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Category Archives: InChI

The Importance of the InChI Identifier as a Foundation Technology for eScience Platforms at the Royal Society of Chemistry

This is a presentation I gave today at Bio-IT 2014 here in Boston. I was in the company of a number of my favorite people to be o the agenda with… Steve Heller, Steve Boyer, Evan Bolton and Chris Southan.

The Importance of the InChI Identifier as a Foundation Technology for eScience Platforms at the Royal Society of Chemistry

The Royal Society of Chemistry hosts one of the largest online chemistry databases containing almost 30 million unique chemical structures. The database, ChemSpider, provides the underpinning for a series of eScience projects allowing for the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it specifically in the ChemSpider project to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a Global Chemistry Network encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.

 

The great promise of navigating the internet using InChIs

This is my presentation at the InChI Symposium today:

The great promise of navigating the internet using InChIs

The InChI, the International Chemical Identifier, has been the basis of both indexing and deduplication of the ChemSpider database since the inception of the platform. When the InChI was adopted we envisaged a future whereby the identifier would proliferate across journals, databases and the internet in general providing us a basis for “structure searching the internet”. This presentation will provide an overview of how the InChI has facilitated the integration of ChemSpider to chemistry on the internet, some of the surprising findings that have resulted from this work and extrapolate the influence of InChIs into the future for a chemically enabled web.

 

An InChIkey Collision is Discovered and NOT Based on Stereochemistry

InChI Strings and InChIKeys are very much the backbone of ChemSpider and have quickly become a way by which online databases are being connected online. The InChIKey is a hash of the InChiString and when the hash was adopted it was suggested that the likelihood that there would be a collision was very small, the estimate being, as quoted from the official InChI site:

“An example of InChI with its InChKey equivalent is shown below. There is a finite, but very small probability of finding two structures with the same InChIKey. For duplication of only the first block of 14 characters this is 1.3% in 109, equivalent to a single collision in one of 75 databases of 109 compounds each.”

At a previous ACS Meeting Prof Jonathan Goodman from University of Cambridge announced that he had identified a collision. The collision was for two isomers of spongistatin, a rather complex chemical structure with many stereocenters.

Jonathan has “done it again”…what a troublemaker he is (in a supremely gentlemanly way!). I was fortunate enough to receive the news about this collision from him just as I was getting on the flight from ACS Denver to home tonight and asked his permission to blog it as it is both exciting and, I believe, quite surprising news. Why? In this case the collision is for two distinctly different chemicals with totally different formulae and with NO stereochemistry! Very surprising!

As you can see in the figure below the two chemical compounds are simply long branched alkyl chains, one an alcohol and one a ketone.

In case Jonathan’s software tool that he was using to connect to the InChI generation software was doing something untoward with the molfile I confirmed the observation myself by drawing the structures in ACD/ChemSketch and generating the InChIKeys there. And, sure enough…I see exactly the same Standard InChIKeys for both molecules as shown in the movie below. VERY interesting!

 

 
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Posted by on September 1, 2011 in General Communications, InChI, InChI

 

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