Clade Ontology

flow “CladeOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > EVOLUTIONARY BIOLOGY > CLADE 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/evolutionary-biology/clade-ontology.html”

type Taxon type Species type Lineage type Ancestor type Descendant type
Clade type CrownGroup type StemGroup type TotalGroup type Phylogeny type
Node type Branch type Character type Synapomorphy type Fossil type
Observation type Evidence type Source

———- CLADE IDENTITY ———-

relation INSTANCE_OF(entity,type) relation CLADE_CONTAINS(clade,taxon)
relation MEMBER_OF_CLADE(taxon,clade) relation
CLADE_ROOTED_AT(clade,node) relation CLADE_IN_PHYLOGENY(clade,phylogeny)
relation HAS_COMMON_ANCESTOR(clade,ancestor)

rule CLADE_MEMBERSHIP_INVERSE(c,t): IF CLADE_CONTAINS(c,t) THEN
MEMBER_OF_CLADE(t,c)

———- MONOPHYLY ———-

relation MONOPHYLETIC(clade) relation INCLUDES_ANCESTOR(clade,ancestor)
relation INCLUDES_ALL_DESCENDANTS(clade,ancestor) relation
DESCENDED_FROM(descendant,ancestor) relation
ANCESTOR_OF(ancestor,descendant)

rule DESCENT_INVERSE(a,b): IF DESCENDED_FROM(a,b) THEN ANCESTOR_OF(b,a)

rule MONOPHYLY_RULE(c,a): IF INCLUDES_ANCESTOR(c,a) AND
INCLUDES_ALL_DESCENDANTS(c,a) THEN MONOPHYLETIC(c)

———- NON-CLADE GROUPINGS ———-

relation PARAPHYLETIC(group) relation POLYPHYLETIC(group) relation
EXCLUDES_DESCENDANT(group,taxon) relation
COMBINES_SEPARATE_LINEAGES(group,lineages)

constraint CLADE_IS_MONOPHYLETIC: IF INSTANCE_OF(c,Clade) THEN
REQUIRE(MONOPHYLETIC(c)) OR MARK_CLADE_STATUS_UNRESOLVED(c)

———- NESTED CLADES ———-

relation SUBCLADE_OF(child,parent) relation SUPERCLADE_OF(parent,child)
relation NESTED_WITHIN(child,parent)

rule SUBCLADE_INVERSE(a,b): IF SUBCLADE_OF(a,b) THEN SUPERCLADE_OF(b,a)

rule SUBCLADE_TRANSITIVITY(a,b,c): IF SUBCLADE_OF(a,b) AND
SUBCLADE_OF(b,c) THEN SUBCLADE_OF(a,c)

———- SISTER CLADES ———-

relation SISTER_CLADE_OF(a,b) relation
SHARES_IMMEDIATE_ANCESTOR(a,b,node)

rule SISTER_CLADE_SYMMETRY(a,b): IF SISTER_CLADE_OF(a,b) THEN
SISTER_CLADE_OF(b,a)

———- COMMON ANCESTRY ———-

relation MOST_RECENT_COMMON_ANCESTOR(a,b,ancestor) relation
SHARES_ANCESTOR_WITH(a,b) relation ORIGINATES_AT_NODE(clade,node)

rule SHARED_ANCESTRY(a,b,c): IF DESCENDED_FROM(a,c) AND
DESCENDED_FROM(b,c) THEN SHARES_ANCESTOR_WITH(a,b)

———- SYNAPOMORPHIES ———-

relation HAS_CHARACTER(taxon,character) relation
SYNAPOMORPHY_OF(character,clade) relation
SUPPORTS_CLADE(character,clade) relation
DERIVED_CHARACTER_STATE(character,state) relation
ANCESTRAL_CHARACTER_STATE(character,state) relation
HOMOPLASY_OF(character,taxa)

rule SYNAPOMORPHY_SUPPORT(ch,c): IF SYNAPOMORPHY_OF(ch,c) THEN
SUPPORTS_CLADE(ch,c)

———- CROWN / STEM / TOTAL GROUPS ———-

relation CROWN_GROUP_OF(crown,clade) relation STEM_GROUP_OF(stem,clade)
relation TOTAL_GROUP_OF(total,clade) relation
EXTANT_MEMBER_OF(taxon,crown) relation
EXTINCT_STEM_MEMBER_OF(taxon,stem)

rule CROWN_GROUP_CONTEXT(c,clade): IF CROWN_GROUP_OF(c,clade) THEN
INSTANCE_OF(c,CrownGroup)

rule STEM_GROUP_CONTEXT(s,clade): IF STEM_GROUP_OF(s,clade) THEN
INSTANCE_OF(s,StemGroup)

