{ "_definitions": { "UUID": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "data_bundle_state": { "default": "submitted", "description": "State of a data bundle.", "enum": [ "submitted", "validated", "error", "released", "suppressed", "redacted" ] }, "data_file_error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "data_file_properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "foreign_key": { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "foreign_key_project": { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": "_definitions", "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "parent_uuids": { "items": { "$ref": "#/UUID" }, "minItems": 1, "type": "array", "uniqueItems": true }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "qc_metrics_state": { "enum": [ "FAIL", "PASS", "WARN" ], "term": { "$ref": "_terms.yaml#/qc_metric_state" } }, "release_state": { "default": "unreleased", "description": "Release state of an entity.", "enum": [ "unreleased", "released", "redacted" ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "to_many": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "to_many_project": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "to_one": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "to_one_project": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "ubiquitous_properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "workflow_properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_end_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_link": { "description": "Link to Github hash for the CWL workflow used.", "type": "string" }, "workflow_start_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_version": { "description": "Major version for a GDC workflow.", "type": "string" } } }, "_settings": { "_dict_commit": "54e573abaa7e67c30cf52d56470fad805a9bee2a", "_dict_version": "4.6.5", "enable_case_cache": false }, "_terms": { "28s_16s_ribosomal_rna_ratio": { "description": "The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "28s/18s Ribosomal RNA Ratio", "term_url": null } }, "RIN": { "description": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products.\n", "termDef": { "cde_id": 5278775, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen RNA Integrity Number Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" } }, "UUID": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "a260_a280_ratio": { "description": "Numeric value that represents the sample ratio of nucleic acid absorbance at 260 nm and 280 nm, used to determine a measure of DNA purity.\n", "termDef": { "cde_id": 5432595, "cde_version": 1.0, "source": "caDSR", "term": "Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" } }, "adapter_name": { "description": "Name of the sequencing adapter.\n" }, "adapter_sequence": { "description": "Base sequence of the sequencing adapter.\n" }, "age_at_diagnosis": { "description": "Age at the time of diagnosis expressed in number of days since birth. If the age at diagnosis is greater than 32872 days (89 years), then see 'age_at_diagnosis_gt89'.\n", "termDef": { "cde_id": 3225640, "cde_version": 2.0, "source": "caDSR", "term": "Patient Diagnosis Age Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" } }, "age_at_diagnosis_gt89": { "description": "Indicate whether the age at the time of diagnosis expressed in number of days since birth is greater than 32872 days (89 years).\n", "termDef": { "cde_id": 3225640, "cde_version": 2.0, "source": "caDSR", "term": "Patient Diagnosis Age Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" } }, "age_at_event_days": { "description": "Age at the time an event occurs expressed in the number of days since birth. If the age at event is greater than 32872 days (89 years), then see 'age_at_event_gt89'.\n" }, "age_at_event_days_gt89": { "description": "Indicate whether the 'Age at the time an event occurs expressed in the number of days since birth' is greater than 32872 days (89 years).\n" }, "ajcc_clinical_m": { "description": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.\n", "termDef": { "cde_id": 3440331, "cde_version": 1.0, "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0" } }, "ajcc_clinical_n": { "description": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.\n", "termDef": { "cde_id": 3440330, "cde_version": 1.0, "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0" } }, "ajcc_clinical_stage": { "description": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.\n", "termDef": { "cde_id": 3440332, "cde_version": 1.0, "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Group Stage", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0" } }, "ajcc_clinical_t": { "description": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.\n", "termDef": { "cde_id": 3440328, "cde_version": 1.0, "source": "caDSR", "term": "Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0" } }, "ajcc_pathologic_m": { "description": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).\n", "termDef": { "cde_id": 3045439, "cde_version": 1.0, "source": "caDSR", "term": "American Joint Committee on Cancer Metastasis Stage Code", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0" } }, "ajcc_pathologic_n": { "description": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.\n", "termDef": { "cde_id": 3203106, "cde_version": 1.0, "source": "caDSR", "term": "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0" } }, "ajcc_pathologic_stage": { "description": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.\n", "termDef": { "cde_id": 3203222, "cde_version": 1.0, "source": "caDSR", "term": "Neoplasm Disease Stage American Joint Committee on Cancer Code", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0" } }, "ajcc_pathologic_t": { "description": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).\n", "termDef": { "cde_id": 3045435, "cde_version": 1.0, "source": "caDSR", "term": "American Joint Committee on Cancer Tumor Stage Code", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0" } }, "alcohol_history": { "description": "A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.\n", "termDef": { "cde_id": 2201918, "cde_version": 1.0, "source": "caDSR", "term": "Alcohol Lifetime History Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0" } }, "alcohol_intensity": { "description": "Category to describe the patient's current level of alcohol use as self-reported by the patient.\n", "termDef": { "cde_id": 3457767, "cde_version": 1.0, "source": "caDSR", "term": "Person Self-Report Alcoholic Beverage Exposure Category", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3457767&version=1.0" } }, "aliquot_quantity": { "description": "The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Biospecimen Aliquot Quantity", "term_url": null } }, "aliquot_volume": { "description": "The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Biospecimen Aliquot Volume", "term_url": null } }, "amount": { "description": "Weight in grams or volume in mL.\n" }, "analyte_quantity": { "description": "The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for sequencing and characterization.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Biospecimen Analyte Quantity", "term_url": null } }, "analyte_type": { "description": "Text term that represents the kind of molecular specimen analyte.\n", "termDef": { "cde_id": 2513915, "cde_version": 2.0, "source": "caDSR", "term": "Molecular Specimen Type Text Name", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" } }, "analyte_type_id": { "description": "A single letter code used to identify a type of molecular analyte.\n", "termDef": { "cde_id": 5432508, "cde_version": 1.0, "source": "caDSR", "term": "Molecular Analyte Identification Code", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0" } }, "analyte_volume": { "description": "The volume in microliters (ml) of the analyte(s) derived from the analyte(s) shipped for sequencing and characterization.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Biospecimen Analyte Volume", "term_url": null } }, "ann_arbor_b_symptoms": { "description": "Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical record.\n", "termDef": { "cde_id": 2902402, "cde_version": 1.0, "source": "caDSR", "term": "Lymphoma B-Symptoms Medical Record Documented Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0" } }, "ann_arbor_clinical_stage": { "description": "The classification of the clinically confirmed anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Ann Arbor Clinical Stage", "term_url": null } }, "ann_arbor_extranodal_involvement": { "description": "Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement of an extranodal site.\n", "termDef": { "cde_id": 3364582, "cde_version": 1.0, "source": "caDSR", "term": "Lymphomatous Extranodal Site Involvement Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0" } }, "ann_arbor_pathologic_stage": { "description": "The classification of the pathologically confirmed anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Ann Arbor Pathologic Stage", "term_url": null } }, "ann_arbor_tumor_stage": { "description": "The classification of the anatomic disease extent of lymphoma (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Ann Arbor Tumor Stage", "term_url": null } }, "assay_instrument": { "description": "The specific instrument type used to perform the assay. If applicable, please also indicate the instrument mode and model in 'assay_instrument_mode' and 'assay_instrument_model'." }, "assay_instrument_model": { "description": "The specific model of instrument used to perform the assay. Please also indicate the instrument and mode in 'assay_instrument' and 'assay_instrument_mode'." }, "assay_method": { "description": "General methodology used to perform the assay." }, "base_caller_name": { "description": "Name of the base caller.\n" }, "base_caller_version": { "description": "Version of the base caller.\n" }, "biomarker_name": { "description": "The name of the biomarker being tested for this specimen and set of test results.\n", "termDef": { "cde_id": 5473, "cde_version": 11.0, "source": "caDSR", "term": "Biomarker Name", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31" } }, "biomarker_result": { "description": "Text term to define the results of genetic testing.\n", "termDef": { "cde_id": 3234680, "cde_version": 1.0, "source": "caDSR", "term": "Laboratory Procedure Genetic Abnormality Test Result Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0" } }, "biomarker_test_method": { "description": "Text descriptor of a molecular analysis method used for an individual.\n", "termDef": { "cde_id": 3121575, "cde_version": 1.0, "source": "caDSR", "term": "Disease Detection Molecular Analysis Method Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0" } }, "biospecimen_anatomic_site": { "description": "Text term that represents the name of the primary disease site of the submitted tumor sample.\n", "termDef": { "cde_id": 4742851, "cde_version": 1.0, "source": "caDSR", "term": "Submitted Tumor Sample Primary Anatomic Site", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4742851&version=1.0" } }, "bmi": { "description": "Body mass index calculated at baseline. (kg/m^2) (HARMONIZED)\n", "termDef": { "cde_id": 4973892, "cde_version": 1.0, "source": "caDSR", "term": "Body Mass Index (BMI)", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" } }, "bucket_path": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "burkitt_lymphoma_clinical_variant": { "description": "Burkitt's lymphoma categorization based on clinical features that differ from other forms of the same disease.\n", "termDef": { "cde_id": 3770421, "cde_version": 1.0, "source": "caDSR", "term": "Burkitt Lymphoma Clinical Variant Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" } }, "callset": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "cause_of_death": { "description": "Text term to identify the cause of death for a patient.\n", "termDef": { "cde_id": 2554674, "cde_version": 3.0, "source": "caDSR", "term": "Patient Death Reason", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0" } }, "cea_level_preoperative": { "description": "Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. [Manually- curated]\n", "termDef": { "cde_id": 2716510, "cde_version": 1.0, "source": "caDSR", "term": "Preoperative Carcinoembryonic Antigen Result Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0" } }, "cigarettes_per_day": { "description": "The average number of cigarettes smoked per day.\n", "termDef": { "cde_id": 2001716, "cde_version": 4.0, "source": "caDSR", "term": "Smoking Use Average Number", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0" } }, "circumferential_resection_margin": { "description": "A value in millimeters indicating the measured length between a malignant lesion of the colon or rectum and the nearest radial (or circumferential) border of tissue removed during cancer surgery.\n", "termDef": { "cde_id": 64202, "cde_version": 3.0, "source": "caDSR", "term": "Colorectal Surgical Margin Circumferential Distance Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0" } }, "classification_of_tumor": { "description": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.\n", "termDef": { "cde_id": 3288124, "cde_version": 1.0, "source": "caDSR", "term": "Tumor Tissue Disease Description Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" } }, "colon_polyps_history": { "description": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).\n", "termDef": { "cde_id": 3107197, "cde_version": 1.0, "source": "caDSR", "term": "Colon Carcinoma Polyp Occurrence Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0" } }, "composition": { "description": "Text term that represents the cellular composition of the sample.\n", "termDef": { "cde_id": 5432591, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Cellular Composition Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" } }, "concentration": { "description": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.\n", "termDef": { "cde_id": 5432594, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" } }, "creation_datetime": { "description": "The datetime of portion creation encoded as seconds from epoch.\n", "termDef": { "cde_id": 5432592, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Portion Creation Seconds Date/Time", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0" } }, "current_weight": { "description": "Numeric value that represents the current weight of the sample, measured in milligrams.\n", "termDef": { "cde_id": 5432606, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Current Weight Milligram Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" } }, "data_category": { "description": "Broad categorization of the contents of the data file.\n" }, "data_file_error_type": { "description": "Type of error for the data file object.\n" }, "data_format": { "description": "Format of the data files.\n" }, "data_type": { "description": "Specific content type of the data file.\n" }, "datetime": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" }, "days_to_birth": { "description": "Time interval from a person's date of birth to the date of initial pathologic diagnosis, represented as a calculated negative number of days.\n", "termDef": { "cde_id": 3008233, "cde_version": 1.0, "source": "caDSR", "term": "Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0" } }, "days_to_collection": { "description": "Time interval from the date of biospecimen collection to the date of initial pathologic diagnosis, represented as a calculated number of days.\n", "termDef": { "cde_id": 3008340, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0" } }, "days_to_death": { "description": "Time interval from a person's date of death to the date of initial pathologic diagnosis, represented as a calculated number of days.\n", "termDef": { "cde_id": 3165475, "cde_version": 1.0, "source": "caDSR", "term": "Death Less Initial Pathologic Diagnosis Date Calculated Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0" } }, "days_to_hiv_diagnosis": { "description": "Time interval from the date of the initial pathologic diagnosis to the date of human immunodeficiency diagnosis, represented as a calculated number of days.\n", "termDef": { "cde_id": 4618491, "cde_version": 1.0, "source": "caDSR", "term": "Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0" } }, "days_to_last_follow_up": { "description": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.\n", "termDef": { "cde_id": 3008273, "cde_version": 1.0, "source": "caDSR", "term": "Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" } }, "days_to_last_known_disease_status": { "description": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.\n", "termDef": { "cde_id": 3008273, "cde_version": 1.0, "source": "caDSR", "term": "Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" } }, "days_to_new_event": { "description": "Time interval from the date of new tumor event including progression, recurrence and new primary malignacies to the date of initial pathologic diagnosis, represented as a calculated number of days.\n", "termDef": { "cde_id": 3392464, "cde_version": 1.0, "source": "caDSR", "term": "New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" } }, "days_to_recurrence": { "description": "Time interval from the date of new tumor event including progression, recurrence and new primary malignancies to the date of initial pathologic diagnosis, represented as a calculated number of days.\n", "termDef": { "cde_id": 3392464, "cde_version": 1.0, "source": "caDSR", "term": "New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" } }, "days_to_sample_procurement": { "description": "The number of days from the date the patient was diagnosed to the date of the procedure that produced the sample.\n" }, "days_to_treatment": { "description": "Number of days from date of initial pathologic diagnosis that treatment began.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Days to Treatment Start", "term_url": null } }, "days_to_treatment_end": { "description": "Time interval from the date of the initial pathologic diagnosis to the date of treatment end, represented as a calculated number of days.\n", "termDef": { "cde_id": 5102431, "cde_version": 1.0, "source": "caDSR", "term": "Treatment End Subtract First Pathologic Diagnosis Day Calculation Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0" } }, "days_to_treatment_start": { "description": "Time interval from the date of the initial pathologic diagnosis to the start of treatment, represented as a calculated number of days.\n", "termDef": { "cde_id": 5102411, "cde_version": 1.0, "source": "caDSR", "term": "Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0" } }, "diagnosis_pathologically_confirmed": { "description": "The histologic description of tissue or cells confirmed by a pathology review of frozen or formalin fixed slide(s) completed after the diagnostic pathology review of the tumor sample used to extract analyte(s).\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Post-Diagnostic Pathology Review Confirmation", "term_url": null } }, "dlco_ref_predictive_percent": { "description": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.\n", "termDef": { "cde_id": 2180255, "cde_version": 1.0, "source": "caDSR", "term": "Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0" } }, "encoding": { "description": "Version of ASCII encoding of quality values found in the file.\n", "termDef": { "cde_id": null, "cde_version": null, "source": "FastQC", "term": "Encoding", "term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" } }, "estrogen_receptor_percent_positive_ihc": { "description": "Classification to represent ER Positive results expressed as a percentage value.\n", "termDef": { "cde_id": 3128341, "cde_version": 1.0, "source": "caDSR", "term": "ER Level Cell Percentage Category", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0" } }, "estrogen_receptor_result_ihc": { "description": "Text term to represent the overall result of Estrogen Receptor (ER) testing.\n", "termDef": { "cde_id": 2957359, "cde_version": 2.0, "source": "caDSR", "term": "Breast Carcinoma Estrogen Receptor Status", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0" } }, "ethnicity": { "description": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino (HARMONIZED). The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.\n", "termDef": { "cde_id": 2192217, "cde_version": 2.0, "source": "caDSR", "term": "Ethnic Group Category Text", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" } }, "experiment_name": { "description": "Submitter-defined name for the experiment.\n" }, "experimental_strategy": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n" }, "fastq_name": { "description": "Names of FASTQs.\n" }, "fev1_fvc_post_bronch_percent": { "description": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.\n", "termDef": { "cde_id": 3302956, "cde_version": 1.0, "source": "caDSR", "term": "Post Bronchodilator FEV1/FVC Percent Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0" } }, "fev1_fvc_pre_bronch_percent": { "description": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.