Feeding and consuming data to support open notebook science via the chem spider platform

Feeding and consuming data to
support Open Notebook Science via
the ChemSpider Platform

Antony Williams, Jean-Claude Bradley, Andrew Lang and
Valery Tkachenko

ACS Philadelphia August 2012

Setting the Stage
 Chemists want access to tools and data

 The more capabilities the better
 The more data the better
 And give us an API with that…
 And it should be free…
 And constantly updated…
 And all data should be Open…
 And make it fully Open Source…
 And it needs to be on my mobile…

Setting the Stage
 Chemists have access to tools and data

 The more capabilities the better – we’ll see
 The more data the better – changing daily
 And give us an API with that… - not just one
 And it should be free… - sure
 And constantly updated… - indeed..please help!
 And all data should be Open…- licensing
 And make it fully Open Source… - kinda, sorta
 And it needs to be on my mobile… - sure

Welcome to ChemSpider
 5 years, 28 million chemicals, linking 400 data
sources and growing daily

 Hosted by the Royal Society of Chemistry
 An important part of our long term strategic vision

 Free to access
 With lots/most/all (?) of the functionality
necessary to support chemists and Open
Notebook Science…

Why Use ChemSpider? LINKING OUT

Work in Progress – 300k Reactions

Storing ONS Reactions
 Working with JC Bradley to host ONS reactions
 Linking directly back to ONS reactions

 What if the links decay?
 Host all related ONS data – benefits of Openness!
 Future applications for RInChIs

What we have been asked for
 “Allow us to grab data”
 “Let us link”
 “Give us web services to integrate”
 “Can we store our data with you?”
 “Can you give us predictions to validate data?”

What we have been asked for
 “Allow us to grab data”
 “Let us link”
 “Give us web services to integrate”
 “Can we store our data with you?”
 “Can you give us predictions to validate data?”

 “Can you build us an ELN?”

Simple Linking to ChemSpider
 Link using ChemSpiderID
 http://www.chemspider.com/1234567

ChemSpider IDs Proliferating Now

Simple Querying Example
 http://
www.chemspider.com/Search.aspx?q=InChIKey=XXO

Or InChI, or SMILES
 http://www.chemspider.com/Search.aspx?q=InChI=1S
m1/s1

 http://www.chemspider.com/Search.aspx?
q=Clc1ccc(cc1)C(O)=C3C(=O)C(=O)N([C@@H]3
c2cccc(F)c2)CCc5c4ccccc4nc5

MANY Web Services for integration

Feeding ONS Data into ChemSpider
 ONS data can be deposited into ChemSpider and
linked out to the ONS pages
 Simply deposit structure(s) and links

Feeding and consuming data to support open notebook science via the chem spider platform

 ONS Solubility Challenge

So isn’t ONS all about ELNs?
 Open Notebook Science is about
 Making records of research publicly available
online as it is recorded

 ONS is enabled by software tools and platforms
 Keep the notebook of the researcher online
with all raw and processed data as it is
generated (close to or near real time)
 Notebooks as Wikis, Commercial or Free ELNs
published to the web (choose public/private –
what data to expose)

Feeding ELN Data into ChemSpider
 Integrate e-Notebooks into ChemSpider

 IDBS e-Workbook plug-in allows direct
deposition of chemical structures
 Can be extended to more ELN content
 Spectra
 Reactions
 Properties etc.

 Integration Video http://tinyurl.com/9xnprqr

Feeding ELN Data into ChemSpider

How much data is lost?
 How many reactions in a thesis never get
published?
 How many spectra of common materials could be
shared?
 How many properties are measured and lost?
 What stands in the way of sharing?
 Is it technology?
 Permissions? “The Boss”, Licensing?

 And yes – there are data quality issues but there
is algorithmic checking and data curation to help

What could the future look like?
 “Publicly funded” research data flows onto the web
 Licensing is clear and NOT a challenge
 Machines are picking up data and depositing

 EXAMPLE project – Any interest?
 Put your spectra/structure in folders (Dropbox)
 ChemSpider robot scoops, processes and
deposits – opportunity with JC Bradley
 While processing also predicts spectra and
compares for validation

Leaving the Stage
 Chemists have access to tools and data

 The more capabilities the better – what’s missing?
 The more data the better – anyone want to share?
 And give us an API with that… - ask us for help
 And it should be free… - it is
 And constantly updated… - help annotate/curate
 And all data should be Open…- licensing
 And make it fully Open Source… - book chapter
 And it needs to be on my mobile… - it is

New URLs to try out
 ChemSpider Reactions:
www.chemspider.com/reactions

 ChemSpider Validation and Standardization
Platform: www.chemspider.com/cvsp

 ChemSpider Google:
www.chemspider.com/google

Acknowledgments
 RSC Cheminformatics team
 JC Bradley’s lab
 Daniel Lowe – reactions
 Commercial Software – GGA Software,
ACD/Labs, OpenEye
 Open Source Components

Thank you

Email: williamsa@rsc.org
Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams

Feeding and consuming data to support open notebook science via the chem spider platform

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