PubChem as an Emerging Toxicological Information Resource
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Presented on October 20, 2020 at the 9th American Society for Cellular and Computational Toxicology (ASCCT) National Meeting. ==== Abstract ==== PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource at the U.S. National Institutes of Health. It collects chemical information from 750+ data sources and disseminates it to the public free of charge. Arguably, PubChem contains the largest amount of chemical information available in the public domain, with more than 265 million depositor-provided substance descriptions, 100 million unique chemical structures, and 270 million bioactivity outcomes from one million assays covering around twenty thousand unique protein target sequences. Included in the many types of content in PubChem is toxicological information about chemicals, e.g., human and animal toxicity, ecotoxicity, exposure limits, exposure symptoms, and antidote & emergency treatment. Notably, a substantial amount of toxicological information from resources formerly offered by the TOXicology data NETwork (TOXNET) is now integrated into PubChem, e.g., the Hazardous Substances Data Bank (HSDB), Genetic Toxicology Data Bank (Gene-Tox), Chemical Carcinogenesis Research Information System (CCRIS), LactMed, and LiverTox. In addition, PubChem contains a large amount of bioactivity and toxicity screening data that can be used to build toxicity prediction models based on statistical and machine-learning approaches. This presentation provides an overview of PubChem’s toxicological information and describes how open data in PubChem can be used to develop prediction models for chemical toxicity.
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ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and curation mechanisms in place for text, structure and spectra ChemSpider intends to be a meeting place and collaborative environment for chemists to work together.ChemSpider Overview SLides August 2007
ChemSpider Overview SLides August 2007US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
11 years old presentation submitted as Project work: Golden Mantra to Perform Worldwide Patent Searches
Patent provides the right to exclude others from making, using, selling, offering for sale, or importing the patented invention for the term of the patent, usually 20 years from the filing date. A patent is, in effect, a limited property right that the government offers to inventors in exchange for their agreement to share the details of their inventions with the public. Like any other property right, it may be sold, licensed, mortgaged, assigned or transferred, given away, or simply abandoned.
In order to obtain a patent, an applicant must provide a written description of his or her invention in sufficient detail for a person skilled in the art (i.e., the relevant area of technology) to make and use the invention. Knowledge is Property- All YOU need to know ABC of Patent Searching
Knowledge is Property- All YOU need to know ABC of Patent SearchingPrity Khastgir IPR Strategic India Patent Attorney Amplify Innovation
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~880,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Web-based technologies coupled with a drive for improved communication between scientists have resulted in the proliferation of scientific opinion, data and knowledge at an ever-increasing rate. The increasing array of chemistry-related computer-based resources now available provides chemists with a direct path to the discovery of information, once previously accessed via library services and limited to commercial and costly resources. We propose that preclinical absorption, distribution, metabolism, excretion and toxicity data as well as pharmacokinetic properties from studies published in the literature (which use animal or human tissues in vitro or from in vivo studies) are precompetitive in nature and should be freely available on the web. This could be made possible by curating the literature and patents, data donations from pharmaceutical companies and by expanding the currently freely available ChemSpider database of over 21 million molecules with physicochemical properties. This will require linkage to PubMed, PubChem and Wikipedia as well as other frequently used public databases that are currently used, mining the full text publications to extract the pertinent experimental data. These data will need to be extracted using automated and manual methods, cleaned and then published to the ChemSpider or other database such that it will be freely available to the biomedical research and clinical communities. The value of the data being accessible will improve development of drug molecules with good ADME/Tox properties, facilitate computational model building for these properties and enable researchers to not repeat the failures of past drug discovery studies.Precompetitive preclinical ADME/tox data and set it free on the web to facili...
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ChemSpider is being built with the intention of being a chemical structure centric community for chemists. With over 16 million chemical structures as of August 2007, and with data deposition and curation mechanisms in place for text, structure and spectra ChemSpider intends to be a meeting place and collaborative environment for chemists to work together.ChemSpider Overview SLides August 2007
ChemSpider Overview SLides August 2007US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
11 years old presentation submitted as Project work: Golden Mantra to Perform Worldwide Patent Searches
Patent provides the right to exclude others from making, using, selling, offering for sale, or importing the patented invention for the term of the patent, usually 20 years from the filing date. A patent is, in effect, a limited property right that the government offers to inventors in exchange for their agreement to share the details of their inventions with the public. Like any other property right, it may be sold, licensed, mortgaged, assigned or transferred, given away, or simply abandoned.
In order to obtain a patent, an applicant must provide a written description of his or her invention in sufficient detail for a person skilled in the art (i.e., the relevant area of technology) to make and use the invention. Knowledge is Property- All YOU need to know ABC of Patent Searching
Knowledge is Property- All YOU need to know ABC of Patent SearchingPrity Khastgir IPR Strategic India Patent Attorney Amplify Innovation
EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project, and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are made available via the EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~880,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectrometry non-targeted screening community, enabling cohesive workflows to support data generation for the detection and assessment of environmental exposures to chemicals contained within the database. The application provides access to segregated lists of chemicals that are of specific interest to relevant stakeholders, including, for example, scientists interested in Per- & Polyfluoroalkyl Substances (PFAS). Added lists include those sourced from the European Union as well as developed in-house and now containing thousands of chemicals. A procured testing library of hundreds of PFAS chemicals annotated into chemical categories has been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and links to the open literature. This presentation will provide an overview of the dashboard, the developing library of PFAS chemicals and associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models developed for these chemicals. The application of the dashboard to support mass spectrometry non-targeted analysis studies for the identification of PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.PFAS Chemistry: Range, Complexity, Groupings, and the CompTox Chemicals Dash...
