Databases

These pages are in development. 

A

Alzheimer's Database

B

Bioinformatics Resource for Oral Pathogens

BioMart: developed jointly by the Ontario Institute for Cancer Research (OiCR) and the European Bioinformatics Institute (EBI).

Bioinformatic Harvester:
4DXp - AceView - BLAST - Biocompare - CDART - CDD - ensEMBL - Entrez - FishMap - Galaxy - UCSC GenomeBrowser - gfp-cDNA - Google-Scholar - gopubmed - Harvester42 - H-Inv - HomoloGene - iHOP - IPI - MapView - MGI - MINT - Mitocheck - OMIM - PolyMeta - PSORT II - RGD - SMART - SOSUI SOURCE - STRING - TAIR - Unigene - UniprotKB - Wikipedia - WikiProtein
Harvester Sequence Search device - YaCy-Sciencenet p2p search engine

C

Cancer Clinical Trials Database: National Cancer Institute
Cancer Genome Atlas Data Portal
Cancer Molecular Analysis Portal: Cancer Biomedical Informatics Grid
Cancer: PDQ Natinal Cancer Institute Comprehensive Cancer Database
Carcinogenic Potency Database
Cell Signalling Information
ChemSpider
Comprehensive Microbial Resource
Collaborative Bio Curation
CRISP (Computer Retrieval of Information on Scientific Projects) is a searchable database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions
Cytokines & Cells Online Pathfinder
Citeline- Worldwide drug development activity
Clinical Trials.gov
CureResearch.com

D

Diabetes Association Researcher Database
Diseases Database
Diseases and Disorders Database: Karolinkska Institutet - Sweden

E

Entrez: Life Sciences Search Engine
ennfsa
Environmental Health and Toxicology
EU Health.net

G

Genetic Association Database
General Practice Notebook: Database of clinical medicine (United Kingdom)
Genomic Variants (Database)

H
Health on the Net Database
HIV Molecular Immunology
HubMed.org
Human Gene Database Database Download

I
Indian Bioresource Information Network
International Classification of Diseases Database
International Protein Index
Intute: Health and Life Sciences

J

Japan Biological Information Research Center
Journal Watch

M

Medical Images: Karolinkska Institutet, Sweden
Medical Journal Library Databases: Washington University in St. Louis School of Medicine
Medline Plus
Medical Subject Headings Browser
Mediscan Image Data Search
Merck Disease Modules
Multilingual Glossary of Medical Terms in 9 European Languages

N

National Cancer Institute 3D Structure Database
National Center for Biotechnology Information
National Library of Medicine Catalog
National Library of Medicine Databases and Resources
National Library of Medicine Locator Plus
National Library of Medicine Gateway
NCBI Resource Guide
NCI Screening Data Miner: A tool for interactive analysis and visualization of the National Cancer Institute anti-tumor datasets. Contains 41,000 chemical compounds versus 155 cancer cell lines.
Neuromuscular Disease Center
New Medicine Oncology Database
National Institute of Diabetes and Digestive and Kidney Diseases Resources

P
Panther: Classification of Genes and Proteins
Parasites:  American Society of Tropical Medicine and Hygene
Proteome Commons

R
Rare Disease Database


S

Science Links Japan
Signaling Gateway, powered by the San Diego Supercomputer Center
Stanford Online Universal Resource for Clones and ESTs

T
tRNA Database

U

UCSC Gene Sorter
USDA Plants Database

V
Visualizing Splices of Genes from EST Data







Adult Acute Liver Failure Study Group (ALFSG)
http://www8.utsouthwestern.edu/utsw/cda/dept25203/files/89624.html

The Acute Liver Failure Study Group is collecting biosamples and information on the natural history, causes and outcomes of Acute Liver Failure in the United States. In addition to the database, a clinical trial conducted to test whether the drug N-acetylcysteine (NAC) improves outcome (survival) for patients with Acute Liver Failure not caused by acetaminophen overdose has recently been completed. Results should be available in the near future.
For more information, contact Dr. Patricia Robuck, DDN, Program Director for Clinical Trials in Digestive Diseases and Nutrition Program


Beta Cell Biology Consortium (BCBC)
http://www.betacell.org/

The mission of the BCBC is to facilitate interdisciplinary approaches that will advance our understanding of pancreatic islet cell development, regenerative capacity and function. The long-term goal is to develop a cell-based therapy, or treatments leading to controlled beta-cell renewal, in order to restore normal insulin production to diabetic patients.
For more information, contact Dr. Olivier Blondel, DEM, Director, Endocrine Systems Biology Program or Dr. Sheryl Sato , DEM, Director, Neurobiology of Obesity and Developmental Biology Programs


Bioinformatics Information Support Contract (BISC)
http://www.niddk.nih.gov/fund/diabetesspecialfunds/consortia/BISC.pdf

The goal of the Bioinformatics Integration Support Contract (BISC) is to advance the discovery and testing of new therapies for immune-mediated diseases and to further the understanding of the basis of innate and adaptive immunity by providing advanced computer support for scientific data handling and disseminating best practices in scientific data analysis.
For more information, contact Dr. Lisa Spain, DEM, Director, Immunobiology of Type 1 Diabetes Program and Autoimmune Endocrine Diseases Program


Central NIDDK Repository for Biosamples and Data
http://www.niddkrepository.org

On July 1, 2003, The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health (NIH) established Central NIDDK Repositories for biosamples and data collected in clinical studies. The purpose of the Central Repositories is to expand the usefulness of these studies by providing access to the biosamples and data to a wider research community beyond the end of the study.
For more information, contact Dr. Rebekah Rasooly, Deputy Director of the Division of Kidney, Urologic, and Hematologic Diseases


Clinical Outcomes Research Inititative (CORI)
http://www.cori.org/

The Clinical Outcomes Research Initiative, CORI, provides gastrointestinal physicians, nurses and researchers with software, research data and tailor-made services aimed to advance the overall practice of endoscopy.
For more information, contact Dr. Jay Everhart, DDN, Director, Epidemiology and Data Systems Branch


Collaborative Islet Transplant Registry (CITR)
http://www.citregistry.org

The mission of CITR is to expedite progress and promote safety in islet/beta cell transplantation through the collection, analysis, and communication of comprehensive and current data on all islet/beta cell transplants performed in North America and soon some transplants in Europe and Australia. An Annual Report that is available on the public web site. This site serves as a repository for general information concerning protocols, clinical transplantation sites, publications, and other information of interest to the general community.
For more information, contact Dr. Michael Appel, DEM, Director, Islet Biology and Transplantation Research Program


Diabetes Genome Anatomy Project (DGAP)
http://www.diabetesgenome.org/

The Diabetes Genome Anatomy Project (DGAP) represents a unique, multidimensional initiative whose goal is to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes. The overall goal of the project is to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes.
For more information, contact Dr. Olivier Blondel, DEM, Director, Endocrine Systems Biology Program


Diabetes in America
http://diabetes.niddk.nih.gov/dm/pubs/america/

A compilation and assessment of epidemiologic, public health, and clinical data on diabetes and its complications in the United States.
For more information, contact Dr. Catherine Cowie, DEM, Director, Diabetes Epidemiology Program


Diabetes Prevention Trial--Type 1 (DPT-1) dataset
https://www.niddkrepository.org/niddk/jsp/public/dataset.jsp#DPT-1

The Diabetes Prevention Type 1 (DPT-1) trial is a NIDDK-funded multi-center clinical trial to determine if treatment with beta-cell antigens can delay the onset of Type 1 Diabetes Mellitus (Type 1 DM) in non-diabetic relatives of persons with Type 1 DM. Insulin is a well characterized antigen specifically produced by beta-cells, and it was used for this purpose in the initial DPT-1 studies. The protocol for high risk subjects uses daily subcutaneous insulin injections and an annual course of intravenous insulin treatment, while the protocol for intermediate risk subjects uses daily doses of insulin administered orally.
For more information, contact Dr. Catherine Cowie, DEM, Director, Diabetes Epidemiology Program


Digestive Diseases in the United States: Epidemiology and Impact
http://digestive.niddk.nih.gov/statistics/statistics.htm

A collection of statistics about specific digestive diseases, including prevalence, mortality, care delivery and cost.


Epidemiology of Diabetes Interventions and Complications (EDIC)
http://www.niddk.nih.gov/patient/edic/edic-public.htm

or http://www.bsc.gwu.edu/bsc/studies/edic.html

An observational study examining the risk factors associated with the long-term complications of type 1 diabetes. The study began in 1994 and follows the 1441 participants previously enrolled in the Diabetes Control and Complications Trial (DCCT).
For more information, contact Dr. Catherine Cowie, DEM, Director, Diabetes Epidemiology Program



Federal Databases for Biomedical and Nutrition Related Research
http://dnrc.nih.gov/highlights/database-page.htm

The Division of Nutrition Research Coordination at NIH provides the HNRIM database (Human Nutrition Research and Information Management), one of a collection of databases of interest to nutrition researchers, including CARDS (Computer Access to Research on Dietary Supplements), CDMRP (Congressionally Directed Medical Research Programs), CRIS (U.S. Department of Agriculture Current Research Information System).


Globin Gene Server
http://globin.cse.psu.edu/

This database provides data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences.
For more information, contact Dr. Terry Rodgers Bishop, KUH, Director, Hematology Research Programs


Healthy People 2010
http://www.healthypeople.gov/

A statement of national objectives for health promotion and disease prevention for the first decade of the 21st century, the book has two overarching goals: increase quality and years of healthy life and eliminate health disparities. Specific parts of Healthy People 2010 relate to prostate and urinary bladder cancer, chronic kidney disease, and diabetes complications.
For more information, contact Dr. Lawrence Agodoa, KUH, Director, Office of Minority Health Research Coordination or Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs


Hembase
http://hembase.niddk.nih.gov/

Hembase is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome. To date, Hembase contains 15,752 entries from erythroblast Expressed Sequenced Tags (ESTs) and 380 referenced genes relevant for erythropoiesis. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology.
For more information, contact Dr. Terry Rodgers Bishop, KUH, Director, Hematology Research Programs


Human Biological Data Interchange
http://www.ndriresource.org/Biospecimens_Programs/HBDI/36/

HBDI maintains a repository of DNA and immortalized cell lines collected from 540 families of subjects with type 1 diabetes. It also houses a database that includes more than 6700 families with diabetes, related complications and other genetic diseases.


Human Nutrition Research Information Management (HNRIM)
http://hnrim.nih.gov/

HNRIM is a searchable database of nutrition research and research training activities supported by the federal government.


Inflammatory Bowel Disease Genetic Consortium (IBDGC)


The NIDDK Inflammatory Bowel Disease Genetics Consortium (IBDGC) consists of investigators from seven sites in the U.S. and Canada, who have recruited a large sample of inflammatory bowel disease patients, their relatives, and control subjects. All of the individuals in this sample have been evaluated according to a standardized protocol for clinical traits related to IBD, and have donated blood samples as a source of DNA. The IBDGC investigators are conducting genetic linkage and association studies to identify genes influencing predisposition to IBD. Phenotype, genotype and pedigree data and DNA samples will be available through the NIDDK Repositories in 2008.
For more information, contact Dr. Robert Karp, DDN, Director, Genetics and Genomics Programs in Digestive Diseases and Obesity Programs


Major Histocompatibility Complex Database (dbMHC)
http://www.ncbi.nlm.nih.gov/projects/mhc/MHC.fcgi?cmd=init

The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC).
For more information, contact Dr. Beena Akolkar, DEM, Director, Immunopathogenesis and Genetics of Type 1 Diabetes Program


