SureChem - Integrating with public and proprietary data sources (ACS Fall 2012)
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Presentation at Fall ACS meeting about upcoming deposition of all SureChem chemical structure data into PubChem
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SureChem - Integrating with public and proprietary data sources (ACS Fall 2012)
- 1. Integrating patent chemistry with public and private non-patent research resources Nicko Goncharoff ACS Fall 2012 Andrew Hinton, PhD 19 August Christopher Southan, PhD
- 4. SureChem Data Collection! Database of automatically mined structure data from text and images! ! • 20M annotated US, EP, WO full text records and Japan patent abstracts! I! • 12M unique chemical structures! • MEDLINE – 19M abstracts (coming Q4)!
- 5. ª Free resource for researchers! ª Professional search needs! ª Enables linking to public and ª Data export, alerts, patent family proprietary content search, chemical relevance filters…! ª API or Data Feed access to chemistry & full text! ª Integrate with internal databases & workflows
- 7. Public Patent Chemistry Landscape!
- 8. Current Patent Sources In PubChem! 4000000 3.7 M 3500000 3000000 Numbers of SID's 2.3 M 2500000 2000000 1500000 1000000 500000 280 K 10 K 0 EPO(Sling) Chemicalize.org IBM Thomson Thompson Pharma
- 9. Patent & Literature Sources in PubChem ! The Big Three Thomson Pharma,! ChEMBL + ! patents and literature ! PubMed + Journals! 3,756,283! 918,077! 41% lead-like! 45% lead-like! 3,291,940 281,920 515,745 52,975 129,448 67,437 2,113,169 IBM, pre-‐2000 patents 2,369,481 32% lead-‐like
- 10. SureChem to Deposit All Structures* into PubChem - 2012! • 1976 to present • Deposition of structures only • View related patents in SureChemOpen • *Some filtering of common chemistry likely
- 11. SureChem and IBM in PubChem (2 Example Patents)! SureChem Total: 776! IBM Total : 527! US583593, Inhibitors of squalene synthetase and protein farnesyltransferase. Abbott ! 478 298 229 SureChem Total: 832 ! IBM Total: 239! 686 146 93 WO-1994018188-A1 ! 4-hydroxy-benzopyran-2-ones and 4- hydroxy-cycloalkyl[b]pyran-2-ones HIV protease inhibitors, Upjohn!
- 12. Identifying Relevant Chemistry - IC50! US-20120035195-A1 BACE2, Hoffman LaRoche
- 13. Structures with IC50 Values! US-20120035195-A1 PDF SureChemOpen Excel
- 14. Search IC50 Structures in PubChem! search
- 15. SureChem Unique Contribution! SureChem Pubchem 79 96 (ThomsonPharma , Chemicalize) Stage! No. of Structures! Available from SureChem (SC)! 1848! Pre-Exist in PubChem! 669! Pre-Exist – not from IC50 table! 573! Pre-Exist – from IC50 table! 96 (12 from TP + 84 via chemicalize.org)! Unique-SC with IC50! 79! Unique-SC – beyond IC50 table! 1100!
- 16. Identifying Relevant Chemistry! Patent US-20120035195-A1! http://opentox.informatik.uni- freiburg.de/ches-mapper/!
- 17. SureChem Chemical Relevance Filtering! • Frequency counts of chemicals within patents • AddiHonal molecular property filtering i.e. Lipinski descriptors ! • Natural Language Processing – based indexing of Exemplified Compounds ! ! Automated indexing of Exemplified Compounds in text!
- 18. Conclusion! SureChem deposition into PubChem will – Significantly expand public patent chemistry scope – Contribute unique and timely MedChem-relevant data – Enable open drug discovery and chemical biology – Advance progress toward a more open, federated chemical information network