Tag: data management

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submissi ...

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 ...

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, Gold Standard Drug D ...

FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of d ...

SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules.

An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Databas ...

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.

Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated ...

The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research ...

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of hundreds of organisms with completely sequenced genomes. Each database contains the genome, predicted metabolic pathways, p ...

Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.

Useful biological numbers

HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.

DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that ...

The Hymenoptera Genome Database (HGD) is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD is divided into three main divisions: BeeBase, which hosts bee genomes and the Bee Pes ...

ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biol ...

The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discove ...

PlanMine is an integrated web resource of data & tools to mine Planarian biology.

HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.

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 ...

BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-cura ...

ZebrafishMine is a tool to customize searches of Zebrafish-related biological data including genes, proteins, fish, and reagents

ccPDB (Compilation and Creation of datasets from PDB) is a collection of commonly used data sets for structural or functional annotation of proteins. There are numerous datasets from the literature and the Protein Data Bank (PDB), which were used for ...

T-psi-C is a database of tRNA sequences and 3D tRNA structures. The T-psi-C database can be continuously updated by any member of the scientific community.

ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using a ...

CHOmine integrates many types of data for Cricetulus griseus, and CHO cells. You can run flexible queries, export results and analyse lists of data.

This tool is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-databas ...

Pathway and Annotated-list Gene-signature Electronic Repository (PAGER) is an repository for pathways, annotated-lists, and gene signatures (PAGs) related to human network biology.

An integrated Omics data warehouse for Locust, Locusta migratoria

A Database of Hemolytic and Non-hemolytic Peptides

Free and extendable opensource platform for objective performance comparison of arbitrary Clustering Methods on different datasets.

RepetDB provides repeat consensus detected and classified by TEdenovo and used by TEannot to annotate copies in genomes.

An InterMine interface to data from Phytozome

XenMine has been created to view, search and analyze Xenopus data, and provides essential information on gene expression changes and regulatory elements present in the genome. It contains published genomic datasets from both Xenopus tropicalis and Xe ...

ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 ...

The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch. Linked to these sequences is information including siRNA thermodynamic prope ...

De-identified publicly available database of chest radiographs with free-text reports. If you use the MIMIC-CXR Database in your work, please cite the following publication:. MIMIC-CXR: A large publicly available database of labeled chest radiograp ...

next generation access point for perturbation-response signatures. The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbatio ...

Wiki database of biological databases

Open access database for rodent cognition data integration and sharing

A database of eukaryotic sequencing projects

Database of zinc binding sites.

System for collecting, preserving and providing bioresources for use as experimental materials for life science research.

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

Non-redundant databases of patent DNA and protein sequences

The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using ...

A database of prokaryotic defense systems related genes. Procaryotic Antiviral Defense System. procaryotic database, defense system database, pangenome database. PADS Arsenal A Database of Prokaryotic Defense Systems Related Genes.

GrapeMine is dedicated to grapevine data. It provides access to many kind of data types like genomic annotation data as well as SNPs, markers and phenotyping data.

This mine integrates many types of data for string bean built from the LIS chado database.

PeanutMine integrates peanut data from LIS PeanutBase and other sources.

MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.

CowpeaMine integrates genomic and genetic data for cowpea, Vigna unguiculata. It is built from the LIS tripal.chado database as well as data from publications.

This mine integrates many types of data for soybean. It is currently under development by LIS, built from the LIS chado database (genomic data) and the SoyBase database (genetic data) as well as other resources

This mine integrates data for multiple legume species. It is under development by NCGR and is built from the LIS and PeanutBase chado databases as well as exports from other sources.

WheatMine integrates many types of data for Triticum aestivum including gene model, markers, and scaffolds. You can run flexible queries, export results and analyse lists of data.

WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.

ChickpeaMine integrates data for chickpea varieties desi and kabuli. It is developed by LIS/NCGR, built from the LIS chado database and the Chickpea Transcriptome Atlas - I.

ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properti ...

RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data.

A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

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 ...

A web-platform for sharing data and software for computational catalysis research.

Database of enhancers identified by high-throughput reporter assays.

The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation

GenoSurf is a metadata driven semantic search system for integrated genomic datasets. Many valuable resources developed by worldwide research institutions and consortia describe genomic datasets that are open, but their metadata search interfaces ar ...

A comprehensive, annotated database of microsatellites. Multiple Loci VNTR Analysis databases and software. Multi Locus VNTR Analysis (MLVA) databases and software. MICAS 3.0, Microsatellite Analysis Server is the online repository of All Bacteria ...

Versatile databases for genomic sequencing and lab management. LabxDB comes with ready-to-use databases. Data is stored in PostgreSQL. LabxDB provides web-browser GUI and a programmatic API for intregration into pipelines. LabxDB for high-throughpu ...

A Focus on the Integrated Interactions Database (IID). Integrated Interactions Database. tissue specific PPI networks across species.

A database portal containing esources that can be used to infer baseline species conditions.

Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables

An integrated resource for metalloenzyme-ligand associations | The Metalloenzyme-Ligand Association Database (MeLAD)

New open data resource for comparative studies of an old insect order. The Odonate Phenotypic DataBase is a resource for dragonfly and damselfly phenotypes. The database consists of a variety of morphological, behavioural, and bio-geographical infor ...

SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500.

SCEptRe provides weekly updated, non-redundant, user customized benchmark datasets with information on the immune receptor features for receptor-specific epitope predictions. This tool extracts weekly updated 3D complexes of antibody-antigen, TCR-pMH ...

An extensive database for pan-species microsatellite investigation and marker development. A Django app for Pan-Species Microsatellite Database. Pan-Species Microsatellite Database. Microsatellites (simple repeat sequences, SSRs or short tandem re ...

A web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for survei ...

A Public Omics Database for Systematic and Comparable Information of CMV. Cytomegalovirus is a double-stranded DNA virus in the same family as herpesvirus found every where,infect people of all ages. Cytomegalovirus Treatment & Management Kauser Ak ...

Integrative database and analysis platform that relates microbiome and phenotypic data. MANTA (Microbiota And pheNotype correlaTion Analysis platform) is an integrative database and analysis platform that relates microbiome and phenotypic data. MANT ...

a database of promiscuous proteins. Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing c ...

A mesocosm database management system for environmental nanosafety.

A Protein Data Bank extension database of pKa and pI theoretical values

A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules.

PlaSMo stands for Plant Systems-biology Modelling and the mission of the project was ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

Automatization and self-maintenance of the O-GlcNAcome catalog.

ResiDB is a user-friendly sequence similarity-dependent database manager for bacteria, fungi, viruses, protozoa, invertebrate, plants, archaea, environmental and whole genome shotgun sequence data. Create a new database Access existing databases Loa ...

A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines. This R script chara-2-sparse.R is used to convert a traditional character genotype matrix into an integer sparse genotype matrix. This R script can be used ...

database of traits of fish to promote advances in fish aquaculture. toff-project – Database of Traits OF Fish. TOFF (i.e. Traits OF Fish) is a curated database focusing on functional trait information for fish that aims at bringing together behavio ...

new binding kinetics database and its integration in an open-source binding analysis software. Kinetics OF Featured Interactions. KOFFI-DB (???) is an article based database for kinetic constants of biomolecular interactions. We focused on interact ...

A database and toolkit for researchers working on environmental mercury geochemistry. AQUA-MER is useful for researchers who want to investigate mercury speciation in defined environments i.e., to which chemical elements and groups it will bind and i ...

A constructing a bilingual website with validated database for Herb and Western medicine interactions using Ginseng, Ginkgo and Dong Quai as examples.

A database of genus characteristics of proteins and RNA. A database of genus characteristics. The Genus database collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given c ...

A repository for scientific information on mesophotic ecosystems. Repository for information on mesophotic coral ecosystems. Mesophotic.org: an information repository on mesophotic coral ecosystems. Mesophotic.org is a curated repository for infor ...

European mutant mice pathology database: histopathology photomicrographs and macroscopic images

Quercus robur annotation database

Aeschynomene evenia genomic data from the Legume Information System

The database of bacterial quality scores.

An integrated Omics data warehouse for FAW, Spodoptera frugiperda

An integrated data warehouse for MaizeGDB

White and narrow-leaf lupin data from the Legume Information System

Intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.

This information system is operated as an Open Access library aimed at archiving, publishing and distributing georeferenced data from earth system research. The system guarantees long-term availability of its content through a commitment of the hosti ...

Biomedical Research Software as a Service that enables biomedical & translational researchers to securely manage and combine datasets, typically for patient cohorts. A suite of cloud enabled & integrated open source applications can be accessed in a ...

DiversityExsiccatae (DWB-DE) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data doma ...

The Viral Host Range database represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the years, countless host range experiments have been perf ...

A Cross-sectional Analysis of the US Food and Drug Administration Manufacturer and User Facility Device Experience Database.

A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.

United States Swine Pathogen Database is integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine.

Staphopia is a database focusing on the genomes of the bacterial pathogen Staphylococcus aureus. Life-threatening Methicillin-resistant S. aureus (MRSA) infections strike across our society, both in the community and hospital settings. In recent year ...

CACHET-CADB is 259 days long contextualised single-channel ECG arrhythmia database from 24 patients recording under a free-living ambulatory setting

An online database for the dragonflies and damselflies of Bangladesh. Welcome to the Odonata of Bangladesh, database of the dragonflies and damselflies of Bangladesh. Situated in the South-east Asia, Bangladesh is gifted with the rich network of wat ...

Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo scrip ...

A cross-sectional analysis of the emergency events database from a pediatric perspective. The international disasters database. Disaster group: Two main groups of disasters are distinguished in EM-DAT: natural disasters and technological disasters. ...