{ "openapi": "3.0.0", "info": { "version": "1.3.0", "title": "Personal Genome Project UK", "termsOfService": "https://www.personalgenomes.org.uk/tos", "contact": { "name": "PGP-UK", "email": "pgp-uk@ucl.ac.uk" }, "license": { "name": "Creative Commons 0 (CC0)", "url": "https://creativecommons.org/share-your-work/public-domain/cc0/" }, "x-logo": { "url": "https://www.personalgenomes.org.uk/images/logo.svg" }, "description": "# Introduction\n\nBelow is the documentation for the [PGP-UK data](https://www.personalgenomes.org.uk/data) restful API, which is compliant with the [OpenAPI 3.0 Specifications](https://swagger.io/specification/) (a language-agnostic standard for RESTful APIs).\n\nThe API simply provides access to the meta data (including download links etc.) associated with the PGP-UK data. As the PGP-UK data are stored at various databases at EBI (e.g. ENA, EVA, ArrayExpress etc.) and the PGP-UK Participant Portal (e.g. Phenotype data and generated reports), this API provides an easy way to bring everything together.\n\nClicking on an endpoint below will provide further information on the format of paramaters (if any) together with information on the expected result format.\n\nAdditionally, it is possible to test the API endpoint on this page by clicking on the \"Try it out\" button, and subsequently clicking on the \"Execute\" button that appears. This will display the server response (body and headers) for the respective endpoint. Furthermore, a curl command will also be displayed that can be run in a terminal.\n" }, "tags": [ { "name": "Participants", "description": "Operations about PGP-UK participants" }, { "name": "Whole Genome Sequencing", "description": "Operations about Whole Genome Sequencing Data" }, { "name": "Variant Data", "description": "Operations about Whole Genome/Exome Sequencing Variant Data" }, { "name": "Genotype Data", "description": "Operations about Genotype Data" }, { "name": "Whole Genome Bisulfite Data", "description": "Operations about Whole Genome Bisulfite Data" }, { "name": "Methylation Array Data", "description": "Operations about Methylation Array Data" }, { "name": "RNA-Seq", "description": "Operations about RNA seq data" }, { "name": "Amplicon RNA-Seq", "description": "Operations about RNA seq data (Amplicon RNA-seq)" }, { "name": "Proton RNA-Seq", "description": "Operations about RNA seq data (Proton RNA-seq)" }, { "name": "Data Direct Urls", "description": "Direct links to all data" }, { "name": "PGP-UK profile", "description": "Operations about Whole Genome Bisulfite Data" }, { "name": "Genome Reports", "description": "Operations about the participant's Genome Reports" }, { "name": "Methylome Reports", "description": "Operations about the participant's Methylation Reports" }, { "name": "Phenotype Data", "description": "Operations about the participant's phenotype data" } ], "servers": [ { "url": "https://www.personalgenomes.org.uk/api/v1.3" }, { "url": "https://www.personalgenomes.org.uk/api/v1.2" }, { "url": "https://www.personalgenomes.org.uk/api/v1.1" }, { "url": "https://www.personalgenomes.org.uk/api/v1.0" } ], "paths": { "/all_participants": { "get": { "tags": [ "Participants" ], "summary": "Get all data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllParicipants", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/Participant" } } } } } }, "404": { "description": "Data not found" } } } }, "/participant/{pgp_hex_id}": { "get": { "tags": [ "Participants" ], "summary": "Get all data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getParicipantByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Participant" } } } }, "404": { "description": "Participant not found" } } } }, "/all_wgs": { "get": { "tags": [ "Whole Genome Sequencing" ], "summary": "Get all whole genome sequencing data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllWgs", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Whole Genome Sequencing data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/WGS" } } } } } }, "404": { "description": "Data not found" } } } }, "/wgs/{pgp_hex_id}": { "get": { "tags": [ "Whole Genome Sequencing" ], "summary": "Get all whole genome sequencing data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getWgsByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/WGS" } } } }, "404": { "description": "Participant not found" } } } }, "/all_variant": { "get": { "tags": [ "Variant Data" ], "summary": "Get all variant data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllVariant", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Variant data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/Variant" } } } } } }, "404": { "description": "Data not found" } } } }, "/variant/{pgp_hex_id}": { "get": { "tags": [ "Variant Data" ], "summary": "Get all variant data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getVariantByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Variant" } } } }, "404": { "description": "Participant not found" } } } }, "/all_genotype": { "get": { "tags": [ "Genotype Data" ], "summary": "Get all genotype data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllGenotype", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Genotype data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/Genotype" } } } } } }, "404": { "description": "Data not found" } } } }, "/genotype/{pgp_hex_id}": { "get": { "tags": [ "Genotype Data" ], "summary": "Get all genotype data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getGenotypeByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Genotype" } } } }, "404": { "description": "Participant not found" } } } }, "/all_wgbs": { "get": { "tags": [ "Whole Genome Bisulfite Data" ], "summary": "Get all whole genome bisulfite data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllWbgs", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Whole Genome Bisulfite Sequencing data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/WGBS" } } } } } }, "404": { "description": "Data not found" } } } }, "/wgbs/{pgp_hex_id}": { "get": { "tags": [ "Whole Genome Bisulfite Data" ], "summary": "Get all whole genome bisulfite data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getWgbsByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/WGBS" } } } }, "404": { "description": "Participant not found" } } } }, "/all_meth_array": { "get": { "tags": [ "Methylation Array Data" ], "summary": "Get all methylation array data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllMethArray", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Methylation Array data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/MethylationArrayData" } } } } } }, "404": { "description": "Data not found" } } } }, "/meth_array/{pgp_hex_id}": { "get": { "tags": [ "Methylation Array Data" ], "summary": "Get all methylation array data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getMethArrayByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/MethylationArrayData" } } } }, "404": { "description": "Participant not found" } } } }, "/all_rna_seq": { "get": { "tags": [ "RNA-Seq" ], "summary": "Get all RNA-seq data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllRnaSeq", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "RNA-Seq data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/RnaSeq" } } } } } }, "404": { "description": "Data not found" } } } }, "/rna_seq/{pgp_hex_id}": { "get": { "tags": [ "RNA-Seq" ], "summary": "Get all RNA-seq data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getRnaSeqByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/RnaSeq" } } } }, "404": { "description": "Participant not found" } } } }, "/all_amplicon_rna_seq": { "get": { "tags": [ "Amplicon RNA-Seq" ], "summary": "Get all amplicon RNA-seq data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllAmpliconRnaSeq", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Amplicon RNA-Seq data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/AmpliconRNAseq" } } } } } }, "404": { "description": "Data not found" } } } }, "/amplicon_rna_seq/{pgp_hex_id}": { "get": { "tags": [ "Amplicon RNA-Seq" ], "summary": "Get all amplicon RNA-seq data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getAmpliconRnaSeqByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/AmpliconRNAseq" } } } }, "404": { "description": "Participant not found" } } } }, "/all_proton_rna_seq": { "get": { "tags": [ "Proton RNA-Seq" ], "summary": "Get all proton RNA-seq data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getAllProtonRnaSeq", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Proton RNA-Seq data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/ProtonRnaSeq" } } } } } }, "404": { "description": "Data not found" } } } }, "/proton_rna_seq/{pgp_hex_id}": { "get": { "tags": [ "Proton RNA-Seq" ], "summary": "Get all proton RNA-seq data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getProtonRnaSeqByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ProtonRnaSeq" } } } }, "404": { "description": "Participant not found" } } } }, "/all_download_url": { "get": { "tags": [ "Data Direct Urls" ], "summary": "Get all file download URL", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getDownloadUrl", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Data containing direct URLs for all data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/DataURLs" } } } } } }, "404": { "description": "Data not found" } } } }, "/download_url/{pgp_hex_id}": { "get": { "tags": [ "Data Direct Urls" ], "summary": "Get all file download URL by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getDownloadUrlByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/DataURLs" } } } }, "404": { "description": "Participant not found" } } } }, "/all_pgp_profile": { "get": { "tags": [ "PGP-UK profile" ], "summary": "Get all PGP-UK profile meta data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getPgpProfile", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Meta data from PGP-UK profile for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/PGPUKProfile" } } } } } }, "404": { "description": "Data not found" } } } }, "/pgp_profile/{pgp_hex_id}": { "get": { "tags": [ "PGP-UK profile" ], "summary": "Get all PGP-UK profile meta data by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getPgpProfileByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PGPUKProfile" } } } }, "404": { "description": "Participant not found" } } } }, "/all_genome_report": { "get": { "tags": [ "Genome Reports" ], "summary": "Get all genome reports", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getGenomeReport", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Genome Report Data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/GenomeReport" } } } } } }, "404": { "description": "Data not found" } } } }, "/genome_report/{pgp_hex_id}": { "get": { "tags": [ "Genome Reports" ], "summary": "Get all genome reports by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getGenomeReportByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/GenomeReport" } } } }, "404": { "description": "Participant not found" } } } }, "/all_methylome_report": { "get": { "tags": [ "Methylome Reports" ], "summary": "Get all methylome reports", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getMethylomeReports", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Methylome Report Data for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/MethylomeReport" } } } } } }, "404": { "description": "Data not found" } } } }, "/methylome_report/{pgp_hex_id}": { "get": { "tags": [ "Methylome Reports" ], "summary": "Get all methylome reports by PGP-UK hex id", "description": "This will return an object containing all the data associated with this PGP-UK participant\n", "operationId": "getMethylomeReportsByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/MethylomeReport" } } } }, "404": { "description": "Participant not found" } } } }, "/all_phenotype": { "get": { "tags": [ "Phenotype Data" ], "summary": "Get all phenotype data", "description": "This will return an object containing all the data for all PGP-UK participants.\n", "operationId": "getPhenotypeData", "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "description": "Phenotype question and answer obtained through a participant-filled questionnaire for all PGP-UK participants", "type": "object", "properties": { "hex_id": { "$ref": "#/components/schemas/HexId" }, "data": { "$ref": "#/components/schemas/Phenotype" } } } } } }, "404": { "description": "Data not found" } } } }, "/phenotype/{pgp_hex_id}": { "get": { "tags": [ "Phenotype Data" ], "summary": "Get all phenotype data by PGP-UK hex id", "description": "This will return an object containing all the data all the data associated with this PGP-UK participant\n", "operationId": "getPhenotypeDataByHexId", "parameters": [ { "name": "pgp_hex_id", "in": "path", "description": "The hex id for the PGP-UK participant for whom the data needs to be fetched", "required": true, "schema": { "$ref": "#/components/schemas/HexId" } } ], "responses": { "200": { "description": "Success", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Phenotype" } } } }, "404": { "description": "Participant not found" } } } } }, "components": { "schemas": { "HexId": { "description": "PGP-UK unique participant id", "type": "string", "example": "uk35C650" }, "Participant": { "description": "All data associated with PGP participant", "type": "array", "items": { "type": "object", "properties": { "wgs": { "$ref": "#/components/schemas/WGS" }, "variant": { "$ref": "#/components/schemas/Variant" }, "genotype": { "$ref": "#/components/schemas/Genotype" }, "wgbs": { "$ref": "#/components/schemas/WGBS" }, "meth_array": { "$ref": "#/components/schemas/MethylationArrayData" }, "rna_seq": { "$ref": "#/components/schemas/RnaSeq" }, "amplicon_rna_seq": { "$ref": "#/components/schemas/AmpliconRNAseq" }, "proton_rna_seq": { "$ref": "#/components/schemas/ProtonRnaSeq" }, "download_url": { "$ref": "#/components/schemas/DataURLs" }, "pgp_profile": { "$ref": "#/components/schemas/PGPUKProfile" }, "genome_report": { "$ref": "#/components/schemas/GenomeReport" }, "methylome_report": { "$ref": "#/components/schemas/MethylomeReport" }, "phenotype": { "$ref": "#/components/schemas/Phenotype" } } } }, "WGS": { "description": "Whole Genome Sequencing data", "type": "array", "items": { "type": "object", "properties": { "study_accession": { "type": "string", "example": "PRJEB17529" }, "secondary_study_accession": { "type": "string", "example": "ERP019394" }, "sample_accession": { "type": "string", "example": "SAMEA4545245" }, "secondary_sample_accession": { "type": "string", "example": "ERS1444424" }, "experiment_accession": { "type": "string", "example": "ERX1796409" }, "run_accession": { "type": "string", "example": "ERR1726424" }, "submission_accession": { "type": "string", "example": "ERA763569" }, "tax_id": { "type": "string", "example": "9606" }, "scientific_name": { "type": "string", "example": "Homo sapiens" }, "instrument_platform": { "type": "string", "example": "ILLUMINA" }, "instrument_model": { "type": "string", "example": "HiSeq X Ten" }, "library_name": { "type": "string", "example": "unspecified" }, "nominal_length": { "type": "string", "example": "350" }, "library_layout": { "type": "string", "example": "PAIRED" }, "library_strategy": { "type": "string", "example": "WGS" }, "library_source": { "type": "string", "example": "GENOMIC" }, "library_selection": { "type": "string", "example": "unspecified" }, "read_count": { "type": "string", "example": "421675357" }, "base_count": { "type": "string", "example": "122196048169" }, "center_name": { "type": "string", "example": "UNIVERSITY COLLEGE LONDON" }, "first_public": { "type": "string", "example": "2016-11-14" }, "last_updated": { "type": "string", "example": "2018-11-16" }, "experiment_title": { "type": "string", "example": "HiSeq X Ten paired end sequencing" }, "study_title": { "type": "string", "example": "Personal Genome Project - United Kingdom" }, "study_alias": { "type": "string", "example": "ena-STUDY-UNIVERSITY COLLEGE LONDON-31-10-2016-15:46:14:765-442" }, "experiment_alias": { "type": "string", "example": "ena-EXPERIMENT-UNIVERSITY COLLEGE LONDON-11-11-2016-16:52:13:609-1" }, "run_alias": { "type": "string", "example": "ena-RUN-UNIVERSITY COLLEGE LONDON-11-11-2016-16:52:13:609-1" }, "fastq_bytes": { "type": "string", "example": "34749676071;39793159517" }, "fastq_md5": { "type": "string", "example": "4251226f83e65e79547998e9f6508125;763cd21e39a58b16ea51229c25ed549d" }, "fastq_ftp": { "type": "string", "example": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR172/004/ERR1726424/ERR1726424_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR172/004/ERR1726424/ERR1726424_2.fastq.gz" }, "fastq_aspera": { "type": "string", "example": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR172/004/ERR1726424/ERR1726424_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR172/004/ERR1726424/ERR1726424_2.fastq.gz" }, "fastq_galaxy": { "type": "string", "example": 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"fasp.sra.ebi.ac.uk:/vol1/err/ERR172/004/ERR1726424" }, "sra_galaxy": { "type": "string", "example": "ftp.sra.ebi.ac.uk/vol1/err/ERR172/004/ERR1726424" }, "cram_index_ftp": { "type": "string", "example": null }, "cram_index_aspera": { "type": "string", "example": null }, "cram_index_galaxy": { "type": "string", "example": null }, "sample_alias": { "type": "string", "example": "uk35C650" }, "broker_name": { "type": "string", "example": null }, "sample_title": { "type": "string", "example": "Personal Genomes Project UK Sample" }, "nominal_sdev": { "type": "string", "example": "0" }, "first_created": { "type": "string", "example": "2016-11-11" }, "type": { "type": "string", "example": "wgs" }, "meta_data_source": { "type": "string", "example": "https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=PRJEB17529&result=read_run" } } } }, "Variant": { "description": "Variant data", "type": "array", "items": { "type": "object", "properties": { "test": { "type": "string", "example": 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"scientific_name": { "type": "string", "example": "Homo sapiens" }, "instrument_platform": { "type": "string", "example": "ILLUMINA" }, "instrument_model": { "type": "string", "example": "HiSeq X Ten" }, "library_name": { "type": "string", "example": "WGBS_PGP-UK1" }, "nominal_length": { "type": "string", "example": "200" }, "library_layout": { "type": "string", "example": "PAIRED" }, "library_strategy": { "type": "string", "example": "Bisulfite-Seq" }, "library_source": { "type": "string", "example": "GENOMIC" }, "library_selection": { "type": "string", "example": "unspecified" }, "read_count": { "type": "string", "example": "331458549" }, "base_count": { "type": "string", "example": "100100481798" }, "center_name": { "type": "string", "example": "UNIVERSITY COLLEGE LONDON" }, "first_public": { "type": "string", "example": "2018-03-02" }, "last_updated": { "type": "string", "example": "2018-11-16" }, "experiment_title": { "type": "string", "example": "HiSeq X Ten paired end 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Genome Bissulfide Sequencing Data" }, "nominal_sdev": { "type": "string", "example": "0" }, "first_created": { "type": "string", "example": "2018-03-02" }, "type": { "type": "string", "example": "wgbs" }, "meta_data_source": { "type": "string", "example": "https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=PRJEB17529&result=read_run" } } } }, "MethylationArrayData": { "description": "Methylation Array data", "type": "array", "items": { "type": "object", "properties": { "source_name": { "type": "string", "example": "Sample 1_PGPUK_B1" }, "characteristicsorganism": { "type": "string", "example": "Homo sapiens" }, "characteristicsindividual": { "type": "string", "example": "uk35C650" }, "commentbiosd_sample": { "type": "string", "example": "SAMEA4545245" }, "characteristicsorganism_part": { "type": "string", "example": "blood" }, "characteristicsage": { "type": "string", "example": "59.67" }, "unittime_unit": { "type": "string", "example": "year" }, "term_source_ref": { "type": 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"example": "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-5377/E-MTAB-5377.raw.1.zip" }, "factor_valueage": { "type": "string", "example": "59.67" }, "factor_value_organism_part": { "type": "string", "example": "blood" }, "factor_value_smoking_status": { "type": "string", "example": "smoked in the past" }, "factor_value_individual": { "type": "string", "example": "uk35C650" }, "type": { "type": "string", "example": "meth_array" }, "accession": { "type": "string", "example": "E-MTAB-5377" }, "meta_data_source": { "type": "string", "example": "https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5377/E-MTAB-5377.sdrf.txt" } } } }, "RnaSeq": { "description": "RNA-Seq data", "type": "array", "items": { "type": "object", "properties": { "source_name": { "type": "string", "example": "Sample_1_PGPUK_B1" }, "commentena_sample": { "type": "string", "example": "ERS2220941" }, "commentbiosd_sample": { "type": "string", "example": "SAMEA4545245" }, "characteristicsorganism": { "type": "string", "example": "Homo