hosting public domain chemicals data online for the community – the challenges of handling...
TRANSCRIPT
Hosting public domain chemicals data online for the community – the
challenges of handling materials
Antony WilliamsOpportunities in Materials Informatics, University of Wisconsin-Madison
February 9th, 2015
0000-0002-2668-4821
About Me…• I am NOT a materials chemist• I am an NMR spectroscopist by training• Worked on a LIMS while at Kodak• 10 years in commercial cheminformatics• Built the ChemSpider database as a hobby• Worked on validating compounds on Wikipedia• Manage cheminformatics team for RSC• Believer in the value of social networking and
Open Data for science• Dane Morgan asked me to tell jokes…
I would tell a chemistry joke…
But all of the good ones…
An ambitious idea….
• Let’s map together all online chemistry data and build systems to integrate it
• Heck, let’s integrate chemistry and biology data and add in disease data too if we can
• Let’s extract property data and model it and see if we can extract new relationships – quantitative and qualitative
• Let’s make it all available on the web…for free
What about this….
• We’re going to map the world
• We’re going to take photos of as many places as we can and link them together
• We’ll let people annotate and curate the map• Then let’s make it available free on the web• We’ll make it available for decision making • Put it on Mobile Devices, give it away…
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• Structure searching DOZENS of websites, each
with different information or…
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• Structure searching DOZENS of websites, each
with different information or…
• Search ONE website integrating the others!
• ~30 million chemicals and growing
• Data sourced from >500 different sources• Crowd sourced curation and annotation• Ongoing deposition of data from our
journals and our collaborators• Structure centric hub for web-searching
• …and a really big dictionary!!!
• Note…NOT all websites connected
ChemSpider
ChemSpider
ChemSpider
Experimental/Predicted Properties
Literature references
Patents references
RSC Books
Google Books
Vendors and data sources
APIs
APIs
Organic Chemistry is hard…
…it has alkynes of trouble
Flavors of Chemistry
Molfiles 10 9 0 0 1 0 0 0 0 0 1 V2000 31.2937 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 26.6526 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 31.2937 -7.7066 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 30.1161 -9.6877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 25.5096 -9.6877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 28.9731 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 27.8163 -9.7016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 26.6664 -7.7066 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 32.4367 -9.6877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 30.1161 -11.0177 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3 1 2 0 0 0 0 4 1 1 0 0 0 0 9 1 1 0 0 0 0 7 2 1 0 0 0 0 5 2 2 0 0 0 0 8 2 1 0 0 0 0 6 4 1 0 0 0 0 4 10 1 6 0 0 0 7 6 1 0 0 0 0M END
Molfiles
• Molfiles are the primary exchange format between structure drawing packages
• Can be different between different drawing packages
• Most commonly carry X,Y coordinates for layout• Can support polymers, organometallics, etc.• Can carry 3D coordinates
SMILES
• SMILES is a common format • Can support polymers,
organometallics, etc.• Does NOT carry X,Y or Z
coordinates for layout so requires layout algorithms – can be problematic!
• Generally different between drawing packages
Stereo
Tautomeric forms
Vendor-dependent SMILESACD/LabsCC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(\C)=C\CC2=C(C)C(=O)c1ccccc1C2=O
OpenEyeCC1=C(C(=O)c2ccccc2C1=O)C/C=C(\C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C
ChEMBLCC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(=C\CC1=C(C)C(=O)c2ccccc2C1=O)\C
Chemists are good…
The InChI Identifier
InChI
• SINGLE code base managed by IUPAC – integrated into drawing packages. 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
Multiple Layers
Tautomers
Stereo
InChIStrings Hash to InChIKeys
Structure search the web
Exact Search
Skeleton Search
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…
Data Quality IssuesWilliams and Ekins, DDT, 16: 747-750 (2011)
Science Translational Medicine 2011
Data quality is a known issue
Data quality is a known issue
Substructure # of
Hits
# of
Correct
Hits
No
stereochemistry
Incomplete
Stereochemistry
Complete but
incorrect
stereochemistry
Gonane 34 5 8 21 0
Gon-4-ene 55 12 3 33 7
Gon-1,4-diene 60 17 10 23 10
Only 34 out of 149 structures were correct!
Patent data in public databases
Patent data in public databases
You just can’t trust atoms!
