Laboratory Metadata Ontology

FLOW ALGEBRA

Ontology: Laboratory Metadata Ontology
Domain: Metadata Ontologies > Scientific Metadata
Canonical URL: https://kirethresearch.org/booksai-core/ontologies/metadata-ontologies/scientific-metadata/laboratory-metadata-ontology.html

Authors: Mark Anthony Higgins — Sky (Recursive AI)

flow "LaboratoryMetadataOntology" v1.0

# ---------- DOMAIN ----------
domain:
  class: MetadataOntology
  category: ScientificMetadata
  subject: LaboratoryMetadata
  purpose:
    - represent metadata describing laboratory environments and activities
    - preserve laboratory, instrument, sample, method, and condition context
    - support traceability, reproducibility, validation, and quality control
    - connect laboratory processes with personnel, equipment, measurements, and results
    - enable machine-readable reasoning over laboratory workflows

# ---------- CORE ENTITY ----------
entity LaboratoryMetadata:
  type: ScientificMetadata
  describes: LaboratoryActivity
  may_include:
    - laboratory_identifier
    - laboratory_name
    - facility
    - location
    - researcher
    - technician
    - instrument
    - equipment
    - sample
    - reagent
    - material
    - protocol
    - procedure
    - environmental_condition
    - calibration
    - maintenance
    - measurement
    - quality_control
    - safety_metadata
    - temporal_metadata
    - provenance
    - version

entity Laboratory:
  type: ScientificFacility
  may_have:
    - LaboratoryIdentifier
    - LaboratoryName
    - Facility
    - Location

entity LaboratoryActivity:
  type: ScientificProcess
  occurs_in: Laboratory
  may_be:
    - Experiment
    - Measurement
    - SamplePreparation
    - CalibrationActivity
    - QualityControlActivity
    - Analysis
    - MaintenanceActivity

entity LaboratoryPersonnel:
  type: Agent
  roles:
    - researcher
    - technician
    - analyst
    - operator
    - supervisor

entity LaboratoryInstrument:
  type: ScientificInstrument
  used_in: LaboratoryActivity

entity LaboratoryEquipment:
  type: Equipment
  supports: LaboratoryActivity

# ---------- RELATIONSHIPS ----------
relationships:
  LaboratoryMetadata -> DESCRIBES -> LaboratoryActivity
  LaboratoryActivity -> OCCURS_IN -> Laboratory
  Laboratory -> LOCATED_AT -> Location
  LaboratoryActivity -> PERFORMED_BY -> LaboratoryPersonnel
  LaboratoryActivity -> MAY_USE -> LaboratoryInstrument
  LaboratoryActivity -> MAY_USE -> LaboratoryEquipment
  LaboratoryActivity -> MAY_USE -> Sample
  LaboratoryActivity -> MAY_USE -> Reagent
  LaboratoryActivity -> FOLLOWS -> LaboratoryProtocol
  LaboratoryActivity -> MAY_HAVE_CONDITION -> EnvironmentalCondition
  LaboratoryInstrument -> MAY_HAVE -> Calibration
  LaboratoryInstrument -> MAY_HAVE -> MaintenanceRecord
  LaboratoryActivity -> MAY_PRODUCE -> Measurement
  LaboratoryActivity -> MAY_PRODUCE -> LaboratoryResult
  LaboratoryActivity -> MAY_HAVE -> QualityControl
  LaboratoryMetadata -> MAY_REFERENCE -> Provenance

# ---------- LABORATORY IDENTITY ----------
rule laboratory_identity:
  Laboratory SHOULD have stable identifier
  where cross-system traceability is required

rule facility_context:
  LaboratoryName alone MUST NOT be assumed globally unique

rule location_context:
  laboratory location SHOULD be preserved
  where environmental, regulatory, or provenance context depends on place

# ---------- PERSONNEL ----------
rule personnel_identity:
  personnel involved in traceable laboratory activities SHOULD have stable identity

rule personnel_role:
  role MUST be associated with specific LaboratoryActivity
  because one Agent MAY hold multiple roles

rule responsibility:
  IF activity requires accountable operator
  THEN responsible Agent SHOULD be explicitly recorded

# ---------- INSTRUMENTS ----------
rule instrument_identity:
  LaboratoryInstrument SHOULD have:
    - instrument_identifier
    - instrument_type
    - manufacturer_optional
    - model_optional

rule instrument_state:
  instrument state MAY include:
    - active
    - calibrated
    - maintenance_due
    - unavailable
    - retired

rule instrument_traceability:
  measurements SHOULD reference instrument identity
  where instrument characteristics affect interpretation

