Amino Acid Ontology

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "AminoAcidOntology" v1.0

ENTITY AminoAcidOntology {
 TYPE: BiologicalOntology
 DOMAIN: Biochemistry
 SUBJECT: AminoAcid
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Amino Acid Ontology"
 PARENT_DOMAIN: "Biochemistry"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biochemistry/amino-acid-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY AminoAcid {
 IS_A: Biomolecule
 HAS: [AminoGroup, CarboxylGroup, SideChain]
 MAY_FUNCTION_AS: [ProteinMonomer, MetabolicIntermediate, BiosyntheticPrecursor]
}

ENTITY AlphaAminoAcid {
 SUBCLASS_OF: AminoAcid
 HAS_FUNCTIONAL_GROUPS_ATTACHED_TO: AlphaCarbon
}

ENTITY SideChain {
 SYMBOL: R
 DETERMINES_MANY: AminoAcidProperties
}

ENTITY ProteinogenicAminoAcid {
 SUBCLASS_OF: AminoAcid
 MAY_BE_INCORPORATED_INTO: Protein
 THROUGH: Translation
}

ENTITY StandardProteinogenicAminoAcid {
 SUBCLASS_OF: ProteinogenicAminoAcid
 MEMBER_COUNT: 20
}

ENTITY NonpolarAminoAcid { SUBCLASS_OF: AminoAcid }
ENTITY PolarUnchargedAminoAcid { SUBCLASS_OF: AminoAcid }
ENTITY AcidicAminoAcid { SUBCLASS_OF: AminoAcid }
ENTITY BasicAminoAcid { SUBCLASS_OF: AminoAcid }
ENTITY AromaticAminoAcid { SUBCLASS_OF: AminoAcid }
ENTITY SulfurContainingAminoAcid { SUBCLASS_OF: AminoAcid }

ENTITY AminoAcidStereochemistry {
 MAY_BE: [LConfiguration, DConfiguration]
}

ENTITY LAminoAcid {
 SUBCLASS_OF: AminoAcid
 HAS: LConfiguration
}

ENTITY DAminoAcid {
 SUBCLASS_OF: AminoAcid
 HAS: DConfiguration
}

ENTITY Glycine {
 SUBCLASS_OF: ProteinogenicAminoAcid
 SIDECHAIN: Hydrogen
 ACHIRAL_AT_ALPHA_CARBON: true
}

ENTITY AminoAcidIonization {
 DEPENDS_ON: [pH, pKaValues]
}

ENTITY Zwitterion {
 HAS: [PositiveCharge, NegativeCharge]
 NET_CHARGE_MAY_BE: Zero
}

ENTITY IsoelectricPoint {
 SYMBOL: pI
 DESCRIBES: pHAtWhichAverageNetChargeIsZero
}

RULE ProtonationRule {
 AminoAcidChargeState := function(pH, amino_group_pKa, carboxyl_group_pKa, ionizable_sidechain_pKa)
}

ENTITY PeptideBond {
 IS_A: CovalentBond
 CONNECTS: AminoAcidResidues
}

PROCESS PeptideBondFormation {
 JOINS: AminoAcids
 PRODUCES: PeptideOrPolypeptide
}

ENTITY AminoAcidResidue {
 DERIVED_FROM: AminoAcid
 PART_OF: PeptideOrProtein
}

ENTITY Protein {
 COMPOSED_OF: AminoAcidResidues
 HAS: AminoAcidSequence
}

ENTITY AminoAcidSequence {
 IS_ORDERED_SEQUENCE_OF: AminoAcidResidues
 DIRECTION: "N-terminus to C-terminus"
}

ENTITY Hydrophobicity {
 DEPENDS_ON: SideChain
}

ENTITY Proline {
 SUBCLASS_OF: ProteinogenicAminoAcid
 MAY_RESTRICT: BackboneConformation
}

ENTITY Cysteine {
 SUBCLASS_OF: ProteinogenicAminoAcid
 HAS: ThiolGroup
 MAY_FORM: DisulfideBond
}

ENTITY Histidine {
 SUBCLASS_OF: ProteinogenicAminoAcid
 HAS: ImidazoleSideChain
 MAY_PARTICIPATE_IN: AcidBaseCatalysis
}

ENTITY EssentialAminoAcid {
 SUBCLASS_OF: AminoAcid
 REQUIRES_DIETARY_SOURCE: organism_and_condition_dependent
}

ENTITY NonessentialAminoAcid {
 SUBCLASS_OF: AminoAcid
 MAY_BE_SYNTHESIZED_ENDOGENOUSLY: true
}

ENTITY ConditionallyEssentialAminoAcid {
 SUBCLASS_OF: AminoAcid
 MAY_REQUIRE_EXTERNAL_SOURCE: specific_physiological_context
}

PROCESS AminoAcidBiosynthesis {
 PRODUCES: AminoAcid
 FROM: MetabolicPrecursors
 MAY_REQUIRE: [Enzyme, Cofactor, Energy]
}

PROCESS AminoAcidDegradation {
 BREAKS_DOWN: AminoAcid
 MAY_INCLUDE: [Transamination, Deamination, CarbonSkeletonMetabolism]
}

PROCESS Transamination {
 TRANSFERS: AminoGroup
 BETWEEN: AminoAcidAndKetoAcid
 CATALYSED_BY: Aminotransferase
}

PROCESS Deamination {
 REMOVES: AminoGroup
 MAY_RELEASE_OR_TRANSFER: Nitrogen
}

ENTITY CarbonSkeleton {
 REMAINS_AFTER: AminoGroupRemoval
 MAY_ENTER: CentralMetabolism
}

PROCESS NitrogenDisposal {
 HANDLES: ExcessNitrogen
 MAY_INCLUDE: UreaCycle
}

ENTITY GlucogenicAminoAcid {
 SUBCLASS_OF: AminoAcid
 DEGRADATION_PRODUCTS_MAY_ENTER: GluconeogenicPathways
}

ENTITY KetogenicAminoAcid {
 SUBCLASS_OF: AminoAcid
 DEGRADATION_PRODUCTS_MAY_FORM: KetoneBodyPrecursors
}

PROCESS AminoAcidTransport {
 MOVES: AminoAcid
 ACROSS: BiologicalMembrane
}

ENTITY AminoAcidTransporter {
 IS_A: MembraneProtein
 TRANSPORTS: AminoAcid
}

ENTITY Aminoacyl_tRNA {
 COMPOSED_OF: [tRNA, CovalentlyAttachedAminoAcid]
 PARTICIPATES_IN: Translation
}

PROCESS tRNACharging {
 ATTACHES: AminoAcid
 TO: tRNA
 CATALYSED_BY: Aminoacyl_tRNA_Synthetase
}

ENTITY Aminoacyl_tRNA_Synthetase {
 IS_A: Enzyme
 RECOGNIZES: [AminoAcid, tRNA]
 CONTRIBUTES_TO: TranslationFidelity
}

PROCESS AminoAcidResidueModification {
 TARGET: AminoAcidResidue
 MAY_INCLUDE: [Phosphorylation, Hydroxylation, Methylation, Acetylation, Ubiquitination]
 MAY_CHANGE: ProteinProperties
}

ENTITY NonProteinAminoAcid {
 SUBCLASS_OF: AminoAcid
 MAY_HAVE: MetabolicOrSignallingRole
}

ENTITY AminoAcidDerivative {
 DERIVED_FROM: AminoAcid
 MAY_FUNCTION_IN: [Metabolism, Signalling, Neurotransmission, Biosynthesis]
}

PROCESS AminoAcidAnalysis {
 MAY_DETERMINE: [Identity, Concentration, Stereochemistry, ModificationState, IsotopicComposition]
 MAY_USE: [Chromatography, MassSpectrometry, Electrophoresis, Spectroscopy]
}

ENTITY Evidence {
 TYPES: [BiochemicalEvidence, StructuralEvidence, MetabolomicEvidence, ProteomicEvidence, MassSpectrometricEvidence, ChromatographicEvidence, GeneticEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
 IF IndependentEvidenceSources AGREE
 THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_assertions
  RECORD amino_acid_identity
  RECORD stereochemistry
  RECORD protonation_state
  RECORD modification_state
  RECORD biological_context
  RECORD analytical_method
  RECORD provenance
  REDUCE confidence
 }
}

RELATION AminoAcid HAS SideChain
RELATION AminoAcid MAY_FORM PeptideBond
RELATION AminoAcidResidue PART_OF Protein
RELATION AminoAcidSequence DEFINES PrimaryProteinStructure
RELATION AminoAcid MAY_BE_ATTACHED_TO tRNA
RELATION AminoAcidTransporter TRANSPORTS AminoAcid
RELATION AminoAcid MAY_HAVE AminoAcidDerivative

