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.

Explore EBI Search data

Some examples of projects using EBI Search APIs:

Statistics

Total number of entries: 1,192,121,304

Domain Name Domain Identifier Category Query on Number of entries Indexed on Updated on Released on
Analysis sra-analysis Nucleotide sequences 9,690 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
ArrayExpress arrayexpress-repository Gene expression 63,485 Feb 08, 2016 Feb 08, 2016 Feb 08, 2016
Assembly genome_assembly Nucleotide sequences 67,745 Feb 06, 2016 Feb 06, 2016 Feb 06, 2016
Assembly contig set wgs_masters Nucleotide sequences 56,992 Feb 06, 2016 Feb 05, 2016 Feb 05, 2016
Assembly scaffold (Release) emblrelease_con Nucleotide sequences 37,522,080 Dec 08, 2015 Nov 19, 2015
Assembly scaffold (Update) emblnew_con Nucleotide sequences 1,367,354 Feb 07, 2016 Feb 06, 2016 Feb 06, 2016
Baseline Expression Atlas Experiments atlas-experiments Gene expression 47 Jan 23, 2016 Jan 22, 2016 Jan 22, 2016
Baseline Expression Atlas Genes atlas-genes Gene expression 469,971 Jan 23, 2016 Jan 22, 2016 Jan 22, 2016
BioModels biomodels Reactions, pathways & diseases 144,367 Sep 04, 2015 Apr 16, 2015 Apr 16, 2015
BioSamples biosamples Samples & ontologies 4,424,329 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
BioSamples groups biosamples-groups Samples & ontologies 51,509 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
ChEBI chebi Small molecules 58,839 Feb 01, 2016 Feb 01, 2016
ChEMBL Activity chembl-activity Small molecules 12,077,491 Sep 04, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Assay chembl-assay Small molecules 734,201 Sep 04, 2015 Oct 04, 2013 Aug 29, 2013
ChEMBL Document chembl-document Small molecules 51,276 Sep 04, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Molecule chembl-molecule Small molecules 1,324,941 Sep 04, 2015 Oct 04, 2013 Aug 29, 2013
ChEMBL Target chembl-target Small molecules 9,356 Sep 04, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Target Component chembl-target_component Small molecules 6,371 Sep 04, 2015 Oct 05, 2013 Aug 29, 2013
Coding (Release) coding_release Nucleotide sequences 176,583,175 Dec 10, 2015 Dec 04, 2015 Dec 04, 2015
Coding (Update) coding_update Nucleotide sequences 21,513,433 Feb 08, 2016 Feb 08, 2016
DGVa dgva Genomes 35,310,378 Dec 09, 2015 Dec 08, 2015 Dec 08, 2015
Differential Expression Atlas Experiments atlas-experiments-differential Gene expression 2,573 Jan 23, 2016 Jan 22, 2016 Jan 22, 2016
Differential Expression Atlas Genes atlas-genes-differential Gene expression 258,093 Jan 23, 2016 Jan 22, 2016 Jan 22, 2016
EFO efo Samples & ontologies 6,209 Jan 19, 2016
EGA ega Genomes 1,900 Dec 09, 2015 Nov 18, 2015 Nov 17, 2015
EMDB emdb Macromolecular structures 3,708 Feb 03, 2016 Feb 03, 2016 Feb 03, 2016
Ensembl Gene ensembl_gene Genomes 1,758,687 Oct 03, 2015 Oct 02, 2015 Sep 23, 2015
Ensembl Genomes Gene ensemblGenomes_gene Genomes 115,868,745 Dec 16, 2015 Dec 15, 2015 Jul 10, 2015
