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Biological and Chemical Sequences: Patents and Extraction

Explore the research creation, processing, and publication of biological sequences and patents, along with extraction of chemical names from patents using innovative tools and databases. Acknowledging funding from the European Commission, EMBL-EBI, and the European Patent Office.

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Biological and Chemical Sequences: Patents and Extraction

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  1. http://www.linkedin.com/in/snauche

  2. Agenda Chemical compounds and Patents Biological Sequences and Patents Acknowledgements: FELICS is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme. Additional funding has been provided by EMBL-EBI and the European Patent Office.

  3. IQ Life sciences - Organizational Structure- President DG2 Operational Support DG4 Administration DG5 Legal/Administration Affairs DG 3 Boards of Appeal DG1 Operations Patent Grant Automation International Affairs Patent Administration IQ Life sciences Services for Examiners Data Acquisition & Verification R&D • Introduction

  4. Biological Sequences and Patents Research Creation Processing Sequence Listing Publication • Biological Sequences and Patents

  5. A Patent Application and its different parts Description Claims SA0000001 Sequence Listing Figures • Biological Sequences and Patents /Sequence Listing

  6. Sequence Listing General Information Part Sequence(s) part • Biological Sequences and Patents /Sequence Listing

  7. Standards Wipo ST25 EMBL ASN.1 General Information Sequence Part • Biological Sequences and Patents /Sequence Presentation Standards

  8. The Submission Tool • Submission • Conversion • Multilingual • Formatting • Verification • Biological Sequences and Patents /Sequence Presentation submission tool

  9. The Submission Tool • Biological Sequences and Patents /Sequence Presentation submission tool

  10. Biological Sequences and Patents Research Creation Processing Sequence Listing Publication

  11. Sequence Listing Verification process Date Stamp Business rules Business rules Business rules Search Environment "Scientific" Publication server Verified Sequences Online filing Relational Database "Non redundant" Patent Sequence Database Process Verification Formatting Legal Publication server Text & Forms OCR Sequence Listing files (ST25) Relational Database Storage of all incoming sequence listing files including versions (Legal version) Sequence Listing version comparison (Trimaran, etc.) Front End Paper Filing and Sequence Listing on Electronic carrier Sequence Listings from National Patent Offices • Biological Sequences and Patents /Sequence Listing Value Chain @ EPO

  12. Sequence Listing Verification process Research Creation Processing Sequence Listing Publication

  13. USPTO JPO EPO KIPO Data Publication: International Cooperation The Trilateral patent offices exchange and publish biological sequence data in collaboration with the Public Database Providers • Biological Sequences and Patents / Published sequences exchange

  14. Non Redundant Patent Sequence Database / Project Overview • Biological Sequences and Patents / Non redundant Patent Sequence Database

  15. Non Redundant Patent Sequence Database / Sequence Capture Sequence Detection Algorithm: Detects the presense of sequences in all incoming EPO applications, using multipass scanning through different detection levels Data Management Pipelines: Enrichment of database coverage avoiding redundancy • Biological Sequences and Patents / Non redundant Patent Sequence Database

  16. Non Redundant Patent Sequence Database / Publicly available 2 types of NR databases PN corrections Database record (L2) Search and Public availability @ EBI • Biological Sequences and Patents / Non redundant Patent Sequence Database

  17. Chemical compounds and Patents Biological Sequences and Patents Extraction of Chemical names in Patents

  18. Extraction of Chemical names in Patents OSCAR Parsing chemicals systematic names trivial names formulae acronyms fragments ► Chemical Structures ► IUPAC name ►Link to Patent numbers • Biological Sequences and Patents / Extraction of chemical names from patents

  19. Chemical Information from Patents • Biological Sequences and Patents / Availability of chemicals from patents

  20. Availability of Patent related Data @ EBI • Biological and Chemical Information from Patents

  21. Acknowledgements: FELICS is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme. Additional funding has been provided by EMBL-EBI and the European Patent Office.

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