You just can’t trust atoms!They make up everything…
ALL variants of Yohimbine!!!
What’s Methane? OLD PUBCHEM
What ELSE is Methane???
NEW PUBCHEM
Depiction vs Accurate Representation
Depiction vs Accurate Representation
What is the Structure of Vitamin K1?
Standardize
• Use the SRS as a guidance document for standardization
• Adjust as necessary to our needs
Nitro groups
Salt and Ionic Bonds
Ammonium salts
Can we MAKE Quality Data?
• We are building systems for everyone to validate and standardize their data
DICTIONARIES are powerful
• Search all forms of structure IDs• Systematic name(s)• Trivial Name(s)• SMILES• InChI Strings• InChIKeys• Database IDs
• Registry Number
Many Names, One Structure
But big and often noisy
Text-Mining and Markup…
Text-Mining and Markup…
With links out to platforms
Dictionaries are invaluable
Text Mining on IUPAC Names
The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-thiadiazol-5-yl)urea prepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer , thermometer and reflux condenser .
The reaction mixture was heated at reflux with stirring , for a period of about one-half hour .
After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
Text Mining on IUPAC Names
The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-thiadiazol-5-yl)urea prepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer , thermometer and reflux condenser .
The reaction mixture was heated at reflux with stirring , for a period of about one-half hour .
After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
Name to Structure Conversion
Name to Structure Conversion
ChemSpider “Annotations”
• Users can add • Descriptions, Syntheses and Commentaries• Links to PubMed articles• Links to articles via DOIs • Add spectral data• Add Crystallographic Information Files• Add photos• Add MP3 files• Add Videos
Spectral Data
• Spectral data to be deposited in standard formats – JCAMP or images
• All spectra available at: http://www.chemspider.com/spectra.aspx
• Data are deposited on a regular basis• Students
• Chemical vendors• Growing collection now
Student Submissions
Data on ChemSpider
Spectral Data EXTRACTION
ORIGINAL
EXTRACTED
It’s exactly the WRONG WAY!
• We should NOT be mining data out of future publications
• Structures should be submitted “correctly” • Spectra should be digital spectral formats,
not images• ESI should be RICH and interactive,
preferably with OPEN DATA
An Adventure into the World of Small but significant contribution..
ChemSpider SyntheticPages
Micropublishing with Peer Review(a chemical synthesis blog?)
Multi-Step Synthesis
Interactive Data
Chemistry data is of value?
• Reference databases generate hundreds of millions of dollars/euros per year
• So much data generated that could go public• Maybe 5% of all data generated is published• There is no “Journal of Failed Experiments”• Funding agencies start to demand Open Data• Scientists want funding but also recognition
A shift to Openness
How will I get recognized?
• Who in the room has an ORCID?
Deposition of Research Data
• If we manage compounds, syntheses and analytical data…
• If we have security and provenance of data…
• If we deliver user interfaces to satisfy the various use cases…
• Then we have delivered electronic lab notebooks for chemistry laboratories. ELNs are research data repositories
Recognition: need to have Impact
Quantitating scientists?
National Information Standards Organization and “Altmetrics”
http://www.niso.org/apps/group_public/download.php/13295/niso_altmetrics_white_paper_draft_v4.pdf
What are we building?
• We are building the “RSC Data Repository”
• Containers for compounds, reactions, analytical data, tabular data
• Algorithms for data validation and standardization • Flexible indexing and search technologies• A platform for modeling data and hosting existing
models and predictive algorithms
Compounds
Reactions
Analytical data
Crystallography data
Deposition of Data
• Developing systems that provides feedback to users regarding data quality• Validate/standardize chemical compounds
• Check for balanced reactions• Checks spectral data
• EXAMPLE Future work• Properties – compare experimental to pred.• Automated structure verification - NMR
So we know about ORGANICS
• 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)?
• Many more I will learn at this workshop..?
Collaboration is key
Internet Data
The Future
Commercial SoftwarePre-competitive Data
Open ScienceOpen DataPublishersEducators
Open DatabasesChemical Vendors
Small organic moleculesUndefined materialsOrganometallicsNanomaterialsPolymersMineralsParticle boundLinks to Biologicals
Thank you
Email: [email protected]: 0000-0002-2668-4821 Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams