Chemical data evaluation: general considerations and approaches for IUPAC projects and the chemistry community (IUPAC Technical Report).

The International Union of Pure and Applied Chemistry (IUPAC) has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international scientific bodies, government agencies and other organizations. The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data (ISCED) has been established to provide guidance on issues related to the evaluation of chemical data. In this first report we define the general principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in chemistry.

Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices.

Research data management (RDM) is needed to assist experimental advances and data collection in the chemical sciences. Many funders require RDM because experiments are often paid for by taxpayers and the resulting data should be deposited sustainably for posterity. However, paper notebooks are still common in laboratories and research data is often stored in proprietary and/or dead-end file formats without experimental context. Data must mature beyond a mere supplement to a research paper. Electronic lab notebooks (ELN) and laboratory information management systems (LIMS) allow researchers to manage data better and they simplify research and publication. Thus, an agreement is needed on minimum information standards for data handling to support structured approaches to data reporting. As digitalization becomes part of curricular teaching, future generations of digital native chemists will embrace RDM and ELN as an organic part of their research.

CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community.

CAS Common Chemistry (https://commonchemistry.cas.org/) is an open web resource that provides access to reliable chemical substance information for the scientific community. Having served millions of visitors since its creation in 2009, the resource was extensively updated in 2021 with significant enhancements. The underlying dataset was expanded from 8000 to 500,000 chemical substances and includes additional associated information, such as basic properties and computer-readable chemical structure information. New use cases are supported with enhanced search capabilities and an integrated application programming interface. Reusable licensing of the content is provided through a Creative Commons Attribution-Non-Commercial (CC-BY-NC 4.0) license allowing other public resources to integrate the data into their systems. This paper provides an overview of the enhancements to data and functionality, discusses the benefits of the contribution to the chemistry community, and summarizes recent progress in leveraging this resource to strengthen other information sources.

Computational Chemistry Data Management Platform Based on the Semantic Web.

This paper presents a formal data publishing platform for computational chemistry using semantic web technologies. This platform encapsulates computational chemistry data from a variety of packages in an Extensible Markup Language (XML) file called CSX (Common Standard for eXchange). On the basis of a Gainesville Core (GC) ontology for computational chemistry, a CSX XML file is converted into the JavaScript Object Notation for Linked Data (JSON-LD) format using an XML Stylesheet Language Transformation (XSLT) file. Ultimately the JSON-LD file is converted to subject-predicate-object triples in a Turtle (TTL) file and published on the web portal. By leveraging semantic web technologies, we are able to place computational chemistry data onto web portals as a component of a Giant Global Graph (GGG) such that computer agents, as well as individual chemists, can access the data.

SciData: a data model and ontology for semantic representation of scientific data.

With the move toward global, Internet enabled science there is an inherent need to capture, store, aggregate and search scientific data across a large corpus of heterogeneous data silos. As a result, standards development is needed to create an infrastructure capable of representing the diverse nature of scientific data. This paper describes a fundamental data model for scientific data that can be applied to data currently stored in any format, and an associated ontology that affords semantic representation of the structure of scientific data (and its metadata), upon which discipline specific semantics can be applied. Application of this data model to experimental and computational chemistry data are presented, implemented using JavaScript Object Notation for Linked Data. Full examples are available at the project website (Chalk in SciData: a scientific data model. http://stuchalk.github.io/scidata/, 2016).

The Open Spectral Database: an open platform for sharing and searching spectral data.

BACKGROUND: A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. RESULTS: The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. CONCLUSION: The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.

The effects of salinity on acute toxicity of zinc to two euryhaline species of fish, Fundulus heteroclitus and Kryptolebias marmoratus.

It is well known that the toxicity of zinc (Zn) varies with water chemistry and that its bioavailability is controlled by ligand interactions and competing ions. Zn toxicity in freshwaters with varying water chemistry has been well characterized; however, far less attention has been paid to the toxicity of Zn in estuarine and marine systems. We performed experiments using two euryhaline species of killifish, Fundulus heteroclitus and Kryptolebias marmoratus, to investigate the effects of changing salinity on acute toxicity of Zn. Larvae (7- to 8-days old) of each species were exposed to various concentrations of Zn for 96 h at salinities ranging from 0 to 36 ppt and survival was monitored. As salinity increased, Zn toxicity decreased in both fish species, and at salinities above 10 ppt, K. marmoratus larvae were generally more sensitive to Zn than were those of F. heteroclitus. The protection of salinity against Zn toxicity in F. heteroclitus was further investigated to determine the role of Ca(2+). Increased Ca(2+) in freshwater protected against Zn toxicity to the same extent as did saline waters with an equal Ca(2+) concentration up to ∼200 mg/L Ca for F. heteroclitus and ∼400 mg/L Ca for K. marmoratus. These results suggest that these two species may have differing Ca(2+) requirements and/or rates of Ca(2+) uptake in water of intermediate to full-strength salinity (∼200-400 mg/L Ca(2+)) and thus differ in their sensitivity to Zn. The overall goal of this study was to better understand Zn toxicity in waters of different salinity and to generate data on acute Zn toxicity from multiple species over a range of salinities, ultimately for use in development of estuarine and marine biotic ligand models.

Spectrophotometric determination of aqueous cyanide using a revised phenolphthalin method.

This paper focuses on a revision of the phenolphthalin method for cyanide analysis, with the intent of producing a robust and sensitive spectrophotometric method. Limitations of the phenolphthalin chemistry were overcome by the addition of EDTA to the reagent. The revised reagent was found to have suitably fast kinetics, a linear dynamic range of 0.01-3.0 ppm cyanide, and a detection limit of 5 ppb. The method was tested for interferences and applied to the determination of cyanide in environmental waters.