About EBI Search

EBI Search, also known as 'EB-eye', is a scalable text search engine that provides easy and uniform access to the biological data resources hosted at the European Bioinformatics Institute (EMBL-EBI).

The data resources represented in EBI Search include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property.

EBI Search presents search results that are up-to-date with the data resources and provides an easy inter-domain navigation via a network of cross-references.

It can be accessed over the web or programmatically using the RESTful Web Services interface. This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. For more information you can have a look at EBI Search help & documentation section.

Some examples of projects using EBI Search APIs:

Statistics

Total number of entries: 1,289,165,757

Domain Name Domain Identifier Category Query on Number of entries Indexed on Updated on Released on
Analysis sra-analysis Nucleotide sequences 62,777 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
ArrayExpress arrayexpress-repository Gene expression 69,365 Oct 21, 2016 Oct 21, 2016
Assembly genome_assembly Nucleotide sequences 98,277 Jan 19, 2017 Jan 18, 2017 Jan 18, 2017
Assembly contig set wgs_masters Nucleotide sequences 85,418 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Assembly scaffold (Release) emblrelease_con Nucleotide sequences 38,162,464 Dec 09, 2016 Nov 19, 2016
Assembly scaffold (Update) emblnew_con Nucleotide sequences 149,383 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Baseline Expression Atlas Genes atlas-genes Gene expression 824,682 Nov 19, 2016 Nov 18, 2016 Nov 18, 2016
BioModels biomodels Reactions, pathways & diseases 144,553 Jul 05, 2016 May 10, 2016 May 10, 2016
BioSamples biosamples Samples & ontologies 4,844,637 Oct 25, 2016 Oct 24, 2016 Oct 24, 2016
BioSamples groups biosamples-groups Samples & ontologies 57,795 Oct 25, 2016 Oct 24, 2016 Oct 24, 2016
ChEBI chebi Small molecules 101,441 Jan 02, 2017 Jan 01, 2017
ChEMBL Activity chembl-activity Small molecules 12,077,491 Jul 05, 2016 Oct 05, 2013 Aug 29, 2013
ChEMBL Assay chembl-assay Small molecules 734,201 Jul 05, 2016 Oct 04, 2013 Aug 29, 2013
ChEMBL Document chembl-document Small molecules 51,276 Jul 05, 2016 Oct 05, 2013 Aug 29, 2013
ChEMBL Molecule chembl-molecule Small molecules 1,324,941 Jul 05, 2016 Oct 04, 2013 Aug 29, 2013
ChEMBL Target chembl-target Small molecules 9,356 Jul 05, 2016 Oct 05, 2013 Aug 29, 2013
ChEMBL Target Component chembl-target_component Small molecules 6,371 Jul 05, 2016 Oct 05, 2013 Aug 29, 2013
Coding (Release) coding_release Nucleotide sequences 252,086,150 Dec 12, 2016 Dec 03, 2016 Dec 03, 2016
Coding (Update) coding_update Nucleotide sequences 17,960,454 Jan 20, 2017 Jan 19, 2017
DGVa dgva Genomes & metagenomes 42,992,846 Aug 25, 2016 Aug 24, 2016 Aug 24, 2016
Differential Expression Atlas Genes atlas-genes-differential Gene expression 370,492 Nov 19, 2016 Nov 18, 2016 Nov 18, 2016
EFO efo Samples & ontologies 7,851 Jan 17, 2017
EGA ega Genomes & metagenomes 1,900 Oct 21, 2016 Oct 21, 2016
Elixir registry elixir-registry Samples & ontologies 2,624 Oct 21, 2016
EMDB emdb Macromolecular structures 4,743 Jan 18, 2017 Jan 18, 2017 Jan 18, 2017
