www.guidetopharmacology.org
Navigating between publications and
databases for drug discovery: IUPHAR/BPS
Guide to PHARMACOLOGY initiatives
Dr Joanna Sharman
20th April 2015
BPS Focused Meeting: Exploiting the new pharmacology and application to drug discovery
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Linking between pharmacology publications
and databases• Making navigation between publications
and databases more seamless offers
major advantages in drug discovery
informatics and pharmacology
• One option is “live linking” where
entities within the text of a manuscript
connect directly via a URL to an
extrinsic database record
• These can be either manually curated
or use automated text-mining
approaches
• Recently added to PubMed Central and
Europe PubMed Central, where protein
or chemical names or IDs linked to
entities in the NCBI databases for the
former and EBI in the latter
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Examples of automated approachesExample of automatic entity mark-up in
EPMC
False negatives
False positives
Unspecific terms
Example of automatic chemical name >
structure recognition using chemicalize.org
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Linking BJP publications to GtoPdb
• Since 2012, all IUPHAR reviews include manually curated
tables of links (ToLs)
• ToLs give the nomenclature of key target proteins and ligands
described in the paper and link to corresponding database
pages on GuidetoPharmacology.org
• Pilot phase begun in second half of 2014 to add ToLs to all BJP
articles as post-acceptance step
• Expert manually curated links ensure relevance and accuracy
• From 2014 - issue 17 - to date, links added to 290 articles
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Example ToLs: IUPHAR endothelin reviewMaguire JJ, Davenport AP. (2014) Endothelin@25 – new agonists, antagonists, inhibitors and emerging research frontiers:
IUPHAR Review 12. Br J Pharmacol. 171: 5555–72.
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Updating the instructions to authors:
adding links during article submission
• In coming months ToLs will be extended to all BJP authors at article
submission stage
• New guidelines for authors are being developed explaining how to
search GtoPdb and add links
• Authors will be asked to submit new targets and ligands not covered to
the database team for consideration – driving database content creation
• Authors will be asked to provide as much information as possible,
including protein accessions for targets and SDF, SMILES, InChI or
PubChem CIDs for ligands
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Retrospective and independent linking
• IUPHAR nomenclature reviews in Pharmacological Reviews currently
have no link mark-up
• Many describe targets and ligands in GtoPdb, such as a recent IUPHAR
review on allosterism
• Experiment: can we retrospectively link the entities in the article to the
database?
• Result: blog post listing the links @ http://tinyurl.com/allostery
• Link between article and blog post using PubMed Commons
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Database to document links
• GtoPdb has introduced compound name <> document ID binding
• E.g. compound 3a [PMID: 12238936]; example 373 [WO2012093101]
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Conclusions/future objectives
• Manually curated links from articles to relevant database
entries have high utility for pharmacologists
• Tables of links highlight key ligands and targets in study
• Other journals would also benefit from links to
target/ligand pages in GtoPdb
• Pilot adding links from IUPHAR Pharmacological Reviews
articles
• Also explore in-line links from entities within article text to
GtoPdb
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Acknowledgements
• Ian McGrath, Editor-in-Chief, British Journal of Pharmacology
• BJP Press Editors and journal staff
• The late Prof Tony Harmar, founder and original PI of GtoPdb
• GtoPdb database team:
• Jamie Davies (Principal Investigator)
• Adam Pawson, Helen Benson, Elena Faccenda and Christopher Southan (Curators)
• Veronika Divincova (Project Administrator)
• Past and present members of NC-IUPHAR and its subcommittees, especially
Michael Spedding, Steve Alexander, Bill Catterall, Anthony Davenport, Colin
Dollery, Doriano Fabbro, Rick Neubig and John Peters
• All Guide to PHARMACOLOGY contributors
• All current and past NC-IUPHAR and GtoPdb sponsors
• IUPHAR/BPS Guide to PHARMACOLOGY funders:
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