CompTox Chemicals Dashboard

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CompTox Chemicals Dashboard
Dashboard image.gif
DescriptionChemicals database targeted towards the environmental sciences and providing access to over 875,000 chemical compounds, properties, bioassay data and associated information.
Research center Environmental Protection Agency
  • National Center for Computational Toxicology
Primary citationThe CompTox Chemistry Dashboard: a community data resource for environmental chemistry. [1]
Download URL
License Public Domain
Data release
Every 6 months
Curation policyManually curated

The CompTox Chemicals Dashboard is a freely accessible online database created and maintained by the U.S. Environmental Protection Agency (EPA). The database provides access to multiple types of data including physicochemical properties, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay. EPA and other scientists use the data and models contained within the dashboard to help identify chemicals that require further testing and reduce the use of animals in chemical testing. The Dashboard is also used to provide public access to information from EPA Action Plans, e.g. around perfluorinated alkylated substances. [2] [3]


Originally titled the Chemistry Dashboard, the first version was released in 2016. [4] The latest release of the database (version 3.0.5) contains manually curated data for over 875,000 chemicals and incorporates the latest data generated from the EPA's Toxicity Forecaster (ToxCast) high-throughput screening program. [5] The Chemicals Dashboard incorporates data from several previous EPA databases into one package including the ToxCast Dashboard, [6] the Endocrine Disruption Screening Program (EDSP) Dashboard [7] and the Chemical and Products Database (CPDat). [8]

Scope and access

The CompTox Chemicals Dashboard database contains high quality chemical structures and information that have been extensively curated and quality checked, which can be used as a resource for analytical scientists involved in structure identification. [9]

ToxCast bioactivity data view for Bisphenol A ToxCast bioactivity data view for Bisphenol A.png
ToxCast bioactivity data view for Bisphenol A

Chemical hazard data in the dashboard comes from both traditional laboratory animal studies and high-throughput screening. Biological data from high-throughput screening is generated by EPA's ToxCast program, [5] the ToxCast data in the database provides information about the assays used and their response potency and efficacy. These data can be found in the bioactivity tab.

The Chemicals Dashboard can be accessed via a web interface or sets of data within it can be downloaded for use offline. The Lists tab can be used to browse and download groups of related chemicals based on their relevance to a specific research topic (such as additives in cigarettes or chemicals demonstrating effects on neurodevelopmental effects) or the specific assay endpoints they are covered by.

Within the online dashboard searches can be performed by product/use categories, assay/gene, systematic name, synonym, CAS number, DSSTox Substance ID or InChiKey. Under the Advanced Search tab chemicals can be searched based on their mass or molecular formula. Searches can also be performed for groups of chemicals based on Chemical Name CASRN, InChIKey, DSSTox Substance ID, DSSTox Compound ID, InChIKey Skeleton, MS-Ready Formula, Exact Formula, or Monoisotopic Mass using the batch search function.

Other functions

Abstract Sifter module Abstract Sifter module.png
Abstract Sifter module

An automated read-across tool called Generalized Read-Across (GenRA) is integrated into The Chemicals Dashboard. GenRA is designed to keep the expert consideration inherent in the read-across method, but automate the chemical selection process to help predict toxicity. [10]

The Dashboard also has the capability to search existing scientific literature sources such as PubMed, via a web-based version of the "Abstract Sifter", [11] Google Scholar and reports from EPA's Provisional Peer Reviewed Toxicity Values (PPRTV) and the EPA Integrated Risk Information System (IRIS).

Real-time QSAR prediction for multiple physicochemical property and toxicity endpoints is available through the predictions tab.

Supporting mass spectrometry

MS-Ready relationships MS-Ready relationships.png
MS-Ready relationships

The dashboard provides support for mass spectrometry providing searches against the chemical data contained in the database based on mass and molecular formula. The dashboard has been applied to non-targeted analysis searching for "known unknowns". [12] Both targeted mass spectrometry and non-targeted mass spectrometry are supported. The searches utilize a search based on "MS-Ready" forms of chemical compounds. Individual chemical substances are collapsed into a form that would be detected by mass spectrometry such that salts are desalted and neutralized and multi-component chemicals are separated into their individual components. [13]

See also

Related Research Articles

<span class="mw-page-title-main">Toxicology</span> Study of substances harmful to living organisms

Toxicology is a scientific discipline, overlapping with biology, chemistry, pharmacology, and medicine, that involves the study of the adverse effects of chemical substances on living organisms and the practice of diagnosing and treating exposures to toxins and toxicants. The relationship between dose and its effects on the exposed organism is of high significance in toxicology. Factors that influence chemical toxicity include the dosage, duration of exposure, route of exposure, species, age, sex, and environment. Toxicologists are experts on poisons and poisoning. There is a movement for evidence-based toxicology as part of the larger movement towards evidence-based practices. Toxicology is currently contributing to the field of cancer research, since some toxins can be used as drugs for killing tumor cells. One prime example of this is ribosome-inactivating proteins, tested in the treatment of leukemia.

