Tag: data management


Found 113 sources
Source Match ReputationScore*

Sequence Read Archive


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 ...
100%

modMine


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.
82%

Database resources of the National Center for Biotechnology Information


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 ...
66%

RxNORM


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 ...
63%

FlyMine


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 ...
63%

Database of MHC Ligands and Peptide Motifs


SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules.
62%

DNA Data Bank of Japan


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 ...
60%

BioSystems


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 ...
60%

Ensembl Fugu Genome Browser


Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.
58%

Protein Interaction Network Analysis platform


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 ...
57%

BioCyc


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 ...
56%

Codon Usage Database


Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
56%

BioNumbers


Useful biological numbers
55%

HumanMine


HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.
55%

YeastMine


Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.
54%

The human DEPhOsphorylation Database


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 ...
53%

COVID-19 Data Portal


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 ...
53%

NCBI BioProject


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 ...
53%

Hymenoptera Genome Database


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 ...
53%

ThaleMine


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.
52%

Golm Metabolome Database


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 ...
51%

PlanMine


PlanMine is an integrated web resource of data & tools to mine Planarian biology.
51%

Alliance of Genome Resources


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 ...
50%

HymenopteraMine


HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.
50%

BovineMine


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 ...
50%

The ITHANET Portal


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 ...
50%

ZebrafishMine


ZebrafishMine is a tool to customize searches of Zebrafish-related biological data including genes, proteins, fish, and reagents
49%

Compilation and Creation of datasets from PDB


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 ...
48%

Chlamydiae Database


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 ...
47%

T-psi-C


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.
47%

CHOmine


CHOmine integrates many types of data for Cricetulus griseus, and CHO cells. You can run flexible queries, export results and analyse lists of data.
46%

BioMart Central


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 ...
46%

Hemolytik


A Database of Hemolytic and Non-hemolytic Peptides
45%

Pathway and Annotated-list Gene-signature Electronic Repository


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.
45%

LocustMine


An integrated Omics data warehouse for Locust, Locusta migratoria
44%

Clusteval


Free and extendable opensource platform for objective performance comparison of arbitrary Clustering Methods on different datasets.
44%

RepetDB


RepetDB provides repeat consensus detected and classified by TEdenovo and used by TEannot to annotate copies in genomes.
43%

PhytoMine


An InterMine interface to data from Phytozome
43%

XenMine


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 ...
43%

siRNAdb


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 ...
43%

ODB - Operon database


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 ...
43%

MetaBase


Wiki database of biological databases
42%

diArk


A database of eukaryotic sequencing projects
41%

LINCS Data Portal 2.0


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 ...
41%

MIMIC-CXR


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 ...
41%

NBRP resources


System for collecting, preserving and providing bioresources for use as experimental materials for life science research.
40%

Alias


A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.
40%

HMS-ICS


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 ...
40%

EBI patent sequences


Non-redundant databases of patent DNA and protein sequences
40%

RaMP


A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.
39%

ZincBind


Database of zinc binding sites.
39%

GrapeMine


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.
39%

BeanMine


This mine integrates many types of data for string bean built from the LIS chado database.
39%

PeanutMine


PeanutMine integrates peanut data from LIS PeanutBase and other sources.
39%

MedicMine


MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.
39%

CowpeaMine


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.
39%

SoyMine


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
39%

LegumeMine


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.
39%

WheatMine


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.
39%

WormMine


WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.
39%

ChickpeaMine


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.
39%

ChemSpider


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 ...
39%

RatMine


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.
39%

Diseasecard


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 ...
39%

MouseBytes


Open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment. Mousebytes-An-open-access-high-throughput-pipeline-and-database-for-rodent-touchscreen-based-data. This code is associated with the paper from Bera ...
38%

FoldamerDB


The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation
38%

PADS Arsenal


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.
38%

RAEdb


Database of enhancers identified by high-throughput reporter assays.
37%

Conservation Archive


A database portal containing esources that can be used to infer baseline species conditions.
37%

VegMarks


Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables
37%

LabxDB


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 ...
37%

ophid


A Focus on the Integrated Interactions Database (IID). Integrated Interactions Database. tissue specific PPI networks across species.
37%

GenoSurf


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 ...
37%

Odonate Phenotypic Database


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 ...
37%

SEQdata-BEACON


SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500.
37%

MAC-INMV-SSR


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 ...
37%

CytoMegaloVirus DataBase (CMVdb)


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 ...
36%

MeLAD


An integrated resource for metalloenzyme-ligand associations | The Metalloenzyme-Ligand Association Database (MeLAD)
36%

SCEptRe


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 ...
36%

ProtMiscuity


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 ...
36%

PSMD


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 ...
36%

Anabel


A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules.
36%

PlaSMo


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.
36%

The O-GlcNAc Database


Automatization and self-maintenance of the O-GlcNAcome catalog.
36%

Catalysis-hub.org


A web-platform for sharing data and software for computational catalysis research.
36%

resiDB


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 ...
36%

KOFFI


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 ...
36%

TOFF


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 ...
36%

AQUA-MER


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 ...
36%

MSDB


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 ...
36%

Drug-herb-interaction


A constructing a bilingual website with validated database for Herb and Western medicine interactions using Ginseng, Ginkgo and Dong Quai as examples.
36%

Genus biomolecules


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 ...
36%

PathBase


European mutant mice pathology database: histopathology photomicrographs and macroscopic images
35%

OakMine


Quercus robur annotation database
33%

JointvetchMine


Aeschynomene evenia genomic data from the Legume Information System
33%

dBBQs


The database of bacterial quality scores.
33%

FawMine


An integrated Omics data warehouse for FAW, Spodoptera frugiperda
33%

MaizeMine


An integrated data warehouse for MaizeGDB
33%

LupinMine


White and narrow-leaf lupin data from the Legume Information System
33%

miRMaid


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.
33%

PANGAEA


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 ...
33%

BRISSKit


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 ...
33%

DiversityExsiccatae


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 ...
33%

pKPDB


A Protein Data Bank extension database of pKa and pI theoretical values
33%

NUCOME


A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.
33%

United States Swine Pathogen Database


United States Swine Pathogen Database is integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine.
33%

MANTA_DB


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 ...
33%

MaizeSNPDB


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 ...
33%

Staphopia


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 ...
33%

OdoBD


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 ...
33%

GenomeHubs


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 ...
33%

EM-DAT


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. ...
33%

mesophotic.org


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 ...
33%

*ReputationScore indicates how established a given datasource is. Find out more.



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