Hot topics: Identifiers for the 21st century

While identifiers are not a traditional “hot topic” in pharmacology the subject is becoming increasingly important. One of the reasons is that for mechanistic pharmacology the community needs to define (and communicate) identifiers for the key entities of model organism species and strains, proteins, protein complexes, genes, sequences, sequence variants, as well as the explicit molecular structures of chemicals, peptides and therapeutic biologicals (including antibodies) used for experimentation. Indeed one of the roles of IUPHAR (as NC-IUPHAR) is to review and recommend protein target nomenclature, in collaboration with the Human Gene Nomenclature Committee (HGNC) [1]. The paper featured here is a technical review [2] of identifier qualities and best practices that facilitate large-scale data integration. It also goes into problems related to persistence and web-accessibility/resolvability. As a database provider, the relevance of this article for GtoPdb is clear (since we are largely about identifiers and their relationships). We are carefully considering its implications and possible consequent changes in our practice. The GtoPdb team has already engaged with this theme some time ago in a blog post [3] that provided an introduction to resolving bioactive ligands and their protein targets from the literature to standardised molecular identifiers.

Comments by Chris Southan (@cdsouthan).

[1] International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification http://www.guidetopharmacology.org/nciuphar.jsp

[2] McMurray et al. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol. 29;15(6). [PMID:28662064].

[3] A Pharmacologists’ Guide to Resolving Chemical Structures and their Protein Targets from the Literature https://blog.guidetopharmacology.org/2014/11/11/a-pharmacologists-guide-to-entity-resolution/