Thiessen, Paul, Bolton, Evan, Williams, Antony, McEwen, Leah Rae
The International Union of Pure and Applied Chemistry (IUPAC) has initiated a community project through the WorldFAIR initiative to define a common protocol for programmatic exchange of chemical representations. Representing chemical substances in the form of distinct chemical structures is fundamental to communicating chemical information. Validation of chemical structure description is an essential requirement for the re-usability of FAIR chemical data. The outcome of this work includes a specification that articulates a shared data model for chemical information exchange through an API that can be implemented by any system that manages chemical structure records. This deliverable outlines a conceptual framework and provides a demo prototype to engage community input and adoption.
This deliverable aims to describe criteria for web-based services that participating organisations can implement based on their existing and/or preferred technologies (e.g., toolkits, programming languages). The services are intended to confirm chemical identity and provide real time feedback on the machine-readability of chemical data and metadata representations based on IUPAC standard rule sets and community best practices. The goal is to support a range of stakeholders engaging in chemical data exchange online, including providers of chemical databases, curators of chemical repositories, chemistry application developers, chemical toolkit developers, and researchers sharing, searching and analysing chemical information programmatically. The initial specification focuses on resolving chemical entities and validating chemical structure representations.
The overarching goal of the WorldFAIR Chemistry Work Package (WP03) is to support the use of chemical data standards in research and curation workflows, between and across disciplines. This will enable downstream data reuse through provision of practical direction and resources. Other deliverables developed under the WorldFAIR Chemistry (WP03) case study further demonstrate and facilitate the use of chemistry data standards, including a framework that can be used by policymakers and developers of services and tools to support FAIR reporting of chemical data (D3.1 Digital guidance), and a digital ‘cookbook’ of interactive recipes demonstrating how to handle digital chemical data (D3.2 Training package).
WP03 activities are coordinated through IUPAC, the world authority on chemical nomenclature and terminology that constitute a common global language for communicating chemistry. In the context of the formal IUPAC process for reviewing and adopting consensus standards in chemistry, this work should be regarded as provisional guidance. Complete review and adoption of standards through IUPAC to reach the status of “Recommendation,” which has a specific meaning in the IUPAC lexicon, will occur after WP03 is complete.
This work was supported (in part) by the U.S. National Center for Biotechnology Information of the National Library of Medicine (NLM), U.S. National Institutes of Health.
This manuscript has been reviewed by the Center for Computational Toxicology and Exposure, United States Environmental Protection Agency and approved for publication. Approval does not signify that the contents necessarily reflect the views and policies of the Agency nor does mention of trade names or commercial products constitute endorsement or recommendation for use. The authors declare no conflict of interest.
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