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Facilitating Scientific Discovery
through Crowdsourcing and
Distributed Participation
Antony Williams
NETTAB
October 17th 2013
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If it was not just about me…
• Together we might:
• build an encyclopedia
• …and rate restaurants
• …share book reviews
• …and movie reviews
• …and reviews of service providers
• …organize sit-ins and social action
• …and more data might just be Open
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If it was not just about me…
• Together we might:
• build an encyclopedia
• …and rate restaurants
• …share book reviews
• …and movie reviews
• …and reviews of service providers
• …organize sit-ins and social action
• …and more data might just be Open
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Crowdsource the galaxy
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Various ways to contribute
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Where Am I From?
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What can be done with Big Data
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Patients Like Me
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Patients Like Me
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Let’s Change the World
• Let’s map together all historical chemistry
data and build systems to integrate new data
• Heck, let’s integrate chemistry and biology
data and add in disease data too
• Lets model the data and see if we can
extract new relationships – quantitative and
qualitative
• Let’s make it all available on the web
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That’s a BIG Request
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What About Something Smaller?
• 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
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I’m from here…
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Wikipedia
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Wikipedia
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Moel-Y-Parc
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I care…I want to contribute…
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The Power of Contribution
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How do you spell Afonwen?
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And the Welsh know!
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Whoa…
• So the world can be mapped…
• We can enter a 3D environment within the map
• We can add annotations
• We can use the data, we can reference it, we
can extract it, we can make decisions with it
• And we can do it on our lap, in our hands
• Let’s crowdsource chemistry
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Chemistry Data is Everywhere
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In a Galaxy far, far away…
• Build a structure-centric hub
• Aggregate structure-based data and integrate
• Link to additional data sources
• Patents
• Publications
• Vendors
• Models
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A LITTLE Chemistry First
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Structural Diagrams
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Structural Diagrams
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Analytical Data
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Does Stereochemistry Matter?
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Does one stereocenter matter?
Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
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Structural Representations
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The InChI Standard
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InChIKeys
Search the Web by Structure
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The Quality of Chemical Data Online
What is the Structure of Vitamin K?
A lipid cofactor that is required for normal
blood clotting. Several forms of vitamin K
have been identified: VITAMIN K1
(phytomenadione) derived from plants,
VITAMIN K2 (menaquinone) from bacteria &
synthetic naphthoquinone provitamins,
VITAMIN K3 (menadione).
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What is the Structure of Vitamin K1?
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What is the Structure of Vitamin K1?
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Chemical Abstracts Service
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Wikipedia
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Wolfram Alpha
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DailyMed
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People Use Trusted Resources…
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We can all help clean it up…
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How will it improve?
Participation
and
contribution
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Building a chemistry hub ..issues
ALL Different, ALL “Domoic Acids”
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ALL Different, ALL “Domoic Acids” ONE is “correct”
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The EXPERTS must get it right?!
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Web 2.0 Contribution
• We have been contributing
to the web for a along time
already – but how much in
chemistry?
• A few blogs, an increasing
amount of tweeting but
what about data sharing in
chemistry?
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Challenging a Publication
This story is only 11 years ago!
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Oops…
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>2 Years to Resolution
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The New Way of Challenging
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Challenging Science…
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Collaboration towards completion
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Detailed constructive dialog
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Oxidation by Sodium Hydride?
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The Blogosphere Analyzes…
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How much is in the archives?
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Data Mine the Archives
• Imagine the power of data-mining the archives
of the publishers
• Generate nanopublications from the articles
and make available to the reasoning engines
• Now imagine extracting all the “data” and
freeing it up to the semantic web.
• MORE LATER ON THAT!
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Open Notebook Science Analysis
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Oxidation by Sodium Hydride?
THIS IS A COP OUT!!!
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What is Hexacyclinol?
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The Blogosphere “Discusses”…
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What is real, what is fake?
http://www.youtube.com/watch?v=hMpAoC-h5SA
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Question Everything Online:
www.dhmo.org
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Chemistry is Dangerous!
http://tinyurl.com/cl2awnj
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Chemistry is Dangerous
Florida DJs May Face Felony for April
Fools' Water Joke
“… told their listeners that "dihydrogen
monoxide" was coming out of the taps
throughout the Fort Myers area.”
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How do you recognize good vs bad?
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Is this real?
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Junk vs Real
• “We then established a collaboration with
professor Sum Ting Wong, a fugitive from
the North Korean University Hu Yu Hai
Ding”
• “..identified as the new protein Wai So
Dim”
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What is real, what is fake?
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Helping to change science
• Participation and contribution
• Immediacy of action
• Platforms for contribution
• Openness…whatever that is
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Getting Called Out in Public…
Rules for Licensing Data
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Challenged in the Twittersphere
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Annotating Articles Today…
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Attribution to me…
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Back to Chemistry….
• ANYBODY can annotate a record on ChemSpider
• Registered users can deposit new data
• Compounds
• Reactions
• Links
• Analytical Data
• Images
• Movies,
• Data sets
• Registered users can validate existing data
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CURATION Search “Vitamin H”
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“Curate” Identifiers
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“Curate” Identifiers
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Data Validation is Exacting Work
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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
• Integrate Chemistry and Biology data by implementing the
standards in a semantic integration hub
• Deliver services to support drug discovery programs in
pharma and public domain
• INITIALLY 22 partners, 8 pharmaceutical companies, 3
biotechs
Guiding principle is open access, open usage, open source
- Key to standards adoption -
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ChemSpider serving RDF and
the semantic web
• Using RDF permalinks
• http://www.chemspider.com/Chemical-
Structure.7787.rdf
• Using a Search Term
• http://www.chemspider.com/rdf.ashx?q=cyclohexane
• http://rdf.chemspider.com/cyclohexane
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RDF and the semantic web
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The issue of identifiers
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Aspirin on ChemSpider
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PubChem Drugbank ChemSpider
Imatinib
Mesylate
What is Gleevec
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Strict Relaxed
Analysing Browsing
LinkSet#1 {
chemspider:gleevec hasParent imatinib ...
drugbank:gleevec exactMatch imatinib ...
}
chemspider:gleevec drugbank:gleevec
Dynamic Equality
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CVSP : chemical validation
Free chemistry validation platform that performs:
• Structure validation • Atoms
• Bonds
• Valence
• Stereo
• If aromatic - check that uniquely dearomatized
• Strongest acid not ionized first in partially-ionized system
• Cross-matching of SDF fields • synonyms
• InChIs
• Smiles
But what about Data Quality???
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Validation
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• Custom processing let’s user to put together workflow from pre-defined standardization modules list
Standardization
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Data Review
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DrugBank dataset (6516 records)
~60 records that can’t be dearomatized unambiguously
DB04283 DB04462
DrugBank
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~30 records with bonds that do not make sense
DB04283
DDB04009
Nonsensical bonds
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~40 records where InChIs did not match the structure DrugBank ID: DB00755 InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+
DruGBank ID: DB00614
Mismatches – which is correct?
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DB08128
J. Brechner, IUPAC Graphical Representation of stereochem. configurations Section: ST-1.1.10
DB06287
7 records with 2 stereo bonds at chiral atoms
Stereobond issues
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Chemistry Validation and Standardization
Platform (CVSP)
at cvsp.chemspider.com
• Validation
• Standardization
• Parent generation
RDF Export
Data
Chemistry Data out to OPS
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Data is being
imported from
ChemSpider to
Open PHACTS in
RDF/turtle
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– VoID is an RDF Schema vocabulary for expressing metadata
about RDF datasets.
• skos:exactMatch (Simple Knowledge Organisation System)
e.g. To link compounds in OPS with compounds in ChEBI.
• skos:closeMatch
e.g. To link Stereo Insensitive Parents to their Children within OPS.
• skos:relatedMatch
e.g. To link Parent compounds that contain others as Fragments.
– Recommendations on VoID specified by Manchester Uni. here: http://www.cs.man.ac.uk/~graya/ops/2012/ED-datadesc/
RDF/VOID
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RDF Export
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Ongoing Updates to Linksets
• Ongoing data checking activities on ChemSpider
• Does Crowdsourcing work?
• But WHY would people validate ChemSpider?
• What can be done to encourage participation?
• How will we deliver on Barend’s Million Minds
approach – he has ideas…see later
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Crowdsourcing – does it work?
• >200 people EVER have deposited or curated
data
• Database hosts make the largest contributions
• ChemSpider staff do the most curation
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Contributions
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Curation Activities
• 2009 – 8255 curations by 43 people
• 2010 – 10014 curations by 66 people
• 2011 – 16025 curations by 116 people
• 2012 – 13127 curations by 74 people
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Depositors
• 2009 91 unique depositors
• 2010 120 unique depositors
• 2011 99 unique depositors
• 2012 120 unique depositors
• “The crowd is small – very small”
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Rewards and Recognition
• The badgesonomy culture of recognition is
growing.
• Badges are commonplace
• FourSquare
• Klout
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Rewards and Recognition
• Rewards and Recognition
integrated across all
ChemSpider related projects
• Including paths to expose
such recognition on
AltMetrics platforms
• MAY work for young
scientists
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The Alt-Metrics Manifesto
http://altmetrics.org/manifesto/
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ImpactStory
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Future Recognition on
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Scientists AltMetrics
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Usage, Citations, Social Media, etc
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Detailed Usage Statistics
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What makes a Scientist Notable?
What will it be in the future???
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We Are All Being Quantified…
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How I am Quantified…
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Likely Enabled by
• Persistent unique digital identifier
• Integrates to workflows such as manuscript
and grant submission
• Supports automated linkages with your
professional activities
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Summary
• A grand vision for semantic data linking is
coming to fruition. We have a lot do.
• Data quality enhancements can come through
crowdsourcing (and intelligent robots)
• Participation may be driven by new
approaches to rewards and recognition
• Publishers are understanding the value of data,
but still guard it, and generally don’t have
systems to handle it. It’s changing.
• There is so much value in the historical data
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Inside our Publication Archive
• How much data is in RSC archive, in the
publications and in the supplementary info?
• How many compounds for ChemSpider?
• How many syntheses for ChemSpider
reactions?
• How many characterization
measurements?
• Property Data
• Spectral Data
• Graphs and charts to be used for modeling?
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What if we could capture it all?
Digitally Enhancing the RSC Archive
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Start with data in publications
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Turn “Figures” Into Data
Spectral
FIGURE
Extracted
Spectrum
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Text Mining
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
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ChemSpider Reactions
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Thank You
Email: [email protected]
Twitter: ChemConnector
Personal Blog: www.chemconnector.com
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