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: 38776 records from 81 Databases.


Database Commons 4 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
MiCroKiTS 22 Midbody, Centrosome, Kinetochore, Telomere and Spindle
AnimalTFDB 38 AnimalTFDB is a comprehensive database including classification and annotation of genome-wide transcription factors
BioCode 5 Archive Bioinformatics Codes for Open Source Projects
BioProject 1 Biological Project Library
BioSample 1 Biological Sample Library
CGDB 1 Circadian Gene Database
dbPAF 7 database of Phospho-sites in Animals and Fungi
DEG 36 Database of Essential Genes
EDK 1 Editome Disease Knowledgebase
GenTree 15 GenTree, the time tree of genes along the evolutionary history
GSA 1 Genome Sequence Archive
hTFtarget 19 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 91 Integrated annotations for Eukaryotic protein Kinases, protein Phosphatases & phosphoprotein-binding Domains
lncRNASNP2 1
MethBank 33 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 32 Methbank, Single-base Resolution Methylomes (SRMs)
nucmap 23 A database of genome-wide nucleosome positioning map across species.
PLMD 5 Protein Lysine Modifications Database
PTMD 4 A database of human disease-associated post-translational modifications
RhesusBase Genes 21
vcg 25 Virtual Chinese Genome Database is a dynamic genome database of Chinese population.

EGA 305 The European Genome-phenome Archive
HGNC 18 HUGO Gene Nomenclature Committee
LRG 3 A stable genomic reference framework for describing sequence variations
MGnify (Analyses) 447 MGnify is the study of all genomes present in any given environment without the need for prior individual identification or amplification.
WormBase ParaSite 198 WormBase ParaSite
Study 475 INSDC Project records from the European Nucleotide Archive
Non-coding (Release) 2 Non-coding (Release) in ENA
SRA Study (Read/Analysis) 198 Next generation sequencing raw data repository from the European Nucleotide Archive (study part)
SRA Sample 225 Next generation sequencing raw data repository from the European Nucleotide Archive (sample part)
SRA Read (Run) 372 Next generation sequencing raw data repository from the European Nucleotide Archive (run part)
SRA Read (Experimentn) 1600 Next generation sequencing raw data repository from the European Nucleotide Archive (experiment part)
SRA Submission (Read/Analysis) 1 Next generation sequencing raw data repository from the European Nucleotide Archive (submission part)
Coding (Release) 2489 Coding (Release) in ENA
Coding (Update) 38 Coding (Update) in ENA
Rfam 2 The Rfam database is a collection of RNA families
RNAcentral 118 The RNAcentral sequences are provided by a group of expert databases and supplemented by sequences from the INSDC.
UniProtKB 1643 UniProt Knowledge Base of protein sequences.
UniRef100 1968 UniProt Non-redundant Reference Databases - mutual sequence identity of 100%.
UniRef90 1038 UniProt Non-redundant Reference Databases - mutual sequence identity of >90%.
UniRef50 351 UniProt Non-redundant Reference Databases - mutual sequence identity of >50%.
UniParc 874 Non-redundant archive of protein sequences
PDBe 30 Macromolecular structures database
ChEMBL Assay 17 Assay details as reported in a scientific document 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 5 ChEMBL Target Component
ArrayExpress 1539 ArrayExpress Archive is a MIAME compliant public database for microarray data.
Expression Atlas Experiments 33 Expression Atlas Experiments
Baseline Expression Atlas Genes 133 Large scale meta-analysis of public transcriptomics data
Differential Expression Atlas Genes 51 Large scale meta-analysis of public transcriptomics data
dbGaP 15 The database of Genotypes and Phenotypes
GEO 761 Gene Expression Omnibus. GEO is a public functional genomics data repository supporting MIAME-compliant data submissions
Human diseases 2 Human diseases
OMIM 370 OMIM Online Mendelian Inheritance in Man
Complex Portal 8 Library of ligands, small molecules and monomers
IntAct Experiments 2 Experimental procedures used to characterise molecular interactions
IntAct Interactions 1267 Descriptions of molecular interactions
IntAct Interactors 35 Proteins taking part in molecular interactions
BioModels 25 Database of Mathematical models of biological interest
Metabolomics Workbench 2 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 1942 Database of core biochemical pathways and reactions
InterPro 19 Database of protein families, domains and functional sites
Interpro domain 9 Database of protein families, domains and functional sites
Interpro family 22 Database of protein families, domains and functional sites
Pfam 5 The protein families contained within the database
TreeFam 9 TreeFam is a database of gene trees of animal protein families.
GPMdb 2 The Global Proteome Machine
MassIVE 12 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 7 PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
PeptideAtlas 60 PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
Enzyme Portal 5 The Enzyme Portal integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds.
Europe PMC 12886 Europe PMC is an archive of life sciences journal literature.
BioSamples 2158 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 2 Experimental Factor Ontology (EFO)
GO 1 Gene Ontology
MESH 1 Medical Subject Headings (MeSH)
Ontology Lookup Service (OLS) 123 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.
Site 5 EBI web corporate

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