SureChEMBL

An open system for exploration of patent chemistry space

Michał Nowotka
ChEMBL Group
EMBL-EBI

Outline

EMBL-EBI Resources

Genes, genomes & variation
European Nucleotide Archive Ensembl European Genome-phenome Archive
1000 Genomes Ensembl Genomes Metagenomocs portal

Gene, protein & metabolite expression
ArrayExpress Expression Atlas Metabolights
PRIDE

Protein sequences, families & motifs
InterPro Pfam UniProt

Molecular structures
Protein Data Bank in Europe
Electron Microscpoy Data Bank

Chemical biology
ChEMBL ChEBI

Systems
BioModels BioSamples
Enzyme Portal

Drug discovery takes time

  • From discovering a target to a drug reaching the market:
     12 years
  • Bioinformatics shortens time to target discovery
  • EMBL-EBI services support all stages of drug discovery

ChEMBL - Data For Drug Discovery

Patent Data

  • Do we include patent data in the ChEMBL database?
    • We do provide cross-references (UniChem), but not the underlying chemical data.
    • Most common question asked about ChEMBL during training and outreach.
  • Why is this so important to Drug Discovery researchers?
    • Patent literature 2-3 years ahead of published literature.
    • Prior art and freedom to operate.
    • Lots more data - but high cost to extract + lots of noisy data.

SureChem = SureChEMBL

  • December 2013 EMBL-EBI acquired SureChem - a leading 'chemistry patent mining' product from Digital Science, Macmillan Group
  • SureChem provides a live (updated daily) view chemical patent space
  • EMBL-EBI will provide an ongoing, free and open resource to entire community
  • Rebranded SureChEMBL

SureChEMBL System

SureChEMBL System

SureChEMBL System

SureChEMBL System

SureChEMBL System

SureChEMBL Data Processing

Technical Challenges

Enhanced Entity Extraction

  • Identify new entity types e.g. proteins, diseases, cell lines, assays
  • Bioactivity Data Extraction
  • Markush Structure Extraction
  • Image Processing

Entity Extraction

Bioactivity Data Extraction

Markush Structure Extraction

Curation Interface

  • Loads compounds to DB, calculates properties
  • Web based application to help scientific curators
  • High level graphical interface, no more SQL
  • Handling many input formats

Curation Interface
handling different file formats

Curation Interface
handling different file formats

Curation Interface
handling different file formats

Curation Interface
handling different file formats

Curation Interface - image extraction

Curation Interface - PDF extraction

Curation Interface - PDF extraction

Curation Interface - PDF extraction

Image segmentation - compound extraction

Image segmentation - compound extraction

Image segmentation - layout detection

Image segmentation - layout detection

Entity classification

  • How to train classifier?
  • SureChEMBL patent data?

ChEMBL Web Services

  • Only data
  • Lack of compound manipulation services

Open source solution - Beaker

  • Server platform and virtual chemistry container
  • Provides cheminformatics tools
  • REST-like HTTP API
  • Easy to use from any programming language
  • Install Beaker on one machine instead of installing RDKit on many hardware/software configurations

Open source solution - Beaker

Trivial installation:

                        
                            pip install chembl_beaker

Beaker code is available as github repository:
https://github.com/mnowotka/chembl_beaker 

                        
    git clone https://github.com/mnowotka/chembl_beaker.git

Beaker - features

  • Format conversion
  • 2D/3D compound rendering
  • Compound recognition (OSRA)
  • Fingerprints, descriptors
  • Marvin 4 JS compilant web services

Beaker - features

Beaker - features

Potential use cases

  • Access from languages like java script, ruby
  • Web applications
  • Mobile apps (camera + OSRA + RDKit)
  • Small desktop apps (clippy)
  • Marvin Backend
  • Part of new web services

Potential use cases

myChEMBL

  • Virtual Machine
  • Contains open data and cheminformatics tools
  • Self contained web interface
  • Complete and free
  • Easy to install

myChEMBL LaunchPad

Available on github:
https://github.com/chembl/mychembl

myChEMBL - contents

  • ChEMBL DB (Postgres + RDKIt Cartridge)
  • Web interface
  • RDKit toolkit
  • Web services + client software
  • Scientific python tools (numpy/scipy etc.)
  • ipython server with many useful notebooks
  • OSRA
  • Beaker

myChEMBL - deployment options

  • ISO image from FTP + VirtualBox
  • vagrant init chembl/myChEMBL && vagrant up
  • bootstrap.sh + bare metal machine

Outline

Acknowledgements

Thank you!

Questions?