Enzyme Portal enzymeportal Enzymes 7,448,296 Jan 21, 2016 Jan 20, 2016 Jan 20, 2016
EPO epo Protein sequences 3,447,948 Dec 08, 2015 Dec 07, 2015
GNPS gnps Protein expression data 247 Jan 28, 2016 Jan 27, 2016 Jan 27, 0016
GO go Samples & ontologies 44,253 Feb 08, 2016
GPCRDB gpcrdb Protein families 62,615 Sep 04, 2015 Mar 26, 0015
GPMdb gpmdb Protein expression data 367 Dec 09, 2015 Dec 05, 2015 Nov 02, 2015
HGNC hgnc Genomes 44,171 Feb 07, 2016
IMGT/HLA imgt-hla Nucleotide sequences 13,641 Sep 04, 2015 Feb 04, 0017
IntAct Complexes intact-complexes Molecular interactions 1,402 Jan 20, 2016 Jan 14, 2016 Jan 14, 2016
IntAct Experiments intact-experiments Molecular interactions 37,168 Jan 20, 2016 Jan 14, 2016 Jan 14, 2016
IntAct Interactions intact-interactions Molecular interactions 356,066 Jan 20, 2016 Jan 14, 2016 Jan 14, 2016
IntAct Interactors intact-interactors Molecular interactions 87,553 Jan 20, 2016 Jan 14, 2016 Jan 14, 2016
IntEnz intenz Enzymes 7,203 Jan 29, 2016 Jan 28, 2016 Jan 26, 2016
InterPro interpro Protein families 28,678 Dec 11, 2015 Dec 04, 2015 Dec 10, 0015
IPD-KIR ipd-kir Nucleotide sequences 709 Sep 04, 2015 Feb 17, 2015
IPD-MHC ipd-mhc Nucleotide sequences 4,003 Sep 04, 2015 Dec 03, 2013
JPO jpo Protein sequences 2,114,455 Dec 18, 2015 Dec 17, 2015
KIPO kipo Protein sequences 292,915 Dec 18, 2015 Dec 17, 2015
Large assembly large-assembly Nucleotide sequences 44,032,859 Sep 04, 2015 Apr 07, 2014 Apr 07, 2014
Ligands pdbechem Small molecules 19,672 Feb 03, 2016 Feb 03, 2016 Apr 06, 2015
LRG lrg Genomes 883 Feb 02, 2016 Feb 01, 2016 Feb 01, 2016
MassIVE massive Protein expression data 248 Jan 28, 2016 Jan 27, 2016 Jan 27, 0016
MEDLINE medline Literature 25,722,940 Feb 08, 2016 Feb 07, 2016
MEROPS Peptidase Clans merops_clan Protein families 88 Sep 04, 2015 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidase Families merops_family Protein families 303 Sep 04, 2015 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidases merops_id Protein families 5,457 Sep 04, 2015 Feb 27, 2012 Jul 04, 2011
MESH mesh Samples & ontologies 27,883 Jan 05, 2016 Dec 17, 2015
MetaboLights metabolights Reactions, pathways & diseases 18,663 Feb 05, 2016 Feb 05, 2016 Feb 05, 2016
MetabolomeExpress metabolome_express Reactions, pathways & diseases 94 Jan 15, 2016 Dec 22, 2015
Metabolomics Workbench metabolomics_workbench Reactions, pathways & diseases 149 Dec 09, 2015 Nov 24, 2015
Metagenomics metagenomics Genomes 3,078 Sep 17, 2015 Sep 16, 2015
Non-coding (Release) non-coding_release Nucleotide sequences 13,374,183 Dec 10, 2015 Dec 04, 2015 Dec 04, 2015
Non-coding (Update) non-coding_update Nucleotide sequences 1,057,272 Feb 08, 2016 Feb 08, 2016
NRNL1 nrnl1 Nucleotide sequences 12,349,772 Sep 04, 2015 Oct 14, 2014
NRNL2 nrnl2 Nucleotide sequences 15,009,374 Sep 04, 2015 Oct 14, 2014
NRPL1 nrpl1 Protein sequences 2,630,721 Sep 04, 2015 Oct 14, 2014
NRPL2 nrpl2 Protein sequences 3,771,578 Sep 04, 2015 Oct 14, 2014
OMIM omim Reactions, pathways & diseases 24,518 Feb 08, 2016
