diff --git a/.travis.yml b/.travis.yml index 974c43a06..0196e399c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,6 +6,8 @@ python: before_script: - yes | python setup.py install - git clone https://github.com/uc-cdis/dictionaryutils +- cd dictionaryutils; git checkout feat/format_upgrade; cd .. + script: - cd dictionaryutils; ./run_tests.sh; cd .. diff --git a/gdcdictionary/schemas/_definitions.yaml b/gdcdictionary/schemas/_definitions.yaml index bd91b5fdc..5208c6360 100644 --- a/gdcdictionary/schemas/_definitions.yaml +++ b/gdcdictionary/schemas/_definitions.yaml @@ -1,8 +1,8 @@ id: _definitions -UUID: +uuid: term: - $ref: "_terms.yaml#/UUID" + $ref: "_terms.yaml#/uuid" type: string pattern: "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$" @@ -10,7 +10,7 @@ parent_uuids: type: array minItems: 1 items: - $ref: "#/UUID" + $ref: "#/uuid" uniqueItems: true foreign_key_project: @@ -18,11 +18,11 @@ foreign_key_project: # Allow true here because we can have other unique keys defined on # a target type additionalProperties: true - # Can either use 'id' which are Gen3 IDs (UUID) or 'code' + # Can either use 'id' which are Gen3 IDs (uuid) or 'code' # which is the user defined ID for project properties: id: - $ref: "#/UUID" + $ref: "#/uuid" code: type: string @@ -48,11 +48,11 @@ foreign_key: # Allow true here because we can have other unique keys defined on # a target type additionalProperties: True - # Can either use 'id' which are GDC IDs (UUID) or 'submitter_id' + # Can either use 'id' which are GDC IDs (uuid) or 'submitter_id' # which are user defined IDs ("submitter IDs in the backend") properties: id: - $ref: "#/UUID" + $ref: "#/uuid" submitter_id: type: string @@ -88,7 +88,7 @@ file_name: file_size: type: integer - term: + term: $ref: "_terms.yaml#/file_size" file_format: @@ -135,7 +135,7 @@ data_file_error_type: state: term: - $ref: "_terms.yaml#/state" + $ref: "_terms.yaml#/state" default: validated downloadable: - uploaded @@ -166,7 +166,7 @@ state: file_state: term: - $ref: "_terms.yaml#/file_state" + $ref: "_terms.yaml#/file_state" default: registered enum: - registered @@ -195,7 +195,7 @@ project_id: data_file_properties: id: - $ref: "#/UUID" + $ref: "#/uuid" systemAlias: node_id submitter_id: type: @@ -211,7 +211,7 @@ data_file_properties: file_size: $ref: "#/file_size" md5sum: - $ref: "#/md5sum" + $ref: "#/md5sum" file_state: $ref: "#/file_state" object_id: @@ -222,7 +222,7 @@ data_file_properties: $ref: "#/data_file_error_type" state_comment: type: string - description: > + description: > Optional comment about why the file is in the current state, mainly for invalid state. project_id: @@ -234,7 +234,7 @@ data_file_properties: workflow_properties: id: - $ref: "#/UUID" + $ref: "#/uuid" systemAlias: node_id submitter_id: type: @@ -264,14 +264,14 @@ ubiquitous_properties: type: type: string id: - $ref: "#/UUID" + $ref: "#/uuid" systemAlias: node_id submitter_id: type: - string 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. + a unit of submission. It can be used in place of the uuid for identifying or recalling a node. state: $ref: "#/state" project_id: diff --git a/gdcdictionary/schemas/_terms.yaml b/gdcdictionary/schemas/_terms.yaml index 0ca296bac..442940b4b 100644 --- a/gdcdictionary/schemas/_terms.yaml +++ b/gdcdictionary/schemas/_terms.yaml @@ -1,1841 +1,2553 @@ + id: _terms 28s_16s_ribosomal_rna_ratio: - description: > - The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA. - termDef: - term: "28s/18s Ribosomal RNA Ratio" - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA. + termDef: + term: >- + 28s/18s Ribosomal RNA Ratio + source: + cde_id: + cde_version: + term_url: 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. - termDef: - term: Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value - source: caDSR - cde_id: 5432595 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" - -adapter_name: # TOREVIEW - description: > - Name of the sequencing adapter. - -adapter_sequence: # TOREVIEW - description: > - Base sequence of the sequencing adapter. + common: + 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. + termDef: + term: >- + Nucleic Acid Absorbance at 260 And Absorbance at 280 DNA Purity Ratio Value + source: caDSR + cde_id: 5432595 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432595&version=1.0" + +adapter_name: + common: + description: >- + Name of the sequencing adapter. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +adapter_sequence: + common: + description: >- + Base sequence of the sequencing adapter. + termDef: + term: + source: + cde_id: + cde_version: + term_url: age_at_diagnosis: - description: > - Age at the time of diagnosis expressed in number of days since birth. - termDef: - term: Patient Diagnosis Age Day Value - source: caDSR - cde_id: 3225640 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" + common: + description: >- + Age at the time of diagnosis expressed in number of days since birth. + termDef: + term: >- + Patient Diagnosis Age Day Value + source: caDSR + cde_id: 3225640 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225640&version=2.0" ajcc_clinical_m: - description: > - Extent of the distant metastasis for the cancer based on evidence obtained from clinical - assessment parameters determined prior to treatment. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage - source: caDSR - cde_id: 3440331 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440331&version=1.0" + common: + description: >- + Extent of the distant metastasis for the cancer based on evidence obtained from + clinical assessment parameters determined prior to treatment. + termDef: + term: >- + Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M + Stage + source: caDSR + cde_id: 3440331 + cde_version: 1.0 + 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. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage - source: caDSR - cde_id: 3440330 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440330&version=1.0" + common: + description: >- + Extent of the regional lymph node involvement for the cancer based on evidence + obtained from clinical assessment parameters determined prior to treatment. + termDef: + term: >- + Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N + Stage + source: caDSR + cde_id: 3440330 + cde_version: 1.0 + 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. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Group Stage - source: caDSR - cde_id: 3440332 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440332&version=1.0" + common: + 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. + termDef: + term: >- + Neoplasm American Joint Committee on Cancer Clinical Group Stage + source: caDSR + cde_id: 3440332 + cde_version: 1.0 + 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. - termDef: - term: Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage - source: caDSR - cde_id: 3440328 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3440328&version=1.0" + common: + description: >- + Extent of the primary cancer based on evidence obtained from clinical assessment + parameters determined prior to treatment. + termDef: + term: >- + Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage + source: caDSR + cde_id: 3440328 + cde_version: 1.0 + 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). - termDef: - term: American Joint Committee on Cancer Metastasis Stage Code - source: caDSR - cde_id: 3045439 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045439&version=1.0" + common: + 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). + termDef: + term: >- + American Joint Committee on Cancer Metastasis Stage Code + source: caDSR + cde_id: 3045439 + cde_version: 1.0 + 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. - termDef: - term: Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code - source: caDSR - cde_id: 3203106 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203106&version=1.0" + common: + 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. + termDef: + term: >- + Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203106 + cde_version: 1.0 + 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. - termDef: - term: Neoplasm Disease Stage American Joint Committee on Cancer Code - source: caDSR - cde_id: 3203222 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3203222&version=1.0" + common: + 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. + termDef: + term: >- + Neoplasm Disease Stage American Joint Committee on Cancer Code + source: caDSR + cde_id: 3203222 + cde_version: 1.0 + 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). - termDef: - term: American Joint Committee on Cancer Tumor Stage Code - source: caDSR - cde_id: 3045435 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3045435&version=1.0" + common: + 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). + termDef: + term: >- + American Joint Committee on Cancer Tumor Stage Code + source: caDSR + cde_id: 3045435 + cde_version: 1.0 + 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. - termDef: - term: Alcohol Lifetime History Indicator - source: caDSR - cde_id: 2201918 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2201918&version=1.0" + common: + 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. + termDef: + term: >- + Alcohol Lifetime History Indicator + source: caDSR + cde_id: 2201918 + cde_version: 1.0 + 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. - termDef: - term: Person Self-Report Alcoholic Beverage Exposure Category - source: caDSR - cde_id: 3457767 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3457767&version=1.0" + common: + description: >- + Category to describe the patient's current level of alcohol use as self-reported + by the patient. + termDef: + term: >- + Person Self-Report Alcoholic Beverage Exposure Category + source: caDSR + cde_id: 3457767 + cde_version: 1.0 + 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. - termDef: - term: Biospecimen Aliquot Quantity - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The quantity in micrograms (ug) of the aliquot(s) derived from the analyte(s) + shipped for sequencing and characterization. + termDef: + term: >- + Biospecimen Aliquot Quantity + source: + cde_id: + cde_version: + term_url: aliquot_volume: - description: > - The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) shipped for - sequencing and characterization. - termDef: - term: Biospecimen Aliquot Volume - source: null - cde_id: null - cde_version: null - term_url: null - -amount: # TOREVIEW - description: > - Weight in grams or volume in mL. + common: + description: >- + The volume in microliters (ml) of the aliquot(s) derived from the analyte(s) + shipped for sequencing and characterization. + termDef: + term: >- + Biospecimen Aliquot Volume + source: + cde_id: + cde_version: + term_url: + +amount: + common: + description: >- + Weight in grams or volume in mL. + termDef: + term: + source: + cde_id: + cde_version: + term_url: analyte_quantity: - description: > - The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) shipped for - sequencing and characterization. - termDef: - term: Biospecimen Analyte Quantity - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The quantity in micrograms (ug) of the analyte(s) derived from the analyte(s) + shipped for sequencing and characterization. + termDef: + term: >- + Biospecimen Analyte Quantity + source: + cde_id: + cde_version: + term_url: analyte_type: - description: > - Text term that represents the kind of molecular specimen analyte. - termDef: - term: Molecular Specimen Type Text Name - source: caDSR - cde_id: 2513915 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2513915&version=2.0" + common: + description: >- + Text term that represents the kind of molecular specimen analyte. + termDef: + term: >- + Molecular Specimen Type Text Name + source: caDSR + cde_id: 2513915 + cde_version: 2.0 + 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. - termDef: - term: Molecular Analyte Identification Code - source: caDSR - cde_id: 5432508 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432508&version=1.0" + common: + description: >- + A single letter code used to identify a type of molecular analyte. + termDef: + term: >- + Molecular Analyte Identification Code + source: caDSR + cde_id: 5432508 + cde_version: 1.0 + 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. - termDef: - term: Biospecimen Analyte Volume - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The volume in microliters (ml) of the analyte(s) derived from the analyte(s) + shipped for sequencing and characterization. + termDef: + term: >- + Biospecimen Analyte Volume + source: + cde_id: + cde_version: + term_url: ann_arbor_b_symptoms: - description: > - Text term to signify whether lymphoma B-symptoms are present as noted in the patient's medical - record. - termDef: - term: Lymphoma B-Symptoms Medical Record Documented Indicator - source: caDSR - cde_id: 2902402 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2902402&version=1.0" + common: + description: >- + Text term to signify whether lymphoma B-symptoms are present as noted in the + patient's medical record. + termDef: + term: >- + Lymphoma B-Symptoms Medical Record Documented Indicator + source: caDSR + cde_id: 2902402 + cde_version: 1.0 + 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. - termDef: - term: Ann Arbor Clinical Stage - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The classification of the clinically confirmed anatomic disease extent of lymphoma + (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: >- + Ann Arbor Clinical Stage + source: + cde_id: + cde_version: + term_url: ann_arbor_extranodal_involvement: - description: > - Indicator that identifies whether a patient with malignant lymphoma has lymphomatous involvement - of an extranodal site. - termDef: - term: Lymphomatous Extranodal Site Involvement Indicator - source: caDSR - cde_id: 3364582 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3364582&version=1.0" + common: + description: >- + Indicator that identifies whether a patient with malignant lymphoma has lymphomatous + involvement of an extranodal site. + termDef: + term: >- + Lymphomatous Extranodal Site Involvement Indicator + source: caDSR + cde_id: 3364582 + cde_version: 1.0 + 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. - termDef: - term: Ann Arbor Pathologic Stage - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The classification of the pathologically confirmed anatomic disease extent of + lymphoma (Hodgkin's and Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: >- + Ann Arbor Pathologic Stage + source: + cde_id: + cde_version: + term_url: 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. - termDef: - term: Ann Arbor Tumor Stage - source: null - cde_id: null - cde_version: null - term_url: null - -base_caller_name: # TOREVIEW - description: > - Name of the base caller. - -base_caller_version: # TOREVIEW - description: > - Version of the base caller. + common: + description: >- + The classification of the anatomic disease extent of lymphoma (Hodgkin's and + Non-Hodgkins) based on the Ann Arbor Staging System. + termDef: + term: >- + Ann Arbor Tumor Stage + source: + cde_id: + cde_version: + term_url: + +base_caller_name: + common: + description: >- + Name of the base caller. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +base_caller_version: + common: + description: >- + Version of the base caller. + termDef: + term: + source: + cde_id: + cde_version: + term_url: biomarker_name: - description: > - The name of the biomarker being tested for this specimen and set of test results. - termDef: - term: Biomarker Name - source: caDSR - cde_id: 5473 - cde_version: 11.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5473&version=2.31" + common: + description: >- + The name of the biomarker being tested for this specimen and set of test results. + termDef: + term: >- + Biomarker Name + source: caDSR + cde_id: 5473 + cde_version: 11.0 + 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. - termDef: - term: Laboratory Procedure Genetic Abnormality Test Result Type - source: caDSR - cde_id: 3234680 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3234680&version=1.0" + common: + description: >- + Text term to define the results of genetic testing. + termDef: + term: >- + Laboratory Procedure Genetic Abnormality Test Result Type + source: caDSR + cde_id: 3234680 + cde_version: 1.0 + 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. - termDef: - term: Disease Detection Molecular Analysis Method Type - source: caDSR - cde_id: 3121575 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121575&version=1.0" + common: + description: >- + Text descriptor of a molecular analysis method used for an individual. + termDef: + term: >- + Disease Detection Molecular Analysis Method Type + source: caDSR + cde_id: 3121575 + cde_version: 1.0 + 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. - termDef: - term: Submitted Tumor Sample Primary Anatomic Site - source: caDSR - cde_id: 4742851 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4742851&version=1.0" + common: + description: >- + Text term that represents the name of the primary disease site of the submitted + tumor sample. + termDef: + term: >- + Submitted Tumor Sample Primary Anatomic Site + source: caDSR + cde_id: 4742851 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4742851&version=1.0" bmi: - description: > - The body mass divided by the square of the body height expressed in units of kg/m^2. - termDef: - term: Body Mass Index (BMI) - source: caDSR - cde_id: 4973892 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" + common: + description: >- + The body mass divided by the square of the body height expressed in units of + kg/m^2. + termDef: + term: >- + Body Mass Index (BMI) + source: caDSR + cde_id: 4973892 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4973892&version=1.0" burkitt_lymphoma_clinical_variant: - description: > - Burkitt's lymphoma categorization based on clinical features that differ from other forms of the - same disease. - termDef: - term: Burkitt Lymphoma Clinical Variant Type - source: caDSR - cde_id: 3770421 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" + common: + description: >- + Burkitt's lymphoma categorization based on clinical features that differ from + other forms of the same disease. + termDef: + term: >- + Burkitt Lymphoma Clinical Variant Type + source: caDSR + cde_id: 3770421 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3770421&version=1.0" cause_of_death: - description: > - Text term to identify the cause of death for a patient. - termDef: - term: Patient Death Reason - source: caDSR - cde_id: 2554674 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2554674&version=3.0" + common: + description: >- + Text term to identify the cause of death for a patient. + termDef: + term: >- + Patient Death Reason + source: caDSR + cde_id: 2554674 + cde_version: 3.0 + 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] - termDef: - term: Preoperative Carcinoembryonic Antigen Result Value - source: caDSR - cde_id: 2716510 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2716510&version=1.0" + common: + description: >- + Numeric value of the Carcinoembryonic antigen or CEA at the time before surgery. + [Manually- curated] + termDef: + term: >- + Preoperative Carcinoembryonic Antigen Result Value + source: caDSR + cde_id: 2716510 + cde_version: 1.0 + 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. - termDef: - term: Smoking Use Average Number - source: caDSR - cde_id: 2001716 - cde_version: 4.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2001716&version=4.0" + common: + description: >- + The average number of cigarettes smoked per day. + termDef: + term: >- + Smoking Use Average Number + source: caDSR + cde_id: 2001716 + cde_version: 4.0 + 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. - termDef: - term: Colorectal Surgical Margin Circumferential Distance Measurement - source: caDSR - cde_id: 64202 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64202&version=3.0" + common: + 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. + termDef: + term: >- + Colorectal Surgical Margin Circumferential Distance Measurement + source: caDSR + cde_id: 64202 + cde_version: 3.0 + 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. - termDef: - term: Tumor Tissue Disease Description Type - source: caDSR - cde_id: 3288124 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + common: + description: >- + Text that describes the kind of disease present in the tumor specimen as related + to a specific timepoint. + termDef: + term: >- + Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + 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). - termDef: - term: Colon Carcinoma Polyp Occurrence Indicator - source: caDSR - cde_id: 3107197 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3107197&version=1.0" + common: + 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). + termDef: + term: >- + Colon Carcinoma Polyp Occurrence Indicator + source: caDSR + cde_id: 3107197 + cde_version: 1.0 + 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. - termDef: - term: Biospecimen Cellular Composition Type - source: caDSR - cde_id: 5432591 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432591&version=1.0" + common: + description: >- + Text term that represents the cellular composition of the sample. + termDef: + term: >- + Biospecimen Cellular Composition Type + source: caDSR + cde_id: 5432591 + cde_version: 1.0 + 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. - termDef: - term: Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter Value - source: caDSR - cde_id: 5432594 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432594&version=1.0" + common: + description: >- + Numeric value that represents the concentration of an analyte or aliquot extracted + from the sample or sample portion, measured in milligrams per milliliter. + termDef: + term: >- + Biospecimen Analyte or Aliquot Extracted Concentration Milligram per Milliliter + Value + source: caDSR + cde_id: 5432594 + cde_version: 1.0 + 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. - termDef: - term: Biospecimen Portion Creation Seconds Date/Time - source: caDSR - cde_id: 5432592 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432592&version=1.0" + common: + description: >- + The datetime of portion creation encoded as seconds from epoch. + termDef: + term: >- + Biospecimen Portion Creation Seconds Date/Time + source: caDSR + cde_id: 5432592 + cde_version: 1.0 + 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. - termDef: - term: Tissue Sample Current Weight Milligram Value - source: caDSR - cde_id: 5432606 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" - -data_category: # TOREVIEW - description: > - Broad categorization of the contents of the data file. - -data_file_error_type: # TOREVIEW - description: > - Type of error for the data file object. - -data_format: # TOREVIEW - description: > - Format of the data files. - -data_type: # TOREVIEW - description: > - Specific content type of the data file. + common: + description: >- + Numeric value that represents the current weight of the sample, measured in + milligrams. + termDef: + term: >- + Tissue Sample Current Weight Milligram Value + source: caDSR + cde_id: 5432606 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432606&version=1.0" + +data_category: + common: + description: >- + Broad categorization of the contents of the data file. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +data_file_error_type: + common: + description: >- + Type of error for the data file object. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +data_format: + common: + description: >- + Format of the data files. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +data_type: + common: + description: >- + Specific content type of the data file. + termDef: + term: + source: + cde_id: + cde_version: + term_url: datetime: - description: > - A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] + common: + description: >- + A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] + termDef: + term: + source: + cde_id: + cde_version: + term_url: 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. - termDef: - term: Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008233 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008233&version=1.0" + common: + 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. + termDef: + term: >- + Person Birth Date Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3008233 + cde_version: 1.0 + 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. - termDef: - term: Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008340 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008340&version=1.0" + common: + description: >- + Time interval from the date of biospecimen collection to the date of initial + pathologic diagnosis, represented as a calculated number of days. + termDef: + term: >- + Biospecimen Collection Date Less Initial Pathologic Diagnosis Date Calculated + Day Value + source: caDSR + cde_id: 3008340 + cde_version: 1.0 + 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. - termDef: - term: Death Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3165475 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3165475&version=1.0" + common: + description: >- + Time interval from a person's date of death to the date of initial pathologic + diagnosis, represented as a calculated number of days. + termDef: + term: >- + Death Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3165475 + cde_version: 1.0 + 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. - termDef: - term: Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis Time Duration Day Calculation Value - source: caDSR - cde_id: 4618491 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4618491&version=1.0" + common: + 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. + termDef: + term: >- + Human Immunodeficiency Virus Diagnosis Subtract Initial Pathologic Diagnosis + Time Duration Day Calculation Value + source: caDSR + cde_id: 4618491 + cde_version: 1.0 + 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. - termDef: - term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008273 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + common: + description: >- + Time interval from the date of last follow up to the date of initial pathologic + diagnosis, represented as a calculated number of days. + termDef: + term: >- + Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated + Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + 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. - termDef: - term: Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3008273 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008273&version=1.0" + common: + description: >- + Time interval from the date of last follow up to the date of initial pathologic + diagnosis, represented as a calculated number of days. + termDef: + term: >- + Last Communication Contact Less Initial Pathologic Diagnosis Date Calculated + Day Value + source: caDSR + cde_id: 3008273 + cde_version: 1.0 + 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. - termDef: - term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3392464 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + common: + 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. + termDef: + term: >- + New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + 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. - termDef: - term: New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value - source: caDSR - cde_id: 3392464 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3392464&version=1.0" + common: + 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. + termDef: + term: >- + New Tumor Event Less Initial Pathologic Diagnosis Date Calculated Day Value + source: caDSR + cde_id: 3392464 + cde_version: 1.0 + 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. + common: + description: >- + The number of days from the date the patient was diagnosed to the date of the + procedure that produced the sample. + termDef: + term: + source: + cde_id: + cde_version: + term_url: days_to_treatment: - description: > - Number of days from date of initial pathologic diagnosis that treatment began. - termDef: - term: Days to Treatment Start - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + Number of days from date of initial pathologic diagnosis that treatment began. + termDef: + term: >- + Days to Treatment Start + source: + cde_id: + cde_version: + term_url: 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. - termDef: - term: Treatment End Subtract First Pathologic Diagnosis Day Calculation Value - source: caDSR - cde_id: 5102431 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102431&version=1.0" + common: + description: >- + Time interval from the date of the initial pathologic diagnosis to the date + of treatment end, represented as a calculated number of days. + termDef: + term: >- + Treatment End Subtract First Pathologic Diagnosis Day Calculation Value + source: caDSR + cde_id: 5102431 + cde_version: 1.0 + 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. - termDef: - term: Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value - source: caDSR - cde_id: 5102411 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102411&version=1.0" + common: + description: >- + Time interval from the date of the initial pathologic diagnosis to the start + of treatment, represented as a calculated number of days. + termDef: + term: >- + Treatment Start Subtract First Pathologic Diagnosis Time Day Calculation Value + source: caDSR + cde_id: 5102411 + cde_version: 1.0 + 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). - termDef: - term: Post-Diagnostic Pathology Review Confirmation - source: null - cde_id: null - cde_version: null - term_url: null + common: + 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). + termDef: + term: >- + Post-Diagnostic Pathology Review Confirmation + source: + cde_id: + cde_version: + term_url: 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. - termDef: - term: Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value Percentage Value - source: caDSR - cde_id: 2180255 - cde_version: 1.0 - 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. - termDef: - term: Encoding - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + common: + description: >- + The value, as a percentage of predicted lung volume, measuring the amount of + carbon monoxide detected in a patient's lungs. + termDef: + term: >- + Lung Carbon Monoxide Diffusing Capability Test Assessment Predictive Value + Percentage Value + source: caDSR + cde_id: 2180255 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2180255&version=1.0" + +encoding: + common: + description: >- + Version of ASCII encoding of quality values found in the file. + termDef: + term: >- + Encoding + source: FastQC + cde_id: + cde_version: + 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. - termDef: - term: ER Level Cell Percentage Category - source: caDSR - cde_id: 3128341 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128341&version=1.0" + common: + description: >- + Classification to represent ER Positive results expressed as a percentage value. + termDef: + term: >- + ER Level Cell Percentage Category + source: caDSR + cde_id: 3128341 + cde_version: 1.0 + 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. - termDef: - term: Breast Carcinoma Estrogen Receptor Status - source: caDSR - cde_id: 2957359 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957359&version=2.0" + common: + description: >- + Text term to represent the overall result of Estrogen Receptor (ER) testing. + termDef: + term: >- + Breast Carcinoma Estrogen Receptor Status + source: caDSR + cde_id: 2957359 + cde_version: 2.0 + 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. 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. - termDef: - term: Ethnic Group Category Text - source: caDSR - cde_id: 2192217 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" - -experiment_name: # TOREVIEW - description: > - Submitter-defined name for the experiment. - -experimental_strategy: # TOREVIEW - description: > - The sequencing strategy used to generate the data file. - -fastq_name: # TOREVIEW - description: > - Names of FASTQs. + common: + description: >- + An individual's self-described social and cultural grouping, specifically whether + an individual describes themselves as Hispanic or Latino. 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. + termDef: + term: >- + Ethnic Group Category Text + source: caDSR + cde_id: 2192217 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192217&version=2.0" + +experiment_name: + common: + description: >- + Submitter-defined name for the experiment. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +experimental_strategy: + common: + description: >- + The sequencing strategy used to generate the data file. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +fastq_name: + common: + description: >- + Names of FASTQs. + termDef: + term: + source: + cde_id: + cde_version: + term_url: 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. - termDef: - term: Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value - source: caDSR - cde_id: 3302948 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302948&version=1.0" + common: + 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. + termDef: + term: >- + Post Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302948 + cde_version: 1.0 + 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. - termDef: - term: Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value - source: caDSR - cde_id: 3302947 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" + common: + 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. + termDef: + term: >- + Pre Bronchodilator Lung Forced Expiratory Volume 1 Test Lab Percentage Value + source: caDSR + cde_id: 3302947 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302947&version=1.0" 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. - termDef: - term: Post Bronchodilator FEV1/FVC Percent Value - source: caDSR - cde_id: 3302956 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302956&version=1.0" + common: + description: >- + Percentage value to represent result of Forced Expiratory Volume in 1 second + (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator. + termDef: + term: >- + Post Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302956 + cde_version: 1.0 + 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. - termDef: - term: Pre Bronchodilator FEV1/FVC Percent Value - source: caDSR - cde_id: 3302955 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&version=1.0" + common: + description: >- + Percentage value to represent result of Forced Expiratory Volume in 1 second + (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator. + termDef: + term: >- + Pre Bronchodilator FEV1/FVC Percent Value + source: caDSR + cde_id: 3302955 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3302955&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. - termDef: - term: Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage - source: caDSR - cde_id: 3225684 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" - -file_name: # TOREVIEW - description: > - The name (or part of a name) of a file (of any type). - -file_size: # TOREVIEW - description: > - The size of the data file (object) in bytes. - -file_state: # TOREVIEW - description: > - The current state of the data file object. - -flow_cell_barcode: # TOREVIEW - description: > - Flow Cell Barcode. + common: + 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. + termDef: + term: >- + Gynecologic Tumor Grouping Cervical Endometrial FIGO 2009 Stage + source: caDSR + cde_id: 3225684 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3225684&version=1.0" + +file_name: + common: + description: >- + The name (or part of a name) of a file (of any type). + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +file_size: + common: + description: >- + The size of the data file (object) in bytes. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +file_state: + common: + description: >- + The current state of the data file object. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +flow_cell_barcode: + common: + description: >- + Flow Cell Barcode. + termDef: + term: + source: + cde_id: + cde_version: + term_url: freezing_method: - description: > - Text term that represents the method used for freezing the sample. - termDef: - term: Tissue Sample Freezing Method Type - source: caDSR - cde_id: 5432607 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" + common: + description: >- + Text term that represents the method used for freezing the sample. + termDef: + term: >- + Tissue Sample Freezing Method Type + source: caDSR + cde_id: 5432607 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432607&version=1.0" gender: - description: > - Text designations that identify gender. Gender is described as the assemblage of properties that - distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification - of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] - termDef: - term: Person Gender Text Type - source: caDSR - cde_id: 2200604 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" + common: + description: >- + Text designations that identify gender. Gender is described as the assemblage + of properties that distinguish people on the basis of their societal roles. + [Explanatory Comment 1: Identification of gender is based upon self-report and + may come from a form, questionnaire, interview, etc.] + termDef: + term: >- + Person Gender Text Type + source: caDSR + cde_id: 2200604 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2200604&version=3.0" height: - description: > - The height of the patient in centimeters. - termDef: - term: Patient Height Measurement - source: caDSR - cde_id: 649 - cde_version: 4.1 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=649&version=4.1" + common: + description: >- + The height of the patient in centimeters. + termDef: + term: >- + Patient Height Measurement + source: caDSR + cde_id: 649 + cde_version: 4.1 + 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. - termDef: - term: HER2 ERBB Positive Finding Cell Percentage Category - source: caDSR - cde_id: 3086980 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3086980&version=1.0" + common: + description: >- + Classification to represent the number of positive HER2/ERBB2 cells in a specimen + or sample. + termDef: + term: >- + HER2 ERBB Positive Finding Cell Percentage Category + source: caDSR + cde_id: 3086980 + cde_version: 1.0 + 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. - termDef: - term: Laboratory Procedure HER2/neu in situ Hybridization Outcome Type - source: caDSR - cde_id: 2854089 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2854089&version=1.0" + common: + description: >- + the type of outcome for HER2 as determined by an in situ hybridization (ISH) + assay. + termDef: + term: >- + Laboratory Procedure HER2/neu in situ Hybridization Outcome Type + source: caDSR + cde_id: 2854089 + cde_version: 1.0 + 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. - termDef: - term: Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status - source: caDSR - cde_id: 2957563 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957563&version=2.0" + common: + 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. + termDef: + term: >- + Laboratory Procedure HER2/neu Immunohistochemistry Receptor Status + source: caDSR + cde_id: 2957563 + cde_version: 2.0 + 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. - termDef: - term: Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable Indicator - source: caDSR - cde_id: 4030799 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4030799&version=1.0" + common: + description: >- + Text term to signify whether a physician has diagnosed HIV infection in a patient. + termDef: + term: >- + Physician Diagnosed HIV Infection Personal Medical History Yes No Not Applicable + Indicator + source: caDSR + cde_id: 4030799 + cde_version: 1.0 + 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. - termDef: - term: Human Papillomavirus Type - source: caDSR - cde_id: 2922649 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2922649&version=1.0" + common: + description: >- + Text classification to represent the strain or type of human papillomavirus + identified in an individual. + termDef: + term: >- + Human Papillomavirus Type + source: caDSR + cde_id: 2922649 + cde_version: 1.0 + 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. - termDef: - term: Oncogenic Human Papillomavirus Result Type - source: caDSR - cde_id: 2230033 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" - -includes_spike_ins: # TOREVIEW - description: > - Spike-in included? + common: + description: >- + The findings of the oncogenic HPV. + termDef: + term: >- + Oncogenic Human Papillomavirus Result Type + source: caDSR + cde_id: 2230033 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2230033&version=1.0" + +includes_spike_ins: + common: + description: >- + Spike-in included? + termDef: + term: + source: + cde_id: + cde_version: + term_url: initial_weight: - description: > - Numeric value that represents the initial weight of the sample, measured in milligrams. - termDef: - term: Tissue Sample Initial Weight Milligram Value - source: caDSR - cde_id: 5432605 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432605&version=1.0" + common: + description: >- + Numeric value that represents the initial weight of the sample, measured in + milligrams. + termDef: + term: >- + Tissue Sample Initial Weight Milligram Value + source: caDSR + cde_id: 5432605 + cde_version: 1.0 + 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. - termDef: - term: Tissue Sample Intermediate Dimension Millimeter Measurement - source: caDSR - cde_id: 5432604 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" - -intermediate_dimension: # TOREVIEW - description: > - Intermediate dimension of the sample, in millimeters. + common: + description: >- + Numeric value that represents the sample dimension that is greater than the + shortest dimension and less than the longest dimension, measured in millimeters. + termDef: + term: >- + Tissue Sample Intermediate Dimension Millimeter Measurement + source: caDSR + cde_id: 5432604 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432604&version=1.0" + +intermediate_dimension: + common: + description: >- + Intermediate dimension of the sample, in millimeters. + termDef: + term: + source: + cde_id: + cde_version: + term_url: is_ffpe: - description: > - Indicator to signify whether or not the tissue sample was fixed in formalin and embedded in - paraffin (FFPE). - termDef: - term: Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator - source: caDSR - cde_id: 4170557 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" - -is_paired_end: # TOREVIEW - description: > - Are the reads paired end? + common: + description: >- + Indicator to signify whether or not the tissue sample was fixed in formalin + and embedded in paraffin (FFPE). + termDef: + term: >- + Specimen Processing Formalin Fixed Paraffin Embedded Tissue Indicator + source: caDSR + cde_id: 4170557 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4170557&version=1.0" + +is_paired_end: + common: + description: >- + Are the reads paired end? + termDef: + term: + source: + cde_id: + cde_version: + term_url: last_known_disease_status: - description: > - Text term that describes the last known state or condition of an individual's neoplasm. - termDef: - term: Person Last Known Neoplasm Status - source: caDSR - cde_id: 5424231 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2759550&version=1.0" + common: + description: >- + Text term that describes the last known state or condition of an individual's + neoplasm. + termDef: + term: >- + Person Last Known Neoplasm Status + source: caDSR + cde_id: 5424231 + cde_version: 1.0 + 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. - termDef: - term: Primary Tumor Laterality - source: caDSR - cde_id: 827 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=827&version=3.0" + common: + description: >- + For tumors in paired organs, designates the side on which the cancer originates. + termDef: + term: >- + Primary Tumor Laterality + source: caDSR + cde_id: 827 + cde_version: 3.0 + 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. - termDef: - term: Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place Value - source: caDSR - cde_id: 2798766 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2798766&version=1.0" + common: + description: >- + The 2 decimal place numeric laboratory value measured, assigned or computed + related to the assessment of lactate dehydrogenase in a specimen. + termDef: + term: >- + Laboratory Procedure Lactate Dehydrogenase Result Integer::2 Decimal Place + Value + source: caDSR + cde_id: 2798766 + cde_version: 1.0 + 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). - termDef: - term: Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value - source: caDSR - cde_id: 2597015 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" - -library_strategy: # TOREVIEW - description: > - Library strategy. - -library_selection: # TOREVIEW - description: > - Library Selection Method - -library_name: # TOREVIEW - description: > - Name of the library. - -library_preparation_kit_name: # TOREVIEW - description: > - Name of Library Preparation Kit - -library_preparation_kit_vendor: # TOREVIEW - description: > - Vendor of Library Preparation Kit - -library_preparation_kit_catalog_number: # TOREVIEW - description: > - Catalog of Library Preparation Kit - -library_preparation_kit_version: # TOREVIEW - description: > - Version of Library Preparation Kit - -library_strand: # TOREVIEW - description: > - Library stranded-ness. + common: + 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). + termDef: + term: >- + Laboratory Procedure Lactate Dehydrogenase Result Upper Limit of Normal Value + source: caDSR + cde_id: 2597015 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2597015&version=1.0" + +library_strategy: + common: + description: >- + Library strategy. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +library_selection: + common: + description: >- + Library Selection Method + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +library_name: + common: + description: >- + Name of the library. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +library_preparation_kit_name: + common: + description: >- + Name of Library Preparation Kit + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +library_preparation_kit_vendor: + common: + description: >- + Vendor of Library Preparation Kit + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +library_preparation_kit_catalog_number: + common: + description: >- + Catalog of Library Preparation Kit + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +library_preparation_kit_version: + common: + description: >- + Version of Library Preparation Kit + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +library_strand: + common: + description: >- + Library stranded-ness. + termDef: + term: + source: + cde_id: + cde_version: + term_url: longest_dimension: - description: > - Numeric value that represents the longest dimension of the sample, measured in millimeters. - termDef: - term: Tissue Sample Longest Dimension Millimeter Measurement - source: caDSR - cde_id: 5432602 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432602&version=1.0" + common: + description: >- + Numeric value that represents the longest dimension of the sample, measured + in millimeters. + termDef: + term: >- + Tissue Sample Longest Dimension Millimeter Measurement + source: caDSR + cde_id: 5432602 + cde_version: 1.0 + 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. - termDef: - term: Lymph Node(s) Positive Number - source: caDSR - cde_id: 89 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=89&version=3.0" + common: + description: >- + The number of lymph nodes involved with disease as determined by pathologic + examination. + termDef: + term: >- + Lymph Node(s) Positive Number + source: caDSR + cde_id: 89 + cde_version: 3.0 + 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 - termDef: - term: Lymphatic/Small vessel Invasion Ind - source: caDSR - cde_id: 64171 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" + common: + description: >- + A yes/no indicator to ask if small or thin-walled vessel invasion is present, + indicating lymphatic involvement + termDef: + term: >- + Lymphatic/Small vessel Invasion Ind + source: caDSR + cde_id: 64171 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64171&version=3.0" method_of_diagnosis: - description: > - The method used to initially the patient's diagnosis. - termDef: - term: Method of Diagnosis - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The method used to initially the patient's diagnosis. + termDef: + term: >- + Method of Diagnosis + source: + cde_id: + cde_version: + term_url: method_of_sample_procurement: - description: > - The method used to procure the sample used to extract analyte(s). - termDef: - term: Method of Sample Procurement - source: null - cde_id: null - cde_version: null - term_url: null - -md5sum: # TOREVIEW - description: > - The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital - fingerprint. + common: + description: >- + The method used to procure the sample used to extract analyte(s). + termDef: + term: >- + Method of Sample Procurement + source: + cde_id: + cde_version: + term_url: + +md5sum: + common: + description: >- + The 128-bit hash value expressed as a 32 digit hexadecimal number used as a + file's digital fingerprint. + termDef: + term: + source: + cde_id: + cde_version: + term_url: microsatellite_instability_abnormal: - description: > - The yes/no indicator to signify the status of a tumor for microsatellite instability. - termDef: - term: Microsatellite Instability Occurrence Indicator - source: caDSR - cde_id: 3123142 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3123142&version=1.0" + common: + description: >- + The yes/no indicator to signify the status of a tumor for microsatellite instability. + termDef: + term: >- + Microsatellite Instability Occurrence Indicator + source: caDSR + cde_id: 3123142 + cde_version: 1.0 + 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. - termDef: - term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code - source: caDSR - cde_id: 3226275 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226275&version=1.0" + common: + 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. + termDef: + term: >- + International Classification of Diseases for Oncology, Third Edition ICD-O-3 + Histology Code + source: caDSR + cde_id: 3226275 + cde_version: 1.0 + 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. - termDef: - term: New Neoplasm Event Occurrence Anatomic Site - source: caDSR - cde_id: 3108271 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3108271&version=2.0" + common: + description: >- + Text term to specify the anatomic location of the return of tumor after treatment. + termDef: + term: >- + New Neoplasm Event Occurrence Anatomic Site + source: caDSR + cde_id: 3108271 + cde_version: 2.0 + 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. - termDef: - term: New Neoplasm Event Type - source: caDSR - cde_id: 3119721 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3119721&version=1.0" + common: + description: >- + Text term to identify a new tumor event. + termDef: + term: >- + New Neoplasm Event Type + source: caDSR + cde_id: 3119721 + cde_version: 1.0 + 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. - termDef: - term: Normal Tumor Genotype Match Indicator - source: caDSR - cde_id: 4588156 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4588156&version=1.0" + common: + description: >- + Text term that represents whether or not the genotype of the normal tumor matches + or if the data is not available. + termDef: + term: >- + Normal Tumor Genotype Match Indicator + source: caDSR + cde_id: 4588156 + cde_version: 1.0 + 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). - termDef: - term: Pathology Review Slide Proliferating Cell Count - source: caDSR - cde_id: 5432636 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432636&version=1.0" + common: + description: >- + Numeric value that represents the count of proliferating cells determined during + pathologic review of the sample slide(s). + termDef: + term: >- + Pathology Review Slide Proliferating Cell Count + source: caDSR + cde_id: 5432636 + cde_version: 1.0 + 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. - termDef: - term: Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator - source: caDSR - cde_id: 5432538 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432538&version=1.0" + common: + description: >- + Indicator of whether or not the sample was embedded in Optimal Cutting Temperature + (OCT) compound. + termDef: + term: >- + Tissue Sample Optimal Cutting Temperature Compound Embedding Indicator + source: caDSR + cde_id: 5432538 + cde_version: 1.0 + 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. - termDef: - term: Person Cigarette Smoking History Pack Year Value - source: caDSR - cde_id: 2955385 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + common: + 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. + termDef: + term: >- + Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + 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. - termDef: - term: Specimen Eosinophilia Percentage Value - source: caDSR - cde_id: 2897700 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897700&version=2.0" + common: + description: >- + Numeric value to represent the percentage of infiltration by eosinophils in + a tumor sample or specimen. + termDef: + term: >- + Specimen Eosinophilia Percentage Value + source: caDSR + cde_id: 2897700 + cde_version: 2.0 + 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. - termDef: - term: "%GC" - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + common: + description: >- + The overall %GC of all bases in all sequences. + termDef: + term: >- + %GC + source: FastQC + cde_id: + cde_version: + 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. - termDef: - term: Specimen Granulocyte Infiltration Percentage Value - source: caDSR - cde_id: 2897705 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897705&version=2.0" + common: + description: >- + Numeric value to represent the percentage of infiltration by granulocytes in + a tumor sample or specimen. + termDef: + term: >- + Specimen Granulocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897705 + cde_version: 2.0 + 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. - termDef: - term: Specimen Inflammation Change Percentage Value - source: caDSR - cde_id: 2897695 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897695&version=1.0" + common: + 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. + termDef: + term: >- + Specimen Inflammation Change Percentage Value + source: caDSR + cde_id: 2897695 + cde_version: 1.0 + 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. - termDef: - term: Specimen Lymphocyte Infiltration Percentage Value - source: caDSR - cde_id: 2897710 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897710&version=2.0" + common: + description: >- + Numeric value to represent the percentage of infiltration by lymphocytes in + a solid tissue normal sample or specimen. + termDef: + term: >- + Specimen Lymphocyte Infiltration Percentage Value + source: caDSR + cde_id: 2897710 + cde_version: 2.0 + 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. - termDef: - term: Specimen Monocyte Infiltration Percentage Value - source: caDSR - cde_id: 5455535 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5455535&version=1.0" + common: + description: >- + Numeric value to represent the percentage of monocyte infiltration in a sample + or specimen. + termDef: + term: >- + Specimen Monocyte Infiltration Percentage Value + source: caDSR + cde_id: 5455535 + cde_version: 1.0 + 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. - termDef: - term: Malignant Neoplasm Necrosis Percentage Value - source: caDSR - cde_id: 2841237 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841237&version=1.0" + common: + description: >- + Numeric value to represent the percentage of cell death in a malignant tumor + sample or specimen. + termDef: + term: >- + Malignant Neoplasm Necrosis Percentage Value + source: caDSR + cde_id: 2841237 + cde_version: 1.0 + 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. - termDef: - term: Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value - source: caDSR - cde_id: 2841267 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841267&version=1.0" + common: + description: >- + Numeric value to represent the percentage of infiltration by neutrophils in + a tumor sample or specimen. + termDef: + term: >- + Malignant Neoplasm Neutrophil Infiltration Percentage Cell Value + source: caDSR + cde_id: 2841267 + cde_version: 1.0 + 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. - termDef: - term: Malignant Neoplasm Normal Cell Percentage Value - source: caDSR - cde_id: 2841233 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841233&version=1.0" + common: + description: >- + Numeric value to represent the percentage of normal cell content in a malignant + tumor sample or specimen. + termDef: + term: >- + Malignant Neoplasm Normal Cell Percentage Value + source: caDSR + cde_id: 2841233 + cde_version: 1.0 + 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. - termDef: - term: Malignant Neoplasm Stromal Cell Percentage Value - source: caDSR - cde_id: 2841241 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841241&version=1.0" + common: + 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. + termDef: + term: >- + Malignant Neoplasm Stromal Cell Percentage Value + source: caDSR + cde_id: 2841241 + cde_version: 1.0 + 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. - termDef: - term: Specimen Tumor Cell Percentage Value - source: caDSR - cde_id: 5432686 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432686&version=1.0" + common: + description: >- + Numeric value that represents the percentage of infiltration by granulocytes + in a sample. + termDef: + term: >- + Specimen Tumor Cell Percentage Value + source: caDSR + cde_id: 5432686 + cde_version: 1.0 + 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. - termDef: - term: Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value - source: caDSR - cde_id: 2841225 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2841225&version=1.0" + common: + description: >- + Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm + sample or specimen. + termDef: + term: >- + Malignant Neoplasm Neoplasm Nucleus Percentage Cell Value + source: caDSR + cde_id: 2841225 + cde_version: 1.0 + 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. - termDef: - term: Tumor Perineural Invasion Ind - source: caDSR - cde_id: 64181 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" - -platform: # TOREVIEW - description: > - Name of the platform used to obtain data. + common: + description: >- + a yes/no indicator to ask if perineural invasion or infiltration of tumor or + cancer is present. + termDef: + term: >- + Tumor Perineural Invasion Ind + source: caDSR + cde_id: 64181 + cde_version: 3.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64181&version=3.0" + +platform: + common: + description: >- + Name of the platform used to obtain data. + termDef: + term: + source: + cde_id: + cde_version: + term_url: portion_number: - description: > - Numeric value that represents the sequential number assigned to a portion of the sample. - termDef: - term: Biospecimen Portion Sequence Number - source: caDSR - cde_id: 5432711 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432711&version=1.0" + common: + description: >- + Numeric value that represents the sequential number assigned to a portion of + the sample. + termDef: + term: >- + Biospecimen Portion Sequence Number + source: caDSR + cde_id: 5432711 + cde_version: 1.0 + 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. - termDef: - term: Biospecimen Portion Weight Milligram Value - source: caDSR - cde_id: 5432593 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432593&version=1.0" + common: + description: >- + Numeric value that represents the sample portion weight, measured in milligrams. + termDef: + term: >- + Biospecimen Portion Weight Milligram Value + source: caDSR + cde_id: 5432593 + cde_version: 1.0 + 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. - termDef: - term: Tissue Sample Preservation Method Type - source: caDSR - cde_id: 5432521 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432521&version=1.0" + common: + description: >- + Text term that represents the method used to preserve the sample. + termDef: + term: >- + Tissue Sample Preservation Method Type + source: caDSR + cde_id: 5432521 + cde_version: 1.0 + 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. - termDef: - term: Neoplasm Histologic Type Name - source: caDSR - cde_id: 3081934 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3081934&version=3.0" + common: + description: >- + Text term for the structural pattern of cancer cells used to define a microscopic + diagnosis. + termDef: + term: >- + Neoplasm Histologic Type Name + source: caDSR + cde_id: 3081934 + cde_version: 3.0 + 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. - termDef: - term: Prior Cancer Diagnosis Occurrence Description Text - source: caDSR - cde_id: 3382736 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3382736&version=2.0" + common: + description: >- + Text term to describe the patient's history of prior cancer diagnosis and the + spatial location of any previous cancer occurrence. + termDef: + term: >- + Prior Cancer Diagnosis Occurrence Description Text + source: caDSR + cde_id: 3382736 + cde_version: 2.0 + 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. - termDef: - term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator - source: caDSR - cde_id: 4231463 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + common: + description: >- + A yes/no/unknown/not applicable indicator related to the administration of therapeutic + agents received before the body specimen was collected. + termDef: + term: >- + Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown + Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + 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. - termDef: - term: Progesterone Receptor Level Cell Percentage Category - source: caDSR - cde_id: 3128342 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3128342&version=1.0" + common: + description: >- + Classification to represent Progesterone Receptor Positive results expressed + as a percentage value. + termDef: + term: >- + Progesterone Receptor Level Cell Percentage Category + source: caDSR + cde_id: 3128342 + cde_version: 1.0 + 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. - termDef: - term: Breast Carcinoma Progesterone Receptor Status - source: caDSR - cde_id: 2957357 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2957357&version=2.0" + common: + description: >- + Text term to represent the overall result of Progresterone Receptor (PR) testing. + termDef: + term: >- + Breast Carcinoma Progesterone Receptor Status + source: caDSR + cde_id: 2957357 + cde_version: 2.0 + 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. - termDef: - term: New Neoplasm Event Post Initial Therapy Indicator - source: caDSR - cde_id: 3121376 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" - -project_id: # TOREVIEW - description: > - Unique ID for any specific defined piece of work that is undertaken or attempted to - meet a single requirement. + common: + description: >- + Yes/No/Unknown indicator to identify whether a patient has had a new tumor event + after initial treatment. + termDef: + term: >- + New Neoplasm Event Post Initial Therapy Indicator + source: caDSR + cde_id: 3121376 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3121376&version=1.0" + +project_id: + common: + description: >- + Unique ID for any specific defined piece of work that is undertaken or attempted + to meet a single requirement. + termDef: + term: + source: + cde_id: + cde_version: + term_url: qc_metric_state: - description: > - State classification given by FASTQC for the metric. Metric specific details about the states - are available on their website. - termDef: - term: QC Metric State - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" + common: + description: >- + State classification given by FASTQC for the metric. Metric specific details + about the states are available on their website. + termDef: + term: >- + QC Metric State + source: FastQC + cde_id: + cde_version: + term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" race: - description: > - An arbitrary classification of a taxonomic group that is a division of a species. It usually - arises as a consequence of geographical isolation within a species and is characterized by - shared heredity, physical attributes and behavior, and in the case of humans, by common history, - nationality, or geographic distribution. 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. - termDef: - term: Race Category Text - source: caDSR - cde_id: 2192199 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" - -read_length: # TOREVIEW - description: > - The length of the reads. - -read_group_name: # TOREVIEW - description: > - The name of the read group. + common: + description: >- + An arbitrary classification of a taxonomic group that is a division of a species. + It usually arises as a consequence of geographical isolation within a species + and is characterized by shared heredity, physical attributes and behavior, and + in the case of humans, by common history, nationality, or geographic distribution. + 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. + termDef: + term: >- + Race Category Text + source: caDSR + cde_id: 2192199 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2192199&version=1.0" + +read_length: + common: + description: >- + The length of the reads. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +read_group_name: + common: + description: >- + The name of the read group. + termDef: + term: + source: + cde_id: + cde_version: + term_url: relationship_age_at_diagnosis: - description: > - The age (in years) when the patient's relative was first diagnosed. - termDef: - term: Relative Diagnosis Age Value - source: caDSR - cde_id: 5300571 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5300571&version=1.0" + common: + description: >- + The age (in years) when the patient's relative was first diagnosed. + termDef: + term: >- + Relative Diagnosis Age Value + source: caDSR + cde_id: 5300571 + cde_version: 1.0 + 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. - termDef: - term: Family Member Relationship Type - source: caDSR - cde_id: 2690165 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2690165&version=2.0" + common: + description: >- + The subgroup that describes the state of connectedness between members of the + unit of society organized around kinship ties. + termDef: + term: >- + Family Member Relationship Type + source: caDSR + cde_id: 2690165 + cde_version: 2.0 + 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. - termDef: - term: Other Cancer Biological Relative History Indicator - source: caDSR - cde_id: 3901752 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3901752&version=1.0" + common: + description: >- + Indicator to signify whether or not an individual's biological relative has + been diagnosed with another type of cancer. + termDef: + term: >- + Other Cancer Biological Relative History Indicator + source: caDSR + cde_id: 3901752 + cde_version: 1.0 + 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. - termDef: - term: Surgical Margin Resection Status - source: caDSR - cde_id: 2608702 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" - -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. - termDef: - term: Biospecimen RNA Integrity Number Value - source: caDSR - cde_id: 5278775 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" + common: + description: >- + Text terms to describe the status of a tissue margin following surgical resection. + termDef: + term: >- + Surgical Margin Resection Status + source: caDSR + cde_id: 2608702 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2608702&version=1.0" + +rin: + common: + 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. + termDef: + term: >- + Biospecimen RNA Integrity Number Value + source: caDSR + cde_id: 5278775 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5278775&version=1.0" sample_type: - description: > - Text term to describe the source of a biospecimen used for a laboratory test. - termDef: - term: Specimen Type Collection Biospecimen Type - source: caDSR - cde_id: 3111302 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" - -sample_type_id: # TOREVIEW - description: > - The accompanying sample type id for the sample type. - -section_location: # TOREVIEW - description: > - Tissue source of the slide. - -sequencing_center: # TOREVIEW - description: > - Name of the center that provided the sequence files. + common: + description: >- + Text term to describe the source of a biospecimen used for a laboratory test. + termDef: + term: >- + Specimen Type Collection Biospecimen Type + source: caDSR + cde_id: 3111302 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3111302&version=2.0" + +sample_type_id: + common: + description: >- + The accompanying sample type id for the sample type. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +section_location: + common: + description: >- + Tissue source of the slide. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +sequencing_center: + common: + description: >- + Name of the center that provided the sequence files. + termDef: + term: + source: + cde_id: + cde_version: + term_url: shortest_dimension: - description: > - Numeric value that represents the shortest dimension of the sample, measured in millimeters. - termDef: - term: Tissue Sample Short Dimension Millimeter Measurement - source: caDSR - cde_id: 5432603 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432603&version=1.0" + common: + description: >- + Numeric value that represents the shortest dimension of the sample, measured + in millimeters. + termDef: + term: >- + Tissue Sample Short Dimension Millimeter Measurement + source: caDSR + cde_id: 5432603 + cde_version: 1.0 + 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. - termDef: - term: International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code - source: caDSR - cde_id: 3226281 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" - -size_selection_range: # TOREVIEW - description: > - Range of size selection. + common: + 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. + termDef: + term: >- + International Classification of Diseases for Oncology, Third Edition ICD-O-3 + Site Code + source: caDSR + cde_id: 3226281 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3226281&version=1.0" + +size_selection_range: + common: + description: >- + Range of size selection. + termDef: + term: + source: + cde_id: + cde_version: + term_url: smoking_history: - description: > - Category describing current smoking status and smoking history as self-reported by a patient. - termDef: - term: Smoking History - source: caDSR - cde_id: 2181650 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + common: + description: >- + Category describing current smoking status and smoking history as self-reported + by a patient. + termDef: + term: >- + Smoking History + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + 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 - termDef: - term: Person Cigarette Smoking History Pack Year Value - source: caDSR - cde_id: 2955385 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" - -source_center: # TOREVIEW - description: > - Name of the center that provided the item. + common: + 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 + termDef: + term: >- + Person Cigarette Smoking History Pack Year Value + source: caDSR + cde_id: 2955385 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2955385&version=1.0" + +source_center: + common: + description: >- + Name of the center that provided the item. + termDef: + term: + source: + cde_id: + cde_version: + term_url: spectrophotometer_method: - description: > - Name of the method used to determine the concentration of purified nucleic acid within a - solution. - termDef: - term: Purification Nucleic Acid Solution Concentration Determination Method Type - source: caDSR - cde_id: 3008378 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" - -spike_ins_fasta: # TOREVIEW - description: > - Name of the FASTA file that contains the spike-in sequences. - -spike_ins_concentration: # TOREVIEW - description: > - Spike in concentration. - -state: # TOREVIEW - description: > - The current state of the object. - -target_capture_kit_name: # TOREVIEW - description: > - Name of Target Capture Kit. - -target_capture_kit_vendor: # TOREVIEW - description: > - Vendor of Target Capture Kit. - -target_capture_kit_catalog_number: # TOREVIEW - description: > - Catalog of Target Capture Kit. - -target_capture_kit_version: # TOREVIEW - description: > - Version of Target Capture Kit. - -target_capture_kit_target_region: # TOREVIEW - description: > - Target Capture Kit BED file. + common: + description: >- + Name of the method used to determine the concentration of purified nucleic acid + within a solution. + termDef: + term: >- + Purification Nucleic Acid Solution Concentration Determination Method Type + source: caDSR + cde_id: 3008378 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3008378&version=1.0" + +spike_ins_fasta: + common: + description: >- + Name of the FASTA file that contains the spike-in sequences. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +spike_ins_concentration: + common: + description: >- + Spike in concentration. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +state: + common: + description: >- + The current state of the object. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +target_capture_kit_name: + common: + description: >- + Name of Target Capture Kit. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +target_capture_kit_vendor: + common: + description: >- + Vendor of Target Capture Kit. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +target_capture_kit_catalog_number: + common: + description: >- + Catalog of Target Capture Kit. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +target_capture_kit_version: + common: + description: >- + Version of Target Capture Kit. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +target_capture_kit_target_region: + common: + description: >- + Target Capture Kit BED file. + termDef: + term: + source: + cde_id: + cde_version: + term_url: therapeutic_agents: - description: > - Text identification of the individual agent(s) used as part of a prior treatment regimen. - termDef: - term: Prior Therapy Regimen Text - source: caDSR - cde_id: 2975232 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2975232&version=1.0" + common: + description: >- + Text identification of the individual agent(s) used as part of a prior treatment + regimen. + termDef: + term: >- + Prior Therapy Regimen Text + source: caDSR + cde_id: 2975232 + cde_version: 1.0 + 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. - termDef: - term: Tissue Sample Clamping and Freezing Elapsed Minute Time - source: caDSR - cde_id: 5432611 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432611&version=1.0" + common: + description: >- + Numeric representation of the elapsed time between the surgical clamping of + blood supply and freezing of the sample, measured in minutes. + termDef: + term: >- + Tissue Sample Clamping and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432611 + cde_version: 1.0 + 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. - termDef: - term: Tissue Sample Excision and Freezing Elapsed Minute Time - source: caDSR - cde_id: 5432612 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432612&version=1.0" + common: + description: >- + Numeric representation of the elapsed time between the excision and freezing + of the sample, measured in minutes. + termDef: + term: >- + Tissue Sample Excision and Freezing Elapsed Minute Time + source: caDSR + cde_id: 5432612 + cde_version: 1.0 + 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. - termDef: - term: Tumor Disease Anatomic Site - source: caDSR - cde_id: 3427536 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3427536&version=3.0" + common: + description: >- + Text term that describes the anatomic site of the tumor or disease. + termDef: + term: >- + Tumor Disease Anatomic Site + source: caDSR + cde_id: 3427536 + cde_version: 3.0 + 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. - termDef: - term: Tissue Sample Description Type - source: caDSR - cde_id: 5432687 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" - -to_trim_adapter_sequence: # TOREVIEW - description: > - Does the user suggest adapter trimming? + common: + description: >- + Text term that represents a description of the kind of tissue collected with + respect to disease status or proximity to tumor tissue. + termDef: + term: >- + Tissue Sample Description Type + source: caDSR + cde_id: 5432687 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432687&version=1.0" + +to_trim_adapter_sequence: + common: + description: >- + Does the user suggest adapter trimming? + termDef: + term: + source: + cde_id: + cde_version: + term_url: tobacco_smoking_onset_year: - description: > - The year in which the participant began smoking. - termDef: - term: Started Smoking Year - source: caDSR - cde_id: 2228604 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228604&version=1.0" + common: + description: >- + The year in which the participant began smoking. + termDef: + term: >- + Started Smoking Year + source: caDSR + cde_id: 2228604 + cde_version: 1.0 + 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. - termDef: - term: Stopped Smoking Year - source: caDSR - cde_id: 2228610 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2228610&version=1.0" + common: + description: >- + The year in which the participant quit smoking. + termDef: + term: >- + Stopped Smoking Year + source: caDSR + cde_id: 2228610 + cde_version: 1.0 + 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. - termDef: - term: Patient Smoking History Category - source: caDSR - cde_id: 2181650 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2181650&version=1.0" + common: + description: >- + Category describing current smoking status and smoking history as self-reported + by a patient. + termDef: + term: >- + Patient Smoking History Category + source: caDSR + cde_id: 2181650 + cde_version: 1.0 + 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. - termDef: - term: Total Sequences - source: FastQC - cde_id: null - cde_version: null - term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html" + common: + description: >- + A count of the total number of sequences processed. + termDef: + term: >- + Total Sequences + source: FastQC + cde_id: + cde_version: + 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. - termDef: - term: Treatment Anatomic Site - source: null - cde_id: null - cde_version: null - term_url: null + common: + description: >- + The anatomic site or field targeted by a treatment regimen or single agent therapy. + termDef: + term: >- + Treatment Anatomic Site + source: + cde_id: + cde_version: + term_url: treatment_intent_type: - description: > - Text term to identify the reason for the administration of a treatment regimen. [Manually-curated] - termDef: - term: Treatment Regimen Intent Type - source: caDSR - cde_id: 2793511 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2793511&version=1.0" + common: + description: >- + Text term to identify the reason for the administration of a treatment regimen. + [Manually-curated] + termDef: + term: >- + Treatment Regimen Intent Type + source: caDSR + cde_id: 2793511 + cde_version: 1.0 + 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. - termDef: - term: Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown Not Applicable Indicator - source: caDSR - cde_id: 4231463 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=4231463&version=1.0" + common: + description: >- + A yes/no/unknown/not applicable indicator related to the administration of therapeutic + agents received before the body specimen was collected. + termDef: + term: >- + Therapeutic Procedure Prior Specimen Collection Administered Yes No Unknown + Not Applicable Indicator + source: caDSR + cde_id: 4231463 + cde_version: 1.0 + 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¿s final outcome after the treatment was administered. - termDef: - term: Treatment Outcome Type - source: caDSR - cde_id: 5102383 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102383&version=1.0" + common: + description: >- + Text term that describes the patient¿s final outcome after the treatment was + administered. + termDef: + term: >- + Treatment Outcome Type + source: caDSR + cde_id: 5102383 + cde_version: 1.0 + 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. - termDef: - term: Treatment Method Type - source: caDSR - cde_id: 5102381 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" + common: + description: >- + Text term that describes the kind of treatment administered. + termDef: + term: >- + Treatment Method Type + source: caDSR + cde_id: 5102381 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5102381&version=1.0" tumor_grade: - description: > - Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation - and aggressiveness. - termDef: - term: Neoplasm Histologic Grade - source: caDSR - cde_id: 2785839 - cde_version: 2.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" - -tumor_code: # TOREVIEW - description: > - Diagnostic tumor code of the tissue sample source. - -tumor_code_id: # TOREVIEW - description: > - BCR-defined id code for the tumor sample. + common: + description: >- + Numeric value to express the degree of abnormality of cancer cells, a measure + of differentiation and aggressiveness. + termDef: + term: >- + Neoplasm Histologic Grade + source: caDSR + cde_id: 2785839 + cde_version: 2.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2785839&version=2.0" + +tumor_code: + common: + description: >- + Diagnostic tumor code of the tissue sample source. + termDef: + term: + source: + cde_id: + cde_version: + term_url: + +tumor_code_id: + common: + description: >- + BCR-defined id code for the tumor sample. + termDef: + term: + source: + cde_id: + cde_version: + term_url: tumor_descriptor: - description: > - Text that describes the kind of disease present in the tumor specimen as related to a specific - timepoint. - termDef: - term: Tumor Tissue Disease Description Type - source: caDSR - cde_id: 3288124 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" + common: + description: >- + Text that describes the kind of disease present in the tumor specimen as related + to a specific timepoint. + termDef: + term: >- + Tumor Tissue Disease Description Type + source: caDSR + cde_id: 3288124 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3288124&version=1.0" 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. - termDef: - term: Tumor Stage - source: NCIt - cde_id: C16899 - cde_version: null - term_url: "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" - -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. - termDef: - term: Universally Unique Identifier - source: NCIt - cde_id: C54100 - cde_version: null - term_url: "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" + common: + 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. + termDef: + term: >- + Tumor Stage + source: NCIt + cde_id: C16899 + cde_version: + term_url: "https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C16899" + +uuid: + common: + 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. + termDef: + term: >- + Universally Unique Identifier + source: NCIt + cde_id: C54100 + cde_version: + term_url: "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=16.02d&ns=NCI_Thesaurus&code=C54100" 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. - termDef: - term: Tumor Vascular Invasion Ind-3 - source: caDSR - cde_id: 64358 - cde_version: 3.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=64358&version=3.0" + common: + description: >- + The yes/no indicator to ask if large vessel or venous invasion was detected + by surgery or presence in a tumor specimen. + termDef: + term: >- + Tumor Vascular Invasion Ind-3 + source: caDSR + cde_id: 64358 + cde_version: 3.0 + 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. - termDef: - term: Patient Vital Status - source: caDSR - cde_id: 5 - cde_version: 5.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" + common: + description: >- + The survival state of the person registered on the protocol. + termDef: + term: >- + Patient Vital Status + source: caDSR + cde_id: 5 + cde_version: 5.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5&version=5.0" weight: - description: > - The weight of the patient measured in kilograms. - termDef: - term: Patient Weight Measurement - source: caDSR - cde_id: 651 - cde_version: 4.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=651&version=4.0" + common: + description: >- + The weight of the patient measured in kilograms. + termDef: + term: >- + Patient Weight Measurement + source: caDSR + cde_id: 651 + cde_version: 4.0 + 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. - termDef: - term: Biospecimen Analyte or Aliquot Plate Well Number - source: caDSR - cde_id: 5432613 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=5432613&version=1.0" + common: + description: >- + Numeric value that represents the the well location within a plate for the analyte + or aliquot from the sample. + termDef: + term: >- + Biospecimen Analyte or Aliquot Plate Well Number + source: caDSR + cde_id: 5432613 + cde_version: 1.0 + 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. + common: + description: >- + Generic name for the workflow used to analyze a data set. + termDef: + term: + source: + cde_id: + cde_version: + term_url: year_of_birth: - description: > - Numeric value to represent the calendar year in which an individual was born. - termDef: - term: Year Birth Date Number - source: caDSR - cde_id: 2896954 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" + common: + description: >- + Numeric value to represent the calendar year in which an individual was born. + termDef: + term: >- + Year Birth Date Number + source: caDSR + cde_id: 2896954 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896954&version=1.0" year_of_diagnosis: - description: > - Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. - termDef: - term: Year of initial pathologic diagnosis - source: caDSR - cde_id: 2896960 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" + common: + description: >- + Numeric value to represent the year of an individual's initial pathologic diagnosis + of cancer. + termDef: + term: >- + Year of initial pathologic diagnosis + source: caDSR + cde_id: 2896960 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2896960&version=1.0" year_of_death: - description: > - Numeric value to represent the year of the death of an individual. - termDef: - term: Year Death Number - source: caDSR - cde_id: 2897030 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" + common: + description: >- + Numeric value to represent the year of the death of an individual. + termDef: + term: >- + Year Death Number + source: caDSR + cde_id: 2897030 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=2897030&version=1.0" years_smoked: - description: > - Numeric value (or unknown) to represent the number of years a person has been smoking. - termDef: - term: Person Smoking Duration Year Count - source: caDSR - cde_id: 3137957 - cde_version: 1.0 - term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" + common: + description: >- + Numeric value (or unknown) to represent the number of years a person has been + smoking. + termDef: + term: >- + Person Smoking Duration Year Count + source: caDSR + cde_id: 3137957 + cde_version: 1.0 + term_url: "https://cdebrowser.nci.nih.gov/CDEBrowser/search?elementDetails=9&FirstTimer=0&PageId=ElementDetailsGroup&publicId=3137957&version=1.0" diff --git a/gdcdictionary/schemas/acknowledgement.yaml b/gdcdictionary/schemas/acknowledgement.yaml index cee5d3d99..03a2a31f1 100644 --- a/gdcdictionary/schemas/acknowledgement.yaml +++ b/gdcdictionary/schemas/acknowledgement.yaml @@ -1,13 +1,14 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "acknowledgement" -title: Acknowledgement +title: Acknowledgement type: object namespace: http://gdc.nci.nih.gov category: administrative program: '*' project: '*' -description: "Acknowledgement of an individual involved in a project." +description: >- + Acknowledgement of an individual involved in a project. additionalProperties: false submittable: true validators: null @@ -21,7 +22,7 @@ systemProperties: links: - name: projects - backref: acknowledgements + backref: acknowledgements label: contribute_to target_type: project multiplicity: many_to_many @@ -33,29 +34,44 @@ required: - projects uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: + type: - enum: [ "acknowledgement" ] + enum: + - acknowledgement + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" + acknowledgee: - description: "The indvidiual or group being acknowledged by the project." + description: >- + The indvidiual or group being acknowledged by the project. type: string - projects: - $ref: "_definitions.yaml#/to_many_project" + project_id: type: string + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + projects: + $ref: "_definitions.yaml#/to_many_project" diff --git a/gdcdictionary/schemas/aligned_reads_index.yaml b/gdcdictionary/schemas/aligned_reads_index.yaml index e09ee3edc..39adda687 100644 --- a/gdcdictionary/schemas/aligned_reads_index.yaml +++ b/gdcdictionary/schemas/aligned_reads_index.yaml @@ -7,7 +7,8 @@ namespace: http://gdc.nci.nih.gov category: index_file program: '*' project: '*' -description: "Data file containing the index for a set of aligned reads." +description: >- + Data file containing the index for a set of aligned reads. additionalProperties: false submittable: true validators: null @@ -25,18 +26,18 @@ links: - exclusive: false required: true subgroup: - - name: submitted_aligned_reads_files - backref: aligned_reads_indexes - label: derived_from - target_type: submitted_aligned_reads - multiplicity: one_to_one - required: false - - name: core_metadata_collections - backref: aligned_reads_indexes - label: data_from - target_type: core_metadata_collection - multiplicity: many_to_many - required: false + - name: submitted_aligned_reads_files + backref: aligned_reads_indexes + label: derived_from + target_type: submitted_aligned_reads + multiplicity: one_to_one + required: false + - name: core_metadata_collections + backref: aligned_reads_indexes + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false required: - submitter_id @@ -49,29 +50,40 @@ required: - data_format uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "aligned_reads_index" ] + enum: + - aligned_reads_index + data_category: - term: - $ref: "_terms.yaml#/data_category" + $ref: + - "_terms.yaml#/data_category/common" enum: - Sequencing Data - Sequencing Reads - Raw Sequencing Data + data_type: - term: - $ref: "_terms.yaml#/data_type" - enum: [ "Aligned Reads Index" ] + $ref: + - "_terms.yaml#/data_type/common" + enum: + - Aligned Reads Index + data_format: - term: - $ref: "_terms.yaml#/data_format" - enum: [ "BAI" ] + $ref: + - "_terms.yaml#/data_format/common" + enum: + - BAI + submitted_aligned_reads_files: $ref: "_definitions.yaml#/to_one" + core_metadata_collections: $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/aliquot.yaml b/gdcdictionary/schemas/aliquot.yaml index 078cb17ac..f4dfcd0ee 100644 --- a/gdcdictionary/schemas/aliquot.yaml +++ b/gdcdictionary/schemas/aliquot.yaml @@ -3,15 +3,16 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "aliquot" title: Aliquot type: object +namespace: null category: biospecimen program: '*' project: '*' -description: > - Pertaining to a portion of the whole; any one of two or more samples of something, of the same - volume or weight. +description: >- + Pertaining to a portion of the whole; any one of two or more samples of something, + of the same volume or weight. additionalProperties: false submittable: true -validators: [] +validators: null systemProperties: - id @@ -20,6 +21,14 @@ systemProperties: - created_datetime - updated_datetime +links: + - name: samples + backref: aliquots + label: derived_from + target_type: sample + multiplicity: many_to_many + required: true + required: - submitter_id - type @@ -29,51 +38,50 @@ uniqueKeys: - [id] - [project_id, submitter_id] -links: - - name: samples - backref: aliquots - label: derived_from - multiplicity: many_to_many - target_type: sample - required: true - -constraints: null - -# Aliquot properties properties: + type: type: string + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" - description: > - The legacy barcode used before prior to the use - UUIDs. For TCGA this is bcraliquotbarcode. + description: >- + The legacy barcode used before prior to the use UUIDs. For TCGA this is bcraliquotbarcode. + oneOf: + - type: string + - type: "null" + aliquot_quantity: - term: - $ref: "_terms.yaml#/aliquot_quantity" + $ref: + - "_terms.yaml#/aliquot_quantity/common" type: number + aliquot_volume: - term: - $ref: "_terms.yaml#/aliquot_volume" + $ref: + - "_terms.yaml#/aliquot_volume/common" type: number + amount: - term: - $ref: "_terms.yaml#/amount" + $ref: + - "_terms.yaml#/amount/common" type: number + analyte_type: - term: - $ref: "_terms.yaml#/analyte_type" + $ref: + - "_terms.yaml#/analyte_type/common" type: string + analyte_type_id: - term: - $ref: "_terms.yaml#/analyte_type_id" + $ref: + - "_terms.yaml#/analyte_type_id/common" enum: - D - E @@ -85,19 +93,28 @@ properties: - W - X - Y + concentration: - term: - $ref: "_terms.yaml#/concentration" + $ref: + - "_terms.yaml#/concentration/common" type: number + project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + source_center: - term: - $ref: "_terms.yaml#/source_center" + $ref: + - "_terms.yaml#/source_center/common" type: string - samples: - $ref: "_definitions.yaml#/to_one" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + samples: + $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/case.yaml b/gdcdictionary/schemas/case.yaml index 3db55f5a3..928063027 100644 --- a/gdcdictionary/schemas/case.yaml +++ b/gdcdictionary/schemas/case.yaml @@ -7,9 +7,9 @@ namespace: http://gdc.nci.nih.gov category: administrative program: '*' project: '*' -description: > - The collection of all data related to a specific subject in the - context of a specific experiment. +description: >- + The collection of all data related to a specific subject in the context of a specific + experiment. additionalProperties: false submittable: true validators: null @@ -22,7 +22,7 @@ systemProperties: - state links: - - name: experiments + - name: experiments backref: cases label: member_of target_type: experiment @@ -38,34 +38,51 @@ uniqueKeys: - [id] - [project_id, submitter_id] -# Case properties properties: + type: type: string + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" + consent_codes: type: array items: type: string + primary_site: - description: "Primary site for the case." + description: >- + Primary site for the case. type: string + disease_type: - description: "Name of the disease for the case." + description: >- + Name of the disease for the case. type: string - experiments: - $ref: "_definitions.yaml#/to_one" + project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + experiments: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/clinical_test.yaml b/gdcdictionary/schemas/clinical_test.yaml index 0ac0376f6..49d28cf9f 100644 --- a/gdcdictionary/schemas/clinical_test.yaml +++ b/gdcdictionary/schemas/clinical_test.yaml @@ -1,16 +1,16 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "clinical_test" -title: Clinical Test +title: Clinical Test type: object namespace: http://gdc.nci.nih.gov -category: clinical -project: '*' +category: clinical program: '*' -description: > - Metadata concerning any clinical tests used in relation to a case diagnosis. +project: '*' +description: >- + Metadata concerning any clinical tests used in relation to a case diagnosis. additionalProperties: false -submittable: true +submittable: true validators: null systemProperties: @@ -21,9 +21,9 @@ systemProperties: - state links: - - name: cases + - name: cases backref: clinical_tests - label: performed_for + label: performed_for target_type: case multiplicity: many_to_one required: true @@ -47,29 +47,33 @@ uniqueKeys: - [project_id, submitter_id] properties: + type: - enum: [ "clinical_test" ] + enum: + - clinical_test id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" biomarker_name: - term: - $ref: "_terms.yaml#/biomarker_name" + $ref: + - "_terms.yaml#/biomarker_name/common" type: string biomarker_result: - term: - $ref: "_terms.yaml#/biomarker_result" + $ref: + - "_terms.yaml#/biomarker_result/common" enum: - Amplification - Gain @@ -82,8 +86,8 @@ properties: - Pending biomarker_test_method: - term: - $ref: "_terms.yaml#/biomarker_test_method" + $ref: + - "_terms.yaml#/biomarker_test_method/common" enum: - Cytogenetics - FISH @@ -99,18 +103,18 @@ properties: - Pending cea_level_preoperative: - term: - $ref: "_terms.yaml#/cea_level_preoperative" + $ref: + - "_terms.yaml#/cea_level_preoperative/common" type: number dlco_ref_predictive_percent: - term: - $ref: "_terms.yaml#/dlco_ref_predictive_percent" + $ref: + - "_terms.yaml#/dlco_ref_predictive_percent/common" type: number estrogen_receptor_percent_positive_ihc: - term: - $ref: "_terms.yaml#/estrogen_receptor_percent_positive_ihc" + $ref: + - "_terms.yaml#/estrogen_receptor_percent_positive_ihc/common" enum: - <1% - 1-10% @@ -125,8 +129,8 @@ properties: - 91-100% estrogen_receptor_result_ihc: - term: - $ref: "_terms.yaml#/estrogen_receptor_result_ihc" + $ref: + - "_terms.yaml#/estrogen_receptor_result_ihc/common" enum: - Negative - Not Performed @@ -134,28 +138,28 @@ properties: - Unknown fev1_ref_post_bronch_percent: - term: - $ref: "_terms.yaml#/fev1_ref_post_bronch_percent" + $ref: + - "_terms.yaml#/fev1_ref_post_bronch_percent/common" type: number fev1_ref_pre_bronch_percent: - term: - $ref: "_terms.yaml#/fev1_ref_pre_bronch_percent" + $ref: + - "_terms.yaml#/fev1_ref_pre_bronch_percent/common" type: number fev1_fvc_post_bronch_percent: - term: - $ref: "_terms.yaml#/fev1_fvc_post_bronch_percent" + $ref: + - "_terms.yaml#/fev1_fvc_post_bronch_percent/common" type: number fev1_fvc_pre_bronch_percent: - term: - $ref: "_terms.yaml#/fev1_fvc_pre_bronch_percent" + $ref: + - "_terms.yaml#/fev1_fvc_pre_bronch_percent/common" type: number her2_erbb2_percent_positive_ihc: - term: - $ref: "_terms.yaml#/her2_erbb2_percent_positive_ihc" + $ref: + - "_terms.yaml#/her2_erbb2_percent_positive_ihc/common" enum: - <1% - 1-10% @@ -170,17 +174,17 @@ properties: - 91-100% her2_erbb2_result_fish: - term: - $ref: "_terms.yaml#/her2_erbb2_result_fish" + $ref: + - "_terms.yaml#/her2_erbb2_result_fish/common" enum: - Negative - - Not Performed + - Not Performed - Positive - Unknown her2_erbb2_result_ihc: - term: - $ref: "_terms.yaml#/her2_erbb2_result_ihc" + $ref: + - "_terms.yaml#/her2_erbb2_result_ihc/common" enum: - Negative - Not Performed @@ -188,26 +192,26 @@ properties: - Unknown ldh_level_at_diagnosis: - term: - $ref: "_terms.yaml#/ldh_level_at_diagnosis" + $ref: + - "_terms.yaml#/ldh_level_at_diagnosis/common" type: number ldh_normal_range_upper: - term: - $ref: "_terms.yaml#/ldh_normal_range_upper" + $ref: + - "_terms.yaml#/ldh_normal_range_upper/common" type: number microsatellite_instability_abnormal: - term: - $ref: "_terms.yaml#/microsatellite_instability_abnormal" + $ref: + - "_terms.yaml#/microsatellite_instability_abnormal/common" enum: - "Yes" - "No" - Unknown progesterone_receptor_percent_positive_ihc: - term: - $ref: "_terms.yaml#/progesterone_receptor_percent_positive_ihc" + $ref: + - "_terms.yaml#/progesterone_receptor_percent_positive_ihc/common" enum: - <1% - 1-10% @@ -222,21 +226,28 @@ properties: - 91-100% progesterone_receptor_result_ihc: - term: - $ref: "_terms.yaml#/progesterone_receptor_result_ihc" + $ref: + - "_terms.yaml#/progesterone_receptor_result_ihc/common" enum: - Negative - Not Performed - Positive - Unknown + project_id: + $ref: + - "_definitions.yaml#/project_id" + + created_datetime: + $ref: + - "_definitions.yaml#/datetime" + + updated_datetime: + $ref: + - "_definitions.yaml#/datetime" + cases: $ref: "_definitions.yaml#/to_one" + diagnoses: $ref: "_definitions.yaml#/to_many" - project_id: - $ref: "_definitions.yaml#/project_id" - created_datetime: - $ref: "_definitions.yaml#/datetime" - updated_datetime: - $ref: "_definitions.yaml#/datetime" diff --git a/gdcdictionary/schemas/core_metadata_collection.yaml b/gdcdictionary/schemas/core_metadata_collection.yaml index 1a2bcebc6..a185faae6 100644 --- a/gdcdictionary/schemas/core_metadata_collection.yaml +++ b/gdcdictionary/schemas/core_metadata_collection.yaml @@ -7,7 +7,7 @@ namespace: https://dcp.bionimbus.org/ category: administrative program: '*' project: '*' -description: > +description: >- Structured description of a collection of several dataset additionalProperties: false submittable: true @@ -28,86 +28,118 @@ links: multiplicity: many_to_one required: true -uniqueKeys: - - [id] - - [project_id, submitter_id] - required: - submitter_id - type - projects +uniqueKeys: + - [id] + - [project_id, submitter_id] + properties: - $ref: "_definitions.yaml#/ubiquitous_properties" + + $ref: + - "_definitions.yaml#/ubiquitous_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. + 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. 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. + 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. type: string 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. + 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. type: string date: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" 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. + 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. 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/). + 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/). 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). + 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). type: string 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. + 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. 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.  + description: >- + A related resource. Recommended best practice is to identify the related resource + by means of a string conforming to a formal identification system. 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. + 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. 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. + 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. type: string 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. + 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. type: string title: - description: > - A name given to the resource. Typically, a Title will be a name by which the resource is formally known. + description: >- + A name given to the resource. Typically, a Title will be a name by which the + resource is formally known. 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. + 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. type: string projects: $ref: "_definitions.yaml#/to_one_project" - diff --git a/gdcdictionary/schemas/demographic.yaml b/gdcdictionary/schemas/demographic.yaml index ea8a2b422..7bd1b1af9 100644 --- a/gdcdictionary/schemas/demographic.yaml +++ b/gdcdictionary/schemas/demographic.yaml @@ -7,9 +7,9 @@ namespace: http://gdc.nci.nih.gov category: clinical program: '*' project: '*' -description: > - Data for the characterization of the patient by means of segementing the population (e.g., - characterization by age, sex, or race). +description: >- + Data for the characterization of the patient by means of segementing the population + (e.g., characterization by age, sex, or race). additionalProperties: false submittable: true validators: null @@ -34,33 +34,32 @@ required: - type - cases -preferred: - - year_of_death - uniqueKeys: - #unclear if want submitter ID for clinical - [id] - [project_id, submitter_id] properties: + type: type: string id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" gender: - term: - $ref: "_terms.yaml#/gender" + $ref: + - "_terms.yaml#/gender/common" enum: - female - male @@ -69,8 +68,8 @@ properties: - not reported race: - term: - $ref: "_terms.yaml#/race" + $ref: + - "_terms.yaml#/race/common" enum: - white - american indian or alaska native @@ -83,8 +82,8 @@ properties: - not allowed to collect ethnicity: - term: - $ref: "_terms.yaml#/ethnicity" + $ref: + - "_terms.yaml#/ethnicity/common" enum: - hispanic or latino - not hispanic or latino @@ -93,22 +92,28 @@ properties: - not allowed to collect year_of_birth: - term: - $ref: "_terms.yaml#/year_of_birth" - type: - - number - - "null" + $ref: + - "_terms.yaml#/year_of_birth/common" + oneOf: + - type: number + - type: "null" year_of_death: - term: - $ref: "_terms.yaml#/year_of_death" + $ref: + - "_terms.yaml#/year_of_death/common" type: number - cases: - $ref: "_definitions.yaml#/to_one" project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + cases: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/diagnosis.yaml b/gdcdictionary/schemas/diagnosis.yaml index 28c424081..28ae602a5 100644 --- a/gdcdictionary/schemas/diagnosis.yaml +++ b/gdcdictionary/schemas/diagnosis.yaml @@ -7,10 +7,10 @@ namespace: http://gdc.nci.nih.gov category: clinical program: '*' project: '*' -description: > - Data from the investigation, analysis and recognition of the presence and nature of disease, - condition, or injury from expressed signs and symptoms; also, the scientific determination of any - kind; the concise results of such an investigation. +description: >- + Data from the investigation, analysis and recognition of the presence and nature + of disease, condition, or injury from expressed signs and symptoms; also, the scientific + determination of any kind; the concise results of such an investigation. additionalProperties: false submittable: true validators: null @@ -48,43 +48,41 @@ required: - days_to_last_known_disease_status - last_known_disease_status -preferred: - - days_to_birth - - site_of_resection_or_biopsy - uniqueKeys: - #unclear if want submitter ID for clinical - [id] - [project_id, submitter_id] properties: + type: type: string id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" age_at_diagnosis: - term: - $ref: "_terms.yaml#/age_at_diagnosis" - type: - - number - - "null" - maximum: 32872 - minimum: 0 + $ref: + - "_terms.yaml#/age_at_diagnosis/common" + oneOf: + - type: number + maximum: 32872 + minimum: 0 + - type: "null" ajcc_clinical_m: - term: - $ref: "_terms.yaml#/ajcc_clinical_m" + $ref: + - "_terms.yaml#/ajcc_clinical_m/common" enum: - M0 - M1 @@ -98,8 +96,8 @@ properties: - Not Allowed To Collect ajcc_clinical_n: - term: - $ref: "_terms.yaml#/ajcc_clinical_n" + $ref: + - "_terms.yaml#/ajcc_clinical_n/common" enum: - N0 - N0 (i+) @@ -130,8 +128,8 @@ properties: - Not Allowed To Collect ajcc_clinical_stage: - term: - $ref: "_terms.yaml#/ajcc_clinical_stage" + $ref: + - "_terms.yaml#/ajcc_clinical_stage/common" enum: - Stage 0 - Stage 0a @@ -166,8 +164,8 @@ properties: - Not Allowed To Collect ajcc_clinical_t: - term: - $ref: "_terms.yaml#/ajcc_clinical_t" + $ref: + - "_terms.yaml#/ajcc_clinical_t/common" enum: - T0 - T1 @@ -208,8 +206,8 @@ properties: - Not Allowed To Collect ajcc_pathologic_m: - term: - $ref: "_terms.yaml#/ajcc_pathologic_m" + $ref: + - "_terms.yaml#/ajcc_pathologic_m/common" enum: - M0 - M1 @@ -224,8 +222,8 @@ properties: - Not Allowed To Collect ajcc_pathologic_n: - term: - $ref: "_terms.yaml#/ajcc_pathologic_n" + $ref: + - "_terms.yaml#/ajcc_pathologic_n/common" enum: - N0 - N0 (i+) @@ -256,8 +254,8 @@ properties: - Not Allowed To Collect ajcc_pathologic_stage: - term: - $ref: "_terms.yaml#/ajcc_pathologic_stage" + $ref: + - "_terms.yaml#/ajcc_pathologic_stage/common" enum: - Stage 0 - Stage 0a @@ -288,8 +286,8 @@ properties: - Stage X ajcc_pathologic_t: - term: - $ref: "_terms.yaml#/ajcc_pathologic_t" + $ref: + - "_terms.yaml#/ajcc_pathologic_t/common" enum: - T0 - T1 @@ -330,8 +328,8 @@ properties: - Not Allowed To Collect ann_arbor_b_symptoms: - term: - $ref: "_terms.yaml#/ann_arbor_b_symptoms" + $ref: + - "_terms.yaml#/ann_arbor_b_symptoms/common" enum: - "Yes" - "No" @@ -340,8 +338,8 @@ properties: - Not Allowed To Collect ann_arbor_clinical_stage: - term: - $ref: "_terms.yaml#/ann_arbor_clinical_stage" + $ref: + - "_terms.yaml#/ann_arbor_clinical_stage/common" enum: - Stage I - Stage II @@ -349,8 +347,8 @@ properties: - Stage IV ann_arbor_extranodal_involvement: - term: - $ref: "_terms.yaml#/ann_arbor_extranodal_involvement" + $ref: + - "_terms.yaml#/ann_arbor_extranodal_involvement/common" enum: - "Yes" - "No" @@ -359,8 +357,8 @@ properties: - Not Allowed To Collect ann_arbor_pathologic_stage: - term: - $ref: "_terms.yaml#/ann_arbor_pathologic_stage" + $ref: + - "_terms.yaml#/ann_arbor_pathologic_stage/common" enum: - Stage I - Stage II @@ -368,34 +366,34 @@ properties: - Stage IV burkitt_lymphoma_clinical_variant: - term: - $ref: "_terms.yaml#/burkitt_lymphoma_clinical_variant" - enum: - - "Endemic" - - "Immunodeficiency-associated, adult" - - "Immunodeficiency-associated, pediatric" - - "Sporadic, adult" - - "Sporadic, pediatric" + $ref: + - "_terms.yaml#/burkitt_lymphoma_clinical_variant/common" + enum: + - Endemic + - Immunodeficiency-associated, adult + - Immunodeficiency-associated, pediatric + - Sporadic, adult + - Sporadic, pediatric - Unknown - Not Reported - Not Allowed To Collect cause_of_death: - term: - $ref: "_terms.yaml#/cause_of_death" + $ref: + - "_terms.yaml#/cause_of_death/common" enum: - - Cancer Related - - Not Cancer Related + - Cancer Related + - Not Cancer Related - Unknown circumferential_resection_margin: - term: - $ref: "_terms.yaml#/circumferential_resection_margin" + $ref: + - "_terms.yaml#/circumferential_resection_margin/common" type: number classification_of_tumor: - term: - $ref: "_terms.yaml#/classification_of_tumor" + $ref: + - "_terms.yaml#/classification_of_tumor/common" enum: - primary - metastasis @@ -406,8 +404,8 @@ properties: - Not Allowed To Collect colon_polyps_history: - term: - $ref: "_terms.yaml#/colon_polyps_history" + $ref: + - "_terms.yaml#/colon_polyps_history/common" enum: - "Yes" - "No" @@ -416,59 +414,59 @@ properties: - Not Allowed To Collect days_to_birth: - term: - $ref: "_terms.yaml#/days_to_birth" - type: - - number - - "null" - maximum: 0 - minimum: -32872 + $ref: + - "_terms.yaml#/days_to_birth/common" + oneOf: + - type: number + maximum: 0 + minimum: -32872 + - type: "null" days_to_death: - term: - $ref: "_terms.yaml#/days_to_death" + $ref: + - "_terms.yaml#/days_to_death/common" type: number maximum: 32872 minimum: 0 days_to_hiv_diagnosis: - term: - $ref: "_terms.yaml#/days_to_hiv_diagnosis" - type: - - number - - "null" + $ref: + - "_terms.yaml#/days_to_hiv_diagnosis/common" + oneOf: + - type: number + - type: "null" days_to_last_follow_up: - term: - $ref: "_terms.yaml#/days_to_last_follow_up" - type: - - number - - "null" + $ref: + - "_terms.yaml#/days_to_last_follow_up/common" + oneOf: + - type: number + - type: "null" days_to_last_known_disease_status: - term: - $ref: "_terms.yaml#/days_to_last_known_disease_status" - type: - - number - - "null" + $ref: + - "_terms.yaml#/days_to_last_known_disease_status/common" + oneOf: + - type: number + - type: "null" days_to_new_event: - term: - $ref: "_terms.yaml#/days_to_new_event" - type: - - number - - "null" + $ref: + - "_terms.yaml#/days_to_new_event/common" + oneOf: + - type: number + - type: "null" days_to_recurrence: - term: - $ref: "_terms.yaml#/days_to_recurrence" - type: - - number - - "null" + $ref: + - "_terms.yaml#/days_to_recurrence/common" + oneOf: + - type: number + - type: "null" figo_stage: - term: - $ref: "_terms.yaml#/figo_stage" + $ref: + - "_terms.yaml#/figo_stage/common" enum: - Stage 0 - Stage I @@ -498,16 +496,16 @@ properties: - Not Allowed To Collect hiv_positive: - term: - $ref: "_terms.yaml#/hiv_positive" + $ref: + - "_terms.yaml#/hiv_positive/common" enum: - "Yes" - - "No" + - "No" - Unknown hpv_positive_type: - term: - $ref: "_terms.yaml#/hpv_positive_type" + $ref: + - "_terms.yaml#/hpv_positive_type/common" enum: - HPV 16 - HPV 18 @@ -515,16 +513,16 @@ properties: - Unknown hpv_status: - term: - $ref: "_terms.yaml#/hpv_status" + $ref: + - "_terms.yaml#/hpv_status/common" enum: - Negative - Positive - Unknown last_known_disease_status: - term: - $ref: "_terms.yaml#/last_known_disease_status" + $ref: + - "_terms.yaml#/last_known_disease_status/common" enum: - Distant met recurrence/progression - Loco-regional recurrence/progression @@ -536,8 +534,8 @@ properties: - Not Allowed To Collect laterality: - term: - $ref: "_terms.yaml#/laterality" + $ref: + - "_terms.yaml#/laterality/common" enum: - Bilateral - Left @@ -545,35 +543,35 @@ properties: - Unknown ldh_level_at_diagnosis: - term: - $ref: "_terms.yaml#/ldh_level_at_diagnosis" - type: - - number - - "null" + $ref: + - "_terms.yaml#/ldh_level_at_diagnosis/common" + oneOf: + - type: number + - type: "null" ldh_normal_range_upper: - term: - $ref: "_terms.yaml#/ldh_normal_range_upper" - type: - - number - - "null" + $ref: + - "_terms.yaml#/ldh_normal_range_upper/common" + oneOf: + - type: number + - type: "null" lymph_nodes_positive: - term: - $ref: "_terms.yaml#/lymph_nodes_positive" - type: integer + $ref: + - "_terms.yaml#/lymph_nodes_positive/common" + type: integer lymphatic_invasion_present: - term: - $ref: "_terms.yaml#/lymphatic_invasion_present" + $ref: + - "_terms.yaml#/lymphatic_invasion_present/common" enum: - "Yes" - "No" - Unknown method_of_diagnosis: - term: - $ref: "_terms.yaml#/method_of_diagnosis" + $ref: + - "_terms.yaml#/method_of_diagnosis/common" enum: - Autopsy - Biopsy @@ -596,13 +594,13 @@ properties: - Not Allowed To Collect morphology: - term: - $ref: "_terms.yaml#/morphology" + $ref: + - "_terms.yaml#/morphology/common" type: string new_event_anatomic_site: - term: - $ref: "_terms.yaml#/new_event_anatomic_site" + $ref: + - "_terms.yaml#/new_event_anatomic_site/common" enum: - Abdomen - Adrenal @@ -708,8 +706,8 @@ properties: - Not Allowed To Collect new_event_type: - term: - $ref: "_terms.yaml#/new_event_type" + $ref: + - "_terms.yaml#/new_event_type/common" enum: - Biochemical Evidence of Disease - Both Locoregional and Distant Metastasis @@ -734,21 +732,21 @@ properties: - Not Allowed To Collect perineural_invasion_present: - term: - $ref: "_terms.yaml#/perineural_invasion_present" + $ref: + - "_terms.yaml#/perineural_invasion_present/common" enum: - "Yes" - "No" - Unknown primary_diagnosis: - term: - $ref: "_terms.yaml#/primary_diagnosis" + $ref: + - "_terms.yaml#/primary_diagnosis/common" type: string prior_malignancy: - term: - $ref: "_terms.yaml#/prior_malignancy" + $ref: + - "_terms.yaml#/prior_malignancy/common" enum: - "yes" - "no" @@ -757,8 +755,8 @@ properties: - Not Allowed To Collect prior_treatment: - term: - $ref: "_terms.yaml#/prior_treatment" + $ref: + - "_terms.yaml#/prior_treatment/common" enum: - "Yes" - "No" @@ -767,8 +765,8 @@ properties: - Not Allowed To Collect progression_or_recurrence: - term: - $ref: "_terms.yaml#/progression_or_recurrence" + $ref: + - "_terms.yaml#/progression_or_recurrence/common" enum: - "yes" - "no" @@ -777,8 +775,8 @@ properties: - Not Allowed To Collect residual_disease: - term: - $ref: "_terms.yaml#/residual_disease" + $ref: + - "_terms.yaml#/residual_disease/common" enum: - R0 - R1 @@ -786,28 +784,28 @@ properties: - RX site_of_resection_or_biopsy: - term: - $ref: "_terms.yaml#/site_of_resection_or_biopsy" + $ref: + - "_terms.yaml#/site_of_resection_or_biopsy/common" type: string tissue_or_organ_of_origin: - term: - $ref: "_terms.yaml#/tissue_or_organ_of_origin" + $ref: + - "_terms.yaml#/tissue_or_organ_of_origin/common" type: string tumor_grade: - term: - $ref: "_terms.yaml#/tumor_grade" + $ref: + - "_terms.yaml#/tumor_grade/common" type: string tumor_stage: - term: - $ref: "_terms.yaml#/tumor_stage" + $ref: + - "_terms.yaml#/tumor_stage/common" type: string vascular_invasion_present: - term: - $ref: "_terms.yaml#/vascular_invasion_present" + $ref: + - "_terms.yaml#/vascular_invasion_present/common" enum: - "Yes" - "No" @@ -816,8 +814,8 @@ properties: - Not Allowed To Collect vital_status: - term: - $ref: "_terms.yaml#/vital_status" + $ref: + - "_terms.yaml#/vital_status/common" enum: - alive - dead @@ -825,20 +823,26 @@ properties: - unknown - not reported - Not Allowed To Collect - - pending # this is from TARGET RT clinical data + - pending year_of_diagnosis: - term: - $ref: "_terms.yaml#/year_of_diagnosis" - type: - - number - - "null" + $ref: + - "_terms.yaml#/year_of_diagnosis/common" + oneOf: + - type: number + - type: "null" - cases: - $ref: "_definitions.yaml#/to_one" project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + cases: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/experiment.yaml b/gdcdictionary/schemas/experiment.yaml index b60cd0682..fa3038004 100644 --- a/gdcdictionary/schemas/experiment.yaml +++ b/gdcdictionary/schemas/experiment.yaml @@ -7,9 +7,9 @@ namespace: http://bloodprofilingatlas.org/bpa/ category: administrative program: '*' project: '*' -description: > - A coordinated set of actions and observations designed to generate data, with the ultimate goal - of discovery or hypothesis testing. +description: >- + A coordinated set of actions and observations designed to generate data, with the + ultimate goal of discovery or hypothesis testing. additionalProperties: false submittable: true validators: null @@ -25,7 +25,7 @@ links: - name: projects backref: experiments label: performed_for - target_type: project + target_type: project multiplicity: many_to_one required: true @@ -35,74 +35,108 @@ required: - projects uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: + type: - enum: [ "experiment" ] + enum: + - experiment + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" + number_experimental_group: - description: "The number denoting this experiment's place within the group within the whole." - type: - - integer + description: >- + The number denoting this experiment's place within the group within the whole. + type: integer + number_samples_per_experimental_group: - description: "The number of samples contained within this experimental group." - type: - - integer + description: >- + The number of samples contained within this experimental group. + type: integer + experimental_description: - description: "A brief description of the experiment being performed." - type: - - string + description: >- + A brief description of the experiment being performed. + type: string + experimental_intent: - description: "Summary of the goals the experiment is designed to discover." - type: - - string + description: >- + Summary of the goals the experiment is designed to discover. + type: string + associated_experiment: - description: "The submitter_id for any experiment with which this experiment is associated, paired, or matched." - type: - - string + description: >- + The submitter_id for any experiment with which this experiment is associated, + paired, or matched. + type: string + type_of_sample: - description: "String indicator identifying the types of samples as contrived or clinical." - type: - - string + description: >- + String indicator identifying the types of samples as contrived or clinical. + type: string + type_of_specimen: - description: "Broad description of the specimens used in the experiment." - type: - - string + description: >- + Broad description of the specimens used in the experiment. + type: string + marker_panel_description: - description: "Brief description of the marker panel used in this experiment." + description: >- + Brief description of the marker panel used in this experiment. type: string + somatic_mutations_identified: - description: "Are somatic mutations identified for this experiment?" + description: >- + Are somatic mutations identified for this experiment? type: boolean + indels_identified: - description: "Are indels identified in this experiment?" + description: >- + Are indels identified in this experiment? type: boolean + copy_numbers_identified: - description: "Are copy number variations identified in this experiment?" + description: >- + Are copy number variations identified in this experiment? type: boolean + type_of_data: - description: "Is the data raw or processed?" + description: >- + Is the data raw or processed? enum: - Raw - Processed + data_description: - description: "Brief description of the data being provided for this experiment." + description: >- + Brief description of the data being provided for this experiment. type: string - projects: - $ref: "_definitions.yaml#/to_one_project" + project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + projects: + $ref: "_definitions.yaml#/to_one_project" diff --git a/gdcdictionary/schemas/experimental_metadata.yaml b/gdcdictionary/schemas/experimental_metadata.yaml index cd4f321a5..c38577663 100644 --- a/gdcdictionary/schemas/experimental_metadata.yaml +++ b/gdcdictionary/schemas/experimental_metadata.yaml @@ -5,9 +5,9 @@ title: Experimental Metadata type: object namespace: http://gdc.nci.nih.gov category: metadata_file -project: '*' program: '*' -description: > +project: '*' +description: >- Data file containing the metadata for the experiment performed. additionalProperties: false submittable: true @@ -26,18 +26,18 @@ links: - exclusive: false required: true subgroup: - - name: core_metadata_collections - backref: experiment_metadata_files - label: data_from - target_type: core_metadata_collection - multiplicity: many_to_many - required: false - - name: experiments - backref: experiment_metadata_files - label: derived_from - target_type: experiment - multiplicity: many_to_many - required: false + - name: core_metadata_collections + backref: experiment_metadata_files + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false + - name: experiments + backref: experiment_metadata_files + label: derived_from + target_type: experiment + multiplicity: many_to_many + required: false required: - submitter_id @@ -50,28 +50,36 @@ required: - data_format uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "experimental_metadata" ] + enum: + - experimental_metadata + data_category: - term: - $ref: "_terms.yaml#/data_category" - type: - - string + $ref: + - "_terms.yaml#/data_category/common" + type: string + data_type: - term: - $ref: "_terms.yaml#/data_type" - enum: [ "Experimental Metadata" ] + $ref: + - "_terms.yaml#/data_type/common" + enum: + - Experimental Metadata + data_format: - term: - $ref: "_terms.yaml#/data_format" - type: - - string - experiments: - $ref: "_definitions.yaml#/to_one" + $ref: + - "_terms.yaml#/data_format/common" + type: string + core_metadata_collections: $ref: "_definitions.yaml#/to_many" + + experiments: + $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/exposure.yaml b/gdcdictionary/schemas/exposure.yaml index 76cfe72c9..0b170024a 100644 --- a/gdcdictionary/schemas/exposure.yaml +++ b/gdcdictionary/schemas/exposure.yaml @@ -7,7 +7,7 @@ namespace: http://gdc.nci.nih.gov category: clinical program: '*' project: '*' -description: > +description: >- Clinically relevant patient information not immediately resulting from genetic predispositions. additionalProperties: false submittable: true @@ -20,10 +20,6 @@ systemProperties: - created_datetime - updated_datetime -required: - - submitter_id - - type - links: - name: cases backref: exposures @@ -32,74 +28,77 @@ links: multiplicity: many_to_one required: true -preferred: - - cigarettes_per_day - - years_smoked +required: + - submitter_id + - type uniqueKeys: - #unclear if want submitter ID for clinical - [id] - [project_id, submitter_id] properties: + type: - enum: [ "exposure" ] + enum: + - exposure id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" alcohol_history: - term: - $ref: "_terms.yaml#/alcohol_history" + $ref: + - "_terms.yaml#/alcohol_history/common" type: string alcohol_intensity: - term: - $ref: "_terms.yaml#/alcohol_intensity" + $ref: + - "_terms.yaml#/alcohol_intensity/common" type: string bmi: - term: - $ref: "_terms.yaml#/bmi" + $ref: + - "_terms.yaml#/bmi/common" type: number cigarettes_per_day: - term: - $ref: "_terms.yaml#/cigarettes_per_day" + $ref: + - "_terms.yaml#/cigarettes_per_day/common" type: number height: - term: - $ref: "_terms.yaml#/height" + $ref: + - "_terms.yaml#/height/common" type: number pack_years_smoked: - term: - $ref: "_terms.yaml#/pack_years_smoked" + $ref: + - "_terms.yaml#/pack_years_smoked/common" type: number tobacco_smoking_onset_year: - term: - $ref: "_terms.yaml#/tobacco_smoking_onset_year" + $ref: + - "_terms.yaml#/tobacco_smoking_onset_year/common" type: integer tobacco_smoking_quit_year: - term: - $ref: "_terms.yaml#/tobacco_smoking_quit_year" + $ref: + - "_terms.yaml#/tobacco_smoking_quit_year/common" type: integer tobacco_smoking_status: - term: - $ref: "_terms.yaml#/tobacco_smoking_status" + $ref: + - "_terms.yaml#/tobacco_smoking_status/common" enum: - "1" - "2" @@ -113,20 +112,26 @@ properties: - Not Allowed To Collect weight: - term: - $ref: "_terms.yaml#/weight" + $ref: + - "_terms.yaml#/weight/common" type: number years_smoked: - term: - $ref: "_terms.yaml#/years_smoked" + $ref: + - "_terms.yaml#/years_smoked/common" type: number - cases: - $ref: "_definitions.yaml#/to_one" project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + cases: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/family_history.yaml b/gdcdictionary/schemas/family_history.yaml index add3a1523..67523f4af 100644 --- a/gdcdictionary/schemas/family_history.yaml +++ b/gdcdictionary/schemas/family_history.yaml @@ -7,7 +7,7 @@ namespace: http://gdc.nci.nih.gov category: clinical program: '*' project: '*' -description: > +description: >- Record of a patient's background regarding cancer events of blood relatives. additionalProperties: false submittable: true @@ -20,10 +20,6 @@ systemProperties: - created_datetime - updated_datetime -required: - - submitter_id - - type - links: - name: cases backref: family_histories @@ -32,31 +28,37 @@ links: multiplicity: many_to_one required: true +required: + - submitter_id + - type uniqueKeys: - #unclear if want submitter ID for clinical - [id] - [project_id, submitter_id] properties: + type: - enum: [ "family_history" ] + enum: + - family_history id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" relative_with_cancer_history: - term: - $ref: "_terms.yaml#/relative_with_cancer_history" + $ref: + - "_terms.yaml#/relative_with_cancer_history/common" enum: - "yes" - "no" @@ -64,13 +66,13 @@ properties: - not reported relationship_type: - term: - $ref: "_terms.yaml#/relationship_type" + $ref: + - "_terms.yaml#/relationship_type/common" type: string relationship_gender: - term: - $ref: "_terms.yaml#/gender" + $ref: + - "_terms.yaml#/gender/common" enum: - female - male @@ -79,20 +81,26 @@ properties: - not reported relationship_age_at_diagnosis: - term: - $ref: "_terms.yaml#/relationship_age_at_diagnosis" + $ref: + - "_terms.yaml#/relationship_age_at_diagnosis/common" type: number relationship_primary_diagnosis: - term: - $ref: "_terms.yaml#/primary_diagnosis" + $ref: + - "_terms.yaml#/primary_diagnosis/common" type: string - cases: - $ref: "_definitions.yaml#/to_one" project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + cases: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/keyword.yaml b/gdcdictionary/schemas/keyword.yaml index 99a3a050f..866a35670 100644 --- a/gdcdictionary/schemas/keyword.yaml +++ b/gdcdictionary/schemas/keyword.yaml @@ -7,7 +7,8 @@ namespace: http://gdc.nci.nih.gov category: administrative program: '*' project: '*' -description: "A keyword for a project." +description: >- + A keyword for a project. additionalProperties: false submittable: true validators: null @@ -33,29 +34,44 @@ required: - projects uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: + type: - enum: [ "keyword" ] + enum: + - keyword + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" + keyword_name: - description: "The name of the keyword." + description: >- + The name of the keyword. type: string - projects: - $ref: "_definitions.yaml#/to_many_project" + project_id: type: string + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + projects: + $ref: "_definitions.yaml#/to_many_project" diff --git a/gdcdictionary/schemas/program.yaml b/gdcdictionary/schemas/program.yaml index 4504f8572..5fc9adf7c 100644 --- a/gdcdictionary/schemas/program.yaml +++ b/gdcdictionary/schemas/program.yaml @@ -3,10 +3,11 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "program" title: Program type: object +namespace: null category: administrative program: '*' project: '*' -description: > +description: >- A broad framework of goals to be achieved. (NCIt C52647) additionalProperties: false submittable: false @@ -15,6 +16,8 @@ validators: null systemProperties: - id +links: [] + required: - name - dbgap_accession_number @@ -23,19 +26,22 @@ uniqueKeys: - [id] - [name] -links: [] - -# Program is the root entity and so it is the only entity -# without a project or parents. properties: + type: type: string + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + name: + description: >- + Full name/title of the program. type: string - description: "Full name/title of the program." + dbgap_accession_number: + description: >- + The dbgap accession number provided for the program. type: string - description: "The dbgap accession number provided for the program." diff --git a/gdcdictionary/schemas/project.yaml b/gdcdictionary/schemas/project.yaml index dc21d32f5..d3ed0be4b 100644 --- a/gdcdictionary/schemas/project.yaml +++ b/gdcdictionary/schemas/project.yaml @@ -3,12 +3,13 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "project" title: Project type: object +namespace: null +category: administrative program: '*' project: '*' -category: administrative -description: > - Any specifically defined piece of work that is undertaken or attempted to meet a single - requirement. (NCIt C47885) +description: >- + Any specifically defined piece of work that is undertaken or attempted to meet a + single requirement. (NCIt C47885) additionalProperties: false submittable: true validators: null @@ -20,16 +21,6 @@ systemProperties: - releasable - intended_release_date -required: - - code - - name - - dbgap_accession_number - - programs - -uniqueKeys: - - [ id ] - - [ code ] - links: - name: programs backref: projects @@ -38,110 +29,111 @@ links: multiplicity: many_to_one required: true -constraints: null +required: + - code + - name + - dbgap_accession_number + - programs + +uniqueKeys: + - [id] + - [code] properties: + type: type: string + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" + description: >- + UUID for the project. systemAlias: node_id - description: "UUID for the project." # TOREVIEW + name: + description: >- + Display name/brief description for the project. type: string - description: "Display name/brief description for the project." # TOREVIEW + code: + description: >- + Unique identifier for the project. type: string - description: "Unique identifier for the project." + investigator_name: - description: "Name of the principal investigator for the project." + description: >- + Name of the principal investigator for the project. type: string + investigator_affiliation: - description: "The investigator's affiliation with respect to a research institution." + description: >- + The investigator's affiliation with respect to a research institution. type: string + date_collected: - description: "The date or date range in which the project data was collected." + description: >- + The date or date range in which the project data was collected. type: string + availability_type: - description: "Is the project open or restricted?" + description: >- + Is the project open or restricted? enum: - Open - Restricted + availability_mechanism: - description: "Mechanism by which the project will be made avilable." + description: >- + Mechanism by which the project will be made avilable. type: string + support_source: - description: "The name of source providing support/grant resources." + description: >- + The name of source providing support/grant resources. type: string + support_id: - description: "The ID of the source providing support/grant resources." + description: >- + The ID of the source providing support/grant resources. type: string - programs: - $ref: "_definitions.yaml#/to_one" - description: > - Indicates that the project is logically part of the indicated project. + state: - description: | - The possible states a project can be in. All but `open` are - equivalent to some type of locked state. + description: >- + The possible states a project can be in. All but `open` are equivalent to some + type of locked state. default: open enum: - # open: the only state users can perform 'upload' actions - # possible actions in `open`: - # - upload (no state change) - # - review -> review - # - release (project.released -> true) - - open - - # locked: admin has locked project for review - # possible actions in `locked`: - # - open -> open - # - submit -> submitted - # - release (project.released -> true) - - review - - # submitted: An admin has submitted project, it is locked against - # upload. - # possible actions in `submitted`: - # - process -> processing - # - release (project.released -> true) - - submitted - - # processing: The system is processing data in the project and - # is locked against upload and submission - # - (system transition to open) - # - release (project.released -> true) - - processing - - - # closed: The closed state is introduced to replace the - # ``legacy`` state and means