Skip to content

exposome-schema

Comprehensive exposome schema for integrating chemical exposures, environmental factors, dietary data, toxicology databases, and health outcomes with support for Adverse Outcome Pathways (AOPs) and multi-granularity measurements

URI: https://w3id.org/diatomsRcool/exposome-schema

Name: exposome-schema

Classes

Class Description
ExposomeDatabase Container for all exposome data including exposures, chemicals, health outcom...
NamedThing A generic grouping for any identifiable entity in the exposome
        AdverseOutcomePathway A sequence of causally linked events at different levels of biological organi...
        Association A relationship between two entities
                ChemicalToGeneAssociation An association between a chemical and a gene
                ExposureToPhenotypeAssociation An association between an exposure and a phenotype
                GeneticVariantToPhenotypeAssociation An association between a genetic variant and a phenotype (e
                GeneToDiseaseAssociation An association between a gene and a disease
                KeyEventRelationship A directional relationship between two key events in an AOP
        BiologicalEntity Biological entities including genes, proteins, cells, and anatomical structur...
                AnatomicalEntity An anatomical structure or system
                CellType A type of cell
                Gene A gene or genetic element
                Organism An individual organism
                Protein A protein or polypeptide
        BiologicalResponse A biological response at the molecular, cellular, or tissue level
                KeyEvent A measurable change in biological state that is a step in an Adverse Outcome ...
                MolecularInitiatingEvent The initial molecular-level perturbation that starts an Adverse Outcome Pathw...
        ChemicalEntity A chemical entity including compounds, drugs, and metabolites
        DatabaseRecord A record from an external database
                AOPWikiRecord A record from the AOP Wiki
                ChEMBLRecord A record from ChEMBL chemical database
                CompToxRecord A record from the EPA CompTox Chemicals Dashboard
                CTDRecord A record from the Comparative Toxicogenomics Database
                GeneExpressionAtlasRecord A record from the Gene Expression Atlas
                GWASRecord A record from the GWAS Catalog
                NHANESRecord A record from the National Health and Nutrition Examination Survey
                ToxCastRecord A record from the ToxCast database
                USDARecord A record from USDA Pesticide Data Program
        ExposureEvent An event in which an organism is exposed to a chemical or environmental facto...
                ChemicalExposure Exposure to a chemical substance
                DietaryExposure Exposure through dietary consumption
                EnvironmentalExposure Exposure to environmental factors
                OccupationalExposure Exposure in an occupational setting
        HealthOutcome A health-related outcome including phenotypes and diseases
                AdverseOutcome An adverse health outcome in the context of an Adverse Outcome Pathway
                Disease A disease or medical condition
                Phenotype An observable characteristic or trait
                        MammalianPhenotype A phenotype observed in mammalian model organisms
                        ZebrafishPhenotype A phenotype observed in zebrafish
        Measurement A measurement or observation
                AggregatedMeasurement An aggregated or summary measurement across a cohort or population
                BiomarkerMeasurement A measurement of a biological marker
                ExposureMeasurement A measurement of exposure to a chemical or environmental factor
                PhenotypeMeasurement A measurement of a phenotypic trait
        StudyEntity Entities related to studies, cohorts, and participants
                Cohort A group of individuals in a study
                Participant An individual participant in a study
                Study A research study or survey

