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

Jacobs, Andrea; Williams, Dustin L.; Hickey, Katherine; Patrick, Nathan; Williams, Antony; Chalk, Stuart; McEwen, Leah; Willighagen, Egon; Walker, Martin A.; Bolton, Evan; Sinclair, Gabriel; Sanford, Adam

doi:10.1021/acs.jcim.2c00268

Cited by 19 publications

(13 citation statements)

References 13 publications

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“…The release of the CAS Common Chemistry data set was heralded by many as a breakthrough for open science. Reflecting on my somewhat less enthusiastic personal reaction to this, I realized that my research career developed in an era where open chemical resources such as PubChem, , ChemSpider, and the Human Metabolome Database (HMDB) , already existed.…”

Section: Fair and Open Chemistrymentioning

confidence: 99%

“…In many ways, the world is “opening” up again, with many colleagues going to their first “in person” conferences since the start of the pandemic in early 2020. A significant leap forward for open chemistry was made in 2021, with the Chemical Abstracts Service (CAS) Registry embracing a hybrid model and releasing half a million chemicals as the CAS Common Chemistry set under an open license .…”

mentioning

confidence: 99%

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Global Challenges: Opening up Chemistry, Pandemics, and Air Pollution

Schymanski

2022

ACS Environ. Au

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Section: Fair and Open Chemistrymentioning

confidence: 99%

mentioning

confidence: 99%

Global Challenges: Opening up Chemistry, Pandemics, and Air Pollution

Schymanski

2022

ACS Environ. Au

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“…Corresponding studies of species conducted under specific conditions were manually extracted from PubMed and systematically reviewed; next, NP content variations were thoroughly examined, and the mechanisms underlying each variation were identified. Then, the data (such as NP and species) were reserved and presented on the NPcVar platform for visualization, fullly referenced by cross-linking to well-established databases. ,,,− ,, Overall, NPcVar provides a valuable resource for understanding the relationship between species, factors, and NP content, and has the potential to improve the yield of high-value NPs and facilitate the development of new therapeutics.…”

Section: Introductionmentioning

confidence: 99%

Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics

Zhang

Zhou

et al. 2023

J. Chem. Inf. Model.

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Natural products (NPs) have long been associated with human production and play a key role in the survival of species. Significant variations in NP content may severely affect the "return on investment" of NP-based industries and render ecological systems vulnerable. Thus, it is crucial to construct a platform that relates variations in NP content to their corresponding mechanisms. In this study, a publicly accessible online platform, NPcVar (http://npcvar.idrblab.net/), was developed, which systematically described the variations of NP contents and their corresponding mechanisms. The platform comprises 2201 NPs and 694 biological resources, including plants, bacteria, and fungi, curated using 126 diverse factors with 26,425 records. Each record contains information about the species, NP, and factors involved, as well as NP content data, parts of the plant that produce NPs, the location of the experiment, and reference information. All factors were manually curated and categorized into 42 classes which belong to four mechanisms (molecular regulation, species factor, environmental condition, and combined factor). Additionally, the cross-links of species and NP to well-established databases and the visualization of NP content under various experimental conditions were provided. In conclusion, NPcVar is a valuable resource for understanding the relationship between species, factors, and NP contents and is anticipated to serve as a promising tool for improving the yield of high-value NPs and facilitating the development of new therapeutics.

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“…This led to the launch of the CAS Common Chemistry data collection and website in 2009, initially providing information for ∼8000 chemicals . The site was recently revamped and the dataset expanded to provide information for nearly 500,000 substances from the CAS Registry. − …”

Section: Introductionmentioning

confidence: 99%

“… 12 The site was recently revamped and the dataset expanded to provide information for nearly 500,000 substances from the CAS Registry. 13 − 15 …”

Section: Introductionmentioning

confidence: 99%

Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data

Sinclair

Thillainadarajah

Meyer

et al. 2022

J. Chem. Inf. Model.

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The online encyclopedia Wikipedia aggregates a large amount of data on chemistry, encompassing well over 20,000 individual Wikipedia pages and serves the general public as well as the chemistry community. Many other chemical databases and services utilize these data, and previous projects have focused on methods to index, search, and extract it for review and use. We present a comprehensive effort that combines bulk automated data extraction over tens of thousands of pages, semiautomated data extraction over hundreds of pages, and fine-grained manual extraction of individual lists and compounds of interest. We then correlate these data with the existing contents of the U.S. Environmental Protection Agency’s (EPA) Distributed Structure-Searchable Toxicity (DSSTox) database. This was performed with a number of intentions including ensuring as complete a mapping as possible between the Dashboard and Wikipedia so that relevant snippets of the article are loaded for the user to review. Conflicts between Dashboard content and Wikipedia in terms of, for example, identifiers such as chemical registry numbers, names, and InChIs and structure-based collisions such as SMILES were identified and used as the basis of curation of both DSSTox and Wikipedia. This work also allowed us to evaluate available data for sets of chemicals of interest to the Agency, such as synthetic cannabinoids, and expand the content in DSSTox as appropriate. This work also led to improved bidirectional linkage of the detailed chemistry and usage information from Wikipedia with expert-curated structure and identifier data from DSSTox for a new list of nearly 20,000 chemicals. All of this work ultimately enhances the data mappings that allow for the display of the introduction of the Wikipedia article in the community-accessible web-based EPA Comptox Chemicals Dashboard, enhancing the user experience for the thousands of users per day accessing the resource.

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

Cited by 19 publications

References 13 publications

Global Challenges: Opening up Chemistry, Pandemics, and Air Pollution

Global Challenges: Opening up Chemistry, Pandemics, and Air Pollution

Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics

Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data

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