Landscape of current toxicity databases and database standards

Current Opinion in Drug Discovery and Development

Volumn 9, Issue 1, 2006, Pages 124-133

  Yang, Chihae ^a   Benz, R Daniel ^b   Cheeseman, Mitchell A ^b  

^a Leadscope Inc   (United States)

^b CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

Controlled vocabulary; Data exchange; Data integration; Data model; Database standard; QSAR; Toxicity database; ToxML

Indexed keywords

COST; DATA BASE; LAW; MODEL; REVIEW; SCREENING; STANDARDIZATION; TOXICITY TESTING;

ANIMALS; COMPUTER COMMUNICATION NETWORKS; DATABASES, FACTUAL; HUMANS; SYSTEMS INTEGRATION; TOXICOLOGY; VOCABULARY, CONTROLLED;

EID: 30744453261     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (66)

1. R & D spending per NME declines: Decision News Media, Montpellier, France (2005). http://www.drugresearcher.com/news/news-ng.asp?id= 61610-r-d-nme-spend
2. Information services: Tufts CSDD outlook report: Tufts Center for the study of drug development, Boston, MA, USA (2005). http://csdd.tufts.edu/ InfoServices/OutlookReports.asp
3. CDER drug and biologic approval reports: US Food and Drug Administration, Rockwell, MD, USA (2005). http://wvm.fda.gov/cder/rdmt
4. REACH: Research Evaluation and Authorisation of Chemicals: European Union (2005). http://ecb.jrc.it/REACH/
5. Cosmetics testing: 7th Amendment to the cosmetics directive (2003/15/EC): European Coalition to End Animal Experiments, London, UK. http://www.eceae.org/ english/cosmetics.html
6. Existing substances evolution: Environment Canada, Ottowa, ON, Canada (2005). http://www.ec.gc.ca/substances/ese/erg/dslprog.cfm
7. Richard AM, Williams CR, Cariello NF: Improving structure-linked access to publicly available chemical toxicity information. Curr Opin Drug Discovery Dev (2002) 5(1):136-143. Assesses toxicity information sources and recognizes that file standardization and linkage to chemical structure are the essential first steps to making a broad impact in the use of toxicity information. Also discusses the DSSTox and other database initiatives to advance approaches in SARs.
8. Wolfgang GH, Johnson DE: Web resources for drug toxicity. Toxicology (2002) 173(1-2):67-74. Provides an excellent overview of the information sources available on the web and in in silico methodology, from a user perspective.
9. Felsot AS: Web resources for pesticide toxicology, environmental chemistry and policy: A utilitarian perspective. Toxicology (2002) 173(1-2):153-166. Analyses resources for risk assessment of pesticide chemicals.
10. Chemical risk information platform: National Institute of Technology and Evaluation, Tokyo, Japan. http://www.safe.nite.go.jp/english/db.html
11. The National Institute for Public Health and the Environment, Bilthoven, the Netherlands. http://www.rivm.nl
12. The advisory list for self-classification of dangerous substances: Danish Environmental Protection Agency, Copenhagen, Denmark (2005). http://www.mst.dk/chemi/01050000.htm
13. Richard AM, Williams CR: Distributed Structure-Searchable Toxicity (DSSTox) public database network: A proposal. Mutat Res (2002) 499(1):27-52. Presents the concept of DSSTox and addresses the issues of the lack of data in the field of (Q)SAR. Also proposes a network of structure-toxicity datasets.
14. Richard AM, Williams CR: Public sources of mutagenicity and carcinogenicity data: Use in structure-activity relationship models. In: QSMRs of Mutagens and Carcinogens. Benigni ER (Ed), CRC Press, Boca Raton, FL, USA (2003). Summarizes public data sources on carcinogenicity and describes the content of the database.
15. Ishidate M: The mutants - mutagenicity/genetic toxicity database. (2005). http://members.jcom.home.ne.jp/mo-ishidate/index.html
16. Pauli A: AmicBase 2005. J Wiley & Sons Ltd, Hoboken, NJ, USA. http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471743925.html
17. CEBS system toxicology home: National Institute of Environmental Health Sciences, Bethesda, MD, USA (2005). http://cebs.niehs.nih.gov/systox/systoxHome. do
18. The Comparative Toxicogenomics Database: National Institute of Environmental Health Sciences, Bethesda, MD, USA (2005). http://ctd.mdibl.org
19. Knudsen KB, Singh AV, Knudsen TB: Data input module for Birth Defects Systems Manager. Reprod Toxicol (2005) 20(3):369-375.
