connecting chemistry across the internet using chemspider
TRANSCRIPT
Connecting Chemistry Across the Internet Using ChemSpider
Antony J Williams and Valery TkachenkoSERMACS, November 15th 2012
Chemistry Data and the Weeds
Tell me about Roundup
So what is Round Up?
The World’s Encyclopedia
Roundup
Where do we Round Up data?
Where can I find the molfile for Roundup? Papers/Patents about Roundup? What are the side effects of Roundup? Where can I order Roundup? What are the physicochemical properties? Metabolic pathways? Different synonyms of Roundup? Synthesis of Roundup? Side effects of Roundup? Etc….
Where do I Round Up Data?
In an increasing LinkedData map….
But I want to aggregate data? So…
ChemSpider
Takes on the role of a structure centric hub:
Connecting, validating, qualifying data Enhancing data with connections to services Provides access to data and services for others
to use (Thermo, Agilent, Bruker, Waters, ACD/Labs, Accelrys, etc.)
Uses available services to integrate, connect and enhance the offering
Roundup on ChemSpider
What will ChemSpider give us??
What will ChemSpider give us??
What will ChemSpider give us??
What will ChemSpider give us??
What will ChemSpider give us??
What will ChemSpider give us??
ChemSpider is Collapsing Data???
What will ChemSpider give us??
For Glyphosate itself
How did we build it?
We deal in Molfiles or SDF files – with coordinates Deposit anything that has an InChI – we support
what InChI can handle, good and bad Standardization based on “InChI standardization” InChIs aggregate (certain) tautomers
How much of ChemSpider is “on ChemSpider”?
Connecting Chemistry across the web
So much of what is seen on ChemSpider is retrieved in real time using services
Connecting Chemistry across the web
Online Predictions
A Comment on Quality
For >28 million chemical compounds there are some errors:
“Incorrect” structure representations Mismatched name-structure relationships Experimental properties (the values, the units) Real vs. virtual compounds – text-mining and
conversion
We have deprecated a LOT of data…
Downsides of InChI
Good for small molecules – but no polymers, issues with inorganics, organometallics, imperfect stereochemistry. ChemSpider is “small molecules”
InChI used as the “deduplicator” – FIRST version of a compound into the database becomes THE structure to deduplicate against…
Side Effects of InChI Usage
SMILES by comparison…
Side Effects of InChI Usage
Standardization IssuesDepiction based on molfile
Downsides of Overall Approach
Meshing data together based on InChIs worked for simple molecules
2D layout errors inherited or limited by algorithm
Complex molecules that are meant to be the same thing were NOT deduplicated. Compounds differing by one stereocenter, named the same, meant to be the same, are not the same
So much data online is “erroneous”
The confusion of name-structures
Collapsing Data – Standardization
What needs to happen?
If we could validate Catch errors in databases (and clean) Proactively catch errors in publications/patents Reduce junk in the ether – improve QUALITY!
If we collectively standardized Interlinking between databases should improve
CVSP – a separate presentation….stick around
Crowdsourcing ChemSpider
ChemSpider is crowdsourced
Community deposition, annotation and curation
Anyone can “Leave Feedback”
Registered users can add data
Internet Data
ChemSpider and Global Chemistry Hub
Commercial SoftwarePre-competitive Data
Open ScienceOpen DataPublishersEducators
Open DatabasesChemical Vendors
Small organic moleculesUndefined materialsOrganometallicsNanomaterialsPolymersMineralsParticle boundLinks to Biologicals
Delivering a Prediction Platform Experimental data will be used as the basis of
model generation – a predictive platform…
The Future of ChemSpider Continued focus on quality over quantity –
but more data is good too! ChemSpider Reactions – work in progress
and includes >300,000 reactions Plugging in a validation and standardization
platform Delivering personal and institutional
repository capabilities
Thank you
Email: [email protected] Twitter: ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams