Fig. 1

Components of the GVto3D portal. The Tools Registry contains a searchable description and metadata for tools, resources, and reference data sets for third-party variant effect prediction and annotation services. Standardized application programming interfaces (APIs) provide interoperability for data input and output of these third-party tools. Custom adapters can provide limited interoperability for tools that cannot adopt the API. A mapping service provides bidirectional mappings from reference genome coordinates to UniProt protein positions and to Protein Data Bank (PDB) residue positions. The tools can use the mapping service to accept variant positions in any of the three coordinate systems. A beacon system enables queries about variant positions where three-dimensional (3D) structural information and annotation are available