Biotechnology

flow “BiotechnologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > BIOTECHNOLOGY

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.html”

type BiologicalEntity type Organism type Cell type Gene type DNA type
Protein type Vector type Construct type Bioprocess type Bioreactor type
Product type Biosensor type Observation type Evidence type Source

relation INSTANCE_OF(entity,type) relation DERIVED_FROM(entity,source)
relation PRODUCED_BY(product,process) relation USES(process,entity)
relation TARGETS(process,target) relation MODIFIES(process,target)

———- GENETIC ENGINEERING ———-

enum GeneticEngineeringMethod: RECOMBINANT_DNA TRANSGENESIS KNOCKOUT
KNOCKIN SITE_DIRECTED_MUTAGENESIS GENOME_EDITING GENE_SILENCING
GENE_OVEREXPRESSION

relation USES_ENGINEERING_METHOD(process,method) relation
GENETICALLY_MODIFIES(process,organism) relation
INTRODUCES_GENE(process,gene) relation DELETES_GENE(process,gene)
relation INSERTS_SEQUENCE(process,sequence) relation
EXPRESSES_GENE(host,gene) relation
CONSTRUCT_CONTAINS(construct,sequence) relation
VECTOR_CARRIES(vector,insert) relation PROMOTER_DRIVES(promoter,gene)

———- GENOME EDITING ———-

enum GenomeEditingSystem: CRISPR_CAS TALEN ZINC_FINGER_NUCLEASE
BASE_EDITOR PRIME_EDITOR

relation USES_EDITING_SYSTEM(process,system) relation
GUIDE_TARGETS(guide,locus) relation NUCLEASE_CUTS(nuclease,locus)
relation EDITS_LOCUS(process,locus) relation
HAS_EDIT_OUTCOME(process,outcome) relation
OFF_TARGET_EVENT(process,locus)

constraint INTENDED_EDIT_NOT_OBSERVED_EDIT: IF intended_edit(p,e) THEN
DO_NOT_INFER(HAS_EDIT_OUTCOME(p,e)) WITHOUT validation_evidence

———- SYNTHETIC / CELL BIOLOGY ———-

relation SYNTHETIC_CIRCUIT(circuit) relation
CIRCUIT_CONTAINS(circuit,component) relation
CIRCUIT_INPUT(circuit,input) relation CIRCUIT_OUTPUT(circuit,output)
relation ENGINEERED_PATHWAY(pathway) relation
PATHWAY_PRODUCES(pathway,product) relation ENGINEERED_CELL(cell)
relation CULTURED_IN(cell,medium) relation
TRANSFECTED_WITH(cell,construct) relation TRANSDUCED_WITH(cell,vector)
relation CELL_PRODUCTIVITY(cell,product,rate)

———- MICROBIAL BIOTECHNOLOGY / FERMENTATION ———-

relation MICROBIAL_HOST(organism) relation FERMENTS(organism,substrate)
relation PRODUCES_METABOLITE(organism,metabolite) relation
ENGINEERED_METABOLIC_PATHWAY(organism,pathway)

enum FermentationMode: BATCH FED_BATCH CONTINUOUS SOLID_STATE

relation HAS_FERMENTATION_MODE(process,mode) relation
FERMENTATION_SUBSTRATE(process,substrate) relation
FERMENTATION_PRODUCT(process,product) relation
FERMENTATION_TEMPERATURE(process,value) relation
FERMENTATION_PH(process,value) relation
FERMENTATION_YIELD(process,value)

———- BIOPROCESS ENGINEERING ———-

relation BIOREACTOR_SUPPORTS(reactor,process) relation
HAS_WORKING_VOLUME(reactor,value) relation AGITATION_RATE(reactor,value)
relation AERATION_RATE(reactor,value) relation
DISSOLVED_OXYGEN(reactor,value) relation
BIOMASS_CONCENTRATION(process,value) relation
PRODUCT_CONCENTRATION(process,value) relation UPSTREAM_PROCESS(step)
relation DOWNSTREAM_PROCESS(step) relation HARVESTS(step,material)
relation SEPARATES(step,component) relation PURIFIES(step,product)
relation FORMULATES(step,product)

———- SCALE-UP ———-

relation SCALE_OF(process,value) relation
SCALED_FROM(process_a,process_b) relation
SCALE_UP_PARAMETER(process,parameter,value) relation
MASS_TRANSFER_COEFFICIENT(process,value) relation
OXYGEN_TRANSFER_RATE(process,value) relation MIXING_TIME(process,value)

