{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T13:32:37Z","timestamp":1769607157309,"version":"3.49.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T00:00:00Z","timestamp":1684281600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HHSN273201500010C"],"award-info":[{"award-number":["HHSN273201500010C"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Access to computationally based visualization tools to navigate chemical space has become more important due to the increasing size and diversity of publicly accessible databases, associated compendiums of high-throughput screening (HTS) results, and other descriptor and effects data. However, application of these techniques requires advanced programming skills that are beyond the capabilities of many stakeholders. Here we report the development of the second version of the ChemMaps.com webserver (https:\/\/sandbox.ntp.niehs.nih.gov\/chemmaps\/) focused on environmental chemical space. The chemical space of ChemMaps.com v2.0, released in 2022, now includes approximately one million environmental chemicals from the EPA Distributed Structure-Searchable Toxicity (DSSTox) inventory. ChemMaps.com v2.0 incorporates mapping of HTS assay data from the U.S. federal Tox21 research collaboration program, which includes results from around 2000 assays tested on up to 10\u00a0000 chemicals. As a case example, we showcased chemical space navigation for Perfluorooctanoic Acid (PFOA), part of the Per- and polyfluoroalkyl substances (PFAS) chemical family, which are of significant concern for their potential effects on human health and the environment.<\/jats:p>","DOI":"10.1093\/nar\/gkad380","type":"journal-article","created":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T10:48:11Z","timestamp":1684320491000},"page":"W78-W82","source":"Crossref","is-referenced-by-count":6,"title":["ChemMaps.com v2.0: exploring the environmental chemical universe"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6499-4540","authenticated-orcid":false,"given":"Alexandre","family":"Borrel","sequence":"first","affiliation":[{"name":"Inotiv , RTP, NC, 27560, USA"}]},{"given":"Mike","family":"Conway","sequence":"additional","affiliation":[{"name":"NIH\/NIEHS\/ODS , RTP, NC 27709, USA"}]},{"given":"Sue Z","family":"Nolte","sequence":"additional","affiliation":[{"name":"NIH\/NIEHS\/ODS , RTP, NC 27709, USA"}]},{"given":"Aswani","family":"Unnikrishnan","sequence":"additional","affiliation":[{"name":"Inotiv , RTP, NC, 27560, USA"}]},{"given":"Charles\u00a0P","family":"Schmitt","sequence":"additional","affiliation":[{"name":"NIH\/NIEHS\/ODS , RTP, NC 27709, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7914-3682","authenticated-orcid":false,"given":"Nicole\u00a0C","family":"Kleinstreuer","sequence":"additional","affiliation":[{"name":"NIH\/NIEHS\/DTT\/NICEATM , RTP, NC 27709, USA"}]}],"member":"286","published-online":{"date-parts":[[2023,5,17]]},"reference":[{"key":"2023070504565915000_B1","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1021\/cc0000388","article-title":"Chemography: the art of navigating in chemical space","volume":"3","author":"Oprea","year":"2001","journal-title":"J. Comb. Chem."},{"key":"2023070504565915000_B2","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1517\/17460441.2015.1060216","article-title":"Progress in visual representations of chemical space","volume":"10","author":"Osolodkin","year":"2015","journal-title":"Expert Opin. Drug Discovery"},{"key":"2023070504565915000_B3","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/s10822-021-00399-1","article-title":"Progress on open chemoinformatic tools for expanding and exploring the chemical space","volume":"36","author":"Medina-Franco","year":"2022","journal-title":"J. Comput. Aided Mol. Des."},{"key":"2023070504565915000_B4","doi-asserted-by":"crossref","first-page":"510","DOI":"10.3389\/fchem.2019.00510","article-title":"Finding constellations in chemical space through core analysis","volume":"7","author":"Naveja","year":"2019","journal-title":"Front. Chem."},{"key":"2023070504565915000_B5","doi-asserted-by":"crossref","first-page":"10895","DOI":"10.1021\/acs.jmedchem.8b01626","article-title":"Computational Method to Evaluate Progress in Lead Optimization","volume":"61","author":"Vogt","year":"2018","journal-title":"J. Med. Chem."},{"key":"2023070504565915000_B6","doi-asserted-by":"crossref","first-page":"D1170","DOI":"10.1093\/nar\/gkaa920","article-title":"DrugSpaceX: a large screenable and synthetically tractable database extending drug space","volume":"49","author":"Yang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023070504565915000_B7","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1038\/nature03193","article-title":"Navigating chemical space for biology and medicine","volume":"432","author":"Lipinski","year":"2004","journal-title":"Nature"},{"key":"2023070504565915000_B8","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1021\/ar500432k","article-title":"The chemical space project","volume":"48","author":"Reymond","year":"2015","journal-title":"Acc. Chem. Res."},{"key":"2023070504565915000_B9","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.trac.2017.09.013","article-title":"The chemical space for non-target analysis","volume":"97","author":"Milman","year":"2017","journal-title":"TrAC Trends Anal. Chem."},{"key":"2023070504565915000_B10","doi-asserted-by":"crossref","first-page":"1800121","DOI":"10.1002\/minf.201800121","article-title":"Filling data gaps by read-across: a mini review on its application, developments and challenges","volume":"38","author":"Kovarich","year":"2019","journal-title":"Mol. Inf."},{"key":"2023070504565915000_B11","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.1093\/bioinformatics\/bty412","article-title":"Exploring drug space with ChemMaps.com","volume":"34","author":"Borrel","year":"2018","journal-title":"Bioinformatics"},{"key":"2023070504565915000_B12","doi-asserted-by":"crossref","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","article-title":"DrugBank 5.0: a major update to the DrugBank database for 2018","volume":"46","author":"Wishart","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023070504565915000_B13","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s13321-017-0247-6","article-title":"The CompTox Chemistry Dashboard: a community data resource for environmental chemistry","volume":"9","author":"Williams","year":"2017","journal-title":"J Cheminform"},{"key":"2023070504565915000_B14","doi-asserted-by":"crossref","first-page":"987848","DOI":"10.3389\/ftox.2022.987848","article-title":"Data curation to support toxicity assessments using the Integrated Chemical Environment","volume":"4","author":"Daniel","year":"2022","journal-title":"Front. Toxicol."},{"key":"2023070504565915000_B15","doi-asserted-by":"crossref","first-page":"100096","DOI":"10.1016\/j.comtox.2019.100096","article-title":"EPA\u2019s DSSTox database: history of development of a curated chemistry resource supporting computational toxicology research","volume":"12","author":"Grulke","year":"2019","journal-title":"Comput. Toxicol."},{"key":"2023070504565915000_B16","doi-asserted-by":"crossref","first-page":"850019","DOI":"10.3389\/fenvs.2022.850019","article-title":"Assembly and curation of lists of per- and polyfluoroalkyl substances (PFAS) to support environmental science research","volume":"10","author":"Williams","year":"2022","journal-title":"Front. Environ. Sci."},{"key":"2023070504565915000_B17","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1021\/acs.chemrestox.0c00264","article-title":"The Tox21 10K compound library: collaborative chemistry advancing toxicology","volume":"34","author":"Richard","year":"2021","journal-title":"Chem. Res. Toxicol."},{"key":"2023070504565915000_B18","doi-asserted-by":"crossref","first-page":"047013","DOI":"10.1289\/EHP8495","article-title":"CATMoS: collaborative Acute Toxicity Modeling Suite","volume":"129","author":"Mansouri","year":"2021","journal-title":"Environ. Health Perspect."},{"key":"2023070504565915000_B19","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1093\/toxsci\/kfac042","article-title":"Evaluation of variability across rat acute oral systemic toxicity studies","volume":"188","author":"Karmaus","year":"2022","journal-title":"Toxicol. Sci."},{"key":"2023070504565915000_B20","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13321-018-0263-1","article-title":"OPERA models for predicting physicochemical properties and environmental fate endpoints","volume":"10","author":"Mansouri","year":"2018","journal-title":"J. Cheminform."},{"key":"2023070504565915000_B21","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1093\/bioinformatics\/btw680","article-title":"tcpl: the ToxCast pipeline for high-throughput screening data","volume":"33","author":"Filer","year":"2017","journal-title":"Bioinformatics"},{"key":"2023070504565915000_B22","doi-asserted-by":"crossref","first-page":"054501","DOI":"10.1289\/EHP1759","article-title":"An integrated chemical environment to support 21st-century toxicology","volume":"125","author":"Bell","year":"2017","journal-title":"Environ. Health Perspect."},{"key":"2023070504565915000_B23","doi-asserted-by":"crossref","first-page":"104916","DOI":"10.1016\/j.tiv.2020.104916","article-title":"An integrated chemical environment with tools for chemical safety testing","volume":"67","author":"Bell","year":"2020","journal-title":"Toxicol. In Vitro"},{"key":"2023070504565915000_B24","doi-asserted-by":"crossref","first-page":"100184","DOI":"10.1016\/j.comtox.2021.100184","article-title":"Application of new approach methodologies: ICE tools to support chemical evaluations","volume":"20","author":"Abedini","year":"2021","journal-title":"Comput. Toxicol."},{"key":"2023070504565915000_B25","doi-asserted-by":"crossref","first-page":"eabg9065","DOI":"10.1126\/science.abg9065","article-title":"Per- and polyfluoroalkyl substances in the environment","volume":"375","author":"Evich","year":"2022","journal-title":"Science"},{"key":"2023070504565915000_B26","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1002\/etc.4890","article-title":"Per- and polyfluoroalkyl substance toxicity and human health review: current state of knowledge and strategies for informing future research","volume":"40","author":"Fenton","year":"2021","journal-title":"Environ. Toxicol. Chem."},{"key":"2023070504565915000_B27","doi-asserted-by":"crossref","first-page":"128243","DOI":"10.1016\/j.jhazmat.2022.128243","article-title":"In Vitro characterization of the endocrine disrupting effects of per- and poly-fluoroalkyl substances (PFASs) on the human androgen receptor","volume":"429","author":"Tachachartvanich","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"2023070504565915000_B28","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1210\/jc.2018-01855","article-title":"Endocrine disruption of androgenic activity by perfluoroalkyl substances: clinical and experimental evidence","volume":"104","author":"Di\u00a0Nisio","year":"2019","journal-title":"J. Clin. Endocrinol. Metab."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W78\/50736402\/gkad380.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W78\/50736402\/gkad380.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T09:02:01Z","timestamp":1688547721000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/W1\/W78\/7167306"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,17]]},"references-count":28,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2023,5,17]]},"published-print":{"date-parts":[[2023,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad380","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,5]]},"published":{"date-parts":[[2023,5,17]]}}}