Bioprocess Engineering Ontology

flow “BioprocessEngineeringOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > BIOTECHNOLOGY > BIOPROCESS 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/bioprocess-engineering-ontology.html”

type Bioprocess type BiologicalHost type Medium type Substrate type
Product type Bioreactor type ProcessStep type Sensor type Controller
type Observation type Evidence type Source

relation INSTANCE_OF(entity,type) relation PART_OF(part,whole) relation
USES(process,entity) relation PRODUCES(process,product) relation
CONSUMES(process,substrate) relation PRECEDES(step_a,step_b)

———- PROCESS / UPSTREAM ———-

enum BioprocessType: MICROBIAL_FERMENTATION MAMMALIAN_CELL_CULTURE
PLANT_CELL_CULTURE INSECT_CELL_CULTURE ENZYME_PROCESS CELL_FREE_PROCESS
BIOCONVERSION

relation HAS_BIOPROCESS_TYPE(process,type) relation
BIOLOGICAL_HOST_OF(host,process) relation
TARGET_PRODUCT(process,product) relation PROCESS_SCALE(process,value)
relation UPSTREAM_STEP(step) relation MEDIA_PREPARATION(step,medium)
relation INOCULUM_PREPARATION(step,inoculum) relation
SEED_TRAIN_OF(seed,process) relation INOCULATES(inoculum,reactor)
relation CULTURE_MEDIUM(process,medium) relation
FEED_SOLUTION(process,feed)

———- BIOREACTORS / MODES ———-

enum BioreactorType: STIRRED_TANK AIRLIFT BUBBLE_COLUMN PACKED_BED
FLUIDISED_BED WAVE_BIOREACTOR PERFUSION_BIOREACTOR SINGLE_USE_BIOREACTOR
PHOTOBIOREACTOR

relation HAS_BIOREACTOR_TYPE(reactor,type) relation
BIOREACTOR_SUPPORTS(reactor,process) relation
TOTAL_VOLUME(reactor,value) relation WORKING_VOLUME(reactor,value)
relation IMPELLER_TYPE(reactor,type)

enum OperationMode: BATCH FED_BATCH CONTINUOUS PERFUSION REPEATED_BATCH

relation HAS_OPERATION_MODE(process,mode) relation
BATCH_DURATION(process,value) relation FEED_RATE(process,value) relation
DILUTION_RATE(process,value) relation PERFUSION_RATE(process,value)
relation RESIDENCE_TIME(process,value)

———- CONDITIONS / KINETICS ———-

relation TEMPERATURE(process,value) relation PH(process,value) relation
DISSOLVED_OXYGEN(process,value) relation DISSOLVED_CO2(process,value)
relation OSMOLALITY(process,value) relation
AGITATION_RATE(process,value) relation AERATION_RATE(process,value)
relation BIOMASS_CONCENTRATION(process,value) relation
VIABLE_CELL_DENSITY(process,value) relation
CELL_VIABILITY(process,value) relation
SPECIFIC_GROWTH_RATE(process,value) relation
DOUBLING_TIME(process,value) relation
SUBSTRATE_CONCENTRATION(process,substrate,value) relation
PRODUCT_CONCENTRATION(process,product,value) relation
METABOLITE_CONCENTRATION(process,metabolite,value)

———- YIELD / PRODUCTIVITY ———-

relation BIOMASS_YIELD_ON_SUBSTRATE(process,value) relation
PRODUCT_YIELD_ON_SUBSTRATE(process,value) relation
PRODUCT_YIELD_ON_BIOMASS(process,value) relation
SPECIFIC_PRODUCTIVITY(process,value) relation
VOLUMETRIC_PRODUCTIVITY(process,value) relation
CONVERSION(process,value)

constraint YIELD_CONTEXT_REQUIRED: IF PRODUCT_YIELD_ON_SUBSTRATE(p,v)
THEN PRESERVE_SUBSTRATE_PRODUCT_TIME_AND_UNIT_CONTEXT(p)

———- MASS TRANSFER / MIXING ———-

relation MASS_TRANSFER_COEFFICIENT(process,value) relation
KLA(process,value) relation OXYGEN_TRANSFER_RATE(process,value) relation
OXYGEN_UPTAKE_RATE(process,value) relation
CRITICAL_DISSOLVED_OXYGEN(process,value) relation
MIXING_TIME(process,value) relation POWER_INPUT(process,value) relation
POWER_PER_VOLUME(process,value) relation SHEAR_RATE(process,value)
relation SHEAR_STRESS(process,value) relation GAS_HOLDUP(process,value)

———- MONITORING / CONTROL ———-

enum ProcessSensorType: PH_SENSOR DO_SENSOR TEMPERATURE_SENSOR
PRESSURE_SENSOR BIOMASS_SENSOR CO2_SENSOR O2_SENSOR RAMAN_SENSOR
NIR_SENSOR CAPACITANCE_SENSOR

relation HAS_SENSOR_TYPE(sensor,type) relation
SENSOR_MEASURES(sensor,variable) relation
SENSOR_INSTALLED_IN(sensor,reactor) relation
SENSOR_READING(sensor,value) relation SENSOR_CALIBRATED_AT(sensor,time)

enum ControlMode: OPEN_LOOP FEEDBACK FEEDFORWARD CASCADE PID
MODEL_PREDICTIVE_CONTROL

relation HAS_CONTROL_MODE(controller,mode) relation
CONTROLLER_REGULATES(controller,variable) relation
SET_POINT(controller,value) relation CONTROL_OUTPUT(controller,value)
relation MANIPULATED_VARIABLE(controller,variable) relation
CONTROL_ERROR(controller,value)

———- PAT / HARVEST ———-

relation PAT_METHOD(method) relation PAT_MEASURES(method,attribute)
relation ONLINE_MEASUREMENT(method) relation INLINE_MEASUREMENT(method)
relation ATLINE_MEASUREMENT(method) relation HARVEST_STEP(step) relation
HARVESTS(step,material) relation CELL_SEPARATION_BY(step,method)
relation CLARIFICATION_YIELD(step,value)

———- DOWNSTREAM PROCESSING ———-

relation DOWNSTREAM_STEP(step) relation CAPTURE_STEP(step) relation
PURIFICATION_STEP(step) relation POLISHING_STEP(step) relation
CONCENTRATION_STEP(step) relation FORMULATION_STEP(step)

enum SeparationMethod: CENTRIFUGATION MICROFILTRATION ULTRAFILTRATION
DIAFILTRATION PRECIPITATION EXTRACTION CHROMATOGRAPHY

relation USES_SEPARATION_METHOD(step,method) relation
STEP_YIELD(step,value) relation STEP_PURITY(step,value) relation
STEP_RECOVERY(step,value)

———- PRODUCT QUALITY ———-

relation PRODUCT_PURITY(product,value) relation
PRODUCT_POTENCY(product,value) relation PRODUCT_STABILITY(product,value)
relation AGGREGATE_LEVEL(product,value) relation
HOST_CELL_PROTEIN(product,value) relation RESIDUAL_DNA(product,value)
relation ENDOTOXIN_LEVEL(product,value) relation
CRITICAL_QUALITY_ATTRIBUTE(product,attribute) relation
QUALITY_ATTRIBUTE_VALUE(product,attribute,value) relation
CRITICAL_PROCESS_PARAMETER(process,parameter) relation
PROCESS_PARAMETER_VALUE(process,parameter,value)

———- SCALE-UP / TECH TRANSFER ———-

relation SCALED_FROM(process_a,process_b) relation
SCALE_FACTOR(process,value) relation
SCALE_UP_CRITERION(process,criterion) relation
SCALE_DOWN_MODEL(model,process) relation GEOMETRIC_SIMILARITY(a,b,value)
relation CONSTANT_POWER_PER_VOLUME(a,b) relation CONSTANT_TIP_SPEED(a,b)
relation CONSTANT_KLA(a,b)

constraint SCALE_UP_NOT_IDENTITY: IF SCALED_FROM(a,b) THEN
DO_NOT_INFER(identical_process_performance(a,b))

relation TECHNOLOGY_TRANSFER_OF(transfer,process) relation
TRANSFER_FROM(transfer,site_a) relation TRANSFER_TO(transfer,site_b)
relation COMPARABILITY_ASSESSMENT(transfer,assessment)

———- VALIDATION / BATCH ———-

relation VALIDATED_PROCESS(process) relation VALIDATION_RUN(process,run)
relation PROCESS_PERFORMANCE_QUALIFICATION(run) relation
ACCEPTANCE_CRITERION(run,criterion) relation
PROCESS_CAPABILITY(process,value) relation DEVIATION_IN(run,event)
relation CONTAMINANT_IN(process,contaminant) relation
BIOBURDEN(process,value) relation STERILITY_TEST_OF(batch,test) relation
ASEPTIC_PROCESS(process) relation BATCH_OF(batch,process) relation
BATCH_START(batch,time) relation BATCH_END(batch,time) relation
BATCH_YIELD(batch,value) relation BATCH_PRODUCTIVITY(batch,value)
relation BATCH_MEETS_SPECIFICATION(batch,specification)

———- MASS BALANCE ———-

relation INPUT_MASS(process,component,value) relation
OUTPUT_MASS(process,component,value) relation
ACCUMULATION(process,component,value) relation
LOSS_OF(process,component,value)

———- EVIDENCE ———-

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: BIOREACTOR_RUN FERMENTATION_RUN CELL_CULTURE_RUN
PROCESS_SENSOR_DATA PAT_DATA MASS_BALANCE KINETIC_ANALYSIS
MASS_TRANSFER_STUDY MIXING_STUDY DOWNSTREAM_RUN CHROMATOGRAPHY_RUN
FILTRATION_RUN QUALITY_ASSAY SCALE_UP_STUDY SCALE_DOWN_STUDY
TECH_TRANSFER_STUDY PROCESS_VALIDATION 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: “bioprocess engineering” ~= “engineering of
biological production processes” “upstream processing” ~= “process
stages involving inoculum preparation culture and biological production”
“downstream processing” ~= “process stages involving harvest recovery
purification and formulation” “bioreactor” ~= “controlled vessel or
system supporting a biological process” “batch culture” ~= “closed
cultivation process without continuous medium feed during production”
“fed-batch culture” ~= “cultivation process with controlled addition of
nutrients during operation” “continuous culture” ~= “cultivation process
with continuous feed and removal” “specific growth rate” ~= “growth rate
normalised to biomass” “volumetric productivity” ~= “product formation
rate per process volume” “oxygen transfer rate” ~= “rate of oxygen
transfer from gas to liquid phase” “kLa” ~= “volumetric mass transfer
coefficient” “PAT” ~= “process analytical technology” “critical quality
attribute” ~= “product property requiring control to assure desired
quality” “critical process parameter” ~= “process parameter whose
variability can affect critical quality attributes” “scale-up” ~=
“translation of a process to a larger operating scale” “technology
transfer” ~= “transfer of process knowledge and operation between
development or manufacturing sites”

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

query BIOPROCESS_PROFILE(p): RETURN: bioprocess_type(p)
biological_host(p) product(p) operation_mode(p) reactor(p) medium(p)
operating_conditions(p) growth_kinetics(p) yields(p) productivity(p)
mass_transfer(p) mixing(p) process_control(p) upstream_steps(p)
downstream_steps(p) quality_attributes(p) scale(p) evidence(p)
confidence(p)

query BIOREACTOR_PROFILE(r): RETURN: reactor_type(r) working_volume(r)
agitation(r) aeration(r) oxygen_transfer(r) mixing(r) sensors(r)
controllers(r)

query DOWNSTREAM_PROFILE(p): RETURN: harvest_steps(p) capture_steps(p)
purification_steps(p) polishing_steps(p) formulation_steps(p)
step_yields(p) purity(p) recovery(p)

