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.
| 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) | 437 | 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 | 468 | INSDC Project records from the European Nucleotide Archive |
| Non-coding (Release) | 2 | 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 | 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) | 2429 | Coding (Release) in ENA |
| Coding (Update) | 73 | 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 | 1646 | UniProt Knowledge Base of protein sequences. |
| UniRef100 | 1894 | UniProt Non-redundant Reference Databases - mutual sequence identity of 100%. |
| UniRef90 | 1014 | UniProt Non-redundant Reference Databases - mutual sequence identity of >90%. |
| UniRef50 | 341 | UniProt Non-redundant Reference Databases - mutual sequence identity of >50%. |
| UniParc | 851 | 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 | 1536 | ArrayExpress Archive is a MIAME compliant public database for microarray data. |
| Expression Atlas Experiments | 33 | Expression Atlas Experiments |
| Baseline Expression Atlas Genes | 155 | Large scale meta-analysis of public transcriptomics data |
| Differential Expression Atlas Genes | 55 | 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 | 369 | 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 | 34 | Proteins taking part in molecular interactions |
| BioModels | 25 | Database of Mathematical models of biological interest |
| Biomodels Parameters | 12 | Biomodels Parameters |
| 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 | 18 | Database of protein families, domains and functional sites |
| Interpro domain | 9 | Database of protein families, domains and functional sites |
| Interpro family | 21 | 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 | 12173 | 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) | 122 | 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 | 15 | EBI web corporate |
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