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The Big Data Challenges
Associated with Building a National
Data Repository for Chemistry

Antony Williams
ICIC Meeting, V...
So what is all this Big Data?
And the World of Chemistry?
And the World of Chemistry?

“The InChIKey indexing has therefore turned
Google into a de-facto open global chemical
infor...
And the World of Chemistry?
RSC’s ChemSpider
>29 million chemicals from >500 sources
…and the world of Openness
Times have changed…
Open Access funder mandates…
Times have changed…
Growth, growth, growth…
Publishers are responding
The world of Open Data…
Open Data are everywhere
• Is Openness and Social Sharing changing
the world?
• The cultural experiments in Open Data and
...
Publications-summary of work
• Scientific publications are a summary of work
•
•
•
•

Is all work reported?
How much scien...
About Me…as a Chemist
• I’ve performed a few dozen chemical
syntheses
• I’ve run thousands of analytical spectra
• I’ve ge...
What of non-abstracted data?
• How much data generated in a lab, that COULD
go public, is lost forever?
What of non-abstracted data?
• How much data generated in a lab, that COULD
go public, is lost forever?
• Public Domain re...
ChemSpider
• ChemSpider allowed the community to
participate in linking the internet of chemistry
& crowdsourcing of data
...
Crowdsourced “Annotations”
• Users can add
•
•
•
•
•
•
•
•

Descriptions, Syntheses and Commentaries
Links to PubMed artic...
An EPSRC Call

“…the identification of the need for a UK
national service for the provision of a
searchable, electronic ch...
National Chemical Database Service
• Service for UK Academics
• “Prepaid access” integrating commercial
databases and serv...
National Chemical Database Service
National Chemical Database Service
• Service for UK Academics
• “Prepaid access” integrating commercial
databases and serv...
Development of Data Repository
•
•
•
•
•

Data repository should not just be a data
dump – should not be a “big disk”
Sear...
What can drive participation?
• What can drive scientists to participate and
contribute?
•
•
•
•
•
•

Ensuring provenance ...
AltMetrics
AltMetrics
AltMetrics as Scientist Impact
AltMetrics
Plum Analytics
Plum Analytics
Rewards and Recognition
The First Step badge is
awarded when a user
submits (& has published)
their 1st CSSP article.

Con...
AltMetrics Feeds
• For our data repository ensure contribution of
data will feed out to the AltMetrics platforms
• Every d...
Domain Specific Challenges
• Creating a platform of value not just dumping
•

Searchability, segregation, tagging, use and...
Domain Specific Challenges
• Quality of data at source
• ensuring chemicals are correct - VALIDATION
• reactions map and b...
Validating Chemicals
• Community service
for validation and
standardization of
chemicals (CVSP)
• Open rules sets but
stan...
Validating chemicals
J. Brechner, IUPAC
Graphical
Representation of
stereochem.
configurations
Section: ST-1.1.10

DB08128...
Standardizing Chemicals
Validated Name-Structure
dictionaries for data checking
• Chemical name dictionaries used for:
• Text-mining (publications...
Difficult to navigate…
IP?
IP?
What’s the
What’s the
structure?
structure?
Are they in
Are they in
our file?
our file?
Wha...
Inside our Publication Archive
• How much data is in the archive, in the
publications and in the supplementary info?
• How...
What if we could capture it all?
Digitally Enhancing the RSC Archive
Linking Names to Structures
Semantic Mark-up of Articles
Hosting Reactions
•
•
•

Seed set of over 1 million reactions from patents to
develop validation and standardization routi...
The challenges of analytical data
• Integration of ChemSpider to analytical
instrumentation vendors already in place
• Agi...
Turning “Figures” Into Data
Community Data Repository
• Automated depositions of data – service-based
deposition, sweep and deposit
• Integrate to Ele...
E-Lab Notebooks
• Integration between ELNs
and:
• ChemSpider
• ChemSpider Reactions
• Chemistry Data Repository
What do we have in place?
• We are testing a data repository on our assets –
ChemSpider and our archive of publications
• ...
The Challenges Ahead
• Chemistry is NOT just nicely defined structures!
• Materials, minerals, attached to beads,
polymers...
The Future
Internet Data

Small organic molecules
Undefined materials
Organometallics
Nanomaterials
Polymers
Minerals
Part...
RSC Open Access Repository

•Imagine applying text-mining to all articles
•Extract all chemicals, syntheses, chemistry
dat...
Thank you
Email: williamsa@rsc.org
ORCID: 0000-0002-2668-4821
Twitter: @ChemConnector
Personal Blog: www.chemconnector.com...
Big data challenges associated with building a national data repository for chemistry
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Big data challenges associated with building a national data repository for chemistry

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At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types ssociated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined.