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

constraint EVIDENCE_REQUIRED: FORALL bioprocess_assertion: REQUIRE
SUPPORTED_BY(bioprocess_assertion,Evidence) OR
MARK_AS_HYPOTHESIS(bioprocess_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 SCALE_CONTEXT_REQUIRED: IF bioprocess_measurement(m) THEN
PRESERVE_PROCESS_SCALE(m)

constraint MODE_CONTEXT_REQUIRED: IF process_performance_result(r) THEN
PRESERVE_OPERATION_MODE(r)

UPDATE_MODEL: on_new_bioprocess(p):
identify_host_product_and_process_type(p)
preserve_operation_mode_and_scale(p)
preserve_reactor_and_medium_context(p) attach_evidence(p)
recalculate_confidence(p)

on_new_process_measurement(m): identify_variable(m)
preserve_value_unit_time_and_scale(m) preserve_sensor_or_method(m)
update_process_state(m)

on_new_downstream_step(s): classify_step_and_method(s)
preserve_input_output_and_operating_context(s)
update_yield_purity_and_recovery(s) attach_evidence(s)

on_new_scale_up_record(s): identify_source_and_target_scale(s)
preserve_scale_up_criteria(s)
compare_mass_transfer_mixing_and_quality(s) attach_evidence(s)

on_new_validation_record(v):
identify_process_batch_and_acceptance_criteria(v) preserve_deviations(v)
update_validation_status(v) attach_evidence(v)

AI_CONSUMPTION: preferred_entity:
canonical_bioprocess_engineering_entity preserve: - bioprocess_type -
biological_host - target_product - process_scale - operation_mode -
upstream_processing - medium - bioreactor - operating_conditions -
growth_kinetics - yields - productivity - mass_transfer - mixing -
heat_transfer - sensors - process_control -
process_analytical_technology - harvesting - downstream_processing -
product_quality - critical_quality_attributes -
critical_process_parameters - scale_up - technology_transfer -
process_validation - contamination_control - batch_context -
mass_balance - evidence - provenance - confidence infer: -
supported_process_step_relations - supported_mass_balance_relations -
supported_quality_relations - semantic_equivalence prohibit: -
scale_up_equals_identical_performance -
correlation_equals_process_causation -
yield_without_substrate_product_context -
process_measurement_without_scale_context -
operation_mode_free_generalisation - confidence_above_evidence
ambiguity: action: preserve_multiple_bioprocess_interpretations
resolution:
prefer_host_product_mode_scale_reactor_method_units_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

FLOW_HASH: ontology: “BioprocessEngineeringOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies >
Biotechnology > Bioprocess Engineering Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biotechnology/bioprocess-engineering-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - bioprocess engineering - biological hosts - upstream
processing - culture media - bioreactors - operation modes - culture
conditions - cell growth kinetics - yield - productivity - mass
transfer - oxygen transfer - mixing - process monitoring - process
control - process analytical technology - harvesting - downstream
processing - product quality - critical quality attributes - critical
process parameters - scale-up - scale-down - technology transfer -
process validation - contamination control - batch processing - mass
balance - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate BioprocessEngineeringOntology when:
process_host_product_mode_and_scale_resolved AND
upstream_reactor_and_operating_context_preserved AND
kinetics_yield_productivity_and_mass_transfer_context_preserved AND
downstream_recovery_purity_and_quality_relations_normalised AND
scale_up_and_process_identity_distinguished AND
validation_batch_and_contamination_context_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_bioprocess_ambiguity_marked

end flow