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Databases

Last updated: April 12, 2016

Alternatives, literature, grants, toxicity data, biomedical, and policy databases containing information of potential use to the development of non-animal alternative methods.

Alternatives Databases


Altbib

AltTox Resource Center

AnimAlt-ZEBET

DB-ALM ECVAM Database Service on Alternative Methods to Animal Experimentation

EUROECOTOX database of bioassays: alternative methods for ecotoxicology testing

MEIC (Multicentre Evaluation of In Vitro Cytotoxicity) and EDIT (Evaluation-guided development of New In vitro Tests) projects (Reference: Toxicol. In Vitro. Volume 24, Issue 8, December 2010, Pages 2060-2062)

SEFREC: database for serum-free cell culture (cells & media)

TSAR (Tracking System for Alternative test methods Review, Validation and Approval in the Context of EU Regulations on Chemicals): tool to provide a transparent view on the status of alternative methods as they progress from purely scientific protocols submitted for pre-validation to being actively used in a regulatory context

Scientific/Technical Literature Databases

BioMed Central: publisher of more than 170 peer-reviewed OPEN access journals

Community of Scholars: 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)

Ethicsweb: European Ethics Documentation Centre: bioethics databases, and bibliographic, laws & regulations and other searchable resources

Infotrieve Online: search for multiple types of content and databases including journal articles, patents, drug pipeline intelligence, laboratory products, and protocols (subscription required)

National Library of Medicine (US) List of Databases & Electronic Information Sources

NCBI Probe Database (ProbeDB): public archive of around 10 million nucleic acid reagents (probes) used in biomedical research

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

Web of Science: index of multidisciplinary research covering scholarly journals, books, proceedings, published data sets, and patents

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

Database Journals

Database: The Journal of Biological Databases and Curation

Nucleic Acids Research 2013 Database issue

Nucleic Acids Research 2016 Database issue

Chemical Toxicity Databases

ACToR (Aggregated Computational Toxicology Resource): US EPA database of structural and toxicological data for environmental chemicals compiled from over 200 sources; launched late 2008

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 Online: allergen protein database

ATSDR ToxProfiles™: information on more than 180 chemicals, hazardous substances, and mixtures (Interaction Profiles) available at no charge from Agency for Toxic Substances and Disease Registry (ATSDR)

BioByte Corp: Bio-Loom (Q)SAR Database

Carcinogenic Potency Database (CPDB): results from 6153 chronic, long-term animal cancer tests on 1485 chemicals; classifies carcinogens based on multi-organ toxicity data summarized as a single record for each chemical

ChemAgora: online portal provided by the European Commission to search for chemical information from multiple databases

Chemical Effects in Biological Systems (CEBS): data of interest to environmental health scientists

Chemical Lists Information System (CheLIST): to support the evaluation of alternative methods, this tool can be used to identify chemicals (or chemical groups) that have been tested in a range of research projects, and also whether the chemical of interest belongs to a regulated group

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

Chemicals Evaluated for Carcinogenic Potential, US EPA

Comparative Toxicogenomics Database: integrates data from curated scientific literature to describe chemical interactions with genes and proteins, and associations between diseases and chemicals, and diseases and genes/proteins; contains over 15 million toxicogenomic relationships; open-access article on 2013 database updates at: http://nar.oxfordjournals.org/content/41/D1/D1104.full

Contact Allergen Database

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

Danish (Q)SAR Database: repository of estimates from over 70 (Q)SAR models for 166,072 chemicals; (Q)SAR models encompass endpoints for physicochemical properties, fate, eco-toxicity, absorption, metabolism, and toxicity

DG-Environment Endocrine Active Substance Database: open-access database covering 428 substances suspected of having the potential for endocrine disruption; content currently being migrated to new IT system by JRC-IHCP

DSSTox, Distributed Structure-Searchable Toxicity Database Network: EPA resource for supporting improved predictive toxicology; maps bioassay and physicochemical property data associated with chemical substances to their chemical structures; incorporates state-of-the-art cheminformatics workflows and provides chemical infrastructure for EPA’s Safer Chemicals Research, including the ToxCast and Tox21 high-throughput efforts

DrugMatrix® and ToxFx®: Proprietary databases acquired and now maintained by the National Toxicology Program (NTP); DrugMatrix® is “one of the world’s largest toxicogenomics references” and ToxFx® is its companion reporting system.

