Literature DB >> 18996453

Chemical databases for environmental health and clinical research.

Carolyn J Mattingly1.   

Abstract

The increasing number of publicly available biological databases reflects the evolving need for managing and evaluating abundant and complex data in biological, clinical and computational research. Currently there are over 1000 biologically relevant databases in the public domain with varied content and diverse approaches to capturing and presenting data. This review summarizes the comparatively small niche of sophisticated databases and other resources that aim to enhance understanding of chemicals and their biological actions. The databases reviewed include 1 that emphasizes environmental chemicals and 9 that emphasize drugs and small molecules. These databases and their associated resources are incrementally strengthening the expanding field of toxicogenomics-based research by providing centralized sources of manually and computationally curated datasets and highly sophisticated tools for the meta-analysis of continually increasing environmental chemical, drug and small-molecule datasets.

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Year:  2008        PMID: 18996453      PMCID: PMC2727625          DOI: 10.1016/j.toxlet.2008.10.003

Source DB:  PubMed          Journal:  Toxicol Lett        ISSN: 0378-4274            Impact factor:   4.372


  15 in total

1.  SuperDrug: a conformational drug database.

Authors:  Andrean Goede; Mathias Dunkel; Nina Mester; Cornelius Frommel; Robert Preissner
Journal:  Bioinformatics       Date:  2005-02-02       Impact factor: 6.937

2.  ChemDB update--full-text search and virtual chemical space.

Authors:  Jonathan H Chen; Erik Linstead; S Joshua Swamidass; Dennis Wang; Pierre Baldi
Journal:  Bioinformatics       Date:  2007-06-28       Impact factor: 6.937

3.  PharmGED: Pharmacogenetic Effect Database.

Authors:  C J Zheng; L Y Han; B Xie; C Y Liew; S Ong; J Cui; H L Zhang; Z Q Tang; S H Gan; L Jiang; Y Z Chen
Journal:  Nucleic Acids Res       Date:  2006-12-06       Impact factor: 16.971

4.  STRING 7--recent developments in the integration and prediction of protein interactions.

Authors:  Christian von Mering; Lars J Jensen; Michael Kuhn; Samuel Chaffron; Tobias Doerks; Beate Krüger; Berend Snel; Peer Bork
Journal:  Nucleic Acids Res       Date:  2006-11-10       Impact factor: 16.971

5.  ChEBI: a database and ontology for chemical entities of biological interest.

Authors:  Kirill Degtyarenko; Paula de Matos; Marcus Ennis; Janna Hastings; Martin Zbinden; Alan McNaught; Rafael Alcántara; Michael Darsow; Mickaël Guedj; Michael Ashburner
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

6.  CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

Authors:  Michael Waters; Stanley Stasiewicz; B Alex Merrick; Kenneth Tomer; Pierre Bushel; Richard Paules; Nancy Stegman; Gerald Nehls; Kenneth J Yost; C Harris Johnson; Scott F Gustafson; Sandhya Xirasagar; Nianqing Xiao; Cheng-Cheng Huang; Paul Boyer; Denny D Chan; Qinyan Pan; Hui Gong; John Taylor; Danielle Choi; Asif Rashid; Ayazaddin Ahmed; Reese Howle; James Selkirk; Raymond Tennant; Jennifer Fostel
Journal:  Nucleic Acids Res       Date:  2007-10-25       Impact factor: 16.971

7.  The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge.

Authors:  Tina Hernandez-Boussard; Michelle Whirl-Carrillo; Joan M Hebert; Li Gong; Ryan Owen; Mei Gong; Winston Gor; Feng Liu; Chuong Truong; Ryan Whaley; Mark Woon; Tina Zhou; Russ B Altman; Teri E Klein
Journal:  Nucleic Acids Res       Date:  2007-11-21       Impact factor: 16.971

8.  PDTD: a web-accessible protein database for drug target identification.

Authors:  Zhenting Gao; Honglin Li; Hailei Zhang; Xiaofeng Liu; Ling Kang; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Xicheng Wang; Hualiang Jiang
Journal:  BMC Bioinformatics       Date:  2008-02-19       Impact factor: 3.169

9.  ChemBank: a small-molecule screening and cheminformatics resource database.

Authors:  Kathleen Petri Seiler; Gregory A George; Mary Pat Happ; Nicole E Bodycombe; Hyman A Carrinski; Stephanie Norton; Steve Brudz; John P Sullivan; Jeremy Muhlich; Martin Serrano; Paul Ferraiolo; Nicola J Tolliday; Stuart L Schreiber; Paul A Clemons
Journal:  Nucleic Acids Res       Date:  2007-10-18       Impact factor: 16.971

10.  The Molecular Biology Database Collection: 2008 update.

Authors:  Michael Y Galperin
Journal:  Nucleic Acids Res       Date:  2007-11-19       Impact factor: 16.971

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  7 in total

1.  Aquatic models, genomics and chemical risk management.

Authors:  Keith C Cheng; David E Hinton; Carolyn J Mattingly; Antonio Planchart
Journal:  Comp Biochem Physiol C Toxicol Pharmacol       Date:  2011-06-28       Impact factor: 3.228

2.  Public data sources to support systems toxicology applications.

Authors:  Allan Peter Davis; Jolene Wiegers; Thomas C Wiegers; Carolyn J Mattingly
Journal:  Curr Opin Toxicol       Date:  2019-03-11

3.  The Comparative Toxicogenomics Database: update 2011.

Authors:  Allan Peter Davis; Benjamin L King; Susan Mockus; Cynthia G Murphy; Cynthia Saraceni-Richards; Michael Rosenstein; Thomas Wiegers; Carolyn J Mattingly
Journal:  Nucleic Acids Res       Date:  2010-09-22       Impact factor: 16.971

4.  CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge.

Authors:  Jessica Ahmed; Thomas Meinel; Mathias Dunkel; Manuela S Murgueitio; Robert Adams; Corinna Blasse; Andreas Eckert; Saskia Preissner; Robert Preissner
Journal:  Nucleic Acids Res       Date:  2010-10-15       Impact factor: 16.971

5.  The Comparative Toxicogenomics Database's 10th year anniversary: update 2015.

Authors:  Allan Peter Davis; Cynthia J Grondin; Kelley Lennon-Hopkins; Cynthia Saraceni-Richards; Daniela Sciaky; Benjamin L King; Thomas C Wiegers; Carolyn J Mattingly
Journal:  Nucleic Acids Res       Date:  2014-10-17       Impact factor: 16.971

6.  Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD).

Authors:  Thomas C Wiegers; Allan Peter Davis; K Bretonnel Cohen; Lynette Hirschman; Carolyn J Mattingly
Journal:  BMC Bioinformatics       Date:  2009-10-08       Impact factor: 3.169

7.  T3DB: a comprehensively annotated database of common toxins and their targets.

Authors:  Emilia Lim; Allison Pon; Yannick Djoumbou; Craig Knox; Savita Shrivastava; An Chi Guo; Vanessa Neveu; David S Wishart
Journal:  Nucleic Acids Res       Date:  2009-11-06       Impact factor: 16.971

  7 in total

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