\n", "termDef": { "cde_id": 3302955, "cde_version": 1.0, "source": "caDSR", "term": "Pre Bronchodilator FEV1/FVC Percent Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0" } }, "fev1_ref_post_bronch_percent": { "description": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.\n", "termDef": { "cde_id": 3302948, "cde_version": 1.0, "source": "caDSR", "term": "Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0" } }, "fev1_ref_pre_bronch_percent": { "description": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.\n", "termDef": { "cde_id": 3302947, "cde_version": 1.0, "source": "caDSR", "term": "Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" } }, "figo_stage": { "description": "The extent of a cervical or endometrial cancer within the body, especially whether the disease has spread from the original site to other parts of the body, as described by the International Federation of Gynecology and Obstetrics (FIGO) stages.\n", "termDef": { "cde_id": 3225684, "cde_version": 1.0, "source": "caDSR", "term": "Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" } }, "file_format": { "description": "The format of the data file object.\n" }, "file_md5sum": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "file_name": { "description": "The name (or part of a name) of a file (of any type).\n" }, "file_size": { "description": "The size of the data file (object) in bytes.\n" }, "file_state": { "description": "The current state of the data file object.\n" }, "file_type": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "flow_cell_barcode": { "description": "Flow Cell Barcode.\n" }, "freezing_method": { "description": "Text term that represents the method used for freezing the sample.\n", "termDef": { "cde_id": 5432607, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Freezing Method Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" } }, "ga4gh_drs_uri": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "gender": { "description": "Subject sex, as recorded by the study. (HARMONIZED)\n", "termDef": { "cde_id": 2200604, "cde_version": 3.0, "source": "caDSR", "term": "Person Gender Text Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" } }, "height": { "description": "Body height at baseline. (cm) (HARMONIZED)\n", "termDef": { "cde_id": 649, "cde_version": 4.1, "source": "caDSR", "term": "Patient Height Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" } }, "her2_erbb2_percent_positive_ihc": { "description": "Classification to represent the number of positive HER2/ERBB2 cells in a specimen or sample.\n", "termDef": { "cde_id": 3086980, "cde_version": 1.0, "source": "caDSR", "term": "HER2 ERBB Positive Finding Cell Percentage Category", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0" } }, "her2_erbb2_result_fish": { "description": "the type of outcome for HER2 as determined by an in situ hybridization (ISH) assay.\n", "termDef": { "cde_id": 2854089, "cde_version": 1.0, "source": "caDSR", "term": "Laboratory Procedure HER2/neu in situ Hybridization Outcome Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0" } }, "her2_erbb2_result_ihc": { "description": "Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 by histochemical localization of immunoreactive substances using labeled antibodies as reagents.\n", "termDef": { "cde_id": 2957563, "cde_version": 2.0, "source": "caDSR", "term": "Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0" } }, "hiv_positive": { "description": "Text term to signify whether a physician has diagnosed HIV infection in a patient.\n", "termDef": { "cde_id": 4030799, "cde_version": 1.0, "source": "caDSR", "term": "Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0" } }, "hpv_positive_type": { "description": "Text classification to represent the strain or type of human papillomavirus identified in an individual.\n", "termDef": { "cde_id": 2922649, "cde_version": 1.0, "source": "caDSR", "term": "Human Papillomavirus Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0" } }, "hpv_status": { "description": "The findings of the oncogenic HPV.\n", "termDef": { "cde_id": 2230033, "cde_version": 1.0, "source": "caDSR", "term": "Oncogenic Human Papillomavirus Result Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" } }, "id": "_terms", "includes_spike_ins": { "description": "Spike-in included?\n" }, "initial_weight": { "description": "Numeric value that represents the initial weight of the sample, measured in milligrams.\n", "termDef": { "cde_id": 5432605, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Initial Weight Milligram Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0" } }, "instrument_model": { "description": "Numeric value that represents the sample dimension that is greater than the shortest dimension and less than the longest dimension, measured in millimeters.\n", "termDef": { "cde_id": 5432604, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Intermediate Dimension Millimeter Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" } }, "intermediate_dimension": { "description": "Intermediate dimension of the sample, in millimeters.\n" }, "is_ffpe": { "description": "Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in paraffin (FFPE).\n", "termDef": { "cde_id": 4170557, "cde_version": 1.0, "source": "caDSR", "term": "Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" } }, "is_paired_end": { "description": "Are the reads paired end?\n" }, "last_known_disease_status": { "description": "Text term that describes the last known state or condition of an individual's neoplasm.\n", "termDef": { "cde_id": 5424231, "cde_version": 1.0, "source": "caDSR", "term": "Person Last Known Neoplasm Status", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0" } }, "laterality": { "description": "For tumors in paired organs, designates the side on which the cancer originates.\n", "termDef": { "cde_id": 827, "cde_version": 3.0, "source": "caDSR", "term": "Primary Tumor Laterality", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0" } }, "ldh_level_at_diagnosis": { "description": "The 2 decimal place numeric laboratory value measured, assigned or computed related to the assessment of lactate dehydrogenase in a specimen.\n", "termDef": { "cde_id": 2798766, "cde_version": 1.0, "source": "caDSR", "term": "Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0" } }, "ldh_normal_range_upper": { "description": "The top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for lactate dehydrogenase (units not specified).\n", "termDef": { "cde_id": 2597015, "cde_version": 1.0, "source": "caDSR", "term": "Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" } }, "library_name": { "description": "Name of the library.\n" }, "library_preparation_kit_catalog_number": { "description": "Catalog of Library Preparation Kit\n" }, "library_preparation_kit_name": { "description": "Name of Library Preparation Kit\n" }, "library_preparation_kit_vendor": { "description": "Vendor of Library Preparation Kit\n" }, "library_preparation_kit_version": { "description": "Version of Library Preparation Kit\n" }, "library_selection": { "description": "Library Selection Method\n" }, "library_strand": { "description": "Library stranded-ness.\n" }, "library_strategy": { "description": "Library strategy.\n" }, "longest_dimension": { "description": "Numeric value that represents the longest dimension of the sample, measured in millimeters.\n", "termDef": { "cde_id": 5432602, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Longest Dimension Millimeter Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0" } }, "lymph_nodes_positive": { "description": "The number of lymph nodes involved with disease as determined by pathologic examination.\n", "termDef": { "cde_id": 89, "cde_version": 3.0, "source": "caDSR", "term": "Lymph Node(s) Positive Number", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0" } }, "lymphatic_invasion_present": { "description": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement\n", "termDef": { "cde_id": 64171, "cde_version": 3.0, "source": "caDSR", "term": "Lymphatic/Small vessel Invasion Ind", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" } }, "md5sum": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "method_of_diagnosis": { "description": "The method used to initially the patient's diagnosis.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Method of Diagnosis", "term_url": null } }, "method_of_sample_procurement": { "description": "The method used to procure the sample used to extract analyte(s).\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Method of Sample Procurement", "term_url": null } }, "microsatellite_instability_abnormal": { "description": "The yes/no indicator to signify the status of a tumor for microsatellite instability.\n", "termDef": { "cde_id": 3123142, "cde_version": 1.0, "source": "caDSR", "term": "Microsatellite Instability Occurrence Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0" } }, "morphology": { "description": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.\n", "termDef": { "cde_id": 3226275, "cde_version": 1.0, "source": "caDSR", "term": "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0" } }, "new_event_anatomic_site": { "description": "Text term to specify the anatomic location of the return of tumor after treatment.\n", "termDef": { "cde_id": 3108271, "cde_version": 2.0, "source": "caDSR", "term": "New Neoplasm Event Occurrence Anatomic Site", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0" } }, "new_event_type": { "description": "Text term to identify a new tumor event.\n", "termDef": { "cde_id": 3119721, "cde_version": 1.0, "source": "caDSR", "term": "New Neoplasm Event Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0" } }, "normal_tumor_genotype_snp_match": { "description": "Text term that represents whether or not the genotype of the normal tumor matches or if the data is not available.\n", "termDef": { "cde_id": 4588156, "cde_version": 1.0, "source": "caDSR", "term": "Normal Tumor Genotype Match Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0" } }, "number_proliferating_cells": { "description": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).\n", "termDef": { "cde_id": 5432636, "cde_version": 1.0, "source": "caDSR", "term": "Pathology Review Slide Proliferating Cell Count", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0" } }, "oct_embedded": { "description": "Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound.\n", "termDef": { "cde_id": 5432538, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" } }, "pack_years_smoked": { "description": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.\n", "termDef": { "cde_id": 2955385, "cde_version": 1.0, "source": "caDSR", "term": "Person Cigarette Smoking History Pack Year Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" } }, "percent_eosinophil_infiltration": { "description": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.\n", "termDef": { "cde_id": 2897700, "cde_version": 2.0, "source": "caDSR", "term": "Specimen Eosinophilia Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0" } }, "percent_gc_content": { "description": "The overall %GC of all bases in all sequences.\n", "termDef": { "cde_id": null, "cde_version": null, "source": "FastQC", "term": "%GC", "term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" } }, "percent_granulocyte_infiltration": { "description": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.\n", "termDef": { "cde_id": 2897705, "cde_version": 2.0, "source": "caDSR", "term": "Specimen Granulocyte Infiltration Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0" } }, "percent_inflam_infiltration": { "description": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by reddness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.\n", "termDef": { "cde_id": 2897695, "cde_version": 1.0, "source": "caDSR", "term": "Specimen Inflammation Change Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0" } }, "percent_lymphocyte_infiltration": { "description": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.\n", "termDef": { "cde_id": 2897710, "cde_version": 2.0, "source": "caDSR", "term": "Specimen Lymphocyte Infiltration Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0" } }, "percent_monocyte_infiltration": { "description": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.\n", "termDef": { "cde_id": 5455535, "cde_version": 1.0, "source": "caDSR", "term": "Specimen Monocyte Infiltration Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0" } }, "percent_necrosis": { "description": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.\n", "termDef": { "cde_id": 2841237, "cde_version": 1.0, "source": "caDSR", "term": "Malignant Neoplasm Necrosis Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0" } }, "percent_neutrophil_infiltration": { "description": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.\n", "termDef": { "cde_id": 2841267, "cde_version": 1.0, "source": "caDSR", "term": "Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0" } }, "percent_normal_cells": { "description": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.\n", "termDef": { "cde_id": 2841233, "cde_version": 1.0, "source": "caDSR", "term": "Malignant Neoplasm Normal Cell Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0" } }, "percent_stromal_cells": { "description": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.\n", "termDef": { "cde_id": 2841241, "cde_version": 1.0, "source": "caDSR", "term": "Malignant Neoplasm Stromal Cell Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0" } }, "percent_tumor_cells": { "description": "Numeric value that represents the percentage of infiltration by granulocytes in a sample.\n", "termDef": { "cde_id": 5432686, "cde_version": 1.0, "source": "caDSR", "term": "Specimen Tumor Cell Percentage Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0" } }, "percent_tumor_nuclei": { "description": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.\n", "termDef": { "cde_id": 2841225, "cde_version": 1.0, "source": "caDSR", "term": "Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0" } }, "perineural_invasion_present": { "description": "a yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.\n", "termDef": { "cde_id": 64181, "cde_version": 3.0, "source": "caDSR", "term": "Tumor Perineural Invasion Ind", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" } }, "platform": { "description": "Name of the platform used to obtain data.\n" }, "portion_number": { "description": "Numeric value that represents the sequential number assigned to a portion of the sample.\n", "termDef": { "cde_id": 5432711, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Portion Sequence Number", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0" } }, "portion_weight": { "description": "Numeric value that represents the sample portion weight, measured in milligrams.\n", "termDef": { "cde_id": 5432593, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Portion Weight Milligram Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0" } }, "preservation_method": { "description": "Text term that represents the method used to preserve the sample.\n", "termDef": { "cde_id": 5432521, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Preservation Method Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" } }, "primary_diagnosis": { "description": "Text term for the structural pattern of cancer cells used to define a microscopic diagnosis.\n", "termDef": { "cde_id": 3081934, "cde_version": 3.0, "source": "caDSR", "term": "Neoplasm Histologic Type Name", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3081934&version=3.0" } }, "prior_malignancy": { "description": "Text term to describe the patient's history of prior cancer diagnosis and the spatial location of any previous cancer occurrence.\n", "termDef": { "cde_id": 3382736, "cde_version": 2.0, "source": "caDSR", "term": "Prior Cancer Diagnosis Occurrence Description Text", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0" } }, "prior_treatment": { "description": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.\n", "termDef": { "cde_id": 4231463, "cde_version": 1.0, "source": "caDSR", "term": "Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" } }, "progesterone_receptor_percent_positive_ihc": { "description": "Classification to represent Progesterone Receptor Positive results expressed as a percentage value.\n", "termDef": { "cde_id": 3128342, "cde_version": 1.0, "source": "caDSR", "term": "Progesterone Receptor Level Cell Percentage Category", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0" } }, "progesterone_receptor_result_ihc": { "description": "Text term to represent the overall result of Progresterone Receptor (PR) testing.\n", "termDef": { "cde_id": 2957357, "cde_version": 2.0, "source": "caDSR", "term": "Breast Carcinoma Progesterone Receptor Status", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0" } }, "progression_or_recurrence": { "description": "Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.\n", "termDef": { "cde_id": 3121376, "cde_version": 1.0, "source": "caDSR", "term": "New Neoplasm Event Post Initial Therapy Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" } }, "project_id": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "qc_metric_state": { "description": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.\n", "termDef": { "cde_id": null, "cde_version": null, "source": "FastQC", "term": "QC Metric State", "term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" } }, "race": { "description": "Harmonized race category of participant. Acceptable values: white,american indian or alaska native,black or african american,asian,native hawaiian or other pacific islander,hispanic,multiple,other,Unknown,not reported,not allowed to collect (HARMONIZED)\n", "termDef": { "cde_id": 2192199, "cde_version": 1.0, "source": "caDSR", "term": "Race Category Text", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" } }, "read_group_name": { "description": "The name of the read group.\n" }, "read_length": { "description": "The length of the reads.\n" }, "relationship_age_at_diagnosis": { "description": "The age (in years) when the patient's relative was first diagnosed.\n", "termDef": { "cde_id": 5300571, "cde_version": 1.0, "source": "caDSR", "term": "Relative Diagnosis Age Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0" } }, "relationship_type": { "description": "The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.\n", "termDef": { "cde_id": 2690165, "cde_version": 2.0, "source": "caDSR", "term": "Family Member Relationship Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" } }, "relative_with_cancer_history": { "description": "Indicator to signify whether or not an individual's biological relative has been diagnosed with another type of cancer.\n", "termDef": { "cde_id": 3901752, "cde_version": 1.0, "source": "caDSR", "term": "Other Cancer Biological Relative History Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0" } }, "residual_disease": { "description": "Text terms to describe the status of a tissue margin following surgical resection.\n", "termDef": { "cde_id": 2608702, "cde_version": 1.0, "source": "caDSR", "term": "Surgical Margin Resection Status", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" } }, "sample_type": { "description": "Text term to describe the source of a biospecimen used for a laboratory test.\n", "termDef": { "cde_id": 3111302, "cde_version": 2.0, "source": "caDSR", "term": "Specimen Type Collection Biospecimen Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" } }, "sample_type_id": { "description": "The accompanying sample type id for the sample type.\n" }, "section_location": { "description": "Tissue source of the slide.\n" }, "sequencing_center": { "description": "Name of the center that provided the sequence files.\n" }, "shortest_dimension": { "description": "Numeric value that represents the shortest dimension of the sample, measured in millimeters.\n", "termDef": { "cde_id": 5432603, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Short Dimension Millimeter Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0" } }, "site_of_resection_or_biopsy": { "description": "The third edition of the International Classification of Diseases for Oncology, published in 2000, used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The description of an anatomical region or of a body part. Named locations of, or within, the body. A system of numbered categories for representation of data.\n", "termDef": { "cde_id": 3226281, "cde_version": 1.0, "source": "caDSR", "term": "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" } }, "size_selection_range": { "description": "Range of size selection.\n" }, "smoking_history": { "description": "Category describing current smoking status and smoking history as self-reported by a patient.