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Supplementary data for our submission "Interpretable Ontology Extension in Chemistry". We present an approach towards ontology extension that uses structural information to train a transformer-based model that predicts new subsumption relations. The ELECTRA model has been pre-trained using a combination of molecules from the ChEBI ontology and a selection of molecules from the PubChem database (chebai/data/SWJpre/raw/smiles.txt). The resulting model has then been fine-truned on a selection of ChEBI classes. The trained model has then been applied to a set of previously unseen chemicals from PubChem (hazardous.txt). The resulting predictions have been used to extend the ChEBI ontology. The extended ontology can be found as an owl file in 'chebi-slim-extended.owl.gz' and as a plot in 'classif-hazardous.png'. The resulting ontology was inconsistent because some of the predicted subsumption relations violated disjointness axioms. Those subsumption relations have been removed ('chebi-slim-extended-fixed.owl.gz'). The README.md file describes how to reproduce our results.

We reviewed the current state of the art of availability and requirements for nanomaterial databases, through reviewing the literature, online resources, engaging in discussions with the NanoSafety Cluster working groups and using the results of a community-based requirement analysis. The eNanoMapper data architecture was developed and consists of a set of web services, providing access to experimental protocols and data, search service and modules, facilitating linking and data transfer between third party databases. This design is expected to facilitate adding new services of any kind, for example supporting different data types and data analysis. The technical solution is able to support the required data types, queries, and annotations, and can enable user friendly applications. The resulting eNanoMapper data access architecture was developed based on the OpenTox framework and Application Programming Interfaces and extensions to them. An eNanoMapper prototype supporting the inclusion of data and protocols was developed and deployed, based on a number of public datasets relevant to Nano Safety.

The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort is developing and disseminating a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as relevant experimental paradigms, biological interactions and safety information. This deliverable report describes the initial release of the ontology, including the content and organization, and the technical and curatorial processes that have been followed to create it.

The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort will develop and disseminate a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as relevant experimental paradigms, biological interactions and safety information. This deliverable report describes the primary content areas within the nanomaterial safety domain which need to be covered by the ontology and comprehensively surveys pre-existing ontology and vocabulary efforts for coverage of those content areas. Gaps and challenging content areas are identified.

The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort will develop and disseminate a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as relevant experimental paradigms, biological interactions and safety information. This deliverable report describes the technical infrastructure that has been created in order to support the development, versioning and dissemination of the ontology. The technical infrastructure also supports the process of the re-use of existing ontologies, as the eNanoMapper objective is to fully harness pre-existing efforts thus avoiding unnecessary and divisive re-implementation. At the same time, re-use poses challenges, thus, our technical infrastructure has been created such as to support modular incorporation of external content from multiple sources while removing duplication and contradictions that can arise from integration. We have implemented an infrastructure for extensive unit and integration testing to ensure that changes in underlying source ontologies do not break the coherence of our offering. All of these aspects are described in this report.