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http://stemcelldb.nih.gov/public.do
Database characterizing and comparing pluripotent human stem cells. The growth and culture conditions of all 21 human embryonic stem cell lines approved under the August 2001 Presidential Executive Order have been analyzed. Available to the scientific community are the results of our rigorous characterization of these cell lines at a more advanced level.
Proper citation: StemCellDB (RRID:SCR_006305) Copy
http://research.nhgri.nih.gov/CGD/
Manually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases.
Proper citation: Clinical Genomic Database (RRID:SCR_006427) Copy
Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service.
Proper citation: GeneTerm Linker (RRID:SCR_006385) Copy
http://www.dartmouth.edu/~rswenson/Atlas/
On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV)
Proper citation: Atlas of the Brain (RRID:SCR_005967) Copy
Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free.
Proper citation: Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) Copy
http://genetrail.bioinf.uni-sb.de/
A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GeneTrail (RRID:SCR_006250) Copy
https://www.clinicaltrialsregister.eu
Database of European clinical trials containing information on interventional clinical trials on medicines. The information available dates from 1 May 2004 when national medicine regulatory authorities began populating the EudraCT database, the application that is used by national medicine regulatory authorities to enter clinical trial data. The EU Clinical Trials Register website launched on 22 March 2011 enables users to search for information which has been included in the EudraCT database. Users are able to: * view the description of a phase II-IV adult clinical trial where the investigator sites are in European Union member states and the European Economic Area; * view the description of any pediatric clinical trial with investigator sites in the European Union and any trials which form part of a pediatric investigation plan (PIP) including those where the investigator sites are outside the European Union. * download up to 20 results (per request) in a text file (.txt). The details in the clinical trial description include: * the design of the trial; * the sponsor; * the investigational medicine (trade name or active substance identification); * the therapeutic areas; * the status (authorized, ongoing, complete).
Proper citation: EU Clinical Trials Register (RRID:SCR_005956) Copy
https://www.facebase.org/facial_norms/
Database of high-quality craniofacial anthropometric normative data for the research and clinical community based on digital stereophotogrammetry. Unlike traditional craniofacial normative datasets that are limited to measures obtained with handheld calipers and tape measurers, the anthropometric data provided here are based on digital stereophotogrammetry, a method of 3D surface imaging ideally suited for capturing human facial surface morphology. Also unlike more traditional normative craniofacial resources, the 3D Facial Norms Database allows users to interact with data via an intuitive graphical interface and - given proper credentials - gain access to individual-level data, allowing users to perform their own analyses.
Proper citation: 3D Facial Norms Database (RRID:SCR_005991) Copy
http://igdb.nsclc.ibms.sinica.edu.tw/
IGDB.NSCLC database is aiming to facilitate and prioritize identified lung cancer genes and microRNAs for pathological and mechanistic studies of lung tumorigenesis and for developing new strategies for clinical interventions. We integrated and curated various lung cancer genomic datasets to present # lung cancer genes with somatic mutations, experimental supports and statistic significance in association with clinicopathological features; # genomic alterations with copy number alterations (CNA) detected by high density SNP arrays, gain or loss regions detected by arrayed comparative genome hybridization (aCGH), and loss of heterozygosity (LOH) detected by microsatellite markers; # aberrant expression of genes and microRNAs detected by various microarrays. IGDB.NSCLC database provides user friendly interfaces and searching functions to display multiple layers of evidence for detecting lung cancer target genes and microRNAs, especially emphasizing on concordant alterations: # genes with altered expression located in the CNA regions; # microRNAs with altered expression located in the CNA regions; # somatic mutation genes located in the CNA regions; and # genes associated with clinicopathological features located in the CNA regions. These concordant altered genes and miRNAs should be prioritized for further basic and clinical studies.
Proper citation: IGDB.NSCLC (RRID:SCR_006048) Copy
http://ki.se/ki/jsp/polopoly.jsp?d=29332&a=31537&l=en
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 4, 2014. Tissue Biobank collects samples from different types of cancers patients prospectively. Blood samples are being sent to KI Biobank for DNA extraction and storage. Number of sample donors: 611 (June 2010)
Proper citation: KI Biobank - Tissue Biobank (RRID:SCR_006043) Copy
http://mint.bio.uniroma2.it/virusmint/
A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.
