Stuart James Chalk

Stuart James Chalk
University of North Florida | UNF · Department of Chemistry

Ph.D.

About

42
Publications
13,478
Reads
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373
Citations
Introduction
I am an analytical chemist by training with research focus in the areas of flow analysis and environment monitoring. In the last eight years however, I have become extremely interested in cheminformatics, which is now my major focus. Current projects include: electronic laboratory notebooks, semantic representation of chemistry data, controlled vocabularies, ontologies, the AnIML and ExptML markup languages, REST interfaces for science data, the ChAMP project, and a new semantic units project.
Additional affiliations
September 2018 - present
University of North Florida
Position
  • Professor
Description
  • Full professor
September 2002 - August 2018
University of North Florida
Position
  • Professor (Associate)
Description
  • Tenure faculty member
August 1996 - August 2002
University of North Florida
Position
  • Professor (Assistant)
Description
  • Faculty member
Education
August 1989 - July 1994
October 1984 - May 1988
Loughborough University
Field of study
  • Chemistry and Analytical Science

Publications

Publications (42)
Article
Full-text available
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 fund...
Article
Full-text available
BackgroundA 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...
Article
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...
Article
Full-text available
This paper details an approach to re-purposing scientific data as presented on a web page for the sole purpose of making the data more available for searching and integration into other websites. Data ‘scraping’ is used to extract metadata from a set of pages on the National Institute of Standards and Technology (NIST) website, clean, organize and...
Conference Paper
Full-text available
The IUPAC Solubility Data Series published its first volume in 1979. Since then over 100 volumes of high quality peer reviewed solubility data has been published, first in hardcopy and subsequently electronically as part of the Journal of Physical and Chemistry Reference Data. In February of this year the National Institute of Standards and Techno...
Article
Full-text available
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 f...
Article
Full-text available
In the age of big data, it is time to ensure that units are routinely documented for easy, unambiguous exchange of information. In the age of big data, it is time to ensure that units are routinely documented for easy, unambiguous exchange of information.
Article
Full-text available
A set of guiding principles for the development of a standard for FAIR management of spectroscopic data are outlined and discussed. The principles form the basis for future recommendations of IUPAC Project 2019-031-1-024 specifying a detailed data model and metadata schema for describing the contents of an “IUPAC FAIRData Collection” and the organi...
Preprint
Full-text available
Human space exploration beyond low Earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in data and space health systems are necessary to enable Earth-independence, rather than Earth-reliance. Promising developments in the fields of artificial intelligence and m...
Preprint
Full-text available
Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the fiel...
Article
Full-text available
The International Committee for Weights and Measures has recognised the need to provide support for digital representations of the International System of Units (SI) and related metrological concepts, such as traceability and measurement uncertainty. A specialised Task Group was established to address this in 2019. This summary reports on the activ...
Article
Full-text available
As 2021 arrives with all the promise of beating COVID-19, mixed with the realities of vaccine delays and the threatened breakdown of international consensus on tackling global pandemics, it is a strange feeling to be writing an article about the ability of all to find, access, understand and re-use spectroscopic data. However, effectively and freel...
Article
The Chemistry Implementation Network (ChIN) is focused on supporting the FAIR Data needs of the research community regarding chemical related data. An Implementation Network is a consortium drawn from a community, in this case the chemistry discipline, committed to defining and constructing standards, materials and software in the spirit of the FAI...
Presentation
Full-text available
Short presentation to the IUPAC Division I Committee meeting
Conference Paper
Full-text available
The IUPAC Compendium of Chemical Terminology or "Gold Book" (http://goldbook.iupac.org/) is an online aggregation of 6414 terms from the IUPAC color books. Each term definition can be accessed by its own unique Digital Object Identifier (DOI) and each term page contains the definition, source information (Pure and Applied Chemistry article(s)) wher...
Conference Paper
Full-text available
The Quantities, Units, Dimensions and Datatypes ontology (QUDT - http://qudt.org/) has evolved into the best representation of scientific units for their identification and use in semantic web applications. However, the burden of generation of units for use in all scientific disciplines is onerous and impractical given the unlimited number of SI (a...
Conference Paper
Full-text available
ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Property Data Curated chemical property data is becoming increasingly valuable as the scientific community moves toward data-driven science. Yet the majority of such datasets are published as PDF files limiting the access and use of such data. This paper will detail an enh...
Article
Full-text available
As IUPAC approaches its 100th anniversary, it is important to re-evaluate the mode(s) in which it operates to sustainably support the standards that are vital to the chemical enterprise–chemical naming, chemical identification, and essential terms for commerce and the community. In addition, the importance of IUPAC’s underpinning of the digital rep...
Article
Full-text available
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). Based on a Gainesville Core (GC) ontology for computational chemi...
Conference Paper
Full-text available
As a mechanism to improve the sharing of data in Flow Injection Analysis, the Flow Analysis Database (http://www.fia.unf.edu) has been re-imagined to improve communication of the research on FIA, SIA, and related technologies across the vibrant communities in Europe, Asia, and the Americas. This talk will present the new version of the Flow Analys...
Conference Paper
Full-text available
In honor of JC Bradley, and the spirit of openness that he inspired, a new online resource called the Open Spectral Database (http://www.osdb.info) was announced in August of this year (aplha version). Built using open source tools, using open code, and open to community input about design and functionality, the OSD is available for anyone to submi...
Conference Paper
Full-text available
Development of the Chemical Analysis Metadata Platform (ChAMP) is a joint project between the University of North Florida and the Royal Society of Chemistry (RSC). In this project, we focused on the development of guidelines for organization, representation, and annotation of analytical science information, based around the definition of a standard...
Conference Paper
Full-text available
The Analytical Information Markup Language (AnIML – http://animl.sourceforge.net) is an XML data standard in development since 2004 and initiated as a replacement for the existing JCAMP data standard. Like JCAMP, AnIML is designed to store the analytical data from the instrument along with appropriate metadata describing the sample and the instrume...
Conference Paper
Full-text available
Computational Chemistry is becoming increasingly important in the scientific process due to its capabilities in predicting molecular properties and reaction pathways, energetics and kinetics. To address this need Chemical Semantics, with grant support from the U.S. Department of Energy, are in the second phase of development of a semantically enabl...
Conference Paper
Full-text available
Scientists are looking for ways to leverage web 2.0 technologies in the research laboratory and as a consequence a number of approaches to web-based electronic notebooks are being evaluated. In this presentation I discuss the Eureka Research Workbench, an electronic laboratory notebook built on semantic technology and XML. Using this approach the c...
Article
Zinc (Zn) is an essential micronutrient to aquatic organisms, but increased concentrations may result in accumulation and toxic effects. Water chemistry is known to influence the uptake of Zn in aquatic biota; therefore, organisms inhabiting environments with variable salinities may exhibit different patterns of Zn accumulation. Likewise, metal upt...
Article
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 per...
Chapter
This chapter summarizes statistics (bibliometrics) on the literature in flow analysis. The flow-analysis database focuses on flow injection analysis (FIA), sequential injection analysis (SIA), lab on valve (LOV), and zone fluidics (ZF). The growth of flow analysis techniques is a testament to the revolutionary approach that the technologies embody....
Chapter
This chapter contains information about online resources for flow analysis available at the time of publication.
Article
A new apparatus for mixing sample and reagent in flow injection analysis (FIA) is described. The continuously variable volume reactor (CVVR) replaces the conventional mixing coil in a flow injection (FI) manifold to provide mixing and dilution. A linear actuator motor allows control of the chamber volume via LabVIEW software. The chamber volume can...
Article
A single line manifold incorporating three Nafion® membrane reactors has been developed for the sequential introduction of components of the mercuric thiocyanate/iron(III)/acid reagent for the determination of chloride. Nitric acid was introduced at the first reactor to give sufficient ionic strength to allow cation exchange of FeSCN2+ at the secon...
Article
Speciated isotope dilution mass spectrometry (SIDMS) improves accuracy in the determination of chemical species in samples. It can be used to measure elements in their oxidation states as well as in organometallics or other molecular forms of species. SIDMS compensates for species transformations that occur in many of the steps of sample processing...
Article
Full-text available
The field of flow injection analysis (FIA) is growing rapidly because much applied research is being conducted around the world. This creates a great need for information dissemination across the globe to keep researchers up to date on current research trends. With the internet becoming the tool for global communication, it seems appropriate that s...
Article
Full-text available
In an attempt to produce complete oxidation of a biological matrix, bovine liver, ozone was investigated as an additional, potentially non-contaminating, oxidizing reagent after nitric acid digestion. Experiments were carried out to determine the decomposition efficiency of residual carbon species, primarily o-, m- and p-nitrobenzoic acids (NBAs),...
Article
Full-text available
An atmospheric pressure microwave digestion method has been developed for the combined analysis of total phosphorus and Kjeldahl nitrogen in complex matrices. In comparison to the digestion steps in EPA Methods 365.4 (total phosphorus) and 351.x (Kjeldahl nitrogen), this method requires less time, eliminates the need for a catalyst, and reduces the...
Article
The use of membrane tubing for the introduction of reagents for the determination of phosphate in waters by flow injection analysis was studied. The use of membranes eliminates the need for confluence points in the design of flow injection manifolds. This increases the sensitivity of the manifold by providing a sufficient reagent excess for the rea...
Article
Three manifold configurations used in flow injection analysis were optimized for maximum sensitivity for the spectrophotometric determination of iron(II) by complexation with 1,10-phenanthroline. The parameters of flow rate(s), injected volume, manifold length, and reagent concentration were studied for single, double, and reverse single line now i...
Article
Full-text available
The use of a permeation tube for the production of liquid stream calibration standards in the flow injection determination of ammonia was investigated. By varying the flow rate from 0.5 to 4.0 ml min–1, calibration standards over the range 1.5–0.18 ppm could be produced. The relationship between concentration of the resulting solution and the recip...

Questions

Question (1)
Question
I am revising the Flow Analysis Database (https://www.fia.unf.edu/) and am interested to know how many of you have an ORCID ID (http://orcid.org/)? Adding ORCIDs to the FAD would make it much easier for me to accurately indicate attribution, link to other papers, and preserve the history of FIA/SIA etc.
Please let me know if you have an ORCID and what it is and if not, consider getting one.  Also, spread the word about this because I want to bring the FAD up to date by the end of the year so it is a much better resource for the community.
Stuart Chalk

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Projects

Projects (4)
Project
This is a research grant to aggregate chemically related datasets using a semantic framework and subsequently develop a website where the graph database can be search using SHACL queries. Grant starts January 1, 2019.
Project
IUPAC Project 2016-046-1-024 entitled 'Backup, Maintenance, and Redevelopment of the IUPAC Gold Book website' started in January 2017 and will run through the end of 2017. Goals are: 1) Create a stable, modern version of the current Gold Book website (http://goldbook.iupac.org/) 2) Create a downloadable vocabulary of Gold Book terms 3) Create a simple website to administer updates to Gold Book terms 4) Create a simple Application Programming Interface (API) to access the Gold Book terms
Project
To develop an on-line portal to administrate the creation and maintenance of semantic unit definitions for use in electronic applications based on the QUDT system. The portal will also allow representations of conversion factors between units, scientific physical constants, and SI prefix definitions. The intent is develop the system to support as many unit implementation approaches as possible.