The document discusses the issue of quality and accuracy of chemical structure information online. It presents ChemSpider, a platform for chemical structure data deposition, curation and linking to other online sources. ChemSpider aims to address the problem of incorrect and inconsistent chemical structure data across different websites through features like chemical structure markup, validation using InChI identifiers, and collaborative curation efforts. The goal is to build a single point of reference for reliable chemical structure information on the internet.

1. Crowdsourcing, Collaborations andCrowdsourcing, Collaborations and
Text-Mining in a World of OpenText-Mining in a World of Open
ChemistryChemistry
Antony WilliamsAntony Williams
Bio-IT World 2009Bio-IT World 2009

2. Building a Structure Centric Community
for Chemists
Linked Data CloudLinked Data Cloud

3. Building a Structure Centric Community
for Chemists
Chemistry on the InternetChemistry on the Internet
 Much of the information online isMuch of the information online is User Beware!User Beware!
 The Quality of information is “diverse”The Quality of information is “diverse”
 Technologies can “link and connect” information butTechnologies can “link and connect” information but
validation and curation is key to providing qualityvalidation and curation is key to providing quality
 The LinkedData web is of less value when the data linkedThe LinkedData web is of less value when the data linked
are “wrong”are “wrong”

4. Building a Structure Centric Community
for Chemists
Quality CostsQuality Costs
 Chemical Abstracts ServiceChemical Abstracts Service (CAS), a division of the(CAS), a division of the
ACS is “Gold Standard” in Chemistry relatedACS is “Gold Standard” in Chemistry related
informationinformation
 101 years of content, $260 million revenue (2006), >40101 years of content, $260 million revenue (2006), >40
million substances and 60 million sequencesmillion substances and 60 million sequences
 But online…But online…

5. Building a Structure Centric Community
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What is “wrong”?What is “wrong”?

6. Building a Structure Centric Community
for Chemists
 A platform for:A platform for:
 Data deposition,Data deposition, curation and annotationcuration and annotation
 Supporting Open Notebook Science effortsSupporting Open Notebook Science efforts
 Chemistry document mark-up with ChemMantisChemistry document mark-up with ChemMantis
 The Open Access ChemSpider Journal of ChemistryThe Open Access ChemSpider Journal of Chemistry

7. Building a Structure Centric Community
for Chemists
Search CholesterolSearch Cholesterol

8. Building a Structure Centric Community
for Chemists
Search CholesterolSearch Cholesterol

9. Building a Structure Centric Community
for Chemists
Search CholesterolSearch Cholesterol

10. Building a Structure Centric Community
for Chemists
Search CholesterolSearch Cholesterol

11. Building a Structure Centric Community
for Chemists
Search CholesterolSearch Cholesterol

12. Building a Structure Centric Community
for Chemists
Search CholesterolSearch Cholesterol

13. Building a Structure Centric Community
for Chemists
Complex Data and InformationComplex Data and Information

14. Building a Structure Centric Community
for Chemists
Online DataOnline Data
 Many websites host structure-based informationMany websites host structure-based information
 Question quality!!!Question quality!!!

15. Building a Structure Centric Community
for Chemists

16. Building a Structure Centric Community
for Chemists
Wikipedia, C&E News, PubChemWikipedia, C&E News, PubChem
C&E News (from ACS)C&E News (from ACS)

17. Building a Structure Centric Community
for Chemists
Does one stereocenter matter?Does one stereocenter matter?

18. Building a Structure Centric Community
for Chemists
VancomycinVancomycin
 Who will curate?Who will curate?
 PubChem is notPubChem is not
resourced to cleanresourced to clean
these errorsthese errors 
 How would youHow would you
clean such a largeclean such a large
dataset?dataset?

19. Building a Structure Centric Community
for Chemists
VancomycinVancomycin
ChemSpider: 1 compound – 3 daysChemSpider: 1 compound – 3 days

20. Building a Structure Centric Community
for Chemists
Question EverythingQuestion Everything
www.dhmo.orgwww.dhmo.org

21. Building a Structure Centric Community
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DailyMedDailyMed
““DailyMed providesDailyMed provides high qualityhigh quality information aboutinformation about
marketed drugs.marketed drugs.
This information includes FDA approved labelsThis information includes FDA approved labels
(package inserts).”(package inserts).”

22. Building a Structure Centric Community
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The FDA’s DailyMedThe FDA’s DailyMed

23. Building a Structure Centric Community
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Structures on DailyMedStructures on DailyMed
Poor RepresentationsPoor Representations

24. Building a Structure Centric Community
for Chemists
Structures on DailyMedStructures on DailyMed
Lack of StereochemistyLack of Stereochemisty

25. Building a Structure Centric Community
for Chemists
Incorrect StructuresIncorrect Structures
Scanning (?) IssuesScanning (?) Issues

26. Building a Structure Centric Community
for Chemists
Incorrect StructuresIncorrect Structures

27. Building a Structure Centric Community
for Chemists
Does it Matter?Does it Matter?
 Does it matter to the consumer that the structures areDoes it matter to the consumer that the structures are
wrong? No…what matters is what is in the bottle is thewrong? No…what matters is what is in the bottle is the
right medication!right medication!
 To make DailyMed structure searchable it DOESTo make DailyMed structure searchable it DOES
mattermatter
 To data mine DailyMed it mattersTo data mine DailyMed it matters
 To mark up DailyMed it mattersTo mark up DailyMed it matters

28. Building a Structure Centric Community
for Chemists
CollaborativeCollaborative Knowledge ManagementKnowledge Management
for Chemistsfor Chemists

29. Building a Structure Centric Community
for Chemists
Wikipedia Links to DrugbankWikipedia Links to Drugbank

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for Chemists
Taxol on PubChemTaxol on PubChem

31. Building a Structure Centric Community
for Chemists
Taxol on Daily MedTaxol on Daily Med

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The InChI IdentifierThe InChI Identifier

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Multiple LayersMultiple Layers
Source: Unofficial InChI FAQ pageSource: Unofficial InChI FAQ page

34. Building a Structure Centric Community
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InChIStrings Hash to InChIKeysInChIStrings Hash to InChIKeys

35. Building a Structure Centric Community
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InChIs for TaxolInChIs for Taxol

36. Building a Structure Centric Community
for Chemists
Back to TaxolBack to Taxol
 DrugBank: RCINICONZNJXQF-CLDWUXIMDDDrugBank: RCINICONZNJXQF-CLDWUXIMDD
 ChEBI:ChEBI: RCINICONZNJXQF-GXKQXQCDDNRCINICONZNJXQF-GXKQXQCDDN
 Wikipedia:Wikipedia: RCINICONZNJXQF-MZXODVADBJ
 Which one is correct???

37. Building a Structure Centric Community
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InChIKeys for TaxolInChIKeys for Taxol
 DrugBank: RCINICONZNJXQF-CLDWUXIMDDDrugBank: RCINICONZNJXQF-CLDWUXIMDD
 ChEBI:ChEBI: RCINICONZNJXQF-GXKQXQCDDNRCINICONZNJXQF-GXKQXQCDDN
 Wikipedia:Wikipedia: RCINICONZNJXQF-MZXODVADBJ
 ChEBI and Wikipedia are the SAME structure
 Drugbank is a DIFFERENT structure – ONE
stereocenter

38. Building a Structure Centric Community
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The InChI ResolverThe InChI Resolver

39. Building a Structure Centric Community
for Chemists

40. Building a Structure Centric Community
for Chemists
Coming Soon…Linked ArticlesComing Soon…Linked Articles

41. Building a Structure Centric Community
for Chemists
How bad can it get???How bad can it get???
And who is right????And who is right????

42. Building a Structure Centric Community
for Chemists
ChemMantisChemMantis
 ChemChemicalical MMarkuparkup AAndnd NNomenclatureomenclature TTransformationransformation
IIntegratedntegrated SSystem –ystem – ChemMantisChemMantis
 A platform for entity extraction for chemistryA platform for entity extraction for chemistry
documents, markup and integration to onlinedocuments, markup and integration to online
information sources – Wikipedia, ChemSpider, Entrez…information sources – Wikipedia, ChemSpider, Entrez…
 Web-based submission, markup and publishing platformWeb-based submission, markup and publishing platform
now hosting thenow hosting the ChemSpider Journal of ChemistryChemSpider Journal of Chemistry

43. Building a Structure Centric Community
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ChemMantis MarkupChemMantis Markup

44. Building a Structure Centric Community
for Chemists
Enable Electronic Articles…Enable Electronic Articles…
 Structures are theStructures are the
language of chemistrylanguage of chemistry
 Show structures toShow structures to
chemists and search/linkchemists and search/link
from there…from there…

45. Building a Structure Centric Community
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Species MarkupSpecies Markup

46. Building a Structure Centric Community
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Dictionaries are Easily EnhancedDictionaries are Easily Enhanced
 Copy-Paste into appropriate Entity DictionaryCopy-Paste into appropriate Entity Dictionary
 Impacts all future markupsImpacts all future markups
 Expanding knowledgebases of informationExpanding knowledgebases of information
 Linked out to rich sources of informationLinked out to rich sources of information

47. Building a Structure Centric Community
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Build DictionariesBuild Dictionaries
Ontologies NextOntologies Next

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for Chemists
Outlinks…Outlinks…

49. Building a Structure Centric Community
for Chemists
Publishers and Document Mark-UpPublishers and Document Mark-Up

50. Building a Structure Centric Community
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ChemSpider EverywhereChemSpider Everywhere
 Linked from WikipediaLinked from Wikipedia
 Linked from Open Notebook Science sites using EMBEDLinked from Open Notebook Science sites using EMBED
 Linked from Blogs using Structure/Spectra EMBEDLinked from Blogs using Structure/Spectra EMBED
 Integrated into structure drawing packages such asIntegrated into structure drawing packages such as
ACD/ChemSketch, Symyx Draw, Open Source appletsACD/ChemSketch, Symyx Draw, Open Source applets
 Integrated to software offerings from Thermo, Waters, Agilent,Integrated to software offerings from Thermo, Waters, Agilent,
BrukerBruker

51. Building a Structure Centric Community
for Chemists
ChemSpider EverywhereChemSpider Everywhere
Embed Functionality (like YouTube)Embed Functionality (like YouTube)

52. Building a Structure Centric Community
for Chemists
ChemSpider EverywhereChemSpider Everywhere
www.spectralgame.comwww.spectralgame.com

53. Building a Structure Centric Community
for Chemists
ChemSpider EverywhereChemSpider Everywhere
Crowdsourced Curation of SpectraCrowdsourced Curation of Spectra

54. Building a Structure Centric Community
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ChemSpider EverywhereChemSpider Everywhere
RSC CompoundsRSC Compounds

55. Building a Structure Centric Community
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ChemSpider EverywhereChemSpider Everywhere
Nature ChemistryNature Chemistry
Nature ChemistryNature Chemistry articles arearticles are
annotated to identify all of theannotated to identify all of the
chemical compounds mentionedchemical compounds mentioned
throughout the text.throughout the text.
Those compounds are linked out toThose compounds are linked out to
other information resourcesother information resources
including PubChem andincluding PubChem and
ChemSpiderChemSpider..

56. Building a Structure Centric Community
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ChemSpider EverywhereChemSpider Everywhere
ChemMobiChemMobi

57. Building a Structure Centric Community
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Structure RSS Feeds with InChIsStructure RSS Feeds with InChIs

58. Building a Structure Centric Community
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59. Building a Structure Centric Community
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AcknowledgmentsAcknowledgments
 Richard Kidd, Royal Society of ChemistryRichard Kidd, Royal Society of Chemistry
 Jason Wilde, Nature Publishing GroupJason Wilde, Nature Publishing Group
 Martin Walker and the Wikipedia Chemistry teamMartin Walker and the Wikipedia Chemistry team
 Microsoft – Rudy PotenzoneMicrosoft – Rudy Potenzone
 Symyx – Keith Taylor and James JackSymyx – Keith Taylor and James Jack
 SureChem – Nicko GoncharoffSureChem – Nicko Goncharoff
 Spectral game - Andrew Lang and Jean-Claude BradleySpectral game - Andrew Lang and Jean-Claude Bradley
 ““The InChI team and Advisory Group”The InChI team and Advisory Group”

60. Building a Structure Centric Community
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ConclusionsConclusions
www.chemspider.comwww.chemspider.com
www.chemspider.com/journalwww.chemspider.com/journal
InChIs and Internet ChemistryInChIs and Internet Chemistry
http://inchis.chemspider.comhttp://inchis.chemspider.com