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Found 33 result(s)

Signature Bank

Banque Signature

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One of the world’s largest banks of biological, psychosocial and clinical data on people suffering from mental health problems. The Signature center systematically collects biological, psychosocial and clinical indicators from patients admitted to the psychiatric emergency and at four points throughout their journey in the hospital: upon arrival to the emergency room (state of crisis), at the end of their hospital stay, as well as at the beginning and the end of outpatient treatment. For all hospital clients who agree to participate, blood specimens are collected for the purpose of measuring metabolic, genetic, toxic and infectious biomarkers, while saliva samples are collected to measure sex hormones and hair samples are collected to measure stress hormones. Questionnaire has been selected to cover important dimensional aspects of mental illness such as Behaviour and Cognition (Psychosis, Depression, Anxiety, Impulsiveness, Aggression, Suicide, Addiction, Sleep),Socio-demographic Profile (Spiritual beliefs, Social functioning, Childhood experiences, Demographic, Family background) and Medical Data (Medication, Diagnosis, Long-term health, RAMQ data). On 2016, May there are more than 1150 participants and 400 for the longitudinal Follow-Up

Human Genetic Variation Repository

HGVD

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The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.

NetPath

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<<<!!!<<< This repository is no longer available. >>>!!!>>> NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering many of the complex networks that govern the machinery inside the cell. Several signaling molecules play an important role in disease processes that are a direct result of their altered functioning and are now recognized as potential therapeutic targets. Understanding how to restore the proper functioning of these pathways that have become deregulated in disease, is needed for accelerating biomedical research. This resource is aimed at demystifying the biological pathways and highlights the key relationships and connections between them. Apart from this, pathways provide a way of reducing the dimensionality of high throughput data, by grouping thousands of genes, proteins and metabolites at functional level into just several hundreds of pathways for an experiment. Identifying the active pathways that differ between two conditions can have more explanatory power than just a simple list of differentially expressed genes and proteins.

Human protein-protein interaction network database search

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<<<!!!<<< This repository is no longer available. >>>!!!>>> A human interactome map. The sequencing of the human genome has provided a surprisingly small number of genes, indicating that the complex organization of life is not reflected in the gene number but, rather, in the gene products – that is, in the proteins. These macromolecules regulate the vast majority of cellular processes by their ability to communicate with each other and to assemble into larger functional units. Therefore, the systematic analysis of protein-protein interactions is fundamental for the understanding of protein function, cellular processes and, ultimately, the complexity of life. Moreover, interactome maps are particularly needed to link new proteins to disease pathways and the identification of novel drug targets.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

Mammalian Transcriptomic Database

MTD

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MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

RADAM database portal

RADiation DAMage database

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RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.

Huntingtin Interaction Network

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<<<!!!<<< This repository is no longer available. >>>!!!>>> The main objective of our work is to understand the pathomechanisms of late onset neurodegenerative disorders such as Huntington's, Parkinson's, Alzheimer's and Machado Joseph disease and to develop causal therapies for them. The disease causing proteins of these illnesses have been identified, but their functions in the unaffected organism are mostly unknown. Here, we have developed a strategy combining library and matrix yeast two-hybrid screens to generate a highly connected PPI network for Huntington's disease (HD).

NONCODE

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NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Now, there are 16 species in NONCODE(human, mouse, cow, rat, chicken, fruitfly, zebrafish, celegans, yeast, Arabidopsis, chimpanzee, gorilla, orangutan, rhesus macaque, opossum and platypus).The source of NONCODE includes literature and other public databases. We searched PubMed using key words ‘ncrna’, ‘noncoding’, ‘non-coding’,‘no code’, ‘non-code’, ‘lncrna’ or ‘lincrna. We retrieved the new identified lncRNAs and their annotation from the Supplementary Material or web site of these articles. Together with the newest data from Ensembl , RefSeq, lncRNAdb and GENCODE were processed through a standard pipeline for each species.

IMGT/LIGM-DBI

IMGT, the international ImMunoGeneTics information system

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IMGT® is a pioneering international information system in immunogenetics and immunoinformatics. It provides databases and tools based on the IMGT-ONTOLOGY to the scientific community for in-depth exploration of the adaptive immune response. IMGT® is dedicated to advancing scientific knowledge through its three main axes of research and development.

