Navigating between publications and databases for drug discovery: IUPHAR/BPS Guide to PHARMACOLOGY initiatives

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IUPHAR Database Meeting

Navigating between publications and databases for drug discovery: IUPHAR/BPS Guide to PHARMACOLOGY initiatives Dr Joanna Sharman20th April 2015 BPS Focused Meeting: Exploiting the new pharmacology and application to drug discovery 1www.guidetopharmacology.orgContents of talk:Linking between pharmacology publications and databasesExamples of automated approachesLinking BJP publications to GtoPdbExample tables of links: IUPHAR endothelin reviewUpdating the instructions to authors: adding links during article submissionRetrospective and independent linkingDatabase to document linksAcknowledgements

1Linking between pharmacology publications and databasesMaking navigation between publications and databases more seamless offers major advantages in drug discovery informatics and pharmacologyOne option is live linking where entities within the text of a manuscript connect directly via a URL to an extrinsic database recordThese can be either manually curated or use automated text-mining approachesRecently 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

2Examples of automated approaches

Example of automatic entity mark-up in EPMCFalse negativesFalse positivesUnspecific terms

Example of automatic chemical name > structure recognition using

3Linking BJP publications to GtoPdbSince 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.orgPilot phase begun in second half of 2014 to add ToLs to all BJP articles as post-acceptance stepExpert manually curated links ensure relevance and accuracyFrom 2014 - issue 17 - to date, links added to 290 articles

4In the pilot phase ToLs were constructed by the BJP Press Editors.4Example ToLs: IUPHAR endothelin review

Maguire JJ, Davenport AP. (2014) Endothelin@25 new agonists, antagonists, inhibitors and emerging research frontiers: IUPHAR Review 12. Br J Pharmacol. 171: 555572.

5Updating the instructions to authors: adding links during article submissionIn coming months ToLs will be extended to all BJP authors at article submission stageNew guidelines for authors are being developed explaining how to search GtoPdb and add linksAuthors will be asked to submit new targets and ligands not covered to the database team for consideration driving database content creationAuthors will be asked to provide as much information as possible, including protein accessions for targets and SDF, SMILES, InChI or PubChem CIDs for ligands


Retrospective and independent linkingIUPHAR nomenclature reviews in Pharmacological Reviews currently have no link mark-upMany describe targets and ligands in GtoPdb, such as a recent IUPHAR review on allosterismExperiment: can we retrospectively link the entities in the article to the database?Result: blog post listing the links @ Link between article and blog post using PubMed Commons


Database to document linksGtoPdb has introduced compound name document ID bindingE.g. compound 3a [PMID: 12238936]; example 373 [WO2012093101]

8Also applies to patents e.g. Example 7 [US8664233]8Conclusions/future objectivesManually curated links from articles to relevant database entries have high utility for pharmacologistsTables of links highlight key ligands and targets in studyOther journals would also benefit from links to target/ligand pages in GtoPdbPilot adding links from IUPHAR Pharmacological Reviews articlesAlso explore in-line links from entities within article text to GtoPdb9AcknowledgementsIan McGrath, Editor-in-Chief, British Journal of PharmacologyBJP Press Editors and journal staffThe late Prof Tony Harmar, founder and original PI of GtoPdbGtoPdb 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 contributorsAll current and past NC-IUPHAR and GtoPdb sponsorsIUPHAR/BPS Guide to PHARMACOLOGY funders:



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