Cheminformatics: Data and Standards

A Pure and Applied Chemistry Special Issue

Vol 94, Issue 6, June 2022

by Vincent F. Scalfani (Guest editor)

Many readers of Pure and Applied Chemistry and Chemistry International are likely familiar with the IUPAC Color Books. The current collection of IUPAC Color Books is comprised of eight volumes, and includes authoritative descriptions of chemical units, nomenclature, terminology, and symbols [1]. IUPAC standards and recommendations exist outside of the Color Books as well, for example, in individual publications and reports from IUPAC Project task groups. Relevant to cheminformatics, two longstanding IUPAC standards and recommendations include the InChI for chemical identification [2], and JCAMP-DX for spectral data exchange [3, 4]. In addition to continued development of InChI and JCAMP-DX within IUPAC, the IUPAC Committee on Publications and Cheminformatics Standards (CPCDS) along with numerous IUPAC task groups have been engaged with advancing cheminformatics, or more broadly, digital chemistry standards over the last two decades. For example, a basic search in the IUPAC Project database [5] for the words ‘cheminformatics’ or ‘digital’ resulted in 26 projects, with 15 of the projects still active. Some examples of current projects include enhancements to the Gold Book, metadata schema for solubility data, FAIR data projects, and efforts to enhance molecular representations (e.g., SMILES and InChI). Clearly, digital standards and cheminformatics are active areas of interest to IUPAC, the contributing volunteers, and the broader chemistry community. Readers are encouraged to visit the IUPAC Digital Standards webpage and submit feedback on current projects or ideas for new standards projects [6].

While the current IUPAC Color Books, publications, and task group reports contain some digital and cheminformatics standards, a need for a dedicated IUPAC Cheminformatics Color Book was recognized by a task group in 2017 [7].The task group completed a review of the current cheminformatics community needs and began preliminary planning for a new Cheminformatics Color Book. In late 2020, the IUPAC Subcommittee on Cheminformatics Data Standards (SCDS) aims were updated to focus on the digital dissemination of IUPAC cheminformatics data standards:

“The Subcommittee on Cheminformatics Data Standards (SCDS) coordinates and leads the digital dissemination of IUPAC cheminformatics data standards. SCDS works collaboratively with relevant IUPAC Divisions, IUPAC Committees, publishers, external scientific organizations, and the chemistry community to manage source reference material for IUPAC outputs related to cheminformatics and data standards. Such outputs may include cheminformatics related theory, policy around digital data/metadata exchange, standards, recommendations, validation data, and community engagement. SCDS maintains a vision for the dissemination of IUPAC cheminformatics standards and works closely with contributors and the community to share and maintain this information.”

In 2021, SCDS was then tasked with continuing the planning and development of a new IUPAC Cheminformatics Color Book. These new goals for SCDS and discussions within the Committee led to this Pure and Applied Chemistry special issue on Cheminformatics: Data and Standards as a first step towards a Cheminformatics Color Book. A call for papers was published in May 2021, with the aim of discussing cheminformatics standards and future needs. The proposed topics for the issue were as follows [8]:

1. Cheminformatics standards use-cases and workflows across disciplines.

2. Discussions around how cheminformatics standards advance research and teaching.

3. Perspectives related to current cheminformatics standards and future needs, for example interoperability and metadata considerations.

4. Cheminformatics datasets useful for teaching and/or validation.

5. Standardization needs related to infrastructure (e.g., repositories), cheminformatics toolkits, or data sharing.

6. Conference, symposia, or workshop based outcomes related to cheminformatics standardization.

How would a Pure and Applied Chemistry special issue on Cheminformatics: Data and Standards lead to an official IUPAC Color Book? Discussions are ongoing within IUPAC. One potential strategy is for the Cheminformatics: Data and Standards special issue to become a virtual “rolling” issue; in other words, articles are continually added. From the collection of cheminformatics articles in Pure and Applied Chemistry, selected articles could then be adapted into a cheminformatics Color Book chapter in collaboration with the author(s) and relevant IUPAC committees. This model for the Cheminformatics Color Book would be similar to an “overlay” journal [9]. Determining which articles would be appropriate for inclusion into the Color Book could be made through a combination of input from the community, IUPAC committees (e.g., SCDS) and related IUPAC task groups. Selected articles would then go through a similar approval process as other IUPAC Color Books. This workflow of completing the Cheminformatics Color Book piece-wise would spread the work across many contributors, while also serving to more quickly disseminate authoritative cheminformatics standards and recommendations to the global community.

Having now described the history and thought behind this special issue and future ideas for an IUPAC Cheminformatics Color Book, let me summarize the content within this issue.

There are four main themes of the contributed articles. The first theme is education with a contributed article on experiences with the Royal Society of Chemistry Chemical Information and Computer Applications interest Group’s open source chemical data and cheminformatics virtual workshops (Swain, see also box on next page), and another contributed article with a detailed account of experiences related to launching a materials informatics program (Lipscomb). The second theme is cheminformatics file formats and use cases. This includes an article on a proposed data model for compounds and assays (Kappler), an article describing a big data use case with RInChI (reaction InChI) (Blanke), and an article on the Reaction Structured Product Labeling format and associated use-cases (Nicklaus). The third theme is spectroscopic data and includes an article with an overview of the JCAMP-DX file format (Davies), and another article describing a proposed IUPAC specification for the FAIR management and sharing of spectroscopic data (Hanson). And the fourth theme was surveying the landscape, including an article reviewing chemical ontologies (Koepler) and a review of analytical data standards (Rauh). I expect that there will be many more contributions and themes that emerge with new submissions. As more machine-readable chemical data is continuing to be shared, standardization efforts will become even more important, and I hope articles collected within this rolling special issue can serve as a starting point toward identifying key chapters for a Cheminformatics Color Book, as well as identifying new IUPAC projects that are needed to advance cheminformatics standardization efforts.

Thank you for reading this special issue. And thank you to the contributing authors, reviewers, and Hugh Burrows, Editor of Pure and Applied Chemistry, for his enthusiasm and help making this issue a reality. Finally, thank you to my colleagues within IUPAC for their encouragement and feedback during the planning of this special issue on Cheminformatics: Data and Standards.

Vincent F. Scalfani <vfscalfani@ua.edu> is Assistant Professor/Science and Engineering Librarian at The University of Alabama, and current Chair of the IUPAC Subcommittee on Cheminformatics Data Standards. ORCID.org/0000-0002-7363-531X

Preface reprinted from PAC

https://www.degruyter.com/PAC ; keyword: Cheminformatics

https://www.degruyter.com/journal/key/pac/94/6/html