# TOP Core — OWL classes and SHACL contract # # Companion to taxonomy/taxonomy.ttl (the SKOS view). This file is the # OWL/SHACL view: the same concepts as the SKOS taxonomy, expressed as # owl:Class declarations with rdfs:subClassOf chains, plus the SHACL # contract that enforces Universal DNA on every TOP entity. # # Mirrors taxonomy/taxonomy.ttl by URI: every concept here is the same # IRI (top:Person, top:Document, …) carrying both views. SKOS-aware # tools (TermBoard / PoolParty / Synaptica) load only the SKOS file; # OWL reasoners and SHACL validators load this file (and may load both). # # WHAT THIS FILE DEFINES (per ADR-0012 and ADR-0013): # # L0 — Root class (top:CommonEntity). # Every TOP entity is rdfs:subClassOf top:CommonEntity, by # construction. The root carries Universal DNA — the three # practitioner-grounded properties every entity answers: # identifier (what is this thing?), observedAt (when was it # captured?), status (is it current?). # # L1 — Universal DNA properties (3). # top:identifier, top:observedAt, top:status. Domain # top:CommonEntity. Required (mandatory) per the SHACL contract # below. # # L1 SHACL — top:UniversalDNAShape. # Targets top:CommonEntity. Requires identifier (xsd:anyURI, # exactly one), observedAt (xsd:dateTime, exactly one), status # (xsd:string, exactly one). The minimum every TOP entity must # carry. # # L2 — Category-Level Object classes (8). # Agent, Location, Resource, Scope, Temporal, Evidence, Outcome, # Constraint. Each rdfs:subClassOf top:CommonEntity and # rdfs:subClassOf prov:Agent | prov:Activity | prov:Entity | # prov:Plan | prov:Location per the PROV-O alignment. Four # categories carry a light-edge BFO subClassOf for OBO interop # (Agent, Location, Temporal, Evidence); the other four # (Resource, Scope, Outcome, Constraint) are mixed-membership, # carry no category-level BFO peer, and declare the edge on # their leaves instead. # # L2 — Category relational extensions (~24 properties). # The verbs each category brings to TOP. Agent gets # hasCredential / memberOf / authorizedBy. Location gets # withinLocation / geoSpatialData / accessRequirement. And so # on per ADR-0012. Domain pinned to the category; range pinned # where the target category is determinable. # # L3 — Leaf classes (28). # The leaves under each category. Each rdfs:subClassOf its L2 # category (which transitively pulls in top:CommonEntity and # the PROV-O alignment) plus its own PROV-O leaf alignment from # taxonomy/taxonomy.ttl (e.g., top:Document rdfs:subClassOf # prov:Entity; top:Log rdfs:subClassOf prov:Collection; # top:Person rdfs:subClassOf prov:Person). # # WHAT THIS FILE DOES NOT DEFINE: # # - Workflow-extension classes. Clinical research / care delivery / # manufacturing / supply chain each live in their own file under # their workflow directory. TOP Core must serve every domain; # workflow-specific declarations belong in their workflow. # - Concrete instances. Walkthroughs (e.g., core/v1/walkthroughs/ # person.ttl) carry single-instance examples of the pattern. # - Record-level metadata properties (creator, created, modified). # Per ADR-0013 those use Dublin Core (dcterms:creator, # dcterms:created, dcterms:modified) — clearly metadata, distinct # from Universal DNA which carries the practitioner shape. # # PROV-O ALIGNMENT (per ADR-0013): # Strict at the class level. Every category and every leaf with an # honest PROV-O peer carries rdfs:subClassOf prov:*. Workflows that # need PROV-O domain provenance (prov:wasAttributedTo on Entities, # prov:wasAssociatedWith on Activities) attach it directly with # proper PROV-O domain semantics. TOP Core does not invent a # record-level vs. domain-level fork — record-level metadata uses # Dublin Core; domain-level provenance uses PROV-O directly. # # BFO ALIGNMENT (per ADR-0013): # Light, edge-only — a single rdfs:subClassOf bfo:* for OBO Foundry # interop, never a heavy axiom set. Four L2 categories have clean BFO # peers and declare them at the category level: # Agent → IndependentContinuant, Location → Site, Temporal → Process, # Evidence → GenericallyDependentContinuant. Their 15 leaves inherit # that peer transitively and add no BFO triple of their own (a more # specific tag would be a modeling decision the category does not # license; an identical one would be redundant). # The other four categories (Resource, Scope, Outcome, Constraint) # are mixed-membership: no honest single peer exists at the category, # so the edge is declared on each of their 13 leaves: # Resource: System → GenericallyDependentContinuant, # Equipment → MaterialEntity, Material → MaterialEntity # Scope: Portfolio / Program / Project → GenericallyDependentContinuant # Outcome: Observation → GenericallyDependentContinuant, # StatusChange → ProcessBoundary, Artifact → MaterialEntity, # Conclusion → GenericallyDependentContinuant # Constraint: PhysicalLimit → Quality, RegulatoryLaw → GDC, # SafetyGuardrail → GDC # Net: every one of the 28 leaves resolves to exactly one BFO # superclass (15 by inheritance, 13 declared). BFO classes use the # readable bfo: local-name convention already established above # (bfo:IndependentContinuant, bfo:Site, …); the SKOS view in # taxonomy/taxonomy.ttl intentionally carries no BFO crosswalk — # BFO lives here, parallel to PROV-O/schema.org living there. @prefix rdf: . @prefix rdfs: . @prefix owl: . @prefix xsd: . @prefix sh: . @prefix prov: . @prefix dct: . @prefix bfo: . @prefix top: . # ==================================================================== # Ontology declaration # ==================================================================== a owl:Ontology ; dct:title "TOP Core — OWL classes and SHACL contract"@en ; dct:description "OWL/SHACL view of the SKOS taxonomy at taxonomy/taxonomy.ttl. Defines the root top:CommonEntity, the eight L2 categories, the 28 L3 leaves, the Universal DNA properties, the category relational extensions, and the SHACL UniversalDNAShape that enforces the three required practitioner-grounded properties on every TOP entity."@en ; dct:created "2026-05-10"^^xsd:date ; dct:license "Apache-2.0" ; rdfs:seeAlso , , . # ==================================================================== # L0 — Root class # ==================================================================== top:CommonEntity a owl:Class ; rdfs:label "Common Entity"@en ; rdfs:comment "The root of every TOP entity. Carries Universal DNA — top:identifier, top:observedAt, top:status — that every Category and every Leaf inherits. Not directly instantiated; serves as the type lattice that lets queries reach across every Category."@en . # ==================================================================== # Extensibility flavor annotation property (per ADR-0019) # ==================================================================== # Every Core property declares one of three flavors: # "Invariant" — semantics cannot drift; tightening allowed; redefinition forbidden # "Tightenable" — shape stays; downstream consumers may add SHACL constraints # (require what's optional, narrow enums, bind value sets) # "Additive" — designed for downstream addition (extends Core values, no replace) # The full per-layer extension contract: governance/extension-contract.md # Linter (forthcoming) enforces the contract at PR time. top:flavor a owl:AnnotationProperty ; rdfs:label "flavor"@en ; rdfs:comment "Extensibility flavor per ADR-0019. Permitted values: 'Invariant', 'Tightenable', 'Additive'."@en . # ==================================================================== # L1 — Universal DNA properties # ==================================================================== # Three properties every TOP entity carries. Per ADR-0013 (practitioner- # first), these are the three an operator universally encounters: # what is this thing, when was it captured, is it current. top:identifier a owl:DatatypeProperty , owl:FunctionalProperty ; rdfs:label "identifier"@en ; top:flavor "Invariant" ; rdfs:domain top:CommonEntity ; rdfs:range xsd:anyURI ; rdfs:comment "Globally unique URI / URN. The opaque, durable, system-of-record handle for the entity. Functional: every TOP entity has exactly one."@en . top:observedAt a owl:DatatypeProperty ; rdfs:label "observed at"@en ; top:flavor "Invariant" ; rdfs:domain top:CommonEntity ; rdfs:range xsd:dateTime ; rdfs:comment "When the system recorded this entity-version — the transaction-time anchor (per ADR-0021), NGSI-LD-style. Distinct from valid time (top:validFrom / top:validUntil, the second clock, opt-in) and from intrinsic activity times (Temporal.startTime / endTime, domain-level)."@en . top:status a owl:DatatypeProperty ; rdfs:label "status"@en ; top:flavor "Tightenable" ; rdfs:domain top:CommonEntity ; rdfs:range xsd:string ; rdfs:comment "Current lifecycle / health state. Each Category narrows the enum at its layer; leaves narrow further. Universal at this layer because every entity has SOME state and the project-wide status query is operationally meaningful."@en . # ==================================================================== # L1 SHACL — Universal DNA contract # ==================================================================== # Enforces the three Universal DNA properties on every top:CommonEntity # instance. Run with pyshacl --advanced (or equivalent SHACL validator). top:UniversalDNAShape a sh:NodeShape ; rdfs:label "Universal DNA Shape"@en ; rdfs:comment "The minimum every TOP entity must carry: a unique identifier, an observation timestamp, and a current status."@en ; sh:targetClass top:CommonEntity ; sh:property [ sh:path top:identifier ; sh:datatype xsd:anyURI ; sh:minCount 1 ; sh:maxCount 1 ; sh:message "Every TOP entity must carry exactly one top:identifier (xsd:anyURI)." ; ] ; sh:property [ sh:path top:observedAt ; sh:datatype xsd:dateTime ; sh:minCount 1 ; sh:maxCount 1 ; sh:message "Every TOP entity must carry exactly one top:observedAt (xsd:dateTime)." ; ] ; sh:property [ sh:path top:status ; sh:datatype xsd:string ; sh:minCount 1 ; sh:maxCount 1 ; sh:message "Every TOP entity must carry exactly one top:status (xsd:string)." ; ] . # ==================================================================== # L2 — Category-Level Object classes (8) # ==================================================================== # Each rdfs:subClassOf top:CommonEntity (carries Universal DNA) and # rdfs:subClassOf prov:* (PROV-O class-level alignment per ADR-0013). # Four carry a light-edge BFO subClassOf for OBO interop; four defer # BFO to leaf level. # --- Agent — authority --- top:Agent a owl:Class ; rdfs:label "Agent"@en ; rdfs:subClassOf top:CommonEntity, prov:Agent, bfo:IndependentContinuant ; rdfs:comment "The entity that holds authority or bears responsibility for what is done: it signs, owns, authorizes, enforces, and can be attributed an action. Persons, Organizations, Groups, Autonomous Agents (software with delegated authority). Capacity to act is not sufficient. A thing that merely acts causally (a pathogen, a compound, a river) is not an Agent unless it can be held to account."@en . top:hasCredential a owl:ObjectProperty ; rdfs:label "has credential"@en ; top:flavor "Tightenable" ; rdfs:domain top:Agent ; rdfs:range top:Credential ; rdfs:comment "Links the Agent to their proof of qualification or identity (license, certificate, training record, role assignment). Range pinned to top:Credential (an Evidence leaf) so audit queries follow uniform paths."@en . top:memberOf a owl:ObjectProperty ; rdfs:label "member of"@en ; top:flavor "Tightenable" ; rdfs:domain top:Agent ; rdfs:range top:Agent ; rdfs:subPropertyOf prov:actedOnBehalfOf ; rdfs:comment "Organizational or group hierarchy the Agent belongs to. PROV-aligned: an Agent acting in their organizational capacity acts on behalf of the parent Agent."@en . top:authorizedBy a owl:ObjectProperty ; rdfs:label "authorized by"@en ; top:flavor "Tightenable" ; rdfs:domain top:Agent ; rdfs:range top:Agent ; rdfs:comment "The authority that granted the Agent permission to act in a specific scope. Investigator authorizedBy IRB; contractor authorizedBy Sponsor; device operator authorizedBy QA Lead."@en . # --- Location — space --- top:Location a owl:Class ; rdfs:label "Location"@en ; rdfs:subClassOf top:CommonEntity, prov:Location, bfo:Site ; rdfs:comment "The spatial or logical context where an Activity occurs or a Resource resides. Physical (ward, manufacturing floor, depot) or logical (data warehouse, system zone, regulatory jurisdiction)."@en . top:withinLocation a owl:ObjectProperty , owl:TransitiveProperty ; rdfs:label "within location"@en ; top:flavor "Tightenable" ; rdfs:domain top:Location ; rdfs:range top:Location ; rdfs:comment "Recursive parent location. Transitive: Room within Building within Campus is queryable as Room within Campus."@en . top:geoSpatialData a owl:DatatypeProperty ; rdfs:label "geo-spatial data"@en ; top:flavor "Tightenable" ; rdfs:domain top:Location ; rdfs:range xsd:string ; rdfs:comment "Physical coordinates or digital path. WKT / GeoJSON for physical spaces; structured locator (URI, file path, network address) for logical spaces."@en . top:accessRequirement a owl:ObjectProperty ; rdfs:label "access requirement"@en ; top:flavor "Tightenable" ; rdfs:domain top:Location ; rdfs:range top:Constraint ; rdfs:comment "Constraints required to enter this Location (clearance, training prerequisite, escort policy, biosafety level). Modeled via Constraint so authorization-failure events produce uniform Evidence."@en . # --- Resource — tools --- # BFO note: Resource is mixed-membership, so the category carries no BFO # peer; the edge is declared per leaf instead. Equipment is a BFO # MaterialEntity; System (software) is a GenericallyDependentContinuant; # Material is a MaterialEntity (the leaf's substances/batches/stocks are # physical — cf. its schema:Substance peer; a purely digital material # would be the rare exception, not the rule). top:Resource a owl:Class ; rdfs:label "Resource"@en ; rdfs:subClassOf top:CommonEntity, prov:Entity ; rdfs:comment "Physical or digital assets used to execute tasks or produce outcomes. Equipment, instruments, software systems, samples, kits, raw materials, consumables."@en . top:ownedBy a owl:ObjectProperty ; rdfs:label "owned by"@en ; top:flavor "Tightenable" ; rdfs:domain top:Resource ; rdfs:range top:Agent ; rdfs:comment "The Agent (Person or Organization) that owns / has custody of the Resource. Chain-of-custody anchor."@en . top:hasMaintenanceLog a owl:ObjectProperty ; rdfs:label "has maintenance log"@en ; top:flavor "Tightenable" ; rdfs:domain top:Resource ; rdfs:range top:Log ; rdfs:comment "Links the Resource to its history of maintenance / calibration / validation Log. Range pinned to top:Log (an Evidence leaf)."