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Facilitating Scientific Discovery through Crowdsourcing and Distributed Participation
The document discusses the potential of crowdsourcing to enhance scientific discovery, particularly in the field of chemistry, by encouraging open participation and data sharing. It emphasizes the importance of building databases, validating data, and integrating diverse sources to improve accessibility and collaboration in scientific research. Additionally, it highlights the role of contributions from individuals and organizations in creating a comprehensive and validated chemistry hub, enabling better decision-making and facilitating innovation.
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Facilitating Scientific Discovery through Crowdsourcing and Distributed Participation
- 1. Facilitating Scientific Discovery throughCrowdsourcing and Distributed Participation Antony Williams NETTAB October 17th 2013
- 2. If it wasnot 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
- 3. If it wasnot 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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- 6. Various ways tocontribute
- 8. Where Am IFrom?
- 9. What can bedone with Big Data
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- 12. Let’s Change theWorld • 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
- 13. That’s a BIGRequest
- 14. What About SomethingSmaller? • 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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- 21. I care…I wantto contribute…
- 22. The Power ofContribution
- 23. How do youspell Afonwen?
- 24. And the Welshknow!
- 25. Whoa… • • • • So the worldcan 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
- 26. Chemistry Data isEverywhere
- 27. In a Galaxyfar, far away… • Build a structure-centric hub • Aggregate structure-based data and integrate • Link to additional data sources • • • • Patents Publications Vendors Models
- 28. A LITTLE ChemistryFirst
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- 33. Does one stereocentermatter? Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
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- 36. InChIKeys Search the Webby Structure
- 37. The Quality ofChemical 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).
- 38. What is theStructure of Vitamin K1?
- 39. What is theStructure of Vitamin K1?
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- 45. People Use TrustedResources…
- 46. We can allhelp clean it up…
- 47. How will itimprove? Participation and contribution
- 48. Building a chemistryhub ..issues ALL Different, ALL “Domoic Acids”
- 49. ONE is “correct” ALLDifferent, ALL “Domoic Acids”
- 50. The EXPERTS mustget it right?!
- 51. 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?
- 52. Challenging a Publication Thisstory is only 11 years ago!
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- 55. >2 Years toResolution
- 56. The New Wayof Challenging
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- 60. Oxidation by SodiumHydride?
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- 63. How much isin the archives?
- 64. Data Mine theArchives • 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!
- 65. Open Notebook ScienceAnalysis
- 66. Oxidation by SodiumHydride? THIS IS A COP OUT!!!
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- 69. What is real,what is fake? http://www.youtube.com/watch?v=hMpAoC-h5SA
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- 72. Chemistry is Dangerous FloridaDJs 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.”
- 73. How do yourecognize good vs bad?
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- 75. Junk vs Real • “Wethen 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”
- 76. What is real,what is fake?
- 77. Helping to changescience • • • • Participation and contribution Immediacy of action Platforms for contribution Openness…whatever that is
- 78. Getting Called Outin Public… Rules for Licensing Data
- 79. Challenged in theTwittersphere
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- 82. 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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- 86. Data Validation isExacting Work
- 87. It is sodifficult to navigate… IP? IP? What’s the What’s the structure? structure? Are they in Are they in our file? our file? What’s What’s similar? similar? Pharmacology Pharmacology data? data? What’s the What’s the target? target? Known Known Pathways? Pathways? Competitors? Competitors? Connections Connections to disease? to disease? Working On Working On Now? Now? Expressed in Expressed in right cell type? right cell type?
- 88. • Open PHACTSProject • 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 Guiding principle is open access, open usage, open source -- Key to standards adoption -Key to standards adoption
- 89. ChemSpider serving RDFand the semantic web • • Using RDF permalinks http://www.chemspider.com/Chemical-Structure.7787.rd • • • Using a Search Term http://www.chemspider.com/rdf.ashx?q=cyclohexane http://rdf.chemspider.com/cyclohexane
- 90. RDF and thesemantic web
- 91. The issue ofidentifiers
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- 97. Dynamic Equality Strict Relaxed Analysing Browsing chemspider:gleevec chemspider:gleevec drugbank:gleevec drugbank:gleevec LinkSet#1 { chemspider:gleevechasParent imatinib ... drugbank:gleevec exactMatch imatinib ... }
- 98. But what aboutData Quality??? 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
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- 100. Standardization • Custom processinglet’s user to put together workflow from pre-defined standardization modules list
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- 102. DrugBank DrugBank dataset (6516 records) ~60records that can’t be dearomatized unambiguously DB04283 DB04462
- 103. Nonsensical bonds ~30 recordswith bonds that do not make sense DB04283 DDB04009
- 104. Mismatches – whichis correct? ~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)11-1218-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,15H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+ DruGBank ID: DB00614
- 105. Stereobond issues 7 recordswith 2 stereo bonds at chiral atoms J. Brechner, IUPAC Graphical Representation of stereochem. configurations Section: ST-1.1.10 DB08128 DB06287
- 106. Chemistry Data outto OPS Data Chemistry Validation and Standardization Platform (CVSP) at cvsp.chemspider.com •Validation •Standardization •Parent generation RDF Export
- 107. Data is being importedfrom ChemSpider to Open PHACTS in RDF/turtle
- 108. RDF/VOID – VoID isan 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/
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- 110. Ongoing Updates toLinksets • • • • 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
- 111. Crowdsourcing – doesit 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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- 113. 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
- 114. Depositors • • • • 2009 2010 2011 2012 91 unique depositors 120unique depositors 99 unique depositors 120 unique depositors • “The crowd is small – very small”
- 115. Rewards and Recognition •The badgesonomy culture of recognition is growing. • Badges are commonplace • FourSquare • Klout
- 116. 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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- 121. Usage, Citations, SocialMedia, etc
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- 123. What makes aScientist Notable? What will it be in the future???
- 124. We Are AllBeing Quantified…
- 125. How I amQuantified…
- 128. Likely Enabled by •Persistent unique digital identifier • Integrates to workflows such as manuscript and grant submission • Supports automated linkages with your professional activities
- 129. Summary • A grandvision 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
- 130. Inside our PublicationArchive • 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?
- 131. What if wecould capture it all? Digitally Enhancing the RSC Archive
- 132. Start with datain publications
- 133. Turn “Figures” IntoData Spectral FIGURE Extracted Spectrum
- 134. Text Mining The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4thiadiazol-5-yl)ureaprepared 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)-Nmethyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
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- 136. Thank You Email: williamsa@rsc.org Twitter:ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams