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Biological Sciences: A Guide to Web Resources: Databases

Databases

ChemBioGrid: Chemistry Databases on the Web

From the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) at Indiana University, this Web site lists and describes many major chemistry and biology databases and resources on the Web. It is classified into these categories: general; 2D structure; specific classes of compounds; drug-related; disease-related; physical properties, spectra, etc.; toxcity and environmental; biomolecules; metabolic pathways; Web services-enabled biosciences; commercial; and miscellaneous. There is also an alphabetical list of databases (resources) that is annotated.

Atlas of Mouse Development & Gene Expression Database

A full 3-D anatomical atlas of mouse development & an associated database of gene expression patterns, cell lineage, & other spatially organized data.

The Borrelia burgdorferiGenome Database (BBDB)

The Institute for Genomic Research has recently released sequence data & related annotation for Borrelia burgdorferi.

BRENDA: The Comprehensive Enzyme Information System

BRENDA is a comprehensive database of enzyme information. It contains enzyme function data from primary literature sources including enzyme name, organism, EC number, literature citations, two dimensional images, and links to other databases. It's free, but users must register.

Canadian Bird Trends Database

Population trends and range distribution information for all species of birds that breed within the Canadian provinces of the North American Breeding Bird Survey.

ChemBank

ChemBank contains data and properties of small molecules, including chemical structure, biological activity, and biological assay.

E. coli Genome Project

The Data and Analysis subsection is the centerpiece of this site with 11 browsable ORF tables that provide information on 12 characteristics of each gene; an additional RNA table includes information on all non-protein encoding RNA species; all tables can be downloaded.

Environmental Data Registry (EDR)

EDR is a comprehensive catalog of major data collections maintained by the U.S. Environmental Protection Agency.

ENZYME

An enzyme nomenclature database based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.

ExPASy Proteomics Tools

Describes & provides access to a comprehensive collection of protein-related databases & research tools.

Human Genome Database from The Institute for Genomic Research

Access to cDNA/EST (human genome) sequence & related data as well as other molecular biology databases.

Human Genome Variation Database

HGVbase seeks to list and summarize known sequence variations in the human genome, and facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.

IOPI Database of Plant Databases (DPD)

Compiled by the International Organization for Plant Information, the DPD is a global list of plant databases including taxonomic databases, collection catalogs, & DELTA datasets.

KEGG: Kyoto Encyclopedia of Genes and Genomes Release

The KEGG Project is an attempt to bridge the gap between the genes and their functional implications; it contains a searchable database of computerized information pathways that consist of interacting genes or molecules.

Klotho: Biochemical Compounds Declarative Database

Klotho is an attempt to model biological processes. The database can be searched or browsed; results include a compound's stereochemical configuration.

LIGAND

The Ligand Chemical Database for Enzyme Reactions (LIGAND) is designed to provide the linkage between chemical & biological aspects of life in light of enzymatic reactions.

The Mendel Database

Searchable database containing more than 20,000 genes, which can be translated into proteins, organized into about 2,000 gene families based on their sequence homology; typical entries include gene family number & gene family name, gene & gene product descriptions & synonyms, and accession numbers with links to SWISS-PROT & EMBL.

National Center for Biotechnology Information

Among the NCBI databases are the GenBank Sequence Database, UniGene: Unique Human Gene Sequence Collection, dbEST: Database of Expressed Sequence Tags, dbGSS: Database of Genome Survey Sequences, dbSTS: Database of Sequence Tagged Sites, Electronic PCR , amd MMDB: Molecular Modelling Database. The NCBI Handbook provides a detailed introduction to NCBI resources with extensive links to help documentation.

NBII Metadata Clearinghouse Gateway

The goal of this National Biological Information Infrastructure site is to help researchers & educators locate repositories of biological data from the following sources: state and federal government agencies, universities, museums, libraries, & private organizations.

The Nucleic Acid Database

The goal of NDB is to assemble & distribute structural information about nucleic acids; it includes the coordinates of nucleic acid-containing crystal structures, including a searchable atlas of structures; Protein Finder, a search-engine for locating protein structures in the PDB database; a macromolecular crystallographic information file, & reports about the structures contained in the database.

REBASE: The Restriction Enzyme Database

A collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, & references.

SCOP: Structural Classification of Proteins

The SCOP database furnishes a detailed description of the structure & evolutionary relationships of proteins.

 

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