@en . top:operationalState a owl:DatatypeProperty ; rdfs:label "operational state"@en ; top:flavor "Tightenable" ; rdfs:domain top:Resource ; rdfs:range xsd:string ; rdfs:comment "Hardware/software-specific readiness beyond top:status. CALIBRATED / DUE_FOR_CALIBRATION / OUT_OF_SERVICE for Equipment; RUNNING / DEGRADED / OFFLINE for System."@en . # --- Scope — intent --- # BFO note: Scope is mixed-membership, so the category carries no BFO # peer; the edge is declared per leaf instead. Portfolio / Program / # Project are all generically dependent continuants in BFO terms. top:Scope a owl:Class ; rdfs:label "Scope"@en ; rdfs:subClassOf top:CommonEntity, prov:Plan ; rdfs:comment "The logical boundary, strategic intent, or organizational container for work. Studies, programs, batch records, projects, campaigns, regulatory submissions — anything that groups Activities under a shared 'why'."@en . top:governedBy a owl:ObjectProperty ; rdfs:label "governed by"@en ; top:flavor "Tightenable" ; rdfs:domain top:Scope ; rdfs:range top:Constraint ; rdfs:comment "Links the Scope to specific Constraints — regulatory, contractual, safety. The legal frame the Scope operates within."@en . top:containsActivity a owl:ObjectProperty ; rdfs:label "contains activity"@en ; top:flavor "Tightenable" ; rdfs:domain top:Scope ; rdfs:range top:Temporal ; rdfs:comment "Links the Scope to the Temporal entities (planned or executed activities) happening within it. Backbone for 'what's in flight under this Scope right now'."@en . top:objectiveStatement a owl:DatatypeProperty ; rdfs:label "objective statement"@en ; top:flavor "Tightenable" ; rdfs:domain top:Scope ; rdfs:range xsd:string ; rdfs:comment "High-level description of the strategic 'why'. Operator-grounded — what an investigator, sponsor, or regulator would say this Scope is for."@en . # --- Temporal — rhythm --- top:Temporal a owl:Class ; rdfs:label "Temporal"@en ; rdfs:subClassOf top:CommonEntity, prov:Activity, bfo:Process ; rdfs:comment "The time-based dimension of operations. Both plans (schedules, milestones, campaigns) and execution (visits, procedures, batches, shipments)."@en . top:startTime a owl:DatatypeProperty ; rdfs:label "start time"@en ; top:flavor "Invariant" ; rdfs:domain top:Temporal ; rdfs:range xsd:dateTime ; rdfs:subPropertyOf prov:startedAtTime ; rdfs:comment "Actual or planned start. PROV-aligned to prov:startedAtTime; for plans this is intended start, for executions this is observed start."@en . top:endTime a owl:DatatypeProperty ; rdfs:label "end time"@en ; top:flavor "Invariant" ; rdfs:domain top:Temporal ; rdfs:range xsd:dateTime ; rdfs:subPropertyOf prov:endedAtTime ; rdfs:comment "Actual or planned end. May be open (null) for ongoing activities."@en . top:precededBy a owl:ObjectProperty ; rdfs:label "preceded by"@en ; top:flavor "Tightenable" ; rdfs:domain top:Temporal ; rdfs:range top:Temporal ; rdfs:subPropertyOf prov:wasInformedBy ; rdfs:comment "Sequence logic — the Temporal that immediately precedes this one. PROV-aligned: this Temporal was informed by its predecessor."@en . top:occursAt a owl:ObjectProperty ; rdfs:label "occurs at"@en ; top:flavor "Tightenable" ; rdfs:domain top:Temporal ; rdfs:range top:Location ; rdfs:subPropertyOf prov:atLocation ; rdfs:comment "Where the Temporal happens. PROV-aligned to prov:atLocation."@en . # --- Evidence — proof --- top:Evidence a owl:Class ; rdfs:label "Evidence"@en ; rdfs:subClassOf top:CommonEntity, prov:Entity, bfo:GenericallyDependentContinuant ; rdfs:comment "Artifacts that provide verifiable proof of an event, state, or action. Lab reports, signed forms, audit logs, calibration certificates, batch records, MedWatch submissions."@en . top:verifiesOutcome a owl:ObjectProperty ; rdfs:label "verifies outcome"@en ; top:flavor "Tightenable" ; rdfs:domain top:Evidence ; rdfs:range top:Outcome ; rdfs:comment "Direct link to the Outcome this Evidence supports. The signed lab report verifies the lab-value Outcome; the calibration certificate verifies the equipment-readiness Outcome."@en . top:integrityHash a owl:DatatypeProperty ; rdfs:label "integrity hash"@en ; top:flavor "Invariant" ; rdfs:domain top:Evidence ; rdfs:range xsd:string ; rdfs:comment "Digital fingerprint (SHA-256 or stronger) ensuring non-repudiation. Anchors GxP / 21 CFR Part 11 audit-trail discipline at the Core layer."@en . top:signedBy a owl:ObjectProperty ; rdfs:label "signed by"@en ; top:flavor "Tightenable" ; rdfs:domain top:Evidence ; rdfs:range top:Agent ; rdfs:subPropertyOf prov:wasAttributedTo ; rdfs:comment "Links the Evidence to the Agent who attested to its truth. E-signature semantics (21 CFR Part 11) and PROV attribution."@en . # --- Outcome — results --- # BFO note: Outcome is mixed-membership, so the category carries no BFO # peer; the edge is declared per leaf instead. Observation is a GDC; # StatusChange is a ProcessBoundary; Artifact is a MaterialEntity; # Conclusion is a GDC. top:Outcome a owl:Class ; rdfs:label "Outcome"@en ; rdfs:subClassOf top:CommonEntity, prov:Entity ; rdfs:comment "Data, state changes, or artifacts produced by a process. Lab values, observations, decisions, batch yields, throughput counts, derived metrics."@en . top:measuredBy a owl:ObjectProperty ; rdfs:label "measured by"@en ; top:flavor "Tightenable" ; rdfs:domain top:Outcome ; rdfs:range top:Resource ; rdfs:subPropertyOf prov:wasGeneratedBy ; rdfs:comment "Links the Outcome to the Resource (Equipment, System) that captured or produced it. Audit-trail anchor — every measured Outcome traces to its measuring Resource."@en . top:satisfiesConstraint a owl:ObjectProperty ; rdfs:label "satisfies constraint"@en ; top:flavor "Tightenable" ; rdfs:domain top:Outcome ; rdfs:range top:Constraint ; rdfs:comment "Links the Outcome to the Constraint(s) it has been validated against. Out-of-range Outcomes surface as the absence of this link to a relevant Constraint."@en . top:variance a owl:DatatypeProperty ; rdfs:label "variance"@en ; top:flavor "Tightenable" ; rdfs:domain top:Outcome ; rdfs:range xsd:string ; rdfs:comment "Delta between expected and actual. Format depends on leaf specialization — numeric for measured values, structured for multi-dimensional. Universal at this layer for cross-leaf trend queries."@en . # --- Constraint — validity --- # BFO note: Constraint is mixed-membership, so the category carries no # BFO peer; the edge is declared per leaf instead. PhysicalLimit is a # Quality; RegulatoryLaw is a GDC; SafetyGuardrail is a GDC. top:Constraint a owl:Class ; rdfs:label "Constraint"@en ; rdfs:subClassOf top:CommonEntity, prov:Entity ; rdfs:comment "Non-negotiable boundaries — physical, legal, regulatory, contractual, safety. Inclusion criteria, dose limits, regulatory deadlines, blinding rules, biosafety floors, SLAs."@en . top:enforcedBy a owl:ObjectProperty ; rdfs:label "enforced by"@en ; top:flavor "Tightenable" ; rdfs:domain top:Constraint ; rdfs:range top:Agent ; rdfs:subPropertyOf prov:wasAssociatedWith ; rdfs:comment "Links the Constraint to the Agent responsible for oversight. The IRB enforces the inclusion criterion; the QA Lead enforces the calibration window; the Pharmacist enforces the dose limit."@en . top:severityLevel a owl:DatatypeProperty ; rdfs:label "severity level"@en ; top:flavor "Tightenable" ; rdfs:domain top:Constraint ; rdfs:range xsd:string ; rdfs:comment "Operational impact of violation. Universal enum — INFORMATIONAL / MINOR / MAJOR / CRITICAL. Workflow extensions can refine."@en . top:appliesTo a owl:ObjectProperty ; rdfs:label "applies to"@en ; top:flavor "Tightenable" ; rdfs:domain top:Constraint ; rdfs:range top:CommonEntity ; rdfs:comment "Targets of the Constraint. Constraints can scope to Agents, Resources, Scopes, or Temporals; range is top:CommonEntity so the targeting is uniform across Categories. Leaf layer narrows by domain."@en . # ==================================================================== # Cross-category role bindings (per ADR-0022) # ==================================================================== # Two role bindings that cut across the eight functional categories. # Neither mints a type; each attaches a role by relation (per ADR-0002). # Domain and range are top:CommonEntity because the role is borne by # different kinds in different contexts — the same Person is an Agent # when they consent and a subject when they are observed. top:hasSubject a owl:ObjectProperty ; rdfs:label "has subject"@en ; top:flavor "Tightenable" ; rdfs:domain top:CommonEntity ; # typically a Scope (a study) or a Temporal (a procedure) rdfs:range top:CommonEntity ; # the entity the work is about (a Person, or a domain living/molecular kind) rdfs:comment "Binds an operation (a Scope such as a study, or a Temporal such as a procedure) to the entity it is performed upon, cares for, or studies: its subject. A role binding, not a type. The same Person is an Agent when they consent and a subject when they are observed; the same virion is a subject in the sequencing lab and a causal participant in an infection. No PROV-O peer (prov:used denotes a tool or consumed entity, not the subject-of-care)."@en . top:denotes a owl:ObjectProperty ; rdfs:label "denotes"@en ; top:flavor "Tightenable" ; rdfs:domain top:CommonEntity ; # an information artifact: a Document / Observation rdfs:range top:CommonEntity ; # the entity it stands for rdfs:comment "Links a representation (a sequence record, a SMILES string, an identifier) to the entity it stands for. A SMILES string (a top:Document) denotes a molecular entity; the string is data, the molecule is the referent. Semiotic relation, no PROV-O peer (declared absence)."@en . # ==================================================================== # L3 — Leaf classes (28) # ==================================================================== # Each rdfs:subClassOf its L2 category (transitively pulling in # top:CommonEntity + Universal DNA + the category's PROV-O alignment) # plus its own PROV-O leaf alignment from taxonomy/taxonomy.ttl. # Leaves under the four mixed-membership categories (Resource, Scope, # Outcome, Constraint) also carry a light-edge BFO peer here, since # their category declares none; see the BFO ALIGNMENT note in the # header for the full leaf → bfo:* map. # --- Agent leaves (4) --- top:Person a owl:Class ; rdfs:label "Person"@en ; rdfs:subClassOf top:Agent, prov:Person ; rdfs:comment "An individual human acting in any role across any workflow."@en . top:Organization a owl:Class ; rdfs:label "Organization"@en ; rdfs:subClassOf top:Agent, prov:Organization ; rdfs:comment "A legal or business entity — corporate parent, operating company, hospital, academic institution, regulator, vendor, sponsor."@en . top:Group a owl:Class ; rdfs:label "Group"@en ; rdfs:subClassOf top:Agent, prov:Agent ; rdfs:comment "A bounded collective acting with shared purpose and accountability — committee, team, working group, oversight body, panel."@en . top:AutonomousAgent a owl:Class ; rdfs:label "Autonomous Agent"@en ; rdfs:subClassOf top:Agent, prov:SoftwareAgent ; rdfs:comment "A software entity acting on delegated authority — robotic process, AI agent, automated decision system, scheduler, monitor."@en . # NOTE (per ADR-0022): top:Organism was removed from Core. Agency is a # role, not a kind: a living non-human (lab animal, microbe, plant) acts # causally but bears no accountability, so it cannot inherit the Agent # authority wiring (signedBy / ownedBy / enforcedBy / hasCredential). # Biological kinds now live in the domains as rdfs:subClassOf # top:CommonEntity (e.g. topcr:StudyAnimal); the "who or what the work is # performed upon" role attaches via top:hasSubject (below). The shared # "Organism" vocabulary anchor is retained in taxonomy/taxonomy.ttl. # --- Location leaves (3) --- top:Physical a owl:Class ; rdfs:label "Physical Location"@en ; rdfs:subClassOf top:Location, prov:Location ; rdfs:comment "A real-world place with geospatial coordinates — building, room, floor, campus, depot, manufacturing line, ward."@en . top:Virtual a owl:Class ; rdfs:label "Virtual Location"@en ; rdfs:subClassOf top:Location, prov:Location ; rdfs:comment "A logical place addressable via URI / path / network identifier — data warehouse, system zone, application namespace, regulatory jurisdiction (logical, not the physical address of the regulator)."@en . top:Storage a owl:Class ; rdfs:label "Storage Location"@en ; rdfs:subClassOf top:Location, prov:Location ; rdfs:comment "A place where Resources reside under controlled conditions — biorepository freezer, IP storage, sample archive, document repository, data vault."@en . # --- Resource leaves (3) --- top:System a owl:Class ; rdfs:label "System"@en ; rdfs:subClassOf top:Resource, prov:Entity, bfo:GenericallyDependentContinuant ; rdfs:comment "A software or operational system used to execute work — EDC, CTMS, IRT, LIMS, MES, ERP."@en . top:Equipment a owl:Class ; rdfs:label "Equipment"@en ; rdfs:subClassOf top:Resource, prov:Entity, bfo:MaterialEntity ; rdfs:comment "A physical device used in operations — analyzer, scale, freezer, infusion pump, imaging modality, sequencer, sensor."@en . top:Material a owl:Class ; rdfs:label "Material"@en ; rdfs:subClassOf top:Resource, prov:Entity, bfo:MaterialEntity ; rdfs:comment "A consumable or substance used or transformed — sample, kit, reagent, raw material, drug substance, dosage unit."@en . # --- Scope leaves (3) --- top:Portfolio a owl:Class ; rdfs:label "Portfolio"@en ; rdfs:subClassOf top:Scope, prov:Plan, bfo:GenericallyDependentContinuant ; rdfs:comment "The widest organizational container — a collection of Programs sharing strategic direction, oversight, or funding."@en . top:Program a owl:Class ; rdfs:label "Program"@en ; rdfs:subClassOf top:Scope, prov:Plan, bfo:GenericallyDependentContinuant ; rdfs:comment "An intermediate container — a coordinated set of Projects sharing therapeutic area, product family, or regulatory pathway."@en . top:Project a owl:Class ; rdfs:label "Project"@en ; rdfs:subClassOf top:Scope, prov:Plan, bfo:GenericallyDependentContinuant ; rdfs:comment "A bounded body of work with a defined start, end, and objective — a study, a campaign, a batch, a submission, a commissioning effort."@en . # --- Temporal leaves (4) --- top:Schedule a owl:Class ; rdfs:label "Schedule"@en ; rdfs:subClassOf top:Temporal, prov:Activity ; rdfs:comment "A planned sequence of activities with intended timing — Schedule of Assessments, manufacturing campaign plan, audit calendar, dosing schedule."