ChemSpider: Building the Premier Online Resource for Chemists University of Toronto June 8th 2010

Overview

The status of chemistry online today The pragmatic vision of ChemSpider The Quality of online chemistry Linking together the internet using InChIs Citizen scientists for deposition and curation ChemSpider as a multimedia container Comparing ChemSpider, Reaxys and SciFinder

Where is chemistry online? Encyclopedic articles (Wikipedia) Chemical vendor databases Metabolic pathway databases Property databases Patents with chemical structures Drug Discovery data Scientific publications Compound aggregators Blogs/Wikis and Open Notebook Science

Chemistry on the Internet TODAY

Chemistry searches are generally limited to text-based searches across the internet

Data are dirty: sorting the wheat from the chaff. Who can you trust?

Too many searches required to resource data

media.obsessable.com

As few interfaces as possible

What do humans want?

A Pragmatic Vision

“Build a Structure Centric Community”

December 2006 – A hobby project initiated to connect chemistry on the web

Integrate chemical structure data on the web Create a “structure-based hub” to information and

data Provide access to structure-based “algorithms” Let chemists contribute their own data Allow the community to curate/correct data

ChemSpider Searches

Search Cholesterol

Search Cholesterol

Search Cholesterol

Search Cholesterol

Search Cholesterol

Linked across the internet

Kyoto Encyclopedia of Genes and Genomes

Links to Patents based on structure

Articles Linked

ChemSpider Complex Searches

Link off a structure in ChemSpider

Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “Everything”

Answering Questions for Chemists Questions a chemist might ask…

What is the melting point of n-butanol? What is the chemical structure of Xanax? Chemically, what is phenolphthalein? What are the stereocenters of cholesterol? Where can I find publications about xylene? What are the different trade names for Ketoconazole? What is the NMR spectrum of Aspirin? What are the safety handling issues for Thymol Blue?

What is a compound?

ChemSpider is a structure-centric hub

ChemSpider aggregates and links out across the internet

Data aggregate based on “structures and links”

What defines a chemical compound?

Linked Data on the Web

Taken from: Rafael Sidis’ Blog

Where Would You look? What Do You Trust?

Chemistry on The Internet Is Messy

It’s Methane…

What’s Methane?

What’s Methane?

What ELSE is Methane???

PubChem

Chemistry is REALLY Messy

Vancomycin

Who will curate?

How would you clean such a large dataset?

Assertions!!!

Vancomycin on ChemSpider 1 compound – 3 days

The EXPERTS must get it right?!

Wikipedia, C&E News, PubChem C&E News (from ACS)

The InChI Identifier

Multiple Layers

InChIStrings Hash to InChIKeys

Vancomycin – Search the Internet

Full Molecule Search: 4 Hits

Full Skeleton Search: 104 Hits

Citizen Scientists

Crowd-sourcing Chemistry Curation

Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate

Citizens as Data Sources

Semantic Markup: Project Prospect

Entity-Extraction, Mark-up, Annotate

Success Depends on Dictionaries

Semantic Linking of Structures

What would you want to link off a structure? Chemical suppliers Other publications Analytical Data Related Reactions Wikipedia Patents “Everything”

Unpublished Chemistry

Only a fraction of chemistry is published

Only a tiny fraction of chemistry is patented

What of the “Lost Chemistry”- never published and cannot be abstracted Reactions performed Structures made and studied Spectra acquired and then disposed of Available chemicals never found

Org Prep Daily (Blog)

ChemSpider SyntheticPages

Submission Process

Submissions reviewed by editorial board

Published as is or comments sent to author

Online Peer Review process

Data supported include web movies, images, live spectra etc.

Micro- and Nano-publications Blogs, wiki entries and even Amazon book reviews

are micro/nano-publications

ChemSpider SyntheticPages will be DOI’ed – students can add these “micro-publications” to their resume

Structures and spectra are nano-publications – these can be tracked and referenced also. (depositions, curations etc). Students participate in building one of the premier sources of chemistry data.

ChemSpider Everywhere:What do computers want?

Web services

flickr.com/photos/microcosmos

ChemSpider Everywhere: ChemMobi

Mobile ChemSpider

Multimedia Content Holder

Periodic Table Images

CAS SciFinder

reaxys

Differences between ChemSpider, Reaxys and SciFinder Everything on Reaxys and Scifinder is curated The data resources can be over a 100 years old The platforms are commercial and “read-only”

ChemSpider is free, to everyone Data are in a state of ongoing curation & annotation Data resources are from the “electronic era” Data are expanded daily and enhanced on an

ongoing basis The platform delivers integrated algorithm access

Community Contribution

We make a bigger contribution to the community if the community shares via ChemSpider

ChemSpider wins “Communitycontribution” best practice award”

How Can You Help ChemSpider?

Encourage students to deposit their data and share with the community Structures – one or many Spectra Links Syntheses into ChemSpider SyntheticPages

Spread the word – ChemSpider is an untapped resource

Chemistry on the Internet FUTURE The semantic web for chemistry is in place Crowdsourced contributions are commonplace Chemists will search by structure/substructure Chemistry articles indexed and searchable Reduced number of searches to find data Data are integrated – compounds, vendors,

syntheses, data, publications and patents A world of Open Access and Open Data

Thank you

antony.williams@chemspider.comTwitter: ChemSpidermanwww.chemspider.com/blogSLIDES: www.slideshare.net/AntonyWilliams