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Linking GtoP <> PubChem <> PubMed


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Presentation for the IUPHAR/BPS/GtoPdb meeting, 18-19 May 2018, Edinburgh, UK

Published in: Science
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Linking GtoP <> PubChem <> PubMed

  1. 1. LinkingGtoP<> PubChem<> PubMed from BPS and other journals:thepowerof dot-joining 1 This presentation (IUPHAR/BPS/GtoPdb meeting, 18-19 May 2018, Edinburgh) covers two main themes • GtoP out-links from BPS journals • GtoP submissions of ligands and references to PubChem and the reciprocal linking between these and PubMed
  2. 2. The Holy Heptet 2
  3. 3. Glossary • GtoP = IUPHAR/BPS Guide to PHARMACOLOGY database • BPS = British Pharmacological Society • BJP = British Journal of Pharmacology • BCCP = British Journal of Clinical Pharmacology • PM = PubMed • PC = PubChem • SID = PubChem substance identifier • CID = PubChem compound identifier • ToLs = Tables of links • Reference citations = added to every paper with GtoP links • Link = a live URL taking users to another database 3
  4. 4. Theme 1 Links from BJP and BJCP out to GtoP 4
  5. 5. Methodology: using NAR reference citation counts 5 • As explained in the link below, the NAR reference citations are included in every paper with outlinks • This means they give a direct count of those papers that have outlinks (see next slides)
  6. 6. The BJP-to- GtoP initiative 6 • The first BJP table of links appeared in Apr 2014 • Since then 1146 BJP papers have links (80%)
  7. 7. From tables to in-line out-links 7 • Transition from Tables of Links to in-line links circa 2017 • ToLs were added by Copy Editors but links now author-specified
  8. 8. BJCP links initiated Nov 2017 8 The total of 284 represents circa 50% of BJCP papers published since linking started
  9. 9. Solving the “missing links” problem • For occasional BJP papers we noted that key ligands and targets that the reports were “about” where not in GtoP (e.g. new ones in primary publications) • In relevant cases we curated those papers but could not add new out-links retrospectively • We recently instigated a process whereby if their key entities are not in GtoP authors notify us and send accepted manuscripts • If within our capture remit we add these new ligands and targets • Depending on timing, we add the authors eventual PMID as a reference within one or two release cycles • The authors thus gain a GtoP reference and links (see later) 9
  10. 10. A recent example from BJCP 10
  11. 11. Theme 2 Reciprocal links between GtoP, PubChem and PubMed 11
  12. 12. Key paper on PC <> PM (wewuzcited :) 12
  13. 13. “Walking” our current GtoP <> PM links 13 • Query establishes that GtoP has 9251 ligand submissions to PC since 2008
  14. 14. GtoP SIDs <> PMIDs 14 • These include 9833 of our reference links
  15. 15. GtoP <>PC <> PM <> BJPs (379) 15
  16. 16. Journal distributions for our PM citations 16 From the 9833 total: 379 are BJP, 18 are BJCP and 10 from PR&P
  17. 17. Linked example 17
  18. 18. Reciprocal links = virtuous circles for users 18 • GtoP users can navigate “out” via PC or PM • NCBI users can navigate “in” via PC or PM
  19. 19. Interesting quirk (I): missing out-links 19 F16357 missing, but note we got the retrospective GtoP in-link
  20. 20. Interestingquirk (II): spurious PMC automated entity link 20
  21. 21. To conclude • The two BPS journals have joined a small but exclusive set of author-specified Journal-to-Database linking efforts • We have recently improved the proportion of reciprocity • There are tangible (e.g. user traffic) and intangible benifits (e.g. big data mining) • Possibility of extending to third journal in the stable Pr&P • The long-standing processes of submitting our ligands to PubChem and the references associated with them brings many important advantages to GtoP • This includes tangible benefits for all the journals and authors we add PubChem links for but need to < awareness • Various options for optimisation can be explored, including automated entity linking if specificity can be ensured 21
  22. 22. Addendum (post-meeting) • Above is intersect of BJP > GtoP and GtoP > BJP = 55 • The 379 GtoP references for ligands (slide 15) go back to 1970 (e.g. PMID: 4189829) • But note only 69 from these 379 are post -Apr 2014 (i.e. could get outlinks) • So the number of reciprocal links is actually high (55/69) • However, the caveat is that not all of the reciprocal links will refer to the same ligand (i.e. the missing link problem from slide 9) • But, via the new process, this should now reach 100% 22