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 a SOAP 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 the EBI Search help & documentation section.

Statistics

Domain Name Domain Identifier Category Number of entries Indexed on Updated on Released on
Analysis sra-analysis Nucleotide sequences 74 01-Oct-2013 01-Oct-2013 01-Oct-2013
ArrayExpress arrayexpress-repository Gene expression 42,729 01-Oct-2013 30-Sep-2013 30-Sep-2013
Assembly genome_assembly Nucleotide sequences 15,813 01-Oct-2013 30-Sep-2013 30-Sep-2013
Assembly contig (Release) emblrelease_wgs Nucleotide sequences 131,247,705 12-Sep-2013 01-Jan-1970
Assembly contig (Update) emblnew_wgs Nucleotide sequences 6,590,740 01-Oct-2013 30-Sep-2013 30-Sep-2013
Assembly contig set wgs_masters Nucleotide sequences 13,781 30-Sep-2013 29-Sep-2013 29-Sep-2013
Assembly scaffold (Release) emblrelease_con Nucleotide sequences 10,125,105 11-Sep-2013 31-Aug-2013
Assembly scaffold (Update) emblnew_con Nucleotide sequences 662,970 01-Oct-2013 30-Sep-2013 30-Sep-2013
BioModels biomodels Reactions, pathways & diseases 143,032 01-Aug-2013 02-Jul-2013 18-Jun-2013
ChEBI chebi Small molecules 38,469 30-Aug-2013 29-Aug-2013
ChEMBL Activity chembl-activity Small molecules 5,479,146 01-Aug-2013 24-Oct-2011 01-Aug-2011
ChEMBL Assay chembl-assay Small molecules 582,982 01-Aug-2013 24-Oct-2011 01-Aug-2011
ChEMBL compound chembl-compound Small molecules 1,060,258 01-Aug-2013 24-Oct-2011 01-Aug-2011
ChEMBL target chembl-target Small molecules 8,603 01-Aug-2013 24-Oct-2011 01-Aug-2011
Coding emblcds Nucleotide sequences 86,726,402 01-Oct-2013 30-Sep-2013 30-Sep-2013
DGVa dgva Genomes 13,987,901 28-Sep-2013 27-Sep-2013
EFO efo Ontologies 4,216 24-Sep-2013
EGA ega Genomes 691 01-Oct-2013 30-Sep-2013 30-Sep-2013
EMDB emdb Macromolecular structures 2,090 25-Sep-2013 25-Sep-2013 25-Sep-2013
Ensembl Gene ensembl_gene Genomes 1,556,803 04-Sep-2013 03-Sep-2013 02-Sep-2013
Ensembl Genomes Gene ensemblGenomes_gene Genomes 35,216,991 19-Sep-2013 18-Sep-2013 17-Sep-2013
EPO epo Protein sequences 2,819,289 09-Sep-2013 08-Sep-2013
Expression Atlas Experiments atlas-experiments Gene expression 2,841 01-Oct-2013 30-Sep-2013 22-Jul-2013
Expression Atlas Genes atlas-genes Gene expression 886,439 01-Oct-2013 30-Sep-2013 22-Jul-2013
GO go Ontologies 39,923 01-Oct-2013 30-Sep-2013
GPCRDB gpcrdb Protein families 32,803 26-Sep-2013 23-Sep-0013
HGNC hgnc Genomes 41,533 01-Oct-2013
IntAct Experiments intact-experiments Molecular interactions 30,975 01-Oct-2013 27-Sep-2013 27-Sep-2013
IntAct Interactions intact-interactions Molecular interactions 279,827 01-Oct-2013 27-Sep-2013 27-Sep-2013
IntAct Interactors intact-interactors Molecular interactions 76,485 01-Oct-2013 27-Sep-2013 27-Sep-2013
IntEnz intenz Enzymes 6,620 06-Sep-2013 05-Sep-2013 04-Sep-2013
InterPro interpro Protein families 25,090 19-Sep-2013 19-Sep-2013 19-Sep-0013
JPO jpo Protein sequences 1,674,104 19-Sep-2013 18-Sep-2013
KIPO kipo Protein sequences 113,599 19-Sep-2013 18-Sep-2013
Ligands pdbechem Small molecules 16,860 25-Sep-2013 25-Sep-2013 23-Sep-2013
LRG lrg Genomes 705 01-Oct-2013 30-Sep-2013 30-Sep-2013
MEDLINE medline Literature 23,122,025 29-Sep-2013 28-Sep-2013
