Abstract
Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the
international, worldwide standard for defined chemical structures. This article will describe the extensive use and
dissemination of the InChI and InChIKey structure representations by and for the world-wide chemistry community,
the chemical information community, and major publishers and disseminators of chemical and related scientific
offerings in manuscripts and databases.
This presentation was given on august 25, 2011 by Steve Heller during the 5th meeting on U.S. Government Chemical Databases and Open Chemistry, which was held in Frederick MD.
This presentation was given June of 2014 at the 10th International Conference on Chemical Structures, which was held in Noordwijkerhout, the Netherlands. https://www.discngine.com/events/2014/5/14/10th-international-conference-on-chemical-structures-iccs
This resource is a simple spreadsheet in Excel that provides a handy interconversion between different chemical identifiers, namely name, InChI, InChIKey and SMILES. It uses some web services to do translations, i.e. PubChem PUG REST and NCI/CADD Chemical Identifier Resolver.
This workbook does not uses macros but makes use of the WEBSERVICE function added to Excel for Windows in Excel 2013.
Comprehensive 2015 article published in Springer’s Journal of Computer-Aided Molecular Design. Here is the abstract,
The IUPAC International Chemical Identifier (InChI) is a non-proprietary, international standard to represent chemical structures. It was conceived 15 years ago, and has been is use for 10 years. The InChI Trust is developing and improving on the current standard, further enabling the interlinking of chemical structures on the web. This mini-review looks at the widespread adoption of InChI in software and databases.
This is an article in Catalan that provides an introduction to chemical information and describes InChI along with other chemical identifiers. Its abstract reads:
“Chemical information, once managed in books paradigmatically in Chemical Abstracts and several handbooks, has now migrated to Internet. Nowadays many large databases, both commercial and freely available, have much more information than we have ever had. But accessing them requires some skills that are not yet taught in the official chemistry degrees. This paper presents a brief introduction to the notations and codes that are currently used to identify the chemical species in computer environments. At the same time, some freely available chemistry databases are presented.”
This submission shows you how to create a smart spreadsheet with Google Sheets that links an IUPAC name to a chemical’s PubChem landing page. You may click here to get a copy of this sheet. This particular sheet uses the Centre for Molecular Informatics OPSIN (Open Parser for Systematic IUPAC nomenclature) web service to convert the name to an InChI key, which is then appended to a hyperlink to PubChem. You will note that some of the names do not work and this is because those names in the sample sheet are incorrect names. If you paste those names directly into the OPSIN web service, it will tell you were an error in parsing the name occurred.
The following video shows you how to create this Google Sheet and below it is the instructions and code needed. This application takes advantage of the canonical nature of the InChI and its key, and the fact that the key allows you to communicate over the web.
Step 1: Paste your IUPAC names into a column of your spread sheet
Step 2: Convert IUPAC name to Standard InChI key
type the following script into the top cell of the column you want to place your keys into, and hit enter”
=IMPORTDATA(“http://opsin.ch.cam.ac.uk/opsin/”&[SPREADSHEET CELL WITH IUPAC NAME]&“.stdinchikey”)
the ampersand(&)concatenates the cell content to the URL
the ampersand must be surrounded by quotation marks
the URL must be in quotation marks
Click on the black box in the bottom right corner of cell and drag down, converting the entire column of names to keys.
Step 3: Hyperlink the key to PubChem Type the following script into the top cell of the column you want to place your links into, and hit enter”n
=HYPERLINK(“https://pubchem.ncbi.nlm.nih.gov/compound/”&[SPREADSHEET CELL WITH INCHIKEY]&“”)
the ampersand (&) concatenates the cell content to the URL
the ampersand must be surrounded by quotation marks
the URL must be in quotation marks
NOTE, these are dynamic cells – And will be recalculated everytime you open the page, or change the chemical name. If you want them to be static, you can copy the block of cells, and paste to another location as text.
You can also download the sheet as an Excel Spreadsheet, but the downloaded sheet will not be dynamic. It will be linked, but will not change if you change the IUPAC name.
This May 2018 open access Journal of Cheminformatics article by Guenter Grethe et al., describes the first official version (RInChI-V1.00) that was released in March of 2017 and is available for download at the InChI Trust (https://www.inchi-trust.org/wp/downloads/).
RInChI provides a standard for the representation of chemical reactions . As different databases use different methods for representing chemical reactions the adoption of RInChI and the ability to transform other representations into RInChI should allow for more thorough discovery across different databases of information related to chemical reactions. This article discusses the layers of the RInChI, the InChIKey and the Web-InChIKey. It also describes generation of RInChI from RD and RXN files, and the generation of RXN from RInChI. A database of over a million RInChI at the University of Cambridge is also described, www-rinchi.ch.cam.ac.uk .
