Patent Knowledge Mining for Drug Repurposing


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Patents contain a huge amount of explicit and implicit information that can be extremely valuable for designing and directing drug repurposing projects. However there are many obstacles to overcome.
Presented at the 2nd Annual Drug Repositioning & Indications Discovery Conference, October 23, 2012 (San Francisco, Cal.)

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Patent Knowledge Mining for Drug Repurposing

  1. 1. Focused Patentomes and Literareomes: Text-Based Knowledge Mining Hermann Mucke for Drug Repurposing 2nd Annual Drug Repositioning & Indications Discovery Conference October 23, 2012 – San Francisco
  2. 2. Presentation Outline Patentomes: totality of all information disclosed in patent documents published in defined fields Exemplary tool for “total recall” prior art research and concept generation in drug repurposing Mapping (and matching) patent and peer review literature ontologies for optimal knowledge merging Patentomes in the biomedical database world 2
  3. 3. Strategy Or Opportunity? On-Target – Off-Target Planned (systematic) repurposing Gap closing in development pipelines Addressing neglected diseases Opportunistic repurposing "Just had this idea..." / "Just found out that..." Can happen in the wet lab, in the clinic – or “in the library” 3
  4. 4. Learn About What Is Already Known - And What Is Not Equally essential for generating and checking ideas Define your repurposing concept Mechanism/target-based Disease-based And then, search the prior art What? - Your idea/finding/concept, obviously Where? - Peer review literature & patents, obviously HOWEVER,...... 4
  5. 5. PubMed & Public Patent Databases Are Not Enough PubMed/Medline is limited to searching: Abstracts (such as there are) Indexed terms (MeSH keywords,...) Patentscope, Esp@acenet, USPTO,... are also limited: No keyword indexing Fulltext available - but as raw OCR output This raw output is the input for Machine translations Datamining 5
  6. 6. Access To Non-English Texts: A Major Hurdle Machine translations can result in total gibberish WO 2012/137870, input is Japanese OCR online text Google Translate Microsoft 6
  7. 7. Solution: Focused Patentomes and Literareomes Totality of patent or peer review publications with relevant information Complete (for the purpose of the search) Searchable in fulltext Indexed for explicit content Annotated for implicit content Only focusing on precisely defined therapeutic fields makes this achievable Document identification must be done by a human expert Impossible for peer review papers (no access rights to >85% of fulltexts) But is a reasonable proposition for patents 7
  8. 8. THIRDSPACE: A Series Of Overlapping Patentomes Primarily a KM tool - patent-legalistic issues secondary Automated entity recognition and linking Patent codes mapped to MeSH codes Search patents on the same level as PubMed - but based on fulltext Chemical information converted to machine-readable format (InChIs) Interactive knowledge discovery software framework 8
  9. 9. REDWING: THIRDSPACE Pilot Module Ophthalmology Ocular pharmacology, drug delivery, tissue technology, and biomarkers 5,333 patent documents captured (Oct. 15, 2012) ~75% with fully expert-corrected machine-readable PDFs in original layout (~160,000 pages) Uses ophthalmology-focused ontology in addition to standard MeSH vocabulary Open-standards ontologies for biomedical investigations 9
  10. 10. REDWING: Drug Repurposing To The Ophthalmology Space (I) Both "idea checking" and "exploratory searches" supported by tailored features Separate searches in claims, body text, and ISR citations Boolean/proximity Semantic/context MeSH & IPC Chemistry Links to H.M. Pharma Consultancy's Discontinued Drug Candidate Database, PubMed, PubChem,... 10
  11. 11. REDWING: Drug Repurposing To The Ophthalmology Space (II) These searches can rapidly answer the key questions for repurposing: Has it been explicitly described already? (novelty) If not, how obvious is the contemplated new use (inventive step) Can invention height and/or utility be improved by new dosing and/or re-formulation? How could we go at obtaining IP for the new use? REDWING can work with implicit contextual information Reveals where "to connect the dots" 11
  12. 12. Further Plans For THIRDSPACE Build additional modules that overlap in a meaningful way e.g., visual cortex, neurodegeneration, photobiochemistry... Extend chemistry integration Fragment-based searches Markush searches Reactions Full integration of Open Access literature in the respective fields 12
  13. 13. The Take-Home Message For drug repurposing, assume that key information has already been published, BUT: Not where it is commonly believed to be Not in easily machine-accessible form Not in an obvious context WE MIGHT NOT KNOW WHAT IS ALREADY KNOWN BUT WE CAN FIND OUT WE MIGHT ALREADY HAVE THE AGENT BUT WE DO NOT (YET) KNOW ALL IT DOES 13
  14. 14. Peer-Review Papers On Ocular Patent Landscaping Towards the Ophthalmology Patentome: A Comprehensive Patent Database of Ocular Drugs and Biomarkers (submitted) Focus, medicinal chemistry, informatics: towards the pharmaceutical patentome Pharm. Pat. Analyst 2012; 1(3): 229-231 Pharmacological therapies for cataract and refractive errors: landscaping niches of ocular drug patenting Pharm. Pat. Analyst 2012; 1(2): 165–75 Current drug patenting for retinal diseases: Beyond VEGF inhibitors IDrugs 2010; 13(1):30-37 New ocular therapeutics: A view from the patenting perspective IDrugs 2007; 10(1):37-41 14
  15. 15. *** THANK YOU FOR YOUR ATTENTION *** 15