number_cluster": "2",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "Neoadjuvant HORM",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "NA",
"nomogram_nomopred_lni": "NA",
"nomogram_nomopred_ocd": "NA",
"nomogram_nomopred_seminal_vesicle_invasion": "97.11015465",
"nomogram_pfp_postrp": "99",
"number_nodes_positive": "0",
"number_nodes_removed": "2",
"pathologic_gleason_score": "8",
"pathologic_primary_gleason": "4",
"pathologic_secondary_gleason": "4",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0016",
"pre_treatment_psa": "12",
"predxbxpsa": "12",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "74.22",
"tnm_stage_n": "Normal_N0"
},
{
"age": "68.12",
"bcr_event": "BCR_Algorithm",
"bcr_freetime": "110.33",
"chemotx": "NA",
"clinical_gleason_score": "7",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "4",
"clinical_tnm_stage_t": "T1C",
"copy_number_cluster": "2",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "NA",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "NA",
"nomogram_nomopred_lni": "NA",
"nomogram_nomopred_ocd": "NA",
"nomogram_nomopred_seminal_vesicle_invasion": "79.85545652",
"nomogram_pfp_postrp": "NA",
"number_nodes_positive": "0",
"number_nodes_removed": "1",
"pathologic_gleason_score": "6",
"pathologic_primary_gleason": "3",
"pathologic_secondary_gleason": "3",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0019",
"pre_treatment_psa": "6.6",
"predxbxpsa": "6.6",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "123.67",
"tnm_stage_n": "Normal_N0"
},
{
"age": "60.57",
"bcr_event": "BCR_Algorithm",
"bcr_freetime": "10.61",
"chemotx": "NA",
"clinical_gleason_score": "7",
"clinical_primary_gleason": "4",
"clinical_secondary_gleason": "3",
"clinical_tnm_stage_t": "T1C",
"copy_number_cluster": "4",
"ethnicity": "Black Non Hispanic",
"event": "DEATH FROM OTHER CANCER",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "PostHORM",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "19.190208",
"nomogram_nomopred_lni": "2.138938",
"nomogram_nomopred_ocd": "77.240045",
"nomogram_nomopred_seminal_vesicle_invasion": "99",
"nomogram_pfp_postrp": "79.85546",
"number_nodes_positive": "0",
"number_nodes_removed": "2",
"pathologic_gleason_score": "9",
"pathologic_primary_gleason": "4",
"pathologic_secondary_gleason": "5",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0023",
"pre_treatment_psa": "3.88",
"predxbxpsa": "4.3",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Positive",
"survtime": "72.84",
"tnm_stage_n": "Normal_N0"
}
],
"totalNumberOfResults": 5
}
Get the locations for a Clinical Dataset Layer
This returns all the locations metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/72/locations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:51 GMT
ETag: -860754461
Server: Apache-Coyote/1.1
Content-Length: 235
Connection: keep-alive
{
"etag": "-860754461",
"id": "72",
"locations": [
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
},
{
"path": "mskcc_prostate_cancer.phenotype.zip",
"type": "awss3"
}
],
"uri": "/repo/v1/dataset/828/layer/72/locations"
}
Get the sageLocation for a Clinical Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/72/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:51 GMT
Server: Apache-Coyote/1.1
Content-Length: 79
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
}
Get the awsS3Location for a Clinical Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/72/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:51 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/mskcc_prostate_cancer.phenotype.zip?Expires=1302055792&AWSAccessKeyId=AKIAI3BTGJG752CCJUVA&Signature=%2BjpZ5thYGTsUdqSvJ5HImyq1X5M%3D",
"type": "awss3"
}
Get a Genetic Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/69'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:52 GMT
ETag: -1684328331
Server: Apache-Coyote/1.1
Content-Length: 682
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/828/layer/69/annotations",
"creationDate": 1302043872000,
"description": null,
"etag": "-1684328331",
"id": "69",
"locations": [
"/repo/v1/dataset/828/layer/69/locations",
"/repo/v1/dataset/828/layer/69/sageLocation",
"/repo/v1/dataset/828/layer/69/awsS3Location"
],
"name": "CNV",
"platform": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"preview": "/repo/v1/dataset/828/layer/69/preview",
"processingFacility": "Agilent 244K array comparative genomic hybridization (aCGH) microarrays",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "G",
"uri": "/repo/v1/dataset/828/layer/69",
"version": "1.0.0"
}
Get Annotations for a Genetic Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/69/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:52 GMT
ETag: 923521
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "69",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/828/layer/69/annotations"
}
Get preview data for a Genetic Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/69/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:52 GMT
ETag: 39598575
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "39598575",
"id": "69",
