Royal Society of Chemistry activities to develop a data repository for chemistry-specific data

Royal Society of Chemistry activities to develop a data repository for chemistry-specific data

Aileen Day, Alexey Pshenichnov, Ken Karapetyan, Colin Batchelor, Peter Corbett, Jon Steele, Valery Tkachenko and Antony Williams,

ACS Dallas

March 2014

Data in a Scientific Publication

• This is not new, you known the story…• So much data of value contained within a

publication and delivered in a PDF form• PDF files, and especially unclear licensing,

don’t allow me at the data so I can rework, reuse, repurpose, text mine etc.

• I specialize in XXXX. I want a database of YYYY extracted from publications and made available, for free, with capabilities I need, and the publishers should just do it

Many useful discussions…

Many good visions…

And over the years, progress…

• There is much progress with open access, data access, licensing, enhanced articles, open data, free online tools, open source codes, publishers waking up, scientists contributing

• We should be excited at what is available now, what the future holds, what opportunities exist in front of us

But it’s NOT easy..technology

But it’s not easy…US

• 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?”

An Initial “Vague” Vision Set

• Manage “all” of the chemistry data associated with chemical substances

• 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

Solving for Authors

I hate text mining data

• DERA: Developing pipelining tools for text-mining so we will be able to process documents for mark-up• Compound extraction/markup• Reaction extraction/conversion• Convert “text spectra” to generate spectral

libraries… AGGHHHHH!

“Where is the real data please?”

FIGURE

DATA

Data Preferences - total bias

• Views of a spectroscopist• Give me the data – interactive, downloadable

spectrum is way more valuable to me (processed spectrum and FID available)

• Spectral header in JCAMP standard is very incomplete (and most spectral standards)

• I want ASSIGNED/ANNOTATED spectra if possible – don’t “textify” a spectrum!

Solving the problem here..

• Binary file formats are problematic – think of the variations in instrumentation and software

• Standards can be defined – are they correctly implemented? CIF and its Checking, Spectral standards - JCAMP versions, Structure formats, etc…

• Metadata is crucial

…and what does it solve?

• “Fixing the data” – data can’t be faked as easily

• Reprocessing of analytical data can be done…weighting functions, baseline correction, deconvolution etc.

• I can convert and store it locally

But solve it for many things

• I want molecules as structure formats not images

• Please don’t make us hack tables of data

• Tell us how you generated your files – software version, software libraries, etc.

Input data pipeline

Deposition Gateway

Staging databases

Compounds

Reactions

Spectra

Materials

Articles / CSSP

Compounds Module

Spectra Module

Reactions Module

Materials Module

TextminingModule

!Module

Web UI for unified depositions

DropBox, Google Drive, SkyDrive, etc

LabTrove and other templated data

Documents

API, FTP, etc

Raw data Validated dataStaging

databases

All databases are sliced by data sources/data

collections and have simple

security model where each data

slice/source is private, public or

embargoed

Depositions Gateway User Interface

Document processing

Input data pipeline

Deposition Gateway

Staging databases

Compounds

Reactions

Spectra

Materials

Articles / CSSP

Compounds Module

Spectra Module

Reactions Module

Materials Module

TextminingModule

!Module

Web UI for unified depositions

DropBox, Google Drive, SkyDrive, etc

LabTrove and other templated data

Documents

API, FTP, etc

Raw data Validated dataStaging

databases

All databases are sliced by data sources/data

collections and have simple

security model where each data

slice/source is private, public or

embargoed

Depositions Gateway User Interface

User Interface Approach

Compounds Reactions Spectra Materials Documents

CompoundsAPI

ReactionsAPI

SpectraAPI

MaterialsAPI

DocumentsAPI

CompoundsWidgets

ReactionsWidgets

SpectraWidgets

MaterialsWidgets

DocumentsWidgets

Data tier

Data access tier

User interface

components tier

Analytical Laboratory application

User interface tier

(examples) Electronic Laboratory Notebook

Paid 3rd party integrations (various platforms – SharePoint, Google, etc)

Chemical Inventory application

Analytical Chemist

Characterize

Measure

Search

Store

<<include>>

<<include>>

<<include>>

Synthetic Chemist

Search(synthetic procedure)

Document(publish synthetic procedure)

Retrosynthetic analysis

Medicinal Chemist

Search(against database of properties)

Source(find vendor)

Analyse(cluster, dock, screen)

Computational Chemist

Search or Develop algorithm

Store results

Run calculations

Synthesize

Measure activity

Addition of Analytical Data

• Spectral Container is in development using componentized widgets for display

• NIST spectra converted into standardized JCAMP format for deposition - 296,103 spectra deposited

• 10% of remaining NIST spectra need to be curated as there are obvious structure issues

Electronic Notebook Data

• 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

Present activities – ACS Fall

• Deposition process development of compounds, reactions and spectral data by Spring• FTP, DropBox, Web-upload, ELN integration

• Compounds, Reactions, Spectral data search, display, download

• Data sharing – private, public, collaborative

• Metadata, metadata, metadata standards!

• Open Sourcing CRD and CVSP

Acknowledgments

• Jeremy Frey and Simon Coles, University of Southampton

• Will Dichtel and Leah McEwan, Cornell University

• Stuart Chalk, University of North Florida

• Bob Hanson and Bob Lancashire, Jmol and JSpecView

Thank you

Email: [email protected]: 0000-0002-2668-4821 Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

mailto:[email protected]

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

https://twitter.com/ChemConnector

http://www.chemconnector.com/

http://www.slideshare.net/AntonyWilliams

Royal Society of Chemistry activities to develop a data repository for chemistry-specific data

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