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: 58944912 records from 131 Databases.


Database Commons 682 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 262089 A knowledgebase of epigenome-wide association studies
EWAS Data Hub 597253 A data hub of DNA methylation array data and metadata
Gene Expression Nebulas 19446 Gene Expression Nebulas (GEN) is a data portal of gene expression profiles under various conditions derived entirely from RNA-Seq data analysis in multiple species.
SEGreg 53156 Database of specifically expressed genes and regulation
BioCode 641 Archive Bioinformatics Codes for Open Source Projects
BioProject 80 Biological Project Library
BioSample 15328 Biological Sample Library
CellMarker 467 CellMarker: a manually curated resource of cell markers in human and mouse.
CGDB 6 Circadian Gene Database
circAltas 610406 circAtlas 2.0
dbPAF 18792 database of Phospho-sites in Animals and Fungi
DEG 28458 Database of Essential Genes
DoriC 2 Database of Replication Origins
EDK 110 Editome Disease Knowledgebase
GenTree 63151 GenTree, the time tree of genes along the evolutionary history
GSA 1048 Genome Sequence Archive
GVM 60088 Genome Variation Map
GWAS Atlas 1 GWAS Atlas is a curated resource of genome-wide variant-trait associations
hTFtarget 13 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
GSA for Human 3 Genome Sequence Archive for Human
iEKPD 29 Integrated annotations for Eukaryotic protein Kinases, protein Phosphatases & phosphoprotein-binding Domains
iUUCD 2 integrated annotations for Ubiquitin and Ubiquitin-like Conjugation Database
lncRNASNP2 4443771
MethBank 45007 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 60499 Methbank, Single-base Resolution Methylomes (SRMs)
PLMD 26 Protein Lysine Modifications Database
PTMD 594 A database of human disease-associated post-translational modifications
RhesusBase Genes 124
vcg 43801 Virtual Chinese Genome Database is a dynamic genome database of Chinese population.

