| See also
DBCAT: The Public Catalog of Databases - (dead link)
Infobiogen
Alcohol Studies Database - (dead link)
" The database contains over 50,000 citations for journal articles, books, book chapters, dissertations, conference papers, and audio-visual material."
Rutgers University Center of Alcohol Studies
APIRS Online
The Database of Aquatic, Wetland and Invasive Plants
"The database includes annotated citations for more than 60,000 research articles, books and reports about plant ecology, physiology, utilization and control. Items in many languages dating back to the 18th century are in this inclusive database."
- University of Florida - Center for Aquatic and Invasive Plants
Bio-DiTRL
"Bio-DiTRL is the Bio-Database of the Digital Imaging and Resource Laboratory. It is an online database with digital media that can be used to teach biology...Bio-DiTRL operates as a non-profit journal of teaching resources. In it you will find images, animations, video clips and text excerpts that may be downloaded for use by subscribers. Anyone may search or browse by the appropriate links."
- University of Alberta, Biological Sciences
Biomedical Acronym Database
"This database was constructed in a purely automated manner, using a set of heuristics to identify acronyms/abbreviations and their definitions within MEDLINE records. Currently, it is the world's largest and most comprehensive catalog of biomedical acronyms and abbreviations, containing approximately 257,000 out of an estimated 277,000 unique acronyms within MEDLINE."
- UT Southwestern Computational Biology Group
Cell Line Data Base (CLDB)
"...contains detailed information on 3838 human and animal cell lines."
ChemBank Initiative for Chemical Genetics
- Small Molecule Bioactives Database
"The ChemBank Small Molecule Bioactives Database is a subproject under the ChemBank umbrella and is being worked on primarily by Jeremy Muhlich, Erik Brauner, Jim Conley, and Caroline Shamu."
Complex Carbohydrate Research Center
- CCCR Spectral Databases - (dead link)
Databases include: Proton NMR Spectra of Xyloglucans and the GC-EIMS of Partially Methylated Alditol Acetates.
Conservation Databases - (dead link)
"a large and varied collection of databases concerning nature conservation."
World Conservation Monitoring Centre
Databases at Harvard University Herbaria - (dead link)
Databases Related to Protistology
Organelle Genome Megasequencing Project, Dept. Biochemistry, University of Montreal
Directory of Research Systematic Collections (DRSC) - (dead link)
"...is a directory of the natural history research collections. This directory is developed and maintained through a partnership between the Association of Systematics Collections (ASC) and the U.S.G.S. Biological Resources Division (BRD) and was developed in part to support the National Biological Information Infrastructure (NBII) and the Electronic Natural History Museum Initiative of the BRD ... "
California Flora Database - (dead link)
"This database contains geographic and ecological distribution information for 8363 California vascular plant taxa, including links to other online sources for California flora data."
Part of the UC Berkeley Digital Library Project
The Comprehensive Microbial Resource Home Page
"These pages have been designed to allow the user to access data from all of the genome sequences completed to date. Accessible here is the Omniome database which contains the sequence and annotation of each of the completed genomes as well as associated information about the organisms (such as taxon and gram stain pattern), the structure and composition of their DNA molecules (such as plasmid vs. chromosome and GC content), and many attributes of the protein sequences predicted from the DNA sequence (such as pI and molecular weight)."
CBS Databases - (dead link)
Includes the following: Filamentous fungi database - (dead link), containing about 28,000 strains; Yeasts database - (dead link), with nearly 6,000 strains total; Bacteria database - (dead link), 8,000 strains; Aphyllophorales database - (dead link), a taxonomical and nomenclatural database of more than 29,000 names; and Fusarium database - (dead link), with over 1,500 names; and the Phabagen databases - (dead link)
Centraalbureau voor Schimmelcultures
DNA Patent Database (DPD) - (dead link)
"The DPD, a joint project of the Georgetown University's Kennedy Institute of Ethics and the Foundation for Genetic Medicine, allows free public access to the full text and analysis of all DNA patents issued by the United States Patent and Trademark Office (PTO)."
E.coli Data Collection (ECDC) - (dead link)
"In this collection you will find all information regarding the entire E.coli K12 chromosome, we possibly could get."
Ralf Wahl, Novartis AG , Basel & Manfred Kroeger, Universitaet Giessen
E. coli Genome Project
"Our goal was to completely sequence the E. coli K-12 genome and several of the E. coli phages using a high-throughput method that is both accurate and rapid. We have achieved that goal and are in the process of analyzing the data acquired."