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

———- BIOPHARMACEUTICALS ———-

enum BiopharmaceuticalType: RECOMBINANT_PROTEIN MONOCLONAL_ANTIBODY
VACCINE NUCLEIC_ACID_THERAPEUTIC CELL_THERAPY GENE_THERAPY
ENZYME_THERAPEUTIC

relation HAS_BIOPHARMACEUTICAL_TYPE(product,type) relation
EXPRESSION_HOST_FOR(host,product) relation PURITY_OF(product,value)
relation POTENCY_OF(product,value) relation STABILITY_OF(product,value)

———- APPLIED BIOTECHNOLOGY ———-

relation BIOCATALYST(enzyme) relation CATALYSES(enzyme,reaction)
relation BIOCONVERSION_OF(substrate,product) relation
BIOBASED_PRODUCT(product) relation BIOFUEL_PRODUCT(product) relation
BIOPLASTIC_PRODUCT(product)

relation ENGINEERED_CROP(organism) relation
ENGINEERED_TRAIT(organism,trait) relation
PLANT_TRANSFORMATION(process,plant) relation
TISSUE_CULTURE_OF(process,plant) relation BIOFERTILISER(entity) relation
BIOPESTICIDE(entity)

relation BIOREMEDIATION_OF(process,contaminant) relation
BIODEGRADES(organism,compound) relation WASTEWATER_BIOTREATMENT(process)
relation BIOAUGMENTATION_OF(process,community)

———- BIOSENSORS / OMICS ———-

relation BIOSENSOR_DETECTS(sensor,analyte) relation
BIORECOGNITION_ELEMENT(sensor,element) relation
TRANSDUCER_OF(sensor,transducer) relation SENSOR_SIGNAL(sensor,signal)
relation DETECTION_LIMIT(sensor,value) relation
SENSITIVITY_OF(sensor,value) relation SELECTIVITY_OF(sensor,value)

relation GENOMIC_DATASET(dataset) relation
TRANSCRIPTOMIC_DATASET(dataset) relation PROTEOMIC_DATASET(dataset)
relation METABOLOMIC_DATASET(dataset) relation
ANALYSED_BY(dataset,method) relation ANNOTATED_AS(sequence,feature)

———- PROTEIN / ENZYME ENGINEERING ———-

relation ENGINEERED_PROTEIN(protein) relation
MUTATION_IN(protein,position,residue) relation
DIRECTED_EVOLUTION_OF(process,protein) relation
SCREENING_SELECTS(process,variant) relation
PROTEIN_ACTIVITY(protein,value) relation
PROTEIN_STABILITY(protein,value) relation
BINDING_AFFINITY(protein,target,value) relation
ENZYME_ACTIVITY(enzyme,value) relation
ENZYME_SPECIFICITY(enzyme,substrate)

———- QUALITY / VALIDATION ———-

relation QUALITY_ATTRIBUTE(product,attribute,value) relation
CRITICAL_QUALITY_ATTRIBUTE(product,attribute) relation
CRITICAL_PROCESS_PARAMETER(process,parameter) relation
IN_PROCESS_CONTROL(process,test) relation RELEASE_TEST(product,test)
relation BATCH_MEETS_SPECIFICATION(batch,specification) relation
VALIDATED_PROCESS(process) relation VALIDATION_RUN(process,run) relation
REPRODUCIBLE_UNDER(process,conditions) relation
DEVIATION_IN(process,event)

———- BIOSAFETY ———-

relation CONTAMINANT_IN(sample,contaminant) relation
STERILITY_TEST_OF(product,test) relation BIOBURDEN_OF(sample,value)
relation ENDOTOXIN_LEVEL(product,value) relation
CONTAINMENT_LEVEL(process,level) relation
BIOSAFETY_MEASURE(process,measure)

———- MEASUREMENT / 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: MOLECULAR_ASSAY SEQUENCING GENOME_EDIT_VALIDATION
EXPRESSION_ASSAY CELL_CULTURE FERMENTATION_RUN BIOREACTOR_RUN
PURIFICATION_RUN ANALYTICAL_ASSAY PROTEIN_ASSAY BIOSENSOR_TEST
OMICS_ANALYSIS PROCESS_VALIDATION QUALITY_CONTROL SCALE_UP_STUDY
PILOT_STUDY 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 ———-

