Human Microbiome Ontology

flow “HumanMicrobiomeOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > HUMAN BIOLOGY > HUMAN MICROBIOME 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/human-biology/human-microbiome-ontology.html”

type Human type Microbiome type MicrobialCommunity type Microorganism
type Taxon type BodySite type Sample type Metabolite type Gene type
Observation type Evidence type Source

———- MICROBIOME IDENTITY ———-

relation INSTANCE_OF(entity,type) relation
HAS_MICROBIOME(human,microbiome) relation
MICROBIOME_AT(microbiome,body_site) relation
COMMUNITY_OF(community,microbiome) relation
COMMUNITY_CONTAINS(community,taxon) relation COLONISES(taxon,body_site)
relation DETECTED_IN(taxon,sample)

enum HumanMicrobiomeSite: ORAL NASAL RESPIRATORY SKIN GASTRIC
SMALL_INTESTINE COLON FECAL UROGENITAL VAGINAL URINARY OCULAR

relation HAS_BODY_SITE_TYPE(site,type) relation SAMPLE_FROM(sample,site)
relation SITE_OF_HOST(site,human)

enum MicrobialGroup: BACTERIA ARCHAEA FUNGI VIRUSES BACTERIOPHAGES
PROTISTS

relation HAS_MICROBIAL_GROUP(entity,group) relation
MEMBER_OF_TAXON(entity,taxon)

———- COMMUNITY COMPOSITION ———-

relation RELATIVE_ABUNDANCE(community,taxon,value) relation
ABSOLUTE_ABUNDANCE(community,taxon,value) relation
MICROBIAL_LOAD(sample,value) relation
PREVALENCE_IN(taxon,population,value) relation
CORE_MEMBER_OF(taxon,community) relation
TRANSIENT_MEMBER_OF(taxon,community)

constraint RELATIVE_ABUNDANCE_BOUNDS: IF RELATIVE_ABUNDANCE(c,t,v) THEN
REQUIRE(0.0 <= v <= 1.0)

———- DIVERSITY ———-

relation ALPHA_DIVERSITY(community,metric,value) relation
BETA_DIVERSITY(community_a,community_b,metric,value) relation
SPECIES_RICHNESS(community,value) relation EVENNESS(community,value)
relation PHYLOGENETIC_DIVERSITY(community,value) relation
FUNCTIONAL_DIVERSITY(community,value)

———- COLONISATION / HOST INTERACTION ———-

relation COLONISATION_EVENT(taxon,site,event) relation
COLONISATION_RESISTANCE(community,value) relation
PERSISTENCE_OF(taxon,site,duration) relation ESTABLISHES_IN(taxon,site)

enum HostMicrobeInteraction: COMMENSAL MUTUALISTIC OPPORTUNISTIC
PATHOGENIC UNKNOWN

relation INTERACTS_WITH_HOST(taxon,human,type) relation
ADHERES_TO(taxon,tissue) relation MODULATES_HOST_PROCESS(taxon,process)
relation HOST_RESPONSE_TO(human,taxon,response)

constraint PRESENCE_NOT_PATHOGENICITY: IF DETECTED_IN(taxon,sample) THEN
DO_NOT_INFER(INTERACTS_WITH_HOST(taxon,human,PATHOGENIC))

———- MICROBIAL INTERACTIONS ———-

relation COMPETES_WITH(a,b) relation COOPERATES_WITH(a,b) relation
INHIBITS(a,b) relation FACILITATES(a,b) relation
CROSS_FEEDS(a,b,metabolite) relation PHAGE_INFECTS(phage,host)

———- METABOLISM ———-

relation PRODUCES(taxon,metabolite) relation CONSUMES(taxon,metabolite)
relation TRANSFORMS(taxon,substrate,product) relation
FERMENTS(taxon,substrate) relation HAS_METABOLIC_PATHWAY(taxon,pathway)
relation COMMUNITY_METABOLIC_CAPACITY(community,pathway,value)

enum MicrobialMetaboliteClass: SHORT_CHAIN_FATTY_ACID
BILE_ACID_DERIVATIVE AMINO_ACID_METABOLITE VITAMIN GAS ORGANIC_ACID
LIPID_DERIVATIVE

relation HAS_METABOLITE_CLASS(metabolite,class) relation
MICROBIAL_METABOLITE_REACHES(metabolite,host_compartment) relation
MICROBIOME_ASSOCIATED_WITH(microbiome,host_trait)

constraint ASSOCIATION_NOT_CAUSATION: IF MICROBIOME_ASSOCIATED_WITH(m,t)
THEN DO_NOT_INFER(CAUSES(m,t)) WITHOUT causal_evidence

———- IMMUNE RELATIONS ———-

relation IMMUNE_SYSTEM_RECOGNISES(host,microbial_feature) relation
MICROBE_STIMULATES(taxon,immune_process) relation
MICROBE_SUPPRESSES(taxon,immune_process) relation
BARRIER_INTERACTION(taxon,epithelium) relation
IMMUNE_TOLERANCE_TO(host,taxon)

