3. Incorporation of toxicity ontologies

The reuse and development of relevant core toxicology and neighbouring biological, chemical and medical ontologies is essential for the effective handling of data and information originating from multiple sources, for ensuring interoperability between different systems, for providing enhanced search and data mining solutions, and supporting the integration of toxicology, „-omics‟, clinical and molecular data.

The ToxBank consortium has started to create a keyword hierarchy that is used in the data warehouse (DW). In addition to its use for facilitating collaborations, the keyword hierarchy is used to support searching, browsing and linking of resources within the warehouse. When information is uploaded into the DW, terms will be selected from this hierarchy and linked to protocols and investigation datasets in the warehouse.

The information generated from the requirements gathering, along with reports and presentations generated by cluster partners was the starting point for this hierarchy. Key concepts are identified and mapped wherever possible onto terms in existing ontologies. Each concept is assigned a unique id number and organized hierarchically. The keyword hierarchy along with definitions, synonyms, links to existing ontology terms, such as ChEBI (http://www.ebi.ac.uk/chebi/), Medical Subject Headings (http://www.nlm.nih.gov/mesh/), the Gene Ontology (http://www.geneontology.org/), and so on), and related links to resources such as the compound and biomaterials wikis are represented using the SKOS format.

The current keyword hierarchy, which contains approximately 600 unique terms, is organized into six main branches:

1. Biomaterials
This branch includes both primary and undifferentiated cell lines, reagents and suppliers.

2. Investigative techniques
These are the diverse experimental techniques that are being used across the cluster including biological assays, molecular and cellular biology techniques, analysis methods, laboratory automation, analytical chemistry, materials testing, sensor development, microscopy and the different –omics approaches.

3. Data and readouts
The above mentioned investigative techniques produce many different types of data. The data types and readouts are defined in this branch including readouts from the different assay systems, dose response analysis, -omics readouts, along with any clinical or pre-clinical data from sources outside the cluster.

4. Modes-of-action (MOA)
This branch includes an organization of adverse outcomes, intermediate effects, mode of action and molecular initiating events.

5. Gold standard compounds
Each compound selected as “Gold” standard reference compounds are included in this branch of the hierarchy.
The entire keyword hierarchy is included as an appendix to the ToxBank Data Warehouse User Guide.

Any suggestion for changes to the keyword hierarchy should be directed to support@lists.toxbank.net.

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