<span class="mw-page-title-main">CAS Registry Number</span> Chemical identifier

A CAS Registry Number is a unique identification number, assigned by the Chemical Abstracts Service (CAS) in the US to every chemical substance described in the open scientific literature, in order to index the substance in the CAS Registry. This registry includes all substances described since 1957, plus some substances from as far back as the early 1800s; it is a chemical database that includes organic and inorganic compounds, minerals, isotopes, alloys, mixtures, and nonstructurable materials. CAS RNs are generally serial numbers, so they do not contain any information about the structures themselves the way SMILES and InChI strings do.

<span class="mw-page-title-main">Toxicity</span> Degree of harmfulness of substances

Toxicity is the degree to which a chemical substance or a particular mixture of substances can damage an organism. Toxicity can refer to the effect on a whole organism, such as an animal, bacterium, or plant, as well as the effect on a substructure of the organism, such as a cell (cytotoxicity) or an organ such as the liver (hepatotoxicity). Sometimes the word is more or less synonymous with poisoning in everyday usage.

Chlordane, or chlordan, is an organochlorine compound that was used as a pesticide. It is a white solid. In the United States, chlordane was used for termite-treatment of approximately 30 million homes until it was banned in 1988. Chlordane was banned 10 years earlier for food crops like corn and citrus, and on lawns and domestic gardens.

In vitro toxicity testing is the scientific analysis of the toxic effects of chemical substances on cultured bacteria or mammalian cells. In vitro testing methods are employed primarily to identify potentially hazardous chemicals and/or to confirm the lack of certain toxic properties in the early stages of the development of potentially useful new substances such as therapeutic drugs, agricultural chemicals and food additives.

<span class="mw-page-title-main">Piperonyl butoxide</span> Chemical compound

Piperonyl butoxide (PBO) is a pale yellow to light brown liquid organic compound used as an adjuvant component of pesticide formulations for synergy. That is, despite having no pesticidal activity of its own, it enhances the potency of certain pesticides such as carbamates, pyrethrins, pyrethroids, and rotenone. It is a semisynthetic derivative of safrole and is produced from the condensation of the sodium salt of 2-(2-butoxyethoxy) ethanol and the chloromethyl derivative of hydrogenated safrole (dihydrosafrole). Although this route of synthesis has faced a lot of criticism in recent times. The new route of synthesis is through 1,2-Methylenedioxybenzene, developed by The Anthea Group and patented in 2019.

Cheminformatics refers to the use of physical chemistry theory with computer and information science techniques—so called "in silico" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields. Such in silico techniques are used, for example, by pharmaceutical companies and in academic settings to aid and inform the process of drug discovery, for instance in the design of well-defined combinatorial libraries of synthetic compounds, or to assist in structure-based drug design. The methods can also be used in chemical and allied industries, and such fields as environmental science and pharmacology, where chemical processes are involved or studied.

<span class="mw-page-title-main">Environmental chemistry</span> Scientific study of the chemical and phenomena that occur in natural places

Environmental chemistry is the scientific study of the chemical and biochemical phenomena that occur in natural places. It should not be confused with green chemistry, which seeks to reduce potential pollution at its source. It can be defined as the study of the sources, reactions, transport, effects, and fates of chemical species in the air, soil, and water environments; and the effect of human activity and biological activity on these. Environmental chemistry is an interdisciplinary science that includes atmospheric, aquatic and soil chemistry, as well as heavily relying on analytical chemistry and being related to environmental and other areas of science.

<span class="mw-page-title-main">There are unknown unknowns</span> Saying associated with the US invasion of Iraq

"There are unknown unknowns" is a phrase from a response United States Secretary of Defense Donald Rumsfeld gave to a question at a U.S. Department of Defense (DoD) news briefing on February 12, 2002, about the lack of evidence linking the government of Iraq with the supply of weapons of mass destruction to terrorist groups. Rumsfeld stated:

Reports that say that something hasn't happened are always interesting to me, because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns—the ones we don't know we don't know. And if one looks throughout the history of our country and other free countries, it is the latter category that tends to be the difficult ones.

<span class="mw-page-title-main">Toxic Substances Control Act of 1976</span> United States federal law

The Toxic Substances Control Act (TSCA) is a United States law, passed by the 94th United States Congress in 1976 and administered by the United States Environmental Protection Agency (EPA), that regulates chemicals not regulated by other U.S. federal statutes, including chemicals already in commerce and the introduction of new chemicals. When the TSCA was put into place, all existing chemicals were considered to be safe for use and subsequently grandfathered in. Its three main objectives are to assess and regulate new commercial chemicals before they enter the market, to regulate chemicals already existing in 1976 that posed an "unreasonable risk of injury to health or the environment", as for example PCBs, lead, mercury and radon, and to regulate these chemicals' distribution and use.

Toxicogenomics is a subdiscipline of pharmacology that deals with the collection, interpretation, and storage of information about gene and protein activity within a particular cell or tissue of an organism in response to exposure to toxic substances. Toxicogenomics combines toxicology with genomics or other high-throughput molecular profiling technologies such as transcriptomics, proteomics and metabolomics. Toxicogenomics endeavors to elucidate the molecular mechanisms evolved in the expression of toxicity, and to derive molecular expression patterns that predict toxicity or the genetic susceptibility to it.

The International Chemical Identifier is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web. Initially developed by the International Union of Pure and Applied Chemistry (IUPAC) and National Institute of Standards and Technology (NIST) from 2000 to 2005, the format and algorithms are non-proprietary. Since May 2009, it has been developed by the InChI Trust, a nonprofit charity from the United Kingdom which works to implement and promote the use of InChI.

PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains multiple substance descriptions and small molecules with fewer than 100 atoms and 1,000 bonds. More than 80 database vendors contribute to the growing PubChem database.

A toxicophore is a chemical structure or a portion of a structure that is related to the toxic properties of a chemical. Toxicophores can act directly or can require metabolic activation.

ChemSpider is a freely accessible online database of chemicals owned by the Royal Society of Chemistry. It contains information on more than 100 million molecules from over 270 data sources, each of them receiving a unique identifier called ChemSpider Identifier.

High production volume chemicals are produced or imported into the United States in quantities of 1 million pounds or 500 tons per year. In OECD countries, HPV chemicals are defined as being produced at levels greater than 1,000 metric tons per producer/importer per year in at least one member country/region. A list of HPV chemicals serves as an overall priority list, from which chemicals are selected to gather data for a screening information dataset (SIDS), for testing and for initial hazard assessment.

The Hazardous Substances Data Bank (HSDB) was a toxicology database on the U.S. National Library of Medicine's (NLM) Toxicology Data Network (TOXNET). It focused on the toxicology of potentially hazardous chemicals, and included information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, and related areas. All data were referenced and derived from a core set of books, government documents, technical reports, and selected primary journal literature. Prior to 2020, all entries were peer-reviewed by a Scientific Review Panel (SRP), members of which represented a spectrum of professions and interests. Last Chairs of the SRP are Dr. Marcel J. Cassavant, MD, Toxicology Group, and Dr. Roland Everett Langford, PhD, Environmental Fate Group. The SRP was terminated due to budget cuts and realignment of the NLM.

<span class="mw-page-title-main">Antony John Williams</span> British chemist

Antony John Williams is a British chemist and expert in the fields of both nuclear magnetic resonance (NMR) spectroscopy and cheminformatics at the United States Environmental Protection Agency. He is the founder of the ChemSpider website that was purchased by the Royal Society of Chemistry in May 2009. He is a science blogger and an author.

Kimberly A. Prather is an American atmospheric chemist. She is a distinguished chair in atmospheric chemistry and a distinguished professor at the Scripps Institution of Oceanography and department of chemistry and biochemistry at UC San Diego. Her work focuses on how humans are influencing the atmosphere and climate. In 2019, she was elected a member of the National Academy of Engineering for technologies that transformed understanding of aerosols and their impacts on air quality, climate, and human health. In 2020, she was elected as a member of the National Academy of Sciences. She is also an elected Fellow of the American Philosophical Society, American Geophysical Union, the American Association for the Advancement of Science, American Philosophical Society, and the American Academy of Arts and Sciences.

<span class="mw-page-title-main">Emma Schymanski</span> Chemist

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