that no further action - # can be taken on the project - # - (system transition to open) - # - release (project.released -> true) - - closed - - # DEPRECATED(2016-03-01): synonymous with closed. included for - # backwards compatibility - - legacy + - open + - review + - submitted + - processing + - closed + - legacy released: - description: | - To release a project is to tell the GDC to include all submitted - entities in the next GDC index. - default: false + description: >- + To release a project is to tell the GDC to include all submitted entities in + the next GDC index. type: boolean + default: false releasable: - description: | + description: >- A project can only be released by the user when `releasable` is true. - default: false type: boolean + default: false intended_release_date: - description: Tracks a Project's intended release date. + description: >- + Tracks a Project's intended release date. type: string format: date-time + dbgap_accession_number: + description: >- + The dbgap accession number provided for the project. type: string - description: "The dbgap accession number provided for the project." + + programs: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/publication.yaml b/gdcdictionary/schemas/publication.yaml index 2feb6a1ab..1b14878a8 100644 --- a/gdcdictionary/schemas/publication.yaml +++ b/gdcdictionary/schemas/publication.yaml @@ -7,7 +7,8 @@ namespace: http://gdc.nci.nih.gov category: administrative program: '*' project: '*' -description: "Publication for a project." +description: >- + Publication for a project. additionalProperties: false submittable: true validators: null @@ -33,30 +34,45 @@ required: - projects uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: + type: - enum: [ "publication" ] + enum: + - publication + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" + pmid: type: string + doi: type: string - projects: - $ref: "_definitions.yaml#/to_many_project" + project_id: type: string + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + projects: + $ref: "_definitions.yaml#/to_many_project" diff --git a/gdcdictionary/schemas/read_group.yaml b/gdcdictionary/schemas/read_group.yaml index d1a8bdd4b..cf43c20f1 100644 --- a/gdcdictionary/schemas/read_group.yaml +++ b/gdcdictionary/schemas/read_group.yaml @@ -3,11 +3,12 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "read_group" title: Read Group type: object -description: "Sequencing reads from one lane of an NGS experiment." namespace: http://gdc.nci.nih.gov category: biospecimen -project: '*' program: '*' +project: '*' +description: >- + Sequencing reads from one lane of an NGS experiment. additionalProperties: false submittable: true validators: null @@ -21,11 +22,11 @@ systemProperties: links: - name: aliquots + backref: read_groups label: derived_from target_type: aliquot multiplicity: many_to_one required: true - backref: read_groups required: - type @@ -33,33 +34,47 @@ required: - aliquots uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" + project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + submitter_id: type: string + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + type: - enum: [ "read_group" ] + enum: + - read_group + experiment_name: - term: - $ref: "_terms.yaml#/experiment_name" + $ref: + - "_terms.yaml#/experiment_name/common" type: string + sequencing_center: - term: - $ref: "_terms.yaml#/sequencing_center" + $ref: + - "_terms.yaml#/sequencing_center/common" type: string + sequencing_date: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + platform: - term: - $ref: "_terms.yaml#/platform" + $ref: + - "_terms.yaml#/platform/common" enum: - Illumina - SOLiD @@ -68,9 +83,10 @@ properties: - Complete Genomics - PacBio - Other + instrument_model: - terms: - $ref: "_terms.yaml#/instrument_model" + $ref: + - "_terms.yaml#/instrument_model/common" enum: - 454 GS FLX Titanium - AB SOLiD 4 @@ -91,9 +107,10 @@ properties: - PacBio RS - Ion S5 XL System, Ion 530 Chip - Other + library_strategy: - term: - $ref: "_terms.yaml#/library_strategy" + $ref: + - "_terms.yaml#/library_strategy/common" enum: - WGS - WXS @@ -104,29 +121,35 @@ properties: - Validation - Amplicon - Other - RIN: - term: - $ref: "_terms.yaml#/RIN" + + rin: + $ref: + - "_terms.yaml#/rin/common" type: number + flow_cell_barcode: - term: - $ref: "_terms.yaml#/flow_cell_barcode" + $ref: + - "_terms.yaml#/flow_cell_barcode/common" type: string + includes_spike_ins: - term: - $ref: "_terms.yaml#/includes_spike_ins" + $ref: + - "_terms.yaml#/includes_spike_ins/common" type: boolean + spike_ins_fasta: - term: - $ref: "_terms.yaml#/spike_ins_fasta" + $ref: + - "_terms.yaml#/spike_ins_fasta/common" type: string + spike_ins_concentration: - term: - $ref: "_terms.yaml#/spike_ins_concentration" + $ref: + - "_terms.yaml#/spike_ins_concentration/common" type: string + library_selection: - term: - $ref: "_terms.yaml#/library_selection" + $ref: + - "_terms.yaml#/library_selection/common" enum: - Hybrid_Selection - PCR @@ -134,92 +157,120 @@ properties: - Poly-T_Enrichment - RNA_Depletion - Other + library_preparation_kit_name: - term: - $ref: "_terms.yaml#/library_preparation_kit_name" + $ref: + - "_terms.yaml#/library_preparation_kit_name/common" type: string + library_preparation_kit_vendor: - term: - $ref: "_terms.yaml#/library_preparation_kit_vendor" + $ref: + - "_terms.yaml#/library_preparation_kit_vendor/common" type: string + library_preparation_kit_catalog_number: - term: - $ref: "_terms.yaml#/library_preparation_kit_catalog_number" + $ref: + - "_terms.yaml#/library_preparation_kit_catalog_number/common" type: string + library_preparation_kit_version: - term: - $ref: "_terms.yaml#/library_preparation_kit_version" + $ref: + - "_terms.yaml#/library_preparation_kit_version/common" type: string + library_name: - term: - $ref: "_terms.yaml#/library_name" + $ref: + - "_terms.yaml#/library_name/common" type: string - target_capture_kit_name: # conditionally required for WXS etc - term: - $ref: "_terms.yaml#/target_capture_kit_name" + + target_capture_kit_name: + $ref: + - "_terms.yaml#/target_capture_kit_name/common" type: string + target_capture_kit_vendor: - term: - $ref: "_terms.yaml#/target_capture_kit_vendor" + $ref: + - "_terms.yaml#/target_capture_kit_vendor/common" type: string + target_capture_kit_catalog_number: - term: - $ref: "_terms.yaml#/target_capture_kit_catalog_number" + $ref: + - "_terms.yaml#/target_capture_kit_catalog_number/common" type: string + target_capture_kit_version: - term: - $ref: "_terms.yaml#/target_capture_kit_version" + $ref: + - "_terms.yaml#/target_capture_kit_version/common" type: string + target_capture_kit_target_region: - term: - $ref: "_terms.yaml#/target_capture_kit_target_region" + $ref: + - "_terms.yaml#/target_capture_kit_target_region/common" type: string + size_selection_range: - term: - $ref: "_terms.yaml#/size_selection_range" + $ref: + - "_terms.yaml#/size_selection_range/common" type: string + adapter_name: - term: - $ref: "_terms.yaml#/adapter_name" + $ref: + - "_terms.yaml#/adapter_name/common" type: string + adapter_sequence: - term: - $ref: "_terms.yaml#/adapter_sequence" + $ref: + - "_terms.yaml#/adapter_sequence/common" type: string + to_trim_adapter_sequence: - term: - $ref: "_terms.yaml#/to_trim_adapter_sequence" + $ref: + - "_terms.yaml#/to_trim_adapter_sequence/common" type: boolean + library_strand: - term: - $ref: "_terms.yaml#/library_strand" + $ref: + - "_terms.yaml#/library_strand/common" enum: - Unstranded - First_Stranded - Second_Stranded + base_caller_name: - term: - $ref: "_terms.yaml#/base_caller_name" + $ref: + - "_terms.yaml#/base_caller_name/common" type: string + base_caller_version: - term: - $ref: "_terms.yaml#/base_caller_version" + $ref: + - "_terms.yaml#/base_caller_version/common" type: string + is_paired_end: - term: - $ref: "_terms.yaml#/is_paired_end" + $ref: + - "_terms.yaml#/is_paired_end/common" type: boolean + read_length: type: integer - read_group_name: # it may be good to assign UUID to read group - description: "Read Group Name" + + read_group_name: + description: >- + Read Group Name type: string + barcoding_applied: - description: "True/False: was barcoding applied?" + description: >- + True/False: was barcoding applied? type: boolean - aliquots: - $ref: "_definitions.yaml#/to_one" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + aliquots: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/read_group_qc.yaml b/gdcdictionary/schemas/read_group_qc.yaml index 9b235528c..f79ea75e2 100644 --- a/gdcdictionary/schemas/read_group_qc.yaml +++ b/gdcdictionary/schemas/read_group_qc.yaml @@ -5,9 +5,10 @@ title: Read Group QC type: object namespace: http://gdc.nci.nih.gov category: notation -project: '*' program: '*' -description: "GDC QC run metadata." +project: '*' +description: >- + GDC QC run metadata. additionalProperties: false submittable: false validators: null @@ -36,11 +37,11 @@ links: multiplicity: one_to_many required: false - name: read_groups + backref: read_group_qcs label: generated_from target_type: read_group multiplicity: many_to_one required: true - backref: read_group_qcs required: - submitter_id @@ -64,70 +65,111 @@ required: - read_groups uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/workflow_properties" + + $ref: + - "_definitions.yaml#/workflow_properties" + type: - enum: [ "read_group_qc" ] + enum: + - read_group_qc + workflow_type: - term: - $ref: "_terms.yaml#/workflow_type" - enum: [ "Read Group Quality Control" ] + $ref: + - "_terms.yaml#/workflow_type/common" + enum: + - Read Group Quality Control + fastq_name: - term: - $ref: "_terms.yaml#/file_name" + $ref: + - "_terms.yaml#/file_name/common" type: string + percent_aligned: - description: "The percent of reads with at least one reported alignment." + description: >- + The percent of reads with at least one reported alignment. type: integer - minimum: 0 maximum: 100 + minimum: 0 + percent_gc_content: - term: - $ref: "_terms.yaml#/percent_gc_content" + $ref: + - "_terms.yaml#/percent_gc_content/common" type: integer - minimum: 0 maximum: 100 + minimum: 0 + encoding: - term: - $ref: "_terms.yaml#/encoding" + $ref: + - "_terms.yaml#/encoding/common" type: string + total_aligned_reads: - description: "The total number of reads with at least one reported alignment." + description: >- + The total number of reads with at least one reported alignment. type: integer + total_sequences: - term: - $ref: "_terms.yaml#/total_sequences" + $ref: + - "_terms.yaml#/total_sequences/common" type: integer + basic_statistics: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + per_base_sequence_quality: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + per_tile_sequence_quality: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + per_sequence_quality_score: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + per_base_sequence_content: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + per_sequence_gc_content: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + per_base_n_content: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + sequence_length_distribution: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + sequence_duplication_levels: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + overrepresented_sequences: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + adapter_content: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + kmer_content: - $ref: "_definitions.yaml#/qc_metrics_state" + $ref: + - "_definitions.yaml#/qc_metrics_state" + submitted_aligned_reads_files: $ref: "_definitions.yaml#/to_one" + submitted_unaligned_reads_files: $ref: "_definitions.yaml#/to_many" + read_groups: $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/sample.yaml b/gdcdictionary/schemas/sample.yaml index 7680e5cb3..3a5d4527e 100644 --- a/gdcdictionary/schemas/sample.yaml +++ b/gdcdictionary/schemas/sample.yaml @@ -7,12 +7,12 @@ namespace: http://gdc.nci.nih.gov category: biospecimen program: '*' project: '*' -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. +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. additionalProperties: false submittable: true validators: null @@ -24,21 +24,12 @@ systemProperties: - created_datetime - updated_datetime -required: - - submitter_id - - type - - cases - -uniqueKeys: - - [id] - - [project_id, submitter_id] - links: - name: cases backref: samples label: derived_from target_type: case - multiplicity: many_to_one #not sure + multiplicity: many_to_one required: true - name: diagnoses backref: samples @@ -47,25 +38,40 @@ links: multiplicity: many_to_one required: false -# Sample properties: keep TCGA-specific fields +required: + - submitter_id + - type + - cases + +uniqueKeys: + - [id] + - [project_id, submitter_id] + properties: + type: type: string + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" - description: > - The legacy barcode used before prior to the use UUIDs, varies by project. - For TCGA this is bcrsamplebarcode. + description: >- + The legacy barcode used before prior to the use UUIDs, varies by project. For + TCGA this is bcrsamplebarcode. + oneOf: + - type: string + - type: "null" + biospecimen_anatomic_site: - term: - $ref: "_terms.yaml#/biospecimen_anatomic_site" + $ref: + - "_terms.yaml#/biospecimen_anatomic_site/common" enum: - Abdomen - Abdominal Wall @@ -348,9 +354,10 @@ properties: - Unknown - Not Reported - Not Allowed To Collect + composition: - term: - $ref: "_terms.yaml#/composition" + $ref: + - "_terms.yaml#/composition/common" enum: - Buccal Cells - Buffy Coat @@ -379,48 +386,56 @@ properties: - Unknown - Not Reported - Not Allowed To Collect + current_weight: - term: - $ref: "_terms.yaml#/current_weight" + $ref: + - "_terms.yaml#/current_weight/common" type: number + days_to_collection: - term: - $ref: "_terms.yaml#/days_to_collection" + $ref: + - "_terms.yaml#/days_to_collection/common" type: integer + days_to_sample_procurement: - term: - $ref: "_terms.yaml#/days_to_sample_procurement" + $ref: + - "_terms.yaml#/days_to_sample_procurement/common" type: integer + diagnosis_pathologically_confirmed: - term: - ref: "_terms.yaml#/diagnosis_pathologically_confirmed" enum: - "Yes" - "No" - Unknown + freezing_method: - term: - $ref: "_terms.yaml#/freezing_method" + $ref: + - "_terms.yaml#/freezing_method/common" type: string + initial_weight: - term: - $ref: "_terms.yaml#/initial_weight" + $ref: + - "_terms.yaml#/initial_weight/common" type: number + intermediate_dimension: - terms: - $ref: "_terms.yaml#/intermediate_dimension" + $ref: + - "_terms.yaml#/intermediate_dimension/common" type: string + is_ffpe: - term: - $ref: "_terms.yaml#/is_ffpe" + $ref: + - "_terms.yaml#/is_ffpe/common" type: boolean + longest_dimension: - terms: - $ref: "_terms.yaml#/longest_dimension" + $ref: + - "_terms.yaml#/longest_dimension/common" type: string + method_of_sample_procurement: - term: - $ref: "_terms.yaml#/method_of_sample_procurement" + $ref: + - "_terms.yaml#/method_of_sample_procurement/common" enum: - Abdomino-perineal Resection of Rectum - Anterior Resection of Rectum @@ -478,13 +493,15 @@ properties: - Unknown - Not Reported - Not Allowed To Collect + oct_embedded: - term: - $ref: "_terms.yaml#/oct_embedded" + $ref: + - "_terms.yaml#/oct_embedded/common" type: string + preservation_method: - term: - $ref: "_terms.yaml#/preservation_method" + $ref: + - "_terms.yaml#/preservation_method/common" enum: - Cryopreserved - FFPE @@ -495,8 +512,10 @@ properties: - Unknown - Not Reported - Not Allowed To Collect + sample_type: - description: "Characterization of the sample as either clinical or contrived." + description: >- + Characterization of the sample as either clinical or contrived. enum: - Additional Metastatic - Additional - New Primary @@ -542,52 +561,59 @@ properties: - Unknown - Not Reported - Not Allowed To Collect + sample_type_id: - term: - $ref: "_terms.yaml#/sample_type_id" + $ref: + - "_terms.yaml#/sample_type_id/common" enum: - - '01' - - '02' - - '03' - - '04' - - '05' - - '06' - - '07' - - '08' - - '09' - - '10' - - '11' - - '12' - - '13' - - '14' - - '15' - - '16' - - '20' - - '40' - - '41' - - '42' - - '50' - - '60' - - '61' - - '99' + - "01" + - "02" + - "03" + - "04" + - "05" + - "06" + - "07" + - "08" + - "09" + - "10" + - "11" + - "12" + - "13" + - "14" + - "15" + - "16" + - "20" + - "40" + - "41" + - "42" + - "50" + - "60" + - "61" + - "99" + sample_volume: - description: "The volume of the sample in mL." + description: >- + The volume of the sample in mL. type: number + shortest_dimension: - term: - $ref: "_terms.yaml#/shortest_dimension" + $ref: + - "_terms.yaml#/shortest_dimension/common" type: string + time_between_clamping_and_freezing: - term: - $ref: "_terms.yaml#/time_between_clamping_and_freezing" + $ref: + - "_terms.yaml#/time_between_clamping_and_freezing/common" type: string + time_between_excision_and_freezing: - term: - $ref: "_terms.yaml#/time_between_excision_and_freezing" + $ref: + - "_terms.yaml#/time_between_excision_and_freezing/common" type: string + tissue_type: - term: - $ref: "_terms.yaml#/tissue_type" + $ref: + - "_terms.yaml#/tissue_type/common" enum: - Tumor - Normal @@ -597,9 +623,10 @@ properties: - Unknown - Not Reported - Not Allowed To Collect + tumor_code: - term: - $ref: "_terms.yaml#/tumor_code" + $ref: + - "_terms.yaml#/tumor_code/common" enum: - Non cancerous tissue - Diffuse Large B-Cell Lymphoma (DLBCL) @@ -632,9 +659,10 @@ properties: - Castration-Resistant Prostate Cancer (CRPC) - Prostate Cancer - Hepatocellular Carcinoma (HCC) + tumor_code_id: - term: - $ref: "_terms.yaml#/tumor_code_id" + $ref: + - "_terms.yaml#/tumor_code_id/common" enum: - "00" - "01" @@ -660,9 +688,12 @@ properties: - "71" - "80" - "81" + tumor_descriptor: - term: - $ref: "_terms.yaml#/tumor_descriptor" + $ref: + - "_terms.yaml#/tumor_descriptor/common" + description: >- + A description of the tumor from which the sample was derived. enum: - Metastatic - Not Applicable @@ -673,14 +704,20 @@ properties: - Unknown - Not Reported - Not Allowed To Collect - description: "A description of the tumor from which the sample was derived." # TOREVIEW - cases: - $ref: "_definitions.yaml#/to_one" - diagnoses: - $ref: "_definitions.yaml#/to_one" + project_id: type: string + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + cases: + $ref: "_definitions.yaml#/to_one" + + diagnoses: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/slide.yaml b/gdcdictionary/schemas/slide.yaml index 2812c2d0f..49428a4ba 100644 --- a/gdcdictionary/schemas/slide.yaml +++ b/gdcdictionary/schemas/slide.yaml @@ -7,8 +7,9 @@ namespace: http://gdc.nci.nih.gov category: biospecimen program: '*' project: '*' -description: > - A digital image, microscopic or otherwise, of any sample, portion, or sub-part thereof. (GDC) +description: >- + A digital image, microscopic or otherwise, of any sample, portion, or sub-part thereof. + (GDC) additionalProperties: false submittable: true validators: null @@ -37,102 +38,148 @@ uniqueKeys: - [id] - [project_id, submitter_id] -# slide properties properties: + type: type: string + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" + apoptotic_concentration: - description: "The concentration, in cells/mL, of apoptotic cells in the slide blood." + description: >- + The concentration, in cells/mL, of apoptotic cells in the slide blood. type: number + ctc_concentration: - description: "The concentration, in cells/mL, of traditional CTC cells (intact and enlarged cell and nucleus, cytokeratin positive, and CD45 negative) in the slide blood." + description: >- + The concentration, in cells/mL, of traditional CTC cells (intact and enlarged + cell and nucleus, cytokeratin positive, and CD45 negative) in the slide blood. type: number + ctc_low_concentration: - description: "The concentration, in cells/mL, of CTC-low cells (those with low cytokeratin levels compared to traditional CTCs) in the slide blood." + description: >- + The concentration, in cells/mL, of CTC-low cells (those with low cytokeratin + levels compared to traditional CTCs) in the slide blood. type: number + ctc_small_concentration: - description: "The concentration, in cells/mL, of CTC-small cells (those with a small nuclear and cellular size relative to traditional CTCs) in the slide blood." + description: >- + The concentration, in cells/mL, of CTC-small cells (those with a small nuclear + and cellular size relative to traditional CTCs) in the slide blood. type: number + section_location: - term: - $ref: "_terms.yaml#/section_location" + $ref: + - "_terms.yaml#/section_location/common" type: string + methanol_added: - description: "True/False indicator for if methanol was used in the slide preparation process." + description: >- + True/False indicator for if methanol was used in the slide preparation process. type: boolean + number_proliferating_cells: - term: - $ref: "_terms.yaml#/number_proliferating_cells" + $ref: + - "_terms.yaml#/number_proliferating_cells/common" type: integer + number_nucleated_cells: - description: "The total number of nucleated cells identified on the slide." + description: >- + The total number of nucleated cells identified on the slide. type: integer + percent_tumor_cells: - term: - $ref: "_terms.yaml#/percent_tumor_cells" + $ref: + - "_terms.yaml#/percent_tumor_cells/common" type: number + percent_tumor_nuclei: - term: - $ref: "_terms.yaml#/percent_tumor_nuclei" + $ref: + - "_terms.yaml#/percent_tumor_nuclei/common" type: number + percent_normal_cells: - term: - $ref: "_terms.yaml#/percent_normal_cells" + $ref: + - "_terms.yaml#/percent_normal_cells/common" type: number + percent_necrosis: - term: - $ref: "_terms.yaml#/percent_necrosis" + $ref: + - "_terms.yaml#/percent_necrosis/common" type: number + percent_stromal_cells: - term: - $ref: "_terms.yaml#/percent_stromal_cells" + $ref: + - "_terms.yaml#/percent_stromal_cells/common" type: number + percent_inflam_infiltration: - term: - $ref: "_terms.yaml#/percent_inflam_infiltration" + $ref: + - "_terms.yaml#/percent_inflam_infiltration/common" type: number + percent_lymphocyte_infiltration: - term: - $ref: "_terms.yaml#/percent_lymphocyte_infiltration" + $ref: + - "_terms.yaml#/percent_lymphocyte_infiltration/common" type: number + percent_monocyte_infiltration: - term: - $ref: "_terms.yaml#/percent_monocyte_infiltration" + $ref: + - "_terms.yaml#/percent_monocyte_infiltration/common" type: number + percent_granulocyte_infiltration: - term: - $ref: "_terms.yaml#/percent_granulocyte_infiltration" + $ref: + - "_terms.yaml#/percent_granulocyte_infiltration/common" type: number + percent_neutrophil_infiltration: - term: - $ref: "_terms.yaml#/percent_neutrophil_infiltration" + $ref: + - "_terms.yaml#/percent_neutrophil_infiltration/common" type: number + percent_eosinophil_infiltration: - term: - $ref: "_terms.yaml#/percent_eosinophil_infiltration" + $ref: + - "_terms.yaml#/percent_eosinophil_infiltration/common" type: number + run_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + run_name: - description: "Name, number, or other identifier given to this slide's run." + description: >- + Name, number, or other identifier given to this slide's run. type: string + slide_identifier: - description: "Unique identifier given to the this slide." + description: >- + Unique identifier given to the this slide. type: string - samples: - $ref: "_definitions.yaml#/to_many" + project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + samples: + $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/slide_count.yaml b/gdcdictionary/schemas/slide_count.yaml index 30002260c..e39678323 100644 --- a/gdcdictionary/schemas/slide_count.yaml +++ b/gdcdictionary/schemas/slide_count.yaml @@ -7,8 +7,9 @@ namespace: http://gdc.nci.nih.gov category: notation program: '*' project: '*' -description: > - Information pertaining to processed results obtained from slides; often in the form of counts. +description: >- + Information pertaining to processed results obtained from slides; often in the form + of counts. additionalProperties: false submittable: true validators: null @@ -34,67 +35,110 @@ required: - slides uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: + type: - enum: [ "slide_count" ] + enum: + - slide_count + id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id + state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" + submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" + cell_type: - description: "The type of cell being counted or measured." + description: >- + The type of cell being counted or measured. type: string + cell_identifier: - description: "An alternative identifier for a given cell type." + description: >- + An alternative identifier for a given cell type. type: string + cell_count: - description: "Raw count of a particular cell type." + description: >- + Raw count of a particular cell type. type: integer + ck_signal: - description: "Numeric quantification of the CK signal." + description: >- + Numeric quantification of the CK signal. type: number + biomarker_signal: - description: "Numeric quantification of the biomarker signal." + description: >- + Numeric quantification of the biomarker signal. type: number + er_localization: - description: "Cellular localization of the endoplasmic reticulum as determined by staining." + description: >- + Cellular localization of the endoplasmic reticulum as determined by staining. enum: - Nuclear - Cytoplasmic - Both - None - - Not Determined + - Not Determined + frame_identifier: - description: "Name, number, or other identifier given to the frame of the slide from which this image was taken." + description: >- + Name, number, or other identifier given to the frame of the slide from which + this image was taken. type: string + relative_nuclear_size: - description: "The ratio of the single cell's nucleus size to the average of the surrounding cells." + description: >- + The ratio of the single cell's nucleus size to the average of the surrounding + cells. type: number + relative_nuclear_intensity: - description: "The ratio of the single cell's nuclear staining intensity to the average of the surrounding cells." + description: >- + The ratio of the single cell's nuclear staining intensity to the average of + the surrounding cells. type: number + relative_cytokeratin_intensity: - description: "The ratio of the single cell's cytokeratin staining intensity to the average of the surrounding cells." + description: >- + The ratio of the single cell's cytokeratin staining intensity to the average + of the surrounding cells. type: number + relative_er_intensity: - description: "The ratio of the single cell's endoplasmic reticulum staining intensity to the average of the surrounding cells." + description: >- + The ratio of the single cell's endoplasmic reticulum staining intensity to the + average of the surrounding cells. type: number + run_name: - description: "The name or identifier given to the run that was used to generate this slide count." + description: >- + The name or identifier given to the run that was used to generate this slide + count. type: string - slides: - $ref: "_definitions.yaml#/to_many" + project_id: type: string + created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + slides: + $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/slide_image.yaml b/gdcdictionary/schemas/slide_image.yaml index 50681f71e..08dacd472 100644 --- a/gdcdictionary/schemas/slide_image.yaml +++ b/gdcdictionary/schemas/slide_image.yaml @@ -7,7 +7,7 @@ namespace: http://gdc.nci.nih.gov category: data_file program: '*' project: '*' -description: > +description: >- Data file containing image of a slide. additionalProperties: false submittable: true @@ -26,18 +26,18 @@ links: - exclusive: false required: true subgroup: - - name: slides - backref: slide_images - label: data_from - target_type: slide - multiplicity: many_to_one - required: false - - name: core_metadata_collections - backref: slide_images - label: data_from - target_type: core_metadata_collection - multiplicity: many_to_many - required: false + - name: slides + backref: slide_images + label: data_from + target_type: slide + multiplicity: many_to_one + required: false + - name: core_metadata_collections + backref: slide_images + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false required: - submitter_id @@ -50,60 +50,87 @@ required: - data_format uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "slide_image" ] + enum: + - slide_image + data_category: - term: - $ref: "_terms.yaml#/data_category" + $ref: + - "_terms.yaml#/data_category/common" enum: - Biospecimen - Slide Image - Mass Cytometry + data_type: - term: - $ref: "_terms.yaml#/data_type" + $ref: + - "_terms.yaml#/data_type/common" enum: - image - Single Cell Image - Raw IMC Data - Single Channel IMC Image - Antibody Panel Added + data_format: - term: - $ref: "_terms.yaml#/data_format" - type: string + $ref: + - "_terms.yaml#/data_format/common" + type: string + experimental_strategy: - description: "Classification of the slide type with respect to its experimental use." + description: >- + Classification of the slide type with respect to its experimental use. enum: - Diagnostic Slide - Tissue Slide + cell_type: - description: "The type of cell being imaged or otherwised analysed." + description: >- + The type of cell being imaged or otherwised analysed. type: string + cell_identifier: - description: "An alternative identifier for a given cell type." + description: >- + An alternative identifier for a given cell type. type: string + cell_count: - description: "Count of the cell type being imaged or otherwise analysed." + description: >- + Count of the cell type being imaged or otherwise analysed. type: integer + frame_identifier: - description: "Name, number, or other identifier given to the frame of the slide from which this image was taken." + description: >- + Name, number, or other identifier given to the frame of the slide from which + this image was taken. type: string + panel_used: - description: "Name or other identifier given to the panel used during an IMC run." + description: >- + Name or other identifier given to the panel used during an IMC run. type: string + protocol_used: - description: "Name or other identifier given to the protocol used during an IMC run." + description: >- + Name or other identifier given to the protocol used during an IMC run. type: string + run_name: - description: "Name, number, or other identifier given to the run that generated this slide image." + description: >- + Name, number, or other identifier given to the run that generated this slide + image. type: string + slides: $ref: "_definitions.yaml#/to_one" + core_metadata_collections: $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/submitted_aligned_reads.yaml b/gdcdictionary/schemas/submitted_aligned_reads.yaml index 59db76bae..80494a5b1 100644 --- a/gdcdictionary/schemas/submitted_aligned_reads.yaml +++ b/gdcdictionary/schemas/submitted_aligned_reads.yaml @@ -7,7 +7,7 @@ namespace: http://gdc.nci.nih.gov category: data_file program: '*' project: '*' -description: > +description: >- Data file containing aligned reads that are used as input to GDC workflows. additionalProperties: false submittable: true @@ -26,18 +26,18 @@ links: - exclusive: false required: true subgroup: - - name: read_groups - backref: submitted_aligned_reads_files # pretty ugly - label: data_from - target_type: read_group - multiplicity: one_to_many - required: false - - name: core_metadata_collections - backref: submitted_aligned_reads_files - label: data_from - target_type: core_metadata_collection - multiplicity: many_to_many - required: false + - name: read_groups + backref: submitted_aligned_reads_files + label: data_from + target_type: read_group + multiplicity: one_to_many + required: false + - name: core_metadata_collections + backref: submitted_aligned_reads_files + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false required: - submitter_id @@ -51,35 +51,43 @@ required: - experimental_strategy uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "submitted_aligned_reads" ] + enum: + - submitted_aligned_reads + data_category: - term: - $ref: "_terms.yaml#/data_category" + $ref: + - "_terms.yaml#/data_category/common" enum: - Sequencing Data - Sequencing Reads - Raw Sequencing Data + data_type: - term: - $ref: "_terms.yaml#/data_type" + $ref: + - "_terms.yaml#/data_type/common" enum: - Aligned Reads - Alignment Coordinates + data_format: - term: - $ref: "_terms.yaml#/data_format" + $ref: + - "_terms.yaml#/data_format/common" enum: - BAM - BED + experimental_strategy: - term: - $ref: "_terms.yaml#/experimental_strategy" + $ref: + - "_terms.yaml#/experimental_strategy/common" enum: - WGS - WXS @@ -89,7 +97,9 @@ properties: - miRNA-Seq - Total RNA-Seq - DNA Panel + read_groups: $ref: "_definitions.yaml#/to_many" + core_metadata_collections: $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/submitted_copy_number.yaml b/gdcdictionary/schemas/submitted_copy_number.yaml index 2bc9d772c..d3109047d 100644 --- a/gdcdictionary/schemas/submitted_copy_number.yaml +++ b/gdcdictionary/schemas/submitted_copy_number.yaml @@ -7,7 +7,7 @@ namespace: http://gdc.nci.nih.gov category: data_file program: '*' project: '*' -description: > +description: >- Data file containing normalized copy number information from an aliquot. additionalProperties: false submittable: true @@ -60,32 +60,43 @@ required: - experimental_strategy uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "submitted_copy_number" ] + enum: + - submitted_copy_number + data_category: - term: - $ref: "_terms.yaml#/data_category" + $ref: + - "_terms.yaml#/data_category/common" type: string + data_type: - term: - $ref: "_terms.yaml#/data_type" - type: string + $ref: + - "_terms.yaml#/data_type/common" + type: string + data_format: - term: - $ref: "_terms.yaml#/data_format" - type: string + $ref: + - "_terms.yaml#/data_format/common" + type: string + experimental_strategy: - term: - $ref: "_terms.yaml#/experimental_strategy" - type: string + $ref: + - "_terms.yaml#/experimental_strategy/common" + type: string + aliquots: $ref: "_definitions.yaml#/to_one" + read_groups: $ref: "_definitions.yaml#/to_many" + core_metadata_collections: $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/submitted_methylation.yaml b/gdcdictionary/schemas/submitted_methylation.yaml index 10408f5f1..4f654753f 100644 --- a/gdcdictionary/schemas/submitted_methylation.yaml +++ b/gdcdictionary/schemas/submitted_methylation.yaml @@ -3,11 +3,15 @@ $schema: "http://json-schema.org/draft-04/schema#" id: "submitted_methylation" title: Submitted Methylation type: object -namespace: https://www.bloodpac.org/ +namespace: https://www.bloodpac.org/ category: data_file program: '*' project: '*' -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." +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. additionalProperties: false submittable: true validators: null @@ -25,18 +29,18 @@ links: - exclusive: false required: true subgroup: - - name: core_metadata_collections - backref: submitted_methylation_files - label: data_from - target_type: core_metadata_collection - multiplicity: many_to_many - required: false - - name: aliquots - backref: submitted_methylation_files - label: data_from - target_type: aliquot - multiplicity: many_to_one - required: false + - name: core_metadata_collections + backref: submitted_methylation_files + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false + - name: aliquots + backref: submitted_methylation_files + label: data_from + target_type: aliquot + multiplicity: many_to_one + required: false required: - submitter_id @@ -49,38 +53,51 @@ required: - data_format uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "submitted_methylation" ] + enum: + - submitted_methylation + data_category: - term: - $ref: "_terms.yaml#/data_category" + $ref: + - "_terms.yaml#/data_category/common" enum: - Methylation Data + data_type: - term: - $ref: "_terms.yaml#/data_type" - enum: [ "Methylation Intensity Values" ] + $ref: + - "_terms.yaml#/data_type/common" + enum: + - Methylation Intensity Values + data_format: - term: - $ref: "_terms.yaml#/data_format" + $ref: + - "_terms.yaml#/data_format/common" enum: - IDAT - assay_method: + + assay_method: enum: - Methylation Array + assay_instrument: enum: - Illumina + assay_instrument_model: enum: - Illumina Infinium HumanMethylation450 - Illumina Infinium HumanMethylation450K - aliquots: - $ref: "_definitions.yaml#/to_one" + core_metadata_collections: $ref: "_definitions.yaml#/to_many" + + aliquots: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/submitted_somatic_mutation.yaml b/gdcdictionary/schemas/submitted_somatic_mutation.yaml index f51b502c4..1aa8e6e73 100644 --- a/gdcdictionary/schemas/submitted_somatic_mutation.yaml +++ b/gdcdictionary/schemas/submitted_somatic_mutation.yaml @@ -7,7 +7,7 @@ namespace: http://gdc.nci.nih.gov category: data_file program: '*' project: '*' -description: > +description: >- Data file containing somatic mutation calls from a read group. additionalProperties: false submittable: true @@ -26,18 +26,18 @@ links: - exclusive: false required: true subgroup: - - name: core_metadata_collections - backref: submitted_somatic_mutations - label: data_from - target_type: core_metadata_collection - multiplicity: many_to_many - required: false - - name: read_groups - backref: submitted_somatic_mutations - label: derived_from - target_type: read_group - multiplicity: many_to_many - required: false + - name: core_metadata_collections + backref: submitted_somatic_mutations + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false + - name: read_groups + backref: submitted_somatic_mutations + label: derived_from + target_type: read_group + multiplicity: many_to_many + required: false required: - submitter_id @@ -51,33 +51,46 @@ required: - experimental_strategy uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "submitted_somatic_mutation" ] + enum: + - submitted_somatic_mutation + data_category: - term: - $ref: "_terms.yaml#/data_category" + $ref: + - "_terms.yaml#/data_category/common" type: string + data_type: - term: - $ref: "_terms.yaml#/data_type" - type: string + $ref: + - "_terms.yaml#/data_type/common" + type: string + data_format: - term: - $ref: "_terms.yaml#/data_format" + $ref: + - "_terms.yaml#/data_format/common" type: string + experimental_strategy: - term: - $ref: "_terms.yaml#/experimental_strategy" - type: string + $ref: + - "_terms.yaml#/experimental_strategy/common" + type: string + total_variants: - description: "The total number of variants detected carrying a base change difference from the reference genome." + description: >- + The total number of variants detected carrying a base change difference from + the reference genome. type: integer - read_groups: - $ref: "_definitions.yaml#/to_many" + core_metadata_collections: $ref: "_definitions.yaml#/to_many" + + read_groups: + $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/submitted_unaligned_reads.yaml b/gdcdictionary/schemas/submitted_unaligned_reads.yaml index 4b72d4653..7978a54af 100644 --- a/gdcdictionary/schemas/submitted_unaligned_reads.yaml +++ b/gdcdictionary/schemas/submitted_unaligned_reads.yaml @@ -7,7 +7,8 @@ namespace: http://gdc.nci.nih.gov category: data_file program: '*' project: '*' -description: "Data file containing unaligned reads that have not been GDC Harmonized." +description: >- + Data file containing unaligned reads that have not been GDC Harmonized. additionalProperties: false submittable: true validators: null @@ -25,18 +26,18 @@ links: - exclusive: false required: true subgroup: - - name: read_groups - backref: submitted_unaligned_reads_files # pretty ugly - label: data_from - target_type: read_group - multiplicity: many_to_one - required: false - - name: core_metadata_collections - backref: submitted_unaligned_reads_files - label: data_from - target_type: core_metadata_collection - multiplicity: many_to_many - required: false + - name: read_groups + backref: submitted_unaligned_reads_files + label: data_from + target_type: read_group + multiplicity: many_to_one + required: false + - name: core_metadata_collections + backref: submitted_unaligned_reads_files + label: data_from + target_type: core_metadata_collection + multiplicity: many_to_many + required: false required: - submitter_id @@ -50,33 +51,42 @@ required: - experimental_strategy uniqueKeys: - - [ id ] - - [ project_id, submitter_id ] + - [id] + - [project_id, submitter_id] properties: - $ref: "_definitions.yaml#/data_file_properties" + + $ref: + - "_definitions.yaml#/data_file_properties" + type: - enum: [ "submitted_unaligned_reads" ] + enum: + - submitted_unaligned_reads + data_category: - term: - $ref: "_terms.yaml#/data_category" + $ref: + - "_terms.yaml#/data_category/common" enum: - Sequencing Data - Sequencing Reads - Raw Sequencing Data + data_type: - term: - $ref: "_terms.yaml#/data_type" - enum: [ "Unaligned Reads" ] + $ref: + - "_terms.yaml#/data_type/common" + enum: + - Unaligned Reads + data_format: - term: - $ref: "_terms.yaml#/data_format" + $ref: + - "_terms.yaml#/data_format/common" enum: - BAM - FASTQ + experimental_strategy: - term: - $ref: "_terms.yaml#/experimental_strategy" + $ref: + - "_terms.yaml#/experimental_strategy/common" enum: - WGS - WXS @@ -86,7 +96,9 @@ properties: - miRNA-Seq - Total RNA-Seq - DNA Panel + read_groups: $ref: "_definitions.yaml#/to_one" + core_metadata_collections: $ref: "_definitions.yaml#/to_many" diff --git a/gdcdictionary/schemas/treatment.yaml b/gdcdictionary/schemas/treatment.yaml index 4ed89da04..2ed0925ae 100644 --- a/gdcdictionary/schemas/treatment.yaml +++ b/gdcdictionary/schemas/treatment.yaml @@ -7,9 +7,9 @@ namespace: http://gdc.nci.nih.gov category: clinical program: '*' project: '*' -description: > - Record of the administration and intention of therapeutic agents provided to a patient to alter - the course of a pathologic process. +description: >- + Record of the administration and intention of therapeutic agents provided to a patient + to alter the course of a pathologic process. additionalProperties: false submittable: true validators: null @@ -21,64 +21,65 @@ systemProperties: - created_datetime - updated_datetime -required: - - submitter_id - - type - links: - name: diagnoses backref: treatments - label: describes #need better term here + label: describes target_type: diagnosis multiplicity: many_to_one required: true - +required: + - submitter_id + - type uniqueKeys: - #unclear if want submitter ID for clinical - [id] - [project_id, submitter_id] properties: + type: - enum: [ "treatment" ] + enum: + - treatment id: - $ref: "_definitions.yaml#/UUID" + $ref: + - "_definitions.yaml#/uuid" systemAlias: node_id state: - $ref: "_definitions.yaml#/state" + $ref: + - "_definitions.yaml#/state" submitter_id: - type: - - string - - "null" + oneOf: + - type: string + - type: "null" days_to_treatment: - term: - $ref: "_terms.yaml#/days_to_treatment" + $ref: + - "_terms.yaml#/days_to_treatment/common" type: number days_to_treatment_end: - term: - $ref: "_terms.yaml#/days_to_treatment_end" + $ref: + - "_terms.yaml#/days_to_treatment_end/common" type: number days_to_treatment_start: - term: - $ref: "_terms.yaml#/days_to_treatment_start" + $ref: + - "_terms.yaml#/days_to_treatment_start/common" type: number therapeutic_agents: - term: - $ref: "_terms.yaml#/therapeutic_agents" + $ref: + - "_terms.yaml#/therapeutic_agents/common" type: string treatment_anatomic_site: - term: - $ref: "_terms.yaml#/treatment_anatomic_site" + $ref: + - "_terms.yaml#/treatment_anatomic_site/common" enum: - Abdomen, total - Arm @@ -159,13 +160,13 @@ properties: - Not Allowed To Collect treatment_intent_type: - term: - $ref: "_terms.yaml#/treatment_intent_type" + $ref: + - "_terms.yaml#/treatment_intent_type/common" type: string treatment_or_therapy: - term: - $ref: "_terms.yaml#/treatment_or_therapy" + $ref: + - "_terms.yaml#/treatment_or_therapy/common" enum: - "yes" - "no" @@ -173,8 +174,8 @@ properties: - not reported treatment_outcome: - term: - $ref: "_terms.yaml#/treatment_outcome" + $ref: + - "_terms.yaml#/treatment_outcome/common" enum: - Complete Response - Partial Response @@ -183,8 +184,8 @@ properties: - Unknown treatment_type: - term: - $ref: "_terms.yaml#/treatment_type" + $ref: + - "_terms.yaml#/treatment_type/common" enum: - Ablation - Chemotherapy @@ -204,14 +205,17 @@ properties: - Not Reported - Not Allowed To Collect - diagnoses: - $ref: "_definitions.yaml#/to_one" - project_id: - $ref: "_definitions.yaml#/project_id" + $ref: + - "_definitions.yaml#/project_id" - # ======== Timestamps ======== created_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + updated_datetime: - $ref: "_definitions.yaml#/datetime" + $ref: + - "_definitions.yaml#/datetime" + + diagnoses: + $ref: "_definitions.yaml#/to_one" diff --git a/setup.py b/setup.py index 28f6decc6..ba7ec72fb 100644 --- a/setup.py +++ b/setup.py @@ -28,6 +28,10 @@ def get_version(): 'jsonschema>=2.5.1', 'dictionaryutils', ], + dependency_links=[ + # for testing purpose + "git+https://github.com/uc-cdis/dictionaryutils.git@feat/format_upgrade#egg=dictionaryutils", + ], package_data={ "gdcdictionary": [ "schemas/*.yaml",