How an Online Chemistry Resource
Could Change Our World
Antony Williams
Triangle Chromatography Discussion Group,
Raleigh, NC, May 2009

Imagine a time when ….
 The internet is searchable by chemical structure and substructure
(e.g.Wikipedia, Google Scholar)
 When there is an online database of NMR, IR, MS spectra and
chromatography methods built by available to the community
 Chemistry articles are indexed and searchable by “chemistry”
 The web is linked together through the “language of chemistry”
 Publicly funded research data can be shared and discussed in the
Open, maybe as Open Notebook Science
 Cheminformatics has as much of a public face and success as
bioinformatics (Protein DataBank, Genbank, etc)
Building a Structure Centric Community for Chemists

The Language of Chemistry
 My language….
Building a Structure Centric Community for Chemists

And its dialects….
Building a Structure Centric Community for Chemists

As a chemist…
 I look for information about chemicals/chemistry
 What is a particular structure ?
 What alternative names/identifiers?
 Reaction synthesis?
 Physical properties?
 Analytical data?
 Purchase?
 Tell me more?
 Similar stuff – what other compounds are “like” mine?
Building a Structure Centric Community for Chemists

Linked Data Cloud
Building a Structure Centric Community for Chemists

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

“Good Stuff” TotallySynthetic.com
Building a Structure Centric Community for Chemists

PubChem
Building a Structure Centric Community 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?
Building a Structure Centric Community for Chemists

Search Cholesterol
Building a Structure Centric Community for Chemists

Search Cholesterol
Building a Structure Centric Community for Chemists

Search Cholesterol
Building a Structure Centric Community for Chemists

Search Cholesterol
Building a Structure Centric Community for Chemists

Search Cholesterol
Building a Structure Centric Community for Chemists

Link outs
Building a Structure Centric Community for Chemists

Complex Data and Information
Building a Structure Centric Community for Chemists

Online Analytical Data
Building a Structure Centric Community for Chemists

Various Searches
 Structure searching
 Substructure searching
 Subset searching – choose from 200 data sources
 Property searching
 Value for Mass Spectrometrists and Chromatographers?
Building a Structure Centric Community for Chemists

ChemSpider for MS Spectrometrists
 What would an MS spectrometrist want to do?
 Search the database based on mass (various forms)
 Search selected subsets of the database based on mass
 Search based on mass and substructure(s)
 Search for structure based on name(s) or database IDs
 Search for structures based on elements/not elements
 Download the structure/structures in standard format
 Search literature for information
 Identify related data sources – chemical vendors, pathway
databases, etc
Building a Structure Centric Community for Chemists

Search Database Based on Mass
Building a Structure Centric Community for Chemists

Mass Based Searches?
 What compounds have a mass of 300+/-0.001?
Building a Structure Centric Community for Chemists

59 hits/1.3 seconds from 21.5 MILLION
Building a Structure Centric Community for Chemists

Substructure and Property
Building a Structure Centric Community for Chemists

Building a Structure Centric Community for Chemists

Elemental Constraints
Building a Structure Centric Community for Chemists

Search based on Data Sources
Building a Structure Centric Community for Chemists

Outlinks – to vendors and other databases
 Example databases of interest to MS Spectrometrists:
 HMDB – Human Metabolome Database
 KEGG – Kyoto Encyclopedia of Genes and Genomes
 BioCyc - collection of Pathway/Genome Databases
 Uni. Minnesota Biodegradation DB - information on
microbial biocatalytic reactions and biodegradation pathways
for primarily xenobiotic, chemical compounds
 WikiPathways – new initiative to build crowdsourced
pathway data management
Building a Structure Centric Community for Chemists

Links out to KEGG
Kyoto Encyclopedia of Genes and Genomes
Building a Structure Centric Community for Chemists

WikiPathways Link
Building a Structure Centric Community for Chemists

Download Structure(s)
 Download individual record – molfile
 Download SDF file (group of structures)
Building a Structure Centric Community for Chemists

Web Service Integration
 ChemSpider integration presently integrated to Bruker,
Waters and Thermo – more vendors coming…
 Direct integration to vendor data processing tools
Building a Structure Centric Community for Chemists

MassSpec API Web Services
 http://www.chemspider.com/MassSpecAPI.asmx
Building a Structure Centric Community for Chemists

Web Services
Building a Structure Centric Community for Chemists

Test Web Services for MassSpec
 http://
www.chemspider.com/WebServices/WSMassSpecAPIDem
Building a Structure Centric Community for Chemists