ECHA Classification & Labeling Inventory Database: classification and labeling information on notified and registered substances received from manufacturers and importers; includes the list of harmonized classifications

ECOTOX, Version 4: US EPA source for locating single chemical toxicity data for aquatic life, terrestrial plants, and wildlife

EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals

Endocrine Active Substances Information System (EASIS): more than 400 substances suspected of having the potential for endocrine disruption

Endocrine Disruptor Knowledge Base: scientific resources including a biological activity database, QSAR training sets, and computational models to predict estrogen and androgen activity

Environmental Bioinformatics Knowledge Base (ebKB)

Environmental Health and Safety freeware: links to free databases and software plus news & events

EPA Chemical Data Access Tool (CDAT): launched in December 2010 to assist the public in retrieving chemical health and safety information submitted to EPA under the Toxic Substances Control Act (TSCA)

EPA TSCA Database

EURL ECVAM Genotoxicity and Carcinogenicity Consolidated Database of Ames Positive Chemicals: curated genotoxicity and carcinogenicity data for 726 Ames positive chemicals compiled from variety of sources; intended to aid in development and evaluation of alternative approaches to animal testing (EURL ECVAM application of this database: https://eurl-ecvam.jrc.ec.europa.eu/news/launch-of-consolidated-database-of-ames-positive-chemicals)

EURL ECVAM KinParDB (ECVAM Kinetic Parameters DataBase) and ECVAM KinCalTool (ECVAM Kinetics Calculation Tool): pilot database of toxicokinetic parameters of compounds used as reference substances in various in vitro toxicity testing programs provided by ECVAM

European chemical Substances Information System (ESIS) database: information on chemicals from various elements/databases, including: EINECS (European Inventory of Existing Commercial chemical Substances); ELINCS (European List of Notified Chemical Substances); BPD (Biocidal Products Directive) active substances; PBT (Persistent, Bioaccumulative, and Toxic) or vPvB (very Persistent and very Bioaccumulative); CLP/GHS (Classification, Labelling and Packaging of substances and mixtures); HPVCs (High Production Volume Chemicals) and LPVCs (Low Production Volume Chemicals); IUCLID Chemical Data Sheets, and others

EXTOXNET: pesticide information profiles database

GHS Reference Exchange and Tool (G.R.E.A.T.): GHS clearinghouse website to collect and provide GHS labelling elements in local languages

Household Products Database: US National Library of Medicine information on toxicity and health risks of common household and automotive products

Human and Environmental Risk Assessments (HERA): toxicity & risk data on ingredients of household cleaning products

IARC Monographs on the Evaluation of Carcinogenic Risks to Humans

Inhalation Database: database for modeling adverse effects of inhaled chemicals; project partner is International QSAR Foundation

Insilicofirst Online Database: collaboration of four organizations in toxicity prediction systems via one simple interface to support the environmental safety assessment of chemicals

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

Interspecies: “interspecies differences can be substantial, hampering reliable extrapolation of the results to the human situation;” this database developed by the National Institute of Public Health and the Environment (RIVM, The Netherlands) provides information on physiological, anatomical, and biochemical parameters, such as organ weights, pH, CYP activities, GST, ventilation rates for humans and various species of laboratory animals

ISSTOX Chemical Toxicity Databases: free databases from Istituto Superiore di Sanita (ISS), Italy designed to be usable for structure-activity relationships studies for toxicity prediction: 1) long-term carcinogenicity bioassay on rodents (rat, mouse) (ISSCAN); 2) in vitro Mutagenesis in Salmonella typhimurium (Ames test) (ISSSTY); 3) in vivo Mutagenesis (micronucleus test) (ISSMIC)

Japan Ministry of Health, Labour and Welfare (MHLW) Chemical Toxicity Database

JRC (Q)SAR Model Reporting Format (QMRF) Database: online database of information on validity of (Q)SAR models submitted to the JRC; intended to help to identify valid (Q)SARs; QMRF is a harmonised template structured according to the OECD principles for validation of (Q)SAR models

Leadscope, Inc.: FDA CDER and CFSAN databases (by license) – marketed drugs, chronic/subchronic toxicity, genetox, repro-developmental, acute toxicity, SAR carcinogenicity, SAR genetox

Livertox: information on the diagnosis, cause, frequency, patterns, and management of liver injury attributable to prescription and nonprescription medications, herbals, and dietary supplements

National Pesticide Information Center: Specific Chemical (Active Ingredient) Information and Active Ingredient Factsheets

NCTR Liver Cancer Database (NCTRlcdb): based on liver-specific carcinogenicity for 999 chemicals; each chemical was assigned one of the following toxicity classifications based on studies of male and female mice and rats: liver carcinogen (273); other carcinogen (293); non-carcinogen (304); other (129)

NICNAS (National Industrial Chemicals Notification and Assessment Scheme) Chemical Assessment Reports (Australia)

NLM Chemical & Drug Information SIS

NLM Environmental Health & Toxicology SIS

NTP Study Reports

NTP toxicology databases: NTP results and status information for all NTP studies

OECD Database on Pesticide/Biocide Reviews

OECD eChemPortal: 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: public repository for information on chemical substances, including their structures and biological activities; consists of three inter-linked databases: Substance, Compound, and BioAssay

RepDose (repeated dose toxicity): relational database on subacute to chronic toxicity; about 904 chemicals representing a subset of the FhG inhouse RepDose database; toxicity of these chemicals is documented in about 3080 studies in rats, mice, or dogs with oral or inhalation exposure
RiskIE, Risk Information Exchange Database: public database currently tracking over 5500 in progress or recently completed risk assessment projects conducted by different organizations

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)

SIDER 4.1: Side Effect Resource: information and adverse drug reactions on marketed medicines; extracted from public documents and package inserts (Kuhn, et al. (2015). Nucleic Acids Res. 44(D1):D1075-9)

Syracuse Research Corporation Databases: Environmental Fate Database, Physical Properties Database, and SMILECAS Database (available for purchase), among others

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)

ToxCast™: US EPA publicly available high-throughput toxicity data on thousands of chemicals

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

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

Toxygates: users can interrogate transcriptome’s response to particular compounds/conditions to explore toxicity mechanisms for data within the Japanese Toxicogenomics Project database, a database of systematically collected microarray samples from rats (liver, kidney, primary hepatocytes) and primary human hepatocytes after exposure to 170 different compounds at different dosages and time intervals

Wildlife Toxicity Reference Values (TRVs) for Ecological Risk Assessments: quantitative measures of toxicity in animals

Grants/Awards Databases

Current Research Information System (CRIS): documentation and reporting for ongoing agricultural, food science, human nutrition, and forestry research, education and extension activities for the USDA

Department of Energy (DOE) Office of Science

EPA Grants Awards Database

EPA NCER Extramural Research Funding

European Research Council Funded Projects

European Commission Awarded Grants, 2001-2011

European Commission Awarded Grants, 2012 and beyond

NIEHS Extramural Research Portfolio

NIH ExPORTER: provides raw data found in RePORTER, which can be loaded to researcher’s own systems for conducting further analysis; CRISP legacy data can also be downloaded here

NIH RePORT (Research Portfolio Online Reporting Tools): provides access to variety of reporting tools, reports, data, and analyses of NIH research activities (includes NIH RePORTER)

NIH RePORTER (RePORT Expenditures and Results): electronic tool to search repository of NIH-funded research projects and access publications and patents resulting from NIH funding; information is drawn from–eRA databases, Medline, PubMed Central, the NIH Intramural Database, and iEdison. The CRISP system was taken off-line and replaced by RePORTER; CRISP legacy data can be downloaded at the ExPORTER site

National Science Foundation (NSF): awards search; awards summaries

TAGGS database: central repository for grants awarded by the eleven US Department of Health & Human Services HHS Operating Divisions

US Small Business Grants (SBIR/STTR)

USA Spending: public access to information on how US tax dollars are spent

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

ArrayTrack: microarray database, data analysis & interpretation tool; free bioinformatics resource for DNA microarray and systems biology; used by FDA for review of genomic data submissions

BLAST (Basic Local Alignment Search Tool): NCBI program for sequence similarity searching that compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches

ELIXIR Tools & Data Services Registry: portal to bioinformatics resources; a community-driven curation effort that provides essential scientific and technical information about analytical tools and data services for bioinformatics

Expression Atlas: integrated database of gene and protein expression in humans, animals, and plants; consists of selected microarray and RNA-sequencing studies from ArrayExpress; recent incorporation of baseline expression profiles of tissues from Human Protein Atlas, GTEx, and FANTOM5, and of cancer cell lines from ENCODE, CCLE, and Genentech projects

National Center for Biotechnology Information (NCBI): National (US) resource for molecular biology information; OPEN access bioinformatics databases; in addition to GenBank, databases include Online Mendelian Inheritance in Man (OMIM), Molecular Modeling Database (MMDB) of 3D protein structures, Unique Human Gene Sequence Collection (UniGene), Gene Map of the Human Genome, Taxonomy Browser, and Cancer Genome Anatomy Project (CGAP); Entrez is NCBI’s search and retrieval system; PubMed provides access to over 11 million journal citations in MEDLINE

RefSeq, NCBI Reference Sequence Database: comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins to provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses

Swiss Institute of Bioinformatics (SIB): more than 150 internationally recognized databases and software tools in proteomics, genomics, systems biology, transcriptomics, etc., including UniProtKB/Swiss-Prot, PROSITE, STRING, SWISS-MODEL Repository

Cell Line Databases

BioSample: descriptions of biological source materials used in experimental assays

Human pluripotent stem cell registry (hPSCreg): public registry and data portal for human embryonic and induced pluripotent stem cell lines; automatically creates a unique standardized name for each cell line registered

ICLAC Database of Cross-Contaminated or Misidentified Cell Lines: from the International Cell Line Authentication Committee (ICLAC)

Genomics Databases

Cancer Genome Atlas (TCGA) Data Portal: platform to search, download, and analyze data sets generated by TCGA (http://cancergenome.nih.gov); contains clinical information, genomic characterization data, and high-throughput sequencing analysis of tumor genomes

CEGA (Conserved Elements from Genomic Alignments): precomputed sets of conserved sequences from different species and at different levels of the vertebrate phylogeny

Database of Genomic Variants: curated catalogue of structural variation in the human genome

DNA data bank of Japan (DDBJ): one of the international nucleotide sequence databases, sharing data with EMBL-Bank/EBI in Europe and GenBank/NCBI in the US

ENCODE Portal: data from the Encyclopedia of DNA Elements (ENCODE) Project to create a comprehensive catalog of functional elements in the human genome; most recent 3rd phase expanded assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a cells and tissues to identify putative regulatory elements

EnsEMBL: European Bioinformatics Institute comparative-genomics database; provides access to data from 87 species; numerous updates across supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish, and rat

European Nucleotide Archive (ENA): repository for the submission, maintenance, and presentation of nucleotide sequence data and related sample and experimental information

GenBank: the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (for over 340,000 formally described species)

Genetic Variation Databases

HUGO Gene Nomenclature Committee (HGNC)

Human Epigenome Atlas (Release 4): includes human reference epigenomes and results of their integrative and comparative analyses; successive releases will include histone marks and DNA methylation marks across specific tissues and cell types, developmental stages, physiological conditions, genotypes, and disease states; produced by NIH Epigenomics Roadmap Consortium

International Nucleotide Sequence Database Collaboration (INSDC): long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI; establishes standards, formats, and protocols for data and metadata to enable reliable data submission to public archives

KEGG (Kyoto Encyclopedia of Genes and Genomes): reference resource for biological interpretation of genome sequences and protein high-throughput data; gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism, and the ecosystem in the forms of molecular networks called KEGG pathway maps, BRITE functional hierarchies, KEGG modules, and KEGG Orthology system

Mammalian Gene Collection (MGC): full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes

MITOMAP: human mitochondrial genome database

NCI’s Cancer Genomics Hub (CGHub): secure repository for storing, cataloging, and accessing cancer genome sequence related data from the Cancer Genome Altas (TCGA) consortium and related projects

PhenomicDB: free multi-organism phenotype-genotype data repository unifying a variety of primary sources to make phenotypic data from different model organisms simultaneously searchable, visible, and comparable. Phenotypic data clusters are mapped to each entry to help further analyze similar phenotypes/diseases caused by different genes or mutations. Gene orthology information is appended to each entry to help suggest a known phenotype/disease to a new or orphan genotype/mutation and thus predict a new unreported phenotypic manifestation

Structural Genomics Knowledgebase: portal for research, news, and events on structural biology and structural genomics

UCSC Genome Browser: integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations; new data sets and software features added frequently

UWash Human Epigenome Browser: next-generation genomic data visualization tool for deriving biological insights from high-quality genomic, epigenomic, and expression data; currently hosts Human Epigenome Atlas and ENCODE data; investigators can upload and visualize their own data as custom tracks

ZFIN, Zebrafish Model Organism Database

Drug Discovery Databases

ChemBank: freely available data derived from small molecules and small-molecule screens; includes varied set of cell measurements derived from cell lines treated with small molecules and other substances; analysis tools are available that allow relationships between cell states, cell measurements, and small molecules to be determined

Drug2Gene: free integrated data repository unifying a number of public resources (PubChem, Chebi, Chembl, NCBI Gene, HGNC, and more) for identified and reported relations between genes/proteins and drugs/compounds. Users can flag, comment, and update relations, or import new drug-gene relations. Gene orthology information helps predict new unreported drug-gene associations

International Serious Adverse Event Consortium Data: genotype data on DNA-variants predictive of drug-related serious adverse events

