Alternatives, literature, grants, toxicity data, and biomedical databases containing information of potential use to the development of non-animal alternative methods.
Alternatives Databases
Altbib
AnimAlt-ZEBET
DB-ALM ECVAM Database Service on Alternative Methods to Animal Experimentation
MEIC (Multicentre Evaluation of In Vitro Cytotoxicity) and EDIT (Evaluation-guided development of New In vitro Tests) projects
Scientific/Technical Literature Databases
BioMed Central: publisher of more than 170 peer-reviewed OPEN access journals
Community of Science: access to range of professional reference databases [subscription required]
DIMDI: 70 databases of scientific literature in medicine, drugs, toxicology, medical devices, biology, psychology [free and fee-based]
EMBASE [subscription required]
Infotrieve Online: search for multiple types of content and databases including journal articles, patents, drug pipeline intelligence, laboratory products, and protocols [subscription required]
Intute, Health and Life Sciences: free online service providing access to web resources for education and research that have been evaluated and selected by a network of subject specialists
National Library of Medicine (US) List of Databases & Electronic Information Sources
NLM Catalog: NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials
NLM Bookshelf: biomedical books that can be searched online
NLM DIRLINE®: directory of organizations and other resources in health and biomedicine
PubMed®/MEDLINE®
ScienceDirect: sign up for alerts to specific new scientific, medical & technical content
SCIRUS: science-specific Internet search engine; searches over 300 million science-specific Web pages
SEFREC: database for serum-free cell culture (cells & media)
Thompson Scientific: current source of BIOSIS databases [subscription required]
WorldWideScience: global science gateway prototype for accelerating scientific discovery and progress to enable searching of national and international scientific databases; more national and international science databases are invited to make their collections accessible
Chemical Toxicity Databases
AcuBase: Pilot database open to ACuteTox Partners containing in vitro and in vivo test data, in vitro protocols and SOPs, human acute toxicity data, and physio-chemical properties for 97 reference chemicals
Acute Toxicity Database: database of aquatic acute toxicity test results for thousands of chemicals in many species conducted by the USGS CERC
Allergen Database
ATSDR Toxicological Profile Information Sheets
Carcinogenic Potency Database (CPDB): results from 6153 chronic, long-term animal cancer tests on 1485 chemicals
Chem.com: access to 127,000 chemical 3D structures from the NCI database
ChemFinder.com: portal of free and subscription scientific databases (reference, chemical, reaction, safety)
Chemical structure indexing of toxicity data on the internet: manuscript by Richard, Gold & Nicklaus in Curr Opin Drug Discov Devel. 9(3), 314-25 (2006); discusses public initiatives with particular reference to toxicology-related chemical information
Contaminant Exposure and Effects-Terrestrial Vertebrates database (CEE-TV): over 18,000 records containing ecotoxicological exposure and effects information on over 460 species of terrestrial vertebrates that reside in US estuarine and coastal habitats
DSSTox, Distributed Structure-Searchable Toxicity Database Network: a project of the US EPA's Computational Toxicology Program; provides a public forum for publishing downloadable, standardized chemical structure files associated with toxicity data
DrugMatrix® and Drug Signatures®: DrugMatrix® proprietary database of microarray and pharmacology data used to identify Drug Signatures®, genomic biomarkers that are predictive of specific toxicological endpoints and mechanisms of action
ECOTOX, Version 4: US EPA source for locating single chemical toxicity data for aquatic life, terrestrial plants, and wildlife
Environmental Health and Safety freeware: links to free databases and software plus news & events
EPAA Working Group 1 (WG1) databases: "In-house Review" and "Research Review," databases of in vitro methods and ongoing research being conducted by industry, are being compiled by EPAA
EXTOXNET: pesticide information profiles database
Human and Environmental Risk Assessments (HERA): toxicity & risk data on ingredients of household cleaning products
Integrated Risk Information System (IRIS): database of human health effects that may result from exposure to various substances found in the environment; hazard identification and dose-response assessments for over 500 chemicals
International Programme on Chemical Safety (IPCS INCHEM): public, searchable, peer-reviewed chemical safety-related publications and database records from international bodies, including: Concise International Chemical Assessment Document (CICADS); International Chemical Safety Cards (ICSCs); Pesticide Data Sheets (PDSs); Screening Information Data Set (SIDS) for High Production Volume Chemicals; and more
