Use case 3
Search and Retrieve Assay Data based on Ontological Terms


Use Case 3 Diagram


Search and Retrieve Molecular Data linked to Key Events in AOPs using assay ontology terms

Brief Description:

A user wants to look up omics data for a particular bioassay. The user supplies a particular assay type, fetches related ontological terms from an ontology service, and retrieves all available assay data associated with assay types and terms. The use case is aimed at nanomaterials, but can be extended to other chemical substances, including compounds.


A researcher with background in toxicology and assay technologies.

Basic Flow:

The user starts with a type of assay, like a genotoxicity assay. This term is looked up in an ontology service (i.e. containing the eNanoMapper ontology or the BioAssay Ontology) and the results are used to retrieve matching assays using the assay service (i.e. containing the nanosafety data repository). Using these results, the assay service is employed to retrieve data annotated with the specific ontology terms. Furthermore, the call to the ontology service may return multiple term IRIs if a full ontological hierarchy is requested. This simplifies asking all genotoxicity assay data, even if data is annotated with more specific genotoxicity assay terms.


  • The supplied assay type is a valid ontological term


Success End Condition:

  • Assay data is found for (engineered) nanomaterials

Failure End Condition:

  • No assay data for the ontological terms can be found within the system

Minimal Guarantee:

  • None

Relationship to other use cases:

Search results will allow downloading of data that may be used (after further preprocessing) as input to QSAR studies.

Alternate Flows:

  • Directly use an ontological term for searching
  • Assay type might occur in multiple ontologies, a workflow for the selection of the intended ontology might be required

Exception Flows:

Possible exceptions:

  • No matching assays are found. An empty set of results


  • Support for chemicals other than nanomaterials.
  • Search for chemicals based on KE-related genes and/or protein targets.
  • Search for chemicals based on Gene Ontology terms (instead of specific genes).
  • An AOP is given and an additional Service is used to request the assays associated or genes/targets associated with the KEs in that AOP.