UniChem: a unified chemical structure cross-referencing and identifier tracking system

By Jon Chambers, M. Davies, Anna Gaulton, Anne Hersey, S. Velankar, R. Petryszak, Janna Hastings, L. Bellis, S. McGlinchey, John P. Overington. 2013

172 citations recorded by the source corpus.

UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources. In the past, the creation and maintenance of such links at EMBL-EBI, where several chemistry-based resources exist, has required independent efforts by each of the separate teams. These efforts were complicated by the different data models, release schedules, and differing business rules for compound normalization and identifier nomenclature that exist across the organization. UniChem, a large-scale, non-redundant database of Standard InChIs with pointers between these structures and chemical identifiers from all the separate chemistry resources, was developed as a means of efficiently sharing the maintenance overhead of creating these links. Thus, for each source represented in UniChem, all links to and from all other sources are automatically calculated and immediately available for all to use. Updated mappings are immediately available upon loading of new data releases from the sources. Web services in UniChem provide users with a single simple automatable mechanism for maintaining all links from their resource to all other sources represented in UniChem. In addition, functionality to track changes in identifier usage allows users to monitor which identifiers are current, and which are obsolete. Lastly, UniChem has been deliberately designed to allow additional resources to be included with minimal effort. Indeed, the recent inclusion of data sources external to EMBL-EBI has provided a simple means of providing users with an even wider selection of resources with which to link to, all at no extra cost, while at the same time providing a simple mechanism for external resources to link to all EMBL-EBI chemistry resources.

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

The ChEMBL bioactivity database: an update (2013, positive): “For compounds, these are now provided by the UniChem service (33), whereas for protein targets cross-references are derived either from UniProt (34) or through manual annotation.”
Systematic integration of biomedical knowledge prioritizes drugs for repurposing (2017, methodology): “UniChem’s ( Chambers et al., 2013 ) Connectivity Search ( Chambers et al., 2014 ) was used to map compounds, which maps by atomic connectivity (based on First InChIKey Hash Blocks ( Heller et al., 2013 )) and ignores small molecular differences.”
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology (2015, background): “These include: (cid:2) Matching proteins in UniProt (16,17), BindingMOAD and DrugBank (18) (cid:2) Matching compounds in ChEMBL, PubChem and UniChem (19), as well as in the ZINC (20) database of commercially available compounds (cid:2) Antibodies against protein targets, in AntibodyPedia (www.antibo”
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers (2014, methodology): “These two changes; the addition of one table, and one field to an existing table, as shown in Figure 1, were the only changes required to implement Connectivity Search in the previously defined UniChem schema [1].”
The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods (2023, methodology): “The detailed nature of these curation processes means that the drug and clinical candidate data is updated approximately every other ChEMBL release with the next drug and clinical candidate data update planned for ChEMBL 34.”
PDBe: improved findability of macromolecular structure data in the PDB (2019, methodology): “◦ CCD mmCIF files with additional cross-references, mapped through the UniChem pipeline (38), to ChEMBL, DrugBank, KEGG, ChEBI, ZINC, Pubchem, NMRShiftDB, BindingDb, MetaboLights, BRENDA and Rhea.”
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources (2022, methodology): “This approach allows for searching ligands using information from different sources of information, such as ligand names, database identifiers matched via UniChem (20), ligand InChIKeys (calculated with RDKit, http://www.rdkit. org), CAS numbers via the Entrez E-utilities (21), UniProt accession num”
InChI, the IUPAC International Chemical Identifier (2015, background): “Of course, for specific targeted databases a lookup service may be added by developers/maintainers (as is implemented, e.g., in the UniChem [31] database Web services [32]).”