"preview": "feature_id\trow\tcol\taccessions\tsubtypemask\tsubtypename\tprobeuid\tcontroltype\tprobename\tgenename\tsystematicname\tdescription\n1\t1\t1\t\t0\t\t0\t1\tHsCGHBrightCorner\tHsCGHBrightCorner\tHsCGHBrightCorner\t\n2\t1\t2\t\t66\tStructural\t1\t1\tDarkCorner\tDarkCorner\tDarkCorner\t\n3\t1\t3\t\t66\tStructural\t1\t1\tDarkCorner\tDarkCorner\tDarkCorner\t\n4\t1\t4\t\t0\t\t3\t0\tA_16_P20527812\tchr16:076331867-076331926\tchr16:076331867-076331926\tUnknown\n5\t1\t5\tref|NM_138295|ref|NM_025031\t0\t\t5\t0\tA_16_P01708709\tPKD1L1\tchr7:047626734-047626793\tHomo sapiens polycystic kidney disease 1 like 1 (PKD1L1), mRNA.\n",
"uri": "/repo/v1/dataset/828/layer/69/preview"
}
Get preview data as a map for a Genetic Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/69/previewAsMap'
Response
HTTP/1.1 500 Internal Server Error
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:54 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{"reason": "Unable to convert preview data to map format"}
Get the locations for a Genetic Dataset Layer
This returns all the locations metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/69/locations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:54 GMT
ETag: -175797184
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "-175797184",
"id": "69",
"locations": [
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
},
{
"path": "mskcc_prostate_cancer.cnv.zip",
"type": "awss3"
}
],
"uri": "/repo/v1/dataset/828/layer/69/locations"
}
Get the sageLocation for a Genetic Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/69/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:54 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
}
Get the awsS3Location for a Genetic Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/69/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:55 GMT
Server: Apache-Coyote/1.1
Content-Length: 196
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/mskcc_prostate_cancer.cnv.zip?Expires=1302055795&AWSAccessKeyId=AKIAI3BTGJG752CCJUVA&Signature=I8NgzJD7WGgWoAHY0KRgsaMmxtA%3D",
"type": "awss3"
}
Get a Expression Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/70'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:55 GMT
ETag: 622767659
Server: Apache-Coyote/1.1
Content-Length: 603
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/828/layer/70/annotations",
"creationDate": 1302043875000,
"description": null,
"etag": "622767659",
"id": "70",
"locations": [
"/repo/v1/dataset/828/layer/70/locations",
"/repo/v1/dataset/828/layer/70/awsS3Location",
"/repo/v1/dataset/828/layer/70/sageLocation"
],
"name": "miRNA expression",
"platform": "Agilent microRNA V2 arrays",
"preview": "/repo/v1/dataset/828/layer/70/preview",
"processingFacility": "Agilent microRNA V2 arrays",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "E",
"uri": "/repo/v1/dataset/828/layer/70",
"version": "1.0.0"
}
Get Annotations for a Expression Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/70/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:56 GMT
ETag: 923521
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "70",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/828/layer/70/annotations"
}
Get preview data for a Expression Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/70/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:56 GMT
ETag: 1056829087
Server: Apache-Coyote/1.1
Content-Length: 753
Connection: keep-alive
{
"etag": "1056829087",
"id": "70",
"preview": "feature_id\tRow\tCol\taccessions\tchr_coord\tSubTypeMask\tSubTypeName\tProbeUID\tControlType\tProbeName\tGeneName\tSystematicName\n1\t1\t1\t\t \t0\t\t0\t1\tmiRNABrightCorner30\tmiRNABrightCorner30\tmiRNABrightCorner30\n2\t1\t2\t\t \t66\tStructural\t2\t1\tDarkCorner\tDarkCorner\tDarkCorner\n3\t1\t3\tmir|hsa-miR-152|mir|MIMAT0000438\tchr17:043469539-043469554\t0\t\t3\t0\tA_25_P00012196\thsa-miR-152\thsa-miR-152\n4\t1\t4\tmir|hsa-miR-627|mir|MIMAT0003296\tchr15:040279120-040279140\t0\t\t5\t0\tA_25_P00011031\thsa-miR-627\thsa-miR-627\n5\t1\t5\tmir|hsa-miR-15a*|mir|MIMAT0004488\tchr13:049521267-049521284\t0\t\t7\t0\tA_25_P00013142\thsa-miR-15a*\thsa-miR-15a*\n",
"uri": "/repo/v1/dataset/828/layer/70/preview"
}
Get preview data as a map for a Expression Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/70/previewAsMap'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:56 GMT
Server: Apache-Coyote/1.1
Content-Length: 1355
Connection: keep-alive
{
"results": [
{
"Col": "1",
"ControlType": "1",
"GeneName": "miRNABrightCorner30",
"ProbeName": "miRNABrightCorner30",
"ProbeUID": "0",
"Row": "1",
"SubTypeMask": "0",
"SubTypeName": "",
"SystematicName": "miRNABrightCorner30",
"accessions": "",
"chr_coord": " ",
"feature_id": "1"
},
{
"Col": "2",
"ControlType": "1",
"GeneName": "DarkCorner",
"ProbeName": "DarkCorner",
"ProbeUID": "2",
"Row": "1",
"SubTypeMask": "66",
"SubTypeName": "Structural",
"SystematicName": "DarkCorner",
"accessions": "",
"chr_coord": " ",
"feature_id": "2"
},
{
"Col": "3",
"ControlType": "0",
"GeneName": "hsa-miR-152",
"ProbeName": "A_25_P00012196",
"ProbeUID": "3",
"Row": "1",
"SubTypeMask": "0",
"SubTypeName": "",
"SystematicName": "hsa-miR-152",
"accessions": "mir|hsa-miR-152|mir|MIMAT0000438",
"chr_coord": "chr17:043469539-043469554",
"feature_id": "3"
},
{
"Col": "4",
"ControlType": "0",
"GeneName": "hsa-miR-627",
"ProbeName": "A_25_P00011031",
"ProbeUID": "5",
"Row": "1",
"SubTypeMask": "0",
"SubTypeName": "",
"SystematicName": "hsa-miR-627",
"accessions": "mir|hsa-miR-627|mir|MIMAT0003296",
"chr_coord": "chr15:040279120-040279140",
"feature_id": "4"
},
{
"Col": "5",
"ControlType": "0",
"GeneName": "hsa-miR-15a*",
"ProbeName": "A_25_P00013142",
"ProbeUID": "7",
"Row": "1",
"SubTypeMask": "0",
"SubTypeName": "",
"SystematicName": "hsa-miR-15a*",
"accessions": "mir|hsa-miR-15a*|mir|MIMAT0004488",
"chr_coord": "chr13:049521267-049521284",
"feature_id": "5"
}
],
"totalNumberOfResults": 5
}
Get the locations for a Expression Dataset Layer
This returns all the locations metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/70/locations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:57 GMT
ETag: -1926145374
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "-1926145374",
"id": "70",
"locations": [
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
},
{
"path": "mskcc_prostate_cancer.mirna.zip",
"type": "awss3"
}
],
"uri": "/repo/v1/dataset/828/layer/70/locations"
}
Get the awsS3Location for a Expression Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/70/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:57 GMT
Server: Apache-Coyote/1.1
Content-Length: 200
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/mskcc_prostate_cancer.mirna.zip?Expires=1302055797&AWSAccessKeyId=AKIAI3BTGJG752CCJUVA&Signature=LHcuI%2B54xmw48oOXo3n6HUeBCxM%3D",
"type": "awss3"
}
Get the sageLocation for a Expression Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/70/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:57 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
}
Get a Clinical Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/67'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:58 GMT
ETag: 1927937721
Server: Apache-Coyote/1.1
Content-Length: 546
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/828/layer/67/annotations",
"creationDate": 1302043868000,
"description": null,
"etag": "1927937721",
"id": "67",
"locations": [
"/repo/v1/dataset/828/layer/67/locations",
"/repo/v1/dataset/828/layer/67/awsS3Location",
"/repo/v1/dataset/828/layer/67/sageLocation"
],
"name": "phenotypes",
"platform": "",
"preview": "/repo/v1/dataset/828/layer/67/preview",
"processingFacility": "",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "C",
"uri": "/repo/v1/dataset/828/layer/67",
"version": "1.0.0"
}
Get Annotations for a Clinical Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/67/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:58 GMT
ETag: 923521
Server: Apache-Coyote/1.1
Content-Length: 185
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "67",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/828/layer/67/annotations"
}
Get preview data for a Clinical Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/67/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 01:59:58 GMT
ETag: 1782170291
Server: Apache-Coyote/1.1
Content-Length: 1999
Connection: keep-alive
{
"etag": "1782170291",
"id": "67",
"preview": "phenotype_id\tsample_type\tmetastatic_site\tethnicity\tpredxbxpsa\tage\tclinical_primary_gleason\tclinical_secondary_gleason\tclinical_gleason_score\tpre_treatment_psa\tclinical_tnm_stage_t\tneoadjradtx\tchemotx\thormtx\tradtxtype\trp_type\tsms\textra_capsular_extension\tseminal_vesicle_invasion\ttnm_stage_n\tnumber_nodes_removed\tnumber_nodes_positive\tpathologic_tnm_stage_t\tpathologic_primary_gleason\tpathologic_secondary_gleason\tpathologic_gleason_score\tbcr_freetime\tbcr_event\tmetsevent\tsurvtime\tevent\tnomogram_pfp_postrp\tnomogram_nomopred_extra_capsular_extension\tnomogram_nomopred_lni\tnomogram_nomopred_ocd\tnomogram_nomopred_seminal_vesicle_invasion\tcopy_number_cluster\texpression_array_tissue_source\r\nPCA0004\tPRIMARY\tNA\tWhite Non Hispanic\t27.5\t68.93\t3\t2\t5\t11.8\tT2B\tNA\tNA\tNA\tNA\tRP\tNegative\tESTABLISHED\tNegative\tNormal_N0\t13\t0\tT3A\t3\t4\t7\t152.55\tNO\tNO\t152.55\tNO\tNA\t37.937846\t3.593974\t55.082939\tNA\t1\tNA\r\nPCA0006\tPRIMARY\tNA\tWhite Non Hispanic\t15.7\t56.64\t3\t3\t6\t8.2\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t4\t0\tT2C\t3\t3\t6\t160.96\tNO\tNO\t160.96\tNO\tNA\tNA\tNA\tNA\tNA\t4\tNA\r\nPCA0016\tPRIMARY\tNA\tWhite Non Hispanic\t12\t67.36\t3\t3\t6\t12\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t4\t8\t74.22\tNO\tNO\t74.22\tNO\t99\tNA\tNA\tNA\t97.11015465\t2\tNA\r\nPCA0019\tPRIMARY\tNA\tWhite Non Hispanic\t6.6\t68.12\t3\t4\t7\t6.6\tT1C\tNA\tNA\tNA\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t1\t0\tT2C\t3\t3\t6\t110.33\tBCR_Algorithm\tNO\t123.67\tNO\tNA\tNA\tNA\tNA\t79.85545652\t2\tNA\r\nPCA0023\tPRIMARY\tNA\tBlack Non Hispanic\t4.3\t60.57\t4\t3\t7\t3.88\tT1C\tNA\tNA\tPostHORM\tNA\tRP\tPositive\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t5\t9\t10.61\tBCR_Algorithm\tNO\t72.84\tDEATH FROM OTHER CANCER\t79.85546\t19.190208\t2.138938\t77.240045\t99\t4\tNA\r\n",
"uri": "/repo/v1/dataset/828/layer/67/preview"
}
Get preview data as a map for a Clinical Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/67/previewAsMap'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:01 GMT
Server: Apache-Coyote/1.1
Content-Length: 5245
Connection: keep-alive
{
"results": [
{
"age": "68.93",
"bcr_event": "NO",
"bcr_freetime": "152.55",
"chemotx": "NA",
"clinical_gleason_score": "5",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "2",
