This document discusses ChemAxon's naming, data curation, and Markush technologies. It describes ChemCurator, which assists in extracting compounds, Markush structures, and assay data from documents. It also outlines ChemAxon's naming technology for converting between structures and names, as well as tools for extracting structures from documents, annotating documents with structures, and indexing structures. Finally, it summarizes ChemAxon's Markush technology capabilities like representing R-groups, atom/bond lists, position variations, and generating Markush structures from input compounds or structural combinations.

1. Markush Techology and Chemical Data
Curation
Surojit Sadhu
1st International Indian Patent Information Conférence
Bangalore, 2-3 Nov, 2017

2. Outline
• The ‘Naming’ Family
• ChemCurator
• Markush Technology

3. THE ‘NAMING’ FAMILY

4. The ‘Naming’ Family
• Convert Structures to IUPAC and Common Names (Structure to Name )
• Convert Names to Structures (Name to Structure )
• Extract Structures from Documents (Document to Structure)
• Display Documents in a web browser (Document Annotator)
• Extract and Index structures in Shared drives and Folders (ChemLocator)
Supported Languages: English, Chinese & Japanese
Inbuilt Chemical OCR error correction feature

5. Structure <> Name

6. Document to Structure
• Detects and extracts Chemical Structures
• Supports PDF, MS office docs, txt, html, xml, etc
• Process a whole document or a single page or a paragraph
• API available.

7. Document Annotator
Input: HTML, XML, Text or PDF
Output: HTML, with Chemical structures highlighted

8. Chemical Indexing and Searching
Documents Structure Database
Marvin JS Search ResultsHTML Annotated Document
Document Annotator
D2S JChem
JChem

9. ChemLocator
Discover the hidden
chemical knowledge in
documents, regardless
whether they are located
on local computer, network
share or in the Cloud
(Google Drive, OneDrive,
DropBox, SharePoint
Online, Office 365).

10. CHEMCURATOR

11. ChemCurator
● Computer assisted document curation and analysis
● Extract compounds, Markush structures and related
assay data.
● Simply drag-and-drop recognized structures and fragments to populate R-
groups, and quickly re-assemble the Markush structures according to the
claim
● Use extracted exemplified structures for Markush validation

12. Compounds extraction view
Compound listCompound list
Project explorerProject explorer
Annotated documentAnnotated document
Selected structuresSelected structures

13. Markush extraction view
Markush editorMarkush editor
Example structuresExample structures
Annotated documentAnnotated document
Selected structuresSelected structures
Structure checkerStructure checker

14. General document curation
● Files (XML, PDF, HTML)
● Google Patents
● IFI CLAIMS
● Images (CLiDE & OSRA)

15. MARKUSH TECHNOLOGY

16. ● R-groups
● Atom lists
● Bond lists
● Position variations
● Link nodes
● Repeating units
● Homology groups
Markush Representation

17. Markush technologies
● Search
● Enumeration
● Hit visualization
● Non-hit visualization
● Overlap
● Composer

18. Automatic Markush generation
Applications
• patent drafting
• combinatorial libraries:
representation & analysis

19. Automatic Markush generation
Task
• generate Markush from a list of
compounds
• it should represent:
• all input molecules
• other similar molecules
(structural combinations)

20. Example for Markush generation

21. ChemAxon provides solutions for:
• Naming Technology
• Data Curation from Patents and other documents
• Markush Technology
• Data Management tools.
Summary

22. THANK YOU
surojit@adventinformatics.com