Allan Peter Davis, Thomas C Wiegers, Daniela Sciaky, Fern Barkalow, Melissa Strong, Brent Wyatt, Jolene Wiegers, Roy McMorran, Sakib Abrar, Carolyn J Mattingly
{"title":"比较毒物基因组学数据库 20 周年:2025 年更新。","authors":"Allan Peter Davis, Thomas C Wiegers, Daniela Sciaky, Fern Barkalow, Melissa Strong, Brent Wyatt, Jolene Wiegers, Roy McMorran, Sakib Abrar, Carolyn J Mattingly","doi":"10.1093/nar/gkae883","DOIUrl":null,"url":null,"abstract":"<p><p>For 20 years, the Comparative Toxicogenomics Database (CTD; https://ctdbase.org) has provided high-quality, literature-based curated content describing how environmental chemicals affect human health. Today, CTD includes over 94 million toxicogenomic connections relating chemicals, genes/proteins, phenotypes, anatomical terms, diseases, comparative species, pathways and exposures. In this 20th year anniversary update, we reflect on CTD's remarkable growth and provide an overview of the increased data content and new features, including enhancements to the curation workflow (e.g. new exposure curation tool and expanded use of natural language processing), added functionality (e.g. improvements to CTD Tetramers and Pathway View tools) and significant upgrades to software and infrastructure. Linking lab-based core curation with real-world human exposure curation via the use of controlled vocabularies facilitates analysis of content across the entire environmental health continuum, from molecular toxicological mechanisms to the population level, and vice versa. The 'prototype database' originally described in 2004 has evolved into a premier, sophisticated, highly cited and well-engineered knowledgebase and discoverybase that is utilized by scientists worldwide to design testable hypotheses about environmental health.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":null,"pages":null},"PeriodicalIF":16.6000,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Comparative toxicogenomics database's 20th anniversary: update 2025.\",\"authors\":\"Allan Peter Davis, Thomas C Wiegers, Daniela Sciaky, Fern Barkalow, Melissa Strong, Brent Wyatt, Jolene Wiegers, Roy McMorran, Sakib Abrar, Carolyn J Mattingly\",\"doi\":\"10.1093/nar/gkae883\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>For 20 years, the Comparative Toxicogenomics Database (CTD; https://ctdbase.org) has provided high-quality, literature-based curated content describing how environmental chemicals affect human health. Today, CTD includes over 94 million toxicogenomic connections relating chemicals, genes/proteins, phenotypes, anatomical terms, diseases, comparative species, pathways and exposures. In this 20th year anniversary update, we reflect on CTD's remarkable growth and provide an overview of the increased data content and new features, including enhancements to the curation workflow (e.g. new exposure curation tool and expanded use of natural language processing), added functionality (e.g. improvements to CTD Tetramers and Pathway View tools) and significant upgrades to software and infrastructure. Linking lab-based core curation with real-world human exposure curation via the use of controlled vocabularies facilitates analysis of content across the entire environmental health continuum, from molecular toxicological mechanisms to the population level, and vice versa. The 'prototype database' originally described in 2004 has evolved into a premier, sophisticated, highly cited and well-engineered knowledgebase and discoverybase that is utilized by scientists worldwide to design testable hypotheses about environmental health.</p>\",\"PeriodicalId\":19471,\"journal\":{\"name\":\"Nucleic Acids Research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":16.6000,\"publicationDate\":\"2024-10-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Nucleic Acids Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/nar/gkae883\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nucleic Acids Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/nar/gkae883","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
For 20 years, the Comparative Toxicogenomics Database (CTD; https://ctdbase.org) has provided high-quality, literature-based curated content describing how environmental chemicals affect human health. Today, CTD includes over 94 million toxicogenomic connections relating chemicals, genes/proteins, phenotypes, anatomical terms, diseases, comparative species, pathways and exposures. In this 20th year anniversary update, we reflect on CTD's remarkable growth and provide an overview of the increased data content and new features, including enhancements to the curation workflow (e.g. new exposure curation tool and expanded use of natural language processing), added functionality (e.g. improvements to CTD Tetramers and Pathway View tools) and significant upgrades to software and infrastructure. Linking lab-based core curation with real-world human exposure curation via the use of controlled vocabularies facilitates analysis of content across the entire environmental health continuum, from molecular toxicological mechanisms to the population level, and vice versa. The 'prototype database' originally described in 2004 has evolved into a premier, sophisticated, highly cited and well-engineered knowledgebase and discoverybase that is utilized by scientists worldwide to design testable hypotheses about environmental health.
期刊介绍:
Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.