Download - Delivering Curated Chemistry to the World via Crowdsourced Deposition and Annotation on ChemSpider
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Delivering Curated Chemistry to the
World via Crowdsourced Deposition
and Annotation on ChemSpider
Antony WilliamsUniversity of Illinois in Chicago, January 27th 2012
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The World of Online Chemistry
Property databases
Compound aggregators
Screening assay results
Scientific publications
Encyclopedic articles (Wikipedia)
Metabolic pathway databases
ADME/Tox data – eTOX for example
Blogs/Wikis and Open Notebook Science
Contributing Open Source code to projects
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We Have …Too Much Data!!!
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e-Science and Primary Data
How much data generated in a lab, that COULDgo public, is lost forever?
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TotallySynthetic.com
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e-Science and Primary Data
How much data generated in a lab, that COULDgo public, is lost forever?
Public Domain reference databases of value?
Syntheses
Properties
Spectra
CIFs
Images
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PubChem
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ChEMBL
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Collaborative Knowledge Management
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e-Science and Primary Data
How much data generated in a lab, that COULDgo public, is lost forever?
Public Domain reference databases of value?
Syntheses
Properties
Spectra
CIFs
Images
Much of chemistry is chemical structure-based –where and how could we host these data?
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RSC’s ChemSpider
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Available Information…
Linked to vendors, safety data, toxicity, metabolism
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Available Information….
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Crowdsourced “Annotations”
Users can add
Descriptions/Syntheses/Commentaries
Links to PubMed articles
Links to articles via DOIs
Add spectral data
Add Crystallographic Information Files
Add photos
Add MP3 files
Add Videos
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Spectra
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Spectra
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Data on the Web
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Chemistry Data online is messy
We have inherited errors
All public compound databases, including ours, have errors
“Incorrect” structures – assertions, timelines etc
“Incorrect” names associated with structures
Properties
Links
Publications
ENORMOUS CHALLENGE
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The Structure of Vitamin K?
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MeSH
A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants, VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K
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The Structure of Vitamin K1?
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What is the Structure of Vitamin K1?
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CAS’s Common Chemistry
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Wikipedia
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ChEBI – Manual Curation
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“2-methyl-3-(3,7,11,15-tetramethylhexadec-2-enyl)naphthalene-1,4-dione”
Variants of systematic names on PubChem
2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E)-3,7,11,15-tetramethyl
2-methyl-3-(3,7,11,15-tetramethyl
2-methyl-3-[(E)-3,7,11,15-tetramethyl
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Question Everything online: www.dhmo.org
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It’s all on Wikipedia…
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Chemistry on The Internet Is Messy
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It’s Methane…
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What’s Methane?
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What’s Methane?
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What ELSE is Methane???
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EPA’s DailyMed
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EPA’s DailyMed
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EPA’s DailyMed
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PHYSPROP Database
The freely downloadable database under the EPI Suite prediction software
Very Basic filters suggest data quality issues
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The Stereochemistry challenge.
12500 chemicals with “missed” stereo
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With Great Fanfare…
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NPC Browser http://tripod.nih.gov/npc/
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NPC Browser http://tripod.nih.gov/npc/
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Openness and Quality IssuesWilliams and Ekins, DDT, 16: 747-750 (2011)
Science Translational Medicine 2011
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Public Domain Databases
Our databases are a mess…
Non-curated databases are proliferating errors
We source and deposit data between databases
Original sources of errors hard to determine
Curation is time-consuming and challenging
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Stop Whining – Fix it
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Crowdsourced Curation
Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
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Search “Vitamin H”
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“Curate” Identifiers
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“Curate” Identifiers
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“Curate” Identifiers
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Standards : Structure Standardization
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Standards : Structure Standardization
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Standards : Structure Standardization
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What needs to happen?