\n", "termDef": { "cde_id": 2181650, "cde_version": 1.0, "source": "caDSR", "term": "Smoking History", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" } }, "smoking_intensity": { "description": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20\n", "termDef": { "cde_id": 2955385, "cde_version": 1.0, "source": "caDSR", "term": "Person Cigarette Smoking History Pack Year Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" } }, "source_center": { "description": "Name of the center that provided the item.\n" }, "spectrophotometer_method": { "description": "Name of the method used to determine the concentration of purified nucleic acid within a solution.\n", "termDef": { "cde_id": 3008378, "cde_version": 1.0, "source": "caDSR", "term": "Purification Nucleic Acid Solution Concentration Determination Method Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" } }, "spike_ins_concentration": { "description": "Spike in concentration.\n" }, "spike_ins_fasta": { "description": "Name of the FASTA file that contains the spike-in sequences.\n" }, "state": { "description": "The current state of the object.\n" }, "target_capture_kit_catalog_number": { "description": "Catalog of Target Capture Kit.\n" }, "target_capture_kit_name": { "description": "Name of Target Capture Kit.\n" }, "target_capture_kit_target_region": { "description": "Target Capture Kit BED file.\n" }, "target_capture_kit_vendor": { "description": "Vendor of Target Capture Kit.\n" }, "target_capture_kit_version": { "description": "Version of Target Capture Kit.\n" }, "therapeutic_agents": { "description": "Text identification of the individual agent(s) used as part of a prior treatment regimen.\n", "termDef": { "cde_id": 2975232, "cde_version": 1.0, "source": "caDSR", "term": "Prior Therapy Regimen Text", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0" } }, "time_between_clamping_and_freezing": { "description": "Numeric representation of the elapsed time between the surgical clamping of blood supply and freezing of the sample, measured in minutes.\n", "termDef": { "cde_id": 5432611, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Clamping and Freezing Elapsed Minute Time", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0" } }, "time_between_excision_and_freezing": { "description": "Numeric representation of the elapsed time between the excision and freezing of the sample, measured in minutes.\n", "termDef": { "cde_id": 5432612, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Excision and Freezing Elapsed Minute Time", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0" } }, "tissue_or_organ_of_origin": { "description": "Text term that describes the anatomic site of the tumor or disease.\n", "termDef": { "cde_id": 3427536, "cde_version": 3.0, "source": "caDSR", "term": "Tumor Disease Anatomic Site", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0" } }, "tissue_type": { "description": "Text term that represents a description of the kind of tissue collected with respect to disease status or proximity to tumor tissue.\n", "termDef": { "cde_id": 5432687, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Description Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" } }, "to_trim_adapter_sequence": { "description": "Does the user suggest adapter trimming?\n" }, "tobacco_smoking_onset_year": { "description": "The year in which the participant began smoking.\n", "termDef": { "cde_id": 2228604, "cde_version": 1.0, "source": "caDSR", "term": "Started Smoking Year", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0" } }, "tobacco_smoking_quit_year": { "description": "The year in which the participant quit smoking.\n", "termDef": { "cde_id": 2228610, "cde_version": 1.0, "source": "caDSR", "term": "Stopped Smoking Year", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0" } }, "tobacco_smoking_status": { "description": "Category describing current smoking status and smoking history as self-reported by a patient.\n", "termDef": { "cde_id": 2181650, "cde_version": 1.0, "source": "caDSR", "term": "Patient Smoking History Category", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" } }, "total_sequences": { "description": "A count of the total number of sequences processed.\n", "termDef": { "cde_id": null, "cde_version": null, "source": "FastQC", "term": "Total Sequences", "term_url": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" } }, "treatment_anatomic_site": { "description": "The anatomic site or field targeted by a treatment regimen or single agent therapy.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Treatment Anatomic Site", "term_url": null } }, "treatment_intent_type": { "description": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]\n", "termDef": { "cde_id": 2793511, "cde_version": 1.0, "source": "caDSR", "term": "Treatment Regimen Intent Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0" } }, "treatment_or_therapy": { "description": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.\n", "termDef": { "cde_id": 4231463, "cde_version": 1.0, "source": "caDSR", "term": "Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" } }, "treatment_outcome": { "description": "Text term that describes the patient\u00bfs final outcome after the treatment was administered.\n", "termDef": { "cde_id": 5102383, "cde_version": 1.0, "source": "caDSR", "term": "Treatment Outcome Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0" } }, "treatment_type": { "description": "Text term that describes the kind of treatment administered.\n", "termDef": { "cde_id": 5102381, "cde_version": 1.0, "source": "caDSR", "term": "Treatment Method Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" } }, "tumor_code": { "description": "Diagnostic tumor code of the tissue sample source.\n" }, "tumor_code_id": { "description": "BCR-defined id code for the tumor sample.\n" }, "tumor_descriptor": { "description": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.\n", "termDef": { "cde_id": 3288124, "cde_version": 1.0, "source": "caDSR", "term": "Tumor Tissue Disease Description Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" } }, "tumor_grade": { "description": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.\n", "termDef": { "cde_id": 2785839, "cde_version": 2.0, "source": "caDSR", "term": "Neoplasm Histologic Grade", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" } }, "tumor_stage": { "description": "The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether lymph nodes contain cancer, and whether the cancer has spread from the original site to other parts of the body. The accepted values for tumor_stage depend on the tumor site, type, and accepted staging system. These items should accompany the tumor_stage value as associated metadata.\n", "termDef": { "cde_id": "C16899", "cde_version": null, "source": "NCIt", "term": "Tumor Stage", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" } }, "vascular_invasion_present": { "description": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.\n", "termDef": { "cde_id": 64358, "cde_version": 3.0, "source": "caDSR", "term": "Tumor Vascular Invasion Ind-3", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0" } }, "vital_status": { "description": "The survival state of the person registered on the protocol.\n", "termDef": { "cde_id": 5, "cde_version": 5.0, "source": "caDSR", "term": "Patient Vital Status", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" } }, "weight": { "description": "Body weight at baseline. (kg) (HARMONIZED).\n", "termDef": { "cde_id": 651, "cde_version": 4.0, "source": "caDSR", "term": "Patient Weight Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" } }, "well_number": { "description": "Numeric value that represents the the well location within a plate for the analyte or aliquot from the sample.\n", "termDef": { "cde_id": 5432613, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Analyte or Aliquot Plate Well Number", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0" } }, "workflow_type": { "description": "Generic name for the workflow used to analyze a data set.\n" }, "year_of_birth": { "description": "Numeric value to represent the calendar year in which an individual was born.\n", "termDef": { "cde_id": 2896954, "cde_version": 1.0, "source": "caDSR", "term": "Year Birth Date Number", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" } }, "year_of_death": { "description": "Numeric value to represent the year of the death of an individual.\n", "termDef": { "cde_id": 2897030, "cde_version": 1.0, "source": "caDSR", "term": "Year Death Number", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" } }, "year_of_diagnosis": { "description": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.\n", "termDef": { "cde_id": 2896960, "cde_version": 1.0, "source": "caDSR", "term": "Year of initial pathologic diagnosis", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" } }, "years_smoked": { "description": "Numeric value (or unknown) to represent the number of years a person has been smoking (HARMONIZED). If the number of years is greater than 89, see 'years_smoked_gt89'.\n", "termDef": { "cde_id": 3137957, "cde_version": 1.0, "source": "caDSR", "term": "Person Smoking Duration Year Count", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" } }, "years_smoked_gt89": { "description": "Indicate whether the numeric value to represent the number of years a person has been smoking (HARMONIZED) is greater than 89 years.\n", "termDef": { "cde_id": 3137957, "cde_version": 1.0, "source": "caDSR", "term": "Person Smoking Duration Year Count", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" } } }, "acknowledgement": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "administrative", "description": "Acknowledgement of an individual involved in a project.", "id": "acknowledgement", "links": [ { "backref": "acknowledgements", "label": "contribute_to", "multiplicity": "many_to_many", "name": "projects", "required": true, "target_type": "project" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "acknowledgee": { "description": "The indvidiual or group being acknowledged by the project.", "type": "string" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "type": "string" }, "projects": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "type": [ "string", "null" ] }, "type": { "enum": [ "acknowledgement" ] }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "projects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Acknowledgement", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "aligned_reads": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Data file containing aligned reads that are generated internally by the GDC.\n", "id": "aligned_reads", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "aligned_reads_files", "label": "data_from", "multiplicity": "many_to_one", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" }, { "backref": "aligned_reads_files", "label": "data_from", "multiplicity": "many_to_one", "name": "alignment_cocleaning_workflows", "required": false, "target_type": "alignment_cocleaning_workflow" }, { "backref": "aligned_reads_files", "label": "data_from", "multiplicity": "many_to_one", "name": "alignment_workflows", "required": false, "target_type": "alignment_workflow" }, { "backref": "aligned_reads_files", "label": "matched_to", "multiplicity": "one_to_many", "name": "submitted_unaligned_reads_files", "required": false, "target_type": "submitted_unaligned_reads" }, { "backref": "aligned_reads_files", "label": "matched_to", "multiplicity": "one_to_one", "name": "submitted_aligned_reads_files", "required": false, "target_type": "submitted_aligned_reads" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "alignment_cocleaning_workflows": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "alignment_workflows": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Sequencing Data", "Sequencing Reads", "Raw Sequencing Data" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "BAM", "CRAM" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Aligned Reads" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "experimental_strategy": { "enum": [ "WGS", "WXS", "Low Pass WGS", "Validation", "RNA-Seq", "miRNA-Seq", "Total RNA-Seq", "scRNA-Seq" ], "term": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "platform": { "enum": [ "Illumina", "SOLiD", "LS454", "Ion Torrent", "Complete Genomics", "PacBio", "Other", "Affymetrix" ], "term": { "description": "Name of the platform used to obtain data.\n" } }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitted_aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitted_unaligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "experimental_strategy", "platform" ], "submittable": false, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Aligned Reads", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "aligned_reads_index": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "index_file", "description": "Data file containing the index for a set of aligned reads.", "id": "aligned_reads_index", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "aligned_reads_indexes", "label": "derived_from", "multiplicity": "one_to_one", "name": "submitted_aligned_reads_files", "required": false, "target_type": "submitted_aligned_reads" }, { "backref": "aligned_reads_indexes", "label": "derived_from", "multiplicity": "one_to_one", "name": "aligned_reads_files", "required": false, "target_type": "aligned_reads" } ] }, { "backref": "aligned_reads_indexes", "label": "data_from", "multiplicity": "many_to_many", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Sequencing Data", "Sequencing Reads", "Raw Sequencing Data" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "BAI", "CRAI" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Aligned Reads Index" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitted_aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Aligned Reads Index", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "alignment_cocleaning_workflow": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "analysis", "description": "Metadata for the alignment and cocleaning pipeline used to align reads in the GDC harmonization pipelines.\n", "id": "alignment_cocleaning_workflow", "links": [ { "exclusive": true, "required": true, "subgroup": [ { "backref": "alignment_cocleaning_workflows", "label": "performed_on", "multiplicity": "one_to_many", "name": "submitted_aligned_reads_files", "required": false, "target_type": "submitted_aligned_reads" }, { "backref": "alignment_cocleaning_workflows", "label": "performed_on", "multiplicity": "one_to_many", "name": "submitted_unaligned_reads_files", "required": false, "target_type": "submitted_unaligned_reads" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitted_aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitted_unaligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_end_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_link": { "description": "Link to Github hash for the CWL workflow used.", "type": "string" }, "workflow_start_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_type": { "enum": [ "BWA with Mark Duplicates and Cocleaning" ], "term": { "description": "Generic name for the workflow used to analyze a data set.\n" } }, "workflow_version": { "description": "Major version for a GDC workflow.", "type": "string" } }, "required": [ "type", "submitter_id", "workflow_link", "workflow_type" ], "submittable": false, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state" ], "title": "Alignment Cocleaning Workflow", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "alignment_workflow": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "analysis", "description": "Metadata for the alignment pipeline used to align reads in the GDC harmonization pipelines.\n", "id": "alignment_workflow", "links": [ { "exclusive": true, "required": true, "subgroup": [ { "backref": "alignment_workflows", "label": "performed_on", "multiplicity": "one_to_many", "name": "submitted_aligned_reads_files", "required": false, "target_type": "submitted_aligned_reads" }, { "backref": "alignment_workflows", "label": "performed_on", "multiplicity": "one_to_many", "name": "submitted_unaligned_reads_files", "required": false, "target_type": "submitted_unaligned_reads" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitted_aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitted_unaligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_end_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_link": { "description": "Link to Github hash for the CWL workflow used.", "type": "string" }, "workflow_start_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_type": { "enum": [ "STAR", "BWA-aln", "BWA-mem", "spinnaker" ] }, "workflow_version": { "description": "Major version for a GDC workflow.", "type": "string" } }, "required": [ "type", "submitter_id", "workflow_type" ], "submittable": false, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state" ], "title": "Alignment Workflow", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "aliquot": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "biospecimen", "constraints": null, "description": "Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight.\n", "id": "aliquot", "links": [ { "backref": "aliquots", "label": "derived_from", "multiplicity": "many_to_many", "name": "samples", "required": true, "target_type": "sample" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "aliquot_quantity": { "term": { "description": "The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Biospecimen Aliquot Quantity", "term_url": null } }, "type": "number" }, "aliquot_volume": { "term": { "description": "The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization.\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Biospecimen Aliquot Volume", "term_url": null } }, "type": "number" }, "amount": { "term": { "description": "Weight in grams or volume in mL.\n" }, "type": "number" }, "analyte_isolation_batch_id": { "description": "Nucleic acid isolation batch ID\n", "type": "string" }, "analyte_isolation_date": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "analyte_isolation_method": { "description": "Type of nucleic acid isolation batch\n", "type": "string" }, "analyte_type": { "term": { "description": "Text term that represents the kind of molecular specimen analyte.\n", "termDef": { "cde_id": 2513915, "cde_version": 2.0, "source": "caDSR", "term": "Molecular Specimen Type Text Name", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" } }, "type": "string" }, "concentration": { "term": { "description": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.\n", "termDef": { "cde_id": 5432594, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" } }, "type": "number" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "exclude": { "description": "Samples flagged for removal from analysis\n", "type": "boolean" }, "exclusion_criteria": { "description": "Additional remarks about flagged samples\n", "type": "string" }, "experiment_batch_id": { "description": "Genotype or expression batch ID\n", "type": "string" }, "experiment_date": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "experimental_strategy": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n", "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "samples": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "samples", "experimental_strategy" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Aliquot", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": [] }, "analyte": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "biospecimen", "description": "Any aspect of an aliquot used in an analysis or assay to characterize the sample. These aspects range from molecules, such as DNA and RNA, that can be extracted from the aliquot to general descriptions of the aliquot's components, such as cell count and morphology.\n", "id": "analyte", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "analytes", "label": "derived_from", "multiplicity": "many_to_many", "name": "aliquots", "required": false, "target_type": "aliquot" }, { "backref": "analytes", "label": "analyzed_for", "multiplicity": "many_to_many", "name": "studies", "required": false, "target_type": "study" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "aliquots": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "analyte_isolation_method": { "description": "The name or general description of the method used to isolate the analyte. Alternatively, if you have provided a protocol, put the file_name here.\n", "type": "string" }, "analyte_type": { "enum": [ "DNA", "RNA", "Peptide", "Protein", "Morphology", "Cell Count" ], "term": { "description": "Text term that represents the kind of molecular specimen analyte.\n", "termDef": { "cde_id": 2513915, "cde_version": 2.0, "source": "caDSR", "term": "Molecular Specimen Type Text Name", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" } } }, "cell_identifier": { "description": "The identifying name or number for the cell being identified.