DGVa 43 Database of Genomic Variants Archive
EGA 2625 The European Genome-phenome Archive
HGNC 14 HUGO Gene Nomenclature Committee
MGnify (Analyses) 44840 MGnify is the study of all genomes present in any given environment without the need for prior individual identification or amplification.
MGnify (Projects) 289 MGnify is the study of all genomes present in any given environment without the need for prior individual identification or amplification.
MGnify (Samples) 42904 MGnify is the study of all genomes present in any given environment without the need for prior individual identification or amplification.
WormBase ParaSite 6898 WormBase ParaSite
Study 40189 INSDC Project records from the European Nucleotide Archive
Non-coding (Release) 1966874 Non-coding (Release) in ENA
Non-coding (Update) 455140 Non-coding (Update) in ENA
SRA Study (Read/Analysis) 18844 Next generation sequencing raw data repository from the European Nucleotide Archive (study part)
SRA Sample 1956629 Next generation sequencing raw data repository from the European Nucleotide Archive (sample part)
SRA Read (Run) 264874 Next generation sequencing raw data repository from the European Nucleotide Archive (run part)
SRA Read (Experimentn) 324034 Next generation sequencing raw data repository from the European Nucleotide Archive (experiment part)
SRA Analysis 6049 Next generation sequencing raw data repository from the European Nucleotide Archive (analysis part)
SRA Submission (Read/Analysis) 826 Next generation sequencing raw data repository from the European Nucleotide Archive (submission part)
Assembly contig set 28011 European Nucleotide Archive(Whole Genome Shotgun Set)
Transcriptome Assembly contig set 2 European Nucleotide Archive(Transcriptome Assembly contig set)
Coding (Release) 16160425 Coding (Release) in ENA
Coding (Update) 3575989 Coding (Update) in ENA
Assembly 33461 Genome Assembly
IMGT/HLA 24218 The IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System.
IPD-KIR 986 The IPD-KIR Database provides a centralised repository for human KIR sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immunoglobulin superfamily (IgSF) formerly called Killer-cell Inhibitory Receptors.
Rfam 18612 The Rfam database is a collection of RNA families
RNAcentral 253566 The RNAcentral sequences are provided by a group of expert databases and supplemented by sequences from the INSDC.
UniProtKB 5945653 UniProt Knowledge Base of protein sequences.
UniRef100 1058679 UniProt Non-redundant Reference Databases - mutual sequence identity of 100%.
UniRef90 482576 UniProt Non-redundant Reference Databases - mutual sequence identity of >90%.
UniRef50 251866 UniProt Non-redundant Reference Databases - mutual sequence identity of >50%.
EPO 1243393 European Patent Office
JPO 789676 Japan Patent Office
KIPO 126593 Korean Intellectual Property Office
USPTO 236693 United States Patent and Trademark Office
EMDB 2227 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 7713 Macromolecular structures database
ChEBI 5798 Chemical Entities of Biological Interest
ChEMBL Assay 364719 Assay details as reported in a scientific document in ChEMBL database
ChEMBL Document 3199 ChEMBL Document in ChEMBL database
ChEMBL Molecule 65 Curated compound set used in ChEMBL database.
ChEMBL Target 189 Curated target set used in ChEMBL database. Includes both protein targets and non-protein targets (e.g., organisms, tissues, cell lines)
ChEMBL Target Component 9 ChEMBL Target Component
ArrayExpress 38098 ArrayExpress Archive is a MIAME compliant public database for microarray data.
Expression Atlas Experiments 1456 Expression Atlas Experiments
Baseline Expression Atlas Genes 1254 Large scale meta-analysis of public transcriptomics data
Differential Expression Atlas Genes 22939 Large scale meta-analysis of public transcriptomics data
dbGaP 719 The database of Genotypes and Phenotypes
GEO 24542 Gene Expression Omnibus. GEO is a public functional genomics data repository supporting MIAME-compliant data submissions
Human diseases 19 Human diseases
OMIM 17412 OMIM Online Mendelian Inheritance in Man
Complex Portal 724 Library of ligands, small molecules and monomers
IntAct Experiments 2477 Experimental procedures used to characterise molecular interactions
IntAct Interactions 1244 Descriptions of molecular interactions
IntAct Interactors 538 Proteins taking part in molecular interactions
BioModels 751 Database of Mathematical models of biological interest
MetaboLights 460 Database for Metabolomics experiments and derived information
MetabolomeExpress 1 MetabolomeExpress: a public place to process, interpret and share GC/MS metabolomics datasets.
Metabolomics Workbench 664 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 8028 Database of core biochemical pathways and reactions
Rhea 8 Manually annotated database of chemical reactions created in collaboration with the Swiss Institute of Bioinformatics (SIB)
GPCRDB 399 Database of G Protein-Coupled Receptors
InterPro 2689 Database of protein families, domains and functional sites
Interpro Active site 7 Database of protein families, domains and functional sites
Interpro Binding site 1 Database of protein families, domains and functional sites
Interpro Conserved site 200 Database of protein families, domains and functional sites
Interpro domain 3208 Database of protein families, domains and functional sites
Interpro family 2195 Database of protein families, domains and functional sites
Interpro Homologous super family 198 Database of protein families, domains and functional sites
Interpro PTM 1 Database of protein families, domains and functional sites
Interpro repeat 40 Database of protein families, domains and functional sites
Interpro unknown 7 Database of protein families, domains and functional sites
Pfam (Clans) 5 The clans contained within the database Pfam
Pfam 1151 The protein families contained within the database
TreeFam 6 TreeFam is a database of gene trees of animal protein families.
MEROPS Peptidases 1279 MEROPS Id Peptidase Database
MEROPS Peptidase Clans 1 MEROPS Clan Peptidase Database
MEROPS Peptidase Families 55 MEROPS Peptidase Families Database
GNPS 190 The Global Natural Product Social Molecular Networking (GNPS) site creates a community for natural product researchers working with mass spectrometry data.
GPMdb 198 The Global Proteome Machine
jPOST 68 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 113 Library of Network-Based Cellular Signatures (LINCS)
MassIVE 882 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.
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Paxdb 13 PaxDB is a comprehensive absolute protein abundance database, which contains whole genome protein abundance information across organisms and tissues.
PeptideAtlas 1448 PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
PeptideAtlas 5177 PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
Enzyme Portal 1669 The Enzyme Portal integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds.
IntEnz 507 Integrated relational Enzyme database.
Europe PMC 2869084 Europe PMC is an archive of life sciences journal literature.
BioSamples 502569 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.
EFO 13 Experimental Factor Ontology (EFO)
GO 238 Gene Ontology
MESH 471 Medical Subject Headings (MeSH)
Ontology Lookup Service (OLS) 19484 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.
SBO 1 Systems Biology Ontology
Taxonomy 5243 NCBI Taxonomy database of Organism names
bio.tools 488 Bioinformatics Tools and Services Discovery Portal
Identifiers.org registry 203 Identifiers.org is a system providing resolvable persistent URIs used to identify data for the scientific community, with a current focus on the Life Sciences domain.
ORCID data claims 177 ORCID is a nonproprietary alphanumeric code to uniquely identify scientific and other academic authors and contributors.
Resources 9 EBI resources
People in EBI 50 EBI people
Site 815 EBI web corporate

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