Markush Techology and Chemical Data

Curation

Surojit Sadhu

1st International Indian Patent Information Conférence

Bangalore, 2-3 Nov, 2017

Outline

• The ‘Naming’ Family

• ChemCurator

• Markush Technology

THE ‘NAMING’ FAMILY

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

Structure <> Name

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.

Document Annotator

Input: HTML, XML, Text or PDF

Output: HTML, with Chemical structures highlighted

Chemical Indexing and Searching

Documents Structure Database

Marvin JS Search ResultsHTML Annotated Document

Document Annotator

D2S JChem

JChem

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).

CHEMCURATOR

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

Compounds extraction view

Compound listCompound listProject explorerProject explorer

Annotated documentAnnotated document

Selected structuresSelected structures

Markush extraction view

Markush editorMarkush editor

Example structuresExample structures

Annotated documentAnnotated document

Selected structuresSelected structures

Structure checkerStructure checker

General document curation

● Files (XML, PDF, HTML)

● Google Patents

● IFI CLAIMS

● Images (CLiDE & OSRA)

MARKUSH TECHNOLOGY

● R-groups

● Atom lists

● Bond lists

● Position variations

● Link nodes

● Repeating units

● Homology groups

Markush Representation

Markush technologies

● Search

● Enumeration

● Hit visualization

● Non-hit visualization

● Overlap

● Composer

Automatic Markush generation

Applications

• patent drafting

• combinatorial libraries:

representation & analysis

Automatic Markush generation

Task

• generate Markush from a list of

compounds

• it should represent:

• all input molecules

• other similar molecules

(structural combinations)

Example for Markush generation

ChemAxon provides solutions for:

• Naming Technology

• Data Curation from Patents and other documents

• Markush Technology

• Data Management tools.

Summary

THANK YOU

surojit@adventinformatics.com