Able to download their version M52 for E. coli K-12
University of Wisconsin-Madison
EcoCyc: Encyclopedia of E. coli Genes and Metabolism
"The project is compiling a large knowledge base (KB) describing the genes and intermediary metabolism of the bacterium E. coli."
A collaborative project between Peter D. Karp of Pangea Systems Inc. and Monica Riley of the Marine Biological Laboratory
Endangered Bryophytes (mosses and liverworts) - (dead link)
Harvard University Herbaria
Electronic Plant Gene Register Index - (dead link)
An electronic publication for articles describing the isolation and DNA sequence determination of plant genes
The eSkeletons Project
"The e-Skeletons Project website enables you to view the bones of a human, chimpanzee, and baboon and gather information about them from our osteology database...This site provides an interactive environment in which to examine and learn about skeletal anatomy. This includes: high-quality images of bones - labels of all muscles, articulations, and morphological features - high-resolution 3-D renderings of the skeletal elements in both animation (Quicktime) and interactive virtual reality (VRML) format."
Created at the University of Texas at Austin
Eukaryotic Promoter Database (EPD)
"...is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references."
By members of the the Bioinformatics Group of the ISREC (Swiss Institute for Experimental Cancer Research).
European Bioinformatics Institute
- CluSTr
"...(Clusters of SWISS-PROT+TrEMBL proteins) database offers an automatic classification of SWISS-PROT + TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam, ProDom, SMART and TIGRFAMs. CluSTr also has cross-references to HSSP and PDB...is a useful resource for whole genome analysis and has already been used for the proteome analysis of a number of completely sequenced genomes. A preliminary proteome analysis was also produced for the human genome."
__________
Expert Center for Taxonomic Identification (ETI)
The Netherlands
- World Biodiversity Database (WBD)
"...is a continuously growing taxonomic database and information system that aims at documenting all presently known species (about 1.7 million) and to make this important biological information worldwide accessible. Access to this online information system is free of charge for noncommercial use: scientific and educational purposes."
- World Taxonomist Database (WTD)
Online taxonomists directory service.
- UNESCO-IOC Register of Marine Organisims - (dead link)
"The register is basically only a list of species names but it is tried to add at least some additional information, including author names, vernacular names, information on geographical and bathymetrical distribution and NODC numerical codes. Synonyms are added but only if they are still in use or were used in recent times."
The Farlow Diatom Collection - (dead link)
Harvard University Herbaria
Flowering Plant Gateway
Texas A&M Bioinformatics Working Group
Gemini Detective
"A collaborative effort of the laboratories of Dr. Judith Brown (University of Arizona) and Dr. Stephen D. Wyatt (Washington State University), this Website serves as a hub of information on whitefly-transmitted geminiviruses in the genus _Begomoviridae_. Resources provided at the site include _Begomovirus_ descriptive information (general information; worldwide distribution; a hyperlinked list of Begomovirus; and a searchable database of begomovirus isolates by geographic location, virus/ isolate name, symptom, and host) and Core Coat Protein Sequence Database (including PCR sequence technical information and Mini-Blast search). In addition to text, several small color images provide illustrations of the effect (symptoms) of geminivirus-related disease on hosts. [LXP]"
From The Scout Report for Science & Engineering [04/12/00], Copyright Internet Scout Project 1994-2000. http://scout.cs.wisc.edu/
GenomeNet WWW Server
"...a Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology...operated jointly by Supercomputer Laboratory (SCL), Institute for Chemical Research (ICR), Kyoto University and the Human Genome Center (HGC), Institute of Medical Science, the University of Tokyo."
Gray Herbarium Index of New World Plants - (dead link)
The Haemophilus influenzae Rd Genome Database (HIDB)
"the first genome of a free living organism to be completed...This page offers access to the latest versions of the sequence data and related annotation."
Harvard University Herbaria Type Specimen Database - (dead link)
HIV Molecular Immunology Database - (dead link)
"...has the epitope alignments, maps and the reference information for the cytotoxic and helper T-cell epitopes and antibody binding sites in HIV-1 immunologically reactive sites along with reviews pertaining to HIV Immunology."
Los Alamos National Laboratory
HIV Sequence Database
Collecting HIV and related genetic sequence data (since 1987)
Los Alamos National Laboratory
IBSO Siberian Luminous Bacteria Database - (dead link)
Index to Plant Chromosome Numbers (IPCN)
"...aims to extract and index original plant chromosome numbers of naturally occurring and cultivated plants published throughout the world. A committee of voluntary contributing editors, located in various parts of the world, reviews sets of serial titles assigned to them and returns the information to the editors for collation in the Index."
Missouri Botanical Garden
INVADERS Database System
"...is a comprehensive database of exotic plant names and weed distribution records for five states in the northwestern United States. The spatial and temporal spread of weeds can be displayed using the historic distribution records in INVADERS. The INVADERS web site contains actual examples of how land management and weed regulatory agencies are using these data to improve their weed management programs. Noxious weed listings are provided for all US states and six southern tier Canadian provinces."
By Division of Biological Sciences, University of Montana
International Centre for Genetic Engineering and Biotechnology (ICGEB)
- Biosafety WebPages - (dead link)
- ICGEB Biosafety News
- Biosafety Database
"The ICGEB bibliographic database on biosafety studies, an index of selected scientific articles published on biosafety and risk assessment from 1990 onward. Featuring records from the applied life sciences database CAB ABSTRACTS[tm] from CABI Publishing."
International Legume Database & Information Service (ILDIS)
"...to provide a service to legume specialists and users of legumes and legume products worldwide. The service includes products obtained from a database of all the species. ILDIS is a collaborative organisation involving experts and institutions all over the world
IOPI Database of Plant Databases (DPD) - (dead link) "The Database of Plant Databases (DPD for short) is a global list of plant databases, to tell you who is putting together what data and where. The DPD contains virtually no plant data as such, but serves to put you in contact with the projects that do. Most, but not all, entries concern databases about higher plants. Roughly speaking, there are three kinds of database: Taxonomic databases, with systematic information on families or genera, or for Flora projects ; Collection catalogues, usually of herbaria ; DELTA datasets. DELTA is the Description Language for Taxonomy, a data format for character data, used for identification, key construction and the generation of descriptions."
International Organization for Plant Information (IOPI)
KMMGU Russia Bacteria Database - (dead link)
Key to the Lichen Genera of the Guianas
The Lichen Type Specimen Register of the U.S. National Herbarium
U.S. National Herbarium
List of Bacterial Names with Standing in Nomenclature - (dead link) "The List of Bacterial Names with Standing in Nomenclature includes, alphabetically and chronologically, the nomenclature of bacteria and the nomenclatural changes as cited in the Approved Lists of Bacterial Names, or published, or validly published in the International Journal of Systematic Bacteriology. It is extensively annotated to clarify the Rules which govern the scientific nomenclature.
By J.P. Euzeby
National Biological Information Infrastructure (NBII)
"...The NBII links diverse, high-quality biological databases, information products, and analytical tools maintained by NBII partners and other contributors in government agencies, academic institutions, non-government organizations, and private industry."
NLM Gateway Search
"The NLM Gateway allows users to search in multiple retrieval systems at the U.S. National Library of Medicine (NLM). The current Gateway searches MEDLINE/PubMed, OLDMEDLINE, LOCATORplus, AIDS Meetings, Health Services Research Meetings, HSRProj, MEDLINEplus and DIRLINE."
National Library of Medicine
Organelle Genome Megasequencing Project
Includes the following databases: Organelle Genome Database (GOBASE), Fungal Mitochondrial Genome Project (FMGP), Protist Image Database (PID), and the Gopher Hole on Organelle Research/Molecular Evolution (MegaGopher).
University of Montreal / Universite de Montreal
Plant Viruses Online
Descriptions and Lists from the VIDE Database
PLANTS National Database
"The PLANTS database includes checklists, distributional data, crop information, plants symbols, plant growth data, references and other plant information."
United States Department of Agriculture, Natural Resources Conservation Service
probeBast.net
An Online Resource for rRNA-targeted Oligonucleotide Probes
"Ribosomal RNA (rRNA) targeted oligonucleotide probes are widely used for fluorescence in situ, dot blot, and microarray hybridization in culture-independent studies of microbial communities and for the identification of uncultured prokaryotes. probeBase is a comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information."
- University of Vienna - Institute of Ecology and Conservation Biology
Protein Data Bank (PDB)
"...the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data." As of 10 October 2001 holdings include 16245 structures.
Research Collaboratory for Structural Bioinformatics (RCSB)
Rainmap Database
Database of genomes for Salmonids (Rainbow Trout)
The Institut National de Recherche Agronomique (France)
Royal Botanic Garden Edinburgh
"this site is a gateway to our science, our horticulture, our education and exhibition programmes, and much much more. Our mission is to explore and explain the world of plants."
The Sanger Centre: Microbial Genomes
"...microbial sequencing effort is concentrated on pathogens and model organisms."