Slots

Slot Description
adverse_outcome The adverse outcome of an AOP
adverse_outcome_pathways Collection of Adverse Outcome Pathways linking exposures to health outcomes
affected_anatomy Anatomical location affected
age Age in years
aopwiki_id AOP Wiki identifier
association_type Type of association
associations Collection of associations between entities
biological_action Biological action or change
biological_entities Collection of biological entities (genes, proteins, cells, anatomical structu...
biological_object Biological object involved
biological_process Biological process involved
biomarker_type Type of biomarker
cas_number CAS Registry Number
category A category or type for a thing
causes_phenotype Phenotypes caused by exposure
chebi_id ChEBI identifier
chembl_id ChEMBL compound identifier
chemical Chemical in association
chemical_entities Collection of chemical entities including compounds, drugs, and metabolites
cl_id Cell Ontology identifier
cohort The cohort for aggregated measurements
cohort_size Number of participants in cohort
cohorts Collection of study cohorts
data_source Source database or repository
database_records Collection of records from external databases
description A human-readable description for a thing
disease Disease in association
disease_category Category of disease
downstream_event Downstream key event
dtxsid EPA CompTox Dashboard identifier
effect_size Effect size of association
encoded_by_gene Gene that encodes this protein
enrollment_period Time period of enrollment
environmental_context Environmental context of exposure
evidence Evidence for association
evidence_support Evidence supporting the relationship
exposed_to_chemical The chemical entity involved in the exposure
exposure Exposure in association
exposure_concentration Concentration of exposure
exposure_duration Duration of exposure
exposure_medium Medium through which exposure occurs
exposure_route Route of exposure
exposures Collection of exposure events (chemical, dietary, environmental, occupational...
food_item Food item consumed
gene Gene in association
genetic_variant Genetic variant identifier
geographic_location Geographic location of study
has_exposure Exposures experienced by participant
health_outcomes Collection of health outcomes including phenotypes and diseases
hp_id Human Phenotype Ontology identifier
id A unique identifier for a thing
in_taxon Taxonomic group
inchi InChI chemical identifier
inclusion_criteria Criteria for cohort inclusion
interaction_type Type of interaction
key_event_relationships Relationships between key events
key_events Key events in an AOP
last_updated Date record was last updated
leads_to_molecular_event Molecular initiating event triggered by exposure
level_of_biological_organization Level of biological organization
measured_entity The entity being measured
measured_in_study Study in which measurement was made
measurement_date Date of measurement
measurement_method Method used for measurement
measurement_unit Unit of measurement
measurement_value Numeric measurement value
measurements Collection of measurements and observations
molecular_formula Molecular formula
molecular_initiating_event The molecular initiating event of an AOP
mondo_id MONDO disease identifier
mp_id Mammalian Phenotype Ontology identifier
name A human-readable name for a thing
ncbigene_id NCBI Gene identifier
occupation Occupation related to exposure
occurs_in_anatomy Anatomical location where event occurs
occurs_in_cell_type Cell type where event occurs
onset_age Age of onset
outcome_level Level of biological organization
p_value Statistical p-value
part_of_cohort Cohort that this participant is part of
part_of_study Study that this cohort is part of
participant The participant being measured
participant_id Participant identifier
participants Collection of study participants
phenotype The phenotype being measured
phenotype_category Category of phenotype
population Study population description
principal_investigator Principal investigator name
pubchem_cid PubChem Compound identifier
publications Related publications
record_url URL to database record
relationship_type Type of relationship
sample_size Number of samples
sample_type Type of biological sample
serving_size Serving size
severity Severity of phenotype or disease
sex Biological sex
smiles SMILES chemical structure
source_database Name of source database
source_database_record Link to original database record
species Species name
statistic_value Value of the summary statistic
stratification Stratification variables
stressors Chemical stressors that trigger the AOP
studies Collection of research studies and surveys
study_type Type of study
summary_statistic Type of summary statistic
survey_cycle NHANES survey cycle
symbol Gene symbol
taxon_id NCBI Taxonomy identifier
triggers_key_event Key events triggered
uberon_id UBERON anatomical identifier
upheno_id Unified phenotype ontology identifier
upstream_event Upstream key event
variable_name Variable name in database
workplace Workplace where exposure occurs
xref External database cross-references
zp_id Zebrafish Phenotype Ontology identifier

Enumerations

Enumeration Description
BiologicalOrganizationLevelEnum Levels of biological organization
DataSourceEnum Data sources and repositories
ExposureMediumEnum Medium through which exposure occurs
ExposureRouteEnum Routes of exposure to chemicals or environmental factors
SampleTypeEnum Types of biological samples
SexEnum Biological sex
StudyTypeEnum Types of research studies
SummaryStatisticEnum Types of summary statistics

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description