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.)

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
www.hmpharmacon.com

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
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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”
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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,......
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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
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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
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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
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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
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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
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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,...
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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"
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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
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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
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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
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15. *** THANK YOU FOR YOUR ATTENTION ***
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