id: https://www.cdisc.org/cosmos/sdtm_v1.0 name: COSMoS-Biomedical-Concepts-SDTM-Schema imports: - linkml:types prefixes: linkml: https://w3id.org/linkml/ cosmos_sdtm: https://www.cdisc.org/cosmos/sdtm_v1.0/ NCIT: http://purl.obolibrary.org/obo/NCIT_ default_prefix: cosmos_sdtm default_range: string classes: SDTMGroup: tree_root: true slots: - packageDate - packageType - datasetSpecializationId - domain - shortName - source - sdtmigStartVersion - sdtmigEndVersion - biomedicalConceptId - variables SDTMVariable: slots: - name - dataElementConceptId - isNonStandard - codelist - subsetCodelist - valueList - assignedTerm - role - relationship - dataType - length - format - significantDigits - mandatoryVariable - mandatoryValue - originType - originSource - comparator - vlmTarget RelationShip: slots: - subject - linkingPhrase - predicateTerm - object CodeList: slots: - conceptId - href - submissionValue CodeListTerm: slots: - termId - termValue SubsetCodeList: slots: - parentCodelist - subsetShortName - subsetLabel - codelistTerm AssignedTerm: attributes: conceptId: description: C-code for assigned term in NCIt or left blank when CDISC terminology does not apply range: string pattern: "^(C[0-9]+|CNEW)$" required: false value: description: Submission value for assigned term in NCIt if it exists, or an assigned value which will be the default value range: string required: true slots: packageDate: description: Biomedical Concept package release date indicating when the BC package was published to production range: date required: true packageType: description: Package type (sdtm for SDTM Dataset Specializations) range: PackageTypeEnum required: true datasetSpecializationId: description: Identifier for SDTM Value Level Metadata group identifier: true range: string pattern: "^[A-Z][A-Z0-9_]*$" required: true domain: description: Domain for the SDTM specialization group range: string required: true source: description: SDTM VLM Source which categorizes VLM groups by topic variable range: string required: true shortName: description: SDTM group short name which provides a user friendly and intuitive name for the vlm_group_id range: string required: true sdtmigStartVersion: description: The earliest SDTMIG version applicable to the BC dataset specialization range: string required: true sdtmigEndVersion: description: The last SDTMIG version that is applicable to the BC dataset specialization range: string biomedicalConceptId: description: Biomedical Concept identifier foreign key range: string pattern: "^(C[0-9]+|NEW_[A-Z_]*[0-9]*)$" recommended: true variables: description: Variable included in the SDTM dataset specialization range: SDTMVariable required: true multivalued: true inlined_as_list: true name: description: Variable included in the SDTM dataset specialization identifier: true range: string pattern: "^[A-Z][A-Z0-9_]*$" required: true dataElementConceptId: description: Biomedical Concept Data Element Concept identifier foreign key range: string pattern: "^(C[0-9]+|NEW_[A-Z_]*[0-9]*)$" isNonStandard: description: Flag that indicates if the variable is a non-standard variable range: boolean codelist: description: Codelist range: CodeList inlined: true subsetCodelist: description: Subset codelist short name range: string pattern: "^[A-Z][A-Z0-9_]*$" conceptId: description: C-code for a codelist in NCIt identifier: true range: string pattern: "^(C[0-9]+|CNEW)$" required: true href: description: Link to NCIt for the codelist range: uri required: false submissionValue: description: CDISC submission value for the codelist range: string pattern: "^[A-Z][A-Z0-9_]*$" required: true parentCodelist: description: Subset codelist parent codelist range: string pattern: "^C[0-9]+$" required: true subsetShortName: description: Subset codelist short name range: string pattern: "^[A-Z][A-Z0-9_]*$" required: true subsetLabel: description: Subset codelist label range: string required: true codelistTerm: description: Term in subset codelist required: true range: CodeListTerm multivalued: true inlined_as_list: true termId: description: C-code term in subset codelist range: string pattern: "^(C[0-9]+)$" required: true termValue: description: Submision value of term in subset codelist range: string required: true valueList: description: List of SDTM submission values used if subset codelist is not applicable range: string multivalued: true inlined_as_list: true assignedTerm: description: Assigned term range: AssignedTerm role: description: SDTM variable role range: RoleEnum relationship: description: Relationship between variables range: RelationShip subject: description: Subject in a variable relationship range: string required: true linkingPhrase: description: Variable relationship descriptive linking phrase range: LinkingPhraseEnum required: true predicateTerm: description: Short variable relationship linking phrase for programming purposes range: PredicateTermEnum required: true object: description: Object in a variable relationship range: string required: true dataType: description: Variable data type range: SDTMVariableDataTypeEnum length: description: Variable length range: integer minimum_value: 1 format: description: Variable display format range: string significantDigits: description: Variable significant_digits range: integer mandatoryVariable: description: Indicator that variable must be present within the SDTM group range: boolean mandatoryValue: description: Indicator that variable must be populated within the SDTM group range: boolean originType: description: Variable origin type (define-XML v21) range: OriginTypeEnum originSource: description: Variable origin source (define-XML v21) range: OriginSourceEnum comparator: description: Comparison operator for SDTM group variables included in VLM range: ComparatorEnum vlmTarget: description: Target variable for VLM range: boolean enums: PackageTypeEnum: permissible_values: sdtm: SDTMVariableDataTypeEnum: permissible_values: datetime: title: datetime durationDatetime: title: durationDatetime float: title: float integer: title: integer text: title: text LinkingPhraseEnum: permissible_values: assesses seriousness of: assesses the severity of: associates the tumor identified in: decodes the value in: describes actions taken: describes relationship of: describes the outcome of: further describes the test in: further specifies the anatomical location in: groups tumor assessments used in overall response identified by: groups values in: groups, within an individual subject, values in: identifies a pattern of: identifies an observation described by: identifies overall response supported by tumor assessments identified by: identifies the image from the procedure in: identifies the reference used in the genomic test in: identifies the tumor found by the test in: indicates heritability of the genetic variant in: indicates occurrence of the value in: indicates pre-specification of the value in: indicates severity of: indicates the location detail for the tumor identified by: indicates the previous irradiation status of the tumor identified by: indicates the progression status of the previous irradiated tumor identified by: is a dictionary-derived class code for the value in: is a dictionary-derived class name for the value in: is a dictionary-derived term for the value in: is a grouping of values in: is a reference range value for: is an identifier for a published reference for the genetic variant in: is an identifier for the copy, on one of two homologous chromosones, of the genetic variant in: is an identifier for the evaluator with the role in: is an identifier for the genetic sequence of the genetic entity represented by: is decoded by the value in: is original text for: is the administered amount of the treatment in: is the administration anatomical location for the treatment in: is the aspect of the event used to define the date in: is the chromosome that is the position of the result in: is the clinical significance interpretation for: is the clinical trial or treatment setting for: is the code for the value in: is the date of occurrence for: is the date of occurrence: is the dictionary code for the test in: is the dictionary-derived class code for the value in: is the dictionary-derived class name for the value in: is the dictionary-derived term for the value in: is the duration for: is the end date for: is the epoch of the performance of the test in: is the frequency of administration of the amount in: is the genetic sub-location of the result in: is the identifier for the device which collected data for the test in: is the identifier for the source data used in the performance of the test in: is the intended disease outcome for: is the material type of the subject of the activity in: is the medical condition that is the reason for the treatment in: is the method for the test in: is the method of secondary analysis of results in: is the name of the reference terminology for: is the numeric location, within a chromosone, genetic entity, or genetic sub-region, of the result in: is the object of the observation in: is the operational objective of the test in: is the part of the body through which is administered the treatment in: is the period of time for the test in: is the period of time to be considered when answering the question in: is the physical form of the product in: is the reason for stopping administration of: is the reason for the status of the value in: is the reason the lesion was not evaluable in: is the result of the test in: is the role of the assessor who performed the test in: is the severity of the toxicity in: is the specimen tested in: is the start date for: is the status of the value in: is the subject position during performance of the test in: is the subject's fasting status during the performance of the test in: is the substance bound to the analyte in: is the symbol for the genomic entity that is the position of the result in: is the textual description of the intended dose regimen for: is the type of genomic entity that is the position of the result in: is the unit for the value in: is the unit for: is the value of the property identified by: is the version of the reference terminology in: specifies the anatomical location in: specifies the anatomical location of the performance of the test in: specifies the anatomical location of the tumor identified by: specifies the anatomical location of: specifies the severity of: values are grouped by: was the subject position during performance of the test in: indicates the inclusion of non-resting time periods: is the analytical method for the test in: is the date of collection for: is the device that performed the test in: is the period of time considered for the test in: is the value for the parameter in: PredicateTermEnum: permissible_values: ASSESSES: CLASSIFIES: DECODES: DESCRIBES: GROUPS: GROUPS_BY: IDENTIFIES: IDENTIFIES_OBSERVATION: IDENTIFIES_PRODUCT_IN: IDENTIFIES_TUMOR_IN: INDICATES: IS_ATTRIBUTE_FOR: IS_DECODED_BY: IS_DERIVED_FROM: IS_EPOCH_OF: IS_GROUPED_BY: IS_INDICATOR_FOR: IS_ORIGINAL_TEXT_FOR: IS_POSITION_FOR: IS_REASON_FOR: IS_RESULT_OF: IS_SPECIMEN_TESTED_IN: IS_SUBJECT_STATE_FOR: IS_TIMING_FOR: IS_UNIT_FOR: PERFORMED: PERFORMS: QUALIFIES: SPECIFIES: IS_VALUE_OF: IS_REFERENCE_TERMINOLOGY_FOR: IS_REFERENCE_VALUE_FOR: IS_DEVICE_FOR: OriginTypeEnum: description: Terminology relevant to the origin type for datasets in the Define-XML document. code_set: NCIT:C170449 permissible_values: Assigned: description: A value that is derived through designation, such as values from a look up table or a label on a CRF. meaning: NCIT:C170547 Collected: description: A value that is actually observed and recorded by a person or obtained by an instrument. meaning: NCIT:C170548 Derived: description: A value that is calculated by an algorithm or reproducible rule, and which is dependent upon other data values. meaning: NCIT:C170549 Predecessor: description: A value that is copied from a variable in another dataset. meaning: NCIT:C170550 Protocol: description: A value that is included as part of the study protocol. meaning: NCIT:C170551 OriginSourceEnum: description: Terminology relevant to the origin source for datasets in the Define-XML document. code_set: NCIT:C170450 permissible_values: Investigator: description: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at the trial site, the investigator is the responsible leader of the team and may be called the principal investigator. meaning: NCIT:C25936 Sponsor: description: An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical study. [After ICH E6, WHO, 21 CFR 50.3 (e), and after IDMP] meaning: NCIT:C70793 Subject: description: An individual who is observed, analyzed, examined, investigated, experimented upon, or/and treated in the course of a particular study. meaning: NCIT:C41189 Vendor: description: A person or agency that promotes or exchanges goods or services for money. (NCI) meaning: NCIT:C68608 RoleEnum: permissible_values: Identifier: Qualifier: Timing: Topic: ComparatorEnum: permissible_values: EQ: IN: