Tag: genotype

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 ...

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 ...

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).

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 European Variation Archive is an open-access archive that accepts submission of, and provides access to, all types of genetic variation data from all species. All users are able to download any dataset, or query our study catalogue via our variat ...

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 ...

VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrat ...

The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...

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 ...

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes as well as the relationship between them, that is freely available and updated daily. The OMIM ontology contains terms used within the OMIM database.

The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

The International Mouse Phenotyping Consortium (IMPC) is an international effort by 21 research institutions to identify the function of every protein-coding gene in the mouse genome. To achieve this, the IMPC is systematically switching off or ‘knoc ...

The NCBI BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials from which data stored in NCBI’s primary data archives are derived. NCBI’s archives host data from diverse types of samples fro ...

The Allele Frequency Net Database (AFND) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunogl ...

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...

The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in the Finnish population. It provides valuable summary data for researchers and clinicians as well as other researchers with an interest in gen ...

The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...

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. ...

Variant Call Format (VCF) is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome.

SNPedia is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). Curati ...

The NIDDK Central Repository stores biosamples, genetic and other data collected in designated NIDDK-funded clinical studies. The purpose of the NIDDK Central Repository is to expand the usefulness of these studies by allowing a wider research commun ...

The Triticeae Toolbox (T3) is a repository for public wheat data generated by the Wheat Coordinated Agricultural Project (Wheat CAP). Funding is provided by the National Institute for Food and Agriculture (NIFA) and the United States Department of Ag ...

A registry of Hereditary Auto-inflammatory Disorder Mutations.

GWAS Central stores genome-wide association study data. The database content comprises direct submissions received from GWAS authors and consortia in addition to actively gathered data sets from various public sources. GWAS data are discoverable from ...

The CHD7 database contains locus-specific, anonymised mutation data on both published and unpublished variants of the CHD7 gene related to the CHARGE syndrome phenotype. It can be searched for patients and their clinical phenotype or for mutations. I ...

GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists togethe ...

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 ...

International Dystrophic Epidermolysis Bullosa Patient Registry (DEB Register) provides phenotypic and genotypic information on DEB and the related COL7A1 mutations. The registry is intended to aid in disease diagnosis, genetic counseling, and discov ...

Panzea provides information on the connection between phenotypes and genotypes of complex traits in maize and its wild relative, teosinte, and specifically in how rare genetic variations contribute to overall plant function.

The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. The JGA contains exclusive data col ...

GeneNet Engine is an exploratory tool to aid hypothesis and biomarker development at a systems-level for genotype-phenotype relationships. Expressed phenotypes may arise due to interactions between multiple genes in a system and effects from the surr ...

SO-Pharm is a formal ontology that represent domain knowledge in pharmacogenomics. To achieve this goal, SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e. genotype, phenotype, drug, trial representations). SO-Pharm enables to ...

The recent genome sequence assemblies of major cucurbit crop species, including cucumber, melon, watermelon and pumpkin have made it feasible to use advanced genomic approaches in cucurbit breeding. Under the CucCAP project (http://cuccap.org), the C ...

The Jackson Laboratory Clinical Knowledgebase (CKB) is a semi-automated/manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and clinical trials related to oncology. CKB not only contains curren ...

FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them ...

This repository provides several plant genomic and phenotypic datasets resulting from IPK and German Plant Phenotyping Network (DPPN) research activities. It was established in January 2015. The background of the study is in plant genetic resources, ...

The GWAS Atlas is a manually curated resource of genome-wide variant-trait associations for a wide range of species.

PGG.Population is a database to aid research on genomic diversity and genetic ancestry of human populations, containing over 7000 genomes, covering more than 350 non-overlapping worldwide populations/groups. It stores information on the genomic diver ...

The Musa Germplasm Information System (MGIS) contains key information on Musa germplasm diversity, including passport data, botanical classification, morpho-taxonomic descriptors, molecular studies, plant photographs and GIS information on 4771 acces ...

MIGen recommends the standard information required to report a genotyping experiment, covering: study and experiment design, subject information, sample collection and processing, genotyping procedure, and data analysis methods, if applicable.

A crowdsourced collection of personal genomics data. Includes SNP genotyping, exome sequencing data, phenotypic annotation and quantified self tracking data.

The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system is an extensible, scalable informatics platform for TBI relevant imaging, assessment, genomics, and other data types. It was developed to share data across the entire ...

TropGENE DB is a database that manages genetic and genomic information about tropical crops studied by Cirad. The database is organised into crop specific modules.

Solanaceae crop phenotypes and traits, developed in collaboration with the research community, especially for breeder traits of agronomic importance.

The Bone Dysplasia ontology provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discrimin ...

MIRING defines the minimum information needed to describe genotyping results for HLA and KIR genes generated using Next Generation Sequencing (NGS) methods, allowing reinterpretation in light of continuous developments in reference sequence and genom ...

The NINDS Parkinson's Disease (PD) Biomarkers Program Data Management Resource enables web-based data entry for clinical studies supporting PD biomarker development, as well as broad data sharing (imaging, clinical, genetic, and biospecimen analysis) ...

The Brassica Information Portal is a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data ...

This site provides access to raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results ar ...

A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene express ...

The SNP Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. The S ...

YamBase is a database containing breeding data for Yam (genus Dioscorea). Yam species that are being used for breeding include Dioscorea rotundata, Dioscorea cayenensis (both are native to Africa and the major cultivated species), Dioscorea aleata (n ...

The wiggle (WIG) format is an older format for display of dense, continuous data such as GC percent, probability scores, and transcriptome data. The bigWig format is the recommended format for almost all graphing track needs. For speed and efficiency ...

The MIQAS set of rules accompanied with the standardized XML and tab-delimited file formats will serve two goals: to encourage research groups that wish to publish a QTL paper to provide and submit the necessary information that would make meta-analy ...

Human disease-related phenotypes in model organisms

The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific m ...

The UK Cystic Fibrosis Registry is a national, secure, centralized database sponsored and managed by the Cystic Fibrosis Trust, with UK National Health Service (NHS) research ethics approval and consent from each person for whom data are collected. F ...

Synthetic data replicating 30,000 ethnically diverse hypertrophic cardiomyopathy patients: This includes clinical and biological phenotyping, co-morbidities, investigations (including ECG, ECHO), any procedures undertaken and outcomes.

Original standard text format for sample pedigree information and genotype calls.

Histoimmunogenetics Markup Language (HML) is intended as a potentially general-purpose XML format for exchanging genetic typing data. This format supports NGS based genotyping methods, raw sequence reads, registered methodologies, reference data, com ...

This format is for displaying SNPs from personal genomes. It is the same as is used for the Genome Variants and Population Variants tracks.

The Drosophila Genetic Reference Panel (DGRP) is a population consisting of more than 200 inbred lines derived from the Raleigh, USA population. The DGRP is a living library of common polymorphisms affecting complex traits, and a community resource f ...

The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for ...

The Drosophila Synthetic Population Resource (DSPR) consists of a new panel of over 1700 recombinant inbred lines (RILs) of Drosophila melanogaster, derived from two highly recombined synthetic populations, each created by intercrossing a different s ...