This document discusses the linking between the Guide to Pharmacology (GtoP) database and other databases including PubChem and PubMed. It covers two main themes: 1) Out-links from British Pharmacology Society journals to GtoP and 2) Submissions of ligands and references from GtoP to PubChem and reciprocal linking between these databases and PubMed. Over 1,100 papers from the British Journal of Pharmacology and 284 papers from the British Journal of Clinical Pharmacology have been linked to GtoP. Reciprocal linking between the databases provides benefits for users by allowing navigation between the resources.

1. LinkingGtoP<> PubChem<> PubMed
from BPS and other journals:thepowerof dot-joining
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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. The Holy Heptet
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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
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4. Theme 1
Links from BJP and BJCP out to GtoP
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5. Methodology:
using NAR reference citation counts
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https://blog.guidetopharmacology.org/2017/02/03/reference-citations-in-bjp/
• 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. The BJP-to-
GtoP
initiative
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• The first BJP
table of links
appeared in
Apr 2014
• Since then 1146
BJP papers
have links (80%)

7. From tables to in-line out-links
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• Transition from Tables of Links to in-line links circa 2017
• ToLs were added by Copy Editors but links now author-specified

8. BJCP links initiated Nov 2017
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The total of 284 represents circa 50% of BJCP papers published since linking
started

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)
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10. A recent example from BJCP
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11. Theme 2
Reciprocal links between GtoP,
PubChem and PubMed
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12. Key paper on PC <> PM (wewuzcited :)
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13. “Walking” our current GtoP <> PM links
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• Query establishes that GtoP has 9251
ligand submissions to PC since 2008

14. GtoP SIDs <> PMIDs
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• These include 9833 of
our reference links

15. GtoP <>PC <> PM <> BJPs (379)
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16. Journal distributions for our PM citations
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From the 9833 total: 379 are BJP, 18 are BJCP and 10 from
PR&P

17. Linked example
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18. Reciprocal links = virtuous circles for users
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• GtoP users can navigate “out” via PC or PM
• NCBI users can navigate “in” via PC or PM

19. Interesting quirk (I): missing out-links
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F16357 missing, but note we got the retrospective GtoP in-link

20. Interestingquirk (II):
spurious PMC automated entity link
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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
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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%
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