ChemSpider Presentation At University Of Toronto

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

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 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 “Community
contribution” 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 [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams

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ChemSpider Presentation At University Of Toronto

by Antony Williams, ChemConnector on Jun 08, 2010

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