Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry Antony Williams

The Language of Chemistry My language….

My language….

And its dialects….

From Yesterday Approaches to linking data RDF’ing, OWL’ing, SPARQL’ing Triples and stores All are appropriate technologies…. Online data linked to by the pharma industry Drugbank, PubChem, Daily Med, KEGG, ChEBI But what of the Quality of data?

Approaches to linking data

RDF’ing, OWL’ing, SPARQL’ing

Triples and stores

All are appropriate technologies….

Online data linked to by the pharma industry

Drugbank, PubChem, Daily Med, KEGG, ChEBI

But what of the Quality of data?

Question Everything www.dhmo.org

PubChem

Quality is a Major Issue- Search Butanol

Caution! Question Everything!

The FDA’s DailyMed

Quality of Structures!!!

Quality of Structures If the “Authority” isn’t doing the work to curate then who will?

If the “Authority” isn’t doing the work to curate then who will?

Collaborative Knowledge Management for Chemists

Drugbank

Taxol on PubChem

Daily Med

The InChI Identifier

Multiple Layers Source: Unofficial InChI FAQ page

Source: Unofficial InChI FAQ page

InChIStrings Hash to InChIKeys

InChIs for Taxol

Back to Taxol DrugBank: RCINICONZNJXQF-CLDWUXIMDD ChEBI: RCINICONZNJXQF-GXKQXQCDDN Wikipedia: RCINICONZNJXQF-MZXODVADBJ Which one is correct???

DrugBank: RCINICONZNJXQF-CLDWUXIMDD

ChEBI: RCINICONZNJXQF-GXKQXQCDDN

Wikipedia: RCINICONZNJXQF-MZXODVADBJ

Which one is correct???

InChIKeys for Taxol DrugBank: RCINICONZNJXQF-CLDWUXIMDD ChEBI: RCINICONZNJXQF-GXKQXQCDDN Wikipedia: RCINICONZNJXQF-MZXODVADBJ ChEBI and Wikipedia are the SAME structure Drugbank is a DIFFERENT structure – ONE stereocenter

DrugBank: RCINICONZNJXQF-CLDWUXIMDD

ChEBI: RCINICONZNJXQF-GXKQXQCDDN

Wikipedia: RCINICONZNJXQF-MZXODVADBJ

ChEBI and Wikipedia are the SAME structure

Drugbank is a DIFFERENT structure – ONE stereocenter

Does one stereocenter matter?

Does one stereocenter matter? Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon

Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon

Does one stereocenter matter? Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon

Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon

Too Much Variability in InChIs Source: Unofficial InChI FAQ page

Source: Unofficial InChI FAQ page

NEW: Resolve Variability with StdInChI StdInChI

Assertion and Chemical Entities Who says what Taxol is? What is the “timeline” for a molecule? How do we clean up the Public data? The Quality source is Chemical Abstracts Service…

Who says what Taxol is?

What is the “timeline” for a molecule?

How do we clean up the Public data?

The Quality source is Chemical Abstracts Service…

Wikipedia Chemistry Curation project > 6000 organic structures Over 1 year of work for a team of 6 Many errors removed in the process Slow and torturous process CAS now collaborating in the process InChIs and InChIKeys will be added

> 6000 organic structures

Over 1 year of work for a team of 6

Many errors removed in the process

Slow and torturous process

CAS now collaborating in the process

InChIs and InChIKeys will be added

Stereoisomers

Content is King and Quality Costs Chemistry “content” is big money – Chemistry publishing and content is worth $100s of millions/year Patent searching Structures and properties Drug databases Literature databases Chemical Abstracts Service (CAS), a division of the ACS is “Gold Standard” in Chemistry related information 101 years of content, $260 million revenue (2006), >40 million substances and 60 million sequences

Chemistry “content” is big money – Chemistry publishing and content is worth $100s of millions/year

Patent searching

Structures and properties

Drug databases

Literature databases

Chemical Abstracts Service (CAS), a division of the ACS is “Gold Standard” in Chemistry related information

101 years of content, $260 million revenue (2006), >40 million substances and 60 million sequences

www.chemspider.com Free access website for chemists to research structure based information Structure/substructure searches Text-based searches Prediction of properties Web service-based integration Platform for deposition, curation, integration of data Structures, analytical data, annotations, links to resources Annotation and curation of data in real-time A platform to assist discovery?

Free access website for chemists to research structure based information

Structure/substructure searches

Text-based searches

Prediction of properties

Web service-based integration

Platform for deposition, curation, integration of data

Structures, analytical data, annotations, links to resources

Annotation and curation of data in real-time

A platform to assist discovery?

ChemSpider Data The database contains > 21.5 million compounds obtained from >150 data sources and growing weekly.– 0.5 million compounds awaiting deposition Chemical vendors Publishers Commercial Database Vendors US and international patents Structure aggregators Scraped from websites Deposited by users

The database contains > 21.5 million compounds obtained from >150 data sources and growing weekly.– 0.5 million compounds awaiting deposition

Chemical vendors

Publishers

Commercial Database Vendors

US and international patents

Structure aggregators

Scraped from websites

Deposited by users

Example Search 1 Is there any information about “Quesnoin”? OR… Type in the name (and there may be many) or other identifier Paste the InChI String, InChIKey or SMILES Draw the structure

Is there any information about “Quesnoin”?

OR…

Type in the name (and there may be many) or other identifier

Paste the InChI String, InChIKey or SMILES

Draw the structure

Example Search 1

Example Search 1

Complex Search

Wikipedia via ChemSpider …

Searching and Reading Articles… Searching articles based on chemical structure and substructure is very expensive.. but is changing The web IS “tool-ready” so when will publishers deliver? Structures can be shown Spectra can be interactive Graphics don’t need to be static Publishers can enhance their articles (Project Prospect from the RSC is an example)

Searching articles based on chemical structure and substructure is very expensive.. but is changing

The web IS “tool-ready” so when will publishers deliver?

Structures can be shown

Spectra can be interactive

Graphics don’t need to be static

Publishers can enhance their articles (Project Prospect from the RSC is an example)

Publishers should adopt/add InChIs RSC and Nature Publishing Group have!

Document Mark-up and Linking

Structure Searching

Species..

Entity Extraction built around modified algorithms from SureChem Optimized for “publications” Dictionaries for chemical entities, groups, reactions, elements, families, species… Dictionaries can be expanded – presently adding PDB

Entity Extraction built around modified algorithms from SureChem

Optimized for “publications”

Dictionaries for chemical entities, groups, reactions, elements, families, species…

Dictionaries can be expanded – presently adding PDB

The InChI Resolver

The InChI “Resolver”

The InChI “Resolver”

Google Searches on InChI – String limit

InChIKey Searches Work

InChIs are incomplete What is NOT supported, yet: polymers organometallics Markush structures 3-D structures excited states interlocking structures (e.g. rotaxanes) host-guest complexes

What is NOT supported, yet:

polymers

organometallics

Markush structures

3-D structures

excited states

interlocking structures (e.g. rotaxanes)

host-guest complexes

Crowdsourcing for Curation Chemistry databases enhanced by crowdsourcing Chemistry databases can be connected to articles, vendors, properties, spectra, etc. A platform for deposition, curation and distribution ? This is the future… existing business models are at risk

Chemistry databases enhanced by crowdsourcing

Chemistry databases can be connected to articles, vendors, properties, spectra, etc.

A platform for deposition, curation and distribution ?

This is the future… existing business models are at risk

Post Comments Anyone can “Post Comments” associated with a structure. To curate data we require login to track

Anyone can “Post Comments” associated with a structure. To curate data we require login to track

Conclusions The internet enables chemistry – and at a reduced cost Web 2.0 is here and improving quality – to benefit 3.0 Question Quality! Crowdsourcing for expansion, curation and integration Classical models may die quite quickly – business models must change soon or fail Publishers – heed the profileration of InChIs for Chemistry

The internet enables chemistry – and at a reduced cost

Web 2.0 is here and improving quality – to benefit 3.0

Question Quality!

Crowdsourcing for expansion, curation and integration

Classical models may die quite quickly – business models must change soon or fail

Publishers – heed the profileration of InChIs for Chemistry

Blogs and Contacts The InChI resolver http://inchis.chemspider.com (goes live at ACS Spring) The ChemSpider blog www.chemspider.com/blog Contact [email_address]

The InChI resolver

http://inchis.chemspider.com (goes live at ACS Spring)

The ChemSpider blog

www.chemspider.com/blog

Contact

[email_address]