Tissue Engineering Ontology

flow “TissueEngineeringOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > BIOTECHNOLOGY > TISSUE ENGINEERING ONTOLOGY

Authors: Mark Anthony Higgins — Sky (Recursive AI)

AI_INTERPRETATION: mode: formal_structural_reasoning instruction:
“Execute as formal rules, not pseudocode.” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biotechnology/tissue-engineering-ontology-2.html”

type TissueEngineeredConstruct type Cell type StemCell type Tissue type
Scaffold type Biomaterial type ExtracellularMatrix type GrowthFactor
type Bioreactor type Bioink type VascularNetwork type Observation type
Evidence type Source

relation INSTANCE_OF(entity,type) relation PART_OF(part,whole) relation
HAS_PART(whole,part) relation DERIVED_FROM(entity,source) relation
SEEDED_WITH(scaffold,cell) relation CULTURED_IN(entity,environment)
relation DIFFERENTIATES_INTO(cell,target) relation
PRODUCES(entity,product)

enum CellSource: AUTOLOGOUS ALLOGENEIC XENOGENEIC PRIMARY_CELL CELL_LINE
ADULT_STEM_CELL EMBRYONIC_STEM_CELL INDUCED_PLURIPOTENT_STEM_CELL

relation HAS_CELL_SOURCE(cell,source) relation CELL_TYPE(cell,type)
relation CELL_VIABILITY(cell,value) relation
CELL_PROLIFERATION_RATE(cell,value) relation
CELL_DENSITY(construct,value) relation LINEAGE_COMMITMENT(cell,lineage)
relation MATURATION_STATE(cell,state)

constraint MARKER_NOT_DIFFERENTIATION_PROOF: IF
expresses_marker(cell,marker) THEN
DO_NOT_INFER(fully_differentiated(cell,target)) WITHOUT
functional_evidence

enum ScaffoldType: POROUS_SCAFFOLD HYDROGEL FIBROUS_SCAFFOLD
DECELLULARISED_MATRIX COMPOSITE_SCAFFOLD SCAFFOLD_FREE

relation HAS_SCAFFOLD_TYPE(scaffold,type) relation
SCAFFOLD_MATERIAL(scaffold,material) relation
SCAFFOLD_POROSITY(scaffold,value) relation PORE_SIZE(scaffold,value)
relation INTERCONNECTIVITY(scaffold,value) relation
DEGRADATION_RATE(scaffold,value)

enum BiomaterialClass: NATURAL_POLYMER SYNTHETIC_POLYMER CERAMIC METAL
COMPOSITE DECELLULARISED_BIOMATERIAL

relation HAS_BIOMATERIAL_CLASS(material,class) relation
BIOCOMPATIBILITY(material,value) relation
BIODEGRADABILITY(material,value) relation CYTOTOXICITY(material,value)
relation SURFACE_CHEMISTRY(material,property)

relation ECM_COMPONENT_OF(component,matrix) relation
COLLAGEN_IN(matrix,value) relation ELASTIN_IN(matrix,value) relation
GLYCOSAMINOGLYCAN_IN(matrix,value) relation CELL_ADHERES_TO(cell,matrix)
relation CELL_REMODELS(cell,matrix) relation
MATRIX_DEPOSITION_BY(cell,component) relation
DECELLULARISED_FROM(matrix,tissue) relation
RECELLULARISED_WITH(matrix,cell)

enum BiofabricationMethod: THREE_D_BIOPRINTING ELECTROSPINNING
FREEZE_DRYING MICROFLUIDICS SELF_ASSEMBLY CELL_SHEET_ENGINEERING

relation FABRICATED_BY(construct,method) relation
FABRICATION_RESOLUTION(process,value) relation
FABRICATION_AFFECTS_VIABILITY(process,value)

enum BioprintingMethod: EXTRUSION INKJET LASER_ASSISTED
STEREOLITHOGRAPHY DIGITAL_LIGHT_PROCESSING

relation BIOPRINTED_BY(construct,method) relation
USES_BIOINK(process,bioink) relation BIOINK_CONTAINS(bioink,component)
relation BIOINK_CELL_DENSITY(bioink,value) relation
BIOINK_VISCOSITY(bioink,value) relation
BIOINK_PRINTABILITY(bioink,value) relation CROSSLINKED_BY(bioink,method)