SEMANTIC_EQUIVALENCE {
 "amino acid" ~= "amino carboxylic acid" WHEN biochemical_context
 "amino acid residue" ~= "residue in peptide or protein" WHEN polymer_context
 "pI" ~= "isoelectric point"
 "aminoacyl-tRNA" ~= "charged tRNA"
 "R group" ~= "amino acid side chain"
}

CONFIDENCE AminoAcidAssertion {
 INPUTS: [chemical_identity_support, stereochemical_support, structural_support, biochemical_support, analytical_quality, metabolic_support, proteomic_support, replication, source_independence, semantic_consistency]
 SCORE := weighted_sum(INPUTS)
 LEVEL :=
  IF SCORE >= 0.90 THEN "very_high"
  ELSE IF SCORE >= 0.75 THEN "high"
  ELSE IF SCORE >= 0.55 THEN "moderate"
  ELSE IF SCORE >= 0.35 THEN "low"
  ELSE "uncertain"
}

RULE AminoAcidClassificationInference {
 IF amino_acid_structure IS_KNOWN
 THEN classify_by [sidechain_polarity, sidechain_charge, aromaticity, sulfur_content, stereochemistry]
}

RULE ChargeInference {
 IF pH AND relevant_pKa_values ARE_KNOWN
 THEN predominant_charge_state MAY_BE_ESTIMATED
}

RULE MetabolicInference {
 IF AminoAcid IS_SUBSTRATE_OR_PRODUCT_OF metabolic_reaction
 THEN AminoAcid PARTICIPATES_IN corresponding_pathway
}

RULE CausalityConstraint {
 IF amino_acid_concentration correlates_with biological_state
 THEN DO_NOT_INFER causal_role
 WITHOUT functional_evidence
}

QUERY AminoAcidLookup(identifier) {
 RETURN [identity, chemical_structure, sidechain, stereochemistry, charge_properties, pKa_values, isoelectric_point, biochemical_class, essentiality, metabolic_pathways, protein_roles, derivatives, evidence, confidence]
}

QUERY AminoAcidResidueLookup(protein_identifier, position) {
 RETURN [amino_acid_identity, residue_position, structural_context, conservation, modification_state, interactions, functional_annotations, variants, evidence, confidence]
}

QUERY AminoAcidMetabolismLookup(identifier) {
 RETURN [biosynthesis, degradation, transamination, nitrogen_fate, carbon_skeleton_fate, transport, enzymes, cofactors, cellular_context, evidence, confidence]
}

UPDATE_MODEL {
 ON new_amino_acid_evidence:
  validate_provenance()
  normalize_amino_acid_identifier()
  identify_organism_and_biological_context()
  capture_stereochemistry()
  capture_protonation_and_modification_state()
  map_protein_and_residue_context()
  map_biosynthetic_and_degradation_pathways()
  map_transport_and_tRNA_relationships()
  record_analytical_method()
  compare_existing_assertions()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_amino_acid_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [amino_acid_identity, sidechain_structure, stereochemistry, protonation_state, biochemical_class, protein_context, metabolic_context, modification_state, analytical_method, evidence_provenance, confidence]
 REQUIREMENTS: [distinguish_free_amino_acid_from_amino_acid_residue, preserve_stereochemistry, preserve_pH_and_protonation_context, preserve_species_context, preserve_modification_state, distinguish_essentiality_by_organism_and_condition, distinguish_structure_from_function, distinguish_concentration_from_activity, distinguish_observed_from_inferred_function, avoid_unsupported_causal_inference]
}

VALIDATE {
 REQUIRE AminoAcid
 REQUIRE AlphaAminoAcid
 REQUIRE ProteinogenicAminoAcid
 REQUIRE SideChain
 REQUIRE AminoAcidStereochemistry
 REQUIRE PeptideBond
 REQUIRE AminoAcidResidue
 REQUIRE AminoAcidBiosynthesis
 REQUIRE AminoAcidDegradation
 REQUIRE Aminoacyl_tRNA
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT AminoAcid != AminoAcidResidue
 ASSERT Glycine.ACHIRAL_AT_ALPHA_CARBON == true
 ASSERT essentiality REQUIRES organism_and_condition_context
 ASSERT concentration != causal_function
}

FLOW_HASH {
 ALGORITHM: SHA-256
 INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
 PURPOSE: integrity_and_version_tracking
}

END flow "AminoAcidOntology"