Proteoglycan Ontology

FLOW ALGEBRA
Proteoglycan Ontology | Kireth Semantic Library
Version: 4.0
Authors: Mark Anthony Higgins — Sky (Recursive AI)
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/macromolecular-entities/proteoglycan-ontology.html
Scope: Biological Entities > Macromolecular Entities > Proteoglycan
Status: Formal semantic model; illustrative inference rules, not laboratory evidence.

1. ONTOLOGY DECLARATION
ontology ProteoglycanOntology {
  domain: MolecularBiology | Glycobiology | ExtracellularMatrix
  primary_entity: Proteoglycan
  parent_entity: Glycoconjugate
  related_entity: Glycoprotein
  semantics: typed_relations + constrained_inference + provenance
}

2. TYPED ENTITIES
entity Proteoglycan <: Glycoconjugate {
  core_protein: Protein
  glycosaminoglycan_chains: Set<Glycosaminoglycan>
  attachment_sites: Set<AminoAcidResidue>
  cellular_location: Optional<Location>
  biological_roles: Set<BiologicalFunction>
}
entity Glycosaminoglycan {
  repeating_disaccharide_units: Sequence<Disaccharide>
  sulphation_pattern: Optional<Pattern>
  polymer_length: Optional<Integer>
}
entity CoreProtein <: Protein
entity LinkerRegion <: CarbohydrateStructure
entity ExtracellularMatrix <: BiologicalStructure
entity CellSurface <: BiologicalLocation
entity Enzyme <: Protein
entity BiosyntheticEvent <: BiologicalProcess
entity DegradationEvent <: BiologicalProcess
entity Evidence { source: String; method: String; date: Optional<Date> }

3. CLASSIFICATION
class SmallLeucineRichProteoglycan <: Proteoglycan
class Lectican <: Proteoglycan
class BasementMembraneProteoglycan <: Proteoglycan
class CellSurfaceProteoglycan <: Proteoglycan
class HeparanSulphateProteoglycan <: Proteoglycan
class ChondroitinSulphateProteoglycan <: Proteoglycan
class DermatanSulphateProteoglycan <: Proteoglycan
class KeratanSulphateProteoglycan <: Proteoglycan
example Decorin : SmallLeucineRichProteoglycan
example Biglycan : SmallLeucineRichProteoglycan
example Aggrecan : Lectican
example Versican : Lectican
example Perlecan : BasementMembraneProteoglycan
example Syndecan : CellSurfaceProteoglycan
example Glypican : CellSurfaceProteoglycan
NOTE: These classes overlap: location, family and GAG composition are separate axes.
NOTE: Hyaluronan is generally not covalently attached to a core protein;
      it can form noncovalent aggregates with proteoglycans such as aggrecan.

4. TYPED RELATIONSHIPS
relation HAS_CORE_PROTEIN(Proteoglycan, Protein)
relation HAS_GAG_CHAIN(Proteoglycan, Glycosaminoglycan)
relation COVALENTLY_ATTACHED_TO(Glycosaminoglycan, Protein)
relation HAS_LINKER(Glycosaminoglycan, LinkerRegion)
relation LOCATED_IN(Proteoglycan, BiologicalLocation)
relation BINDS(Proteoglycan, MolecularEntity)
relation PARTICIPATES_IN(Proteoglycan, BiologicalProcess)
relation MODULATES(Proteoglycan, BiologicalProcess)
relation SYNTHESISED_BY(BiologicalEntity, BiologicalProcess)
relation DEGRADED_BY(BiologicalEntity, BiologicalProcess)
relation SUPPORTED_BY(Assertion, Evidence)
relation DERIVED_FROM(Assertion, Assertion)

5. STRUCTURAL RULES
rule PG_CORE:
  Proteoglycan(p) -> exists c:Protein, HAS_CORE_PROTEIN(p,c)
rule PG_GAG:
  Proteoglycan(p) -> exists g:Glycosaminoglycan, HAS_GAG_CHAIN(p,g)
rule GAG_ATTACHMENT:
  HAS_GAG_CHAIN(p,g) -> COVALENTLY_ATTACHED_TO(g,core_protein(p))
rule GAG_CHAIN_CARDINALITY:
  Proteoglycan(p) -> count(g | HAS_GAG_CHAIN(p,g)) >= 1
constraint CoreProteinIsProtein:
  HAS_CORE_PROTEIN(p,c) -> Protein(c)
constraint GAGIsGlycosaminoglycan:
  HAS_GAG_CHAIN(p,g) -> Glycosaminoglycan(g)
NOTE: Glycosylation alone does not establish proteoglycan identity;
      the attached carbohydrate must include qualifying GAG chain(s).

6. BIOSYNTHESIS AND MODIFICATION
process CoreProteinTranslation:
  inputs: mRNA, ribosome, amino_acids
  outputs: core_protein
process GAGChainInitiation:
  inputs: core_protein, activated_sugar_donors, relevant_enzymes
  outputs: initiated_glycan_linker
process GAGPolymerisation:
  inputs: initiated_glycan_linker, nucleotide_sugars, glycosyltransferases
  outputs: elongated_GAG_chain
process GAGModification:
  inputs: GAG_chain, modification_enzymes, cofactors
  outputs: modified_GAG_chain
process ProteoglycanAssembly:
  inputs: core_protein, GAG_chains
  outputs: mature_or_maturing_proteoglycan
rule BIOSYNTHESIS_DEPENDENCY:
  GAGPolymerisation(e) -> requires(e, initiated_glycan_linker)
rule MODIFICATION_CONTEXT:
  GAGModification(e) -> context_dependent(e, cell_type, enzyme_expression)
NOTE: Biosynthetic details vary by GAG family; keratan sulphate differs
      from the canonical xylose-based linker used by several other GAGs.

7. BIOLOGICAL FUNCTIONS
function MatrixHydration
function MechanicalResistance
function GrowthFactorPresentation
function CellAdhesionRegulation
function ReceptorCoSignalling
function MatrixOrganisation
function FiltrationBarrierSupport
rule MATRIX_ROLE:
  LOCATED_IN(p,ExtracellularMatrix) AND HAS_GAG_CHAIN(p,g)
  -> candidate_role(p,MatrixHydration)
rule CELL_SURFACE_ROLE:
  LOCATED_IN(p,CellSurface)
  -> candidate_role(p,ReceptorCoSignalling)
rule CONTEXTUAL_FUNCTION:
  candidate_role(p,f) AND evidence_supports(p,f)
  -> PARTICIPATES_IN(p,f)
NOTE: Candidate roles are hypotheses until context-specific evidence exists.

8. DEGRADATION AND TURNOVER
process Proteolysis:
  target: core_protein
  agent: protease
process GAGDepolymerisation:
  target: GAG_chain
  agent: relevant_glycosidase_or_lyase
process LysosomalCatabolism:
  target: internalised_proteoglycan_components
  context: lysosome
rule TURNOVER:
  degradation_event(d,p) AND validated(d)
  -> DEGRADED_BY(p,d)

9. SEMANTIC_EQUIVALENCE
SEMANTIC_EQUIVALENCE("proteoglycan", "protein bearing glycosaminoglycan chains")
SEMANTIC_EQUIVALENCE("GAG", "glycosaminoglycan")
SEMANTIC_EQUIVALENCE("heparan sulfate", "heparan sulphate")
SEMANTIC_EQUIVALENCE("chondroitin sulfate", "chondroitin sulphate")
SEMANTIC_DIFFERENCE("proteoglycan", "glycoprotein"):
  Proteoglycan requires one or more GAG chains;
  glycoprotein is a broader term for proteins bearing glycans.
SEMANTIC_DIFFERENCE("proteoglycan", "hyaluronan"):
  Hyaluronan is a GAG but not itself a core-protein-linked proteoglycan.

10. INFERENCE AND RECURSIVE REASONING
rule CLASSIFY_PROTEOGLYCAN:
  Protein(c) AND Glycosaminoglycan(g)
  AND COVALENTLY_ATTACHED_TO(g,c)
  AND verified_identity(c,g)
  -> infer ProteoglycanComplex(c,g)
rule RECURSIVE_COMPONENT_TRAVERSAL:
  HAS_COMPONENT(x,y) AND HAS_COMPONENT(y,z)
  -> INDIRECT_COMPONENT(x,z)
rule PROVENANCE_PROPAGATION:
  DERIVED_FROM(a,b) AND SUPPORTED_BY(b,e)
  -> INHERITED_EVIDENCE(a,e)
constraint RECURSION_SAFETY:
  traversal_uses_visited_set = true
  maximum_depth = configured_limit
  cycles_do_not_create_new_facts = true

11. CONFIDENCE
CONFIDENCE {
  score_range: [0.0,1.0]
  dimensions: [source_reliability, method_quality, biological_context,
               replication, directness]
  direct_observation: prefer_to_inference
  missing_evidence: do_not_assume_true
  conflict_resolution: preserve_competing_claims_and_provenance
}
rule CONFIDENCE_PROPAGATION:
  inferred_claim(a, premises)
  -> confidence(a) <= min(confidence(each premise))
NOTE: Confidence values require calibrated evidence; no numerical values
      are assigned merely from the existence of an ontology rule.

12. FLOW_HASH
FLOW_HASH {
  canonicalisation: UTF-8 + LF + stable_field_order
  hash_algorithm: SHA-256
  input: canonical_ontology_content_excluding_hash_field
  output: lowercase_hex_digest
  recompute_on_semantic_change: true
}
NOTE: No digest is asserted until the canonical serialisation is hashed.

13. UPDATE_MODEL
UPDATE_MODEL {
  change_types: [add_entity, revise_relation, revise_rule,
                 add_evidence, deprecate_assertion, correct_definition]
  require: provenance + timestamp + version_increment
  preserve_prior_versions: true
  invalidate_affected_inferences: true
  rerun_type_validation: true
  recompute_flow_hash: true
}

14. AI_CONSUMPTION
AI_CONSUMPTION {
  parse_mode: typed_semantic_graph
  interpret_rules_as: declarative_constraints_and_inference_templates
  entity_resolution: canonical_name_plus_aliases
  distinguish: [observed_fact, inferred_claim, illustrative_example]
  output_requirements: [claim, provenance, confidence, ontology_version]
  forbid: [invented_experimental_results, unsupported_causal_claims]
  query_examples: [
    "Which proteoglycans contain heparan sulphate?",
    "How does aggrecan contribute to cartilage matrix properties?",
    "Which GAG attachment claims have direct evidence?"
  ]
}

15. VALIDATION
assert every Proteoglycan has a typed core protein and at least one GAG chain
assert each HAS_GAG_CHAIN target is a Glycosaminoglycan
assert inferred classifications retain supporting evidence
assert structural classes may overlap without contradiction
assert semantic aliases do not collapse biologically distinct entities
assert recursive traversal terminates on cyclic graphs
assert no inferred claim is represented as a direct measurement

END FLOW ALGEBRA