Test results
Building a Structure Centric Community for Chemists

Waters Integration
Building a Structure Centric Community for Chemists

Waters Integration
Building a Structure Centric Community for Chemists

Outlinks from Table
Building a Structure Centric Community for Chemists

For Chromatographers?
 “Structure-based methods” being linked
 Structure-centric searching of methods
 We can host chromatograms for display
 LogPs and LogDs (pH5.5 and 7.4) calculated for >21
million compounds using ACD/Labs software
 We’d love to host collections from the column vendors!
tony@chemspider.com
Building a Structure Centric Community for Chemists

From 21.5 MILLION molecules…
 Data are gathered/deposited from >200 data sources
 Government databases
 Chemical vendors
 Wikipedia
 There are “imperfections” in all online data sources
 How bad can it get????
Building a Structure Centric Community for Chemists

What is “wrong”?
Building a Structure Centric Community for Chemists

Quality is a Major Issue- Search Butanol
OLD EXAMPLE..now fixed
Building a Structure Centric Community for Chemists

Vancomycin
 Who will curate?
 PubChem is not
resourced to clean
these errors 
 How would you
clean such a large
dataset?
Building a Structure Centric Community for Chemists

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

Building a Structure Centric Community for Chemists

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

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

DailyMed
“DailyMed provides high quality information about
marketed drugs.
This information includes FDA approved labels
(package inserts).”
Building a Structure Centric Community for Chemists

The FDA’s DailyMed
Building a Structure Centric Community for Chemists

Structures on DailyMed
Poor Representations
Building a Structure Centric Community for Chemists

Incorrect Structures
Scanning (?) Issues
Building a Structure Centric Community for Chemists

Incorrect Structures
Building a Structure Centric Community for Chemists

Wikis for Science
 Who in the room hasn’t used Wikipedia?
 Is it trustworthy?
 What are the advantages and disadvantages of the Wiki
environment?
 How suitable is it for Chemistry?
Building a Structure Centric Community for Chemists

Collaborative Knowledge Management
for Chemists
Building a Structure Centric Community for Chemists

Wikipedia Curation
 Looking for self-consistency
across a Wikipedia Page
 Primary key is the article TITLE
 The chemical shown needs to
match the title
 Cyclic self-consistency – and
decisions must get made
Building a Structure Centric Community for Chemists

Taxol on PubChem
Building a Structure Centric Community for Chemists

When are things “wrong”?
 Structures have a timeline…..
Building a Structure Centric Community for Chemists

Building a Structure Centric Community for Chemists

Building a Structure Centric Community for Chemists

Building a Structure Centric Community for Chemists

Creating a trusted source…
 Small databases can be curated by the hosts – EPA’s
DSSTox, Wikipedia, etc.
 Who will curate an enormous database?
Building a Structure Centric Community for Chemists

Crowdsourcing
Building a Structure Centric Community for Chemists

Curating ChemSpider
 Anyone can “Post Comments” associated with a
structure. To curate data we require login to track
Building a Structure Centric Community for Chemists

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

ChemMantis
 Chemical Markup And Nomenclature Transformation
Integrated System
Building a Structure Centric Community for Chemists

On the fly conversion
Building a Structure Centric Community for Chemists

Nature Publications
Building a Structure Centric Community for Chemists

Integrations Out to Other Sources
Building a Structure Centric Community for Chemists

Reactions
Building a Structure Centric Community for Chemists

ChemSpider Everywhere
RSC Compounds
Building a Structure Centric Community for Chemists

ChemSpider Everywhere
Nature Chemistry
Nature Chemistry articles are
annotated to identify all of the
chemical compounds mentioned
throughout the text.
Those compounds are linked out to
other information resources
including PubChem and
ChemSpider.
Building a Structure Centric Community for Chemists

ChemSpider Everywhere
ChemMobi
Building a Structure Centric Community for Chemists

Building a Structure Centric Community for Chemists

It Happened in a Basement!!
 Homebuilt servers
 Cable internet
 Software donations
 Lots of hard work
 >8000 users per day
 >80,000 transactions per day
Building a Structure Centric Community for Chemists

And now…
 The Royal Society of Chemistry announced on May 11th that it
has acquired ChemSpider, heralding a breakthrough investment
for the organisation and for the Chemistry Community. This
acquisition reflects RSC's commitment to providing access to rich
resources of chemistry data and information.
Building a Structure Centric Community for Chemists