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: 1,379,173,341

Domain Name Domain Identifier Category Query on Number of entries Indexed on Updated on Released on
Analysis sra-analysis Nucleotide sequences 1,533 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
ArrayExpress arrayexpress-repository Gene expression 58,582 Aug 03, 2015 Aug 03, 2015 Aug 03, 2015
Assembly genome_assembly Nucleotide sequences 45,331 Aug 01, 2015 Jul 31, 2015 Jul 31, 2015
Assembly contig (Release) emblrelease_wgs Nucleotide sequences 316,661,330 Jun 20, 2015 Jun 15, 2015
Assembly contig (Update) emblnew_wgs Nucleotide sequences 17,712,831 Aug 01, 2015 Jul 31, 2015 Jul 31, 2015
Assembly contig set wgs_masters Nucleotide sequences 48,800 Jul 29, 2015 Jul 27, 2015 Jul 27, 2015
Assembly scaffold (Release) emblrelease_con Nucleotide sequences 36,777,227 Jul 01, 2015 Jun 04, 2015
Assembly scaffold (Update) emblnew_con Nucleotide sequences 640,505 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
Baseline Expression Atlas Experiments atlas-experiments Gene expression 30 Jul 01, 2015 Jun 28, 2015 Jun 27, 2015
Baseline Expression Atlas Genes atlas-genes Gene expression 372,465 Jul 01, 2015 Jun 28, 2015 Jun 27, 2015
BioModels biomodels Reactions, pathways & diseases 144,367 Jul 01, 2015 Apr 16, 2015 Apr 16, 2015
BioSamples biosamples Samples & ontologies 4,357,262 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
BioSamples groups biosamples-groups Samples & ontologies 103,148 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
ChEBI chebi Small molecules 55,360 Aug 02, 2015 Aug 01, 2015
ChEMBL Activity chembl-activity Small molecules 12,077,491 Jul 01, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Assay chembl-assay Small molecules 734,201 Jul 01, 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 Jul 01, 2015 Oct 04, 2013 Aug 29, 2013
ChEMBL Target chembl-target Small molecules 9,356 Jul 01, 2015 Oct 05, 2013 Aug 29, 2013
ChEMBL Target Component chembl-target_component Small molecules 6,371 Jul 01, 2015 Oct 05, 2013 Aug 29, 2013
Coding (Release) coding_release Nucleotide sequences 151,244,310 Jul 01, 2015 Jun 24, 2015 Jun 24, 2015
Coding (Update) coding_update Nucleotide sequences 52,584,483 Aug 03, 2015 Aug 03, 2015
DGVa dgva Genomes 21,950,995 Jul 01, 2015 Feb 04, 2015 Feb 04, 2015
Differential Expression Atlas Experiments atlas-experiments-differential Gene expression 1,077 Jul 01, 2015 Jun 28, 2015 Jun 27, 2015
Differential Expression Atlas Genes atlas-genes-differential Gene expression 117,595 Jul 01, 2015 Jun 28, 2015 Jun 27, 2015
EFO efo Samples & ontologies 5,351 Jul 16, 2015
EGA ega Genomes 763 Jul 01, 2015 Jun 17, 2014 Jun 17, 2014
EMDB emdb Macromolecular structures 3,291 Jul 29, 2015 Jul 29, 2015 Jul 29, 2015
Ensembl Gene ensembl_gene Genomes 1,756,591 Jul 17, 2015 Jul 16, 2015 Jul 06, 2015
Ensembl Genomes Gene ensemblGenomes_gene Genomes 92,337,668 Jul 01, 2015 Jun 19, 2015 Jun 25, 2015
Enzyme Portal enzymeportal Enzymes 1,399,744 Jul 01, 2015 Jun 05, 2015 May 27, 2015
EPO epo Protein sequences 3,402,268 Jul 02, 2015 Jul 01, 2015
GO go Samples & ontologies 43,507 Aug 03, 2015
GPCRDB gpcrdb Protein families 62,615 Mar 26, 2015 Mar 26, 0015
HGNC hgnc Genomes 43,731 Jul 27, 2015
IMGT/HLA imgt-hla Nucleotide sequences 10,095 Jan 17, 2015 Oct 11, 2013
IntAct Complexes intact-complexes Molecular interactions 1,203 Jul 01, 2015 Jun 26, 2015 Jun 26, 2015
IntAct Experiments intact-experiments Molecular interactions 36,254 Jul 01, 2015 Jun 26, 2015 Jun 26, 2015
IntAct Interactions intact-interactions Molecular interactions 350,009 Jul 01, 2015 Jun 26, 2015 Jun 26, 2015
IntAct Interactors intact-interactors Molecular interactions 84,801 Jul 01, 2015 Jun 26, 2015 Jun 26, 2015
IntEnz intenz Enzymes 7,044 Jul 30, 2015 Jul 29, 2015 Jul 28, 2015
InterPro interpro Protein families 27,542 Jul 23, 2015 Jul 16, 2015 Jul 23, 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 2,003,628 Jul 15, 2015 Jul 14, 2015