Mammalian Gene Collection (MGC)
http://mgc.nci.nih.gov/

Mammalian Gene Collection (MGC) and Zebrafish Gene Collection (ZGC) The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes ( http://mgc.nci.nih.gov/). The companion Zebrafish Gene Collection (ZGC) project is providing FL-ORF clones for zebrafish genes (http://zgc.nci.nih.gov).
For more information, contact Dr. Rebekah Rasooly, Deputy Director of the Division of Kidney, Urologic, and Hematologic Diseases


Mouse Metabolic Phenotyping Centers (MMPC)
http://www.mmpc.org

The Centers are housed at outstanding academic institutions, staffed by experts in state-of-the-art technology. Researchers can ship mice to one of the four Centers and obtain on a fee-for-service basis a range of complex exams used to characterize mouse metabolism, blood composition including hormones, energy balance, eating and exercise, organ function and morphology, physiology and histology. Many tests are done in living animals and are designed to elucidate subtle to complex traits that would define models of metabolic disease.
For more information, contact Dr. Maren Laughlin, DEM, Senior Advisor for Integrative Metabolism


Murine Atlas of Genitourinary Development (GUDMAP)
http://www.gudmap.org/

The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research. The key components are:
  • a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract
  • a high resolution molecular anatomy that highlights development of the GU system
  • mouse strains to facilitate developmental and functional studies within the GU system
  • tutorials describing GU organogenesis
  • rapid access to primary data via the GUDMAP database

For more information, contact Dr. Elizabeth Wilder, KUH, Director, Developmental Biology of the Kidney and Urogenital Tract Program


National Diabetes Education Program (NDEP)
http://www.ndep.nih.gov/

The NDEP is the leading federal government public education program that promotes diabetes prevention and control. The mission of the NDEP is to reduce the morbidity and mortality associated with diabetes and its complications. The NDEP is jointly sponsored by the National Institutes of Health and the Centers for Disease Control and Prevention and over 200 partner organizations. Target audiences include people with diabetes and those at risk, including the racial and ethnic populations disproportionately affected by the disease, health care providers and payers and purchasers of health care.
For more information, contact Ms. Joanne Gallivan, Director, National Diabetes Education Program (NDEP)


National Diabetes Information Clearinghouse (NDIC)
http://www.diabetes.niddk.nih.gov

The diabetes clearinghouse provides comprehensive information about diabetes for the public: online, in booklets and fact sheets, by email, and over the phone.
For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses


National Digestive Diseases Information Clearinghouse (NDDIC)
http://www.digestive.niddk.nih.gov

The digestive diseases clearinghouse provides comprehensive information about digestive health and disease for the public: online, in booklets and fact sheets, by email, and over the phone.
For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses


National Gene Vector Laboratories (NGVL)
http://www.ngvl.org/

The National Gene Vector Laboratories (NGVL) are composed of an interactive group of academic production and pharm/tox laboratories whose primary goal is to provide eligible investigators with clinical grade vectors for phase I/II gene therapy clinical trials and to provide support for relevant pharmacology/toxicology studies leading up to clinical gene transfer protocols. If the application is approved, clinical grade material will be produced at no cost to the investigator.
For more information, contact Dr. Catherine McKeon, DEM, Senior Advisor for Genetic Research in Diabetes, Endocrinology and Metabolic Diseases


National Kidney and Urologic Diseases Information Clearinghouse (NKUDIC)
http://kidney.niddk.nih.gov

or http://www.urologic.niddk.nih.gov The kidney and urologic diseases clearinghouse provides comprehensive information about bladder and renal health and disease for the public: online, in booklets and fact sheets, by email, and over the phone.
For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses


National Kidney Diseases Education Program (NKDEP)
http://www.nkdep.nih.gov/

The National Kidney Disease Education Program (NKDEP) aims to increase awareness of kidney disease and its risk factors, the importance of testing those at risk, and the availability of treatment to prevent or slow the progression to kidney failure. NKDEP’s target audiences include individuals at risk, particularly those with diabetes, high blood pressure, and a family history of kidney disease, and primary care providers.
For more information, contact Dr. Andrew Narva, Director, National Kidney Disease Education Program; Senior Scientific Advisor or Ms. Eileen Newman, Associate Director, National Kidney Diseases Education Program


NIDDK Endocrine and Metabolic Diseases Information Service
http://www.endocrine.niddk.nih.gov

This public service provides information about endocrine and metabolic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone.
For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses


NIDDK Hematologic Diseases Information Service
http://www.hematologic.niddk.nih.gov

This service provides information about certain hematologic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone. Additional hematologic information for the public is available at http://www.nhlbi.nih.gov.
For more information, contact Ms. Kathy Kranzfelder, OCPL, Director, NIDDK Information Clearinghouses


Nuclear Receptor Resource Project (NRR)
http://nrr.georgetown.edu/NRR/nrrhome.htm

The Nuclear Receptor Resource (NRR) Project is a collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily.
For more information, contact Dr. Ronald Margolis, DEM, Senior Advisor, Molecular Endocrinology


Nuclear Receptor Signaling Atlas (NURSA)
http://www.nursa.org/

Commensurate with this directive, NURSA's goals can be distilled into two broad aims: (i) to execute research strategies designed to rapidly and efficiently elucidate those facets of orphan nuclear receptor biology we deem most critical to its understanding; and (ii) to facilitate the generation of hypotheses, design of experiments and communication of results by scientists active in this field. We anticipate that this initiative will provide a valuable service to the nuclear receptor community by developing a web-accessible bioinformatics resource, in which current and emerging data will be organized into more accessible and "user-mineable" forms.
For more information, contact Dr. Ronald Margolis, DEM, Senior Advisor, Molecular Endocrinology


Organ Procurement and Transplantation Network (OPTN)
http://www.optn.org/

The U.S. Organ Procurement and Transplantation Network (OPTN) maintains a registry of human tissues in order to ensure the success and efficiency of the U.S. organ transplant system.
For more information, contact Dr. Thomas Eggerman, DEM, Director, Islet Transplantation Clinical Trials Program


Pediatric Acute Liver Failure Study Group (PALF)
http://www.palfstudy.org

This multi-center, multi-national collaborative group of pediatric clinical liver centers is aimed at identifying, characterizing, and developing management strategies for infants, children, and adolescents who present with acute liver failure (ALF). In addition to a database of pediatric patients with ALF, a clinical trial is being conducted to test whether the drug N-acetylcysteine (NAC) improves outcome (survival) for patients with ALF not caused by acetaminophen overdose.
For more information, contact Dr. Patricia Robuck, DDN, Program Director for Clinical Trials in Digestive Diseases and Nutrition Program


United States Renal Data System (USRDS)
http://www.usrds.org/

The United States Renal Data System (USRDS) is a national data system that collects, analyzes, and distributes information about chronic kidney disease and end-stage renal disease (ESRD) in the United States. The USRDS publishes and Annual data report which can be downloaded at http://www.usrds.org/adr.htm. The missions of the USRDS are: (1) To characterize the total renal patient population and describe the distribution of patients by socio-demographic variables across treatment modalities; (2) To report on the incidence, prevalence, mortality rates, and trends over time of renal disease by primary diagnosis, treatment modality and other variables; (3) To develop and analyze data on the effect of various modalities of treatment by disease and patient group categories; (4) To identify problems and opportunities for more focused special studies of renal research issues; (5) To conduct cost effectiveness studies and other economic studies of ESRD; and (6) To make the data available to investigators, and by supporting investigator-initiated projects, to conduct biomedical and economic analyses of ESRD patients. For more information, contact Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs, or Dr. Lawrence Agodoa, KUH, Director, Office of Minority Health Research Coordination.
For more information, contact Dr. Lawrence Agodoa, KUH, Director, Office of Minority Health Research Coordination or Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs


Urologic Diseases in America Compendium (UDA)
http://kidney.niddk.nih.gov/statistics/uda/

Urologic diseases cover a wide range of conditions, symptoms, and problems that include such diverse diagnoses as cancer, pelvic pain, sexual dysfunction, urinary incontinence, kidney stones, and benign prostatic hyperplasia (BPH). To remedy this lack of information, NIDDK initiated the Urologic Disease in America (UDA) project. The UDA compendium delineates the changes in the epidemiology, health economic impact, and practice patterns for the diseases currently included within the scope of practice of the specialty of urology, analyzed retrospectively over a ten-year period. The UDA compendium consists of data tables annotated in chapters that amplify the data analyses. The objectives of the UDA project include secondary data analyses of the following topics: (1) changes in the overall health care burden for individual urologic diseases; (2) changes in physician practice patterns for each urologic disease; (3) changes in demographics of persons with urologic disease; (4) the impact of specific urologic diseases, especially diseases of the prostate, on the minority populations of the U.S.; (5) documentation of new and evolving therapies for urologic disease and their potential impact on treatment outcomes and health care costs. The resultant compendium can be found at the above web address. In addition to updating the original compendium, the second phase of the UDA is to focus less on descriptive analyses and more on analytical outcomes analyses, and it will also attempt to increase involvement of the urologic community in analytical activities.
For more information, contact Dr. Paul Eggers, KUH, Director, Kidney and Urology Epidemiology Programs or Dr. Leroy Nyberg, KUH, Director, Urology Programs



PubMed.gov
PubMed Central: A free archive of Life Sciences Journals.
PubMed Tutorials

RX Centric

ToxNet

Unified Medical Language System
Visible Human Project

Max Planck Institute for Infection Biology, Berlin, Germany - DE 

Access databases:

US Dept of Health and Human Services:
Practitioner Databanks
Practitioner's Guide to the Databanks - PDF

National Institutes of Health

Tools & Resources

General Scientific Support

Partnerships

Collaborative Research

Computational SIGs

Research Studies

Publications

Projects

Supercomputing

  • The Biowulf supercomputer provides NIH researchers with a world-class system to assist in solving complex biomedical problems as diverse as gene variation in worldwide human populations and PET brain scan processing to identify plaques associated with Alzheimer's disease. The Biowulf cluster requires a Helix System account and a justification describing the research project and why the cluster is necessary to perform the computations.

  • Helix Managed Storage is provided for NIH Helix user login directory and includes seamless access to files among Helix Systems computational platforms, convenient access from users desktop computers, regular snapshots of files for online access and backup to offline tapes, and high performance using highly redundant network file servers.

  • The NIH Helix System is a high-performance computer running Linux that provides a comprehensive set of scientific applications and biomedical databases tailored to the needs of NIH researchers.

  • Imaris services allow researchers and scientists to visualize and analyze microscopic image data. Imaris services also provides licenses to use Imaris and associated modules including MeasurementPro, Coloc, Track, FilamentTracer, and XT.

  • MASCOT Server and Support. The Mascot search engine uses mass spectrometry data to identify proteins from primary sequence databases. The CIT-managed Mascot server provides a centralized, shared resource with updated databases, and allows NIH researchers to run Mascot searches directly on the NIH Mascot website or by using the Mascot daemon on a desktop PC.

NIH Computational Molecular Biology
Database Catalogs

Helix Systems Scientific Databases - locally available databases (NIH only)
WHALES - Web Homology Alert Service (NIH only)

Genomic

UCSC Genome Browser - the gold standard of genome browsers
National Center for Biotechnology Information (NCBI) - clearinghouse for all genomic information
Ensembl - joint project between EBI and Sanger Institute
GAD - The Genetic Association Database, at NIA
COMPARE - multi organism information system, at the Developmental Biology Institute of Marseille
The Cancer Genome Atlas Data Portal - clinical information associated with cancer tumors and human subjects, genomic characterization, and high-throughput sequencing analysis of the tumor genomes.

Nucleic Acids

Entrez - The Life Sciences Search Engine, at NCBI
SRS - Sequence Retrieval System, at EBI
dbEST - sequence and mapping data on partial, "single-pass" cDNA sequences or ESTs
NDB - Nucleic Acids Database, at Rutgers
Tumor Gene Database - information about targets for cancer-causing mutations
Riboapt DB - Ribozymes & Aptamer Database, at Univ. of Southern Mississippi
SILVA - Quality checked and aligned rRNA sequence data, at Max Planck Institute
ASPicDB - Alternative Splicing Prediction Data Base, at Univ. of Bari

Proteins

SwissProt - at ExPASy.org
Entrez - The Life Sciences Search Engine, at NCBI
SRS - Sequence Retrieval System, at EBI
Molecules To Go - text-based interface to the PDB on Helix Systems
MEROPS - The Peptidase Database, at the Wellcome Trust Sanger Institute
Human Mitochondria l Protein Database - multiple query types available, at NIST
HIV Protease Database - at NCI-Frederick
Human Protein Reference Database - at Johns Hopkins University and the Institute of Bioinformatics
SCOP - Structural Classifications of Proteins
CATH - Hierarchical classification of protein structural relationships
FSSP - Families of structurally similar proteins
PFAM - Database of multiple sequence alignments
GPCRDB - Database of G-protein coupled proteins
ModBase - Database of 3D protein models
HOMSTRAD - Homologous Structure Alignment Database
Database of Macromolecular Movements - with online analysis tools, at Yale Univ.
gpDB - Database of G-proteins and their interactions with GPCRs, at Univ. of Athens
Proteopedia - The Collaborative, 3D Encyclopedia of proteins and other molecules
Microbial Protein Interaction Database - at the J. Craig Venter Institute
OPM - Orientations of Proteins in Membranes Database, at Univ. of Michigan

Factors and Motifs

Transfac Professional - transcription activation factor database (NIH only)
BIOBASE - free registration required

Pathways

Reactome - a curated knowledgebase of biological pathways
KEGG - Kyoto Encyclopedia of Genes and Genomes
PID - Pathway Interaction Database, at NCI
BioCyc - Large collection of pathway/genome databases

Enzymes

REBASE - good old New England Biolabs
ENZYME Database - at ExPASy.org
IntEnz - at EBI
Biology-oriented newsgroups - at Indiana University
CATRES - Database of catalytic residues, at EBI
CSA - Catalytic Site Atlas, at EBI

Plasmids

Genome Database of Naturally Occurring Plasmids

Organism-Specific Databases

Mammalian

Mouse Genome Database - synoptic descriptions with bibliographic citations
Portable Dictionary of the Mouse Genome - compact, downloadable database

Worm

Worm Base - biology and genome of C. elegans
Caenorhabditis elegans WWW Server - one-stop shopping for C. elegans

Insect

FlyBase - comprehensive database for genetics and molecular biology of Drosophila

Yeast

Saccharomyces Genome Database - at Stanford

Protozoan

PlasmoGF - Plasmodium gene families, at Wenzhou Medical College

Fungi/Mycobacteria

MycoperonDB - Predicted operon and transcriptional units of Mycobacteria

Prokaryote

IECA Database Portal - collection of E. coli servers around the world
SubtiList WWW Server - all about B. subtilis, Pasteur Institute
Entrez Microbial Genomes - 348 completed genomes and counting...
BAGET - very nice tool for getting sequence & info from prokaryotic genomes, from Université Paris

Plants

Arabidopsis Information Resource - very nice gateway to our favorite mustard weed
Grain genes - database for triticaea and avena
The Korea Rice Genome Database - at Myongii University
ChromDB - the plant chromatin database, at University of Arizona

Other

Ribosomal Database Project - at Michigan State University
National Human Genome Research Institute - ongoing research into genomics