@en . top:Window a owl:Class ; rdfs:label "Window"@en ; rdfs:subClassOf top:Temporal, prov:Activity ; rdfs:comment "A bounded interval within which an activity must occur — visit window, dose window, regulatory submission window, calibration window."@en . top:Activity a owl:Class ; rdfs:label "Activity"@en ; rdfs:subClassOf top:Temporal, prov:Activity ; rdfs:comment "An executed unit of operational work — a procedure performed, a batch run, a shipment received, a review completed."@en . top:Milestone a owl:Class ; rdfs:label "Milestone"@en ; rdfs:subClassOf top:Temporal, prov:Activity ; rdfs:comment "A point-in-time marker of significant progress — first-patient-in, last-patient-last-visit, batch release, regulatory approval."@en . # --- Evidence leaves (4) --- top:Document a owl:Class ; rdfs:label "Document"@en ; rdfs:subClassOf top:Evidence, prov:Entity ; rdfs:comment "A formal artifact carrying recorded content — protocol, SOP, IB, ICF, CAPA report, batch record, regulatory submission."@en . top:Log a owl:Class ; rdfs:label "Log"@en ; rdfs:subClassOf top:Evidence, prov:Collection ; rdfs:comment "A time-ordered collection of recorded events — audit log, communication log, calibration log, equipment log, system event log."@en . top:Attestation a owl:Class ; rdfs:label "Attestation"@en ; rdfs:subClassOf top:Evidence, prov:Entity ; rdfs:comment "A formal declaration by an Agent affirming a fact — signed consent, regulatory attestation, compliance declaration, e-signature on a record."@en . top:Credential a owl:Class ; rdfs:label "Credential"@en ; rdfs:subClassOf top:Evidence, prov:Entity ; rdfs:comment "Proof of qualification or identity for an Agent — license, certification, training record, role assignment, e-credential."@en . # --- Outcome leaves (4) --- top:Observation a owl:Class ; rdfs:label "Observation"@en ; rdfs:subClassOf top:Outcome, prov:Entity, bfo:GenericallyDependentContinuant ; rdfs:comment "A captured data point — vital sign, lab value, sensor reading, qualitative assessment, computed metric."@en . top:StatusChange a owl:Class ; rdfs:label "Status Change"@en ; rdfs:subClassOf top:Outcome, prov:Entity, bfo:ProcessBoundary ; rdfs:comment "A discrete transition in lifecycle state — enrollment, withdrawal, batch release, IRB approval, record finalization."@en . top:Artifact a owl:Class ; rdfs:label "Artifact"@en ; rdfs:subClassOf top:Outcome, prov:Entity, bfo:MaterialEntity ; rdfs:comment "A produced object — a manufactured batch unit, a generated dataset, a derived report, a synthesized substance."@en . top:Conclusion a owl:Class ; rdfs:label "Conclusion"@en ; rdfs:subClassOf top:Outcome, prov:Entity, bfo:GenericallyDependentContinuant ; rdfs:comment "A reasoned determination — adjudication outcome, root-cause finding, regulatory decision, eligibility determination."@en . # --- Constraint leaves (3) --- top:PhysicalLimit a owl:Class ; rdfs:label "Physical Limit"@en ; rdfs:subClassOf top:Constraint, prov:Entity, bfo:Quality ; rdfs:comment "A bound rooted in physical reality — temperature range, dose ceiling, pressure limit, mass tolerance, biological viability window."@en . top:RegulatoryLaw a owl:Class ; rdfs:label "Regulatory Law"@en ; rdfs:subClassOf top:Constraint, prov:Entity, bfo:GenericallyDependentContinuant ; rdfs:comment "A rule rooted in legal or regulatory authority — 21 CFR clause, ICH guideline, EU CTR provision, contractual SLA, jurisdictional reporting requirement."@en . top:SafetyGuardrail a owl:Class ; rdfs:label "Safety Guardrail"@en ; rdfs:subClassOf top:Constraint, prov:Entity, bfo:GenericallyDependentContinuant ; rdfs:comment "A boundary rooted in safety discipline — biosafety floor, blinding rule, contamination boundary, escalation threshold, stop-rule."@en . # ==================================================================== # Bitemporal model (per ADR-0021) # ==================================================================== # Core carries two clocks. TRANSACTION TIME — top:observedAt (above), # Universal DNA, always required — is when the system recorded an # entity-version. VALID TIME — top:validFrom / top:validUntil (here) — # is when that recorded state was true in the world. The two are # independently queryable ("as we knew it at T1" vs. "as it was true at # T2"). # # Valid time is OPT-IN: it attaches to versioned nodes (top:Versioned) # via top:BitemporalShape and is NOT folded into the always-on # UniversalDNAShape, so mono-temporal entities stay valid and the # minimum contract does not move. # # Versioning is append-only and PROV-native: a correction mints a new # immutable top:Versioned node, prov:wasRevisionOf the prior, both # prov:specializationOf a stable identity, the prior closed with # prov:invalidatedAtTime. The grain is the attribute-value-at-a-time; # the composed entity is a prov:Collection assembled at query time. # # WHICH values get versioned (ADR-0021 triggering): # Tier 1 (here, always-on, enforced): a value carrying top:integrityHash # or top:signedBy, or a top:Attestation / top:StatusChange, MUST be a # version — you cannot hash or sign a value and then mutate it. # Tiers 2-3 (follow-on PRs): propagation along regulated edges, and # workflow opt-in per ADR-0019. Default-off otherwise. top:Versioned a owl:Class ; rdfs:label "Versioned"@en ; rdfs:comment "Marker for an immutable, bitemporally-tracked value-version — an attribute-value-at-a-time (or whole-entity snapshot) carrying valid time and a stable identity via prov:specializationOf. Applied where Tier-1 entailment fires or where a workflow opts an attribute in. Not every TOP entity is Versioned; only those that need full bitemporal history."@en . top:validFrom a owl:DatatypeProperty ; rdfs:label "valid from"@en ; top:flavor "Invariant" ; rdfs:domain top:Versioned ; rdfs:range xsd:dateTime ; rdfs:comment "Start of the valid-time interval — when this version's state became true in the world. Distinct from top:observedAt (transaction time). Invariant per ADR-0019, like top:startTime/top:endTime. No PROV-O peer: PROV models system time, not valid-time-of-a-fact (declared absence, per ADR-0021)."@en . top:validUntil a owl:DatatypeProperty ; rdfs:label "valid until"@en ; top:flavor "Invariant" ; rdfs:domain top:Versioned ; rdfs:range xsd:dateTime ; rdfs:comment "End of the valid-time interval; open (absent) for the currently-valid version. Invariant per ADR-0019."@en . # --- The opt-in bitemporal contract --- # Requires a valid-time start and a stable identity on a versioned node. # Invoked directly on top:Versioned instances, and via sh:node from the # Tier-1 enforcement shapes below. top:BitemporalShape a sh:NodeShape ; rdfs:label "Bitemporal Shape"@en ; rdfs:comment "The contract a versioned value satisfies: a valid-time start, an optional (open) valid-time end, and a stable identity via prov:specializationOf. Opt-in — NOT targeted at top:CommonEntity, so it never burdens mono-temporal entities."@en ; sh:targetClass top:Versioned ; sh:property [ sh:path top:validFrom ; sh:datatype xsd:dateTime ; sh:minCount 1 ; sh:maxCount 1 ; sh:message "A versioned value must state when its state became valid (top:validFrom, exactly one)." ; ] ; sh:property [ sh:path top:validUntil ; sh:datatype xsd:dateTime ; sh:maxCount 1 ; sh:message "top:validUntil is open (absent) for the current version, or exactly one xsd:dateTime when closed." ; ] ; sh:property [ sh:path prov:specializationOf ; sh:minCount 1 ; sh:maxCount 1 ; sh:message "A versioned value must point at its stable identity (prov:specializationOf, exactly one)." ; ] . # --- Tier-1 entailment: committed markers force versioning (hard) --- # Always-on in Core, at sh:Violation. Mechanism is sh:targetSubjectsOf / # sh:targetClass -> sh:node top:BitemporalShape; SHACL Core, no SPARQL. top:HashedMustVersionShape a sh:NodeShape ; rdfs:label "Hashed values must be versioned"@en ; sh:targetSubjectsOf top:integrityHash ; sh:severity sh:Violation ; sh:node top:BitemporalShape ; sh:message "A value carrying top:integrityHash must be an immutable version (top:Versioned: top:validFrom + prov:specializationOf). You cannot hash a value and leave it mutable." . top:SignedMustVersionShape a sh:NodeShape ; rdfs:label "Signed values must be versioned"@en ; sh:targetSubjectsOf top:signedBy ; sh:severity sh:Violation ; sh:node top:BitemporalShape ; sh:message "A value carrying top:signedBy must be an immutable version. You cannot sign a value and leave it mutable." . top:AttestationMustVersionShape a sh:NodeShape ; rdfs:label "Attestations must be versioned"@en ; sh:targetClass top:Attestation ; sh:severity sh:Violation ; sh:node top:BitemporalShape ; sh:message "A top:Attestation is a committed, signed declaration and must be an immutable version." . top:StatusChangeMustVersionShape a sh:NodeShape ; rdfs:label "Status changes must be versioned"@en ; sh:targetClass top:StatusChange ; sh:severity sh:Violation ; sh:node top:BitemporalShape ; sh:message "A top:StatusChange is the audit event of a transition and must be an immutable version." . # --- Tier-1 lifecycle calibration: in-progress evidence warns (soft) --- # A draft Document/Log/Credential is legitimately mutable until it is # committed; warn (not fail) until it carries a valid-time start. Once # hashed or signed, the hard shapes above take over at sh:Violation. # Direct property check (not sh:node) so the result stays at Warning. top:EvidenceShouldVersionShape a sh:NodeShape ; rdfs:label "Evidence should be versioned once committed"@en ; sh:targetClass top:Document, top:Log, top:Credential ; sh:property [ sh:path top:validFrom ; sh:minCount 1 ; sh:severity sh:Warning ; sh:message "This evidentiary value is not yet a version. Drafts may stay mutable; once finalized (and certainly once hashed or signed) it must be versioned (top:Versioned with top:validFrom)." ; ] . # === End of TOP Core OWL/SHACL ===