Standards
Standardization of structures ChEBI/PubChem sharing
InChI adoption
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The InChI Identifier
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Multiple Layers
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InChIStrings Hash to InChIKeys
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Vancomycin – Search the Internet
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Vancomycin
Search Molecular
SKELETON
Search Full Molecule
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Full Skeleton Search: 104 Hits
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Full Molecule Search: 4 Hits
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Crowdsourcing Works
>130 people have deposited data and participated in data curation
Different level curators check each other
More curators and depositors are encouraged!
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What needs to happen?
Standards
Standardization of structures ChEBI/PubChem sharing
InChI adoption
Collaboration
Stop reinventing the wheel
Share data, share efforts and speed the process
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Antony Williams vs Identifiers
Passport ID
Dad, Tony, others
SSN
Green Card
License5 email addresses
ChemSpiderman (blog,
Twitter account,
Facebook, Friendfeed)
OpenID
….
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Aspirin names and synonyms
• Text searches depend on correct association
• 335 suggested identifiers for Aspirin just on PubChem!
• Disambiguation dictionaries are necessary, not just for authors!
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The Final Search Strategy
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All Those Names, One Structure
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Ambiguity in Identifiers
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Curated Dictionaries Matter
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Success Depends on Dictionaries
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Validated Name-Structure Dictionaries
Chemical name dictionaries are used for: Text-mining (publications, patents)
Used to index PubMed and link to Google Patents
Linking to other databases – think Biology! When structures are not available drug names link
Searching the web Names link to structures link to InChIs
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I want to know about “Vincristine”
If all algorithms work then
everything on the page is
correct by default except the
name-structure relationship!
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Vincristine: Identifiers and Properties
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Vincristine: Vendors and SourcesLinked by Structure
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Vincristine: PatentsLinked by Name
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Vincristine: ArticlesLinked by Name
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Challenges of Complex Molecules
Yohimbine
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Originally 15 compounds “called” Yohimbine
54 Skeletons for Yohimbine
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Internal and external content
Built to meet primary use-case
Tailored indexes and GUIs
Internal unique language & metadata
Poor interoperability/integration
Powerpoint, Documents, Excel
Many suppliers of systems and content in a single workflow
Literature Patents NewsPipeline SAR CSRs SafetyIn vivo Etc
Pharma Information Tombs
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What could create change?
Harvard Business Review (2010)
“One change would make a substantial difference [to drug R&D]: the creation of
agreed-upon standards for digitally representing drug assets.”
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It is so difficult to navigate…
What’s the
structure?
Are they in
our file?
What’s
similar?
What’s the
target?Pharmacology
data?
Known
Pathways?
Working On
Now?Connections
to disease?
Expressed in
right cell type?
Competitors?
IP?
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Open PHACTS Project Develop a set of robust standards…
Implement the standards in a semantic integration hub
Deliver services to support drug discovery programs in pharma and public domain
22 partners, 8 pharmaceutical companies, 3 biotechs
36 months project
Guiding principle is open access, open usage, open source
- Key to standards adoption -
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ChemSpider Resources for Chemistry
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Internet Data
The Future
Commercial Software
Pre-competitive Data
Open Science
Open Data
Publishers
Educators
Open Databases
Chemical Vendors
Small organic molecules
Undefined materials
Organometallics
Nanomaterials
Polymers
Minerals
Particle bound
Links to Biologicals
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The Future of Chemistry on the Web?
Public compound databases federate & build a linked environment of validated data!
Data validation needs are not ignored
Publishers layer on information to make publications discoverable
Public-Private databases can be linked
Open Data proliferate
The “Semantic Web” in action
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Acknowledgments
The ChemSpider team
Our data providers, depositors, collaborators and curators
Software providers – OpenEye, ChemDoodle, ACD/Labs, GGA Software, Open Source (Jmol, JSpecView, OpenBabel)
Sean Ekins @collabchem
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Thank you
Email: [email protected]
Twitter: ChemConnector
Blog: www.chemspider.com/blog
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams