Dealing with the complex challenge of managing diverse chemistry data online
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Transcript of Dealing with the complex challenge of managing diverse chemistry data online
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
CAS Counter http://www.cas.org/content/counter
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…
• 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!!
Think about chemistry a mo’
Consider a shift to Openness
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
• Manage “all” of the chemistry data associated with chemical substances – PUBLISHED and UNPUBLISHED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
We set a vision…
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 Architecturedoi: 10.1007/s10822-014-9784-5
New Repository Architecture
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
Input data pipeline
Deposition Gateway
Staging databases
Compounds
Reactions
Spectra
Materials
Articles / CSSP
Compounds Module
Spectra Module
Reactions Module
Materials Module
TextminingModule
1Module
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
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
Deposition Gateway
Staging databases
Compounds
Reactions
Spectra
Materials
Articles / CSSP
Compounds Module
Spectra Module
Reactions Module
Materials Module
TextminingModule
1Module
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
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
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
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
Display Widgets
Work in Progress
Work in Progress
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
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
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.
The First Step badge is awarded when a user submits (& has published) their 1st CSSP article.
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: [email protected]: 0000-0002-2668-4821 Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams