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 SOAP or RESTful Web Services interfaces. 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: 1,310,735,349

Domain Name Domain Identifier Category Query on Number of entries Indexed on Updated on Released on
Analysis sra-analysis Nucleotide sequences 1,356 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
ArrayExpress arrayexpress-repository Gene expression 58,140 Jun 03, 2015 Jun 03, 2015 Jun 03, 2015
Assembly genome_assembly Nucleotide sequences 38,041 May 30, 2015 May 29, 2015 May 29, 2015
Assembly contig (Release) emblrelease_wgs Nucleotide sequences 248,503,231 Mar 20, 2015 Mar 12, 2015
Assembly contig (Update) emblnew_wgs Nucleotide sequences 88,134,298 Jun 03, 2015 Jun 03, 2015 Jun 03, 2015
Assembly contig set wgs_masters Nucleotide sequences 44,804 May 26, 2015 May 26, 2015 May 26, 2015
Assembly scaffold (Release) emblrelease_con Nucleotide sequences 36,354,922 Mar 19, 2015 Mar 06, 2015
Assembly scaffold (Update) emblnew_con Nucleotide sequences 470,366 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
Baseline Expression Atlas Experiments atlas-experiments Gene expression 28 Mar 31, 2015 Mar 30, 2015 Mar 30, 2015
Baseline Expression Atlas Genes atlas-genes Gene expression 375,571 Mar 31, 2015 Mar 30, 2015 Mar 30, 2015
BioModels biomodels Reactions, pathways & diseases 144,367 Apr 17, 2015 Apr 16, 2015 Apr 16, 2015
BioSamples biosamples Samples & ontologies 4,328,498 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
BioSamples groups biosamples-groups Samples & ontologies 131,419 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
ChEBI chebi Small molecules 54,376 Jun 01, 2015 Jun 01, 2015
ChEMBL Activity chembl-activity Small molecules 12,077,491 Jan 17, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Assay chembl-assay Small molecules 734,201 Jan 17, 2015 Oct 04, 2013 Aug 29, 2013
ChEMBL Document chembl-document Small molecules 51,276 Jan 17, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Molecule chembl-molecule Small molecules 1,324,941 Jan 17, 2015 Oct 04, 2013 Aug 29, 2013
ChEMBL Target chembl-target Small molecules 9,356 Jan 17, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Target Component chembl-target_component Small molecules 6,371 Jan 17, 2015 Oct 05, 2013 Aug 29, 2013
Coding (Release) coding_release Nucleotide sequences 109,938,339 Mar 26, 2015 Mar 25, 2015 Mar 25, 2015
Coding (Update) coding_update Nucleotide sequences 47,194,476 Jun 03, 2015 Jun 03, 2015
DGVa dgva Genomes 21,950,995 Feb 07, 2015 Feb 04, 2015 Feb 04, 2015
Differential Expression Atlas Experiments atlas-experiments-differential Gene expression 909 Mar 31, 2015 Mar 30, 2015 Mar 30, 2015
Differential Expression Atlas Genes atlas-genes-differential Gene expression 98,944 Mar 31, 2015 Mar 30, 2015 Mar 30, 2015
EFO efo Samples & ontologies 4,882 May 18, 2015
EGA ega Genomes 763 Jan 17, 2015 Jun 17, 2014 Jun 17, 2014
EMDB emdb Macromolecular structures 3,196 Jun 03, 2015 Jun 03, 2015 Jun 03, 2015
Ensembl Gene ensembl_gene Genomes 1,751,773 May 23, 2015 May 22, 2015 May 13, 2015
Ensembl Genomes Gene ensemblGenomes_gene Genomes 80,147,100 Apr 15, 2015 Mar 25, 2015 Mar 13, 2013
Enzyme Portal enzymeportal Enzymes 1,472,376 Mar 20, 2015 Mar 19, 2015 Mar 04, 2015
EPO epo Protein sequences 3,383,669 Mar 24, 2015 Mar 23, 2015
GO go Samples & ontologies 43,141 Jun 03, 2015
GPCRDB gpcrdb Protein families 62,615 Mar 26, 2015 Mar 26, 0015
HGNC hgnc Genomes 43,695 Jun 03, 2015
IMGT/HLA imgt-hla Nucleotide sequences 10,095 Jan 17, 2015 Oct 11, 2013
IntAct Complexes intact-complexes Molecular interactions 1,116 Apr 12, 2015 Apr 08, 2015 Apr 08, 2015
IntAct Experiments intact-experiments Molecular interactions 35,799 Apr 12, 2015 Apr 08, 2015 Apr 08, 2015
IntAct Interactions intact-interactions Molecular interactions 348,389 Apr 11, 2015 Apr 08, 2015 Apr 08, 2015
IntAct Interactors intact-interactors Molecular interactions 84,384 Apr 11, 2015 Apr 08, 2015 Apr 08, 2015
IntEnz intenz Enzymes 7,044 May 27, 2015 May 26, 2015 May 21, 2015
InterPro interpro Protein families 27,463 May 22, 2015 May 21, 2015 May 28, 0015
IPD-KIR ipd-kir Nucleotide sequences 656 Jan 17, 2015 Oct 11, 2013
IPD-MHC ipd-mhc Nucleotide sequences 4,003 Jan 17, 2015 Dec 03, 2013
JPO jpo Protein sequences 1,890,835 Jan 17, 2015 Jan 12, 2015
KIPO kipo Protein sequences 246,459 Jan 17, 2015 Jan 12, 2015
Large assembly large-assembly Nucleotide sequences 44,032,859 Jan 17, 2015 Apr 07, 2014 Apr 07, 2014
Ligands pdbechem Small molecules 19,672 Jun 03, 2015 Jun 03, 2015 Apr 06, 2015
LRG lrg Genomes 812 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
MEDLINE medline Literature 24,950,707 Jun 03, 2015 Jun 02, 2015
MEROPS Peptidase Clans merops_clan Protein families 88 Jan 17, 2015 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidase Families merops_family Protein families 303 Jan 17, 2015 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidases merops_id Protein families 5,457 Jan 17, 2015 Feb 27, 2012 Jul 04, 2011
MESH mesh Samples & ontologies 27,455 Jan 17, 2015 Jan 05, 2015
MetaboLights metabolights Reactions, pathways & diseases 16,943 Jun 03, 2015 Jun 03, 2015 Jun 03, 2015
Non-coding (Release) non-coding_release Nucleotide sequences 11,285,972 Mar 26, 2015 Mar 25, 2015 Mar 25, 2015
Non-coding (Update) non-coding_update Nucleotide sequences 499,390 Jun 03, 2015 Jun 03, 2015
NRNL1 nrnl1 Nucleotide sequences 12,349,772 Jan 17, 2015 Oct 14, 2014
NRNL2 nrnl2 Nucleotide sequences 15,009,374 Jan 17, 2015 Oct 14, 2014
NRPL1 nrpl1 Protein sequences 2,630,721 Jan 17, 2015 Oct 14, 2014
NRPL2 nrpl2 Protein sequences 3,771,578 Jan 17, 2015 Oct 14, 2014
OMIM omim Reactions, pathways & diseases 24,139 Jun 03, 2015
Patent Families patentFamilies Literature 119,710 Jan 17, 2015 Feb 01, 2013
Patents patentdb Literature 4,239,074 Jan 17, 2015 Nov 24, 2012
PDBe pdbe Macromolecular structures 107,958 Jun 03, 2015 Jun 03, 2015 Mar 09, 0017
People ebiweb_people EBI web 598 Jun 03, 2015 Jun 03, 2015
PomBase pombase Genomes 7,019 May 28, 2015 May 27, 2015
PRIDE pride Protein expression data 1,474 Jun 03, 2015 Jun 02, 2015 Feb 17, 2015
Reactome reactome Reactions, pathways & diseases 488,279 Mar 24, 2015
Read (Experiment) sra-experiment Nucleotide sequences 1,010,440 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
Read (Run) sra-run Nucleotide sequences 1,245,208 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
Resources ebiweb_resources EBI web 160 Jun 03, 2015 Jun 03, 2015
Rhea rhea Reactions, pathways & diseases 32,420 May 27, 2015 May 26, 2015 May 21, 2015
RNAcentral rnacentral Nucleotide sequences 8,446,855 May 06, 2015 Feb 26, 2015 Feb 23, 2015
Sample sra-sample Nucleotide sequences 965,161 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
SBO sbo Samples & ontologies 630 Jun 03, 2015
Sequence (Release) emblrelease_standard Nucleotide sequences 181,851,498 Mar 19, 2015 Mar 08, 2015
Sequence (Update) emblnew_standard Nucleotide sequences 2,569,128 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
Site ebiweb_corporate EBI web 5,427 Jun 03, 2015 Jun 03, 2015
Study project Nucleotide sequences 140,198 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
Study (Read/Analysis) sra-study Nucleotide sequences 52,548 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
Submission (Read/Analysis) sra-submission Nucleotide sequences 389,842 Jun 03, 2015 Jun 02, 2015 Jun 02, 2015
Taxonomy taxonomy Samples & ontologies 1,287,670 Jun 03, 2015 Jun 02, 2015
Transcriptome assembly contig (Release) emblrelease_tsa Nucleotide sequences 66,008,524 Mar 19, 2015 Mar 13, 2015
Transcriptome assembly contig (Update) emblnew_tsa Nucleotide sequences 7,618,959 Jun 02, 2015 Jun 01, 2015 Jun 01, 2015
Transcriptome assembly contig set tsa_masters Nucleotide sequences 1,003 May 25, 2015 May 24, 2015 May 24, 2015
TreeFam treefam Protein families 15,736 Jan 17, 2015 Sep 11, 2013 May 10, 2013
UniParc uniparc Protein sequences 94,914,534 May 26, 2015 May 25, 2015 May 27, 2015
UniProtKB uniprot Protein sequences 49,293,307 May 26, 2015 May 25, 2015 May 27, 2015
UniRef100 uniref100 Protein sequences 60,885,128 May 26, 2015 May 25, 2015 May 27, 2015
UniRef50 uniref50 Protein sequences 14,286,742 May 26, 2015 May 25, 2015 May 27, 2015
UniRef90 uniref90 Protein sequences 33,691,329 May 26, 2015 May 25, 2015 May 27, 2015
USPTO uspto Protein sequences 3,071,045 Jan 17, 2015 Sep 26, 2014
WormBase ParaSite wormbaseParasite Genomes 1,766,334 Mar 17, 2015 Mar 16, 2015 Mar 11, 2015
Total 1,310,735,349

EBISearch ver: 26.4