20. Elmasri R, Shamkant BN: Fundamentals of Database Systems, 4th Edition, Addison-Wesley, New York, NY, USA (2004).
21. Johnson JL: Database: Models, Languages, Design. Oxford University Press, Oxford, UK (1997).
22. Hill DP, Blake JA, Richardson JE, Ringwald M: Extension and Integration of the gene ontology (GO): Combining GO vocabularies with external vocabularies. Genome Res (2002) 12(12):1982-1991. Addresses the methods and challenges involved in the creation of a larger Gene Ontology vocabulary by combining concepts from two orthogonal vocabularies.
23. Cosmides GJ: Electronic surveillance of the pharmacology-toxicology literature: The need for controlled vocabularies and registry systems. Regul Toxicol Pharmacol (1995) 21(2):208-210. Describes the need to use controlled vocabulary for storing, searching and retrieving the literature from databases for pharmacology-toxicology. Also describes the International Union of Pharmacology guidelines for the classification of drugs and receptors.
24. Medical Subject Headings: US National Library of Medicine, Bethesda, MD, USA. http://www.nlm.nih.gov/mesh/meshhome.html
25. Unified Medical Language System: SNOMED Clinical Terms®: US National Library of Medicine, Bethesda, MD, USA. http://www.nlm.nih.gov/research/umls/ Snomed/snomed_main.html
26. Chem abstracts® (CA): CA index guide: American Chemical Society, Washington, DC, USA. http://www.cas.org/PRINTED/caissues.html
27. Solecki R, Bergmann B, Burgin H, Buschmann J, Clark R, Druga A, Van Duijnhoven EA, Duverger M, Edwards J, Freudenberger H, Guittin P et al: Harmonization of rat fetal external and visceral terminology and classification: Report of the fourth workshop on the terminology in developmental toxicology, Berlin, 18-20 April 2002. Reprod Toxicol (2003) 17(5):625-637. Provides a synopsis of four workshops conducted over a span of seven years, which became the foundation of the Fraunhofer developmental toxicology nomenclature.
28. Yang C, Arvidson K, Benz RD, Matthews E, Cheeseman MA, Kruhlak N, Mayer J, Nelson C, Twaroski ML, Dierkes P, Patlewicz G et al: ToxML, a domain intelligent database standard for linking toxicology to chemistry: manuscript in preparation. Presents in detail the use of ToxML modeling using genetic toxicity. The schema for ToxML listed in this manuscript can be accessed from the Leadscope Inc web site, www.leadscope.com.
29. CDISC: Clinical Data Interchange Standards Consortium - Standard for exchange of nonclinical data (SEND): CDISC Inc, Austin, TX, USA (2004). http://www.cdisc.org/models/send/v2.2/index.html
30. IUCLID: International Uniform Chemical Information Database: Technidata America LLC, Wilmington, DE, USA. http://www.technidata-america.com/iuclid/
31. Electronic tools for data submission, evaluation and exchange in the OECD HPV chemicals programme: Organisation for Economic Co-operation and Development, Paris, France, http://www.oecd.org/document/46/0,2340, en_2649_34379_2501870_1_1_1_1,00.html#IUCL ID_guidance_document
32. Mattes WB, Pettit SD, Sansone S-A, Bushel PR, Waters MD: Database development in toxicogenomics: Issues and efforts. Environ Health Perspect (2004) 112(4):495-505.
33. Fostel J, Choi D, Zwickl C: Chemical Effects in Biological Systems - data dictionary (CEBS-DD): A compendium of terms for the capture and integration of biological study design description, conventional phenotypes and 'omics data. Toxicol Sci (2005) 88(2):585-601. Describes in detail the development of a toxicity data model within toxicogenomics database, and also explains the construction of a data dictionary by assimilating other data standards such as SEND, Lilly TDM, ToxML and SEND.
34. Bailey AB, Chanderbhan R, Collazo-Brier N, Cheeseman, MA, Twaroski ML: The use of structure-activity relationship analysis in the food contact notification program. Regul Toxicol Pharmacol (2005) 42(2):225-235.
35. IARC monographs on the evaluation of carcinogenic risks to humans: International Agency for Research on Cancer, Lyon, France. http://www-cie.iarc. fr/
36. Integrated risk information system: US Environmental Protection Agency, Washington, DC, USA. http://www.epa.gov/iris/index.html
37. Toxicology excellence for risk assessment: Concurrent Technologies Corporation, Johnstown, PA, USA. http://iter.ctcnet. net/publicurl/ pub_search_list. cfm
38. Risk assessment information system: US Department of Energy, Oak Ridge, TN, USA. http://risk.lsd.ornl.gov/index.shtml
39. Drugs@FDA: US Food and Drug Administration, Rockwell, MD, USA. http://www.accessdata.fda.gov/scripts/cder/drugsatfda/
40. Cooperative Research and Development Agreement (CRADA): US Food and Drug Administration, Rockwell, MD, USA. http://www.fda.gov/oc/ofacs/partnership/ techtran/policyst.htm FDA CRADA Databases are available from Leadscope (http://www. leadscope.com).
41. National toxicology program: National Institute of Environmental Health Science, Research Triangle Park, NC, USA. http://ntp-server.niehs.nih.gov/
42. Mutagenicity of Food Additives: Mutagenicity of food additives in the Ames Salmonella/microsome assay: Tokyo Metropolitan Institute of Public Health, Tokyo, Japan. http://www.tokyo-eiken.go.jp/henigen/index.htm
43. ECOTOX Database: US Environmental Protection Agency, Washington, DC, USA. http://www.epa.gov/ecotox/
44. TOXNET: Toxicology data network: US National Library of Medicine, Bethesda, MD, USA. http://toxnet.nlm.nih.gov/index.html
45. National Library of Medicine, specialized information services: ChemlDplus advanced: US National Library of Medicine, Bethesda, MD, USA. http://chem.sis.nlm.nih.gov/chemidplus/
46. IPCS INCHEM: International Programme on Chemical Safety, Canada. http://www.inchem.org/
47. Historical control database - of preclinical developmental teratology and reproductive toxicity parameters: Middle Atlantic Reproduction and Teratology Association, King of Prussia, PA/Midwest Teratology Association, Perrysville, OH, USA. http://www.hcd.org
48. National Toxicology Program: Study data searches - historical controls: National Institute of Environmental Health Science, Research Triangle Park, NC, USA. http://ntp-server.niehs.nih.gov/ntpweb/index.cfm?objectid=92E61F1B-F1F6- 975E-7D3BED551F07DCOA
49. RITA - Registry of Industrial Toxicology Animal-data: Fraunhofer ITEM, Hannover, Germany. http://www.item.fraunhofer.de/reni/public/nita/index.html
50. Distributed Structure-Searchable Toxicity (DSSTox) public database network: US Environmental Protection Agency, Washington, DC, USA. http://www.epa.gov/nheerl/dsstox/index.html
51. QSARs: The European Chemicals Bureau, Ispra, Italy. http://ecb.jrc.it/ QSAR/
52. CDER: Informatics and Computational Safety Analysis Staff (ICSAS) Programs and Activities: US Food and Drug Administration, Rockwell, MD, USA. http://www.fda.gov/cder/Offices/OPS_IO/ICSAS.htm
53. Datasets (which are, in contrast to other dataset lists, available in a structural format): Cheminformatics.org. http://cheminformatics.org/datasets/ index.shtml
54. Leadscope Inc, Columbus, OH, USA. http://www.leadscope.com
55. MultiCASE Inc, Beachwood, OH, USA. http://www.multicase.com/
56. MDL® carcinogenicity module: Elsevier MDL, San Leandro, CA, USA. http://mdl.com/products/predictive/carc_module/index.jsp
57. PASS (prediction of activity spectrum for substance): AKos Consulting and Solutions GmbH, Basel, Switzerland. http://www. akosgmbh.de/pass/PASS_OV.htm
58. TOPKAT®: Accelrys Inc, San Diego, CA, USA. http://www.accelrys. com/products/topkat/index.html
59. VITIC: General information: Lhasa Ltd, Leeds, UK. http://www. lhasalimited.org/index.php?cat=2&sub_cat=72
60. CCRIS (chemical carcinogenesis research information system): US National Library of Medicine, Bethesda, MD, USA. http://toxnet.nlm.nih.gov/cgi-bin/sis/ htmlgen?CCRIS
61. The carcinogenic potency database: Carcinogenic Potency Database Project, Berkeley, CA, USA. http://potency.berkeley.edu/cpdb.html
62. Developmental and reproductive toxicology database (DART): US National Library of Medicine, Bethesda, MD, USA. http://toxnet. nlm.nih.gov/cgi-bin/sis/ htmlgen?DARTETIC.htm
63. Genetic toxicology data bank (GENE-TOX): US National Library of Medicine, Bethesda, MD, USA. http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?GENETOX
64. PAN pesticides database: Pesticide Action Network North America, San Francisco, CA, USA. http://www.pesticideinfo.org/index.html
65. RTECS®: Elsevier MDL, San Leandro, CA, USA. http://mdl.com/products/ predictive/rtecs/index.jsp
66. TERIS: Teratogen Information system: University of Washington, Seattle, WA, USA. http://depts.washington.edu/~terisweb/teris/