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.

InChI version 1.06: now more than 99.99% reliable

“…Changes to the InChI can be readily incorporated in Reaction Fig. 7 All molecules with numbering instability that lack "/p" and "/q" layers InChI (RInChI) [6,7] and into ongoing work to develop an InChI-based description of mixtures [17].…”

“…InChI v1.06 provides substantial new functionality and corrects some issues with earlier releases, whilst retaining a very high level of backwards compatibility. Changes to the InChI can be readily incorporated in Reaction InChI (RInChI) [ 6 , 7 ] and into ongoing work to develop an InChI-based description of mixtures [ 17 ].…”

Using Machine Learning to Parse Chemical Mixture Descriptions

“…The mixture data structure that is created by the machine learning method is based on the openly available Mixfile format, which is accompanied by open source tools for editing and manipulating the content. 1 The marked-up data used for training these methods has also been made openly available. The Mixfile format, and the data created using it, has been designed intentionally to serve as the first of many upstream sources for the Mixtures InChI (MInChI) notation.…”

“…Once the tree processing algorithm described above is complete, the tree structure can be converted directly into the Mixfile data structure, which we have previously described in detail. 1 The material and quantity fields should ideally contain enough information to recreate the structure (if applicable) and to parse out the quantity with its corresponding modifiers and units.…”

“…We have previously described an open format called Mixfile , which is the mixture analog of the de facto industry standard Molfile , as well as a suite of open-source tools and generation of the Mixtures InChI (MInChI) standard notation, which is layered atop the well-known InChI identifier. 1 As part of the preliminary research, we described a proof-of-concept technique for extracting marked-up mixture descriptions from text descriptions, and in this work, we describe a much more sophisticated and robust algorithm for automated text-to-mixture transformation at scale.…”