———- MICROBIAL GENETICS / RESISTOME ———-

relation HAS_GENE(taxon,gene) relation COMMUNITY_GENE(community,gene)
relation GENE_ENCODES(gene,function) relation
HAS_RESISTANCE_GENE(taxon,gene) relation
HAS_VIRULENCE_FACTOR(taxon,factor)

enum HorizontalTransferMechanism: CONJUGATION TRANSFORMATION
TRANSDUCTION

relation HORIZONTAL_GENE_TRANSFER(event,donor,recipient) relation
TRANSFER_MECHANISM(event,mechanism) relation TRANSFERS_GENE(event,gene)
relation RESISTOME_OF(resistome,community) relation
RESISTOME_CONTAINS(resistome,gene)

———- VIROME / MYCOBIOME ———-

relation VIROME_OF(virome,microbiome) relation PHAGE_HOST(phage,taxon)
relation LYTIC_CYCLE(phage,host) relation LYSOGENIC_CYCLE(phage,host)
relation MYCOBIOME_OF(mycobiome,microbiome) relation
FUNGAL_MEMBER_OF(fungus,community)

———- DYSBIOSIS ———-

relation COMMUNITY_STATE(community,state) relation
DYSBIOSIS_STATE(community,state) relation COMMUNITY_SHIFT(from,to,event)
relation LOSS_OF_DIVERSITY(community,value) relation
BLOOM_OF_TAXON(community,taxon,value)

constraint DYSBIOSIS_REQUIRES_REFERENCE: IF DYSBIOSIS_STATE(c,s) THEN
REQUIRE(reference_state(c)) OR MARK_REFERENCE_UNSPECIFIED(c)

———- TRANSMISSION / DEVELOPMENT ———-

relation TRANSMITTED_FROM_TO(taxon,source,recipient) relation
VERTICAL_TRANSMISSION(taxon,parent,offspring) relation
HORIZONTAL_TRANSMISSION(taxon,source,recipient) relation
ENVIRONMENTAL_ACQUISITION(taxon,environment,host) relation
MICROBIOME_DEVELOPS_OVER(microbiome,period) relation
EARLY_LIFE_COLONISATION(host,event) relation
MATURATION_OF_MICROBIOME(host,period) relation
AGEING_ASSOCIATED_SHIFT(host,change)

———- EXPOSURES / TEMPORAL DYNAMICS ———-

relation DIET_ASSOCIATED_WITH(diet,community,change) relation
ENVIRONMENT_ASSOCIATED_WITH(environment,community,change) relation
MEDICATION_ASSOCIATED_WITH(medication,community,change) relation
SAMPLED_AT(sample,time) relation COMMUNITY_AT_TIME(community,time,state)
relation TEMPORAL_STABILITY(community,value) relation
TEMPORAL_VARIABILITY(community,value) relation
RECOVERS_AFTER(community,disturbance)

———- SAMPLING / METHODS ———-

enum SampleType: STOOL SALIVA ORAL_SWAB NASAL_SWAB SKIN_SWAB SPUTUM
BRONCHOALVEOLAR_LAVAGE INTESTINAL_BIOPSY VAGINAL_SWAB URINE
TISSUE_BIOPSY

relation HAS_SAMPLE_TYPE(sample,type) relation
SAMPLE_FROM_HOST(sample,human) relation
SAMPLE_COLLECTION_METHOD(sample,method) relation
SAMPLE_STORAGE(sample,condition) relation
SAMPLE_PROCESSING(sample,method)

enum MicrobiomeMethod: CULTURE MICROSCOPY QPCR SIXTEEN_S_RRNA_SEQUENCING
ITS_SEQUENCING SHOTGUN_METAGENOMICS METATRANSCRIPTOMICS METAPROTEOMICS
METABOLOMICS LONG_READ_SEQUENCING

relation ANALYSED_BY(sample,method) relation
DETECTION_LIMIT(method,value) relation TAXONOMIC_RESOLUTION(method,rank)
relation FUNCTIONAL_RESOLUTION(method,value)

———- CONTAMINATION / BIAS ———-

relation CONTAMINANT_IN(sample,taxon) relation
EXTRACTION_BIAS(method,taxon,value) relation
AMPLIFICATION_BIAS(method,taxon,value) relation
BATCH_EFFECT(dataset,batch,value) relation
NEGATIVE_CONTROL_FOR(control,batch)

constraint DETECTION_NOT_TRUE_COLONISATION: IF DETECTED_IN(t,s) THEN
DO_NOT_INFER(ESTABLISHES_IN(t,site)) WITHOUT colonisation_evidence

constraint RELATIVE_ABUNDANCE_NOT_ABSOLUTE_LOAD: IF
RELATIVE_ABUNDANCE(c,t,v) THEN DO_NOT_INFER(ABSOLUTE_ABUNDANCE(c,t,v))

