Tag: data submission, annotation and curation

The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and expe ...

DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBas ...

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

The Chemical Effects in Biological Systems (CEBS) database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial, and governmental laboratories.

A public resource for knowledge on the timescale and evolutionary history of life.A search utility allows exploration of the thousands of divergence times among organisms in the published literature. A tree-based (hierarchical) system is used to iden ...

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for compre ...

SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.

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 ...

bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources.

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...

The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts. Our mission is to both aggregate the scarce TCR specificity in ...

ViruSurf is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A G ...

Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.

Experimentally validated anticancer peptides

VIRsiRNAdb contains information on experimentally validated Viral siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic ...

tRNA Gene DataBase Curated by Experts

Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multiv ...

proGenomes is a database providing consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes belonging to over 12,000 species. These can be interactively explored and downloaded, whereby subsets can be customized, e.g. ...

The Chemotion-repository is a repository for chemistry research data. The repository was founded at the Karlsruhe Institute of Technology (KIT) in Germany as a project funded by the German Research Foundation. The repository is domain specific, offer ...

A database of curated biomolecular interactions.

Human Integrated Pathway Database (hiPathDB) provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. The entity-level integration creates a super ...

Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

HypoxiaDB is a manually-curated non-redundant catalogue of human hypoxia-regulated proteins with a goal of collecting proteins whose expression patterns are altered in hypoxic conditions.

Experimentally Characterized Protein annotations

Comparison system for cancer stem cell analysis

a database of curated and consistently annotated human gut metagenomes | GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and acce ...

Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies.

Protein-protein interactions for mammalian TRP channels

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, a ...

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionisation equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play ...

Curated database to annotate gene promoters identified from ChIP-seq results. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, ...

GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.

CellTalkDB is a manually curated database of ligand-receptor interactions in humans and mice. CellTalkDB contains literature-supported ligand-receptor (LR) pairs for human and mouse, which are curated from protein-protein interactions (PPIs) in STRIN ...

Protein stability data

CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset.

A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides. More and more evidences have shown that non-coding RNAs (ncRNAs), such as lncRNAs, circRNAs and primary miRNAs, could encode proteins or peptides. ncEP is a ...

A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies. VariCarta is a curated, web-based database housing ASD-linked genes created from the meta-analysis of -omic sequencing literature. VariCar ...

ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.

Curated Protein Aggregation Database (CPAD) is an integrated database which contains information related to amyloidogenic proteins, Aggregation prone regions, aggregation kinetics and structure of proteins relevant to aggregation. Authors are encoura ...

a curated database for intrapatient tumor heterogeneity. CancerTracer is a manually curated and integrated database aims to help researchers to decipher tumor heterogeneity at individual patient level. It contains two types of tumor heterogeneity da ...

An open-access curated barcode library for diatoms. Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge dive ...

A unified and manually curated repertoire of GRIN variants. A CURATED DATABASE FOR GRIN VARIANTS.

A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome. Murine microbiome database (MMDB) contains 16S rRNA gene-based microbiome taxonomic profiles of the healthy mouse gut microbiota with manually curated meta ...

A Comprehensive Database for Association Between Microbiota and Disease.

A curated database for microbes across human body and their associations with health and diseases.

A knowledgebase of human long non-coding RNAs with enhanced curation model and database system.

Database and resource of protein families in Arthropod genomes.

A curated database of reconstructed individual patient-level data from 153 oncology clinical trials.

The Colorado Richly Annotated Full Text Corpus (CRAFT) is a manually annotated corpus consisting of 67 full-text biomedical journal articles from the PubMed Central Open Access Subset.

CSDB_GT, a curated glycosyltransferase database with close-to-full coverage on three most studied non-animal species.

A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Datab ...

A manually curated database for experimentally validated non-coding RNAs in inflammation. Non-coding RNAs in Inflammation (ncRI) provides a manually curated database for experimentally validated non-coding RNAs in inflammatary disease. Recently, inf ...

A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications. miR2Diabetes aims to provide a comprehensive resource of miRNA dysregulation in diabetic microvascular complications (DMC). Each entry in the miR2 ...

Gene expression regulation database curated by mining abstracts from literature. Gene Expression Regulation Database. Gene Expression Regulation Database (GREDB) has been developed to facilitate systems-level analyses that will provide insights int ...

Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools index bioinformatics tools that can extract knowledge from thes ...

A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China

A curated database of molecular tastants.

Search engine for exploratory searches in heterogeneous biological databases.

A database for drug-resistant probiotic bacteria.

A manually curated database of human and mouse essential lncRNA genes.

This is the Schizosaccharomyces japonicus genome database.

Database and Tool for Metataxonomics with Long-Read Sequence.

A database of manually curated biomarkers for Prostate Cancer.

A manually curated database for the differential methylation in Alzheimer's disease.

Database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects

Semantic-based detection of redundancies to unify protein-protein interaction databases.

An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution.

Machine learning approach to classify genes and genera in the family Geminiviridae.

A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis.

Scaling up oligogenic diseases research with OLIDA.

A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing.

A Database Extension to Visualize Structural Interactome in One-to-many Manner

A high-throughput database of macromolecular host-pathogen interactions on the Web.

REVA as a Well-curated Database for Human Expression-modulating Variants.

AnimalTraits is a curated database containing body mass, metabolic rate and brain size measurements across a wide range of terrestrial animal taxa.

AGODB is a comprehensive domain annotation database of argonaute (Ago) proteins, which contains extensive information about 1902 Ago proteins manually extracted from research articles and public databases.

ClinGen Variant Curation Interface is a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.

circR2Cancer is a manually curated database of associations between circRNAs and cancers. circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase.

CNGB (China National GeneBank) Nucleotide Sequence Archive (CNSA) is a service that provides online data submitting of data and metadata of projects, samples, experiments and sequencing. The CNSA is a system for archiving global omics data, dedicated ...

A curated database for binding affinity and neutralization profiles of coronavirus related antibodies.

Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB str ...

A web-based application for molecular identification of Prototheca species.

a curated lung disease gene expression database | An accessible R package to download PulmonDB data | PulmonDB is a transcriptomic database of IPF and COPD with curated annotation | PulmonDB is a gene expression database with Chronic Obstructive Pulm ...

MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems ...

TFcancer is a manually curated database of transcription factors associated with human cancer. TFcancer features in comprehensive annotations of TFs in human cancers. TFcancer mainly focused on the influence of transcription factors on four dimension ...

Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons.

A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence | cAb-Rep is a database of curated antibody repertoires. It currently includes 306 B cell repertoires collected from 121 human individuals, ...

LBD (Lymphoma Biomarker Database) is a manually curated database of literature-supported biomarkers for lymphoma. It contains 793 biomarkers (715 single biomarkers and 78 combined biomarkers) for different subtypes of lymphoma which have been verifie ...