Clinical Genomic Database

CGD

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Clinical Genomic Database (CGD) is a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.

International HapMap Project

国际人类基因组单体型图计划

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<<<!!!<<< OFFLINE >>>!!!>>> A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain. The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs. In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. The Project officially started with a meeting in October 2002 (https://www.genome.gov/10005336/) and is expected to take about three years.

The Adaptive Evolution Database

TAED

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TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios model in PAML3, and labels for each node of speciation or duplication from gene tree/species tree reconciliation using SoftParsMap4. The phylogenetic indexing enables simultaneous viewing of lineages with high dN/dS that occurred along the same species tree branches. Resources from the Protein Data Bank (PDB) and the Kyoto Encyclopedia of Genes and Genomes (KEGG)5, have been incorporated into the TAED analysis to detect substitutions along each branch within the phylogenetic tree and to assess selection within pathways.

Virtual Liver Network

VLN

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<<<!!!<<<no longer avialable>>>!!!>>>

Biosearch

Marine Biodiversity Database of India

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Boola Boola Forest bird study

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This study assessed differences in avian biodiversity across different forest age-classes, including mature stands (> 100 years), in a managed, mixed-species eucalypt forest located in Gippsland, south-eastern Australia. Avian surveys and detailed habitat measurements were initially carried out in 50 two hectare stands ranging in age from 100 years. Extensive wildfire which occurred during the study reduced the number of sites to 28 (seven in each of four age classes) upon which analyses and inferences were made. Mature vegetation (> 100 years) had the greatest richness, abundance and biomass of birds. Key ecological resources, such as tree-hollows for nesting, generally occurred mostly in stands > 60 years. There were quantum increases in all measures of avian biodiversity in mature stands (> 100 years). The visualisation of the survey data is part of an interoperable web-GIS maintained by the Centre for eResearch and Digital Innovation (CeRDI) at Federation University Australia (FedUni).

Harvard Medical School, Library of Integrated Network-Based Cellular Signatures Database

HMS, LINCS database

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The Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.

IMGT/PRIMER-DB

International ImMunoGeneTics information system/PRIMER-Database

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The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).

Biobank of blood donors

Biobank der Blutspender

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With its “Blood Donor BIOBANK”, the Bavarian Red Cross (BRK) Blood Donor Service offers a unique and innovative resource for biomarker research: the world’s first blood donor based biobank. Biobanks as collections of biological material together with associated medical data open new possibilities for the development of new targeted diagnostics and therapies. The BRK Blood Donor Service maintains a unique collection of over 3 million blood samples, making it one of the largest sample collections worldwide. Every working day 2,000 new samples are added to the collection.

The Taenia solium Genome Project

T. solium Genome Project

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<<<!!!<<< 2021-08; The repository is no longer available. >>>!!!>>> Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

Clinical Proteomic Tumor Analysis Consortium Data Portal

CPTAC Data Portal

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The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP).

T3DB

Toxin and Toxin Target Database

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The Toxin and Toxin Target Database is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases.

LifeMap Discovery

Embryonic development & stem cell Compendium

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LifeMap Discovery® is a compendium of embryonic development for stem cell research and regenerative medicine, constructed by integrating extensive molecular, cellular, anatomical and medical data curated from scientific literature and high-throughput data sources.

NAGRP Blast Center

National Animal Genome Research Program Blast Center

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NAGRP Blast Center aggregates various sequence databases and makes them accessible via its website.

COVID-19 Interactive Map

Johns Hopkins Coronavirus Resource Center

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JHU has stopped collecting data as of 03/10/2023 After three years of around-the-clock tracking of COVID-19 data from around the world, Johns Hopkins has discontinued the Coronavirus Resource Center’s operations. The site’s two raw data repositories will remain accessible for information collected from 1/22/20 to 3/10/23 on cases, deaths, vaccines, testing and demographics. Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). Johns Hopkins experts in global public health, infectious disease, and emergency preparedness have been at the forefront of the international response to COVID-19. This website is a resource to help advance the understanding of the virus, inform the public, and brief policymakers in order to guide a response, improve care, and save lives. All data collected and displayed are made freely available through a GitHub repository https://github.com/CSSEGISandData/COVID-19, along with the feature layers of the dashboard, which are now included in the ESRI Living Atlas: https://livingatlas.arcgis.com/en/home/