"clinical_tnm_stage_t": "T2B",
"copy_number_cluster": "1",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "ESTABLISHED",
"hormtx": "NA",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "37.937846",
"nomogram_nomopred_lni": "3.593974",
"nomogram_nomopred_ocd": "55.082939",
"nomogram_nomopred_seminal_vesicle_invasion": "NA",
"nomogram_pfp_postrp": "NA",
"number_nodes_positive": "0",
"number_nodes_removed": "13",
"pathologic_gleason_score": "7",
"pathologic_primary_gleason": "3",
"pathologic_secondary_gleason": "4",
"pathologic_tnm_stage_t": "T3A",
"phenotype_id": "PCA0004",
"pre_treatment_psa": "11.8",
"predxbxpsa": "27.5",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "152.55",
"tnm_stage_n": "Normal_N0"
},
{
"age": "56.64",
"bcr_event": "NO",
"bcr_freetime": "160.96",
"chemotx": "NA",
"clinical_gleason_score": "6",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "3",
"clinical_tnm_stage_t": "T2B",
"copy_number_cluster": "4",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "Neoadjuvant HORM",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "NA",
"nomogram_nomopred_lni": "NA",
"nomogram_nomopred_ocd": "NA",
"nomogram_nomopred_seminal_vesicle_invasion": "NA",
"nomogram_pfp_postrp": "NA",
"number_nodes_positive": "0",
"number_nodes_removed": "4",
"pathologic_gleason_score": "6",
"pathologic_primary_gleason": "3",
"pathologic_secondary_gleason": "3",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0006",
"pre_treatment_psa": "8.2",
"predxbxpsa": "15.7",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "160.96",
"tnm_stage_n": "Normal_N0"
},
{
"age": "67.36",
"bcr_event": "NO",
"bcr_freetime": "74.22",
"chemotx": "NA",
"clinical_gleason_score": "6",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "3",
"clinical_tnm_stage_t": "T2B",
"copy_number_cluster": "2",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "Neoadjuvant HORM",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "NA",
"nomogram_nomopred_lni": "NA",
"nomogram_nomopred_ocd": "NA",
"nomogram_nomopred_seminal_vesicle_invasion": "97.11015465",
"nomogram_pfp_postrp": "99",
"number_nodes_positive": "0",
"number_nodes_removed": "2",
"pathologic_gleason_score": "8",
"pathologic_primary_gleason": "4",
"pathologic_secondary_gleason": "4",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0016",
"pre_treatment_psa": "12",
"predxbxpsa": "12",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "74.22",
"tnm_stage_n": "Normal_N0"
},
{
"age": "68.12",
"bcr_event": "BCR_Algorithm",
"bcr_freetime": "110.33",
"chemotx": "NA",
"clinical_gleason_score": "7",
"clinical_primary_gleason": "3",
"clinical_secondary_gleason": "4",
"clinical_tnm_stage_t": "T1C",
"copy_number_cluster": "2",
"ethnicity": "White Non Hispanic",
"event": "NO",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "NA",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "NA",
"nomogram_nomopred_lni": "NA",
"nomogram_nomopred_ocd": "NA",
"nomogram_nomopred_seminal_vesicle_invasion": "79.85545652",
"nomogram_pfp_postrp": "NA",
"number_nodes_positive": "0",
"number_nodes_removed": "1",
"pathologic_gleason_score": "6",
"pathologic_primary_gleason": "3",
"pathologic_secondary_gleason": "3",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0019",
"pre_treatment_psa": "6.6",
"predxbxpsa": "6.6",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Negative",
"survtime": "123.67",
"tnm_stage_n": "Normal_N0"
},
{
"age": "60.57",
"bcr_event": "BCR_Algorithm",
"bcr_freetime": "10.61",
"chemotx": "NA",
"clinical_gleason_score": "7",
"clinical_primary_gleason": "4",
"clinical_secondary_gleason": "3",
"clinical_tnm_stage_t": "T1C",
"copy_number_cluster": "4",
"ethnicity": "Black Non Hispanic",
"event": "DEATH FROM OTHER CANCER",
"expression_array_tissue_source\r": "NA\r",
"extra_capsular_extension": "NONE",
"hormtx": "PostHORM",
"metastatic_site": "NA",
"metsevent": "NO",
"neoadjradtx": "NA",
"nomogram_nomopred_extra_capsular_extension": "19.190208",
"nomogram_nomopred_lni": "2.138938",
"nomogram_nomopred_ocd": "77.240045",
"nomogram_nomopred_seminal_vesicle_invasion": "99",
"nomogram_pfp_postrp": "79.85546",
"number_nodes_positive": "0",
"number_nodes_removed": "2",
"pathologic_gleason_score": "9",
"pathologic_primary_gleason": "4",
"pathologic_secondary_gleason": "5",
"pathologic_tnm_stage_t": "T2C",
"phenotype_id": "PCA0023",
"pre_treatment_psa": "3.88",
"predxbxpsa": "4.3",
"radtxtype": "NA",
"rp_type": "RP",
"sample_type": "PRIMARY",
"seminal_vesicle_invasion": "Negative",
"sms": "Positive",
"survtime": "72.84",
"tnm_stage_n": "Normal_N0"
}
],
"totalNumberOfResults": 5
}
Get the locations for a Clinical Dataset Layer
This returns all the locations metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/67/locations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:01 GMT
ETag: -860754461
Server: Apache-Coyote/1.1
Content-Length: 235
Connection: keep-alive
{
"etag": "-860754461",
"id": "67",
"locations": [
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
},
{
"path": "mskcc_prostate_cancer.phenotype.zip",
"type": "awss3"
}
],
"uri": "/repo/v1/dataset/828/layer/67/locations"
}
Get the awsS3Location for a Clinical Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/67/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:02 GMT
Server: Apache-Coyote/1.1
Content-Length: 202
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/mskcc_prostate_cancer.phenotype.zip?Expires=1302055802&AWSAccessKeyId=AKIAI3BTGJG752CCJUVA&Signature=fVbJl6R8mIZN2DoKMG1IZzKVgKc%3D",
"type": "awss3"
}
Get the sageLocation for a Clinical Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/67/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:02 GMT
Server: Apache-Coyote/1.1
Content-Length: 79
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
}
Get a Genetic Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:03 GMT
ETag: -1498813326
Server: Apache-Coyote/1.1
Content-Length: 577
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/828/layer/68/annotations",
"creationDate": 1302043870000,
"description": null,
"etag": "-1498813326",
"id": "68",
"locations": [
"/repo/v1/dataset/828/layer/68/awsS3Location",
"/repo/v1/dataset/828/layer/68/sageLocation",
"/repo/v1/dataset/828/layer/68/locations"
],
"name": "sequencing",
"platform": "iPLEX Sequenom ",
"preview": "/repo/v1/dataset/828/layer/68/preview",
"processingFacility": "iPLEX Sequenom ",
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "G",
"uri": "/repo/v1/dataset/828/layer/68",
"version": "1.0.0"
}
Get Annotations for a Genetic Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:03 GMT
ETag: 923521
Server: Apache-Coyote/1.1
Content-Length: 185
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "68",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/828/layer/68/annotations"
}
Get preview data for a Genetic Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:03 GMT
ETag: -306095595
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "-306095595",
"id": "68",
"preview": "marker_id\tDU145\tLAPC4-1\tLAPC9\tLNCaP\tLNM971\tPC3\tPCA0002\tPCA0004\tPCA0005\tPCA0015\tPCA0024\tPCA0027\tPCA0037\tPCA0044\tPCA0056\tPCA0068\tPCA0083\tPCA0087\tPCA0092\tPCA0094\tPCA0099\tPCA0100\tPCA0112\tPCA0115\tPCA0118\tPCA0119\tPCA0122\tPCA0123\tPCA0125\tPCA0126\tPCA0127\tPCA0128\tPCA0129\tPCA0130\tPCA0132\tPCA0136\tPCA0159\tPCA0162\tPCA0173\tPCA0188\tPCA0194\tPCA0197\tPCA0199\tPCA0209\tPCA0212\tPCA0213\tPCA0215\tPCA0216\tPCA0218\tVcap\n25\tNA\tH897R\tNA\tNA\tN789S\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tG725S\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n27\tNA\tNA\tNA\tR135Q\tNA\tNA\tS1098N\tNA\tNA\tNA\tNA\tS1098N\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n208\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\te10+2\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\n238\tNA\tNA\tNA\tNA\tNA\tF1174L\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tP36S\n324\tNA\tNA\tNA\tR2714C\tR2714C\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tD1748N\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tE1577*\tNA\n",
"uri": "/repo/v1/dataset/828/layer/68/preview"
}
Get preview data as a map for a Genetic Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/previewAsMap'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:03 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"DU145": "NA",
"LAPC4-1": "H897R",
"LAPC9": "NA",
"LNCaP": "NA",
"LNM971": "N789S",
"PC3": "NA",
"PCA0002": "NA",
"PCA0004": "NA",
"PCA0005": "NA",
"PCA0015": "NA",
"PCA0024": "NA",
"PCA0027": "NA",
"PCA0037": "NA",
"PCA0044": "NA",
"PCA0056": "NA",
"PCA0068": "NA",
"PCA0083": "NA",
"PCA0087": "NA",
"PCA0092": "NA",
"PCA0094": "NA",
"PCA0099": "NA",
"PCA0100": "NA",
"PCA0112": "G725S",
"PCA0115": "NA",
"PCA0118": "NA",
"PCA0119": "NA",
"PCA0122": "NA",
"PCA0123": "NA",
"PCA0125": "NA",
"PCA0126": "NA",
"PCA0127": "NA",
"PCA0128": "NA",
"PCA0129": "NA",
"PCA0130": "NA",
"PCA0132": "NA",
"PCA0136": "NA",
"PCA0159": "NA",
"PCA0162": "NA",
"PCA0173": "NA",
"PCA0188": "NA",
"PCA0194": "NA",
"PCA0197": "NA",
"PCA0199": "NA",
"PCA0209": "NA",
"PCA0212": "NA",
"PCA0213": "NA",
"PCA0215": "NA",
"PCA0216": "NA",
"PCA0218": "NA",
"Vcap": "NA",
"marker_id": "25"
},
{
"DU145": "NA",
"LAPC4-1": "NA",
"LAPC9": "NA",
"LNCaP": "R135Q",
"LNM971": "NA",
"PC3": "NA",
"PCA0002": "S1098N",
"PCA0004": "NA",
"PCA0005": "NA",
"PCA0015": "NA",
"PCA0024": "NA",
"PCA0027": "S1098N",
"PCA0037": "NA",
"PCA0044": "NA",
"PCA0056": "NA",
"PCA0068": "NA",
"PCA0083": "NA",
"PCA0087": "NA",
"PCA0092": "NA",
"PCA0094": "NA",
"PCA0099": "NA",
"PCA0100": "NA",
"PCA0112": "NA",
"PCA0115": "NA",
"PCA0118": "NA",
"PCA0119": "NA",
"PCA0122": "NA",
"PCA0123": "NA",
"PCA0125": "NA",
"PCA0126": "NA",
"PCA0127": "NA",
"PCA0128": "NA",
"PCA0129": "NA",
"PCA0130": "NA",
"PCA0132": "NA",
"PCA0136": "NA",
"PCA0159": "NA",
"PCA0162": "NA",
"PCA0173": "NA",
"PCA0188": "NA",
"PCA0194": "NA",
"PCA0197": "NA",
"PCA0199": "NA",
"PCA0209": "NA",
"PCA0212": "NA",
"PCA0213": "NA",
"PCA0215": "NA",
"PCA0216": "NA",
"PCA0218": "NA",
"Vcap": "NA",
"marker_id": "27"
},
{
"DU145": "NA",
"LAPC4-1": "NA",
"LAPC9": "NA",
"LNCaP": "NA",
"LNM971": "NA",
"PC3": "NA",
"PCA0002": "NA",
"PCA0004": "NA",
"PCA0005": "NA",
"PCA0015": "NA",
"PCA0024": "NA",
"PCA0027": "NA",
"PCA0037": "NA",
"PCA0044": "NA",
"PCA0056": "NA",
"PCA0068": "NA",
"PCA0083": "NA",
"PCA0087": "NA",
"PCA0092": "NA",
"PCA0094": "NA",
"PCA0099": "NA",
"PCA0100": "NA",
"PCA0112": "e10+2",
"PCA0115": "NA",
"PCA0118": "NA",
"PCA0119": "NA",
"PCA0122": "NA",
"PCA0123": "NA",
"PCA0125": "NA",
"PCA0126": "NA",
"PCA0127": "NA",
"PCA0128": "NA",
"PCA0129": "NA",
"PCA0130": "NA",
"PCA0132": "NA",
"PCA0136": "NA",
"PCA0159": "NA",
"PCA0162": "NA",
"PCA0173": "NA",
"PCA0188": "NA",
"PCA0194": "NA",
"PCA0197": "NA",
"PCA0199": "NA",
"PCA0209": "NA",
"PCA0212": "NA",
"PCA0213": "NA",
"PCA0215": "NA",
"PCA0216": "NA",
"PCA0218": "NA",
"Vcap": "NA",
"marker_id": "208"
},
{
"DU145": "NA",
"LAPC4-1": "NA",
"LAPC9": "NA",
"LNCaP": "NA",
"LNM971": "NA",
"PC3": "F1174L",
"PCA0002": "NA",
"PCA0004": "NA",
"PCA0005": "NA",
"PCA0015": "NA",
"PCA0024": "NA",
"PCA0027": "NA",
"PCA0037": "NA",
"PCA0044": "NA",
"PCA0056": "NA",
"PCA0068": "NA",
"PCA0083": "NA",
"PCA0087": "NA",
"PCA0092": "NA",
"PCA0094": "NA",
"PCA0099": "NA",
"PCA0100": "NA",
"PCA0112": "NA",
"PCA0115": "NA",
"PCA0118": "NA",
"PCA0119": "NA",
"PCA0122": "NA",
"PCA0123": "NA",
"PCA0125": "NA",
"PCA0126": "NA",
"PCA0127": "NA",
"PCA0128": "NA",
"PCA0129": "NA",
"PCA0130": "NA",
"PCA0132": "NA",
"PCA0136": "NA",
"PCA0159": "NA",
"PCA0162": "NA",
"PCA0173": "NA",
"PCA0188": "NA",
"PCA0194": "NA",
"PCA0197": "NA",
"PCA0199": "NA",
"PCA0209": "NA",
"PCA0212": "NA",
"PCA0213": "NA",
"PCA0215": "NA",
"PCA0216": "NA",
"PCA0218": "NA",
"Vcap": "P36S",
"marker_id": "238"
},
{
"DU145": "NA",
"LAPC4-1": "NA",
"LAPC9": "NA",
"LNCaP": "R2714C",
"LNM971": "R2714C",
"PC3": "NA",
"PCA0002": "NA",
"PCA0004": "NA",
"PCA0005": "NA",
"PCA0015": "NA",
"PCA0024": "NA",
"PCA0027": "NA",
"PCA0037": "NA",
"PCA0044": "NA",
"PCA0056": "NA",
"PCA0068": "NA",
"PCA0083": "NA",
"PCA0087": "NA",
"PCA0092": "NA",
"PCA0094": "NA",
"PCA0099": "NA",
"PCA0100": "NA",
"PCA0112": "NA",
"PCA0115": "NA",
"PCA0118": "NA",
"PCA0119": "NA",
"PCA0122": "NA",
"PCA0123": "NA",
"PCA0125": "NA",
"PCA0126": "NA",
"PCA0127": "NA",
"PCA0128": "NA",
"PCA0129": "NA",
"PCA0130": "D1748N",
"PCA0132": "NA",
"PCA0136": "NA",
"PCA0159": "NA",
"PCA0162": "NA",
"PCA0173": "NA",
"PCA0188": "NA",
"PCA0194": "NA",
"PCA0197": "NA",
"PCA0199": "NA",
"PCA0209": "NA",
"PCA0212": "NA",
"PCA0213": "NA",
"PCA0215": "NA",
"PCA0216": "NA",
"PCA0218": "E1577*",
"Vcap": "NA",
"marker_id": "324"
}
],
"totalNumberOfResults": 5
}
Get the locations for a Genetic Dataset Layer
This returns all the locations metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/locations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:04 GMT
ETag: 1163248688
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "1163248688",
"id": "68",
"locations": [
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
},
{
"path": "mskcc_prostate_cancer.sequence.zip",
"type": "awss3"
}
],
"uri": "/repo/v1/dataset/828/layer/68/locations"
}
Get the awsS3Location for a Genetic Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:04 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/mskcc_prostate_cancer.sequence.zip?Expires=1302055805&AWSAccessKeyId=AKIAI3BTGJG752CCJUVA&Signature=xon92PSnbWOfKG%2FKben7cRpfo5Y%3D",
"type": "awss3"
}
Get the sageLocation for a Genetic Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:04 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_011__sawyers_prostate_cancer",
"type": "sage"
}
Query API Schema
Query Response Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:04 GMT
Server: Apache-Coyote/1.1
Content-Length: 191
Connection: keep-alive
{
"optional": true,
"properties": {
"results": {
"items": {
"optional": true,
"type": "object"
},
"optional": true,
"type": "array"
},
"totalNumberOfResults": {
"optional": true,
"type": "integer"
}
},
"type": "object"
}
REST API Schemas
Datasets List Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:05 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"paging": {
"optional": true,
"type": "object"
},
"results": {
"items": {
"optional": true,
"type": "any"
},
"optional": true,
"type": "array"
},
"totalNumberOfResults": {
"optional": true,
"type": "integer"
}
},
"type": "object"
}
Dataset Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:05 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"annotations": {
"optional": true,
"type": "string"
},
"creationDate": {
"optional": true,
"type": "number"
},
"creator": {
"optional": true,
"type": "string"
},
"description": {
"optional": true,
"type": "string"
},
"etag": {
"optional": true,
"type": "string"
},
"hasClinicalData": {
"optional": true,
"type": "boolean"
},
"hasExpressionData": {
"optional": true,
"type": "boolean"
},
"hasGeneticData": {
"optional": true,
"type": "boolean"
},
"id": {
"optional": true,
"type": "string"
},
"layer": {
"optional": true,
"type": "string"
},
"name": {
"optional": true,
"type": "string"
},
"releaseDate": {
"optional": true,
"type": "number"
},
"status": {
"optional": true,
"type": "string"
},
"uri": {
"optional": true,
"type": "string"
},
"version": {
"optional": true,
"type": "string"
}
},
"type": "object"
}
Dataset Annotations Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/annotations/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:05 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"creationDate": {
"optional": true,
"type": "number"
},
"dateAnnotations": {
"optional": true,
"type": "object"
},
"doubleAnnotations": {
"optional": true,
"type": "object"
},
"etag": {
"optional": true,
"type": "string"
},
"id": {
"optional": true,
"type": "string"
},
"longAnnotations": {
"optional": true,
"type": "object"
},
"stringAnnotations": {
"optional": true,
"type": "object"
},
"uri": {
"optional": true,
"type": "string"
}
},
"type": "object"
}
Dataset Layers List Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:05 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"paging": {
"optional": true,
"type": "object"
},
"results": {
"items": {
"optional": true,
"type": "any"
},
"optional": true,
"type": "array"
},
"totalNumberOfResults": {
"optional": true,
"type": "integer"
}
},
"type": "object"
}
Layer Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:05 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"annotations": {
"optional": true,
"type": "string"
},
"creationDate": {
"optional": true,
"type": "number"
},
"description": {
"optional": true,
"type": "string"
},
"etag": {
"optional": true,
"type": "string"
},
"id": {
"optional": true,
"type": "string"
},
"locations": {
"items": {
"optional": true,
"type": "string"
},
"optional": true,
"type": "array"
},
"name": {
"optional": true,
"type": "string"
},
"platform": {
"optional": true,
"type": "string"
},
"preview": {
"optional": true,
"type": "string"
},
"processingFacility": {
"optional": true,
"type": "string"
},
"publicationDate": {
"optional": true,
"type": "number"
},
"qcBy": {
"optional": true,
"type": "string"
},
"qcDate": {
"optional": true,
"type": "number"
},
"releaseNotes": {
"optional": true,
"type": "string"
},
"tissueType": {
"optional": true,
"type": "string"
},
"type": {
"optional": true,
"type": "string"
},
"uri": {
"optional": true,
"type": "string"
},
"version": {
"optional": true,
"type": "string"
}
},
"type": "object"
}
Layer Preview Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/preview/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:05 GMT
Server: Apache-Coyote/1.1
Content-Length: 212
Connection: keep-alive
{
"optional": true,
"properties": {
"etag": {
"optional": true,
"type": "string"
},
"id": {
"optional": true,
"type": "string"
},
"preview": {
"optional": true,
"type": "string"
},
"uri": {
"optional": true,
"type": "string"
}
},
"type": "object"
}
Layer Preview as Map Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/previewAsMap/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:05 GMT
Server: Apache-Coyote/1.1
Content-Length: 191
Connection: keep-alive
{
"optional": true,
"properties": {
"results": {
"items": {
"optional": true,
"type": "object"
},
"optional": true,
"type": "array"
},
"totalNumberOfResults": {
"optional": true,
"type": "integer"
}
},
"type": "object"
}
Layer Locations Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/locations/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:06 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"etag": {
"optional": true,
"type": "string"
},
"id": {
"optional": true,
"type": "string"
},
"locations": {
"items": {
"optional": true,
"properties": {
"path": {
"optional": true,
"type": "string"
},
"type": {
"optional": true,
"type": "string"
}
},
"type": "object"
},
"optional": true,
"type": "array"
},
"uri": {
"optional": true,
"type": "string"
}
},
"type": "object"
}
Get the awsS3Location for a Dataset Layer
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/awsS3Location/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:06 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"path": {
"optional": true,
"type": "string"
},
"type": {
"optional": true,
"type": "string"
}
},
"type": "object"
}
Get the sageLocation for a Dataset Layer
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/828/layer/68/sageLocation/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 06 Apr 2011 02:00:06 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"path": {
"optional": true,
"type": "string"
},
"type": {
"optional": true,
"type": "string"
}
},
"type": "object"
}
REST API Usage Examples (Read/Write and slightly out of date)
This is a REST api (see Service API Design for more details as to what this means). You can create entities, updated entities, read entities, and delete entities. More advanced querying will be implemented as a separate API. Partial updates (e.g., just updating two fields in a dataset) are not supported. In a nutshell, when you update something like a dataset, you GET the dataset first, modify the properties you want to change, and then send the entire object back to the service so that this revised entity overwrites the previously stored entity.
Create a Dataset
Request:
curl -i -H Accept:application/json -H Content-Type:application/json
-d '{"name":"test dataset", "creator":"fake creator", "releaseDate":"2009-10-01", "status":"not curated"}'
http://localhost:8080/repo/v1/dataset
Response
HTTP/1.1 201 Created
ETag: 1736839268
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBAw
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"name":"test dataset",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"version":"0.0.1",
"creator":"fake creator",
"description":null,
"creationDate":1296595870715,
"status":"not curated",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"etag":"1309185941",
"releaseDate":1254355200000,
"layers":[]
}
Update a Dataset
Note that in the example below the creator and description fields have been changed but all others remain the same.