———- NODE / BRANCH STRUCTURE ———-

relation HAS_NODE(clade,node) relation HAS_BRANCH(clade,branch) relation
BRANCHES_FROM(lineage,node) relation NODE_AGE(node,time) relation
BRANCH_LENGTH(branch,value)

———- DIVERGENCE ———-

relation DIVERGES_FROM(a,b) relation DIVERGENCE_TIME(a,b,time) relation
DIVERSIFICATION_RATE(clade,rate) relation SPECIATION_RATE(clade,rate)
relation EXTINCTION_RATE(clade,rate)

———- TAXONOMIC RELATION ———-

relation REPRESENTED_BY_TAXON(clade,taxon) relation
TAXON_CORRESPONDS_TO_CLADE(taxon,clade) relation TAXON_RANK(taxon,rank)

constraint TAXON_NOT_ALWAYS_CLADE: IF INSTANCE_OF(t,Taxon) THEN
DO_NOT_INFER(TAXON_CORRESPONDS_TO_CLADE(t,c)) WITHOUT monophyly_evidence

———- FOSSIL MEMBERS ———-

relation FOSSIL_OF(fossil,taxon) relation
INCLUDED_IN_CLADE(fossil,clade) relation DATED_TO(fossil,time) relation
PRESERVES_CHARACTER(fossil,character) relation
STEM_MEMBER_OF(fossil,clade) relation CROWN_MEMBER_OF(fossil,clade)

———- CLADE AGE ———-

relation CLADE_ORIGIN_TIME(clade,time) relation CROWN_AGE(clade,time)
relation STEM_AGE(clade,time) relation CALIBRATED_BY(clade,evidence)

———- CLADE SUPPORT ———-

relation SUPPORT_VALUE(clade,value) relation
BOOTSTRAP_SUPPORT(clade,value) relation
POSTERIOR_PROBABILITY(clade,value) relation
JACKKNIFE_SUPPORT(clade,value)

constraint POSTERIOR_BOUNDS: IF POSTERIOR_PROBABILITY(c,p) THEN
REQUIRE(0.0 <= p <= 1.0)

———- CLADE COMPARISON ———-

relation OVERLAPS_WITH(clade_a,clade_b) relation
DISJOINT_FROM(clade_a,clade_b) relation SHARES_MEMBERS_WITH(a,b,members)
relation TOPOLOGICALLY_CONFLICTS_WITH(a,b)

———- BIOGEOGRAPHY ———-

relation DISTRIBUTED_IN(clade,region) relation
ANCESTRAL_RANGE(clade,region) relation DISPERSAL_EVENT(clade,region)
relation VICARIANCE_EVENT(clade,region_a,region_b) relation
ENDEMIC_TO(clade,region)

———- TRAIT EVOLUTION ———-

relation TRAIT_ORIGINATES_IN(trait,clade) relation
TRAIT_LOST_IN(trait,clade) relation TRAIT_DIVERSIFIES_IN(trait,clade)
relation CHARACTER_EVOLVES_ON(character,branch)

———- EXTINCTION ———-

relation CLADE_EXTINCT(clade) relation EXTINCTION_TIME(clade,time)
relation SURVIVING_MEMBER_OF(taxon,clade) relation
EXTINCTION_EVENT_AFFECTS(event,clade)

———- OBSERVATION / EVIDENCE ———-

relation OBSERVES(observation,entity) relation
SUPPORTED_BY(assertion,evidence) relation DERIVED_FROM(evidence,source)
relation HAS_CONFIDENCE(assertion,score) relation
OBSERVED_AT(observation,location) relation
OBSERVED_ON(observation,datetime)

enum EvidenceType: MOLECULAR_PHYLOGENY MORPHOLOGICAL_PHYLOGENY GENOMIC
FOSSIL DEVELOPMENTAL BIOGEOGRAPHIC SYNAPOMORPHY BOOTSTRAP
POSTERIOR_SUPPORT COMPARATIVE 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: “clade” ~= “monophyletic group” “monophyly” ~=
“common ancestor plus all descendants” “subclade” ~= “nested clade”
“sister clades” ~= “clades sharing an immediate common ancestor”
“synapomorphy” ~= “shared derived character” “crown group” ~= “most
recent common ancestor of living members and all descendants” “stem
group” ~= “extinct lineages closer to a crown group than to its living
sister group” “total group” ~= “crown group plus its stem lineage”
“MRCA” ~= “most recent common ancestor” “clade support” ~= “phylogenetic
support for a clade” “crown age” ~= “age of crown-group common ancestor”

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

———- QUERY MODEL ———-

query CLADE_PROFILE(c): RETURN: root_node(c) common_ancestor(c)
members(c) subclades(c) sister_clades(c) synapomorphies(c)
crown_group(c) stem_group(c) origin_time(c) support(c) evidence(c)
confidence(c)

query CLADE_MEMBERSHIP(t): RETURN: clades_containing(t)
immediate_clade(t) nested_superclades(t) crown_or_stem_status(t)

query COMPARE_CLADES(a,b): RETURN: shared_ancestor(a,b)
shared_members(a,b) sister_relationship(a,b) nesting_relationship(a,b)
topology_conflict(a,b)

query CLADE_SUPPORT_PROFILE(c): RETURN: synapomorphies(c)
molecular_support(c) morphological_support(c) fossil_support(c)
bootstrap(c) posterior_probability(c)

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

———- CONSISTENCY ———-

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

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

constraint SISTER_NOT_ANCESTOR: IF SISTER_CLADE_OF(a,b) THEN
DO_NOT_INFER(DESCENDED_FROM(a,b)) AND DO_NOT_INFER(DESCENDED_FROM(b,a))

constraint NESTING_ACYCLIC: IF SUBCLADE_OF(a,b) THEN NOT
SUBCLADE_OF(b,a)

constraint SUPPORT_NOT_CERTAINTY: IF SUPPORT_VALUE(c,value) THEN
PRESERVE_SUPPORT_AS_STATISTICAL_EVIDENCE(c,value)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_clade(c): identify_root_node(c)
identify_common_ancestor(c) identify_members(c) validate_monophyly(c)
attach_synapomorphies(c) preserve_provenance(c)

on_new_phylogeny(p): update_clade_membership(p) update_sister_clades(p)
update_nested_clades(p) preserve_support_values(p)

on_new_fossil(f): validate_taxonomic_assignment(f) preserve_age(f)
preserve_character_data(f) evaluate_stem_or_crown_membership(f)

on_clade_revision(old,new): preserve(old) link_revision(old,new)
compare_membership(old,new) compare_topology(old,new)
update_current_hypothesis(new)

on_conflicting_clades(a,b): preserve(a) preserve(b)
compare_datasets(a,b) compare_methods(a,b) compare_synapomorphies(a,b)
compare_support_values(a,b) flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_clade preserve: -
clade_identity - root_node - common_ancestor - membership - monophyly -
nested_clades - sister_clades - synapomorphies - crown_group -
stem_group - total_group - divergence_time - support_values -
fossil_membership - evidence - provenance - confidence infer: -
valid_membership_inverse - valid_nested_clade_relations -
supported_common_ancestry - semantic_equivalence prohibit: -
taxon_equals_clade_without_monophyly_evidence -
sister_clade_equals_ancestor - cyclic_clade_nesting -
support_equals_absolute_certainty - unsupported_clade_membership -
confidence_above_evidence ambiguity: action:
preserve_multiple_clade_hypotheses resolution:
prefer_phylogenetic_data_synapomorphies_and_support missing_data:
action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “CladeOntology” version: “1.0” domain_path: “AI
Core > Ontologies > Biological Ontologies > Evolutionary Biology > Clade
Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/evolutionary-biology/clade-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - clades - monophyly - common ancestry - clade
membership - nested clades - sister clades - synapomorphies - crown
groups - stem groups - total groups - nodes and branches - divergence -
fossil membership - clade age - phylogenetic support - biogeography -
trait evolution - extinction - evidence deterministic_normalisation:
true provenance_required: true confidence_required: true

terminate CladeOntology when: clade_identity_resolved AND
common_ancestor_resolved AND monophyly_status_preserved AND
membership_and_nesting_normalised AND support_and_uncertainty_preserved
AND evidence_links_preserved AND confidence_values_validated AND
unresolved_clade_hypotheses_marked

end flow