About EBI Search

The EBI Search engine, 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 EMBL-EBI.

The data resources represented in the EBI Search engine 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.

The 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 the EBI Search help & documentation section.

Statistics

Total number of entries: 1,138,640,384

Domain Name Domain Identifier Category Query on Number of entries Indexed on Updated on Released on
Analysis sra-analysis Nucleotide sequences 758 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
ArrayExpress arrayexpress-repository Gene expression 52,185 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Assembly genome_assembly Nucleotide sequences 29,841 Sep 02, 2014 Sep 01, 2014 Sep 01, 2014
Assembly contig (Release) emblrelease_wgs Nucleotide sequences 200,560,885 Aug 27, 2014 Jun 09, 2014
Assembly contig (Update) emblnew_wgs Nucleotide sequences 95,065,937 Sep 03, 2014 Sep 03, 2014 Sep 03, 2014
Assembly contig set wgs_masters Nucleotide sequences 26,192 Aug 27, 2014 Aug 25, 2014 Aug 25, 2014
Assembly scaffold (Release) emblrelease_con Nucleotide sequences 33,223,010 Aug 27, 2014 Jun 10, 2014
Assembly scaffold (Update) emblnew_con Nucleotide sequences 22,961,331 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Baseline Expression Atlas Experiments atlas-experiments Gene expression 13 Aug 27, 2014 Aug 22, 2014 Aug 22, 2014
Baseline Expression Atlas Genes atlas-genes Gene expression 980,913 Aug 27, 2014 Aug 22, 2014 Aug 22, 2014
BioModels biomodels Reactions, pathways & diseases 144,254 Aug 27, 2014 Apr 15, 2014 Apr 11, 2014
BioSamples biosamples Samples & ontologies 3,425,408 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
BioSamples groups biosamples-groups Samples & ontologies 108,955 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
ChEBI chebi Small molecules 43,295 Sep 01, 2014 Aug 31, 2014
ChEMBL Activity chembl-activity Small molecules 12,077,491 Aug 27, 2014 Oct 05, 2013 Aug 29, 2013
ChEMBL Assay chembl-assay Small molecules 734,201 Aug 27, 2014 Oct 04, 2013 Aug 29, 2013
ChEMBL Document chembl-document Small molecules 51,276 Aug 27, 2014 Oct 05, 2013 Aug 29, 2013
ChEMBL Molecule chembl-molecule Small molecules 1,324,941 Aug 27, 2014 Oct 04, 2013 Aug 29, 2013
ChEMBL Target chembl-target Small molecules 9,356 Aug 27, 2014 Oct 05, 2013 Aug 29, 2013
ChEMBL Target Component chembl-target_component Small molecules 6,371 Aug 27, 2014 Oct 05, 2013 Aug 29, 2013
Coding (Release) coding_release Nucleotide sequences 90,769,699 Aug 27, 2014 Jun 20, 2014 Jun 20, 2014
Coding (Update) coding_update Nucleotide sequences 10,188,535 Sep 03, 2014 Sep 03, 2014
DGVa dgva Genomes 14,401,456 Aug 27, 2014 Jun 05, 2014 Jun 05, 2014
Differential Expression Atlas Experiments atlas-experiments-differential Gene expression 696 Aug 27, 2014 Aug 22, 2014 Aug 22, 2014
Differential Expression Atlas Genes atlas-genes-differential Gene expression 980,913 Aug 27, 2014 Aug 22, 2014 Aug 22, 2014
EFO efo Samples & ontologies 4,498 Aug 27, 2014
EGA ega Genomes 763 Aug 27, 2014 Jun 17, 2014 Jun 17, 2014
EMDB emdb Macromolecular structures 2,648 Sep 03, 2014 Sep 03, 2014 Sep 03, 2014
Ensembl Gene ensembl_gene Genomes 1,697,150 Aug 27, 2014 Aug 06, 2014 Jul 21, 2014
Ensembl Genomes Gene ensemblGenomes_gene Genomes 57,605,933 Aug 27, 2014 Aug 18, 2014 Aug 13, 2014
EPO epo Protein sequences 3,303,073 Aug 27, 2014 Jun 14, 2014
GO go Samples & ontologies 41,694 Sep 03, 2014
GPCRDB gpcrdb Protein families 32,803 Aug 27, 2014 Sep 23, 0013
HGNC hgnc Genomes 43,186 Sep 03, 2014
IMGT/HLA imgt-hla Nucleotide sequences 10,095 Aug 27, 2014 Oct 11, 2013
IntAct Complexes intact-complexes Molecular interactions 917 Aug 27, 2014 Jul 17, 2014 Jul 17, 2014
IntAct Experiments intact-experiments Molecular interactions 33,731 Aug 27, 2014 Jul 17, 2014 Jul 17, 2014
IntAct Interactions intact-interactions Molecular interactions 295,567 Aug 27, 2014 Jul 17, 2014 Jul 17, 2014
IntAct Interactors intact-interactors Molecular interactions 79,199 Aug 27, 2014 Jul 17, 2014 Jul 17, 2014
IntEnz intenz Enzymes 6,878 Aug 27, 2014 Jul 17, 2014 Jul 15, 2014
InterPro interpro Protein families 26,238 Aug 27, 2014 Jul 08, 2014 Jul 17, 0014
IPD-KIR ipd-kir Nucleotide sequences 656 Aug 27, 2014 Oct 11, 2013