Ensembl Gene ensembl_gene Genomes & metagenomes 2,466,658 Dec 08, 2016 Dec 07, 2016 Nov 22, 2016
Ensembl Genomes Gene ensemblGenomes_gene Genomes & metagenomes 162,309,705 Oct 28, 2016 Oct 26, 2016 Oct 24, 2016
Enzyme Portal enzymeportal Enzymes 9,301,716 Nov 08, 2016 Nov 07, 2016 Nov 04, 2016
Enzyme Portal - Enzymes enzymeportal_enzymes Enzymes 7,006 Nov 08, 2016 Nov 07, 2016 Nov 01, 2016
EPO epo Protein sequences 3,785,264 Dec 03, 2016 Dec 02, 2016
Expression Atlas Experiments atlas-experiments Gene expression 2,913 Oct 21, 2016 Oct 21, 2016
GNPS gnps Protein expression data 318 Oct 21, 2016 Oct 21, 2016
GO go Samples & ontologies 46,055 Jan 20, 2017
GPCRDB gpcrdb Protein families 62,615 Jul 05, 2016 Mar 26, 0015
GPMdb gpmdb Protein expression data 367 Jul 05, 2016 Dec 05, 2015 Nov 02, 2015
HGNC hgnc Genomes & metagenomes 44,989 Jan 20, 2017
IMGT/HLA imgt-hla Nucleotide sequences 13,641 Jul 05, 2016 Feb 04, 0017
IntAct Complexes intact-complexes Molecular interactions 1,735 Dec 21, 2016 Dec 12, 2016 Dec 12, 2016
IntAct Experiments intact-experiments Molecular interactions 38,595 Dec 21, 2016 Dec 12, 2016 Dec 12, 2016
IntAct Interactions intact-interactions Molecular interactions 417,785 Dec 21, 2016 Dec 12, 2016 Dec 12, 2016
IntAct Interactors intact-interactors Molecular interactions 91,974 Dec 21, 2016 Dec 12, 2016 Dec 12, 2016
IntEnz intenz Enzymes 7,435 Jan 18, 2017 Jan 17, 2017 Jan 13, 2017
InterPro interpro Protein families 29,700 Nov 03, 2016 Nov 02, 2016 Nov 03, 0016
IPD-KIR ipd-kir Nucleotide sequences 709 Jul 05, 2016 Feb 17, 2015
IPD-MHC ipd-mhc Nucleotide sequences 4,003 Jul 05, 2016 Dec 03, 2013
JPO jpo Protein sequences 2,114,455 Sep 15, 2016 Dec 17, 2015
KIPO kipo Protein sequences 292,915 Sep 16, 2016 Dec 17, 2015
Large assembly large-assembly Nucleotide sequences 44,032,859 Jul 05, 2016 Apr 07, 2014 Apr 07, 2014
Ligands pdbechem Small molecules 19,672 Jan 18, 2017 Jan 18, 2017 Apr 06, 2015
LRG lrg Genomes & metagenomes 958 Jan 17, 2017 Jan 16, 2017 Jan 16, 2017
MassIVE massive Protein expression data 361 Oct 21, 2016 Oct 21, 2016
MEDLINE medline Literature 26,495,432 Oct 04, 2016 Oct 03, 2016
MEROPS Peptidase Clans merops_clan Protein families 88 Jul 05, 2016 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidase Families merops_family Protein families 303 Jul 05, 2016 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidases merops_id Protein families 5,457 Jul 05, 2016 Feb 27, 2012 Jul 04, 2011
MESH mesh Samples & ontologies 28,472 Jan 04, 2017 Jan 03, 2017
MetaboLights metabolights Reactions, pathways & diseases 24,481 Jan 20, 2017 Jan 20, 2017 Jan 20, 2017
MetabolomeExpress metabolome_express Reactions, pathways & diseases 58 Oct 21, 2016 Oct 21, 2016
Metabolomics Workbench metabolomics_workbench Reactions, pathways & diseases 283 Oct 21, 2016 Oct 21, 2016
Metagenomics Projects metagenomics_projects Genomes & metagenomes 862 Jan 20, 2017 Jan 20, 2017
Metagenomics Runs metagenomics_runs Genomes & metagenomes 73,988 Jan 20, 2017 Jan 20, 2017
Metagenomics Samples metagenomics_samples Genomes & metagenomes 54,967 Jan 20, 2017 Jan 20, 2017
Non-coding (Release) non-coding_release Nucleotide sequences 15,872,819 Dec 12, 2016 Dec 03, 2016 Dec 03, 2016
Non-coding (Update) non-coding_update Nucleotide sequences 328,953 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
NRNL1 nrnl1 Nucleotide sequences 12,349,772 Jul 05, 2016 Oct 14, 2014
NRNL2 nrnl2 Nucleotide sequences 15,009,374 Jul 05, 2016 Oct 14, 2014
NRPL1 nrpl1 Protein sequences 2,630,721 Jul 05, 2016 Oct 14, 2014
NRPL2 nrpl2 Protein sequences 3,771,578 Jul 05, 2016 Oct 14, 2014
OMIM omim Reactions, pathways & diseases 24,518 Jan 20, 2017
Patent Families patentFamilies Literature 119,710 Jul 05, 2016 Feb 01, 2013
Patents patentdb Literature 4,239,074 Jul 05, 2016 Nov 24, 2012
PDBe pdbe Macromolecular structures 107,958 Jan 18, 2017 Jan 18, 2017 Mar 09, 0017
People ebiweb_people EBI web 692 Jan 19, 2017 Jan 19, 2017
PeptideAtlas peptide_atlas Protein expression data 2,365 Oct 21, 2016 Oct 21, 2016
Pfam pfam Protein families 16,306 Jul 05, 2016 Jun 17, 2016
PomBase pombase Genomes & metagenomes 6,995 Oct 21, 2016 Oct 20, 2016
PRIDE pride Protein expression data 3,000 Nov 01, 2016 Oct 31, 2016
Reactome reactome Reactions, pathways & diseases 578,939 Dec 22, 2016
Read (Experiment) sra-experiment Nucleotide sequences 2,579,861 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Read (Run) sra-run Nucleotide sequences 2,936,396 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Resources ebiweb_resources EBI web 269 Jan 20, 2017 Jan 20, 2017
Rhea rhea Reactions, pathways & diseases 38,644 Jan 18, 2017 Jan 17, 2017 Jan 13, 2017
RNAcentral rnacentral Nucleotide sequences 12,215,144 Jan 15, 2017 Jan 14, 2017 Dec 16, 2016
Sample sra-sample Nucleotide sequences 2,307,159 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
SBO sbo Samples & ontologies 645 Jan 20, 2017
Sequence (Release) emblrelease_standard Nucleotide sequences 198,426,387 Dec 09, 2016 Nov 22, 2016
Sequence (Update) emblnew_standard Nucleotide sequences 742,193 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Site ebiweb_corporate EBI web 9,556 Jan 20, 2017 Jan 20, 2017
Study project Nucleotide sequences 195,191 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Study (Read/Analysis) sra-study Nucleotide sequences 94,208 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Submission (Read/Analysis) sra-submission Nucleotide sequences 772,861 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
Taxonomy taxonomy Samples & ontologies 1,551,831 Jan 20, 2017 Jan 19, 2017
Transcriptome assembly contig set tsa_masters Nucleotide sequences 2,082 Jan 20, 2017 Jan 19, 2017 Jan 19, 2017
TreeFam treefam Protein families 15,736 Jul 05, 2016 Sep 11, 2013 May 10, 2013
UniParc uniparc Protein sequences 143,389,247 Jan 17, 2017 Jan 16, 2017 Jan 18, 2017
UniProtKB uniprot Protein sequences 74,265,355 Jan 17, 2017 Jan 16, 2017 Jan 18, 2017
UniRef100 uniref100 Protein sequences 94,756,963 Jan 17, 2017 Jan 16, 2017 Jan 18, 2017
UniRef50 uniref50 Protein sequences 20,083,468 Jan 17, 2017 Jan 16, 2017 Jan 18, 2017
UniRef90 uniref90 Protein sequences 49,122,202 Jan 17, 2017 Jan 16, 2017 Jan 18, 2017
USPTO uspto Protein sequences 4,077,368 Sep 16, 2016 Sep 15, 2016
WormBase ParaSite wormbaseParasite Genomes & metagenomes 2,509,935 Dec 06, 2016 Nov 16, 2016 Dec 05, 2016
Total 1,289,165,757

EBISearch ver: 34.2