The molecular entities in linked data dataset

The Molecular Entities in Linked Data (MEiLD) dataset comprises data of distinct atoms, molecules, ions, ion pairs, radicals, radical ions, and others that can be identifiable as separately distinguishable chemical entities. The dataset is provided in a JSON-LD format and was generated by the SDFEater, a tool that allows parsing atoms, bonds, and other molecule data. MEiLD contains 349,960 of ‘small’ chemical entities. Our dataset is based on the SDF files and is enriched with additional ontologies and line notation data. As a basis, the Molecular Entities in Linked Data dataset uses the Resource Description Framework (RDF) data model. Saving the data in such a model allows preserving the semantic relations, like hierarchical and associative, between them. To describe chemical molecules, vocabularies such as Chemical Vocabulary for Molecular Entities (CVME) and Simple Knowledge Organization System (SKOS) are used. The dataset can be beneficial, among others, for people concerned with research and development tools for cheminformatics and bioinformatics. In this paper, we describe various methods of access to our dataset. In addition to the MEiLD dataset, we publish the Shapes Constraint Language (SHACL) schema of our dataset and the CVME ontology. The data is available in Mendeley Data.