The Subterranean Amphipod Database - (dead link)
"The goal of this site is to add data stepwise to all the listed subterranean families. The individual databases differ per family, depending on the information available. They range from simple species lists to detailed specimen databases, which, for example, include biogeographic data and bibliographies."
Department of Biological Sciences, Old Dominion University
TreeBASE
A Database of Phylogenetic Knowledge
"...is a relational database of phylogenetic information sponsored by Harvard University Herbaria, Leiden University EEW - (dead link), and the University of California, Davis. TreeBASE stores phylogenetic trees and the data matrices used to generate them from published research papers."
TRITON Project - (dead link)
Taxonomy Resource & Index To Organism Names
"...is a system under development by BIOSIS UK - (dead link) as a mechanism for making data related to names of both fossil and recent organisms, and in particular animal nomenclatural data from the Zoological Record (ZR), available on the www. TRITON accesses a database of over a million animal names, at all taxonomic ranks, reported from the scientific literature of the last 18 years, plus some 400,000 names of other non-animal organisms provided by collaborating organisations."
UniProt - The Universal Protein Resource
"...is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR."
University College London - Biomolecular Structure and Modelling Group
- Enzyme Structures Database
"This database contains the known enzyme structures that have been deposited in the Brookhaven Protein Data Bank (the PDB). There are currently 7432 PDB-enzyme entries in the PDB (as at 13 April 2001) involving 7109 separate PDB files - some files having more than one E.C. number associated with them."
University of Minnesota Department of Entomology
- Insect Collection
Sections include: Collection Info ; People ; Projects ; Systematic Databases ; Visits & Tours ; Links.
Virtual Genome Center - (dead link)
"The Virtual Genome Center is a place where molecular biologists can access tools and databases to do their work. The VGC has no director, staff, grant support, or corporate sponsors. It simply exists."
Virus Databases On-Line
BioInformatics Group, Research School of Biological Sciences Institute of Advanced Studies, Australian National University
WWW Virtual Library: E. coli - (dead link)
The E. coli Index
"These pages contain a comprehensive guide to information relating to the bacterium Escherichia coli on the WWW."
This Megellan 4 Star Site is very extensive collection of academic resources. Sections include Databases, Individual Researchers, The E. coli Abstracts, Journals, Full Research Papers, Societies, Protocols, International Universities, and more
International Nucleotide Sequence Database Collaboration:
DNA Data Bank of Japan
"One of the International DNA Databases, including EBI (European Bioinformatics Institute; responsible for EMBL database) in Europe and NCBI (National Center for Biotechnology Information; responsible for GenBank database) in the USA as the two other members."
European Bioinformatics Institute
"The EBI maintains the EMBL and SWISS-Prot databases as well as various other databases such as IMGT, NDB, PDB, Flybase and RHDB. Data can also be submitted to EBI via the WWW. "
GenBank
"GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. There are approximately 1,258,000,000 bases in 1,892,000 sequence records as of December 1997."
ImMunoGeneTics Database (IMGT)
"IMGT, the international ImMunoGeneTics database, is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc (UniversitÈ Montpellier II, CNRS). IMGT, a European project since 1992, works in close collaboration with EBI. At present, IMGT includes two databases: IMGT/LIGM-DB, a comprehensive database of Ig and TcR from human and other vertebrates, with translation for fully annotated sequences, and IMGT/HLA-DB, a database of the human MHC referred to as HLA (Human Leucocyte Antigens). The IMGT server provides a common access to all Immunogenetics data."
NBII Metadata Clearinghouse Gateway
"...contains standardized metadata-based descriptions of biological data sets and information products. Metadata descriptions follow the NBII's Biological Profile of the Federal Geographic Data Committee's (FGDC's) Content Standards for Digital Geospatial Metadata - (dead link)."
Databases from the National Center for Biotechnology Information:
Blast
"NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases."
Entrez
"WWW Entrez allows you to retrieve molecular biology data and bibliographic citations from the NCBI's integrated databases."
Molecular Modeling Database (MMDB)
"Contains 3-dimensional structures determined by X-ray crystallography and NMR spectroscopy. "
PubMed
"Bibliographic database containing citations for nearly 9 million biomedical articles from the National Library of Medicine's MEDLINE and pre-MEDLINE databases"
The BioCatalog
"...a software directory of general interest in molecular biology and genetics."
Areas include DNA, Proteins, Alignments, Genomes, Genetic, Mapping, Molecular Evolution, Molecular Graphics, Databases, and Servers.
European Bioinformatics Institute
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