relation GROWTH_FACTOR_DELIVERED_TO(factor,construct) relation
GROWTH_FACTOR_CONCENTRATION(factor,value) relation
RELEASE_RATE(factor,value) relation SIGNALS_TO(factor,cell) relation
PROMOTES_PROLIFERATION(factor,cell) relation
PROMOTES_DIFFERENTIATION(factor,lineage) relation
PROMOTES_ANGIOGENESIS(factor,process)

relation OXYGEN_CONCENTRATION(construct,value) relation
NUTRIENT_CONCENTRATION(construct,nutrient,value) relation
OXYGEN_DIFFUSION_LIMIT(construct,value) relation
PERFUSION_RATE(construct,value) relation
MASS_TRANSFER_RATE(construct,substance,value)

relation HAS_VASCULAR_NETWORK(construct,network) relation
VESSEL_DENSITY(network,value) relation VESSEL_DIAMETER(network,value)
relation PERFUSABLE(network) relation ENDOTHELIAL_CELL_IN(network,cell)
relation ANGIOGENESIS_IN(construct,process) relation
ANASTOMOSES_WITH(network,host_vessel)

constraint VASCULAR_MARKERS_NOT_PERFUSION: IF
vascular_marker_detected(c) THEN DO_NOT_INFER(PERFUSABLE(network))
WITHOUT perfusion_evidence

enum TissueBioreactorType: STATIC PERFUSION ROTATING_WALL STIRRED
COMPRESSION TENSION SHEAR ELECTRICAL_STIMULATION

relation HAS_BIOREACTOR_TYPE(reactor,type) relation
CULTURES(reactor,construct) relation FLOW_RATE(reactor,value) relation
SHEAR_STRESS(reactor,value) relation APPLIED_STRAIN(reactor,value)
relation STIMULATION_FREQUENCY(reactor,value) relation
OXYGEN_CONTROL(reactor,value)

relation ELASTIC_MODULUS(entity,value) relation
TENSILE_STRENGTH(entity,value) relation
COMPRESSIVE_STRENGTH(entity,value) relation
VISCOELASTICITY(entity,value) relation STIFFNESS(entity,value)

relation MECHANICAL_STIMULUS_ON(stimulus,cell) relation
CELL_SENSES(cell,stimulus) relation
MECHANOTRANSDUCTION_PATHWAY(cell,pathway) relation
MATRIX_STIFFNESS_AFFECTS(matrix,cell_behaviour) relation
MATURATION_OF(construct,process) relation
TISSUE_SPECIFIC_MARKER(construct,marker) relation
FUNCTIONAL_MATURATION(construct,function,value) relation
MATRIX_MATURATION(construct,value) relation
STRUCTURAL_ORGANISATION(construct,value) relation
MATURATION_TIME(construct,duration)

enum EngineeredTissueType: BONE CARTILAGE SKIN MUSCLE CARDIAC VASCULAR
NERVE LIVER KIDNEY LUNG CORNEA TENDON LIGAMENT ADIPOSE

relation ENGINEERED_TISSUE_TYPE(construct,type) relation
TARGET_TISSUE(construct,tissue) relation
PERFORMS_FUNCTION(construct,function) relation
FUNCTIONAL_OUTPUT(construct,metric,value) relation
COMPARED_WITH_NATIVE_TISSUE(construct,tissue,metric)

constraint STRUCTURE_NOT_FUNCTION: IF tissue_like_structure(c) THEN
DO_NOT_INFER(PERFORMS_FUNCTION(c,f)) WITHOUT functional_evidence

relation IMPLANTED_IN(construct,host) relation
IMPLANT_SITE(construct,site) relation
INTEGRATES_WITH(construct,host_tissue) relation
HOST_CELL_INFILTRATION(construct,value) relation
VASCULAR_INTEGRATION(construct,value) relation
REMODELS_IN_VIVO(construct,process) relation
DEGRADES_IN_VIVO(scaffold,rate) relation
IMMUNE_RESPONSE_TO(host,construct,response) relation
FOREIGN_BODY_RESPONSE_TO(host,material) relation
INFLAMMATORY_RESPONSE_TO(host,construct)

