{"_id":"5b0e13ffc4664e0003c75cc2","__v":0,"parentDoc":null,"version":{"_id":"5b0e13ffc4664e0003c75a67","project":"5b0e13ffc4664e0003c75a66","__v":4,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["5b0e13ffc4664e0003c75a68","5b0e13ffc4664e0003c75a69","5b0e13ffc4664e0003c75a6a","5b0e13ffc4664e0003c75a6b","5b0e13ffc4664e0003c75a6c","5b0e13ffc4664e0003c75a6d","5b0e13ffc4664e0003c75a6e","5b0e13ffc4664e0003c75a6f","5b0e13ffc4664e0003c75a70","5b0e13ffc4664e0003c75a71","5b0e13ffc4664e0003c75a72","5b0e13ffc4664e0003c75a73","5b0e13ffc4664e0003c75a74","5b0e13ffc4664e0003c75a75","5b0e13ffc4664e0003c75a76","5b0e13ffc4664e0003c75a77","5b0e13ffc4664e0003c75a89","5b0e13ffc4664e0003c75a8a","5b0e13ffc4664e0003c75a9d","5b0e13ffc4664e0003c75a9e","5b0e13ffc4664e0003c75a9f","5b0e13ffc4664e0003c75aa0","5b0e13ffc4664e0003c75aa1","5b0e13ffc4664e0003c75aa2","5b0e13ffc4664e0003c75aa3","5b0e13ffc4664e0003c75aa4","5b0e13ffc4664e0003c75aa5","5b0e13ffc4664e0003c75aa6","5b0e13ffc4664e0003c75aa7","5b0e13ffc4664e0003c75aa8","5b0e13ffc4664e0003c75aa9","5b0e13ffc4664e0003c75aaa","5b0e13ffc4664e0003c75aab","5b0e13ffc4664e0003c75aac","5b0e13ffc4664e0003c75aad","5b0e13ffc4664e0003c75aae","5b0e13ffc4664e0003c75aaf","5b0e13ffc4664e0003c75ab2","5bb3374f4306ad0003eb18e7","5bbf3c5373e72a000318362b","5bc065567d1cb0000384c649","5cbf19a5f9181f0033fbb968"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"5b0e13ffc4664e0003c75aaa","project":"5b0e13ffc4664e0003c75a66","version":"5b0e13ffc4664e0003c75a67","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"user":"5613e4f8fdd08f2b00437620","project":"5b0e13ffc4664e0003c75a66","githubsync":"","metadata":{"title":"","description":"","image":[]},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-12-05T15:56:26.428Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":32,"body":"##Overview\n\nMetadata is data that describes other data. On this page, we've detailed TOPMed studies metadata that are available for viewing and filtering TOPMed studies data in the Data Browser. TOPMed studies metadata on the DataSTAGE powered by Seven Bridges consists of properties which describe the entities.\n\n* **Entities** are particular resources such as files, samples, subjects, and studies.\n\n* **Properties** can either describe an entity or relate that entity to another entity. For instance, properties include an entity's gender, data format, or biospecimen repository.\n\n## Entities for TOPMed studies\n\nThe following are entities for TOPMed studies. They represent clinical data, biospecimen data and data about TOPMed studies files. Learn more about TOPMed studies data.\n\n* Study  \n* TOPMed project\n* Subject\n* Sample\n* File name\n    \n \nRead more about these entities and related properties below. \n\n##Study\n\nThe **Study** entity represents.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Study name\",\n    \"0-1\": \"TOPMed-assigned short study name (1:1 with phs number).\",\n    \"1-0\": \"Study design\",\n    \"1-1\": \"Study design is a process wherein the trial methodology and statistical analysis are organized to ensure that the null hypothesis is either accepted or rejected and the conclusions arrived at reflect the truth.\",\n    \"2-0\": \"Biospecimen repository\",\n    \"3-0\": \"Study disease\",\n    \"4-0\": \"dbGap Accession\",\n    \"2-1\": \"A biorepository is a biological materials repository that collects, processes, stores, and distributes biospecimens to support future scientific investigation.\",\n    \"3-1\": \"Disease that is being investigated.\",\n    \"4-1\": \"dbGaP study accession number.\"\n  },\n  \"cols\": 2,\n  \"rows\": 5\n}\n[/block]\n##Subject\n\nThe Subject entity represents person from whom the sample was taken and analyzed.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Consent\",\n    \"0-1\": \"Consent group as determined by Data Access Committee (DAC).\",\n    \"1-0\": \"Sex\",\n    \"1-1\": \"Self-reported sex or gender identity.\",\n    \"3-0\": \"Subject is affected\",\n    \"2-0\": \"Organism\",\n    \"2-1\": \"A living thing, such as an animal, a plant, a bacterium, or a fungus. (NCI Thesaurus Code:  C14250)\",\n    \"3-1\": \"Case or control status of the subject.\"\n  },\n  \"cols\": 2,\n  \"rows\": 4\n}\n[/block]\n## Sample\n\nThe **Sample** entity represents an analyte or biological specimen sampled from a subject (e.g. DNA from blood).\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"BioSample ID\",\n    \"0-1\": \"A biosample ID assigned by dbGaP. These are unique across all studies in dbGaP.\",\n    \"1-0\": \"Body Site\",\n    \"1-1\": \"Body site where sample was collected.\",\n    \"2-0\": \"Analyte type\",\n    \"2-1\": \"Analyte type(e.g. DNA, RNA).\",\n    \"3-0\": \"Histological type\",\n    \"3-1\": \"Cell or tissue type or subtype - e.g. melanocytes, buccal cells, embryonic stem cells).\",\n    \"4-0\": \"Is tumor\",\n    \"4-1\": \"The tumor status.\"\n  },\n  \"cols\": 2,\n  \"rows\": 5\n}\n[/block]\n## File name\n\nThe **File name** entity refers to the files in TOPMed project produced by aliquot analysis. Find the properties of the file entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Access level\",\n    \"0-1\": \"A Boolean value indicating Controlled Data or Open Data. Controlled Data is data from public studies that has limitations on use and requires approval by dbGaP. Open Data is data from public studies that doesn't have limitations on its use.\",\n    \"1-0\": \"Assembly name\",\n    \"1-1\": \"The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.\",\n    \"2-0\": \"Platform\",\n    \"2-1\": \"The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying.\",\n    \"3-0\": \"Molecular data type\",\n    \"3-1\": \"Molecular data type (e.g. SNP/CNV Genotypes).\",\n    \"4-0\": \"Freeze\",\n    \"5-0\": \"Sequencing center\",\n    \"5-1\": \"Name of the center which conducted sequencing.\",\n    \"6-0\": \"Assay type\",\n    \"7-0\": \"Instrument\",\n    \"8-0\": \"File type\",\n    \"9-0\": \"Library name\",\n    \"10-0\": \"Library layout\",\n    \"11-0\": \"Library selection\",\n    \"12-0\": \"Library source\",\n    \"13-0\": \"Alignment provider\",\n    \"14-0\": \"Release date\",\n    \"15-0\": \"Consent\",\n    \"9-1\": \"Name of the library.\",\n    \"10-1\": \"Library layout of a project (SINGLE or PAIRED end reads.)\",\n    \"11-1\": \"The method used to select and/or enrich the material being sequenced.\",\n    \"12-1\": \"The type of source material that is being sequenced.\",\n    \"4-1\": \"TOPMed WGS genotype call sets.\",\n    \"6-1\": \"DNA sequencing technique that was applied ( e.g. WGS ,WES).\",\n    \"7-1\": \"Type of instrument that was being used for sequencing.\",\n    \"8-1\": \"File Type (e.g. CRAM, VCF).\",\n    \"13-1\": \"Information about who did the alignment.\",\n    \"14-1\": \"Date when the  sequencing data was released to SRA.\",\n    \"15-1\": \"Consent group as determined by Data Access Committee (DAC).\"\n  },\n  \"cols\": 2,\n  \"rows\": 16\n}\n[/block]","excerpt":"","slug":"topmed-metadata","type":"basic","title":"TOPMed studies metadata"}

TOPMed studies metadata


##Overview Metadata is data that describes other data. On this page, we've detailed TOPMed studies metadata that are available for viewing and filtering TOPMed studies data in the Data Browser. TOPMed studies metadata on the DataSTAGE powered by Seven Bridges consists of properties which describe the entities. * **Entities** are particular resources such as files, samples, subjects, and studies. * **Properties** can either describe an entity or relate that entity to another entity. For instance, properties include an entity's gender, data format, or biospecimen repository. ## Entities for TOPMed studies The following are entities for TOPMed studies. They represent clinical data, biospecimen data and data about TOPMed studies files. Learn more about TOPMed studies data. * Study * TOPMed project * Subject * Sample * File name Read more about these entities and related properties below. ##Study The **Study** entity represents. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Study name", "0-1": "TOPMed-assigned short study name (1:1 with phs number).", "1-0": "Study design", "1-1": "Study design is a process wherein the trial methodology and statistical analysis are organized to ensure that the null hypothesis is either accepted or rejected and the conclusions arrived at reflect the truth.", "2-0": "Biospecimen repository", "3-0": "Study disease", "4-0": "dbGap Accession", "2-1": "A biorepository is a biological materials repository that collects, processes, stores, and distributes biospecimens to support future scientific investigation.", "3-1": "Disease that is being investigated.", "4-1": "dbGaP study accession number." }, "cols": 2, "rows": 5 } [/block] ##Subject The Subject entity represents person from whom the sample was taken and analyzed. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Consent", "0-1": "Consent group as determined by Data Access Committee (DAC).", "1-0": "Sex", "1-1": "Self-reported sex or gender identity.", "3-0": "Subject is affected", "2-0": "Organism", "2-1": "A living thing, such as an animal, a plant, a bacterium, or a fungus. (NCI Thesaurus Code: C14250)", "3-1": "Case or control status of the subject." }, "cols": 2, "rows": 4 } [/block] ## Sample The **Sample** entity represents an analyte or biological specimen sampled from a subject (e.g. DNA from blood). [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "BioSample ID", "0-1": "A biosample ID assigned by dbGaP. These are unique across all studies in dbGaP.", "1-0": "Body Site", "1-1": "Body site where sample was collected.", "2-0": "Analyte type", "2-1": "Analyte type(e.g. DNA, RNA).", "3-0": "Histological type", "3-1": "Cell or tissue type or subtype - e.g. melanocytes, buccal cells, embryonic stem cells).", "4-0": "Is tumor", "4-1": "The tumor status." }, "cols": 2, "rows": 5 } [/block] ## File name The **File name** entity refers to the files in TOPMed project produced by aliquot analysis. Find the properties of the file entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Access level", "0-1": "A Boolean value indicating Controlled Data or Open Data. Controlled Data is data from public studies that has limitations on use and requires approval by dbGaP. Open Data is data from public studies that doesn't have limitations on its use.", "1-0": "Assembly name", "1-1": "The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.", "2-0": "Platform", "2-1": "The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying.", "3-0": "Molecular data type", "3-1": "Molecular data type (e.g. SNP/CNV Genotypes).", "4-0": "Freeze", "5-0": "Sequencing center", "5-1": "Name of the center which conducted sequencing.", "6-0": "Assay type", "7-0": "Instrument", "8-0": "File type", "9-0": "Library name", "10-0": "Library layout", "11-0": "Library selection", "12-0": "Library source", "13-0": "Alignment provider", "14-0": "Release date", "15-0": "Consent", "9-1": "Name of the library.", "10-1": "Library layout of a project (SINGLE or PAIRED end reads.)", "11-1": "The method used to select and/or enrich the material being sequenced.", "12-1": "The type of source material that is being sequenced.", "4-1": "TOPMed WGS genotype call sets.", "6-1": "DNA sequencing technique that was applied ( e.g. WGS ,WES).", "7-1": "Type of instrument that was being used for sequencing.", "8-1": "File Type (e.g. CRAM, VCF).", "13-1": "Information about who did the alignment.", "14-1": "Date when the sequencing data was released to SRA.", "15-1": "Consent group as determined by Data Access Committee (DAC)." }, "cols": 2, "rows": 16 } [/block]