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Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY

preprint
submitted on 02.05.2018 and posted on 03.05.2018 by Christopher Southan, Joanna L Sharman, Elena Faccenda, Adam J Pawson, Simon D Harding, Jamie A Davies
Connecting chemistry to pharmacology (c2p) has been an objective of GtoPdb and its precursor IUPHAR-DB since 2003. This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical structures, their locations within the documents and the protein targets in the assays (D-A-R-C-P). A wide range of challenges associated with this are described in this perspective, using illustrative examples from GtoPdb entries. Our selection process begins with judgements of pharmacological relevance and scientific quality. Even though we have a stringent focus for our small-data extraction we note that assessing the quality of papers has become more difficult over the last 15 years. We discuss ambiguity issues with the resolution of authors’ descriptions of A-R-C-P entities to standardised identifiers. We also describe developments that have made this somewhat easier over the same period both in the publication ecosystem as well as enhancements of our internal processes over recent years. This perspective concludes with a look at challenges for the future including the wider capture of mechanistic nuances and possible impacts of text mining on automated entity extraction

Funding

Wellcome Trust 108420/Z/15/Z

History

Email Address of Submitting Author

cdsouthan@hotmail.com

Institution

University of Edinburgh

Country

UK

ORCID For Submitting Author

0000-0001-9580-0446

Declaration of Conflict of Interest

No conflict of interest

Exports