InChI Tag: InChI Modification

7 posts

International chemical identifier for reactions (RInChI)

Abstract

The Reaction InChI (RInChI) extends the idea of the InChI, which provides a unique descriptor of molecular structures, towards reactions. Prototype versions of the RInChI have been available since 2011. The frst ofcial release (RInChIV1.00), funded by the InChI Trust, is now available for download (http://www.inchi-trust.org/downloads/). This release defnes the format and generates hashed representations (RInChIKeys) suitable for database and web operations. The RInChI provides a concise description of the key data in chemical processes, and facilitates the manipulation and analysis of reaction data.

Capturing mixture composition: an open machine-readable format for representing mixed substances

Abstract: We describe a file format that is designed to represent mixtures of compounds in a way that is fully machine readable. This Mixfile format is intended to fill the same role for substances that are composed of multiple components as the venerable Molfile does for specifying individual structures. This much needed datastructure is intended to replace current practices for communicating information about mixtures, which usually relies on human-readable text descriptions, drawing several species within a single molecular diagram, or mutually incompatible ad hoc solutions. We describe an open source software application for editing mixture files, which can also be used as web-ready tools for manipulating the file format. We also present a corpus of mixture examples, which we have extracted from collections of text-based descriptions. Furthermore, we present an early look at the proposed IUPAC Mixtures InChI specification, instances of which can be automatically generated using the Mixfile format as a precursor.

UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers

Chambers et al. Journal of Cheminformatics 2014, 6:43

Abstract

UniChem is a low-maintenance, fast and freely available compound identifier mapping service, recently made available on the Internet. Until now, the criterion of molecular equivalence within UniChem has been on the basis of complete identity between Standard InChIs. However, a limitation of this approach is that stereoisomers, isotopes and salts of otherwise identical molecules are not considered as related. Here, we describe how we have exploited the layered structural representation of the Standard InChI to create new functionality within UniChem that integrates these related molecular forms. The service, called ‘Connectivity Search’ allows molecules to be first matched on the basis of complete identity between the connectivity layer of their corresponding Standard InChIs, and the remaining layers then compared to highlight stereochemical and isotopic differences. Parsing of Standard InChI sub-layers permits mixtures and salts to also be included in this integration process. Implementation of these enhancements required simple modifications to the schema, loader and web application, but none of which have changed the original UniChem functionality or services. The scope of queries may be varied using a variety of easily configurable options, and the output is annotated to assist the user to filter, sort and understand the difference between query and retrieved structures. A RESTful web service output may be easily processed programmatically to allow developers to present the data in whatever form they believe their users will require, or to define their own level of molecular equivalence for their resource, albeit within the constraint of identical connectivity.

Keywords: UniChem, Standard InChI, InChIKey, Chemical databases, Data integration, Connectivity search

Data Formats for Elementary Gas Phase Kinetics, Part 1: Unique Representations of Species at the Molecular Level

BURGESS, D. R., MANION, J. A. and HAYES, C. J. (2014), Data Formats for Elementary Gas Phase Kinetics, Part 1: Unique Representations of Species at the Molecular Level. Int. J. Chem. Kinet., 46: 640-650. doi:10.1002/kin.20875

Abstract

Standardized electronic formats for data are needed to efficiently and transparently communicate the results of scientific studies. A format for the unique identification of chemical species is a requirement in the field of chemistry, and the IUPAC International Chemical Identifier (InChI) has been widely adopted for this purpose. The InChI identifier has proved to be very useful. The InChI identifier, however, is currently insufficient to uniquely specify some types of molecular entities at a detailed molecular level needed to fully characterize their chemical nature, to differentiate between chemically distinct conformers, to uniquely identify structures used in quantum chemical calculations, and to completely describe elementary chemical reactions. To address this limitation, we propose an augmented form of InChI, denoted as InChI–ER, which contains additional optional layers that allow the unique and unambiguous identification of molecules at a detailed molecular level. The new layers proposed herein are optional extensions of the existing InChI formalism and, like all other InChI layers, would not interfere with InChI identifiers currently in use. The focus of the present work is the better specification of required molecular entities such as rotational conformations, ring conformations, and electronic states. In companion articles, we propose additional reaction layers using an extended InChI format that will enable the unique identification of elementary chemical reactions, including specification of associated transition states, specification of the changes in bonds that occur during reaction, and classification of reaction types.

Many InChIs and quite some feat

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.

International Chemical Identifier for Reactions (RInChI)

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/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 .