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The InChI Key Has Been Unveiled – and now there are 17.2 MILLION of them online

08 Sep

ChemSpider users will likely have seen InChIs exposed on the record view for any chemical structure. The majority of you will know what an InChI is..for those of you who don’t I recommend seeing the Wikipedia description. This week the support of InChI was extended by introducing the InChI key in the version 1.02 beta release.

The definition of the InChI key is given as:

“A fixed-length (25-character) condensed digital representation of the Identifier to be known as InChIKey. In particular, this will

* facilitate web searching, previously complicated by unpredictable breaking of InChI character strings by search engines
* allow development of a web-based InChI lookup service
* permit an InChI representation to be stored in fixed length fields
* make chemical structure database indexing easier
* allow verification of InChI strings after network transmission.

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.

Caffeine:
InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
InChIKey=RYYVLZVUVIJVGH-UHFFFAOYAW
First block (14 letters), encodes molecular skeleton (connectivity): RYYVLZVUVIJVGH
Second block (8 letters), encodes proton positions (tautomers), stereochemistry, isotopes, reconnected layer: UHFFFAOY
Flag character, indicates InChI version, presence/absence of fixed H layer, isotopes, and stereochemistry: A
Check character: W”

Egon Willinghagen, as prolific as ever (!) has already provided feedback on the beta version on his blog. We have been waiting for the InChI key for a while since we heard of of its development. We’ve been given some grief about the length of some of the InChIs for the molecules on ChemSpider.For example, see this record – the InChI is:

InChI=1/C74H114O37/c1-17-27-94-36-19-23-38(24-20-36)96-34-45-52-59(85-8)67
(93-16)74(104-45)109-51-44(33-79)100-70(63(89-12)58(51)84-7)107-49-42(31-77)
102-72(65(91-14)56(49)82-5)111-53-46(35-97-39-25-21-37(22-26-39)95-28-18-2)
103-73(66(92-15)60(53)86-9)108-50-43(32-78)99-69(62(88-11)57(50)83-6)105-47-40
(29-75)98-68(61(87-10)54(47)80-3)106-48-41(30-76)101-71(110-52)64(90-13)55(48)
81-4/h17-26,40-79H,1-2,27-35H2,3-16H3/t40-,41+,42-,43-,44+,45+,46-,47+,48+,49+,
50+,51+,52+,53+,54-,55+,56-,57-,58-,59-,60-,61+,62+,63+,64-,65+,66+,67-,68+,69+,
70+,71+,72+,73+,74+/m0/s1
(This InChI is word-wrapped to allow it to stay within the WordPress display)

and the InChI key is: CINKENNKQKVJAW-LJIFKLEWBD

Which do you prefer?

Some of you might have read about my analysis about erectile dyscfunction and how the size of the InChI does give a bigger SMILES in general. This IS an R-rated blog-posting so maybe not… Now, with the InChI key all of these issues will be resolved for different erectile dysfunction drugs…everything will now be the same length.

The ChemSpider database online has expanded to over 17.2 Million compounds. The last record in the database is 17628589….there are no properties yet generated for the last 800,000 structures added and the zoom view is not yet available….these are coming shortly.

We have already downloaded the InChi 1.02 beta version and in a few hours have generated and populated the database with 17.2 million InChi Keys. This coming week we will check for duplicates as part of our validation process. What we can say so far is that the generation process was fast and efficient. More reports to come…now, if anyone out there from Google wants to point their indexing of InChI keys our way feel free!

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on September 8, 2007 in ChemSpider Services

 

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