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zebrafish-toxicology-atlas-schema

Schema to represent metadatcha associated with the Zebrafish Toxicology Atlas

URI: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema

Name: zebrafish-toxicology-atlas-schema

Classes

Class Description
Entity The base class for all entities in the Zebrafish Toxicology Atlas Schema
        ChemicalEntity The chemical used as the stressor chemical in an exposure event
        Control A subject serves as a reference for assessing phenotypic outcome in the pheno...
        ControlImage An image associated with a control, taken at the same developmental stage as ...
        Experiment A group of observations (phenotypic outcomes and their control) that are link...
        ExposureEvent An occurrence in a study where a subject is exposed to a stressor under defin...
        Fish Zebrafish used as subject in the study
        Image An image associated with a phenotype observation
        Phenotype Any measurable or visible trait change in the subject as a result of exposure
        PhenotypeObservationSet An observation set containing control and phenotypic outcome resulting from a...
        Regimen The schedule and pattern of an exposure event
        StressorChemical A chemical, that elicit a response (a phenotype) in a subject when when encou...
        Study A toxicological investigation, including the experimental conditions and phen...
QuantityValue A value of an attribute that is quantitative and measurable, expressed as a c...

Slots

Slot Description
additional_exposure_condition Additional information about the conditions under which exposure event occurr...
annotator ORCID identifier of the indidvidual submitting the study data
cas_id CAS identifier for the chemical
chebi_id CHEBI identifier for the chemical
chemical_id Chemical identifier (CHEBI, CAS, or UUID)
chemical_name Name of the chemical
comment Additional comments
concentration The dose or concentration of the chemical to which the subject was exposed to
control An observation that serves as the reference for assessing phenotypic outcome
control_id Identifier for the control, used to link control images to specific controls
control_image Image associated with this control
control_type Type of control (e
experiment The experiment in a study
exposure_end_stage The developmental stage of fish when exposure ended
exposure_event The exposure event in an experiment
exposure_regimen_type The type of exposure regimen (e
exposure_start_stage The developmental stage of fish when exposure started
exposure_type An instance of exposure specifying the type of stressor a subject was exposed...
fish The fish subject of the experiment
id
image Images associated with this observation
individual_exposure_duration Individual exposure duration
interval_between_individual_exposures Interval between individual exposures
lab ZFIN lab identifier of the laboratory that produced the study data
magnification The factor by which a microscope enlarges the apparent size of a subject comp...
manufacturer The manufacturer of the chemical
name Name or label of an entity
number_of_individual_exposure Total number of individual exposures
numeric_value The numeric value of the quantity value
phenotype The phenotype observed
phenotype_comments Comments about the phenotype in the control image
phenotype_id Foreign key reference to the PhenotypeObservationSet uuid (for database repre...
phenotype_observation The phenotype observation resulting from an exposure event
phenotype_term_id The phenotype ontology term identifier
prevalence The percentage of subject exhibiting this phenotype
publication The publication identifier (e
rearing_condition_comment Comments on rearing conditions, for example, about how conditions deviated fr...
regimen The regimen for the exposure
resolution The level of detail in the image
route The route of exposure
scale_bar Scale bar information, including the physical length it represents and the un...
severity The intensity of the observed phenotype
stage The developmental stage of fish when the phenotype was observed
standard_rearing_condition An indication of whether the subject was maintained under standard conditions...
stressor Substance, chemical or toxicant that elicits a response (a phenotype) in a su...
synonym Other names for the chemical
total_exposure_duration Time between first and last individual exposure
unit The unit of the quantity value
uuid UUID identifier
vehicle The substance or medium used to deliver a stressor
vehicle_if_treated The vehicle used in a control

Enumerations

Enumeration Description
ExposureRegimenTypeEnum An enumeration of exposure regimen types
ExposureRouteEnum An enumeration of exposure routes derived from the EXO ontology
ExposureTypeEnum An enumeration of exposure types derived from the ECTO ontology
SeverityEnum An enumeration of severity levels for phenotypes
VehicleEnumeration An enumeration of vehicles used in exposures

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