Single Nucleotide Polymorphisms (SNPS)

RNA and RNAi

Drosophila RNAi Screening Center

SM2miR: curated database of small molecules’ effects on miRNA expression

Proteins and Proteomics

AbMiner: public database on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies

CASBAH (CAspase Substrate dataBAse)

Community Structure-Activity Resource (CSAR): NIGMS-funded data resource providing experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes

dbPTM: resource for experimentally-verified post-translational modification of proteins (PTMs)

DeathBase: manually curated database of proteins involved in cell death in several species

ExPASy Proteomics Server

Human Protein Atlas: public resource of protein expression profiles in human normal and diseased tissues, cells, and cell lines through immunohistochemistry and immunofluorescence-based methods; contains protein expression profiles for ~33% of the human protein-coding genes

Human Protein Reference Database (HPRD): centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks, and disease association for each protein in the human proteome; data has been manually extracted from the literature by expert biologists; Reference: Prasad, T. S. K. et al. (2009) Human Protein Reference Database – 2009 Update. Nucleic Acids Research 37, D767-72

Human Proteinpedia: community portal for sharing and integration of human protein data; allows research laboratories to contribute and maintain protein annotations

Immune Epitope Database: bioinformatics resource useful to the development of vaccines, immunotherapeutics, and diagnostics

KiNET: cell signalling protein expression and phosphorylation results from Kinetworks multi-immunoblots

miRWalk2.0: freely available collection of predicted and experimentally verified microRNA (miRNA)-target interactions with various unique features (see: Dweep, H., et al. (2015). miRWalk2.0: a comprehensive atlas of microRNA-target interactions, Nature Methods 12, 697-697)

National Cancer Institute Drug Information System 3D Database: collection of 3D structures for over 400,000 drugs

P53 Database

PANTHER (Protein ANalysis THrough Evolutionary Relationships): resource for comprehensive protein evolutionary and functional classification; classify proteins (and their genes) in order to facilitate high-throughput analysis; proteins classified according to: family and subfamily, molecular function, biological process, and pathway

PDBeChem Database: library of ligands and small molecules found in Protein Data Bank (PDB)

POLYVIEW-3D: protein structure visualization/annotation resource

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

Metabolomics

Human Metabolome Database detailed information about small molecule metabolites found in the human body

Metabolomics Workbench: repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources; part of the data coordinating effort of NIH Common Fund’s Metabolomics Program

Pathways Databases

HumanCyc: Stanford Research Institute human pathway database

KEGG Pathway Database

KEGGconverter: tool for in silico modeling of metabolic networks of the KEGG Pathway Database

NCI-Nature Pathway Interaction Database: OPEN access database of human cellular signaling pathways

Pathway Commons: point of access to biological pathway information collected from multiple sources and represented in a common language; pathways include biochemical reactions, complex assembly, transport, and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules, and complexes

Pathway Commons 2 (Version 3): PC2 will replace Pathway Commons portal around mid-2013 as the point of access to biological pathway information

Reactome Knowledgebase: provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations—an extended version of a classic metabolic map; functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data

Science Database of Cell Signaling: information on components of cellular signaling pathways and their relations; organized into pathways called Connections Maps

UCSD-Nature Signaling Gateway Molecule Pages: information on more than 3900 proteins involved in cellular signaling

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

WikiPathways: open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis; support provided via popular standalone tools, i.e. PathVisio and Cytoscape, web applications, and common programming environments

Database Lists

European Bioinformatics Institute: biological databases

Israel Science and Technology Directory: links to many biomedical databases

Labome

Nucleics Acid Research (NAR) Database List: links to many biomedical 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

CompuCell 3D: computational modeling of multi-scale, multicell simulations of biological phenomena occurring at single cell to tissue levels

Effectopedia: open knowledge aggregation and collaboration tool that provides a means of describing adverse outcome pathways in an encyclopedic manner

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

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; encompasses clinical information including dosing guidelines and drug labels, potentially clinically actionable gene-drug associations, and genotype-phenotype relationships

Phish-Pharm Database of Pharmacokinetics Data in Fish (HTML version)

Policy Databases


ECOLEX, The Gateway to Environmental Law: comprehensive, global source of information on environmental law; operated jointly by FAO, IUCN, and UNEP

Environmental Legislation: Inter-American Forum on Environmental Law (Spanish acronym FIDA) database on Environmental Legislation in the Americas

National Pesticide Information Center, Pesticide Regulations

University of Massachusetts at Lowell Database: state, county, and city chemical control regulations and policies that have been enacted, pending & failed ranging from 1999 to the present