Patent Families patentFamilies Literature 119,710 Sep 04, 2015 Feb 01, 2013
Patents patentdb Literature 4,239,074 Sep 04, 2015 Nov 24, 2012
PDBe pdbe Macromolecular structures 107,958 Feb 03, 2016 Feb 03, 2016 Mar 09, 0017
People ebiweb_people EBI web 615 Feb 08, 2016 Feb 08, 2016
PeptideAtlas peptide_atlas Protein expression data 84 Dec 09, 2015 Nov 16, 2015 Nov 16, 2015
Pfam pfam Protein families 16,295 Dec 22, 2015 Dec 22, 2015
PomBase pombase Genomes 7,015 Jan 19, 2016 Jan 18, 2016
PRIDE pride Protein expression data 1,614 Dec 09, 2015 Nov 24, 2015 Nov 06, 2015
Reactome reactome Reactions, pathways & diseases 471,389 Dec 16, 2015
Read (Experiment) sra-experiment Nucleotide sequences 1,536,496 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
Read (Run) sra-run Nucleotide sequences 1,822,019 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
Resources ebiweb_resources EBI web 155 Feb 08, 2016 Feb 08, 2016
Rhea rhea Reactions, pathways & diseases 35,464 Jan 29, 2016 Jan 28, 2016 Jan 26, 2016
RNAcentral rnacentral Nucleotide sequences 9,321,083 Dec 04, 2015 Dec 03, 2015 Nov 27, 2015
Sample sra-sample Nucleotide sequences 1,434,362 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
SBO sbo Samples & ontologies 632 Feb 08, 2016
Sequence (Release) emblrelease_standard Nucleotide sequences 189,132,748 Dec 08, 2015 Nov 24, 2015
Sequence (Update) emblnew_standard Nucleotide sequences 2,706,233 Feb 08, 2016 Feb 08, 2016 Feb 08, 2016
Site ebiweb_corporate EBI web 9,709 Feb 08, 2016 Feb 08, 2016
Study project Nucleotide sequences 160,390 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
Study (Read/Analysis) sra-study Nucleotide sequences 64,290 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
Submission (Read/Analysis) sra-submission Nucleotide sequences 511,226 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
Taxonomy taxonomy Samples & ontologies 1,415,897 Feb 08, 2016 Feb 07, 2016
Transcriptome assembly contig (Release) emblrelease_tsa Nucleotide sequences 89,802,153 Dec 08, 2015 Nov 23, 2015
Transcriptome assembly contig (Update) emblnew_tsa Nucleotide sequences 42,071,918 Feb 08, 2016 Feb 08, 2016 Feb 08, 2016
Transcriptome assembly contig set tsa_masters Nucleotide sequences 1,361 Feb 08, 2016 Feb 07, 2016 Feb 07, 2016
TreeFam treefam Protein families 15,736 Sep 04, 2015 Sep 11, 2013 May 10, 2013
UniParc uniparc Protein sequences 111,569,591 Jan 19, 2016 Jan 18, 2016 Jan 20, 2016
UniProtKB uniprot Protein sequences 60,268,458 Jan 19, 2016 Jan 18, 2016 Jan 20, 2016
UniRef100 uniref100 Protein sequences 72,946,704 Jan 19, 2016 Jan 18, 2016 Jan 20, 2016
UniRef50 uniref50 Protein sequences 16,038,089 Jan 19, 2016 Jan 18, 2016 Jan 20, 2016
UniRef90 uniref90 Protein sequences 39,362,473 Jan 19, 2016 Jan 18, 2016 Jan 20, 2016
USPTO uspto Protein sequences 3,071,045 Sep 04, 2015 Jul 15, 2015
WormBase ParaSite wormbaseParasite Genomes 2,070,948 Jan 20, 2016 Jan 19, 2016 Jan 20, 2016
Total 1,192,121,304

EBISearch ver: 29.2