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Hosting public domain chemicals
data online for the community – the
challenges of handling materials
Antony Williams
NIST Diffusion/CALPHAD Data Informatics and Tools Workshop
May 14th
, 2015
ORCID ID:0000-0002-2668-4821
Disclaimer…
• Previously at the Royal Society of Chemistry
• Now I am here…
Many challenges are the same
• What I will discuss in terms of publisher,
public domain databases, curated chemistry
challenges etc. are the same…
• Need capable tools to handle the data
• Need standards for data exchange
• Meshing data without review is dangerous!
• Quality costs – time, effort and money
• Algorithms can help clean data
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…
• Most searching for chemistry on the internet…
• Name searching Google/Bing/Yahoo
• Name searching Wikipedia
• Name searching Wolfram Alpha
• Name, name, name, name…searching
The issue of identifiers
Hosting Public Domain Chemicals Data Online for the Community – the Challenges of Handling Materials
Hosting Public Domain Chemicals Data Online for the Community – the Challenges of Handling Materials
Some names for Aspirin..
The CAS Number
• MUCH integration is done using CAS Numbers
• MANY searches are CAS Numbers and Names
CAS Numbers are GREAT!
The CAS Number Index grows…
Scifinder
Prophetic Enumeration
CAS Numbers are “Trademarked”?
• From http://www.cas.org/legal/infopolicy
CAS and Wikipedia
• http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/CAS_validation
CAS and Wikipedia
CAS and Wikipedia
7900 CAS Chemicals Online…
How many CAS Numbers?
How many CAS Numbers?
• >34 million chemicals from >500 sources
But CAS is hard to “Resolve”
Why CAS Numbers are not great
• There is no free service…like DOIs
• The resolver is a “Google Search”
• Maybe we need another “identifier”?
• And thanks to IUPAC/NIST….
The InChI Identifier
Multiple Layers
InChI
• SINGLE code base managed by IUPAC –
integrated into drawing packages and used by
MANY databases. No variability as with
SMILES
Vendor-dependent SMILES
ACD/Labs
CC(C)CCC[C@@H](C)CCC[C@@H]
(C)CCCC(C)=CCC2=C(C)C(=O)c1ccccc1C2
=O
OpenEye
CC1=C(C(=O)c2ccccc2C1=O)C/C=C(C)/CC
C[C@H](C)CCC[C@H](C)CCCC(C)C
ChEMBL
CC(C)CCC[C@@H](C)CCC[C@@H]
(C)CCCC(=CCC1=C(C)C(=O)c2ccccc2C1=
InChI
• SINGLE code base managed by IUPAC –
integrated into drawing packages and used by
MANY databases. No variability as with
SMILES
• InChI Strings can be reversed to structures –
same problem as with SMILES – no layout
• Adopted by the community (databases, blogs,
Wikipedia) – good for searching the internet
InChIStrings Hash to InChIKeys
InChIs for small molecules…
• InChIs are good for “small molecules”
• Read here: http://www.jcheminf.com/series/InChI
A Vision in December 2006
Lots of data coming online…
ChemSpider
ChemSpider
ChemSpider
Experimental/Predicted Properties
Literature references
Patents references
Google Books
Vendors and data sources
Structure search the web
Exact Search
Skeleton Search
6 years ago this week…
ChemSpider strengths
• Serves over 40,000 unique users per day
• Advanced searching of >34 million chemicals
Fully documented APIs
Fully documented APIs
Data Quality/Standardization
• MANY structures meant to be something
online are MISREPRESENTED.
• Commonly you will have better success finding
information by name searches than structure –
with many caveats of course…
• Validating chemical structure representations
is laborious work – and it’s shocking to review
data…
What is the Structure of Vitamin K1?
Data Quality Issues
Williams and Ekins, DDT, 16: 747-750 (2011)
Science Translational Medicine 2011
Data quality is a known issue
Data quality is a known issue
Patent data in public databases
Patent data in public databases
Depiction vs Accurate Representation
Depiction vs Accurate Representation
There are Unused Standards!
There are Unused Standards!
There are Unused Standards!
Nitro groups
Salt and Ionic Bonds
Ammonium salts
Can we MAKE Quality Data?
• Systems for everyone to validate and
standardize their data would be useful
• Would improve structure data in publications,
databases etc. and make searching across
resources better
• Collaboration to establish community rules
would be good!
Chemical Validation and
Standardization:
http://cvsp.chemspider.com
CVSP Rules Sets
CVSP Filtering of DrugBank
CVSP Filtering of DrugBank
CVSP is Open to Anyone!
ChemSpider limitations
• Supports “small molecules” only – no
InChI, no possibility to register a compound
• SO MUCH of chemistry is “materials”
• Severe limitation in chemistry coverage:
• Monomers but no polymers
• Inorganic and organometallic handling
• Ambiguous structures – “Markush”
• Nanomaterials
• Minerals
• Bound to beads, surfaces etc
ORGANICS vs. Materials
• Comment – you don’t know all of the
challenges until you start to work in the area!
• We, and cheminformatics companies, have
solved MANY, but not all of the issues
regarding organic chemistry management
• The majority of our approaches do not map to
materials
• No standard ways to represent compounds
• No InChI for materials
Questions to consider…
• Organics are hard enough!
• What are your best dictionaries of materials?
• We have chemical ontologies. Status for
materials?
• Is open annotation of your databases possible?
• What standards do you have for materials data
exchange?
Polymorphism is common
Known Challenges
• Many materials are non-stoichiometric
• How to represent composite materials (e.g.
supported catalysts)?
• Methods to distinguish novelty in materials
(equivalent to diversity in organic structures)?
• Lots of challenges ahead..a curated
“community dictionary” would be of value…
Mapped DICTIONARIES…
• Structure IDs
• Systematic name(s)
• Trivial Name(s)
• SMILES
• InChI Strings
• InChIKeys
• Database IDs
• Registry Number
Hosting Public Domain Chemicals Data Online for the Community – the Challenges of Handling Materials
Hosting Public Domain Chemicals Data Online for the Community – the Challenges of Handling Materials
Pragmatism wins
Collaboration is key
Wouldn’t it be nice if…
Thank you
Email: tony27587@gmail.com
ORCID: 0000-0002-2668-4821
Twitter: @ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams

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