Copyright©2007 Antony Williams
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.
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:
(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!Stumble it!