International Toxicity Estimates for Risk (ITER) Database: database of human health risk values and cancer classifications for over 600 chemicals of environmental concern; now a part of TOXNET
Japan Ministry of Health, Labour and Welfare (MHLW) Chemical Toxicity Database
NLM Chemical Information SIS
NLM Environmental Health & Toxicology SIS
NTP Study Reports
NTP toxicology databases
OECD Database on Pesticide/Biocide Reviews
OECD eChemPortal: new 2006; free public access to data submitted to government chemical review programmes at national, regional, and international levels: physical chemical properties; environmental fate and behaviour; ecotoxicity; toxicity
OECD EXICHEM Database: resource for identifying activities on existing chemicals (e.g. information gathering, testing, evaluation) by OECD Member countries and thereby assist in identifying opportunities for co-operation and avoiding duplication of work
PAN Pesticides Database: current toxicity and regulatory information for pesticides; a project of Pesticide Action Network North America
PubChem: new database of chemical structures and their biological activities that is part of the NIH Molecular Libraries Roadmap; provides information on biological activities of small molecules, including substance information, compound structures, and bioactivity data in three primary databases, PCSubstance, PCCompound, and PCBioAssay; a future goal is to include predictive ADME/toxicology for the small molecule modulators
TETRATOX: fish LC50 alternative database of toxic potency for more than 2400 chemicals [Schultz, T.W. 1997. TETRATOX: Tetrahymena pyriformis population growth impairment endpoint-A surrogate for fish lethality. Toxicol. Methods 7: 289-309]
TOXNET® Toxicology Data Network: NLM's collection of toxicology and environmental health databases including: Hazardous Substances Data Bank (HSDB); Integrated Risk Information System (IRIS); Genetic Toxicology Data Bank (GENE-TOX); Chemical Carcinogenesis Research Information System (CCRIS); Household Products Database; TOXLINE® containing references to the world's toxicology literature; ChemIDplus, a chemical dictionary and structure database
Toxic Substance Control Act Test Submission database (TSCATS): database of information on unpublished technical reports submitted by industry to EPA under the Toxic Substances Control Act (TSCA); search for chemicals by CAS#, formula, or chemical name
RTECS®, The Registry of Toxic Effects of Chemical Substances: toxicity information for over 150,000 chemical substances; includes toxic effects, general toxicology reviews, data on skin and/or eye irritation, mutation, reproductive consequences and tumorigenicity [fee based]
Syracuse Research Corporation Databases: Environmental Fate Data Base; Physical Properties Database; Solvents Database; SMILECAS Database [available for purchase]
Grants/Awards Databases
NIEHS Extramural Research Portfolio
NIH CRISP (Computer Retrieval of Information on Scientific Projects): US federally funded biomedical research projects
National Science Foundation (NSF)
Genome and Other Biomedical Databases
Bioinformatics Databases (multiple types)
Argonne National Laboratory Computational Biology Group: databases and tools for analysis of genomes and metabolic networks
BioChipNet database: OPEN source, comprehensive and searchable information platform on microarrays and related fields such as microfluidics and bioinformatics
National Center for Biotechnology Information (NCBI): National (US) resource for molecular biology information; OPEN access bioinformatics databases
Genomics Databases
Database of Genomic Variants: curated catalogue of structural variation in the human genome
EnsEMBL at European Bioinformatics Institute (EBI): comparative-genomics database
Entrez at NCBI: comparative-genomics database
GenBank: DNA sequence database
Genetic Variation Databases
Genome Browser at University of California: comparative-genomics database
HUGO Gene Nomenclature Committee (HGNC)
Mammalian Gene Collection (MGC): full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes
UCSC Genome Browser: research tool that integrates work of hundreds of scientists worldwide into graphical display of genome sequences and aligned annotations on multitude of mammalian and model organism genomes
Single Nucleotide Polymorphisms (SNPS)
GeneSNPs
Mouse SNP and Genotype Data Download: NTP Mouse Genome Resequencing Project
NCBI SNP
RNA interference (RNAi)
Drosophila RNAi Screening Center
Proteomics and Related
AbMiner: public database on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies
ExPASy Proteomics Server
Immune Epitope Database: bioinformatics resource useful to the development of vaccines, immunotherapeutics, and diagnostics
SIB-HTPSELEX: public database of high-throughput SELEX libraries for transcription factor binding sites
YASARA: protein molecular graphics, modeling, and simulation program for Windows, Linux, and Mac OS X; YASARA View is free, and several more powerful versions are available via license