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Transcript of "Big data challenges associated with building a national data repository for chemistry"

  1. 1. The Big Data Challenges Associated with Building a National Data Repository for Chemistry Antony Williams ICIC Meeting, Vienna October 14th 2013
  2. 2. So what is all this Big Data?
  3. 3. And the World of Chemistry?
  4. 4. And the World of Chemistry? “The InChIKey indexing has therefore turned Google into a de-facto open global chemical information hub by merging links to most significant sources, including over 50 million PubChem and ChemSpider records.”
  5. 5. And the World of Chemistry?
  6. 6. RSC’s ChemSpider >29 million chemicals from >500 sources
  7. 7. …and the world of Openness
  8. 8. Times have changed… Open Access funder mandates…
  9. 9. Times have changed… Growth, growth, growth…
  10. 10. Publishers are responding
  11. 11. The world of Open Data…
  12. 12. Open Data are everywhere • Is Openness and Social Sharing changing the world? • The cultural experiments in Open Data and exchange are almost daily • Mobile platforms enhance participation • And then what of Chemistry Data???
  13. 13. Publications-summary of work • Scientific publications are a summary of work • • • • Is all work reported? How much science is lost to pruning? What of value sits in notebooks and is lost? Publications offering access to “real data”? • How much data is lost? • • • How many compounds never reported? How many syntheses fail or succeed? How many characterization measurements?
  14. 14. About Me…as a Chemist • I’ve performed a few dozen chemical syntheses • I’ve run thousands of analytical spectra • I’ve generated thousands of NMR assignments • I’ve probably published <5% of all work • Most of it has been lost • But things can be different today…. • But it still needs to be associated with me…
  15. 15. What of non-abstracted data? • How much data generated in a lab, that COULD go public, is lost forever?
  16. 16. What of non-abstracted data? • How much data generated in a lab, that COULD go public, is lost forever? • Public Domain reference databases of value? • Syntheses • Properties • Spectra and CIFs • Images • Raw data vs. representations of data
  17. 17. ChemSpider • ChemSpider allowed the community to participate in linking the internet of chemistry & crowdsourcing of data • Successful experiment in terms of building a central hub for integrated web search • More people are “users” than “contributors” • Yet basic feedback and game-play helps
  18. 18. Crowdsourced “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
  19. 19. An EPSRC Call “…the identification of the need for a UK national service for the provision of a searchable, electronic chemical database for the UK academic research community.”
  20. 20. National Chemical Database Service • Service for UK Academics • “Prepaid access” integrating commercial databases and services • Access to curated data sets • Provision of prediction algorithms
  21. 21. National Chemical Database Service
  22. 22. National Chemical Database Service • Service for UK Academics • “Prepaid access” integrating commercial databases and services • Access to curated data sets • Provision of prediction algorithms • Ultimate goal is to federate search • Development of “data repository”
  23. 23. Development of Data Repository • • • • • Data repository should not just be a data dump – should not be a “big disk” Searchable, integrated, segregated repository of data types Data access including private, shared embargoed and public Delivery of derived models from data Integrated to AltMetrics models
  24. 24. What can drive participation? • What can drive scientists to participate and contribute? • • • • • • Ensuring provenance of their data for reuse Mandates from funding agencies Improved systems to ease contribution Additional contributions to science Improved publishing processes Recognition for contributions
  25. 25. AltMetrics
  26. 26. AltMetrics
  27. 27. AltMetrics as Scientist Impact
  28. 28. AltMetrics
  29. 29. Plum Analytics
  30. 30. Plum Analytics
  31. 31. Rewards and Recognition The First Step badge is awarded when a user submits (& has published) their 1st CSSP article. Congratulations! Your 1st CSSP article has been published. Philosopher Lao Tzu said “A journey of a thousand miles begins with a single step”. In the same way we hope that this will be the first of many submissions that you make to CSSP.
  32. 32. AltMetrics Feeds • For our data repository ensure contribution of data will feed out to the AltMetrics platforms • Every data point, every data download, use and reuse will be associated with the scientist • Data will be DOI’ed (presently under review) • Services provided will allow for AltMetrics use
  33. 33. Domain Specific Challenges • Creating a platform of value not just dumping • Searchability, segregation, tagging, use and reuse, collaboration, low barrier to participation • Quality of chemistry data at source • • • • ensuring chemicals are correct reactions map and balance as appropriate file format handling for analytical data types – binary file formats are proprietary valid interpretation of data
  34. 34. Domain Specific Challenges • Quality of data at source • ensuring chemicals are correct - VALIDATION • reactions map and balance as appropriate – VALIDATION and STANDARDIZATION • file format handling for analytical data types – binary file formats are proprietary STANDARDIZATION • valid interpretation of data – VALIDATION and ANNOTATION
  35. 35. Validating Chemicals • Community service for validation and standardization of chemicals (CVSP) • Open rules sets but standard set based on FDA substance registry system
  36. 36. Validating chemicals J. Brechner, IUPAC Graphical Representation of stereochem. configurations Section: ST-1.1.10 DB08128 DB06287
  37. 37. Standardizing Chemicals
  38. 38. Validated Name-Structure dictionaries for data checking • Chemical name dictionaries used for: • Text-mining (publications, patents) • Linking to other databases – think Biology • Drug names are incredibly valuable links • Searching the web • Names link to structures
  39. 39. Difficult 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?
  40. 40. Inside our Publication Archive • How much data is in the 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?
  41. 41. What if we could capture it all? Digitally Enhancing the RSC Archive
  42. 42. Linking Names to Structures
  43. 43. Semantic Mark-up of Articles
  44. 44. Hosting Reactions • • • Seed set of over 1 million reactions from patents to develop validation and standardization routines. Reactions to be extracted from RSC journal articles, ESI and reaction databases will be examined Resulting validation algorithms used at deposition
  45. 45. The challenges of analytical data • Integration of ChemSpider to analytical instrumentation vendors already in place • Agilent, Bruker, Thermo, Waters • Vendors produce complex proprietary data formats and standard formats are required (JCAMP, NetCDF, AniML) • • • • ChemSpider already hosts thousands of JCAMP spectra Support of “assigned spectra” in place Data validation approaches understood There are a myriad of analytical data types…
  46. 46. Turning “Figures” Into Data
  47. 47. Community Data Repository • Automated depositions of data – service-based deposition, sweep and deposit • Integrate to Electronic Lab Notebooks as feeds • High value would be databases of reference data, but validated by model validation and the community • National services feeding the repository – crystallography, mass spectrometry
  48. 48. E-Lab Notebooks • Integration between ELNs and: • ChemSpider • ChemSpider Reactions • Chemistry Data Repository
  49. 49. What do we have in place? • We are testing a data repository on our assets – ChemSpider and our archive of publications • Working with many collaborators to define needs • Deposition system for deposition of chemical compounds – hosts >29 million chemicals • Crowdsourcing curation & annotation platform • Chemical validation & standardization platform • Chemical reactions database with >1 million reactions and presently developing RVSP • Analytical data handling formats (JCAMP preferred) • And lots in development…
  50. 50. The Challenges Ahead • Chemistry is NOT just nicely defined structures! • Materials, minerals, attached to beads, polymers, ambiguous materials • Domain-specific measurements • File format standards are limited in application • Encouraging scientists to free up their data • AltMetrics, open data mandates, systems • The data explosion continues • 4 years ahead to expand capability
  51. 51. The Future Internet Data Small organic molecules Undefined materials Organometallics Nanomaterials Polymers Minerals Particle bound Links to Biologicals Commercial Software Pre-competitive Data Open Science Open Data Publishers Educators Open Databases Chemical Vendors
  52. 52. RSC Open Access Repository •Imagine applying text-mining to all articles •Extract all chemicals, syntheses, chemistry data and link to OA articles •Provide additional data handling tools
  53. 53. Thank you Email: williamsa@rsc.org ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams
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