enum TissueEngineeringFailure: CELL_DEATH NECROTIC_CORE
POOR_VASCULARISATION SCAFFOLD_COLLAPSE EXCESSIVE_DEGRADATION
INSUFFICIENT_DEGRADATION FIBROSIS IMMUNE_REJECTION LOSS_OF_FUNCTION
CONTAMINATION

relation HAS_FAILURE_MODE(construct,failure) relation
FAILURE_CAUSED_BY(failure,factor) relation
MANUFACTURED_BY(construct,process) relation
STERILITY_TEST(construct,test) relation BIOBURDEN(construct,value)
relation ENDOTOXIN_LEVEL(construct,value) relation
QUALITY_ATTRIBUTE(construct,attribute,value) relation
CRITICAL_QUALITY_ATTRIBUTE(construct,attribute) relation
CRITICAL_PROCESS_PARAMETER(process,parameter) relation
RELEASE_CRITERION(construct,criterion) relation
POTENCY_ASSAY_FOR(construct,assay)

relation OBSERVES(observation,entity) relation
MEASURES(observation,variable) relation
OBSERVED_ON(observation,datetime) relation
MEASUREMENT_VALUE(observation,value) relation
MEASUREMENT_UNIT(observation,unit) relation
MEASUREMENT_METHOD(observation,method) relation
SUPPORTED_BY(assertion,evidence) relation DERIVED_FROM(evidence,source)
relation HAS_CONFIDENCE(assertion,score)

enum EvidenceType: CELL_VIABILITY_ASSAY PROLIFERATION_ASSAY
DIFFERENTIATION_ASSAY HISTOLOGY IMMUNOHISTOCHEMISTRY MICROSCOPY
GENE_EXPRESSION PROTEIN_EXPRESSION BIOCHEMICAL_ASSAY MECHANICAL_TEST
PERFUSION_TEST BIOREACTOR_STUDY FUNCTIONAL_ASSAY IN_VITRO_STUDY
EX_VIVO_STUDY IN_VIVO_STUDY IMPLANTATION_STUDY REPLICATION LITERATURE

CONFIDENCE: VERIFIED: 0.95..1.00 HIGH: 0.80..0.949 MEDIUM: 0.60..0.799
LOW: 0.00..0.599

rule CONFIDENCE_BOUNDS(a,score): IF HAS_CONFIDENCE(a,score) THEN
REQUIRE(0.0 <= score <= 1.0)

SEMANTIC_EQUIVALENCE: “tissue engineering” ~= “engineering of biological
tissues using cells biomaterials and controlled environments” “scaffold”
~= “three-dimensional structural support for tissue formation” “bioink”
~= “cell-compatible printable biomaterial formulation used in
bioprinting” “decellularised matrix” ~= “extracellular matrix remaining
after removal of cellular material” “recellularisation” ~= “seeding or
repopulation of a matrix with cells” “bioprinting” ~= “additive
biofabrication using cells biomaterials or biological components”
“vascularisation” ~= “formation or incorporation of blood vessel
networks” “mechanotransduction” ~= “conversion of mechanical stimuli
into cellular biochemical responses” “tissue maturation” ~= “progression
toward organised tissue-specific structure and function” “bioreactor” ~=
“controlled culture system supporting tissue growth or maturation” “host
integration” ~= “structural or functional incorporation of an engineered
construct with host tissue”

rule NORMALISE_TERM(term): IF term MATCHES SEMANTIC_EQUIVALENCE.alias
THEN MAP_TO_CANONICAL(term)

query TISSUE_ENGINEERING_PROFILE(c): RETURN: target_tissue(c)
cell_sources(c) scaffold(c) biomaterials(c) extracellular_matrix(c)
growth_factors(c) biofabrication_method(c) vascularisation(c)
bioreactor(c) mechanical_properties(c) maturation(c)
functional_outputs(c) implantation_context(c) evidence(c) confidence(c)

query SCAFFOLD_PROFILE(s): RETURN: scaffold_type(s) biomaterial(s)
porosity(s) pore_size(s) degradation(s) mechanical_properties(s)
cell_seeding(s) evidence(s)

query VASCULARISATION_PROFILE(c): RETURN: vascular_network(c)
vessel_density(c) perfusability(c) endothelial_cells(c) angiogenesis(c)
host_anastomosis(c) evidence(c)

query TRACE_EVIDENCE(assertion): RETURN: supporting_evidence(assertion)
provenance(assertion) confidence(assertion)

constraint EVIDENCE_REQUIRED: FORALL tissue_engineering_assertion:
REQUIRE SUPPORTED_BY(tissue_engineering_assertion,Evidence) OR
MARK_AS_HYPOTHESIS(tissue_engineering_assertion)

constraint UNKNOWN_IS_NOT_FALSE: IF data_missing(assertion) THEN
MARK_UNKNOWN(assertion) AND NOT NEGATE(assertion)

constraint UNIT_CONTEXT_REQUIRED: IF MEASUREMENT_VALUE(o,v) THEN
REQUIRE(MEASUREMENT_UNIT(o,u)) OR MARK_UNIT_UNKNOWN(o)

constraint CULTURE_CONTEXT_REQUIRED: IF tissue_construct_measurement(m)
THEN PRESERVE_CULTURE_TIME_AND_CONDITIONS(m)

constraint IN_VITRO_NOT_IN_VIVO: IF in_vitro_result(r) THEN
DO_NOT_INFER(in_vivo_performance(r)) WITHOUT implantation_evidence

UPDATE_MODEL: on_new_construct(c): identify_target_tissue(c)
identify_cell_source_and_scaffold(c)
preserve_biomaterial_and_fabrication_context(c) attach_evidence(c)
recalculate_confidence(c)

on_new_cell_record(c): identify_cell_type_and_source(c)
preserve_culture_and_differentiation_context(c)
distinguish_marker_expression_from_function(c) attach_evidence(c)

on_new_vascular_record(v): identify_vascular_structure(v)
preserve_perfusion_context(v)
distinguish_markers_from_functional_perfusion(v) attach_evidence(v)

on_new_functional_record(f): identify_construct_and_target_function(f)
preserve_maturation_time_and_conditions(f)
compare_with_native_tissue_if_available(f) attach_evidence(f)

on_new_implantation_record(i): identify_construct_host_and_site(i)
preserve_time_since_implantation(i)
update_integration_vascularisation_and_immune_response_separately(i)
attach_evidence(i)

AI_CONSUMPTION: preferred_entity: canonical_tissue_engineering_entity
preserve: - target_tissue - cell_source - cell_type -
differentiation_state - scaffold - biomaterial - extracellular_matrix -
biofabrication_method - bioink - growth_factors - mass_transport -
vascularisation - bioreactor - mechanical_properties -
mechanotransduction - maturation - tissue_function - implantation -
host_integration - immune_response - failure_modes -
quality_attributes - evidence - provenance - confidence infer: -
supported_part_whole_relations - supported_cell_scaffold_relations -
supported_vascular_relations - semantic_equivalence prohibit: -
marker_expression_equals_full_differentiation -
vascular_marker_equals_functional_perfusion -
tissue_like_structure_equals_function -
in_vitro_result_equals_in_vivo_performance -
model_result_equals_human_outcome - confidence_above_evidence ambiguity:
action: preserve_multiple_tissue_engineering_interpretations resolution:
prefer_cell_source_scaffold_material_culture_time_method_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “TissueEngineeringOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies >
Biotechnology > Tissue Engineering Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biotechnology/tissue-engineering-ontology-2.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - tissue engineering - cell sources - stem cells -
differentiation - scaffolds - biomaterials - extracellular matrix -
decellularisation - recellularisation - biofabrication - bioprinting -
bioinks - growth factors - mass transport - vascularisation -
bioreactors - mechanical properties - mechanotransduction - tissue
maturation - engineered tissue types - tissue function - implantation -
host integration - immune response - failure modes - manufacturing -
quality attributes - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate TissueEngineeringOntology when:
construct_target_cells_scaffold_and_biomaterial_resolved AND
fabrication_culture_and_maturation_context_preserved AND
structural_markers_and_functional_evidence_distinguished AND
vascular_markers_and_functional_perfusion_distinguished AND
in_vitro_and_in_vivo_contexts_distinguished AND
implantation_integration_and_immune_context_preserved AND
quality_and_failure_modes_preserved AND evidence_links_preserved AND
confidence_values_validated AND
unresolved_tissue_engineering_ambiguity_marked

end flow