KIPO kipo Protein sequences 246,459 Jul 15, 2015 Jul 14, 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 Jul 29, 2015 Jul 29, 2015 Apr 06, 2015
LRG lrg Genomes 821 Jul 30, 2015 Jul 29, 2015 Jul 29, 2015
MEDLINE medline Literature 25,142,013 Aug 03, 2015 Aug 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 Jul 01, 2015 Jan 05, 2015
MetaboLights metabolights Reactions, pathways & diseases 17,459 Aug 03, 2015 Aug 03, 2015 Aug 03, 2015
Non-coding (Release) non-coding_release Nucleotide sequences 12,336,207 Jul 01, 2015 Jun 24, 2015 Jun 24, 2015
Non-coding (Update) non-coding_update Nucleotide sequences 431,789 Aug 03, 2015 Aug 03, 2015
NRNL1 nrnl1 Nucleotide sequences 12,349,772 Jul 01, 2015 Oct 14, 2014
NRNL2 nrnl2 Nucleotide sequences 15,009,374 Jul 01, 2015 Oct 14, 2014
NRPL1 nrpl1 Protein sequences 2,630,721 Jul 01, 2015 Oct 14, 2014
NRPL2 nrpl2 Protein sequences 3,771,578 Jul 01, 2015 Oct 14, 2014
OMIM omim Reactions, pathways & diseases 24,245 Aug 03, 2015
Patent Families patentFamilies Literature 119,710 Jul 01, 2015 Feb 01, 2013
Patents patentdb Literature 4,239,074 Jul 01, 2015 Nov 24, 2012
PDBe pdbe Macromolecular structures 107,958 Jul 29, 2015 Jul 29, 2015 Mar 09, 0017
People ebiweb_people EBI web 607 Aug 03, 2015 Aug 03, 2015
PomBase pombase Genomes 7,019 Jul 01, 2015 Jun 16, 2015
PRIDE pride Protein expression data 1,640 Aug 01, 2015 Jul 31, 2015 Feb 17, 2015
Reactome reactome Reactions, pathways & diseases 499,509 Jul 03, 2015
Read (Experiment) sra-experiment Nucleotide sequences 1,186,319 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
Read (Run) sra-run Nucleotide sequences 1,434,545 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
Resources ebiweb_resources EBI web 161 Aug 03, 2015 Aug 03, 2015
Rhea rhea Reactions, pathways & diseases 33,396 Jul 30, 2015 Jul 29, 2015 Jul 28, 2015
RNAcentral rnacentral Nucleotide sequences 8,607,919 Jun 05, 2015 Jun 04, 2015 May 29, 2015
Sample sra-sample Nucleotide sequences 1,101,119 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
SBO sbo Samples & ontologies 630 Aug 03, 2015
Sequence (Release) emblrelease_standard Nucleotide sequences 184,160,814 Jul 01, 2015 Jun 07, 2015
Sequence (Update) emblnew_standard Nucleotide sequences 2,626,492 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
Site ebiweb_corporate EBI web 5,523 Aug 03, 2015 Aug 03, 2015
Study project Nucleotide sequences 145,350 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
Study (Read/Analysis) sra-study Nucleotide sequences 56,372 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
Submission (Read/Analysis) sra-submission Nucleotide sequences 436,714 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
Taxonomy taxonomy Samples & ontologies 1,318,975 Aug 03, 2015 Aug 02, 2015
Transcriptome assembly contig (Release) emblrelease_tsa Nucleotide sequences 70,894,017 Jul 01, 2015 Jun 08, 2015
Transcriptome assembly contig (Update) emblnew_tsa Nucleotide sequences 344,109 Jul 29, 2015 Jul 27, 2015 Jul 27, 2015
Transcriptome assembly contig set tsa_masters Nucleotide sequences 1,010 Aug 03, 2015 Aug 02, 2015 Aug 02, 2015
TreeFam treefam Protein families 15,736 Jan 17, 2015 Sep 11, 2013 May 10, 2013
UniParc uniparc Protein sequences 98,024,676 Jul 21, 2015 Jul 20, 2015 Jul 22, 2015
UniProtKB uniprot Protein sequences 50,560,035 Jul 21, 2015 Jul 20, 2015 Jul 22, 2015
UniRef100 uniref100 Protein sequences 63,391,201 Jul 21, 2015 Jul 20, 2015 Jul 22, 2015
UniRef50 uniref50 Protein sequences 15,065,016 Jul 21, 2015 Jul 20, 2015 Jul 22, 2015
UniRef90 uniref90 Protein sequences 35,218,174 Jul 21, 2015 Jul 20, 2015 Jul 22, 2015
USPTO uspto Protein sequences 3,071,045 Jul 16, 2015 Jul 15, 2015
WormBase ParaSite wormbaseParasite Genomes 1,790,573 Jul 29, 2015 Jul 28, 2015 Jul 28, 2015
Total 1,379,173,341

EBISearch ver: 27.3