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GtoPDB_ELIXIR_UK_AllHands_update_Dec2019

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Update on Guide to Pharmacology during the ELIXIR UK All Hands Meeting in Dundee in Dec 2019

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GtoPDB_ELIXIR_UK_AllHands_update_Dec2019

  1. 1. IUPHAR/BPS Guide to PHARMACOLOGY Simon Harding & Chris Southan University of Edinburgh, UK www.guidetopharmacology.org 10 DECEMBER ELIXIR-UK ALL-HANDS, DUNDEE, 2019 1WWW.GUIDETOPHARMACOLOGY.ORG
  2. 2. www.guidetoimmunopharmacology.org A knowledge-base that connects immunology with pharmacology Targets and ligands linked to immunological processes, cell type and disease IUPHAR/BPS Guide to Pharmacology www.guidetopharmacology.org Open, expert-driven database of pharmacological targets and the substances that act on them: ~1,700 human drug targets, ~9,700 ligands, including ~1,300 approved drugs Updated quarterly, accessible via website, download and web service API Includes Bioschemas mark-up for ligands (Molecular Entities) IUPHAR/MMV Guide to Malaria Pharmacology Curation of antimalarial compounds and Plasmodium molecular targets for approved drugs: www.guidetomalariapharmacology.org
  3. 3. WWW.GUIDETOPHARMACOLOGY.ORG 3 Database report https://www.guidetopharmacology.org/pdfs/GtoPdb_Database_Report_April_2019.pdf
  4. 4. Guide to MALARIA PHARMACOLOGY 4 Aim to curate antimalarial compounds and Plasmodium molecular targets for approved drugs Developed with funding and scientific support from the Medicines for Malaria Venture (MMV) www.guidetomalariapharmacology.org WWW.GUIDETOPHARMACOLOGY.ORG
  5. 5. Guide to MALARIA PHARMACOLOGY • Our last database release (2019.4) contains: • 72 ligands tagged as in GtoMPdb • 30 targets tagged as in GtoMPdb • Curated ligands include • antimalarial leads • drugs in preclinical and clinical development • approved medicines ble 4. GtoMPdb data counts for targets, ligands and interactions (database release 2019.4). Guide to Malaria Pharmacology Content Breakdown Targets 30 Ligands 72 Ligands (Approved drugs) 19 Ligands (WHO essential lists) 17 Targets with quantitative ligand interactions 20 Targets with approved drug interactions 4 Ligands with interactions 67 Ligands with interaction to known targets 38 Ligands with interaction to unknown targets 34 Ligands with quantitative interactions (approved drugs) 65 (18) Ligands with clinical use summaries (approved drugs) 39 (19)
  6. 6. WWW.GUIDETOPHARMACOLOGY.ORG 6 BioSchemas <!-- BioSchemas Mark-Up For Ligands --> <script type="application/ld+json"> { "@context": "http://schema.org", "@id": "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=5535", "@type": "MolecularEntity", "@type": "DataRecord", "dct:conformsTo": "https://bioschemas.org/types/MolecularEntity/", "includedInDataset" : { "@type": "Dataset", "@id": "https://www.guidetopharmacology.org/index.jsp#dataset" }, "mainEntity": { "@id": "https://identifiers.org/iuphar.ligand:5535", "name": "chloroquine", "alternateName": [ "Aralen&reg;","chloraquine","Malaquin&reg;" ], "description": "Chloroquine is a 4-aminoquinoline and used primarily as an antimalarial drug. <br>The approved drug is a racemic mixture and we show the chemical structure without stereochemistry to represent the mixture. The non-isomeric structure is also represented in the PubChem, ChEMBL and ChEBI entries listed in the links table below, while the two enantiomers forming the racemate are represented by <a href="https://pubchem.ncbi.nlm.nih.gov/compound/444810">PubChem CID 444810</a> and <a href="https://pubchem.ncbi.nlm.nih.gov/compound/639540">PubChem CID 639540</a>.<br>Marketed formulations may contain chloroquine phosphate (<a href="https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=64927&loc=ec_rcs" target="_blank">PubChem CID 64927</a>).<br><br>The <b>Malaria</b> tab on this ligand page provides additional curator comments of relevance to the Guide to MALARIA PHARMACOLOGY.", "identifier": "5535", "inChI": "InChI=1S/C18H26ClN3/c1-4-22(5-2)12-6-7-14(3)21-17-10-11-20-18-13-15(19)8-9-16(17)18/h8-11,13-14H,4-7,12H2,1-3H3,(H,20,21)", "inChIKey": "WHTVZRBIWZFKQO-UHFFFAOYSA-N", "iupacName": "N'-(7-chloroquinolin-4-yl)-N,N-diethylpentane-1,4-diamine", "molecularWeight": 319.18, "smiles": "CCN(CCCC(Nc1ccnc2c1ccc(c2)Cl)C)CC", "url": https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=5535 } } </script> Addingschema.org semantic mark-up to GtoPdb Our current focus is on implementing mark-up on all ligand summary pages but also beginning to engage on including mark-up for proteins. Thanks to Alasdair Gray! (https://bioschemas.org/specifications/drafts/Molec ularEntity).
  7. 7. 7 Publications WWW.GUIDETOPHARMACOLOGY.ORG
  8. 8. 8 Publications WWW.GUIDETOPHARMACOLOGY.ORG Immunology paper submitted! Connecting pharmacology and immunology Update on GtoPdb published in NAR last month and…
  9. 9. Interoperable entities between ELIXIR resources 9WWW.GUIDETOPHARMACOLOGY.ORG Document > assay > result > compound > protein target We can compare D-A-R-C-P between GtoPdb and ChEMBL
  10. 10. Document X-refs in UniProt 10WWW.GUIDETOPHARMACOLOGY.ORG
  11. 11. UniProt x-ref protein counts 11WWW.GUIDETOPHARMACOLOGY.ORG 17695389 ChEMBL 7158 GtoPdb 2013 244
  12. 12. PubChem Compound (CIDs) 12WWW.GUIDETOPHARMACOLOGY.ORG
  13. 13. Substance (SID) tagging in PubChem 13WWW.GUIDETOPHARMACOLOGY.ORG
  14. 14. PubChem CID counts 14WWW.GUIDETOPHARMACOLOGY.ORG 53721866798 ChEMBL 1872170 GtoPdb 7662 2290
  15. 15. Further info 15WWW.GUIDETOPHARMACOLOGY.ORG https://cdsouthan.blogspot.com/2018/08/an-initial-look-at-elixir-chemistry.html https://europepmc.org/article/PPR/PPR102764

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