sapiens" }, "characteristicsdisease": { "type": "string", "example": "normal" }, "characteristicssex": { "type": "string", "example": "male" }, "characteristicsindividual": { "type": "string", "example": "uk35C650" }, "characteristicsage": { "type": "string", "example": "59.67" }, "unittime_unit": { "type": "string", "example": "year" }, "term_source_ref": { "type": "string", "example": "EFO" }, "term_accession_number": { "type": "string", "example": "UO_0000036" }, "characteristicsclinical_history": { "type": "string", "example": "smoked in the past" }, "characteristicsorganism_part": { "type": "string", "example": "blood" }, "material_type": { "type": "string", "example": "RNA" }, "protocol_ref": { "type": "string", "example": " " }, "extract_name": { "type": "string", "example": "Sample_1_PGPUK_B1" }, "commentlibrary_layout": { "type": "string", "example": "PAIRED" }, "commentlibrary_selection": { "type": "string", "example": "PolyA" }, "commentlibrary_source": { "type": "string", "example": "TRANSCRIPTOMIC" }, "commentlibrary_strategy": { "type": "string", "example": "RNA-Seq" }, "commentnominal_length": { "type": "string", "example": "150" }, "commentnominal_sdev": { "type": "string", "example": "1.92" }, "commentorientation": { "type": "string", "example": "5'-3'-3'-5'" }, "performer": { "type": "string", "example": "UCL" }, "assay_name": { "type": "string", "example": "Sample_1_PGPUK_B1" }, "technology_type": { "type": "string", "example": "sequencing assay" }, "commentena_experiment": { "type": "string", "example": "ERX2373316" }, "scan_name": { "type": "string", "example": "PGP_UK_RNAseq_P5_R1.fastq.gz" }, "commentsubmitted_file_name": { "type": "string", "example": "PGP_UK_RNAseq_P5_R1.fastq.gz" }, "commentena_run": { "type": "string", "example": "ERR2322363" }, "commentfastq_uri": { "type": "string", "example": "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR232/003/ERR2322363/ERR2322363_1.fastq.gz" }, "commentspot_length": { "type": "string", "example": "302" }, "commentread_index_1_base_coord": { "type": "string", "example": "152" }, "derived_array_data_file": { "type": "string", "example": " " }, "comment_derived_arrayexpress_ftp_file": { "type": "string", "example": " " }, "factor_valueclinical_history": { "type": "string", "example": "smoked in the past" }, "factor_valueindividual": { "type": "string", "example": "uk2E2AAE" }, "factor_valueprotocol": { "type": "string", "example": "RNA-seq" }, "type": { "type": "string", "example": "rna_seq" }, "accession": { "type": "string", "example": "E-MTAB-6523" }, "meta_data_source": { "type": "string", "example": "https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6523/E-MTAB-6523.sdrf.txt" } } } }, "AmpliconRNAseq": { "description": "Amplicon RNA-Seq data", "type": "array", "items": { "type": "object", "properties": { "study_accession": { "type": "string", "example": "PRJEB25139" }, "secondary_study_accession": { "type": "string", "example": "ERP107030" }, "sample_accession": { "type": "string", "example": "SAMEA104609659" }, "secondary_sample_accession": { "type": "string", "example": "ERS2220941" }, "experiment_accession": { "type": "string", "example": "ERX2373326" }, "run_accession": { "type": "string", "example": "ERR2322353" }, "submission_accession": { "type": "string", "example": "ERA1221153" }, "tax_id": { "type": "string", "example": "9606" }, "scientific_name": { "type": "string", "example": "Homo sapiens" }, "instrument_platform": { "type": "string", "example": "ION_TORRENT" }, "instrument_model": { "type": "string", "example": "Ion Torrent Proton" }, "library_name": { "type": "string", "example": "Sample_1_PGPUK_B1_targeted_s" }, "nominal_length": { "type": "string", "example": null }, "library_layout": { "type": "string", "example": "SINGLE" }, "library_strategy": { "type": "string", "example": "AMPLICON" }, "library_source": { "type": "string", "example": "TRANSCRIPTOMIC" }, "library_selection": { 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participant-filled questionnaire", "type": "array", "items": { "type": "object", "properties": { "name": { "type": "string", "example": "General Questionnaire" }, "data": { "type": "array", "items": { "type": "object", "properties": { "question": { "type": "string", "example": "Age at Sample Collection" }, "answer": { "type": "string", "example": 60 } } } } } } } }, "headers": { "ExpiresAfter": { "description": "date in UTC when token expires", "schema": { "type": "string", "format": "date-time" } } } } }