Dealing with the complex challenge of managing diverse chemistry data online Antony Williams, Valery Tkachenko, Alexey Pshenichnov and Ken Karapetyan ACS San Francisco August 2014

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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…

Think about chemistry a mo’ If we imagine that permission exists… (i.e. forget IP, chemical and pharma companies etc…think students…) How many syntheses are performed How many spectra are run How many properties are measured How many compounds are made How many, how much, how big??..... Let’s go manage it all!!

Consider a shift to Openness

Open Access funder mandates… Times have changed… Open Access funder mandates…

Publishers are responding

The world of Open Data is here

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???

An Experiment - 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

An Experiment - CSSP

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.”

National Chemical Database Service

We set a vision… Manage “all” of the chemistry data associated with chemical substances – PUBLISHED and UNPUBLISHED Based on user selected licensing the data to be downloadable, reusable, interactive Build a platform that enables the scientist Data storage, validation, standardization and curation Collaborative data sharing Provide data platform that can enable and enhance publishing of scientific papers

Data Repository Registration of chemical compounds Deposition of chemical syntheses Addition of analytical data Integration to electronic notebooks Rewards and recognition for data sharing Document processing Hosting of data as private, embargoed or public

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

New Repository Architecture doi: 10.1007/s10822-014-9784-5

New Repository Architecture

Input data pipeline

Compounds

Reactions

Analytical data

Crystallography data

For Deposition of Data 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

Input data pipeline

Depositions Gateway User Interface

Deposition of Data

Validate and Standardize

CVSP Filtering

CVSP Filtering of DrugBank

ChEMBL (1.3 million records) 11,020 records with 4 bonds and zero charge, e.g. CHEMBL501101 or CHEMBL501973 271 records with hypervalent oxygen (e.g. , CHEMBL2219679), carbon (e.g. 1005895), boron, chlorine, iodine or phosphine 6,177 records where direction of bond makes no sense, e.g. CHEMBL12760 and CHEMBL34704

Depositions User Interface

The challenges of analytical data 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…

ChemSpider ID 24528095 H1 NMR

ChemSpider ID 24528095 C13 NMR

ChemSpider ID 24528095 HHCOSY

ChemSpider ID 24528095 HSQC

ChemSpider ID 24528095 HMBC

Managing Assignments?

Depositions User Interface

Depositions from ELNs Development work integrating chemistry into the Southampton Labtrove notebook Stoichiometry table development Analytical data integration “ChemTrove” rolled out to a small test group in January

Document deposition/processing

Experimental data checker

User Interface Approach

User Interface Approach

Display Widgets

Work in Progress

Work in Progress

User Interface Approach

A Compounds Repository Interface

A Reactions/Document Interface

The PharmaSea Website

The Open PHACTS community ecosystem

Open Source Drug Discovery India

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

Scientists are Increasingly Quantified…

AltMetrics as Scientist Impact

AltMetrics

Detailed Usage Statistics

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.

http://orcid.org/0000-0002-2668-4821

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

What do we have in place? We are testing an early form of the data repository on our data – ChemSpider and our archive of publications Working with collaborators to define needs Testing and enhancing deposition systems Chemical validation & standardization platform Analytical data handling formats And lots in development…

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

But it’s not easy of course Not everything we would like around data handling is there for sure Many systems, tools, platforms are already available but we don’t know about them or even if we did contributing us “more work” “What’s in it for me?”, “It’s my data”, “It’s too much work”, “What credit do I get?”

And yes…we know…

Thank you Email: williamsa@rsc.org ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams 79