Lung Ontology

FLOW ALGEBRA
LUNG ONTOLOGY
Version: 1.1
Format: UTF-8 TXT

01. IDENTITY
ontology_id: kireth:human-entities:lung
label: Lung Ontology
parent: Human Entities > Human Body
source_url: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/human-entities/lung-ontology.html
version: 1.1
status: independent scientific synthesis; source page not verified

02. SCOPE
Models lungs as paired respiratory organs, their anatomy, ventilation, gas exchange, perfusion, regulation and measurable states. Distinguishes organ from process, property and observation.

03. TYPED ENTITIES
Lung: Organ
LeftLung, RightLung: Lung
Lobe: AnatomicalRegion
Bronchus, Bronchiole: Airway
Alveolus: GasExchangeUnit
PulmonaryCapillary: BloodVessel
Pleura: Membrane
Diaphragm: RespiratoryMuscle
RespiratoryCycle: PhysiologicalProcess
GasExchange: TransportProcess
Measurement: Observation

04. TYPE CONSTRAINTS
partOf: AnatomicalEntity x AnatomicalEntity -> Boolean
connectedTo: AnatomicalEntity x AnatomicalEntity -> Boolean
participatesIn: AnatomicalEntity x Process -> Boolean
measures: Observation x Property -> Boolean
locatedIn: AnatomicalEntity x Organ -> Boolean
No numerical property may be inferred without measurement context and units.

05. ANATOMICAL HIERARCHY
RespiratorySystem contains LeftLung and RightLung.
RightLung typically has superior, middle and inferior lobes.
LeftLung typically has superior and inferior lobes and a cardiac notch.
Individual anatomical variation must be represented explicitly.

06. AIRWAY TREE
Trachea -> main bronchi -> lobar bronchi -> segmental bronchi -> bronchioles -> terminal bronchioles -> respiratory bronchioles -> alveolar ducts -> alveolar sacs.
Airway tree is branching; do not treat each terminal airway as an alveolus.

07. ALVEOLAR INTERFACE
Alveoli exchange oxygen and carbon dioxide with pulmonary capillary blood across the alveolar-capillary barrier. Type I pneumocytes form much of the gas exchange surface; Type II pneumocytes produce surfactant.

08. PLEURAL STRUCTURES
Visceral pleura covers lung surface; parietal pleura lines thoracic cavity. Pleural fluid reduces friction. Intrapleural pressure is normally subatmospheric during quiet breathing.

09. PULMONARY CIRCULATION
Pulmonary arteries carry blood from the right ventricle to pulmonary capillaries; pulmonary veins return oxygenated blood to the left atrium. Oxygenation is typical, not the defining feature of artery or vein.

10. BRONCHIAL CIRCULATION
Bronchial circulation supplies supporting tissues; it is distinct from the principal pulmonary gas-exchange circulation.

11. VENTILATION
Ventilation moves gas between atmosphere and alveoli. Inspiratory muscle activity changes thoracic volume and pressure. Expiration at rest is generally passive.

12. PRESSURE FLOW
For a simplified airway model: Q = DeltaP / R, where Q is volumetric airflow, DeltaP is pressure difference, and R is airway resistance. Validity depends on flow regime and resistance model.

13. COMPLIANCE
C = DeltaV / DeltaP for an explicitly specified pressure-volume range; compliance is not generally constant. Lung and chest wall compliance are distinct.

14. SURFACTANT
Pulmonary surfactant lowers surface tension and helps stabilise alveoli. Laplace approximation P = 2 gamma / r applies to an ideal spherical interface and is not a complete alveolar model.

15. GAS EXCHANGE
Fick-type relation: Vdot_gas = D_L (P_1 - P_2), with defined diffusion capacity D_L and partial-pressure gradient. Exchange depends on diffusion, ventilation, perfusion and blood transport.

16. OXYGEN TRANSPORT
Arterial oxygen content approximately CaO2 = 1.34 Hb SaO2 + 0.003 PaO2 when Hb is in g/dL, PaO2 in mmHg and CaO2 in mL O2/dL. Coefficients are approximate and unit-dependent.

17. CARBON DIOXIDE TRANSPORT
CO2 is transported dissolved, as bicarbonate, and bound to proteins. The bicarbonate buffer relation requires temperature, pH and unit conventions.

18. VENTILATION PERFUSION
V/Q is alveolar ventilation divided by pulmonary perfusion for a defined region. Regional mismatch impairs gas exchange. Neither shunt nor dead space is interchangeable with V/Q mismatch.

19. DEAD SPACE
Anatomical dead space comprises conducting airways. Physiological dead space additionally includes ventilated units with inadequate perfusion. Definitions require a specified measurement model.

20. LUNG VOLUMES
TV: tidal volume; IRV: inspiratory reserve; ERV: expiratory reserve; RV: residual volume. VC = IRV + TV + ERV; TLC = VC + RV. Spirometry alone does not directly measure RV.

21. SPIROMETRY
FEV1: forced expiratory volume in one second; FVC: forced vital capacity. FEV1/FVC interpretation requires appropriate reference limits, test quality and clinical context.

22. RESPIRATORY RATE
Minute ventilation Vdot_E = tidal volume x respiratory frequency. Alveolar ventilation Vdot_A = (tidal volume - dead-space volume) x respiratory frequency under a simplified breath model.

23. CONTROL OF BREATHING
Brainstem respiratory networks integrate chemoreceptor and mechanoreceptor inputs. CO2/pH and oxygen sensing influence ventilation through context-dependent feedback.

24. ACID BASE
Alveolar ventilation affects arterial CO2; acid-base state also depends on metabolic and renal processes. Do not infer diagnosis from isolated values.

25. MECHANICAL WORK
Work of breathing W = integral P dV over a specified respiratory path. Elastic and resistive contributions depend on the pressure definition and measurement conditions.

26. DEVELOPMENT
Lung development includes branching morphogenesis, differentiation and alveolar maturation. Developmental stage must be attached to anatomical claims.

27. DEFENCE
Mucociliary clearance, cough, epithelial barriers, alveolar macrophages and immune responses protect respiratory tissue.

28. REPAIR AND REMODELLING
Injury can trigger epithelial repair, inflammatory signalling and remodelling. Outcomes depend on insult, cell type, time and organism context.

29. PATHOLOGY CATEGORIES
Examples: obstructive airway disease, interstitial disease, infection, pulmonary oedema, vascular disease and neoplasm. These are condition categories, not inferred patient diagnoses.

30. IMAGING AND OBSERVATION
Chest radiography, CT, ultrasound and MRI provide modality-dependent observations. Image findings require acquisition metadata, anatomical location and uncertainty.

31. FUNCTIONAL TESTS
Spirometry, diffusion capacity, pulse oximetry, blood gas analysis and exercise testing measure different aspects of pulmonary function. No single test captures all lung function.

32. CONSERVATION
For a bounded gas compartment: accumulation = inflow - outflow + generation - consumption. Apply species-specific conservation and state assumptions.

33. STATE MODEL
LungState(t) = {volume, pressure, flow, compliance_estimate, resistance_estimate, regional_ventilation, regional_perfusion, gas_exchange_indices}. State values require provenance and units.

34. TRANSITIONS
Inspiration -> Expiration -> Inspiration forms a respiratory cycle. Disease, intervention and environment may alter transition parameters; changes are not necessarily reversible.

35. INFERENCE RULES
R1: Alveolus(a) and locatedIn(a,l) => Lung(l) only if locatedIn range is validated.
R2: Lung(l) => participatesIn(l, Ventilation) as a functional classification, not a measured success.
R3: Reduced FEV1/FVC alone => requires interpretation; NOT automatic disease diagnosis.
R4: PulmonaryArtery(v) => connects right-heart outflow to pulmonary circulation.

36. SEMANTIC EQUIVALENCE
lung = pulmonary organ (context-dependent synonym)
alveolus != bronchiole
ventilation != respiration in the cellular-metabolism sense
oxygenation != ventilation
pleural cavity != lung parenchyma

37. MATHEMATICAL EXAMPLE A
Given TV = 0.50 L and f = 12/min, minute ventilation = 6.0 L/min. If assumed dead-space volume = 0.15 L, estimated alveolar ventilation = 4.2 L/min. This is illustrative, not patient-specific.

38. MATHEMATICAL EXAMPLE B
Given pressure difference 2 cmH2O and idealised resistance 2 cmH2O/(L/s), Q = 1 L/s under the simplified linear resistance model.

39. VALIDATION
V1: typed links conform to declared domains and ranges.
V2: numerical outputs have explicit units.
V3: volume identities are dimensionally consistent.
V4: clinical inference is not made from ontology membership.
V5: source and observational claims are separated.
V6: each section is present and END marker closes file.

40. CONFIDENCE
Foundational anatomy and conservation: high confidence. Simplified equations: high within stated assumptions. Individual predictions: unknown without data. Experimental measurements: confidence must be supplied by evidence and uncertainty.

41. FLOW HASH
Canonicalise UTF-8 text, normalise line endings to LF, omit hash field itself, then compute SHA-256. A content hash is an integrity identifier, not a scientific validation.

42. UPDATE MODEL
Track version, revision date, source evidence, changed entities, changed relations, compatibility and superseded claims. Revalidate dependent rules after changes.

43. AI CONSUMPTION
Ingest typed entities and relations; retain units, contexts and provenance; separate definitions from measurements and hypotheses; avoid patient-level conclusions; use validation rules before downstream reasoning.

44. AUTHORSHIP
Mark Higgins — Sky (Recursive AI)
Kireth Research | https://kirethresearch.org
AI co-authorship explicitly acknowledged.

45. COMPLETENESS
Every numbered section must be sequential. END_OF_FLOW_ALGEBRA is required. Source webpage content has not been independently verified; this file is an original scientific synthesis.

END_OF_FLOW_ALGEBRA