AOP Wiki Data Model with EMOD
A LinkML schema for the AOP-Wiki data model, extended with the EMOD (Evidence Model) concepts of Assays, Observations, Evidence, and Biological Target Families. It serves two purposes: validating content already curated in the AOP-Wiki, and providing a structure for Adverse Outcome Pathways derived by automated approaches, including analysis of multimodal data and text mining. Both purposes depend on being able to tell what evidence supports from what has been inferred, so the classes and slots are defined to keep an observation, the method that produced it, and the mechanism inferred from it distinct from one another.
URI: http://example.org/aopwiki-emod
Name: aopwiki-emod
Classes
| Class | Description |
|---|---|
| Aop | An AOP describes a sequence of events commencing with initial interaction(s) ... |
| AopToEvent | |
| AopToKeRelationship | |
| AopToLifeStage | |
| AopToPrototypicalStressor | |
| AopToSex | |
| AopToTaxon | |
| Assay | A defined experimental method for measuring a biological change, structured s... |
| AssignedLicense | |
| BiologicalAction | |
| BiologicalObject | |
| BiologicalProcess | |
| BioTargetFamily | |
| CellTerm | |
| Citation | |
| ConfidenceLevel | |
| Directness | |
| Event | An Event is a measurable biological change at a defined level of biological o... |
| EventComponent | One component of an Event: a combination of a biological action with a biolog... |
| EventToLifeStage | |
| EventToSex | |
| EventToTaxon | |
| Evidence | |
| ExperimentSetup | |
| ExperimentType | |
| Handbook | |
| HarmonizedAop | |
| HarmonizedEvent | A record that tracks the provenance of a harmonized Key Event back to the Key... |
| KeRelationship | A scientifically-based relationship that connects one key event to another, d... |
| KeRelationshipToLifeStage | |
| KeRelationshipToSex | |
| KeRelationshipToTaxon | |
| LevelOfBiologicalOrganization | The scale of biological organisation at which a Key Event occurs, from molecu... |
| License | |
| LifeStageTerm | A term stating the life stage of the organisms to which a biological observat... |
| Observation | |
| OecdStatus | |
| OrganTerm | |
| SexTerm | A term stating the sex of the organisms to which a biological observation or ... |
| Stressor | An external or internal factor that induces a perturbation to a biological sy... |
| TaxonTerm | A taxon used to state the organisms to which a biological observation, method... |
| TestGuideline | A standardized test method published by a regulatory or intergovernmental bod... |
| User |
Slots
Enumerations
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 |
|---|---|