\n", "type": "string" }, "cell_type": { "description": "In the case of single cell analysis, this is the type of cell being analyzed.\n", "enum": [ "All CTC Populations", "Apoptotic CTC", "Biomarker Positive All CTC Populations", "Biomarker Positive Traditional CTC", "Cytokeratin Negative CTC", "Cytokeratin Negative CTC Cluster", "Cytokeratin Positive CTC", "Cytokeratin Positive CTC Cluster", "Nucleated Cell", "Small CTC", "Small CTC Cluster", "Traditional CTC", "Traditional CTC Cluster", "White Blood Cell" ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "days_to_assay": { "description": "The amount of time, in days, between the date used for index and the assay used to address this analyte.\n", "type": "integer" }, "frame_identifier": { "description": "In an analysis of a slide, the frame denotes the region of the slide that is being examined. Within a frame are multiple cells.\n", "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "llod": { "description": "The lower limit of detection. The lowest quantity of a substance that can be distinguished from the absence of that substance (a blank value) within a stated confidence limit (generally 1%). If the lower limit of detection is not a number ('WT', for example), see 'llod_other'.", "type": "number" }, "llod_other": { "description": "If the lower limit of detection is not a number (for example, 'WT'), enter the text here.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "run_identifier": { "description": "The identifier given to the run during which this particular analyte was tested or evaluated. If you analyze multiple analytes through the same experimentation run, this is a good way to keep track.\n", "type": "string" }, "sensitivity": { "description": "The true positive rate. If this value is not a number ('WT', for example), see 'sensitivity_other'.", "type": "number" }, "sensitivity_other": { "description": "If the true positive rate is not a numnber (for example, 'WT'), enter the text here.", "type": "string" }, "specificity": { "description": "The true negative rate. If this value is not a number ('WT', for example), see 'specificty_other'.", "type": "number" }, "specificity_other": { "description": "If the true negative rate is something other than a number (for example, 'WT'), enter the text here.", "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "studies": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "submitter_id", "type", "analyte_type", "analyte_isolation_method" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Analyte", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "blood_pressure_test": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "Resting blood pressure will be measured in the right arm after five minutes in the seated position. An automated oscillometric method (Dinamap) and appropriate cuff size will be used. Three readings will be taken; the second and third readings will be averaged to obtain the blood pressure levels used in analyses. An additional systolic blood pressure will be measured in both the right and left brachial, posterior tibial, and dorsalis pedis arteries with a Doppler instrument. \n", "id": "blood_pressure_test", "links": [ { "backref": "blood_pressure_test", "label": "describes", "multiplicity": "many_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "http://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "age_at_bp_diastolic": { "description": "age at measurement of bp_diastolic (years) (HARMONIZED)\n", "type": "number" }, "age_at_bp_systolic": { "description": "age at measurement of bp_systolic (years) (HARMONIZED)\n", "type": "number" }, "bp_diastolic": { "description": "Resting diastolic blood pressure from the upper arm in a clinical setting. (mmHg) (HARMONIZED)\n", "type": "number" }, "bp_systolic": { "description": "Resting systolic blood pressure from the upper arm in a clinical setting. (mmHg) (HARMONIZED)\n", "type": "number" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "unit_bp_diastolic": { "description": "harmonization unit for bp_diastolic (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.)\n", "type": "string" }, "unit_bp_systolic": { "description": "harmonization unit for bp_systolic (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "submitter_id", "type", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Blood Pressure Test", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "cardiac_mri": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "Cardiac MRI used to obtain measures of left ventricular mass, wall thickness, ejection fraction, cardiac output, aortic atherosclerosis, and aortic distensibility.\n", "id": "cardiac_mri", "links": [ { "backref": "cardiac_mris", "label": "describes", "multiplicity": "one_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "http://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "cardiac_output": { "description": "RV Cardiac output (l/min) (HARMONIZED)\n", "type": "number" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "submitter_id", "type", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Cardiac Magnetic Resonance Image", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "core_metadata_collection": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "administrative", "description": "Structured description of a collection of several dataset\n", "id": "core_metadata_collection", "links": [ { "backref": "core_metadata_collections", "label": "data_from", "multiplicity": "many_to_one", "name": "projects", "required": true, "target_type": "project" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "contributor": { "description": "An entity responsible for making contributions to the resource. Examples of a Contributor include a person, an organization, or a service. Typically, the name of a Contributor should be used to indicate the entity.\n", "type": "string" }, "coverage": { "description": "The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant. Spatial topic and spatial applicability may be a named place or a location specified by its geographic coordinates. Temporal topic may be a named period, date, or date range. A jurisdiction may be a named administrative entity or a geographic place to which the resource applies. Recommended best practice is to use a controlled vocabulary such as the Thesaurus of Geographic Names [TGN] (http://www.getty.edu/research/tools/vocabulary/tgn/index.html). Where appropriate, named places or time periods can be used in preference to numeric identifiers such as sets of coordinates or date ranges.\n", "type": "string" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "creator": { "description": "An entity primarily responsible for making the resource. Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.\n", "type": "string" }, "data_type": { "description": "The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMITYPE]. To describe the file format, physical medium, or dimensions of the resource, use the Format element.\n", "type": "string" }, "date": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "description": { "description": "An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.\n", "type": "string" }, "format": { "description": "The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/).\n", "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "language": { "description": "A language of the resource. Recommended best practice is to use a controlled vocabulary such as RFC 4646 (http://www.ietf.org/rfc/rfc4646.txt).\n", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "projects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "publisher": { "description": "An entity responsible for making the resource available. Examples of a Publisher include a person, an organization, or a service. Typically, the name of a Publisher should be used to indicate the entity.\n", "type": "string" }, "relation": { "description": "A related resource. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.\u00a0\n", "type": "string" }, "rights": { "description": "Information about rights held in and over the resource. Typically, rights information includes a statement about various property rights associated with the resource, including intellectual property rights.\n", "type": "string" }, "source": { "description": "A related resource from which the described resource is derived. The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.\n", "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subject": { "description": "The topic of the resource. Typically, the subject will be represented using keywords, key phrases, or classification codes. Recommended best practice is to use a controlled vocabulary.\n", "type": "string" }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "title": { "description": "A name given to the resource. Typically, a Title will be a name by which the resource is formally known.\n", "type": "string" }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "submitter_id", "type", "projects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Core Metadata Collection", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "data_release": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "internal", "description": "Internal node to store different data releases.\n", "id": "data_release", "links": [ { "backref": "data_releases", "label": "describes", "multiplicity": "many_to_one", "name": "roots", "required": true, "target_type": "root" } ], "namespace": "http://gdc.nci.nih.gov", "program": "*", "project": "*", "properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "major_version": { "description": "The number identifying the major version.\n", "type": "integer" }, "minor_version": { "description": "The number identifying the minor version.\n", "type": "integer" }, "name": { "description": "String representing release name.\n", "type": "string" }, "release_date": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "released": { "default": false, "description": "Indicates if it is the current release.\n", "type": "boolean" }, "roots": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "type": { "enum": [ "data_release" ] }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "name", "major_version", "minor_version", "type" ], "submittable": false, "systemProperties": [ "id", "created_datetime", "updated_datetime" ], "title": "Data Release", "type": "object", "uniqueKeys": [ [ "id" ] ], "validators": null }, "demographic": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "Data for the characterization of the patient by means of segementing the population (e.g., characterization by age, sex, or race).\n", "id": "demographic", "links": [ { "backref": "demographics", "label": "describes", "multiplicity": "one_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "age_at_bmi_baseline": { "description": "age at measurement of bmi (years) (HARMONIZED)\n", "type": "number" }, "age_at_height_baseline": { "description": "age at measurement of height_baseline (years) (HARMONIZED)\n", "type": "number" }, "age_at_index": { "description": "The subject's age (in years) on the reference or anchor date used during date obfuscation (HARMONIZED). If age is greater than 89 years, see 'age_at_index_gt89'.\n", "maximum": 89, "minimum": 0, "type": "number" }, "age_at_index_gt89": { "description": "Indicate whether the subject's age (in years) on the reference or anchor date used during date obfuscation (HARMONIZED) is greater than 89 years.\n", "enum": [ "Yes", "No" ] }, "age_at_weight_baseline": { "description": "age at measurement of weight_baseline (years) (HARMONIZED)\n", "type": "number" }, "annotated_sex": { "enum": [ "female", "male", "unknown", "unspecified", "not reported" ], "term": { "description": "Subject sex, as recorded by the study. (HARMONIZED)\n", "termDef": { "cde_id": 2200604, "cde_version": 3.0, "source": "caDSR", "term": "Person Gender Text Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" } } }, "bmi_baseline": { "term": { "description": "Body mass index calculated at baseline. (kg/m^2) (HARMONIZED)\n", "termDef": { "cde_id": 4973892, "cde_version": 1.0, "source": "caDSR", "term": "Body Mass Index (BMI)", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" } }, "type": "number" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "ethnicity": { "enum": [ "hispanic or latino", "inconsistent/contradictory", "not hispanic or latino", "Unknown", "not reported", "not allowed to collect" ], "term": { "description": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino (HARMONIZED). The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.\n", "termDef": { "cde_id": 2192217, "cde_version": 2.0, "source": "caDSR", "term": "Ethnic Group Category Text", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" } } }, "height_baseline": { "term": { "description": "Body height at baseline. (cm) (HARMONIZED)\n", "termDef": { "cde_id": 649, "cde_version": 4.1, "source": "caDSR", "term": "Patient Height Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" } }, "type": "number" }, "hispanic_subgroup": { "description": "classification of Hispanic/Latino background for Hispanic/Latino subjects where country or region of origin information is available (HARMONIZED)\n", "enum": [ "CentralAmerican", "CostaRican", "Cuban", "Dominican", "Mexican", "PuertoRican", "SouthAmerican", "Multiple" ] }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "population": { "description": "CHB Han Chinese in Beijing, China EAS; JPT Japanese in Tokyo, Japan EAS; CHS Southern Han Chinese EAS; CDX Chinese Dai in Xishuangbanna, China EAS; KHV Kinh in Ho Chi Minh City, Vietnam EAS; CEU Utah Residents (CEPH) with Northern and Western European Ancestry EUR; TSI Toscani in Italia EUR; FIN Finnish in Finland EUR; GBR British in England and Scotland EUR; IBS Iberian Population in Spain EUR; YRI Yoruba in Ibadan, Nigeria AFR; LWK Luhya in Webuye, Kenya AFR; GWD Gambian in Western Divisions in the Gambia AFR; MSL Mende in Sierra Leone AFR; ESN Esan in Nigeria AFR; ASW Americans of African Ancestry in SW USA AFR; ACB African Caribbeans in Barbados AFR; MXL Mexican Ancestry from Los Angeles USA AMR; PUR Puerto Ricans from Puerto Rico AMR; CLM Colombians from Medellin, Colombia AMR; PEL Peruvians from Lima, Peru AMR; GIH Gujarati Indian from Houston, Texas SAS; PJL Punjabi from Lahore, Pakistan SAS; BEB Bengali from Bangladesh SAS; STU Sri Lankan Tamil from the UK SAS; ITU Indian Telugu from the UK\n", "enum": [ "CHB", "JPT", "CHS", "CDX", "KHV", "CEU", "TSI", "FIN", "GBR", "IBS", "YRI", "LWK", "GWD", "MSL", "ESN", "ASW", "ACB", "MXL", "PUR", "CLM", "PEL", "GIH", "PJL", "BEB", "STU", "ITU", "other", "Unknown", "not reported", "not allowed to collect" ] }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "race": { "description": "Harmonized race category of participant. Acceptable values: white,american indian or alaska native,black or african american,asian,native hawaiian or other pacific islander,hispanic,multiple,other,Unknown,not reported,not allowed to collect (HARMONIZED)\n", "items": { "enum": [ "white", "american indian or alaska native", "black or african american", "asian", "native hawaiian or other pacific islander", "hispanic", "multiple", "other", "Unknown", "not reported", "not allowed to collect" ] }, "term": { "description": "Harmonized race category of participant. Acceptable values: white,american indian or alaska native,black or african american,asian,native hawaiian or other pacific islander,hispanic,multiple,other,Unknown,not reported,not allowed to collect (HARMONIZED)\n", "termDef": { "cde_id": 2192199, "cde_version": 1.0, "source": "caDSR", "term": "Race Category Text", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" } }, "type": "array" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subcohort": { "description": "A distinct subgroup within a study, generally indicating subjects who share similar characteristics due to study design. Subjects may belong to only one subcohort. (HARMONIZED)\n", "enum": [ "Amish_HAPI", "Amish_Longevity", "Amish_Wellness", "ARIC_NoSubcohortStructure", "CARDIA_NoSubcohortStructure", "CFS_NoSubcohortStructure", "CHS_AfricanAmerican", "CHS_Original", "COPDGene_NoSubcohortStructure", "CRA_NoSubcohortStructure", "FHS_Gen3", "FHS_NewOffspringSpouse", "FHS_Offspring", "FHS_Omni1", "FHS_Omni2", "FHS_Original", "GENOA_AfricanAmerican", "GENOA_EuropeanAmerican", "GOLDN_NoSubcohortStructure", "HCHS_SOL_NoSubcohortStructure", "HVH_NoSubcohortStructure", "JHS_NoSubcohortStructure", "Mayo_VTE_GENEVA", "MESA_AirNR", "MESA_Classic", "MESA_Family", "SAS_NoSubcohortStructure", "WHI_ClinicalTrial", "WHI_ObservationalStudy" ] }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "unit_annotated_sex": { "description": "harmonization unit for annotated_sex (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_bmi_baseline": { "description": "harmonization unit for bmi_baseline (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_ethnicity": { "description": "harmonization unit for ethnicity (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_height_baseline": { "description": "harmonization unit for height_baseline (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_hispanic_subgroup": { "description": "harmonization unit for hispanic_subgroup (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_race": { "description": "harmonization unit for race (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_subcohort": { "description": "harmonization unit for subcohort (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_weight_baseline": { "description": "harmonization unit for weight_baseline (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "weight": { "term": { "description": "Body weight at baseline. (kg) (HARMONIZED).\n", "termDef": { "cde_id": 651, "cde_version": 4.0, "source": "caDSR", "term": "Patient Weight Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" } }, "type": "number" }, "weight_baseline": { "description": "Body weight at baseline. (kg) (HARMONIZED)\n", "type": "number" } }, "required": [ "type", "submitter_id", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Demographic", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "electrocardiogram_test": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "A 12-lead ECG will be obtained and transmitted to the ECG Reading Center via telephone lines for Minnesota coding.\n", "id": "electrocardiogram_test", "links": [ { "backref": "electrocardiogram_tests", "label": "describes", "multiplicity": "one_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "http://dcp.bionimbus.org", "program": "*", "project": "*", "properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "gtc_duration": { "description": "QTC interval (msec) (HARMONIZED)\n", "type": "number" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "pr_duration": { "description": "PR interval (msec) (HARMONIZED)\n", "type": "number" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "qrs_duration": { "description": "QRS interval (msec) (HARMONIZED)\n", "type": "number" }, "qt_duration": { "description": "QT interval (msec) (HARMONIZED)\n", "type": "number" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "submitter_id", "type", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Electrocardiogram", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "exposure": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "Clinically relevant patient information not immediately resulting from genetic predispositions.\n", "id": "exposure", "links": [ { "backref": "exposures", "label": "describes", "multiplicity": "many_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "http://dcp.bionimbus.org/", "preferred": [ "cigarettes_per_day", "years_smoked" ], "program": "*", "project": "*", "properties": { "age_at_current_smoker_baseline": { "description": "age at measurement of current_smoker_baseline (years) (HARMONIZED)\n", "type": "number" }, "age_at_ever_smoker_baseline": { "description": "age at measurement of ever_smoker_baseline (years) (HARMONIZED)\n", "type": "number" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "current_smoker_baseline": { "description": "Indicates whether subject currently smokes cigarettes. (HARMONIZED)\n", "type": "boolean" }, "ever_smoker_baseline": { "description": "Indicates whether subject ever regularly smoked cigarettes. (HARMONIZED)\n", "enum": [ "Never a cigarette smoker", "Current or former cigarette smoker" ] }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "smoking_status": { "description": "Smoking condition (HARMONIZED)\n", "enum": [ "NEVER", "FORMER", "CURRENT" ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "unit_current_smoker_baseline": { "description": "harmonization unit for current_smoker_baseline (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_ever_smoker_baseline": { "description": "harmonization unit for ever_smoker_baseline (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "years_smoked": { "maximum": 89, "minimum": 0, "term": { "description": "Numeric value (or unknown) to represent the number of years a person has been smoking (HARMONIZED). If the number of years is greater than 89, see 'years_smoked_gt89'.