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Web-based technologies coupled with a drive for improved communication between scientists have resulted in the proliferation of scientific opinion, data and knowledge at an ever-increasing rate. The increasing array of chemistry-related computer-based resources now available provides chemists with a direct path to the discovery of information, once previously accessed via library services and limited to commercial and costly resources. We propose that preclinical absorption, distribution, metabolism, excretion and toxicity data as well as pharmacokinetic properties from studies published in the literature (which use animal or human tissues in vitro or from in vivo studies) are precompetitive in nature and should be freely available on the web. This could be made possible by curating the literature and patents, data donations from pharmaceutical companies and by expanding the currently freely available ChemSpider database of over 21 million molecules with physicochemical properties. This will require linkage to PubMed, PubChem and Wikipedia as well as other frequently used public databases that are currently used, mining the full text publications to extract the pertinent experimental data. These data will need to be extracted using automated and manual methods, cleaned and then published to the ChemSpider or other database such that it will be freely available to the biomedical research and clinical communities. The value of the data being accessible will improve development of drug molecules with good ADME/Tox properties, facilitate computational model building for these properties and enable researchers to not repeat the failures of past drug discovery studies.Precompetitive preclinical ADME/tox data and set it free on the web to facili...
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PubChem as an Emerging Toxicological Information Resource
- 1. PubChem as an Emerging Toxicological Information Resource Sunghwan Kim (sunghwan.kim@nih.gov), Jian Zhang, Paul A. Thiessen, Asta Gindulyte, Pertti J. Hakkinen & Evan E. Bolton Tools and Services Classification browser https://pubchem.ncbi.nlm.nih.gov/classification Identifier exchange service https://pubchemdocs.ncbi.nlm.nih.gov/identifier- exchange-service Score matrix service https://pubchemdocs.ncbi.nlm.nih.gov/score-matrix- service Structure download https://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi Assay download https://pubchem.ncbi.nlm.nih.gov/assay/assaydownload.cgi Bulk download vis FTP ftp://ftp.ncbi.nlm.nih.gov/pubchem Programmatic access PUG-REST https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest PUG-View https://pubchemdocs.ncbi.nlm.nih.gov/pug-view PubChem RDF https://pubchem.ncbi.nlm.nih.gov/rdf PubChem (https://pubchem.ncbi.nlm.nih.gov) Public chemical database at the U.S. National Institutes of Health. Contains a large amount of chemical information, collected from 750+ data sources. Organizes its data into three major databases: • Substance: archives depositor-submitted descriptions of substances. • Compound: contains unique chemical structures extracted from the Substance database. • BioAssay: stores biological assay descriptions and test results. Has additional data collections that provide information on genes, proteins, pathways, scientific articles, and patents related to chemicals. • Gene (ex. EGFR) https://pubchem.ncbi.nlm.nih.gov/gene/1956 • Protein (ex. HMG-CoA reductase) https://pubchem.ncbi.nlm.nih.gov/protein/P04035 • Pathway (ex. TCA Cycle) • https://pubchem.ncbi.nlm.nih.gov/pathway/Reacto me:R-HSA-1428517 • US Patent (ex. US7030151B2) • https://pubchem.ncbi.nlm.nih.gov/patent/US- 7030151-B2 Acknowledgements This work was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health. Predictive Toxicology Modelling Using PubChem Bioactivity data in PubChem High-throughput screening data • Molecular Libraries Program • Tox21 Literature-extracted bioactivity data • Scientific articles • Patent documents PubChem’s bioactivity data have been used to develop computational models for chemical toxicity prediction (with machine-learning algorithms, such as neural network, support vector machine, random forest, etc.). Toxicological Information in PubChem Human/non-human toxicity Health effects (short- and long-term) Populations at special risk Exposure routes, symptoms & limits (REL, PEL) Average daily Intake, body burden & target organs Ecotoxicity & environmental concentration/degradation Many others → All of these data are collected from authoritative sources, including U.S. NLM/NIH, EPA, CDC, USGS, OSHA, etc. Summary PubChem contains a large amount of publicly available chemical information. It has a wide range of toxicological information, collected from many authoritative sources. Data from several ToxNet databases have been integrated into PubChem (e.g., HSDB, ChemIDPlus, CCRIS, GeneTox, LiverTox, and LactMed) . PubChem’s bioactivity data are used to develop computational models for chemical toxicity prediction. Efforts to add additional toxicology-related data sources are underway. ToxNet Data in PubChem (https://pubchemdocs.ncbi.nlm.nih.gov/toxnet) TOXicology Data NETwork. Consisted of toxicological databases at NLM. Retired in December 2019 as part of a broader NLM reorganization. Most of its content have been integrated into other NLM products and services. Toxicological information on chemicals are integrated into PubChem. ChemIDPlus HSDB (Hazardous Substances Data Bank) → Integrated as annotations of compounds. Available through the Compound Summary page. (ex.) HSDB data for benzene: https://pubchem.ncbi.nlm.nih.gov/compound/241# source=Hazardous%20Substances%20Data%20B ank%20(HSDB) Gene-Tox (Genetic Toxicology Data Bank) CCRIS (Chemical Carcinogenesis Research Information System) → Integrated as bioassays and substances tested in them. (ex.) Mutagenicity study data from CCRIS https://pubchem.ncbi.nlm.nih.gov/bioassay/12 59407 (ex.) Aniline data in CCRIS https://pubchem.ncbi.nlm.nih.gov/substance/3 63897994 LiverTox & LactMed → Data downloadable from PubChem Sources: https://pubchem.ncbi.nlm.nih.gov/source/23224 https://pubchem.ncbi.nlm.nih.gov/source/15404