BIG Search

BIG Search is a scalable text search engine built based on ElasticSearch (a highly scalable open-source full-text search and analytics engine based on Apache Lucene). It features cross-domain search and facilitates users to gain access to a wide range of biomedical data, not only from BIGD databases but also partner databases throughout the world.

e.g., PRJCA000126;SAMC000385;tp53;EGFR; human; KaKs_Calculator; GenBank

Total: 104357 records from 89 Databases.


Database Commons 1 Database Commons is a curated catalogue of biological databases, providing people with easy access to a comprehensive collection of publicly available biological databases encompassing different data types and spanning diverse organisms.
EWAS Atlas 1 A knowledgebase of epigenome-wide association studies
EWAS Data Hub 1 A data hub of DNA methylation array data and metadata
SEGreg 11 Database of specifically expressed genes and regulation
AnimalTFDB 48 AnimalTFDB is a comprehensive database including classification and annotation of genome-wide transcription factors
BioCode 5 Archive Bioinformatics Codes for Open Source Projects
dbPAF 3 database of Phospho-sites in Animals and Fungi
DEG 5 Database of Essential Genes
EDK 1 Editome Disease Knowledgebase
EKPD 109 Eukaryotic Kinase and Phosphatase Database
GenTree 2 GenTree, the time tree of genes along the evolutionary history
hTFtarget 4 In this hTFtarget database, we collected comprehensive human TF ChIP-Seq data and customized an analysis workflow to identify reliable TF targets with taking epigenomic states into account
iEKPD 323 Integrated annotations for Eukaryotic protein Kinases, protein Phosphatases & phosphoprotein-binding Domains
lncRNASNP2 2
MethBank 6 A database that integrates genome-wide DNA methylomes across a variety of species and provides an interactive browser for visualization of high-resolution DNA methylation data.
Methbank SRMs 7 Methbank, Single-base Resolution Methylomes (SRMs)
nucmap 14 A database of genome-wide nucleosome positioning map across species.
PLMD 2 Protein Lysine Modifications Database
PTMD 2 A database of human disease-associated post-translational modifications
RhesusBase Genes 7
vcg 7 Virtual Chinese Genome Database is a dynamic genome database of Chinese population.

EGA 55 The European Genome-phenome Archive
HGNC 4 HUGO Gene Nomenclature Committee
LRG 1 A stable genomic reference framework for describing sequence variations
MGnify (Analyses) 533 MGnify is the study of all genomes present in any given environment without the need for prior individual identification or amplification.
WormBase ParaSite 16 WormBase ParaSite
Study 581 INSDC Project records from the European Nucleotide Archive
Non-coding (Release) 1 Non-coding (Release) in ENA
SRA Study (Read/Analysis) 192 Next generation sequencing raw data repository from the European Nucleotide Archive (study part)
SRA Sample 308 Next generation sequencing raw data repository from the European Nucleotide Archive (sample part)
SRA Read (Run) 1164 Next generation sequencing raw data repository from the European Nucleotide Archive (run part)
SRA Read (Experimentn) 1397 Next generation sequencing raw data repository from the European Nucleotide Archive (experiment part)
SRA Submission (Read/Analysis) 19 Next generation sequencing raw data repository from the European Nucleotide Archive (submission part)
Coding (Release) 1341 Coding (Release) in ENA
Coding (Update) 46 Coding (Update) in ENA
RNAcentral 16 The RNAcentral sequences are provided by a group of expert databases and supplemented by sequences from the INSDC.
UniProtKB 1058 UniProt Knowledge Base of protein sequences.
UniRef100 92 UniProt Non-redundant Reference Databases - mutual sequence identity of 100%.
UniRef90 51 UniProt Non-redundant Reference Databases - mutual sequence identity of >90%.
UniRef50 42 UniProt Non-redundant Reference Databases - mutual sequence identity of >50%.
EPO 1811 European Patent Office
JPO 4470 Japan Patent Office
KIPO 1912 Korean Intellectual Property Office
USPTO 1219 United States Patent and Trademark Office
UniParc 1322 Non-redundant archive of protein sequences
EMDB 1 The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.
PDBe 360 Macromolecular structures database
ChEBI 9 Chemical Entities of Biological Interest
ChEMBL Assay 2784 Assay details as reported in a scientific document in ChEMBL database
ChEMBL Document 158 ChEMBL Document in ChEMBL database
ChEMBL Molecule 2 Curated compound set used in ChEMBL database.
ChEMBL Target 1 Curated target set used in ChEMBL database. Includes both protein targets and non-protein targets (e.g., organisms, tissues, cell lines)
ChEMBL Target Component 2 ChEMBL Target Component
ArrayExpress 1365 ArrayExpress Archive is a MIAME compliant public database for microarray data.
Expression Atlas Experiments 51 Expression Atlas Experiments
Baseline Expression Atlas Genes 57 Large scale meta-analysis of public transcriptomics data
Differential Expression Atlas Genes 2937 Large scale meta-analysis of public transcriptomics data
dbGaP 7 The database of Genotypes and Phenotypes
GEO 395 Gene Expression Omnibus. GEO is a public functional genomics data repository supporting MIAME-compliant data submissions
OMIM 230 OMIM Online Mendelian Inheritance in Man
Complex Portal 2 Library of ligands, small molecules and monomers
IntAct Experiments 106 Experimental procedures used to characterise molecular interactions
IntAct Interactions 969 Descriptions of molecular interactions
IntAct Interactors 13 Proteins taking part in molecular interactions
BioModels 54 Database of Mathematical models of biological interest
MetaboLights 1 Database for Metabolomics experiments and derived information
Metabolomics Workbench 5 The Metabolomics Workbench will serve as a national and international repository for metabolomics data and metadata and will provide analysis tools and access to metabolite standards, protocols, tutorials, training, and more.
Reactome 825 Database of core biochemical pathways and reactions
InterPro 34 Database of protein families, domains and functional sites
Interpro domain 88 Database of protein families, domains and functional sites
Interpro family 27 Database of protein families, domains and functional sites
Interpro Homologous super family 3 Database of protein families, domains and functional sites
Pfam 10 The protein families contained within the database
TreeFam 2 TreeFam is a database of gene trees of animal protein families.
MEROPS Peptidases 1 MEROPS Id Peptidase Database
GPMdb 7 The Global Proteome Machine
jPOST 1 The ProteomeXchange Consortium has been set up to provide a globally coordinated submission of mass spectrometry proteomics data to the main existing proteomics repositories, and to encourage optimal data dissemination.
LINCS 220 Library of Network-Based Cellular Signatures (LINCS)
MassIVE 26 The Mass spectrometry Interactive Virtual Environment (MassIVE) is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.
PeptideAtlas 13 PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
PeptideAtlas 113 PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
Enzyme Portal 3 The Enzyme Portal integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds.
IntEnz 1 Integrated relational Enzyme database.
Europe PMC 57916 Europe PMC is an archive of life sciences journal literature.
BioSamples 2173 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 links to assays for specific samples, and accepts direct submissions of samples.
GO 42 Gene Ontology
Ontology Lookup Service (OLS) 526 The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. The user can browse the ontologies through the website as well as programmatically via the OLS API.
bio.tools 1 Bioinformatics Tools and Services Discovery Portal
Site 10 EBI web corporate

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