MEROPS Peptidase Clans merops_clan Protein families 88 01-Aug-2013 27-Feb-2012 04-Jul-2011
MEROPS Peptidase Families merops_family Protein families 303 01-Aug-2013 27-Feb-2012 04-Jul-2011
MEROPS Peptidases merops_id Protein families 5,457 01-Aug-2013 27-Feb-2012 04-Jul-2011
MetaboLights metabolights Reactions, pathways & diseases 6,294 01-Aug-2013 27-Jun-2013 27-Jun-2013
NRNL1 nrnl1 Nucleotide sequences 12,349,772 01-Aug-2013 01-Feb-2013
NRNL2 nrnl2 Nucleotide sequences 15,009,374 01-Aug-2013 01-Feb-2013
NRPL1 nrpl1 Protein sequences 2,630,721 01-Aug-2013 01-Feb-2013
NRPL2 nrpl2 Protein sequences 3,771,578 01-Aug-2013 01-Feb-2013
OMIM omim Reactions, pathways & diseases 23,141 01-Oct-2013
Patent Families patentFamilies Literature 119,710 01-Aug-2013 01-Feb-2013
Patents patentdb Literature 4,239,074 19-Aug-2013 24-Nov-2012
PDBe pdbe Macromolecular structures 94,143 25-Sep-2013 25-Sep-2013 09-Mar-0017
People ebiweb_people EBI web 578 01-Oct-2013 01-Oct-2013
PomBase pombase Genomes 7,017 13-Sep-2013 12-Sep-2013
PRIDE pride Protein sequences 452,696 25-Sep-2013 24-Sep-2013 06-Mar-0030
Reactome reactome Reactions, pathways & diseases 83,765 24-Sep-2013 19-Sep-2013
Read (Experiment) sra-experiment Nucleotide sequences 377,936 01-Oct-2013 01-Oct-2013 01-Oct-2013
Read (Run) sra-run Nucleotide sequences 510,402 01-Oct-2013 01-Oct-2013 01-Oct-2013
RESID resid Small molecules 611 19-Sep-2013 17-Sep-2013
Resources ebiweb_resources EBI web 149 01-Oct-2013 01-Oct-2013
Rhea rhea Reactions, pathways & diseases 23,380 06-Sep-2013 05-Sep-2013 04-Sep-2013
Sample sra-sample Nucleotide sequences 398,319 01-Oct-2013 01-Oct-2013 01-Oct-2013
SBO sbo Ontologies 604 01-Oct-2013 01-Oct-2013
Sequence (Release) emblrelease_standard Nucleotide sequences 167,424,681 11-Sep-2013 03-Sep-2013
Sequence (Update) emblnew_standard Nucleotide sequences 759,720 27-Sep-2013 26-Sep-2013 26-Sep-2013
Site ebiweb_corporate EBI web 8,809 30-Sep-2013 30-Sep-2013
Study project Nucleotide sequences 54,055 01-Oct-2013 01-Oct-2013 01-Oct-2013
Study (Read/Analysis) sra-study Nucleotide sequences 25,246 01-Oct-2013 01-Oct-2013 01-Oct-2013
Submission (Read/Analysis) sra-submission Nucleotide sequences 160,387 01-Oct-2013 01-Oct-2013 01-Oct-2013
Taxonomy taxonomy Ontologies 1,078,029 01-Oct-2013 30-Sep-2013
Transcriptome assembly contig (Release) emblrelease_tsa Nucleotide sequences 15,403,753 11-Sep-2013 05-Sep-2013 05-Sep-2013
Transcriptome assembly contig (Update) emblnew_tsa Nucleotide sequences 705,191 01-Oct-2013 30-Sep-2013 30-Sep-2013
Transcriptome assembly contig set tsa_masters Nucleotide sequences 253 30-Sep-2013 29-Sep-2013 29-Sep-2013
TreeFam treefam Protein families 15,736 12-Sep-2013 11-Sep-2013 10-May-2013
UniParc uniparc Protein sequences 48,705,074 17-Sep-2013 16-Sep-2013 18-Sep-2013
UniProtKB uniprot Protein sequences 43,362,837 17-Sep-2013 16-Sep-2013 18-Sep-2013
UniRef100 uniref100 Protein sequences 26,599,709 17-Sep-2013 16-Sep-2013 18-Sep-2013
UniRef50 uniref50 Protein sequences 8,082,957 17-Sep-2013 16-Sep-2013 18-Sep-2013
UniRef90 uniref90 Protein sequences 16,269,649 17-Sep-2013 16-Sep-2013 18-Sep-2013
USPTO uspto Protein sequences 2,550,327 01-Aug-2013 07-Jan-2013
Total 693,987,144

EBISearch ver: 15.2