\n", "termDef": { "cde_id": 3137957, "cde_version": 1.0, "source": "caDSR", "term": "Person Smoking Duration Year Count", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" } }, "type": [ "number", "null" ] }, "years_smoked_gt89": { "enum": [ "Yes", "No" ], "term": { "description": "Indicate whether the numeric value to represent the number of years a person has been smoking (HARMONIZED) is greater than 89 years.\n", "termDef": { "cde_id": 3137957, "cde_version": 1.0, "source": "caDSR", "term": "Person Smoking Duration Year Count", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" } } } }, "required": [ "type", "submitter_id", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Exposure", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "germline_mutation_calling_workflow": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "analysis", "description": "Metadata for the germline mutation calling pipeline used to call variants in the GDC DNA-Seq pipelines.\n", "id": "germline_mutation_calling_workflow", "links": [ { "exclusive": true, "required": true, "subgroup": [ { "backref": "germline_mutation_calling_workflows", "label": "performed_on", "multiplicity": "many_to_many", "name": "submitted_aligned_reads_files", "required": false, "target_type": "submitted_aligned_reads" }, { "backref": "germline_mutation_calling_workflows", "label": "performed_on", "multiplicity": "many_to_many", "name": "aligned_reads_files", "required": false, "target_type": "aligned_reads" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitted_aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_end_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_link": { "description": "Link to Github hash for the CWL workflow used.", "type": "string" }, "workflow_start_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "workflow_type": { "enum": [ "HaplotypeCaller" ], "term": { "description": "Generic name for the workflow used to analyze a data set.\n" } }, "workflow_version": { "description": "Major version for a GDC workflow.", "type": "string" } }, "required": [ "type", "submitter_id", "workflow_link", "workflow_type" ], "submittable": false, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state" ], "title": "Germline Mutation Calling Workflow", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "germline_variation_index": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "index_file", "description": "Data file containing the index for a set of germline variants.", "id": "germline_variation_index", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "germline_variation_indexes", "label": "derived_from", "multiplicity": "one_to_one", "name": "simple_germline_variations", "required": false, "target_type": "simple_germline_variation" }, { "backref": "germline_variation_indexes", "label": "data_from", "multiplicity": "many_to_many", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" } ] } ], "namespace": "https://dcp.bionimbus.org", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Simple Nucleotide Variation" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "TBI", "CSI" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Germline Variation Index" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "simple_germline_variations": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Germline Variation Index", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "imaging_file": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Data file containing raw imaging data\n", "id": "imaging_file", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "imaging_files", "label": "data_from", "multiplicity": "many_to_one", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" }, { "backref": "imaging_files", "label": "data_from", "multiplicity": "many_to_one", "name": "subjects", "required": false, "target_type": "subject" } ] } ], "namespace": "https://niaid.bionimbus.org", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "term": { "description": "Broad categorization of the contents of the data file.\n" }, "type": "string" }, "data_format": { "term": { "description": "Format of the data files.\n" }, "type": "string" }, "data_type": { "term": { "description": "Specific content type of the data file.\n" }, "type": "string" }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "experimental_strategy": { "term": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n" }, "type": "string" }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_phase": { "description": "The image file's data release Phase for a particular study. \n", "type": "integer" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "image_quality": { "description": "Good, poor, or average image quality\n", "enum": [ "Good image quality", "Average image quality", "Poor image quality", "Not Reported" ] }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "series_instance_number": { "description": "order number for this image or other content.\n", "type": "integer" }, "series_instance_uid": { "description": "Formal identifier for this image or other content.\n", "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "experimental_strategy" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Imaging File", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "imaging_file_reference": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Reference data file for raw imaging data\n", "id": "imaging_file_reference", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "imaging_file_references", "label": "data_from", "multiplicity": "many_to_one", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" }, { "backref": "imaging_file_references", "label": "data_from", "multiplicity": "many_to_many", "name": "imaging_files", "required": false, "target_type": "imaging_file" } ] } ], "namespace": "https://gen3.biodatacatalyst.nhlbi.nih.gov/", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "term": { "description": "Broad categorization of the contents of the data file.\n" }, "type": "string" }, "data_format": { "term": { "description": "Format of the data files.\n" }, "type": "string" }, "data_type": { "term": { "description": "Specific content type of the data file.\n" }, "type": "string" }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "imaging_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime", "file_state", "error_type" ], "title": "Imaging File Reference", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "lab_result": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "Measurements obtained from blood or other laboratory tests required by a medical professional. These will include lipids and lipid metabolism parameters, lipid oxidation markers, cytokines, adhesion molecules, nitric oxide, and hemostasis/fibrinolysis markers.\n", "id": "lab_result", "links": [ { "backref": "lab_results", "label": "describes", "multiplicity": "one_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "http://dcp.bionimbus.org", "program": "*", "project": "*", "properties": { "age_at_basophil_ncnc_bld": { "description": "age at measurement of basophil_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_eosinophil_ncnc_bld": { "description": "age at measurement of eosinophil_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_hdl": { "description": "age at measurement of hdl (years) (HARMONIZED)\n", "type": "number" }, "age_at_hematocrit_vfr_bld": { "description": "Measurement of hematocrit, the fraction of volume (vfr) of blood (bld) that is composed of red blood cells. (years) (HARMONIZED)\n", "type": "number" }, "age_at_hemoglobin_mcnc_bld": { "description": "age at measurement of hemoglobin_mcnc_bld. (years) (HARMONIZED)\n", "type": "number" }, "age_at_ldl": { "description": "age at measurement of ldl (years) (HARMONIZED)\n", "type": "number" }, "age_at_lymphocyte_ncnc_bld": { "description": "age at measurement of lymphocyte_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_mch_entmass_rbc": { "description": "age at measurement of mch_entmass_rbc (years) (HARMONIZED)\n", "type": "number" }, "age_at_mchc_mcnc_rbc": { "description": "age at measurement of mchc_mcnc_rbc (years) (HARMONIZED)\n", "type": "number" }, "age_at_mcv_entvol_rbc": { "description": "age at measurement of mcv_entvol_rbc (years) (HARMONIZED)\n", "type": "number" }, "age_at_monocyte_ncnc_bld": { "description": "age at measurement of monocyte_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_neutrophil_ncnc_bld": { "description": "age at measurement of neutrophil_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_platelet_ncnc_bld": { "description": "age at measurement of platelet_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_pmv_entvol_bld": { "description": "age at measurement of pmv_entvol_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_rbc_ncnc_bld": { "description": "age at measurement of rbc_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "age_at_rdw_ratio_rbc": { "description": "age at measurement of rdw_ratio_rbc (years) (HARMONIZED)\n", "type": "number" }, "age_at_total_cholesterol": { "description": "age at measurement of total_cholesterol (years) (HARMONIZED)\n", "type": "number" }, "age_at_triglycerides": { "description": "age at measurement of triglycerides (HARMONIZED)\n", "type": "number" }, "age_at_wbc_ncnc_bld": { "description": "age at measurement of wbc_ncnc_bld (years) (HARMONIZED)\n", "type": "number" }, "basophil_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of basophils in the blood (bld). (thousands / microliter) (HARMONIZED)\n", "type": "number" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "eosinophil_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of eosinophils in the blood (bld). (thousands / microliter) (HARMONIZED)\n", "type": "number" }, "hdl": { "description": "Hdl cholesterol (mg/dl) (HARMONIZED)\n", "type": "number" }, "hematocrit_vfr_bld": { "description": "Measurement of hematocrit, the fraction of volume (vfr) of blood (bld) that is composed of red blood cells. (percentage) (HARMONIZED)\n", "type": "number" }, "hemoglobin_mcnc_bld": { "description": "Measurement of mass per volume, or mass concentration (mcnc), of hemoglobin in the blood (bld). (g / dL = grams per deciliter) (HARMONIZED)\n", "type": "number" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "ldl": { "description": "Ldl cholesterol (mg/dl) (HARMONIZED)\n", "type": "number" }, "lymphocyte_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of lymphocytes in the blood (bld). (thousands / microliter) (HARMONIZED)\n", "type": "number" }, "mch_entmass_rbc": { "description": "Measurement of the average mass (entmass) of hemoglobin per red blood cell(rbc), known as mean corpuscular hemoglobin (MCH). (pg = picogram) (HARMONIZED)\n", "type": "number" }, "mchc_mcnc_rbc": { "description": "Measurement of the mass concentration (mcnc) of hemoglobin in a given volume of packed red blood cells (rbc), known as mean corpuscular hemoglobin concentration (MCHC). (g /dL = grams per deciliter) (HARMONIZED)\n", "type": "number" }, "mcv_entvol_rbc": { "description": "Measurement of the mass concentration (mcnc) of hemoglobin in a given volume of packed red blood cells (rbc), known as mean corpuscular hemoglobin concentration (MCHC). (g /dL = grams per deciliter) (HARMONIZED)\n", "type": "number" }, "monocyte_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of monocytes in the blood (bld). (HARMONIZED)\n", "type": "number" }, "neutrophil_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of neutrophils in the blood (bld). (HARMONIZED)\n", "type": "number" }, "platelet_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of platelets in the blood (bld). (thousands / microliter) (HARMONIZED)\n", "type": "number" }, "pmv_entvol_bld": { "description": "Measurement of the mean volume (entvol) of platelets in the blood (bld), known as mean platelet volume (MPV or PMV). (fL = femtoliter) (HARMONIZED)\n", "type": "number" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "rbc_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of red blood cells in the blood (bld). (millions / microliter) (HARMONIZED)\n", "type": "number" }, "rdw_ratio_rbc": { "description": "Measurement of the ratio of variation in width to the mean width of the red blood cell (rbc) volume distribution curve taken at +/- 1 CV, known as red cell distribution width (RDW). (percentage) (HARMONIZED)\n", "type": "number" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "total_cholesterol": { "description": "Total cholesterol (mg/dl) (HARMONIZED)\n", "type": "number" }, "triglycerides": { "description": "Triglycerides (mg/dl) (HARMONIZED)\n", "type": "number" }, "type": { "type": "string" }, "unit_basophil_ncnc_bld": { "description": "harmonization unit for basophil_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_eosinophil_ncnc_bld": { "description": "harmonization unit for eosinophil_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_hdl": { "description": "harmonization unit for hdl (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_hematocrit_vfr_bld": { "description": "harmonization unit for hematocrit_vfr_bld. (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_hemoglobin_mcnc_bld": { "description": "Measurement of hematocrit, the fraction of volume (vfr) of blood (bld) that is composed of red blood cells. (percentage) (HARMONIZED)\n", "type": "string" }, "unit_ldl": { "description": "harmonization unit for ldl (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_lymphocyte_ncnc_bld": { "description": "harmonization unit for lymphocyte_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_mch_entmass_rbc": { "description": "harmonization unit for mch_entmass_rbc (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_mchc_mcnc_rbc": { "description": "harmonization unit for mchc_mcnc_rbc (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_mcv_entvol_rbc": { "description": "harmonization unit for mcv_entvol_rbc (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_monocyte_ncnc_bld": { "description": "harmonization unit for monocyte_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_neutrophil_ncnc_bld": { "description": "harmonization unit for neutrophil_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_platelet_ncnc_bld": { "description": "harmonization unit for platelet_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_pmv_entvol_bld": { "description": "harmonization unit for pmv_entvol_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_rbc_ncnc_bld": { "description": "harmonization unit for rbc_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_rdw_ratio_rbc": { "description": "harmonization unit for rdw_ratio_rbc (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED) \n", "type": "string" }, "unit_total_cholesterol": { "description": "harmonization unit for total_cholesterol (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_triglycerides": { "description": "harmonization unit for triglycerides (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_wbc_ncnc_bld": { "description": "harmonization unit for wbc_ncnc_bld (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "wbc_ncnc_bld": { "description": "Count by volume, or number concentration (ncnc), of white blood cells in the blood (bld). (thousands / microliter) (HARMONIZED)\n", "type": "number" } }, "required": [ "type", "submitter_id", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Laboratory Results", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "medical_history": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "Standard questionnaire used to collect medical records from the subject\n", "id": "medical_history", "links": [ { "backref": "medical_histories", "label": "describes", "multiplicity": "one_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "http://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "age_at_cac_score": { "description": "age at measurement of cac_score (years) (HARMONIZED)\n", "type": "number" }, "age_at_cac_volume": { "description": "age at measurement of cac_volume (years) (HARMONIZED)\n", "type": "number" }, "age_at_carotid_plaque": { "description": "age at measurement of carotid_plaque (years) (HARMONIZED)\n", "type": "number" }, "age_at_carotid_stenosis": { "description": "age at measurement of carotid_stenosis (years) (HARMONIZED)\n", "type": "number" }, "age_at_cimt_1": { "description": "age at measurement of cimt_1 (years) (HARMONIZED)\n", "type": "number" }, "age_at_cimt_2": { "description": "age at measurement of cimt_2 (years) (HARMONIZED)\n", "type": "number" }, "age_at_vte_case_status": { "description": "age at measurement of vte_case_status (HARMONIZED)\n", "type": "number" }, "age_at_vte_prior_history": { "description": "age at measurement of vte_prior_history (years) (HARMONIZED)\n", "type": "number" }, "asthma": { "description": "Reported Asthma condition in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "asthma", "term_id": "HP:0002099", "term_version": "2019-04-15" } ] }, "atrial_fibrillation": { "description": "Reported atrial fibrillation condition in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "atrial fibrillation", "term_id": "HP:0005110", "term_version": "2019-04-15" } ] }, "cabg_presence": { "description": "Reported presence of coronary artery bypass graft (CABG) in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "coronary_artery_disease", "term_id": "HP:0001677", "term_version": "2019-04-15" } ] }, "cac_score": { "description": "Coronary artery calcification (CAC) score using Agatston scoring of CT scan(s) of coronary arteries decimal (HARMONIZED)\n", "type": "number" }, "cac_volume": { "description": "Coronary artery calcium volume using CT scan(s) of coronary arteries (HARMONIZED)\n", "type": "number" }, "carotid_plaque": { "description": "Presence or absence of carotid plaque. (HARMONIZED)\n", "enum": [ "Plaque not present", "Plaque present" ] }, "carotid_stenosis": { "description": "Extent of narrowing of the carotid artery. (HARMONIZED)\n", "enum": [ "None", "1%-24%", "25%-49%", "50%-74%", "75%-99%", "100%" ] }, "cerebrovascular_disease": { "description": "Reported Cerebrovascular disease in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "cerebrovascular_disease", "term_id": null, "term_version": null } ] }, "chronic_bronchitis": { "description": "Reported chronic bronchitis condition in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "chronic bronchitis", "term_id": "HP:0004469", "term_version": "2019-04-15" } ] }, "chronic_respiratory_disease": { "description": "Reported Chronic Respiratory disease in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "chronic_respiratory_disease", "term_id": null, "term_version": null } ] }, "cimt_1": { "description": "Common carotid intima-media thickness, calculated as the mean of two values: mean of multiple thickness estimates from the left far wall and from the right far wall. (HARMONIZED)\n", "type": "number" }, "cimt_2": { "description": "Common carotid intima-media thickness, calculated as the mean of four values: maximum of multiple thickness estimates from the left far wall, left near wall, right far wall, and right near wall. (mm) (HARMONIZED)\n", "type": "number" }, "copd": { "description": "Reported Chronic Obstructive Pulmonary Disease (COPD) in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "copd", "term_id": "HP:0006510", "term_version": "2019-04-15" } ] }, "coronary_artery_disease": { "description": "Reported Coronary Artery disease in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "coronary_artery_disease", "term_id": "HP:0001677", "term_version": "2019-04-15" } ] }, "covid_hospital_admission": { "description": "Did COVID-19 contribute to need for hospital admission?\n", "enum": [ "Yes", "No" ] }, "covid_hospital_admission_age": { "description": "Age on hospital admit (years, age \u22651 year)\n", "type": "integer" }, "covid_icu": { "description": "Was patient admitted to ICU during hospitalization?\n", "enum": [ "Yes", "No" ] }, "covid_icu_stay_length": { "description": "Total ICU length of stay (from hospital admit)\n", "type": "integer" }, "covid_pos_ever_yn": { "description": "Any positive COVID-19 test?\n", "enum": [ "Yes", "No" ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "diabetes": { "description": "Reported Diabetes in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "diabetes", "term_id": "HP:0000819", "term_version": "2019-04-15" } ] }, "emphysema": { "description": "Reported Emphysema in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "emphysema", "term_id": "HP:0002097", "term_version": "2019-04-15" } ] }, "heart_failure": { "description": "Reported Heart failure in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "heart_failure", "term_id": "HP:0001635", "term_version": "2019-04-15" } ] }, "hyperlipidemia": { "description": "Reported Hyperlipidemia condition in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "hyperlipidemia", "term_id": "HP:0003077", "term_version": "2019-04-15" } ] }, "hypertension": { "description": "Reported Hypertension condition in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "hypertension", "term_id": "HP:0000822", "term_version": "2019-04-15" } ] }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "myocardial_infarction": { "description": "Reported Myocardial Infarction in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "myocardial_infarction", "term_id": "HP:0001658", "term_version": "2019-04-15" } ] }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "stroke": { "description": "Reported Stroke in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "stroke", "term_id": "HP:0001297", "term_version": "2019-04-15" } ] }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "type1_diabetes": { "description": "Reported Type-1 Diabetes in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "type1_diabetes", "term_id": "HP:0100651", "term_version": "2019-04-15" } ] }, "type2_diabetes": { "description": "Reported Type-2 Diabetes in the participant (HARMONIZED)\n", "enum": [ "Yes", "No", "Not reported", "Unknown" ], "enumDef": [ { "enumeration": true, "source": "NCI Thesaurus", "term_id": "C49488", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": false, "source": "NCI Thesaurus", "term_id": "C49487", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Not reported", "source": "NCI Thesaurus", "term_id": "C43234", "version_date": "19.03d (Release date:2019-03-25)" }, { "enumeration": "Unknown", "source": "NCI Thesaurus", "term_id": "C17998", "version_date": "19.03d (Release date:2019-03-25)" } ], "termDef": [ { "source": "hp", "term": "type2_diabetes", "term_id": "HP:0005978", "term_version": "2019-04-15" } ] }, "unit_cac_score": { "description": "harmonization unit for cac_score (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_cac_volume": { "description": "harmonization unit for cac_volume (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_carotid_plaque": { "description": "harmonization unit for carotid_plaque (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_carotid_stenosis": { "description": "harmonization unit for carotid_stenosis (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_cimt_1": { "description": "harmonization unit for cimt_1 (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_cimt_2": { "description": "harmonization unit for cimt_2 (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_vte_case_status": { "description": "harmonization unit for vte_case_status (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_vte_followup_start_age": { "description": "harmonization unit for vte_followup_start_age (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_vte_prior_history": { "description": "harmonization unit for vte_prior_history (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "vte_case_status": { "description": "An indicator of whether a subject experienced a venous thromboembolismevent (VTE) that was verified by adjudication or by medical professionals. (HARMONIZED)\n", "type": "boolean" }, "vte_followup_start_age": { "description": "Age of subject at the start of the follow up period during which venousthromboembolism (VTE) events were reviewed and adjudicated. (years) (HARMONIZED)\n", "type": "number" }, "vte_prior_history": { "description": "An indicator of whether a subject had a venous thromboembolism (VTE)event prior to the start of the medical review process (includingself-reported events). (HARMONIZED)\n", "type": "boolean" } }, "required": [ "submitter_id", "type", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Medical History", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "medication": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "clinical", "description": "Recods about historical medication use\n", "id": "medication", "links": [ { "backref": "medication_records", "label": "describes", "multiplicity": "one_to_one", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "http://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "age_at_antihypertensive_meds": { "description": "age at measurement of antihypertensive_meds (years) (HARMONIZED)\n", "type": "number" }, "age_at_fasting_lipids": { "description": "age at measurement of fasting_lipids (years) (HARMONIZED)\n", "type": "number" }, "age_at_lipid_lowering_medication": { "description": "age at measurement of age_at_lipid1c (years) (HARMONIZED)\n", "type": "number" }, "antihypertensive_meds": { "description": "Indicator for use of antihypertensive medication at the time of blood pressure measurement. (HARMONIZED)\n", "enum": [ "Not taking antihypertensive medication", "Taking antihypertensive medication" ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "fasting_lipids": { "description": "Indicates whether participant fasted for at least eight hours prior to blood draw to measure lipids phenotypes. (HARMONIZED)\n", "type": "boolean" }, "hypertension_meds": { "description": "Take medication for hypertension (HARMONIZED)\n", "type": "boolean" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "lipid_lowering_medication": { "description": "Any lipid-lowering medication (HARMONIZED)\n", "type": "boolean" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "unit_antihypertensive_meds": { "description": "harmonization unit for antihypertensive_meds (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_fasting_lipids": { "description": "harmonization unit for fasting_lipids (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "unit_lipid_lowering_medication": { "description": "harmonization unit for unit_lipid1c (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "submitter_id", "type", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Medication Use Record", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "metaschema": { "$schema": "http://json-schema.org/draft-04/schema#", "allOf": [ { "$ref": "http://json-schema.org/draft-04/schema#" } ], "definitions": { "link": { "additionalProperties": false, "properties": { "backref": { "$ref": "#/field" }, "label": { "$ref": "#/field" }, "multiplicity": { "enum": [ "one_to_one", "one_to_many", "many_to_one", "many_to_many" ], "type": "string" }, "name": { "$ref": "#/field" }, "required": { "type": "boolean" }, "target_type": { "$ref": "#/field" } }, "required": [ "name", "target_type", "backref", "label", "multiplicity", "required" ], "type": "object" }, "link_subgroup": { "properties": { "exclusive": { "type": "boolean" }, "required": { "type": "boolean" }, "subgroup": { "items": { "oneOf": [ { "$ref": "#/definitions/link" }, { "$ref": "#/definitions/link_subgroup" } ] }, "type": "array" } }, "required": [ "exclusive", "required", "subgroup" ] }, "validator_def": { "properties": { "link_to_type": { "type": "string" }, "multiplicity": { "enum": [ "one_to_one", "one_to_many", "many_to_one", "many_to_many" ], "type": "string" } }, "required": [ "property", "function" ], "title": "Define a validator to be used on a property", "type": "object" } }, "field": { "pattern": "^[_a-zA-Z0-9]*$", "type": "string" }, "id": "metaschema", "properties": { "category": { "$ref": "#/field", "enum": [ "administrative", "analysis", "biospecimen", "clinical", "data", "data_bundle", "data_file", "index_file", "metadata_file", "notation", "qc_bundle", "TBD" ] }, "links": { "items": { "oneOf": [ { "$ref": "#/definitions/link" }, { "$ref": "#/definitions/link_subgroup" } ] }, "title": "Define a link to other GDC entities", "type": "array" }, "properties": { "additionalProperties": false, "patternProperties": { "^[_a-zA-Z0-9]*$": { "type": "object" } }, "type": "object" }, "submittable": { "type": "boolean" }, "system_properties": { "type": "array" }, "unique_keys": { "items": { "items": { "type": "string" }, "type": "array" }, "type": "array" }, "validators": { "items": { "$ref": "#/definitions/validator_def" }, "type": [ "array", "null" ] } }, "required": [ "category", "program", "project", "uniqueKeys", "links", "validators", "systemProperties", "id" ], "title": "GDC JSON schema extension" }, "original_file": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "original_data", "description": "A storage node for the original, raw contents of a study ingested into our system.", "id": "original_file", "links": [ { "backref": "original_data", "label": "data_from", "multiplicity": "many_to_one", "name": "projects", "required": true, "target_type": "project" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "projects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "ga4gh_drs_uri" ], "submittable": true, "systemProperties": [ "id", "state", "project_id", "created_datetime", "updated_datetime" ], "title": "Original File", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "program": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "administrative", "description": "A broad framework of goals to be achieved. (NCIt C52647)\n", "id": "program", "links": [], "program": "*", "project": "*", "properties": { "dbgap_accession_number": { "description": "The dbgap accession number provided for the program.", "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "name": { "description": "Full name/title of the program.", "type": "string" }, "type": { "type": "string" } }, "required": [ "name", "dbgap_accession_number" ], "submittable": false, "systemProperties": [ "id" ], "title": "Program", "type": "object", "uniqueKeys": [ [ "id" ], [ "name" ] ], "validators": null }, "project": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "administrative", "constraints": null, "description": "Any specifically defined piece of work that is undertaken or attempted to meet a single requirement. (NCIt C47885)\n", "id": "project", "links": [ { "backref": "projects", "label": "member_of", "multiplicity": "many_to_one", "name": "programs", "required": true, "target_type": "program" } ], "program": "*", "project": "*", "properties": { "availability_mechanism": { "description": "Mechanism by which the project will be made avilable.", "type": "string" }, "availability_type": { "description": "Is the project open or restricted?", "enum": [ "Open", "Restricted" ] }, "code": { "description": "Unique identifier for the project.", "type": "string" }, "date_collected": { "description": "The date or date range in which the project data was collected.", "type": "string" }, "dbgap_accession_number": { "description": "The dbgap accession number provided for the project.", "type": "string" }, "id": { "description": "UUID for the project.", "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "intended_release_date": { "description": "Tracks a Project's intended release date.", "format": "date-time", "type": "string" }, "investigator_affiliation": { "description": "The investigator's affiliation with respect to a research institution.", "type": "string" }, "investigator_name": { "description": "Name of the principal investigator for the project.", "type": "string" }, "name": { "description": "Display name/brief description for the project.", "type": "string" }, "programs": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ], "description": "Indicates that the project is logically part of the indicated project.\n" }, "releasable": { "default": false, "description": "A project can only be released by the user when `releasable` is true.\n", "type": "boolean" }, "released": { "default": false, "description": "To release a project is to tell the GDC to include all submitted\nentities in the next GDC index.\n", "type": "boolean" }, "state": { "default": "open", "description": "The possible states a project can be in. All but `open` are\nequivalent to some type of locked state.\n", "enum": [ "open", "review", "submitted", "processing", "closed", "legacy" ] }, "support_id": { "description": "The ID of the source providing support/grant resources.", "type": "string" }, "support_source": { "description": "The name of source providing support/grant resources.", "type": "string" }, "type": { "type": "string" } }, "required": [ "code", "name", "programs", "dbgap_accession_number" ], "submittable": true, "systemProperties": [ "id", "state", "released", "releasable", "intended_release_date" ], "title": "Project", "type": "object", "uniqueKeys": [ [ "id" ], [ "code" ] ], "validators": null }, "publication": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "administrative", "description": "Publication for a project.", "id": "publication", "links": [ { "backref": "publications", "label": "refers_to", "multiplicity": "many_to_many", "name": "projects", "required": true, "target_type": "project" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "doi": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "pmid": { "type": "string" }, "project_id": { "type": "string" }, "projects": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "type": [ "string", "null" ] }, "type": { "enum": [ "publication" ] }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "projects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Publication", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "read_group": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "biospecimen", "description": "Sequencing reads from one lane of an NGS experiment.", "id": "read_group", "links": [ { "backref": "read_groups", "label": "derived_from", "multiplicity": "many_to_one", "name": "aliquots", "required": true, "target_type": "aliquot" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "RIN": { "term": { "description": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products.\n", "termDef": { "cde_id": 5278775, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen RNA Integrity Number Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" } }, "type": "number" }, "adapter_name": { "term": { "description": "Name of the sequencing adapter.\n" }, "type": "string" }, "adapter_sequence": { "term": { "description": "Base sequence of the sequencing adapter.\n" }, "type": "string" }, "aliquots": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "barcoding_applied": { "description": "True/False: was barcoding applied?", "type": "boolean" }, "base_caller_name": { "term": { "description": "Name of the base caller.\n" }, "type": "string" }, "base_caller_version": { "term": { "description": "Version of the base caller.\n" }, "type": "string" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "experiment_name": { "term": { "description": "Submitter-defined name for the experiment.\n" }, "type": "string" }, "flow_cell_barcode": { "term": { "description": "Flow Cell Barcode.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "includes_spike_ins": { "term": { "description": "Spike-in included?\n" }, "type": "boolean" }, "instrument_model": { "enum": [ "454 GS FLX Titanium", "AB SOLiD 4", "AB SOLiD 2", "AB SOLiD 3", "Complete Genomics", "Illumina HiSeq X Ten", "Illumina HiSeq X Five", "Illumina Genome Analyzer II", "Illumina Genome Analyzer IIx", "Illumina HiSeq 2000", "Illumina HiSeq 2500", "Illumina HiSeq 4000", "Illumina MiSeq", "Illumina NextSeq", "Illumina NovaSeq 6000", "Ion Torrent PGM", "Ion Torrent Proton", "NextSeq 500", "PacBio RS", "Ion S5 XL System, Ion 530 Chip", "Other" ], "terms": { "description": "Numeric value that represents the sample dimension that is greater than the shortest dimension and less than the longest dimension, measured in millimeters.\n", "termDef": { "cde_id": 5432604, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Intermediate Dimension Millimeter Measurement", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" } } }, "is_paired_end": { "term": { "description": "Are the reads paired end?\n" }, "type": "boolean" }, "library_name": { "term": { "description": "Name of the library.\n" }, "type": "string" }, "library_preparation_kit_catalog_number": { "term": { "description": "Catalog of Library Preparation Kit\n" }, "type": "string" }, "library_preparation_kit_name": { "term": { "description": "Name of Library Preparation Kit\n" }, "type": "string" }, "library_preparation_kit_vendor": { "term": { "description": "Vendor of Library Preparation Kit\n" }, "type": "string" }, "library_preparation_kit_version": { "term": { "description": "Version of Library Preparation Kit\n" }, "type": "string" }, "library_selection": { "enum": [ "Hybrid_Selection", "PCR", "Affinity_Enrichment", "Poly-T_Enrichment", "RNA_Depletion", "Other" ], "term": { "description": "Library Selection Method\n" } }, "library_strand": { "enum": [ "Unstranded", "First_Stranded", "Second_Stranded" ], "term": { "description": "Library stranded-ness.\n" } }, "library_strategy": { "enum": [ "Amplicon", "Bisulfite-Seq", "ChIP-Seq", "Exclude", "miRNA-Seq", "OMNI", "Other", "RNA-Seq", "scATAC-Seq", "scRNA-Seq", "snRNA-Seq", "Validation", "WES", "WGS" ], "term": { "description": "Library strategy.\n" } }, "platform": { "enum": [ "Illumina", "SOLiD", "LS454", "Ion Torrent", "Complete Genomics", "PacBio", "Other", "Affymetrix" ], "term": { "description": "Name of the platform used to obtain data.\n" } }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "read_group_name": { "description": "Read Group Name", "type": "string" }, "read_length": { "type": "integer" }, "sequencing_center": { "term": { "description": "Name of the center that provided the sequence files.\n" }, "type": "string" }, "sequencing_date": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "size_selection_range": { "term": { "description": "Range of size selection.\n" }, "type": "string" }, "spike_ins_concentration": { "term": { "description": "Spike in concentration.\n" }, "type": "string" }, "spike_ins_fasta": { "term": { "description": "Name of the FASTA file that contains the spike-in sequences.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "target_capture_kit_catalog_number": { "term": { "description": "Catalog of Target Capture Kit.\n" }, "type": "string" }, "target_capture_kit_name": { "term": { "description": "Name of Target Capture Kit.\n" }, "type": "string" }, "target_capture_kit_target_region": { "term": { "description": "Target Capture Kit BED file.\n" }, "type": "string" }, "target_capture_kit_vendor": { "term": { "description": "Vendor of Target Capture Kit.\n" }, "type": "string" }, "target_capture_kit_version": { "term": { "description": "Version of Target Capture Kit.\n" }, "type": "string" }, "to_trim_adapter_sequence": { "term": { "description": "Does the user suggest adapter trimming?\n" }, "type": "boolean" }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "aliquots" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state" ], "title": "Read Group", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "reference_file": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Data file containing any type of reference required for a data analysis.", "id": "reference_file", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "reference_files", "label": "data_from", "multiplicity": "many_to_one", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" }, { "backref": "reference_files", "label": "data_from", "multiplicity": "many_to_one", "name": "projects", "required": false, "target_type": "project" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Analysis Information", "Annotation Reference", "Clinical Data", "Familial Reference", "Sequencing Reference", "Variant Calling Reference", "Other" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "ALT", "AMB", "ANN", "AVRO", "BCF", "BED", "BIM", "BNP", "BWT", "C", "CSI", "CSV", "CTR", "DAT", "DB", "DCM", "DESC", "DOC", "DOCX", "DTA", "FAI", "FAM", "FASTA", "FMT", "FOR", "GDS", "GRD", "GZ", "HTM", "HTML", "HWE", "JSON", "MD", "PAC", "PDF", "PNG", "POS", "PPT", "PPTX", "R", "RAR", "RDATA", "RTF", "SA", "SAS", "SAS7BCAT", "SAS7BDAT", "SAV", "STM", "TAR", "TBI", "TBL", "TSV", "TXT", "VCF", "WPD", "XLS", "XLSX", "XML", "ZIP" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Kinship Matrix", "Principal Component", "Script", "Sequencing Reference", "Unharmonized Clinical Data", "Variant Annotation", "Variant Call", "Other" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "projects": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "source_file": { "description": "The originating compressed file's name.\n", "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "study_version": { "description": "The version of the study that was released by data source (e.g., dbGaP)\n", "type": "number" }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Reference File", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "reference_file_index": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "index_file", "description": "Data file containing the index for a set of germline variants.", "id": "reference_file_index", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "reference_file_indexes", "label": "derived_from", "multiplicity": "many_to_many", "name": "reference_files", "required": false, "target_type": "reference_file" }, { "backref": "reference_file_indexes", "label": "data_from", "multiplicity": "many_to_many", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" } ] } ], "namespace": "https://dcp.bionimbus.org", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Simple Nucleotide Variation" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "BCF.CSI", "CSI", "TBI", "VCF.CSI", "ZIP" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Germline Variation Index", "Sequencing Reference Index", "Variant Reference Index" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "reference_files": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "source_file": { "description": "The originating compressed file's name.