# ---------- CALIBRATION ----------
entity Calibration:
  type: QualityMetadata
  may_include:
    - calibration_date
    - calibration_method
    - reference_standard
    - calibration_result
    - valid_from
    - valid_until
    - calibration_agent

rule calibration_validity:
  IF measurement depends on valid calibration
  THEN measurement_time SHOULD fall within Calibration validity period

rule calibration_trace:
  Calibration SHOULD reference applicable instrument and reference standard

rule expired_calibration:
  IF measurement occurs outside calibration validity
  THEN flag measurement quality context
  rather_than automatically discarding measurement

# ---------- MAINTENANCE ----------
entity MaintenanceRecord:
  type: EquipmentMetadata
  may_include:
    - maintenance_date
    - maintenance_type
    - action
    - parts_replaced
    - technician
    - next_due_date

rule maintenance_history:
  maintenance records SHOULD remain historically traceable

rule maintenance_effect:
  instrument maintenance MAY require recalibration
  according_to instrument policy

# ---------- SAMPLES ----------
entity Sample:
  type: ScientificSample
  may_include:
    - sample_identifier
    - sample_type
    - source
    - collection_time
    - preparation_state
    - storage_condition
    - chain_of_custody

rule sample_identity:
  each traceable Sample SHOULD have stable identifier

rule sample_lineage:
  derived Sample SHOULD reference parent Sample or source material

rule sample_state:
  sample preparation and storage state SHOULD be preserved
  where they affect measurement or analysis

# ---------- REAGENTS / MATERIALS ----------
entity Reagent:
  type: LaboratoryMaterial
  may_include:
    - reagent_identifier
    - chemical_identity
    - concentration
    - lot_number
    - supplier
    - preparation_date
    - expiry_date
    - storage_condition

rule reagent_traceability:
  reagents affecting result SHOULD be traceable by identity or lot where applicable

rule reagent_validity:
  IF expiry_date exists
  AND use_time > expiry_date
  THEN flag reagent validity issue

# ---------- PROTOCOL ----------
entity LaboratoryProtocol:
  type: ScientificMethod
  defines:
    - procedure
    - sequence
    - materials
    - equipment
    - conditions
    - measurement_method

rule protocol_version:
  material protocol changes SHOULD create distinguishable version

rule protocol_deviation:
  deviations from LaboratoryProtocol SHOULD be recorded with:
    - deviation
    - reason
    - authorising_agent
    - timestamp

# ---------- ENVIRONMENT ----------
entity EnvironmentalCondition:
  type: ContextMetadata
  may_include:
    - temperature
    - humidity
    - pressure
    - light_level
    - contamination_state
    - atmospheric_condition

rule environmental_context:
  conditions affecting scientific validity SHOULD be recorded

rule environmental_units:
  quantitative environmental values SHOULD have units

# ---------- QUALITY CONTROL ----------
entity QualityControl:
  type: QualityMetadata
  may_include:
    - control_sample
    - blank
    - reference_material
    - acceptance_criteria
    - quality_flag
    - corrective_action

rule qc_evaluation:
  IF acceptance criteria exist
  THEN QualityControl result SHOULD be evaluated against criteria

rule failed_qc:
  IF QualityControl fails
  THEN affected results SHOULD be flagged
  AND corrective action SHOULD be traceable where available

# ---------- MEASUREMENT ----------
rule measurement_context:
  LaboratoryMeasurement SHOULD preserve:
    - sample
    - instrument
    - method
    - operator
    - time
    - value
    - unit
    - uncertainty
    - quality_state

rule raw_measurement:
  raw measurement SHOULD remain distinguishable from processed result

# ---------- PROVENANCE ----------
rule provenance:
  LaboratoryActivity SHOULD preserve provenance for:
    - personnel
    - sample
    - instrument
    - reagent
    - protocol
    - environmental_condition
    - processing
    - result

rule chain_of_custody:
  IF sample custody matters
  THEN transfers SHOULD preserve:
    - from_agent
    - to_agent
    - timestamp
    - location
    - condition

# ---------- VALIDATION ----------
validation:
  require:
    - identifiable_laboratory_activity

  validate_if_present:
    - laboratory
    - personnel
    - instruments
    - equipment
    - calibration
    - samples
    - reagents
    - protocol
    - environmental_conditions
    - measurements
    - quality_control
    - provenance

  reject:
    - unresolved_sample_identity where traceability is mandatory
    - measurement_without_interpretable_unit where unit is required
    - contradictory_instrument_state
    - invalid_calibration_period
    - impossible_sample_lineage
    - protocol_version_contradiction
    - broken_chain_of_custody where custody is mandatory

