Ccdh-Mvp schema

Classes

• CodeableConcept
• Coding - A structured representation of a coded/enumerated data value, that includes additional metadata about the code and code system.
• Entity - Any resource that has its own identifier
  • Patient
  • Project
  • ResearchSubject - A research subject is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject’s privacy.
  • Specimen - Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation.
• Identifier
• Quantity - A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit.

Mixins

Slots

• ➞coding - A reference to a code defined by a terminology system
• ➞text - A human language representation of the concept represented by the Coding
• ➞code - The value of the code itself.
• ➞display - A human-readable name for the code.
• ➞system - The code system where the code is defined.
• ➞version - The version of the code system.
• id
  • Patient➞id - The ‘logical’ identifier of the entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system. The identified entity may have a different ‘id’ in a different system.
  • Project➞id
  • ResearchSubject➞id - The ‘logical’ identifier of the entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system. The identified entity may have a different ‘id’ in a different system.
  • Specimen➞id - The ‘logical’ identifier of the entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system. The identified entity may have a different ‘id’ in a different system.
• ➞system - The system or namespace that defines the identifier.
• ➞type - A code that defines the type of the identifier.
• ➞value - The value of the identifier, as defined by the system.
• ➞identifier - A ‘business’ identifier for the entity, typically as provided by an external system or authority, that persists across implementing systems.
• ➞taxon - The taxonomic group (e.g. species) of the patient.

• ➞comparator - How to understand the value . . . <

  <=

  >=

  >

• ➞unit - Unit representation (e.g. mg, mL)
• ➞value - Numerical value (with implicit precision)
• ➞associated_patient - A reference to the Patient that is this ResearchSubject
• ➞associated_project - A reference to the Project(s) of which this ResearchSubject is a member
• ➞identifier - A ‘business’ identifier for the entity, typically as provided by an external system or authority, that persists across implementing systems (i.e. a ‘logical’ identifier). Uses a specialized, complex ‘Identifier’ data type to capture information about the source of the business identifier.
• ➞primary_disease_site - The text term used to describe the primary site of disease, as categorized by the World Health Organization’s (WHO) International Classification of Diseases for Oncology (ICD-O). This categorization groups cases into general categories.
• ➞primary_disease_type - The text term used to describe the type of malignant disease, as categorized by the World Health Organization’s (WHO) International Classification of Diseases for Oncology (ICD-O).
• ➞analyte_concentration - The concentration of an extracted analyte that is present in a specimen (specifically, in a specimen of type ‘analyte’, or an ‘aliquot’ derived from an analyte). e.g. the concentration of DNA in a specimen created through extracting DNA from a blood sample.
• ➞analyte_concentration_method - The method used to determine the concentration of purified analyte within a solution.
• ➞analyte_type - When the specimen is of type ‘analyte’ or ‘aliquot’, this is the type of substance the analyte represents (e.g. DNA, RNA)
• ➞associated_project - The Project associated with the specimen.
• ➞cellular_composition - The cellular composition of the sample
• ➞current_volume - The current total volume of the specimen, at the time of recording.
• ➞current_weight - The current weight of the specimen, at the time of recording (as opposed to an initial weight before its processing or portioning).
• ➞derived_from_specimen - A source/parent specimen from which this one was directly derived.
• ➞derived_from_subject - The Patient/ResearchSubject, or Biologically Derived Materal (e.g. a cell line, tissue culture, organoid) from which the specimen was directly or indirectly derived.
• ➞general_tissue_morphology - A term describing at a high-level the kind of tissue collected in a specimen, with respect to disease status or proximity to tumor tissue (e.g. is it normal, abnormal, tumor, tumor-adjacent).
• ➞identifier - A ‘business’ identifier or accession number for the entity, typically as provided by an external system or authority, that persists across implementing systems (i.e. a ‘logical’ identifier).
• ➞matched_normal_flag - A flag indicating that there is no matched normal aliquot for this case that can be used for variant calling purposes.
• ➞qualification_status_flag - A flag indicating whether the specimen is qualified or disqualified for data analysis in a study.
• ➞source_material_type - The general kind of material from which the specimen was derived, indicating the physical nature of the source material.
• ➞specific_tissue_morphology - A term describing the specific pathology exhibited by the tissue in a specimen.
• ➞specimen_type - The high-level type of the specimen, based on its how it has been derived from the original extracted sample.

Types

Built in

• Bool
• Decimal
• ElementIdentifier
• NCName
• NodeIdentifier
• URI
• URIorCURIE
• XSDDate
• XSDDateTime
• XSDTime
• float
• int
• str

Defined

• Boolean (Bool) - A binary (true or false) value
• Date (XSDDate) - a date (year, month and day) in an idealized calendar
• Datetime (XSDDateTime) - The combination of a date and time
• Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
• Double (float) - A real number that conforms to the xsd:double specification
• Float (float) - A real number that conforms to the xsd:float specification
• Integer (int) - An integer
• Ncname (NCName) - Prefix part of CURIE
• Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
• Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
• String (str) - A character string
• Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
• Uri (URI) - a complete URI
• Uriorcurie (URIorCURIE) - a URI or a CURIE
• Url (String)