IPD-MHC ipd-mhc Nucleotide sequences 4,003 Aug 27, 2014 Dec 03, 2013
JPO jpo Protein sequences 1,807,126 Aug 27, 2014 Jun 26, 2014
KIPO kipo Protein sequences 161,181 Aug 27, 2014 Jun 26, 2014
Large assembly large-assembly Nucleotide sequences 44,032,859 Aug 27, 2014 Apr 07, 2014 Apr 07, 2014
Ligands pdbechem Small molecules 18,657 Sep 03, 2014 Sep 03, 2014 Sep 02, 2014
LRG lrg Genomes 760 Aug 27, 2014 Aug 14, 2014 Aug 14, 2014
MEDLINE medline Literature 24,151,527 Sep 03, 2014 Sep 02, 2014
MEROPS Peptidase Clans merops_clan Protein families 88 Aug 27, 2014 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidase Families merops_family Protein families 303 Aug 27, 2014 Feb 27, 2012 Jul 04, 2011
MEROPS Peptidases merops_id Protein families 5,457 Aug 27, 2014 Feb 27, 2012 Jul 04, 2011
MESH mesh Samples & ontologies 27,149 Aug 27, 2014 Dec 16, 2013
MetaboLights metabolights Reactions, pathways & diseases 11,254 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Non-coding (Release) non-coding_release Nucleotide sequences 11,012,304 Aug 27, 2014 Jun 20, 2014 Jun 20, 2014
Non-coding (Update) non-coding_update Nucleotide sequences 1,053,864 Sep 03, 2014 Sep 03, 2014
NRNL1 nrnl1 Nucleotide sequences 12,349,772 Aug 27, 2014 May 16, 2014
NRNL2 nrnl2 Nucleotide sequences 15,009,374 Aug 27, 2014 May 16, 2014
NRPL1 nrpl1 Protein sequences 2,630,721 Aug 27, 2014 May 16, 2014
NRPL2 nrpl2 Protein sequences 3,771,578 Aug 27, 2014 May 16, 2014
OMIM omim Reactions, pathways & diseases 23,692 Sep 03, 2014
Patent Families patentFamilies Literature 119,710 Aug 27, 2014 Feb 01, 2013
Patents patentdb Literature 4,239,074 Aug 27, 2014 Nov 24, 2012
PDBe pdbe Macromolecular structures 103,015 Sep 03, 2014 Sep 03, 2014 Mar 09, 0017
People ebiweb_people EBI web 589 Sep 03, 2014 Sep 03, 2014
PomBase pombase Genomes 7,017 Aug 27, 2014 Aug 20, 2014
PRIDE pride Protein sequences 456,161 Aug 27, 2014 Jan 21, 2014 Jul 07, 0026
Reactome reactome Reactions, pathways & diseases 94,136 Aug 27, 2014 Nov 30, 0002
Read (Experiment) sra-experiment Nucleotide sequences 660,295 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Read (Run) sra-run Nucleotide sequences 858,257 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Resources ebiweb_resources EBI web 158 Sep 03, 2014 Sep 03, 2014
Rhea rhea Reactions, pathways & diseases 27,912 Aug 27, 2014 Jul 17, 2014 Jul 15, 2014
RNAcentral rnacentral Nucleotide sequences 7,704,884 Aug 27, 2014 Jul 31, 2014
Sample sra-sample Nucleotide sequences 723,418 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
SBO sbo Samples & ontologies 609 Sep 03, 2014
Sequence (Release) emblrelease_standard Nucleotide sequences 172,452,930 Aug 27, 2014 Jun 05, 2014
Sequence (Update) emblnew_standard Nucleotide sequences 2,828,700 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Site ebiweb_corporate EBI web 3,711 Sep 03, 2014 Sep 03, 2014
Study project Nucleotide sequences 118,339 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Study (Read/Analysis) sra-study Nucleotide sequences 40,206 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Submission (Read/Analysis) sra-submission Nucleotide sequences 263,745 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Taxonomy taxonomy Samples & ontologies 1,196,482 Sep 03, 2014 Sep 02, 2014
Transcriptome assembly contig (Release) emblrelease_tsa Nucleotide sequences 35,345,750 Aug 27, 2014 Jun 08, 2014 Jun 08, 2014
Transcriptome assembly contig (Update) emblnew_tsa Nucleotide sequences 6,508,173 Sep 03, 2014 Sep 02, 2014 Sep 02, 2014
Transcriptome assembly contig set tsa_masters Nucleotide sequences 632 Aug 27, 2014 Aug 24, 2014 Aug 24, 2014
TreeFam treefam Protein families 15,736 Aug 27, 2014 Sep 11, 2013 May 10, 2013
UniParc uniparc Protein sequences 70,740,512 Sep 02, 2014 Sep 01, 2014 Sep 03, 2014
UniProtKB uniprot Protein sequences 82,673,135 Sep 02, 2014 Sep 01, 2014 Sep 03, 2014
UniRef100 uniref100 Protein sequences 44,408,603 Sep 02, 2014 Sep 01, 2014 Sep 03, 2014
UniRef50 uniref50 Protein sequences 11,862,245 Sep 02, 2014 Sep 01, 2014 Sep 03, 2014
UniRef90 uniref90 Protein sequences 25,890,643 Sep 02, 2014 Sep 01, 2014 Sep 03, 2014
USPTO uspto Protein sequences 2,870,997 Aug 27, 2014 Nov 19, 2013
Total 1,138,640,384

EBISearch ver: 23.14