# ---------- SEMANTIC EQUIVALENCE ----------
SEMANTIC_EQUIVALENCE:
  "laboratory metadata" ~= "lab metadata"
  "laboratory instrument" ~= "lab instrument"
  "laboratory protocol" ~= "lab protocol"
  "quality control" ~= "QC" WHEN laboratory context applies
  "sample preparation" ~= "specimen preparation" WHEN domain semantics match
  "equipment maintenance" ~= "instrument maintenance" WHEN equipment is instrument

  PRESERVE distinctions:
    laboratory != experiment
    instrument != equipment
    calibration != maintenance
    sample != reagent
    raw_measurement != processed_result
    protocol != procedure_execution
    quality_control != calibration
    sample_identifier != sample_type

# ---------- CONFIDENCE ----------
CONFIDENCE:
  explicit_laboratory_metadata:
    score: 1.00

  explicit_sample_and_instrument_trace:
    score: 1.00

  valid_calibration_context:
    score: 0.95

  complete_chain_of_custody:
    score: 0.95

  inferred_instrument_from_method:
    score: 0.75

  inferred_sample_relationship:
    score: 0.75

  incomplete_laboratory_context:
    score: <= 0.60
    action: preserve uncertainty

# ---------- UPDATE MODEL ----------
UPDATE_MODEL:
  on_instrument_update:
    - preserve instrument history
    - update state
    - update maintenance
    - update calibration
    - reassess dependent measurements
    - record provenance

  on_sample_update:
    - preserve prior sample state
    - update preparation or storage state
    - maintain lineage
    - update chain_of_custody
    - record provenance

  on_protocol_update:
    - preserve previous protocol version
    - create new version
    - reassess affected activities
    - record provenance

  on_quality_control_update:
    - preserve previous QC state
    - reassess affected results
    - record corrective action
    - update provenance

# ---------- FLOW HASH ----------
FLOW_HASH:
  inputs:
    - ontology
    - laboratory_entities
    - relationships
    - instrument_rules
    - sample_rules
    - protocol_rules
    - quality_rules
    - provenance_rules
    - validation
    - semantic_equivalence
    - confidence
    - update_model

  canonicalisation:
    - normalise_whitespace
    - preserve_case_sensitive_identifiers
    - sort_unordered_property_sets
    - preserve_rule_order

  output:
    deterministic_semantic_hash

# ---------- AI CONSUMPTION ----------
AI_CONSUMPTION:
  interpret_as:
    - scientific metadata ontology
    - laboratory workflow model
    - sample and instrument traceability structure
    - laboratory quality model
    - reproducibility support structure

  operations:
    - identify laboratory activities
    - resolve laboratory and personnel
    - trace instruments and equipment
    - validate calibration context
    - trace sample lineage
    - resolve reagents and materials
    - interpret protocols
    - evaluate environmental conditions
    - evaluate quality control
    - trace measurements and results
    - preserve provenance
    - expose uncertainty

  constraints:
    - do_not_invent_sample_identity
    - do_not_assume_instrument_is calibrated
    - do_not_equate_maintenance_with calibration
    - do_not_discard_failed_QC context
    - do_not_merge raw and processed results
    - preserve sample lineage, protocol version, and laboratory provenance

# ---------- QUERY MODEL ----------
query:
  input:
    - laboratory
    - activity
    - personnel
    - instrument
    - sample
    - reagent
    - protocol
    - measurement
    - quality_control
    - time_constraint

  resolve:
    1. identify LaboratoryActivity
    2. resolve Laboratory
    3. resolve responsible personnel
    4. resolve instruments and calibration
    5. trace samples and reagents
    6. resolve protocol and deviations
    7. inspect environmental conditions
    8. retrieve measurements
    9. evaluate quality control
    10. trace provenance and confidence

  output:
    - laboratory_activity
    - laboratory
    - personnel
    - instruments
    - samples
    - reagents
    - protocol
    - measurements
    - quality_state
    - provenance
    - confidence

# ---------- INFERENCE ----------
inference:
  IF measurement references instrument
  AND valid calibration covers measurement time
  THEN infer calibration_context = valid
  WITH confidence = 0.95

  IF derived sample references parent sample
  THEN construct SampleLineage relationship

  IF reagent use occurs after declared expiry
  THEN infer reagent_validity_issue

  IF QC result violates acceptance criteria
  THEN infer quality_flag = failed
  AND associate affected laboratory results where traceable

  IF critical laboratory context is absent
  THEN reduce confidence
  AND preserve missing metadata requirements

# ---------- OUTPUT CONTRACT ----------
output:
  ontology_entity: LaboratoryMetadata
  laboratory_context: machine_interpretable
  personnel: traceable
  instruments: traceable
  calibration: explicit
  samples: lineage_preserved
  reagents: traceable
  protocols: versioned
  quality_control: reportable
  measurements: source_linked
  provenance: preserved
  uncertainty: explicit
  semantic_retrieval: enabled

end flow