Pathways Databases
BIND: University of Toronto pathway database
BioSilico: web-based database system that facilitates the search and analysis of metabolic pathways
HumanCyc: Stanford Research Institute human pathway database
KEGG Pathway Database
NCI-Nature Pathway Interaction Database: OPEN access database of human cellular signaling pathways
PANTHER Pathways: Applied Biosystems pathway database
Reactome: curated collection of human biological pathways such as energy metabolism, DNA replication, RNA transcription, protein translation, cell cycle regulation, and the blood-clotting cascade
Science Database of Cell Signaling: information on components of cellular signaling pathways and their relations; organized into pathways called Connections Maps
VisANT: open-source interface for published data sets on biomolecular interactions, including those entered by users; integrated with standard databases for organized annotation; suitable for a wide range of applications: pathways, gene regulation, systems biology
Database Lists
Biomedical databases of the Entrez Molecular Biology System
DoD2006 Database of Databases: biomedical databases
Harvard University: list of biomolecular databases
Israel Science and Technology Directory: links to many biomedical databases
LabVelocity Bioinformatics Links
Molecular Cross-Database System
Nucleic Acids Research (NAR), 2006 Database Issue
NAR Molecular Biology Database Collection: links to ~858 databases featured in NAR, and selected other databases
NAR Database List: links to many biomedical databases
Physiome Project list of databases: databases for bioinformatics, proteins, cell signaling, and physiome
Biomedical Simulation Projects/Software
Allen Brain Atlas (ABA): OPEN access database of gene expression maps for about 20,000 mouse brain genes; RNA in situ hybridization data, detailed Reference Atlases, and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression; "for exploration of the brain at the cellular and molecular level"
Cell Electrophysiology Simulation Environment (CESE): framework to perform computational electrophysiological simulations; useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations
Gepasi Biochemical Simulation: software package for modeling biochemical systems
MGED Open Source Projects: Site for distribution of Open Source Software developed by Microarray Gene Expression Data Society:
MAGE software, MISFISHIE (the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments), MIAME (Minimum Information About a Microarray Experiment)
National Resource for Cell Analysis and Modeling (NRCAM): OPEN access Virtual Cell software for quantitative cell biological research; couples computational cell biology approaches and high resolution light microscopy; models can be based on experimental data and theoretical assumptions
National Simulation Resource (NSR) for Transport, Metabolism and Reaction: collection of material of interest to biological modelers
Ontology Viewer: Physiome Project organizes biological knowledge and access to databases in the form of the following ontological trees: Organ systems; Tissues; Cells; Organelles; Cell function; Proteins; Protein domains; Genes
Physiome Project (http://www.physiome.org.nz/ OR http://www.physiome.org): worldwide public domain effort to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations
PK-Sim®: physiologically based pharmacokinetic whole body model
Protégé: open source ontology editor and knowledge-base framework
Protein Lounge: interactive web-based databases and software for systems biology…"focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis" [subscription required]
Systems Biology Markup Language (SBML): free and open language used to represent quantitative models of metabolic networks, cell-signaling pathways, regulatory networks, and others to allow models to be shared in a form useable to other researchers
Pharmacokinetics and Pharmacogenomics Databases
Connectivity Map: genomic tool "that relies on genes to connect diseases with potential drugs to treat them and to predict how new drugs function in cells"
Human Genome Project (HGP) Gene Gateway: Internet tools "to investigate genetic disorders, chromosomes, genome maps, genes, sequence data, genetic variants, and molecular structures"
Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB): interactive tool for investigating how genetic variation effects drug response; displays genotype, molecular, and clinical primary data integrated with literature, pathway representations, protocol information, and links to additional external resources [Reference: Thorn, C.F., Klein, T.E. & Altman, R.B. (2005). PharmGKB: The pharmacogenetics and pharmacogenomics knowledge base. Methods Mol. Biol. 311, 179-91.]
Phish-Pharm Database of Pharmacokinetics Data in Fish [HTML version]
Phish-Pharm on CVM: Reference: Reimschuessel, R., et al. Available at: http://www.aapsj.org/view.asp?art=aapsj070230
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