Tag: data submission, annotation and curation


Found 62 sources
Source Match ReputationScore*

European Nucleotide Archive


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 ...
100%

TarBase


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 ...
92%

Gene Ontology Annotation Database


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 ...
90%

Open Targets


The Open Targets Platform is a comprehensive and robust data integration for access to and visualisation of potential drug targets associated with disease. It brings together multiple data types and aims to assist users to identify and prioritise tar ...
90%

MGI Mouse Gene Expression Database


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 ...
76%

SABIO-RK Biochemical Reaction Kinetics Database


SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
76%

GlycomeDB


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.
72%

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 ...
70%

Ascidian Network for In Situ Expression and Embryological Data


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 ...
68%

Signaling Pathway Integrated Knowledge Engine


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 ...
68%

bio.tools


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.
66%

Dragon Antimicrobial Peptide Database


Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.
64%

VDJdb: a curated database of T-cell receptors with known antigen specificity


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 ...
61%

VIRsiRNAdb


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 ...
61%

CancerPPD


Experimentally validated anticancer peptides
61%

tRNADB-CE


tRNA Gene DataBase Curated by Experts
60%

TimeTree


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 ...
59%

Chemotion repository


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 ...
58%

BINDTranslation


A database of curated biomolecular interactions.
58%

Human Integrated Pathway Database


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 ...
57%

CharProtDB


Experimentally Characterized Protein annotations
57%

LocDB


Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana
57%

PhaSePro


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 ...
56%

Stem Cell Discovery Engine


Comparison system for cancer stem cell analysis
56%

HypoxiaDB


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.
56%

proGenomes


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. ...
56%

Aber-OWL


Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies.
55%

TRIP


Protein-protein interactions for mammalian TRP channels
55%

Mammalian Promoter Database (MPromDb)


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, ...
54%

GoMapMan


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.
53%

GMrepo


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 ...
51%

FireProtDB


Protein stability data
51%

ENdb


A manually curated database of experimentally supported enhancers for human and mouse. Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons
50%

VariCarta


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 ...
50%

CIViCmine


CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset.
49%

ARGminer


ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.
49%

MMDB_Mouse


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 ...
49%

ncEP


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 ...
49%

CancerTracer


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 ...
49%

Diat.barcode


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 ...
49%

CellTalkDB


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 ...
49%

ProtoBug


Database and resource of protein families in Arthropod genomes.
47%

CRAFT


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.
47%

PCOSBase


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 ...
47%

miR2Diabetes


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 ...
47%

GEREDB


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 ...
47%

Datasets2Tools


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 ...
46%

PPD


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 ...
46%

ODNA


A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China
43%

BioCarian


Search engine for exploratory searches in heterogeneous biological databases.
43%

Fangorn Forest (F2)


Machine learning approach to classify genes and genera in the family Geminiviridae.
43%

GRINdb


A unified and manually curated repertoire of GRIN variants. A CURATED DATABASE FOR GRIN VARIANTS.
43%

REVA


REVA as a Well-curated Database for Human Expression-modulating Variants.
43%

CSDB_GT


CSDB_GT, a curated glycosyltransferase database with close-to-full coverage on three most studied non-animal species.
43%

circR2Cancer


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.
43%

CPAD


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 ...
43%

CNSA


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 ...
43%

3DBIONOTES


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 ...
43%

PulmonDB


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 ...
43%

M-IOLITE


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 ...
43%

ncRI


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 ...
43%

cAb-Rep


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, ...
43%

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