Tag: rare diseases

Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the ...

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public ...

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations an ...

MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT ...

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data.

Online Mendelian Inheritance in Man. It is an authoritative compendium of human genes and phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 15,000 genes. OMIM focuses on the relation ...

The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular dia ...

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://githu ...

The Genome-Wide Association Studies (GWAS) Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, ...

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts publish ...

Genome Aggregation Database (gnomAD) - browser that aggregates exome and whole-genome sequencing data from a wide variety of large-scale sequencing projects. It enables search of genetic variation information by gene, variant or region.

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variat ...

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignm ...

Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues.

The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications i ...

InterMine was formed in 2002 at the University of Cambridge, originally as a Drosophila-dedicated resource, before expanding to become organism-agnostic, enabling a large range of organisations around the world to create their own InterMines. There a ...

BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interacti ...

The SIGnaling Network Open Resource. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are comp ...

Orphanet is a unique resource, gathering and improving knowledge on rare diseases so as to improve the diagnosis, care and treatment of patients with rare diseases. Orphanet aims to provide high-quality information on rare diseases, including ...

neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

Genomics England PanelApp is a publicly-available knowledgebase that allows virtual gene panels related to human disorders to be created, stored and queried. It includes a crowdsourcing tool that allows genes and genomic entities (short tandem repeat ...

The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes.

PubMed® comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. ...

Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activit ...

ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization. It contains codes for diseases, signs and symptoms, abnormal fi ...

Method to assess the outcome of non-synonymous SNVs using a CONsensus DELeteriousness score that combines various tools.

Database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs) in the human genome. It also facilitates the steps of filtering and prioritizing SNVs fr ...

mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated ...

The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information ...

HmtDB is an open resource created to support population genetics and mitochondrial disease studies. The database hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the applica ...

The database of Disease-Gene Associations with annotated Relationships (eDGAR) is a database for collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar. For each heterogeneous or polygenic disease, ...

The ITHANET Portal represents an expanding resource for clinicians and researchers dealing with haemoglobinopathies and a port of call for patients in search of professional advice. The ITHANET Portal integrates information on news, events, clinical ...

UK Biobank is a large-scale biomedical database and research resource that provides researchers access to detailed longitudinal phenotype, medical and genetic data from 500,000 volunteer participants.

Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.

DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.

Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.

NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.

A global search engine for genetic mutations.

Universal Mutation Database (UMD) is a database for mutations. UMD-predictor is a tool that enables functional annotation of variants to find the relevant ones.

DISNOR is a resource that uses a comprehensive collection of disease associated genes, as annotated in DisGeNET, to interrogate SIGNOR (https://signor.uniroma2.it) in order to assemble disease-specific logic networks linking disease associated genes ...

Integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research.

This catalogue is intended to facilitate the discovery of samples and samples data from Rare Diseases biobanks. It also provides information about sample collections and studies done on the registered samples.

Polymorphic inversions in the human genome

Repository for clinicians and scientists working in the rare disorder community. It enables secure sharing of case records by clinicians and rare disease scientists and helps the user to find additional cases of the same unnamed disorder. The reposit ...

Autosomal monoallelic expression (MAE) refers to mitotically stable, epigenetically controlled allele-specific expression of autosomal genes, with the initial non-predetermined ('random') choice of thetranscriptional activity of the two alleles maint ...

NHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders.

Emory Genetics Laboratory's (EGL) Variant Classification Catalog contains variants of the gene of interest that has been seen and analysed by EGL Genetics.

Genetic mutation database for rare diseases that enables to search, sort and filter genetic variants from clinically diagnosed individuals worldwide and make symptoms-based queries.

Inborn Errors of Metabolism Knowledgebase (IEMbase) accepts an array of biochemical and clinical symptoms from a user and returns a ranked list of possible IEM disorders that match the input profile. In addition, the system can explain the rationale ...

Review and classification of published variants in the ARSB gene. The purpose of this database is to support researchers and clinicians. understand structural changes on alylsulfatase B (ASB) caused by Mucopolysaccharidosis type VI (MPS6) mutations ...

A database of interactors and mutations of the human von Hippel-Lindau tumor suppressor protein (pVHL).

PhenoDis is a manually annotated database providing symptomatic, genetic and imprinting information about rare cardiac diseases. PhenoDis is primarily concerned with the assignment of clinical symptoms to rare diseases using the biomedical literature ...

The Canadian Rare Diseases Models and Mechanisms (RDMM) Network. Japanese Rare Disease Models & Mechanisms Network.

The FDA Adverse Event Reporting System (FAERS) is a database that contains information on adverse event and medication error reports submitted to FDA.

Information retrieval tool for accessing and integrating genetic and medical information for health applications. Resorting to this integrated environment, clinicians are able to access and relate diseases data already available in the Internet, scat ...

Semantic web application network that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems. In a single package, it provides the tools to create new applications, including advanced integratio ...

Liege Acromegaly Survey (LAS) database includes anonymous historical and prospective data on liege acromegaly patients, pathophysiology, clinical features, responses to therapy and long term outcomes of acromegaly.

The RAMEDIS system is a platform independent, web-based information system for rare metabolic diseases based on filed case reports. It was developed in close cooperation with clinical partners to allow them to collect information on rare metabolic di ...

It is a a joint ISA-CNR/UniSA project: a database in which information are collected and freely available about structural features of the enzymes involved in the galactose metabolism, i.e. galactose-1-phosphate uridylyltransferase (GALT, E.C. 2.7.7. ...

The NEW ESID online database network. European Society for Immunodeficiencies. Exchange of ideas and information among doctors, nurses, biomedical investigators, patients and their families concerned with primary immunodeficiency diseases (PID). E ...

LORD (linking opendata for rare diseases) - tool for browsing information about rare diseases. It aggregates the information from Orphanet, HPO and OMIM database.

a manually curated database of lysosomal enzymes associated with rare diseases. RareLSD: Database for Human Lysosomal Enzymes. RareLSD: A Database for Human Lysosomal Enzymes. RareLSD is a manually curated database of 63 lysosomal enzymes present i ...

The first integrated database of gene annotation and expression profiles for variants related to human diseases. An integrated database of variants and gene expression profiles for genetic diseases.

Orphadata provides the scientific community with comprehensive, quality datasets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.

Longitudinal, routine data for UHB NHSFT patients recruited to the 100K Genomes project that accessed Acute Care at UHB: This includes data for cancer and rare diseases in adults and children, with investigations undertaken and outcomes.

A rare skin disease database to link drugs with potential drug targets for rare skin diseases.

ModelMatcher is a scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research.

A search engine for human genomic variants.

Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.

Data portal for standardized stem cell information. ICSCB is operated by CiRA,Kyoto University. It is an Intergerated Collection of Stem Cell Bank data by miacarm, standard data format for all the stem cell lines with minimum necessary information f ...

Software that includes powerful bioinformatics applications for genetic analysis and offers a comprehensive solution to the tasks of genomic variants annotation, filtration, interpretation and reporting. It includes Alamut Batch, which is a high-thro ...

Diagnostic Variant Database (DVD) is a nation-wide human genomic variant database launched by Dutch University Medical Centers. Its purpose is to share all genetic variants detected in the course of next-generation sequencing (NGS) applications betwe ...