eugm 2014 - Árpád figyelmesi, daniel bonniot de ruisselet (chemaxon): chemical patent curation and...
TRANSCRIPT
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Chemical Patent Curation and Management
New Tools and Capabilities
Árpád Figyelmesi, Daniel Bonniot de Ruisselet
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Motivation
Knowing the chemical space covered by competitors’ patents is essential for successful drug discovery.
This information can be useful for: ● Idea generation ● Lead candidates selection ● Drug design ● Patent claims construction
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Challenges
● The existing databases are optimized for patent searching
● Manual processing and analysing is time consuming and needs special expertise
● Automatic processing quality is not good enough ● No tools for editing complex Markush structures
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Computer-assisted data extraction
● English, Chinese and Japanese Name to Structure dramatically speeds up the extraction process
● Markush Editor helps to draw complex Markush structures
● Structure Checker and Markush Validation guarantees the high quality of extracted information
● Markush Representation, Search and Enumeration
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Name to Structure
● Support for many nomenclatures (common, drug names, …) ● IUPAC names used for exemplified structures ● Essential to extract chemical information from patents
● English (2008, Marvin 5.1) ● Chinese (2013, Marvin 5.12) ● Japanese (2014, Marvin 6.3)
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Why other languages?
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Validation on patent data
Measuring overlap between English and Chinese patents Using different data sources and tools
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Document Annotation
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Document Annotation
● Upcoming API in 6.4 ● Display annotated patents and documents (PDF, XML) ● Integrated in ChemCurator
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Markush Editor Functions
● Editing complex patent markush structures ● Hierarchical representation of fragments’ relationships ● Visualization of nesting view, preview ● Editing separately the individual fragments ● Integrated structure checker ● Available as a desktop application and as an
integratable component (6.3)
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Markush Editor
R-group definitions
Tree view
Scaffold
Structure checker
Nesting view & Preview
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ChemCurator Functions
● Compound and Markush editor component ● Annotated documents from pdf, html, xml. ● Drag and drop structures from the document ● Connection between the document and extracted data ● Markush validation against the examples ● Support for multi-display environment ● Available as a desktop application (6.4)
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ChemCurator
Markush editor
Example structures
Annotated document
Project explorer
Selected structures
Structure checker
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Workflow
IP experts ● Search ● Analyze
IP experts ● Extract ● Validate
Database ● Markushes ● Examples ● Documents
Drug discovery team ● IJC ● Plexus ● JChem for Office
● IP experts can represent the chemical space ● Chemical representation is comprehensible for Medicinal Chemists ● High quality project specific database ● New opportunities, less risk, faster communication
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Non patent Curation
Mode optimized for extracting specific structures ● Exemplified structures in patents ● Scientific journal articles ● Internal company reports ● … Wizard to automatically detect relevant structures ● Exclude fragments, chemical elements, …
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Non patent Curation
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Future plans
Naming: ● Keep improving accuracy in all languages (en,cn,jp) ● Add requested languages Markush: ● Overlap analysis ● Non-hit visualization ● Markush generation wizard ● Claim generation wizard
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Acknowledgment