\n", "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "study_version": { "description": "The version of the study that was released by data source (e.g., dbGaP)\n", "type": "number" }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Reference File Index", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "root": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "internal", "constraints": null, "id": "root", "links": [], "program": "*", "project": "*", "properties": { "id": { "enum": [ "root" ] }, "schema_version": { "type": "string" }, "type": { "type": "string" } }, "required": [ "type" ], "root": "*", "submittable": false, "systemProperties": [ "id" ], "title": "Root", "type": "object", "uniqueKeys": [ [ "id" ] ], "validators": null }, "sample": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "biospecimen", "description": "Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products.\n", "id": "sample", "links": [ { "backref": "samples", "label": "derived_from", "multiplicity": "many_to_many", "name": "subjects", "required": true, "target_type": "subject" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "autolysis_score": { "description": "Autolysis Score\n", "enum": [ "None", "Mild", "Moderate", "Severe" ] }, "biospecimen_anatomic_site": { "enum": [ "Abdomen", "Abdominal Wall", "Acetabulum", "Adenoid", "Adipose", "Adrenal", "Alveolar Ridge", "Amniotic Fluid", "Ampulla Of Vater", "Anal Sphincter", "Ankle", "Anorectum", "Antecubital Fossa", "Antrum", "Anus", "Aorta", "Aortic Body", "Appendix", "Aqueous Fluid", "Arm", "Artery", "Ascending Colon", "Ascending Colon Hepatic Flexure", "Auditory Canal", "Autonomic Nervous System", "Axilla", "Back", "Bile Duct", "Bladder", "Blood", "Blood Vessel", "Bone", "Bone Marrow", "Bowel", "Brain", "Brain Stem", "Breast", "Broad Ligament", "Bronchiole", "Bronchus", "Brow", "Buccal Cavity", "Buccal Mucosa", "Buttock", "Calf", "Capillary", "Cardia", "Carina", "Carotid Artery", "Carotid Body", "Cartilage", "Cecum", "Cell-Line", "Central Nervous System", "Cerebellum", "Cerebral Cortex", "Cerebrospinal Fluid", "Cerebrum", "Cervical Spine", "Cervix", "Chest", "Chest Wall", "Chin", "Clavicle", "Clitoris", "Colon", "Colon (Mucosa Only)", "Common Duct", "Conjunctiva", "Connective Tissue", "Dermal", "Descending Colon", "Diaphragm", "Duodenum", "Ear", "Ear Canal", "Ear, Pinna (External)", "Effusion", "Elbow", "Endocrine Gland", "Epididymis", "Epidural Space", "Esophagogastric Junction", "Esophagus", "Esophagus (Mucosa Only)", "Eye", "Fallopian Tube", "Femoral Artery", "Femoral Vein", "Femur", "Fibroblasts", "Fibula", "Finger", "Floor Of Mouth", "Fluid", "Foot", "Forearm", "Forehead", "Foreskin", "Frontal Cortex", "Frontal Lobe", "Fundus Of Stomach", "Gallbladder", "Ganglia", "Gastroesophageal Junction", "Gastrointestinal Tract", "Groin", "Gum", "Hand", "Hard Palate", "Head & Neck", "Head (Face Or Neck) NOS", "Heart", "Hepatic", "Hepatic Duct", "Hepatic Vein", "Hip", "Hippocampus", "Humerus", "Hypopharynx", "Ileum", "Ilium", "Index Finger", "Ischium", "Islet Cells", "Jaw", "Jejunum", "Joint", "Kidney", "Knee", "Lacrimal Gland", "Large Bowel", "Laryngopharynx", "Larynx", "Leg", "Leptomeninges", "Ligament", "Lip", "Liver", "Lumbar Spine", "Lung", "Lymph Node", "Lymph Node(s) Axilla", "Lymph Node(s) Cervical", "Lymph Node(s) Distant", "Lymph Node(s) Epitrochlear", "Lymph Node(s) Femoral", "Lymph Node(s) Hilar", "Lymph Node(s) Iliac-Common", "Lymph Node(s) Iliac-External", "Lymph Node(s) Inguinal", "Lymph Node(s) Internal Mammary", "Lymph Node(s) Mammary", "Lymph Node(s) Mesenteric", "Lymph Node(s) Occipital", "Lymph Node(s) Paraaortic", "Lymph Node(s) Parotid", "Lymph Node(s) Pelvic", "Lymph Node(s) Popliteal", "Lymph Node(s) Regional", "Lymph Node(s) Retroperitoneal", "Lymph Node(s) Scalene", "Lymph Node(s) Splenic", "Lymph Node(s) Subclavicular", "Lymph Node(s) Submandibular", "Lymph Node(s) Supraclavicular", "Lymph Nodes(s) Mediastinal", "Mandible", "Maxilla", "Mediastinal Soft Tissue", "Mediastinum", "Mesentery", "Mesothelium", "Middle Finger", "Mitochondria", "Muscle", "Nails", "Nasal Cavity", "Nasal Soft Tissue", "Nasopharynx", "Neck", "Nerve", "Nerve(s) Cranial", "Occipital Cortex", "Ocular Orbits", "Omentum", "Oral Cavity", "Oral Cavity (Mucosa Only)", "Oropharynx", "Other", "Ovary", "Palate", "Pancreas", "Paraspinal Ganglion", "Parathyroid", "Parotid Gland", "Patella", "Pelvis", "Penis", "Pericardium", "Periorbital Soft Tissue", "Peritoneal Cavity", "Peritoneum", "Pharynx", "Pineal", "Pineal Gland", "Pituitary Gland", "Placenta", "Pleura", "Popliteal Fossa", "Prostate", "Pylorus", "Rectosigmoid Junction", "Rectum", "Retina", "Retro-Orbital Region", "Retroperitoneum", "Rib", "Ring Finger", "Round Ligament", "Sacrum", "Salivary Gland", "Scalp", "Scapula", "Sciatic Nerve", "Scrotum", "Seminal Vesicle", "Shoulder", "Sigmoid Colon", "Sinus", "Sinus(es), Maxillary", "Skeletal Muscle", "Skin", "Skull", "Small Bowel", "Small Bowel (Mucosa Only)", "Small Finger", "Small Intestine", "Soft Tissue", "Spinal Column", "Spinal Cord", "Spleen", "Splenic Flexure", "Sternum", "Stomach", "Stomach (Mucosa Only)", "Subcutaneous Tissue", "Synovium", "Temporal Cortex", "Tendon", "Testis", "Thigh", "Thoracic Spine", "Thorax", "Throat", "Thumb", "Thymus", "Thyroid", "Tibia", "Tongue", "Tonsil", "Tonsil (Pharyngeal)", "Trachea / Major Bronchi", "Transverse Colon", "Trunk", "Umbilical Cord", "Ureter", "Urethra", "Urinary Tract", "Uterus", "Uvula", "Vagina", "Vas Deferens", "Vein", "Venous", "Vertebra", "Vulva", "White Blood Cells", "Wrist", "Unknown", "Not Reported", "Not Allowed To Collect" ], "term": { "description": "Text term that represents the name of the primary disease site of the submitted tumor sample.\n", "termDef": { "cde_id": 4742851, "cde_version": 1.0, "source": "caDSR", "term": "Submitted Tumor Sample Primary Anatomic Site", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4742851&version=1.0" } } }, "biospecimen_anatomic_site_detail": { "description": "Tissue type, more specific detail of tissue tyep\n", "enum": [ "Adipose - Subcutaneous", "Adipose - Visceral (Omentum)", "Adrenal Gland", "Artery - Aorta", "Artery - Coronary", "Artery - Tibial", "Bladder", "Brain - Amygdala", "Brain - Anterior cingulate cortex (BA24)", "Brain - Caudate (basal ganglia)", "Brain - Cerebellar Hemisphere", "Brain - Cerebellum", "Brain - Cortex", "Brain - Frontal Cortex (BA9)", "Brain - Hippocampus", "Brain - Hypothalamus", "Brain - Nucleus accumbens (basal ganglia)", "Brain - Putamen (basal ganglia)", "Brain - Spinal cord (cervical c-1)", "Brain - Substantia nigra", "Breast - Mammary Tissue", "Cells - EBV-transformed lymphocytes", "Cells - Transformed fibroblasts", "Cervix - Ectocervix", "Cervix - Endocervix", "Colon - Sigmoid", "Colon - Transverse", "Esophagus - Gastroesophageal Junction", "Esophagus - Mucosa", "Esophagus - Muscularis", "Fallopian Tube", "Heart - Atrial Appendage", "Heart - Left Ventricle", "Kidney - Cortex", "Liver", "Lung", "Minor Salivary Gland", "Muscle - Skeletal", "Nerve - Tibial", "Ovary", "Pancreas", "Pituitary", "Prostate", "Skin - Not Sun Exposed (Suprapubic)", "Skin - Sun Exposed (Lower leg)", "Small Intestine - Terminal Ileum", "Spleen", "Stomach", "Testis", "Thyroid", "Uterus", "Vagina", "Whole Blood" ] }, "biospecimen_anatomic_site_uberon_id": { "description": "Uberon ID, anatomical location as described by the Uber Anatomy Ontology (UBERON)\n", "type": "string" }, "biospecimen_anatomic_site_uberon_term": { "description": "Uberon Term, anatomical location as described by the Uber Anatomy Ontology (UBERON)\n", "type": "string" }, "biospecimen_physical_site": { "description": "Tissue location\n", "type": "string" }, "biospecimen_type": { "description": "Original material type of the collected sample\n", "type": "string" }, "collection_kit": { "description": "Category or classifier of a set of responses, indicates the color of the sample collection kit\n", "enum": [ "Aqua Kit:Organ and Tissue donation", "Green Kit: Brain donation", "Yellow Kit: Skin and Blood donation" ] }, "collection_site": { "description": "Code for BSS collection site. Indicates the site that enrolled the donor, brain subregions may have more than one site.\n", "type": "string" }, "composition": { "enum": [ "B-lymphocyte", "Buccal Cells", "Buffy Coat", "Bone Marrow Components", "Bone Marrow Components NOS", "Control Analyte", "Cell", "Circulating Tumor Cell (CTC)", "Derived Cell Line", "EBV Immortalized", "Fibroblasts from Bone Marrow Normal", "Granulocytes", "Human Original Cells", "Lymphocytes", "Mononuclear Cells from Bone Marrow Normal", "Peripheral Blood Components NOS", "Peripheral Blood Nucleated Cells", "Pleural Effusion", "Plasma", "Peripheral Whole Blood", "Serum", "Saliva", "Sputum", "Solid Tissue", "Whole Bone Marrow", "Unknown", "Not Reported", "Not Allowed To Collect" ], "term": { "description": "Text term that represents the cellular composition of the sample.\n", "termDef": { "cde_id": 5432591, "cde_version": 1.0, "source": "caDSR", "term": "Biospecimen Cellular Composition Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" } } }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "current_weight": { "term": { "description": "Numeric value that represents the current weight of the sample, measured in milligrams.\n", "termDef": { "cde_id": 5432606, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Current Weight Milligram Value", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" } }, "type": "number" }, "freezing_method": { "term": { "description": "Text term that represents the method used for freezing the sample.\n", "termDef": { "cde_id": 5432607, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Freezing Method Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" } }, "type": "string" }, "hours_to_collection": { "description": "Total Ischemic time for a sample\n", "type": "integer" }, "hours_to_sample_procurement": { "description": "Time a sample spent in the PAXgene fixative\n", "type": "integer" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "internal_notes": { "description": "Internal notes about the sample generated by the LDACC\n", "type": "string" }, "is_ffpe": { "term": { "description": "Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in paraffin (FFPE).\n", "termDef": { "cde_id": 4170557, "cde_version": 1.0, "source": "caDSR", "term": "Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" } }, "type": "boolean" }, "method_of_sample_procurement": { "enum": [ "Abdomino-perineal Resection of Rectum", "Anterior Resection of Rectum", "Aspirate", "Biopsy", "Blood Draw", "Bone Marrow Aspirate", "Core Biopsy", "Cystectomy", "Endo Rectal Tumor Resection", "Endoscopic Biopsy", "Endoscopic Mucosal Resection (EMR)", "Enucleation", "Excisional Biopsy", "Fine Needle Aspiration", "Full Hysterectomy", "Gross Total Resection", "Hand Assisted Laparoscopic Radical Nephrectomy", "Hysterectomy NOS", "Incisional Biopsy", "Indeterminant", "Laparoscopic Biopsy", "Laparoscopic Partial Nephrectomy", "Laparoscopic Radical Nephrectomy", "Laparoscopic Radical Prostatectomy with Robotics", "Laparoscopic Radical Prostatectomy without Robotics", "Left Hemicolectomy", "Lobectomy", "Local Resection (Exoresection; wall resection)", "Lumpectomy", "Modified Radical Mastectomy", "Needle Biopsy", "Open Craniotomy", "Open Partial Nephrectomy", "Open Radical Nephrectomy", "Open Radical Prostatectomy", "Orchiectomy", "Other", "Other Surgical Resection", "Pan-Procto Colectomy", "Pneumonectomy", "Right Hemicolectomy", "Sigmoid Colectomy", "Simple Mastectomy", "Subtotal Resection", "Surgical Resection", "Thoracoscopic Biopsy", "Total Colectomy", "Total Mastectomy", "Transplant", "Transurethral resection (TURBT)", "Transverse Colectomy", "Tumor Resection", "Wedge Resection", "Unknown", "Not Reported", "Not Allowed To Collect" ], "term": { "description": "The method used to procure the sample used to extract analyte(s).\n", "termDef": { "cde_id": null, "cde_version": null, "source": null, "term": "Method of Sample Procurement", "term_url": null } } }, "oct_embedded": { "term": { "description": "Indicator of whether or not the sample was embedded in Optimal Cutting Temperature (OCT) compound.\n", "termDef": { "cde_id": 5432538, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" } }, "type": "string" }, "pathology_notes": { "description": "Pathology Notes, notes from PRC Report\n", "type": "string" }, "preservation_method": { "enum": [ "Cryopreserved", "FFPE", "Fresh", "OCT", "Snap Frozen", "Frozen", "Unknown", "Not Reported", "Not Allowed To Collect" ], "term": { "description": "Text term that represents the method used to preserve the sample.\n", "termDef": { "cde_id": 5432521, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Preservation Method Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" } } }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "prosector_notes": { "description": "Prosector comments\n", "type": "string" }, "sample_type": { "description": "Current material type of the sample as stored at the LDACC\n", "enum": [ "PAXgene Preserved tissue", "Fresh frozen tissue", "Whole blood", "PAXgene Preserved whole blood", "Pellet frozen cells", "DNA genomic", "Fresh skin punch" ] }, "specimen_id": { "description": "Unique identifier that can be used to retrieve more information for a specimen.\n", "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "tissue_type": { "enum": [ "Tumor", "Normal", "Abnormal", "Peritumoral", "Contrived", "Unknown", "Not Reported", "Not Allowed To Collect" ], "term": { "description": "Text term that represents a description of the kind of tissue collected with respect to disease status or proximity to tumor tissue.\n", "termDef": { "cde_id": 5432687, "cde_version": 1.0, "source": "caDSR", "term": "Tissue Sample Description Type", "term_url": "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" } } }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "subjects" ], "submittable": true, "systemProperties": [ "id", "project_id", "state", "created_datetime", "updated_datetime" ], "title": "Sample", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "simple_germline_variation": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Data file containing simple germline variations called from aligned reads.\n", "id": "simple_germline_variation", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "simple_germline_variations", "label": "data_from", "multiplicity": "many_to_one", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" }, { "backref": "simple_germline_variations", "label": "data_from", "multiplicity": "many_to_one", "name": "germline_mutation_calling_workflows", "required": false, "target_type": "germline_mutation_calling_workflow" }, { "backref": "simple_germline_variations", "label": "data_from", "multiplicity": "many_to_many", "name": "read_groups", "required": false, "target_type": "read_group" }, { "backref": "simple_germline_variations", "label": "data_from", "multiplicity": "many_to_many", "name": "submitted_aligned_reads_files", "required": false, "target_type": "submitted_aligned_reads" }, { "backref": "simple_germline_variations", "label": "data_from", "multiplicity": "many_to_many", "name": "aligned_reads_files", "required": false, "target_type": "aligned_reads" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Simple Nucleotide Variation" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "VCF" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Simple Germline Variation" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "experimental_strategy": { "enum": [ "WGS", "WXS", "Low Pass WGS", "Validation" ], "term": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "germline_mutation_calling_workflows": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "read_groups": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitted_aligned_reads_files": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "experimental_strategy" ], "submittable": false, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Simple Germline Variation", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "sleep_test_file": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Polysomnography data containing signal files and event scoring and event staging annotation files.", "id": "sleep_test_file", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "sleep_test_files", "label": "data_from", "multiplicity": "many_to_many", "name": "subjects", "required": false, "target_type": "subject" }, { "backref": "sleep_test_files", "label": "data_from", "multiplicity": "many_to_many", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" } ] } ], "namespace": "https://gen3.biodatacatalyst.nhlbi.nih.gov/", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Polysomnography Data", "Actigraphy Data" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "EDF", "XML", "CSV" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Signal Data", "Annotation Data" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "experimental_strategy": { "enum": [ "Polysomnography", "Actigraphy" ], "term": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "subjects": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "experimental_strategy" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Sleep Test File", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "study": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "administrative", "description": "A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing.\n", "id": "study", "links": [ { "backref": "studies", "label": "performed_for", "multiplicity": "many_to_one", "name": "projects", "required": true, "target_type": "project" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "authz": { "description": "The authz string (example, [\"/programs/Program.name/projects/Project.code\"] ).\n", "items": { "type": "string" }, "type": "array" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_description": { "description": "Brief description of the data being provided for this study. Free text", "type": "string" }, "dbgap_accession": { "description": "The dbgap accession number provided for the project (example, phs123456.v1.p1.c1).\n", "type": "string" }, "dbgap_consent": { "description": "The dbGaP consent number (example, c1).\n", "type": "string" }, "dbgap_consent_text": { "description": "The dbGaP consent text (example, HMB-IRB).\n", "type": "string" }, "dbgap_participant_set": { "description": "The dbGaP participant set (example, p1).\n", "type": "string" }, "dbgap_phs": { "description": "The dbGaP phs accession (example, phs123456).\n", "type": "string" }, "dbgap_version": { "description": "The dbGaP version (example, v1).\n", "type": "string" }, "exclude_from_aggregations": { "description": "Should the study be excluded from aggregations (e.g., Counts of total numbers of studies or total numbers of subjects) for users who are not authorized to access this study?", "type": "boolean" }, "full_name": { "description": "The full name for the project.\n", "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "projects": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "code": { "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" } }, "type": "object" } ] }, "short_name": { "description": "The shorthand name for the project.\n", "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "study_description": { "description": "A brief description of the study being performed. Free text", "type": "string" }, "study_id": { "description": "Unique identifier that can be used to retrieve more information for a study.\n", "type": "string" }, "study_registration": { "description": "External source from which the identifier included in study_id originates.\n", "type": "string" }, "study_setup": { "description": "A high level description of the setup used to achieve the study objectives.