ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of Chemistry On The Internet

ChemSpider: How the Wisdom of the Crowd Can Improve the Quality of Chemistry on the Internet

Overview
Chemistry on the Internet
An introduction to ChemSpider
How crowds can enhance quality of public databases
The DailyMed Project on ChemSpider
Observed Quality Issues
The Curation Platform
Semantic Markup and Integration

Linked Data on the Web Taken from: Rafael Sidis’ Blog

Where Would You look? What Do You Trust?

Lots of “Public Compound” Databases
PubChem
Drugbank
ChEBI/ChEMBL
KEGG
LipidMAPs
ChemIDPlus
eMolecules
ZINC
Lots of chemical vendors
ChemSpider

What is a compound?

Connecting Chemistry on the Web
The internet is searchable by chemical structure and substructure (e.g.Wikipedia, Google Scholar)
Chemistry articles are indexed and searchable by a free online service
The web is linked together through the “language of chemistry”

Antony Williams vs Identifiers Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .

Aspirin vs Chemical Identifiers

Aspirin names and synonyms
Text searches depend on correct association
335 suggested identifiers for Aspirin just on PubChem!
Disambiguation dictionaries are necessary

The Final Search Strategy

All Those Names, One Structure

Connections Can Lead Anywhere

The InChI Identifier

Multiple Layers

InChIStrings Hash to InChIKeys

Oleoylethanolamine

Search Engine Dependencies

InChIs have traction…

Vancomycin

Vancomycin
Who will curate?
How would you clean such a large dataset?

What is ChemSpider?
ChemSpider is:
Building a Structure Centric Community for Chemists
Ca. 23 million compounds, ca. 300 data sources
A deposition and curation platform
A publishing platform for the community
Grows daily – more depositions, more links, more data sources

Search Cholesterol

Linked across the internet

Kyoto Encyclopedia of Genes and Genomes

Link off a structure in ChemSpider
Chemical suppliers
Other publications
Analytical Data
Related Reactions
Wikipedia
Patents
“ Everything”

Links to Patents based on structure

Pubmed Articles Linked

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?

Complex Data and Information

ChemSpider Searches

ChemSpider Complex Searches

Chemistry on the Internet
Much of the information is based on assertions and User Beware!
The Quality of information available is diverse and how does the user know what is and is not “correct”?

Question Everything online: www.dhmo.org

Vancomycin

Vancomycin on ChemSpider

Vancomycin

Vancomycin Search Molecular SKELETON Search Full Molecule

Full Skeleton Search: 104 Hits

Full Molecule Search: 4 Hits

The InChI “Resolver”

The EXPERTS must get it right?!

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

Feedback from Steve Ritter
“ Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access, strangely enough.”
“ It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day .”

What About Digitonin?

CAS as an authority

The Blogging Community Participate

Collaborative Knowledge Management

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

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

Multi-level Curation and Approval Building a Structure Centric Community for Chemists

DailyMed

The Intention
Make DailyMed structure searchable via ChemSpider
In the process curate data on ChemSpider and validate data on DailyMed
Improve the curation platform on ChemSpider
Perform markup of DailyMed articles to enhance the reading experience

Poor Representations

Lack of Stereochemisty

Simply Wrong

Missing Fragments?

Hmmmm….

Does it Matter?
Does it matter to the consumer that the structures are wrong? No…what matters is what is in the bottle is the right medication!
To make DailyMed structure searchable it DOES matter
To data mine DailyMed it matters
To mark up DailyMed it matters

The Process
Import all XML files from DailyMed
Use “Home built” entity extraction based on our dictionary of chemical names
Articles online here:
http://www.chemspider.com/DailyMed.aspx
Example Article: http://www.chemspider.com/DailyMedArticle.aspx?id=2

State of the Data

Tolinase: DailyMed on ChemSpider

OTHER Mentioned Chemicals

One Name – Multiple Structures NO Stereo Full Stereo Partial Stereo Partial Stereo

Editing a Record
Do NOT deprecate record…remove association between name and chemical structure

Partial Stereochemistry

Loop of Assertions
Reduce to ONE structure – with full explicit stereo

How bad can it get??? And who is right????

Name-Structure Pairs
Cleaning up the associations of names and structures is torturous and time-consuming
Decisions get made and can be challenged
Names are not “removed” …they are still on the database
Such a curated “dictionary” is very valuable

ChemMantis
Chem ical M arkup A nd N omenclature T ransformation I ntegrated S ystem – ChemMantis
A platform for entity extraction for chemistry documents, markup and integration to online information sources – Wikipedia, ChemSpider, Entrez…
Web-based submission, markup and publishing platform

Name-Structure Pairs

Species – linked to Wikipedia

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

Outlinks…

Back to DailyMed

The Difference…

ChemMantis Markup

Species Markup

Dictionaries are Easily Enhanced
Copy-Paste into appropriate Entity Dictionary
Impacts all future markups
Expanding knowledgebases of information
Linked out to rich sources of information

Expand Dictionaries

Where To From Here?
The platform is built…it’s all eyeballs for curation now
As structure-identifier pairs are curated DailyMed will improve
The project is now on hold – no resources to continue

If We Had Our Way…
Convert every DailyMed Label to a ChemMantis marked up document
Use the XML segregation of the Tablet Labels to tag where chemicals are in the label
Allow data mining based on “where” in a label the chemicals are..drug-drug interactions etc
Markup and mine property data out of the labels using new dictionaries related to properties such as IC50 and toxicity

Citizen Scientists

Become a Data Source

Synthesis Procedures

Links to Data or Deposit Data

ChemSpider Everywhere : Embed

ChemSpider Everywhere: Spectral Game

ChemSpider Everywhere Crowdsourced Curation of Spectra

ChemSpider Everywhere ChemMobi Building a Structure Centric Community for Chemists

ChemSpider Web Services

Linked Data on the Web Taken from: Rafael Sidis’ Blog

Linking to Resources
Linking to resources by structures or name
Example integration: HSDB or ChemIDPlus

It’s a long road ahead…

Conclusions
The internet enables chemistry, at a reduced cost
Web 2.0 is here and improving quality
Question Quality! All data sources are imperfect – some more imperfect than others
Crowdsourcing to expand, curate and integrate
Structures submitted to DailyMed need checking

Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams

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ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of Chemistry On The Internet

by Antony Williams, ChemConnector on Dec 02, 2009

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ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of Chemistry On The Internet — Presentation Transcript