usdm-overlay

https://kerfors.github.io/usdm-overlay/

Terms for an overlay graph that classifies and comments on the CDISC USDM v4 model as rendered in RDF/OWL by usdm-rdf. The overlay only points at usdm-rdf IRIs; it never changes them. Every assertion carries an evidence tier, so model-stated facts stay apart from readings of the model.

Draft. Not a CDISC artifact. RDF: graphs/overlay.ttl (whole graph).

Classes by role

• Aggregate (8): InterventionalStudyDesign, ObservationalStudyDesign, ScheduleTimeline, Study, StudyAmendment, StudyDefinitionDocumentVersion, StudyDesign, StudyVersion
• Extension (2): ExtensionAttribute, ExtensionClass
• Structured entity (49): Activity, AdministrableProduct, AdministrableProductIdentifier, AdministrableProductProperty, Administration, AssignedPerson, BiomedicalConcept, BiomedicalConceptCategory, BiomedicalConceptProperty, BiomedicalConceptSurrogate, BiospecimenRetention, DocumentContentReference, Duration, EligibilityCriterion, Encounter, Estimand, GovernanceDate, Identifier, Indication, Ingredient, MedicalDevice, MedicalDeviceIdentifier, NarrativeContent, Organization, PopulationDefinition, Procedure, ProductOrganizationRole, ReferenceIdentifier, ResponseCode, ScheduleTimelineExit, ScheduledActivityInstance, ScheduledDecisionInstance, ScheduledInstance, Strength, StudyAmendmentImpact, StudyArm, StudyCell, StudyCohort, StudyDefinitionDocument, StudyDesignPopulation, StudyEpoch, StudyIdentifier, StudyIntervention, StudyRole, StudySite, SubjectEnrollment, Substance, SyntaxTemplateDictionary, Timing
• Templated text (7): Characteristic, Condition, EligibilityCriterionItem, Endpoint, IntercurrentEvent, Objective, SyntaxTemplate
• Text carrier (10): AnalysisPopulation, CommentAnnotation, ConditionAssignment, Masking, NarrativeContentItem, StudyAmendmentReason, StudyChange, StudyElement, StudyTitle, TransitionRule
• Value type (10): Abbreviation, Address, AliasCode, Code, GeographicScope, ParameterMap, PersonName, Quantity, QuantityRange, Range

Findings

Ready to raise (4)

The published artefacts contradict themselves, or leave undefined something they rely on. The pinned files alone show it, and the ask is to make the artefacts consistent.

• Abstract-class attributes carry a subclass's C-code
• Extension classes carry no definitions
• Population-level summary: term and definition disagree
• Procedure type is an uncoded classification

For discussion (17)

Depends on a modelling choice CDISC may have made on purpose, or on content of the published example files.

• Biomedical concept property datatypes are uncontrolled names
• Biomedical concept references are relative API paths
• Code systems are named by free strings
• Schedule conditions are strings, not Condition instances
• Objectives, endpoints and criteria have no link to document sections
• Section references are used only for amendment changes
• Eligibility identifier identifies only together with the category
• No link between Endpoint and what it requires
• Intercurrent event strategy: fixed set, specified as text
• NarrativeContent holds its text by reference
• Narrative refers to model instances by markup in text
• Syntax-template parameters resolve through markup
• Amendment number: definition says numerals, an example uses a letter
• Syntax-template parameters are rarely used
• Template parameters are matched by name inside text
• Timing values follow ISO 8601 by convention only
• Timing labels are typed, not generated from the value

Concept schemes

• Class roles: Aggregate, Extension, Structured entity, Templated text, Text carrier, Unassigned role, Value type
• Content kinds: Business identifier, Citation, Classification as text, Code component, Coded, Companion text, Composition, Contact detail, Display label, Document position, Embedded reference, Encoded value, Extension content, Extension point, Housekeeping, Identity, Lexical variant, Logic as text, Naming, Narrative text (definition-stated), Prose, Reference, Structured text (definition-stated), Text, Type discriminator, Typed value, Unclassified string, Unstructured text (definition-stated)
• Evidence tiers: Authored, Definition-stated, Example-observed, Model-stated
• Finding standing: For discussion, Ready to raise

Collections

Read text, Structure held in a string

Classes and properties

Assessment, Class-role rule, Finding, Rule

about, assigned kind, by rule, companion of, evidence tier, label of, refines, standing, tested against, check function, composed in count, expected result, has naming, holds, is referenced, observation, order, part count, quote, rationale, read text count, reference count, standing rationale, statement, string structure count, syntax, test query, value count, class role, content kind

Rules

rule-coded, rule-composition, rule-extension-point, rule-identity, rule-naming, rule-narrative-text, rule-reference, rule-structured-text, rule-type-discriminator, rule-typed-value, rule-unclassified-string, rule-unstructured-text

rule-role-aggregate, rule-role-extension, rule-role-structured-entity, rule-role-templated-text, rule-role-text-carrier, rule-role-unassigned, rule-role-value-type