\n", "enum": [ "Genotyping", "Expression" ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "type_of_data": { "description": "Is the data raw or processed?", "enum": [ "Raw", "Processed", "Raw/Processed" ] }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "projects", "study_id", "study_registration" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state" ], "title": "Study", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "subject": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "administrative", "description": "The collection of all data related to a specific subject in the context of a specific experiment. \n", "id": "subject", "links": [ { "backref": "subjects", "label": "member_of", "multiplicity": "many_to_many", "name": "studies", "required": true, "target_type": "study" } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "amputation_type": { "description": "If amputated, the amputation type for leg, above the knee or below the knee. \u00a0 \n", "type": "string" }, "cohort_id": { "description": "The study subgroup that the participant belongs to. This indicates whether the participant was a postmortem donor, an organ donor, or a surgical donor. \u00a0 \n", "enum": [ "Postmortem", "Organ Donor (OPO)", "Surgical Donor" ] }, "consent_codes": { "description": "Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. \\n Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html \\n GRU - For general research use for any research purpose. Example of usage: This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research. \\n HMB - Use of the data is limited to health/medical/biomedical purposes; does not include the study of population origins or ancestry. \\n DS-X - Use of the data must be related to [disease]. \\n NPU - Use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. \\n IRB - Requestor must provide documentation of local IRB/REC approval.\n", "items": { "type": "string" }, "type": "array" }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_submission_guid": { "description": "A Globally Unique IDentifier (GUID) provided by the data submitter, used to identify this subject across multiple projects, commons, etc.\n", "type": "string" }, "derived_parent_subject_id": { "description": "Unique subject identifier associated with parent project; derived from parent accession and submitted subject ID.\n", "type": "string" }, "derived_topmed_subject_id": { "description": "Unique subject identifier associated with TOPMed project; derived from TOPMed accession and submitted subject ID.\n", "type": "string" }, "eligibility": { "description": "A verification field of whether the Donor has met the overall eligibility criteria for GTEx collection based on answers to eligibility questions. All Eligibility conditions require confirmation from the donor procurement team (staff team where tissue collection and data abstraction takes place) and must be met in order for donor to eligible. \u00a0\n", "type": "boolean" }, "geographic_site": { "description": "\"Site where the subject was recruted. ARIC_A=field center A representing one of four anonymized centers (Forsyth County, NC, USA; Jackson, MS, USA; the northwest suburbs of Minneapolis, MN, USA; and Washington County, MD, USA) where baseline exam was conducted for ARIC (Atherosclerosis Risk in Communities), ARIC_B=field center B representing one of four anonymized centers (Forsyth County, NC, USA; Jackson, MS, USA; the northwest suburbs of Minneapolis, MN, USA; and Washington County, MD, USA) where baseline exam was conducted for ARIC (Atherosclerosis Risk in Communities), ARIC_C=field center C representing one of four anonymized centers (Forsyth County, NC, USA; Jackson, MS, USA; the northwest suburbs of Minneapolis, MN, USA; and Washington County, MD, USA) where baseline exam was conducted for ARIC (Atherosclerosis Risk in Communities), ARIC_D=field center D representing one of four anonymized centers (Forsyth County, NC, USA; Jackson, MS, USA; the northwest suburbs of Minneapolis, MN, USA; and Washington County, MD, USA) where baseline exam was conducted for ARIC (Atherosclerosis Risk in Communities), CARDIA_1=field center 1 representing one of four anonymized field centers (University of Alabama, Birmingham, AL, USA; Northwestern University, IL, USA; University of Minnesota, MN, USA; Kaiser Foundation Research Institute, Oakland, CA, USA) for subjects in the CARE project within CARDIA (Coronary Artery Risk Development in Young Adults), CARDIA_2=field center 2 representing one of four anonymized field centers (University of Alabama, Birmingham, AL, USA; Northwestern University, IL, USA; University of Minnesota, MN, USA; Kaiser Foundation Research Institute, Oakland, CA, USA) for subjects in the CARE project within CARDIA (Coronary Artery Risk Development in Young Adults), CARDIA_3=field center 3 representing one of four anonymized field centers (University of Alabama, Birmingham, AL, USA; Northwestern University, IL, USA; University of Minnesota, MN, USA; Kaiser Foundation Research Institute, Oakland, CA, USA) for subjects in the CARE project within CARDIA (Coronary Artery Risk Development in Young Adults), CARDIA_4=field center 4 representing one of four anonymized field centers (University of Alabama, Birmingham, AL, USA; Northwestern University, IL, USA; University of Minnesota, MN, USA; Kaiser Foundation Research Institute, Oakland, CA, USA) for subjects in the CARE project within CARDIA (Coronary Artery Risk Development in Young Adults), CHS_BOWMAN.GRAY=clinic at Bowman Gray University (Forsyth County, NC, USA) for CHS (Cardiovascular Health Study), CHS_DAVIS=clinic at Davis University (Sacramento County, CA, USA) for CHS (Cardiovascular Health Study), CHS_HOPKINS=clinic at Johns Hopkins University (Washington County, MD, USA) for CHS (Cardiovascular Health Study), CHS_PITT=clinic at University of Pittsburgh (Pittsburgh, PA, USA) for CHS (Cardiovascular Health Study), COPDGene_C01=clinical center C01 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C02=clinical center C02 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C03=clinical center C03 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C04=clinical center C04 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C05=clinical center C05 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C06=clinical center C06 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C07=clinical center C07 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C08=clinical center C08 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C09=clinical center C09 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C10=clinical center C10 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C11=clinical center C11 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C12=clinical center C12 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C13=clinical center C13 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C14=clinical center C14 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C15=clinical center C15 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C16=clinical center C16 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C17=clinical center C17 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C18=clinical center C18 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C19=clinical center C19 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C20=clinical center C20 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), COPDGene_C21=clinical center C21 representing one of 21 de-identified clinical centers for COPDGene (Genetic Epidemiology of COPD), GENOA_MN=recruitment from Rochester, MN, US, GENOA_MS=recruitment from Jackson, MS, US, GOLDN_MN=recruitment center at Minneapolis, MN, USA for GOLDN (Genetics of Lipid Lowering Drugs and Diet Network Lipodemics Study), GOLDN_UT=recruitment center at Salt Lake City, UT, USA for GOLDN (Genetics of Lipid Lowering Drugs and Diet Network Lipodemics Study), HCHS_SOL_Bronx=recruitment center Bronx, NY, USA for HCHS/SOL (Hispanic Community Health Study/Study of Latinos), HCHS_SOL_Chicago=recruitment center Chicago, IL, USA for HCHS/SOL (Hispanic Community Health Study/Study of Latinos), HCHS_SOL_Miami=recruitment center Miami, FL, USA for HCHS/SOL (Hispanic Community Health Study/Study of Latinos), HCHS_SOL_SanDiego=recruitment center San Diego, CA, USA for HCHS/SOL (Hispanic Community Health Study/Study of Latinos), JHS_Hinds=recruitment from urban and rural areas of Hinds county, MS, USA for JHS (Jackson Heart Study), JHS_Madison=recruitment from urban and rural areas of Madison county, MS, USA for JHS (Jackson Heart Study), JHS_Rankin=recruitment from urban and rural areas of Rankin county, MS, USA for JHS (Jackson Heart Study), JHS_Unknown=recruitment from unknown county in MS, USA for JHS (Jackson Heart Study), Mayo_VTE_Midwest_US=state of residence (at time of enrollment for Mayo_VTE study) is in the South region of the USA as defined by the Census Bureau, Mayo_VTE_Northeast_US=state of residence (at time of enrollment for Mayo_VTE study) is in the Northeast region of the USA as defined by the Census Bureau, Mayo_VTE_non_US=state of residence (at time of enrollment for Mayo_VTE study) is from a country outside the USA, Mayo_VTE_South_US=state of residence (at time of enrollment for Mayo_VTE study) is in the Midwest region of the USA as defined by the Census Bureau, Mayo_VTE_West_US=state of residence (at time of enrollment for Mayo_VTE study) is in the West region of the USA as defined by the Census Bureau, MESA_COL=field center/baseline clinic at Columbia University, NY, USA for MESA (Multi-Ethnic Study of Atherosclerosis Cohort), MESA_JHU=field center/baseline clinic at Johns Hopkins University, MD, USA for MESA (Multi-Ethnic Study of Atherosclerosis Cohort), MESA_NWU=field center/baseline clinic at Northwestern University, IL, USA for MESA (Multi-Ethnic Study of Atherosclerosis Cohort), MESA_UCLA=field center/baseline clinic at University of California, Los Angeles, CA, USA for MESA (Multi-Ethnic Study of Atherosclerosis Cohort), MESA_UMN=field center/baseline clinic at University of Minnesota, MN, USA for MESA (Multi-Ethnic Study of Atherosclerosis Cohort), MESA_WFU=field center/baseline clinic at Wake Forest University, NC, USA for MESA (Multi-Ethnic Study of Atherosclerosis Cohort), SAS_Apia.urban=recruitment census region of Apia Urban Area in Samoa for SAS (Genome-wide Association Study of Adiposity in Samoans), SAS_NW.Upola=recruitment census region of Northwest Upola in Samoa for SAS (Genome-wide Association Study of Adiposity in Samoans), SAS_rest.Upola=recruitment census region including rest of Upola in Samoa for SAS (Genome-wide Association Study of Adiposity in Samoans), SAS_Savaii=recruitment census region of Savaii in Samoa for SAS (Genome-wide Association Study of Adiposity in Samoans), WHI_Midwest=recruitment from Midwest region of the USA for WHI (Womens Health Initiative), WHI_Northeast=recruitment from Northeast region of the USA for WHI (Womens Health Initiative), WHI_South=recruitment from South region of the USA for WHI (Womens Health Initiative), WHI_West=recruitment from West region of the USA for WHI (Womens Health Initiative)\" (HARMONIZED)\n", "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "index_date": { "description": "\"Indicates whether the time point reference begins at the donor's actual death, presumed death, or when the cross clamp was applied in the case of surgical donors.\"\n", "enum": [ "Actual Death", "Presumed Death", "Cross Clamp", "Study Enrollment", "Diagnosis", "First Patient Visit" ] }, "participant_id": { "description": "Unique identifier that can be used to retrieve more information for a participant.\n", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "studies": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "transplanted_organ": { "description": "If the Donor was an Organ Donor, which Organs were donated.\n", "type": "string" }, "type": { "type": "string" }, "unit_geographic_site": { "description": "harmonization unit for site (A \"harmonization unit\" is a defined group of subjects whose phenotypes can be similarly processed.) (HARMONIZED)\n", "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "studies", "consent_codes", "participant_id" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state" ], "title": "Subject", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "submitted_aligned_reads": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Data file containing aligned reads that are used as input to GDC workflows.\n", "id": "submitted_aligned_reads", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "submitted_aligned_reads_files", "label": "data_from", "multiplicity": "many_to_many", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" }, { "backref": "submitted_aligned_reads_files", "label": "data_from", "multiplicity": "many_to_many", "name": "read_groups", "required": false, "target_type": "read_group" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Sequencing Data", "Sequencing Reads", "Raw Sequencing Data" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "BAM", "CRAM" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Aligned Reads" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "experimental_strategy": { "enum": [ "WGS", "WXS", "Low Pass WGS", "Validation", "RNA-Seq", "miRNA-Seq", "Total RNA-Seq", "Amplicon", "scRNA-Seq", "Other" ], "term": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "read_groups": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "experimental_strategy" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Submitted Aligned Reads", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "submitted_methylation": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "DNA methylation data files contain information on raw and normalized signal intensities, detection confidence and calculated beta values for methylated and unmethylated probes. DNA methylation is an epigenetic mark which can be associated with transcriptional inactivity when located in promoter regions.", "id": "submitted_methylation", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "submitted_methylation_files", "label": "data_from", "multiplicity": "many_to_one", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" }, { "backref": "submitted_methylation_files", "label": "data_from", "multiplicity": "one_to_one", "name": "analytes", "required": false, "target_type": "analyte" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "analytes": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "assay_instrument": { "enum": [ "Illumina" ], "term": { "description": "The specific instrument type used to perform the assay. If applicable, please also indicate the instrument mode and model in 'assay_instrument_mode' and 'assay_instrument_model'." } }, "assay_instrument_model": { "enum": [ "Illumina Infinium HumanMethylation450", "Illumina Infinium HumanMethylation450K" ], "term": { "description": "The specific model of instrument used to perform the assay. Please also indicate the instrument and mode in 'assay_instrument' and 'assay_instrument_mode'." } }, "assay_method": { "enum": [ "Methylation Array" ], "term": { "description": "General methodology used to perform the assay." } }, "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "maxItems": 1, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Methylation Data" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "IDAT" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Methylation Intensity Values" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "submitter_id", "type", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Submitted Methylation", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null }, "submitted_unaligned_reads": { "$schema": "http://json-schema.org/draft-04/schema#", "additionalProperties": false, "category": "data_file", "description": "Data file containing unaligned reads that have not been GDC Harmonized.", "id": "submitted_unaligned_reads", "links": [ { "exclusive": false, "required": true, "subgroup": [ { "backref": "submitted_unaligned_reads_files", "label": "data_from", "multiplicity": "many_to_many", "name": "read_groups", "required": false, "target_type": "read_group" }, { "backref": "submitted_unaligned_reads_files", "label": "data_from", "multiplicity": "many_to_many", "name": "core_metadata_collections", "required": false, "target_type": "core_metadata_collection" } ] } ], "namespace": "https://dcp.bionimbus.org/", "program": "*", "project": "*", "properties": { "bucket_path": { "items": { "type": "string" }, "term": { "description": "The directory levels of the file as it would be found in the AWS and/or GCP bucket.\n" }, "type": "array" }, "callset": { "term": { "description": "Periodically, the TOPMed Informatics Research Center (IRC) performs variant identification and genotype calling on all samples available at a given time and the resulting call set is referred to as a genotype \"Freeze\".\n" }, "type": "string" }, "core_metadata_collections": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "created_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } }, "data_category": { "enum": [ "Sequencing Data", "Sequencing Reads", "Raw Sequencing Data" ], "term": { "description": "Broad categorization of the contents of the data file.\n" } }, "data_format": { "enum": [ "BAM", "FASTQ" ], "term": { "description": "Format of the data files.\n" } }, "data_type": { "enum": [ "Unaligned Reads" ], "term": { "description": "Specific content type of the data file.\n" } }, "error_type": { "enum": [ "file_size", "file_format", "md5sum" ], "term": { "description": "Type of error for the data file object.\n" } }, "experimental_strategy": { "enum": [ "Amplicon", "Low Pass WGS", "miRNA-Seq", "Other", "RNA-Seq", "scATAC-Seq", "scRNA-Seq", "snRNA-Seq", "Total RNA-Seq", "Validation", "WGS", "WXS" ], "term": { "description": "The sequencing strategy used to generate the data file referred to by the ga4gh_drs_uri.\n" } }, "file_format": { "term": { "description": "The format of the data file object.\n" }, "type": "string" }, "file_md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "file_name": { "term": { "description": "The name (or part of a name) of a file (of any type).\n" }, "type": "string" }, "file_size": { "term": { "description": "The size of the data file (object) in bytes.\n" }, "type": "integer" }, "file_state": { "default": "registered", "enum": [ "registered", "uploading", "uploaded", "validating", "validated", "submitted", "processing", "processed", "released", "error" ], "term": { "description": "The current state of the data file object.\n" } }, "file_type": { "term": { "description": "Specific content type of the data file. This version of the property is used for interoperation purposes.\n" }, "type": "string" }, "ga4gh_drs_uri": { "term": { "description": "DRS URI as defined by GA4GH DRS spec for pointers to file objects.\n" }, "type": "string" }, "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "systemAlias": "node_id", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "md5sum": { "pattern": "^[a-f0-9]{32}$", "term": { "description": "The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint.\n" }, "type": "string" }, "object_id": { "description": "The GUID of the object in the index service.", "type": "string" }, "project_id": { "term": { "description": "Unique ID for any specific defined piece of work that is undertaken or attempted to meet a single requirement.\n" }, "type": "string" }, "read_groups": { "anyOf": [ { "items": { "additionalProperties": true, "minItems": 1, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" }, "type": "array" }, { "additionalProperties": true, "properties": { "id": { "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", "term": { "description": "A 128-bit identifier. Depending on the mechanism used to generate it, it is either guaranteed to be different from all other UUIDs/GUIDs generated until 3400 AD or extremely likely to be different. Its relatively small size lends itself well to sorting, ordering, and hashing of all sorts, storing in databases, simple allocation, and ease of programming in general.\n", "termDef": { "cde_id": "C54100", "cde_version": null, "source": "NCIt", "term": "Universally Unique Identifier", "term_url": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" } }, "type": "string" }, "submitter_id": { "type": "string" } }, "type": "object" } ] }, "state": { "default": "validated", "downloadable": [ "uploaded", "md5summed", "validating", "validated", "error", "invalid", "released" ], "oneOf": [ { "enum": [ "uploading", "uploaded", "md5summing", "md5summed", "validating", "error", "invalid", "suppressed", "redacted", "live" ] }, { "enum": [ "validated", "submitted", "released" ] } ], "public": [ "live" ], "term": { "description": "The current state of the object.\n" } }, "submitter_id": { "description": "A project-specific identifier for a node. This property is the calling card/nickname/alias for a unit of submission. It can be used in place of the UUID for identifying or recalling a node.\n", "type": [ "string" ] }, "type": { "type": "string" }, "updated_datetime": { "oneOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "term": { "description": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]\n" } } }, "required": [ "type", "submitter_id", "file_name", "file_size", "md5sum", "data_category", "data_type", "data_format", "experimental_strategy" ], "submittable": true, "systemProperties": [ "id", "project_id", "created_datetime", "updated_datetime", "state", "file_state", "error_type" ], "title": "Submitted Unaligned Reads", "type": "object", "uniqueKeys": [ [ "id" ], [ "project_id", "submitter_id" ] ], "validators": null } }