SEMANTIC_EQUIVALENCE: “biotechnology” ~= “application of biological
systems organisms or components to develop useful processes and
products” “genetic engineering” ~= “direct modification of genetic
material” “recombinant DNA” ~= “DNA assembled from sequences originating
from different sources” “genome editing” ~= “targeted alteration of
genomic sequence” “synthetic biology” ~= “engineering of biological
systems using designed components and circuits” “bioprocessing” ~= “use
of biological systems in controlled production processes” “fermentation”
~= “microbial or cellular conversion process under controlled
conditions” “upstream processing” ~= “biological production stages
before product recovery” “downstream processing” ~= “recovery
purification and formulation stages” “biopharmaceutical” ~= “therapeutic
product produced using biological systems” “biocatalysis” ~= “use of
enzymes or biological catalysts for chemical transformation” “biosensor”
~= “analytical device combining biological recognition with signal
transduction” “scale-up” ~= “translation of a process to a larger
operating scale”

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

———- QUERIES ———-

query BIOTECHNOLOGY_PROFILE(x): RETURN: entity_type(x)
engineering_method(x) host_system(x) construct(x) bioprocess(x)
product(x) analytical_methods(x) quality_attributes(x) evidence(x)
confidence(x)

query GENETIC_ENGINEERING_PROFILE(p): RETURN: target(p)
engineering_method(p) vector_or_editor(p) construct(p) intended_edit(p)
observed_edit(p) off_target_events(p) validation(p)

query BIOPROCESS_PROFILE(p): RETURN: host(p) reactor(p)
fermentation_mode(p) operating_conditions(p) biomass(p)
product_concentration(p) yield(p) upstream_steps(p) downstream_steps(p)
scale(p) quality_controls(p)

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

———- CONSISTENCY / UPDATE ———-

constraint EVIDENCE_REQUIRED: FORALL biotechnology_assertion: REQUIRE
SUPPORTED_BY(biotechnology_assertion,Evidence) OR
MARK_AS_HYPOTHESIS(biotechnology_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_result(r) THEN
PRESERVE_PROCESS_SCALE(r)

UPDATE_MODEL: on_new_biotechnology_record(r):
identify_biological_system(r) identify_engineering_or_process_context(r)
preserve_measurement_and_scale_context(r) attach_evidence(r)
recalculate_confidence(r)

on_new_genetic_engineering_record(g): identify_target_and_method(g)
preserve_construct_or_editor(g)
distinguish_intended_from_observed_edit(g)
preserve_off_target_context(g) attach_evidence(g)

on_new_bioprocess_record(p): identify_host_and_product(p)
preserve_reactor_scale_and_mode(p) preserve_operating_conditions(p)
update_yield_and_productivity(p) attach_evidence(p)

on_conflicting_biotechnology_evidence(a,b): preserve(a) preserve(b)
compare_host_systems(a,b) compare_process_scales(a,b)
compare_methods(a,b) compare_measurement_units(a,b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_biotechnology_entity
preserve: - biological_system - genetic_engineering_method -
recombinant_construct - genome_editing_context -
synthetic_biology_context - cell_engineering - microbial_host -
fermentation_mode - bioreactor - upstream_processing -
downstream_processing - process_scale - biopharmaceutical_product -
industrial_biotechnology - agricultural_biotechnology -
environmental_biotechnology - biosensor_context -
omics_and_bioinformatics - protein_engineering - enzyme_technology -
quality_control - validation - biosafety - evidence - provenance -
confidence infer: - supported_construct_relations -
supported_process_relations - supported_product_relations -
semantic_equivalence prohibit: - intended_edit_equals_observed_edit -
scale_up_equals_identical_performance - detection_equals_function -
process_output_without_unit_context - unsupported_causal_claim -
confidence_above_evidence ambiguity: action:
preserve_multiple_biotechnology_interpretations resolution:
prefer_system_method_construct_scale_measurement_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “BiotechnologyOntology” version: “1.0” domain_path:
“AI Core > Ontologies > Biological Ontologies > Biotechnology”
canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biotechnology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - biotechnology - genetic engineering - recombinant
DNA - genome editing - synthetic biology - cell engineering - microbial
biotechnology - fermentation - bioprocess engineering - upstream
processing - downstream processing - scale-up - biopharmaceuticals -
industrial biotechnology - agricultural biotechnology - environmental
biotechnology - biosensors - omics - bioinformatics - protein
engineering - enzyme technology - quality control - process validation -
biosafety - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate BiotechnologyOntology when:
biotechnology_entities_and_systems_resolved AND
engineering_construct_and_edit_context_preserved AND
intended_and_observed_outcomes_distinguished AND
bioprocess_scale_and_operating_context_preserved AND
product_quality_and_validation_context_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_biotechnology_ambiguity_marked

end flow