mdf-reader

Handle: CRDC URI: https://datacommons.cancer.gov/ Version: v1.0.0 Tags: Model: Sample Nodes: diagnosis: Props: - diagnosis_id - diagnosis - case_type Desc: Properties that describe a participant's disease(s). Tags: Category: clinical Class: primary number: 1 cool: true Term: - Origin: caDSR Code: "7058670" Value: Diagnosis Version: "1.00" - Origin: UFP Value: Disease or Disorder Diagnosis - Origin: NBA Code: "23" Value: Disorder Diagnosis Version: "2.00" Handle: disorder_diagnosis Desc: Term used by NBA to describe a diagnosis of a disorder. Tags: category: clinical Definition: A diagnosis of a disorder. nanoid: jordan nanoid: abc123 file: Props: - file_size - list_of_strings - list_of_integers - list_of_numbers - list_of_datetimes - list_of_urls - list_of_booleans - list_of_TBDs - file_id - file_name - md5sum Term: - Origin: CRDC Value: file participant: Props: - participant_id - height - weight - age_at_first_diagnosis - race - participant_bmis Tags: Template: "Yes" visit: CompKey: - participant.participant_id - visit_date Props: - visit_id - visit_date finding: CompKey: - participant.participant_id - visit.visit_id - test_name - test_value Props: - finding_id - test_name - test_value study: Props: - study_data_types - study_data_types_enum - experimental_strategy_and_data_subtype - study_payments - adult_or_childhood_study - study_id sample: Props: - sample_weight - sample_length - sample_id - sample_type - sample_tumor_status - anatomic_site - collection_method placeholder: Props: null Relationships: of_participant: Mul: many_to_one Ends: - Src: diagnosis Dst: participant - Src: file Dst: participant Mul: one_to_one - Src: study Dst: participant Mul: many_to_many Tags: Display: false Desc: A participant can have many diagnoses. Props: - of_participant_id - of_participant_type - of_file_id Tags: Reltag: test Term: - Origin: caDSR Code: '2953639' Value: Of participant Version: '1.00' of_diagnosis: Mul: one_to_many Ends: - Src: file Dst: diagnosis Props: null nanoid: "111222" UniversalNodeProperties: mustHave: - id - date mayHave: - transaction_id - transaction_date UniversalRelationshipProperties: mustHave: - id mayHave: - transaction_id PropDefinitions: id: Type: string Req: true date: Type: datetime Req: Yes visit_date: Type: datetime Req: Yes visit_id: Type: string Key: true finding_id: Type: string Key: true test_name: Type: string Req: Yes test_value: Type: number Req: Yes transaction_id: Type: url Nul: true Req: false transaction_date: Type: datetime Key: false Req: No diagnosis_id: Type: number Desc: A unique identifier for a diagnosis. Src: CRDC Key: true Nul: false diagnosis: Enum: [https:/icdo3.org/diagnosis_codes_and_terms/123] Req: Preferred Strict: false participant_id: Type: string Key: true case_type: Type: TBD of_participant_id: Type: boolean of_participant_type: Enum: - a_participant_type Deprecated: false of_file_id: Enum: - C:/path/to/file/id.txt Deprecated: true height: Type: value_type: number units: - cm weight: Type: value_type: number units: [mg, kg, lbs, stone] Term: - Origin: CRDC Code: 'weight123' Value: Weight Handle: weight file_size: Type: value_type: integer units: - https://www.every_file_size_unit.com/bytesandstuff Term: - Origin: CRDC Code: 'file123' Value: File Size - Origin: caDSR Code: '11479876' Value: Electronic Data File Size Integer Version: '1.00' Tags: include_units: true nanoid: nanoid age_at_first_diagnosis: Type: value_type: integer units: - years - months - days Term: - Origin: CRDC Value: Age at First Diagnosis (years) - Origin: caDSR Value: Age at First Diagnosis in Years - Origin: CCDI Value: age at first diagnosis Tags: include_units: true pref_units: days race: Enum: - "American Indian or Alaska Native" - "Asian" - "Black or African American" - "Hispanic or Latino" - "Native Hawaiian or other Pacific Islander" - "Not Allowed to Collect" - "Not Reported" - "Unknown" - "White" Strict: true Term: - Origin: caDSR Code: '2192199' Value: Race Category Text Version: '1.00' sample_weight: Type: value_type: number units: - pattern: ^\\d+(mg|kg|g)$ flavor: Perl sample_length: Type: value_type: number units: - path/to/sample/length/units/ sample_id: Type: pattern: ^[A-Z]{2,5}-\d{4,8}(_[A-Z\d]{2,4})?$ flavor: JS Key: true sample_type: Type: https://sample_types.com/api/v1/ sample_tumor_status: Type: - Normal - Peritumoral - Tumor anatomic_site: Type: - https://anatomic_sites.gov/uberon/ collection_method: Type: - /path/to/collection/methods list_of_strings: Type: value_type: list item_type: string list_of_integers: Type: value_type: list item_type: integer list_of_numbers: Type: value_type: list item_type: number list_of_datetimes: Type: value_type: list item_type: datetime list_of_urls: Type: value_type: list item_type: url list_of_booleans: Type: value_type: list item_type: boolean list_of_TBDs: Type: value_type: list item_type: TBD study_data_types: Type: value_type: list item_type: - Genomic - Imaging - Clinical study_data_types_enum: Type: value_type: list Enum: - Genomic - Imaging - Clinical experimental_strategy_and_data_subtype: Type: value_type: list item_type: - http://research.activity/experimental/method/type/1 participant_bmis: Type: value_type: list item_type: value_type: integer units: [kg, lbs, stone] study_payments: Type: value_type: list item_type: value_type: number units: [$, dollars, USD] adult_or_childhood_study: Enum: - Adult - Pediatric Tags: display_color: blue file_id: Type: string Key: true study_id: Type: string Key: true file_name: Type: string md5sum: Type: string Terms: american_indian_or_alaska_native: Origin: caDSR Definition: A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB) Code: '2572232' Version: '1' Value: 'American Indian or Alaska Native' Handle: american_indian_or_alaska_native Desc: A person with origins in any of the original peoples of the Americas. nanoid: '125722' asian: Origin: caDSR Definition: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB) Code: '2572233' Version: '1' Value: Asian black_or_african_american: Origin: caDSR Definition: A person having origins in any of the Black racial groups of Africa. Terms such as \"Haitian\" or \"Negro\" can be used in addition to \"Black or African American\". (OMB) Code: '2572313' Version: '1' Value: 'Black or African American' hispanic_or_latino: Origin: caDSR Definition: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. The term, \"Spanish origin,\" can be used in addition to \"Hispanic or Latino.\" (OMB) Code: '2581176' Version: '1' Value: Hispanic or Latino native_hawaiian_or_other_pacific_islander: Origin: caDSR Definition: Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuukese (Trukese), Fijian, Kosraean, Melanesian, Micronesian, Northern Mariana Islander, Palauan, Papua New Guinean, Pohnpeian, Polynesian, Solomon Islander, Tahitian, Tokelauan, Tongan, Yapese, or Pacific Islander, not specified. Code: '2572235' Version: '1' Value: Native Hawaiian or Other Pacific Islander not_allowed_to_collect: Origin: caDSR Definition: An indicator that specifies that a collection event was not permitted. Code: '6662191' Version: '1' Value: Not Allowed To Collect not_reported: Origin: NCIt Value: Not Reported unknown: Origin: caDSR Definition: Not known, not observed, not recorded, or refused. Code: '4266671' Version: '1' Value: Unknown Tags: display: grey_out white: Origin: caDSR Definition: Denotes person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. Code: '2572236' Version: '1' Value: White normal: Origin: caDSR Value: Normal Tissue peritumoral: Origin: caDSR Definition: Located in tissues surrounding a tumor. Code: '4633527' Version: '1' Value: Peritumoral tumor: Origin: caDSR Definition: A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. Code: '3071117' Version: '1' Value: Neoplasm genomic: Origin: NWM Value: Genomic Data imaging: Origin: NWM Value: Imaging Data clinical: Origin: NWM Value: Clinical Data Adult: Origin: MAJ Value: Adult Study Pediatric: Origin: MAJ Value: Pediatric Study