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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