———- EVIDENCE ———-

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

enum EvidenceType: CULTURE MICROSCOPY QPCR AMPLICON_SEQUENCING
SHOTGUN_METAGENOMICS METATRANSCRIPTOMICS METAPROTEOMICS METABOLOMICS
ISOLATE_GENOMICS FUNCTIONAL_ASSAY GNOTOBIOTIC_MODEL LONGITUDINAL_STUDY
COHORT_STUDY CASE_CONTROL_STUDY INTERVENTION_STUDY META_ANALYSIS
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: “human microbiome” ~= “microbial communities and
their genetic material associated with the human body” “microbiota” ~=
“community of microorganisms in a defined habitat” “gut microbiome” ~=
“microbiome of the gastrointestinal tract” “oral microbiome” ~=
“microbiome of the oral cavity” “skin microbiome” ~= “microbiome of the
skin” “virome” ~= “viral component of a microbiome” “mycobiome” ~=
“fungal component of a microbiome” “resistome” ~= “collection of
antimicrobial resistance genes” “dysbiosis” ~= “microbial community
state altered relative to a specified reference” “alpha diversity” ~=
“within-sample microbial diversity” “beta diversity” ~= “between-sample
microbial community difference” “metagenomics” ~= “sequencing and
analysis of community genetic material” “colonisation resistance” ~=
“community-mediated resistance to incoming microorganisms”

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

———- QUERY MODEL ———-

query HUMAN_MICROBIOME_PROFILE(m): RETURN: host(m) body_site(m)
microbial_groups(m) community_composition(m) diversity(m)
functional_capacity(m) metabolites(m) host_interactions(m)
temporal_dynamics(m) sampling_method(m) analytical_method(m) evidence(m)
confidence(m)

query TAXON_PROFILE(t): RETURN: taxonomy(t) body_sites(t) abundance(t)
prevalence(t) metabolic_functions(t) host_interactions(t)
microbial_interactions(t) genes(t) evidence(t)

query SAMPLE_PROFILE(s): RETURN: host(s) body_site(s) sample_type(s)
collection_method(s) storage(s) processing(s) analytical_methods(s)
controls(s)

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 BODY_SITE_CONTEXT_REQUIRED: IF microbiome_assertion(a) THEN
PRESERVE_BODY_SITE(a)

constraint SAMPLE_METHOD_CONTEXT_REQUIRED: IF microbiome_measurement(m)
THEN PRESERVE_SAMPLE_AND_ANALYTICAL_METHOD(m)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_microbiome_record(r):
identify_host_and_body_site(r) identify_sample(r)
preserve_collection_processing_and_method(r) attach_evidence(r)
recalculate_confidence(r)

on_new_taxon_detection(d): identify_taxon(d) identify_sample_and_site(d)
preserve_detection_method(d) distinguish_detection_from_colonisation(d)
attach_evidence(d)

on_new_community_profile(c): preserve_abundance_measure_type(c)
calculate_or_attach_diversity(c) preserve_reference_state(c)
attach_method_context(c)

on_new_host_association(a):
identify_microbiome_feature_and_host_trait(a)
preserve_population_and_body_site(a)
distinguish_association_from_causality(a) attach_evidence(a)

on_conflicting_microbiome_results(a,b): preserve(a) preserve(b)
compare_body_sites(a,b) compare_sample_types(a,b)
compare_processing(a,b) compare_analytical_methods(a,b)
compare_populations(a,b) flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_human_microbiome_entity
preserve: - host_identity - body_site - microbial_taxonomy -
microbial_group - community_composition - relative_abundance -
absolute_abundance - diversity - colonisation_status -
host_microbe_interaction - microbial_interaction - metabolic_function -
metabolites - immune_relations - microbial_genetics - resistome -
virome - mycobiome - dysbiosis_reference - transmission -
developmental_context - temporal_dynamics - sample_type -
sampling_method - analytical_method - contamination_controls -
evidence - provenance - confidence infer: -
supported_taxonomic_relations - supported_metabolic_relations -
supported_transmission_relations - semantic_equivalence prohibit: -
microbial_detection_equals_colonisation -
microbial_presence_equals_pathogenicity -
relative_abundance_equals_absolute_load - association_equals_causation -
dysbiosis_without_reference_state - method_free_microbiome_comparison -
confidence_above_evidence ambiguity: action:
preserve_multiple_microbiome_interpretations resolution:
prefer_body_site_sample_method_population_time_and_evidence
missing_data: action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “HumanMicrobiomeOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies > Human
Biology > Human Microbiome Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/human-biology/human-microbiome-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - human microbiome - body-site microbiomes - bacteria -
archaea - fungi - viruses - bacteriophages - community composition -
microbial abundance - microbial diversity - colonisation - host-microbe
interactions - microbial interactions - microbial metabolism - immune
relations - microbial genetics - horizontal gene transfer - resistome -
virome - mycobiome - dysbiosis - transmission - microbiome development -
temporal dynamics - sampling - sequencing and multi-omics -
contamination and bias - evidence deterministic_normalisation: true
provenance_required: true confidence_required: true

terminate HumanMicrobiomeOntology when:
host_body_site_and_microbiome_identity_resolved AND
microbial_taxonomy_and_community_composition_normalised AND
abundance_measure_types_preserved AND
detection_colonisation_and_pathogenicity_distinguished AND
association_and_causality_distinguished AND
sampling_method_and_contamination_context_preserved AND
evidence_links_preserved AND confidence_values_validated AND
unresolved_microbiome_ambiguity_marked

end flow