Request:
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1309185941 -d '{
"name":"test dataset",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"version":"0.0.1",
"creator":"updated creator",
"description":"I just added a description",
"creationDate":1296595870715,
"status":"not curated",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"etag":"1309185941",
"releaseDate":1254355200000,
"layers":[]
}
' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw
Response
HTTP/1.1 200 OK
ETag: -852418664
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"name":"test dataset",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"version":"0.0.1",
"creator":"updated creator",
"description":"I just added a description",
"creationDate":1296595870715,
"status":"not curated",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"etag":"-852418664",
"releaseDate":1254355200000,
"layers":[]
}
Add Annotations to a Dataset
First get the empty annotations container for your newly created dataset
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations
Response
HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"creationDate":null,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
"etag":"923521",
"stringAnnotations":{
},
"floatAnnotations":{
},
"dateAnnotations":{
}
}
Then you add/modify the annotations of interest and do a PUT. Note that annotation values must always be list values even if the list is only of length one.
Request
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '{
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
"creationDate":null,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
"etag":"923521",
"stringAnnotations":{
"Experimental Design Templates":["exp-122887", "exp-97765"]
},
"floatAnnotations":{
"Number of Samples":[500]
},
"dateAnnotations":{
"Publication Date":["2011-01-15"]
}
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations
Response
HTTP/1.1 200 OK
ETag: -1638393853
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww",
"creationDate":null,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww/annotations",
"etag":"-1638393853",
"stringAnnotations":{
"Experimental Design Templates":[
"exp-122887",
"exp-97765"
]
},
"floatAnnotations":{
"Number of Samples":[
500.0
]
},
"dateAnnotations":{
"Publication Date":[
1295049600000
]
}
}
Delete a Dataset
Request
curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw
Response
HTTP/1.1 204 No Content Server: Jetty(6.1.x)
Get a Layers for a Dataset
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer
Response
HTTP/1.1 200 OK
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"results":[
{
"name":"Flint HS Mice Affy",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"type":"E",
"version":"0.0.1",
"description":"this is a description",
"creationDate":1296690778880,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"etag":"1424771925",
"publicationDate":null,
"releaseNotes":"this is a release note",
"tissueType":"liver",
"platform":null,
"processingFacility":null,
"qcBy":null,
"qcDate":null
},
{
"name":"Flint HS Mice Phenotypes",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",
"type":"C",
"version":"0.0.1",
"description":"this is a description",
"creationDate":1296693007167,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",
"etag":"1445062754",
"publicationDate":null,
"releaseNotes":"this is a release note",
"tissueType":null,
"platform":null,
"processingFacility":null,
"qcBy":null,
"qcDate":null
}
],
"totalNumberOfResults":2,
"paging":{
}
}
Get a Layer
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
Response
HTTP/1.1 200 OK
ETag: 1240467407
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"name":"Flint HS Mice Affy",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"type":"E",
"version":"0.0.1",
"description":"this is a description",
"creationDate":1296690778880,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"etag":"1240467407",
"publicationDate":null,
"releaseNotes":"this is a release note",
"tissueType":null,
"platform":null,
"processingFacility":null,
"qcBy":null,
"qcDate":null
}
Get annotations for a layer
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations
Response
HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"creationDate":null,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"etag":"923521",
"stringAnnotations":{
},
"floatAnnotations":{
},
"dateAnnotations":{
}
}
Create a layer
Request
curl -i -H Accept:application/json -H Content-Type:application/json -d '{"name":"Flint HS Mice Affy", "type":"E", "description":"this is a description", "releaseNotes":"this is a release note"}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer
Response
HTTP/1.1 201 Created
ETag: 1240467407
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"name":"Flint HS Mice Affy",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"type":"E",
"version":"0.0.1",
"description":"this is a description",
"creationDate":1296690778880,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"etag":"1240467407",
"publicationDate":null,
"releaseNotes":"this is a release note",
"tissueType":null,
"platform":null,
"processingFacility":null,
"qcBy":null,
"qcDate":null
}
Now ask for the owning dataset and you can see the preview of the layer
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww
Response
HTTP/1.1 200 OK
ETag: -801135512
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"name":"Flint HS Mice",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
"version":"0.0.1",
"creator":"Jonathan Flint",
"description":null,
"creationDate":1296690549675,
"status":"Future",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
"etag":"-801135512",
"releaseDate":null,
"layers":[
{
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"type":"E",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww"
},{
"id":"use this uri to make a new layer",
"type":"hack",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer"
}
]
}
Update a Layer
In the example below we updated the tissue type.
Request
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1240467407 -d '
{
"name":"Flint HS Mice Affy",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"type":"E",
"version":"0.0.1",
"description":"this is a description",
"creationDate":1296690778880,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"etag":"1240467407",
"publicationDate":null,
"releaseNotes":"this is a release note",
"tissueType":"liver",
"platform":null,
"processingFacility":null,
"qcBy":null,
"qcDate":null
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
Response
HTTP/1.1 200 OK
ETag: 1424771925
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"name":"Flint HS Mice Affy",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"type":"E",
"version":"0.0.1",
"description":"this is a description",
"creationDate":1296690778880,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"etag":"1424771925",
"publicationDate":null,
"releaseNotes":"this is a release note",
"tissueType":"liver",
"platform":null,
"processingFacility":null,
"qcBy":null,
"qcDate":null
}
Delete a layer
Request
curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
Response
HTTP/1.1 204 No Content Server: Jetty(6.1.x)
Add annotations to a layer
Request
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '
{
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"creationDate":null,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"etag":"923521",
"stringAnnotations":{
"notes":["I threw away 6 samples during the curation process due to gender chromosome mismatches"]
},
"floatAnnotations":{
},
"dateAnnotations":{
}
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations
Response
HTTP/1.1 200 OK
ETag: -1897035229
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)
{
"id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
"creationDate":null,
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
"etag":"-1897035229",
"stringAnnotations":{
"notes":[
"I threw away 6 samples during the curation process due to gender chromosome mismatches"
]
},
"floatAnnotations":{
},
"dateAnnotations":{
}
}