Proper citation: VirusMINT (RRID:SCR_005987) Copy
http://compbio.charite.de/phenomizer/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 31,2026. Phenomizer offers three different approaches to find the appropriate term for a phenotypic abnormality, indicated by the three tabs on the left hand side: Feature, Disease and Ontology. The Phenomizer is intended to be used by qualified and licensed physicians in order to provide assistance in reaching the correct diagnosis in patients with hereditary diseases and for use as a teaching aid. The Phenomizer does not make diagnoses. Rather, it produces a ranked list of possibilities that can be used by physicians as a part of the diagnostic workup. The Phenomizer does not contain information about all possible diagnoses or even all possible hereditary diseases. The Phenomizer should not be used to make medical decisions without the advice of a physician.
Proper citation: Phenomizer (RRID:SCR_006157) Copy
Biobank Ireland Trust promotes the development of an Irish Hospital Biobank Network to coordinate collection of small samples of cancer and normal tissue and coded patient data from those having a cancer operation. This will facilitate international molecular research collaborations, which may help identify the best treatment for each individual patient - personalized medicine. Biobank Ireland is promoting the development of a Hospital Biobank Network throughout the island of Ireland as a bridge between cancer research and care. This new infrastructure will facilitate large national and international translational research collaborations that will raise Ireland''s research profile and benefit those with cancer. Researchers will have online access to samples and to restricted patient data from participating hospitals and an equitable withdrawal process for scientifically and ethically approved projects. Important research results will be explained to the public. Other Objectives: * To facilitate (inter)national translational research collaborations that may lead to new tests and better, less toxic treatments for those with cancer * To enable molecular research on cancer tissue from clinical trials patients identify the best treatment for each individual patient ������??personalized medicine������?? * Researchers will have online access to samples and restricted patient data from participating hospitals, and a fair release process for scientifically and ethically approved projects * Biobank Ireland recognizes the need to have harmonization in biobanking around the world * Important research results will be explained to the public * Biobank Ireland will seek to have the hospital-based Biobank Network funded by government as standard of care
Proper citation: Biobank Ireland Trust (RRID:SCR_006430) Copy
http://www.alphaone.ufl.edu/dna_tissue_bank1.html
The Alpha-1 Foundation DNA and Tissue Bank, established in 2000 by the Alpha-1 Foundation, is a repository specifically for medical information (hyperlink to data points) and tissue samples (DNA, plasma, lung/liver) for alpha-1-antitrypsin deficient individuals, their family and friends. The Bank serves the international scientific community. Currently the Bank has the largest collection of DNA in the world for Alpha-1-antitrypsin research studies. The Alpha-1 Foundation has established a Tissue Bank Advisory Committee which includes a wide representation of physicians, ethicists, attorneys, consumers as well as international experts in tissue banking. Collectively this Advisory Committee reviews requests for research. At this time the Bank has over 2400 members who have provided valuable medical and/or tissue samples. For investigators interested in obtaining tissue samples with phenotypes from the Bank, please contact the Alpha-1 Foundation or our research staff at the University of Florida.
Proper citation: University of Florida DNA and Tissue Bank (RRID:SCR_006581) Copy
http://www.physionet.org/physiobank/database/gaitndd/
Database of records from patients with Parkinson's disease (n = 15), Huntington's disease (n = 20), or amyotrophic lateral sclerosis (n = 13). Records from 16 healthy control subjects are also included here. The raw data were obtained using force-sensitive resistors, with the output roughly proportional to the force under the foot. Stride-to-stride measures of footfall contact times were derived from these signals.
Proper citation: Gait Dynamics in Neuro-Degenerative Disease Data Base (RRID:SCR_006979) Copy
https://sites.google.com/site/bipolardatabase/
Database of 141 studies which have investigated brain structure (using MRI and CT scans) in patients with bipolar disorder compared to a control group. Ninety-eight studies and 47 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website.
Proper citation: Bipolar Disorder Neuroimaging Database (RRID:SCR_007025) Copy
http://www.ncbi.nlm.nih.gov/CCDS/
Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly.
Proper citation: Consensus CDS (RRID:SCR_006729) Copy
http://cbl-gorilla.cs.technion.ac.il/
A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes.
Proper citation: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) Copy
http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/
A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication.
Proper citation: HIV-1 Human Protein Interaction Database (RRID:SCR_006879) Copy
http://www.mc.vanderbilt.edu/root/vumc.php?site=chtn%20western%20division
The Cooperative Human Tissue Network- Western Division at Vanderbilt University Medical Center is one of six institutions throughout the country funded by the National Cancer Institutes to procure and distribute remnant human tissues to biomedical researchers throughout the United States and Canada. CHTN operates through a shared networking system which allows investigators greater access to available research specimens. CHTN offers a variety of preparation and preservation techniques to ensure investigators are receiving the quality specimens needed for research. Remnant tissues are obtained from surgical resections and autopsies and are procured to the specifications of the investigator.
Proper citation: Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center (RRID:SCR_006661) Copy
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