| Data resources |
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| General |
All |
www.ebi.ac.uk/services/ |
www.ebi.ac.uk/Submissions/ |
www.ebi.ac.uk/FTP/ |
www.ebi.ac.uk/help/ |
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www.ebi.ac.uk/support/ |
| DNA and RNA sequences |
EMBL-Bank |
www.ebi.ac.uk/embl/ |
www.ebi.ac.uk/embl/Submission/ |
ftp.ebi.ac.uk/pub/databases/embl/ |
www.ebi.ac.uk/embl/Documentation/ |
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datalib@ebi.ac.uk |
| Vertebrate genomes |
Ensembl |
www.ensembl.org |
Ensembl does not accept direct submissions; genome sequences should be submitted to EMBL-Bank (see above) |
www.ensembl.org/Download/ |
www.ensembl.org/Docs/ |
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www.ensembl.org/helpdesk |
| Prokaryotic genomes |
Genome Reviews |
www.ebi.ac.uk/GenomeReviews/ |
Genome Reviews does not accept direct submissions; genome sequences should be submitted to EMBL-Bank (see above) |
ftp.ebi.ac.uk/pub/databases/genome_reviews/ |
www.ebi.ac.uk/GenomeReviews/userman.html |
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genome_reviews@ebi.ac.uk |
| Transcriptomes |
ArrayExpress |
www.ebi.ac.uk/arrayexpress/ |
www.ebi.ac.uk/arrayexpress/Submissions |
ftp.ebi.ac.uk/pub/databases/arrayexpress/ |
www.ebi.ac.uk/arrayexpress/Help |
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arrayexpress@ebi.ac.uk |
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arraysubs@ebi.ac.uk (submission enquiries) |
| Protein sequences |
UniProt |
www.uniprot.org |
Directly sequenced protein sequences can be submitted to UniProt/SwissProt at www.ebi.ac.uk/swissprot/Submissions
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www.ebi.uniprot.org/database/download.shtml |
www.ebi.uniprot.org/support/ |
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UniProt does not provide accession numbers, in advance, for protein sequences that are the result of translation of nucleic acid sequences. |
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help@uniprot.org datalib@ebi.ac.uk (submission enquiries) |
| Protein structures |
MSD |
www.ebi.ac.uk/msd/ |
www.ebi.ac.uk/msd/Deposition.html |
www.ebi.ac.uk/msd/services/FTPdownload.html |
www.ebi.ac.uk/msd/Documentation.html |
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msd@ebi.ac.uk |
| Protein–protein interactions |
IntAct |
www.ebi.ac.uk/intact/ |
www.ebi.ac.uk/intact/index.html#submission |
www.ebi.ac.uk/intact/index.html#soft (for software) |
www.ebi.ac.uk/intact/doc/html/documentation.html |
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ftp.ebi.ac.uk/pub/databases/intact/ (for data) |
Intact-help@ebi.ac.uk |
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datasubs@ebi.ac.uk (submission enquiries) |
| Pathways |
Reactome |
www.reactome.org |
Contact the Reactome Development team at dev@reactome.org |
www.reactome.org/download |
www.reactome.org/userguide/userguide.html |
| Small molecules |
ChEBI |
www.ebi.ac.uk/chebi/ |
ChEBI does not accept direct submissions |
ftp.ebi.ac.uk/pub/databases/chebi/ |
www.ebi.ac.uk/chebi/pages/html/help.html |
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www.ebi.ac.uk/chebi/emailChebi.do?toolBarForward=true |
| Controlled vocabularies describing functional attributes of gene products |
Gene Ontology |
www.geneontology.org |
GO does not accept direct submissions but you can submit suggestions for new terms by clicking on the Curator Requests Tracker link at www.geneontology.org
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www.geneontology.org/index.shtml#downloads |
www.geneontology.org/GO.contents.doc.html |
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go@geneontology.org |
| Annotations of gene products with GO terms |
Gene Ontology Annotation Database |
www.ebi.ac.uk/GOA/ |
GOA does not accept direct submissions, but users are encouraged to send updates and corrections to goa@ebi.ac.uk |
ftp.ebi.ac.uk/pub/databases/GO/goa/ |
www.ebi.ac.uk/GOA/goaHelp.html |
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goa@ebi.ac.uk |
| Integrated access to data resources |
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| Genomes and proteomes |
Integr8 |
www.ebi.ac.uk/integr8 |
Integr8 does not accept direct submissions |
First use QuickSearch to find the relevant species, then click on the downloads link |
www.ebi.ac.uk/integr8/ContentsHelpPage.do or click on local help in the left-hand menu bar for context-dependent help. www.ebi.ac.uk/support/
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| Complex queries across several databases |
BioMart |
www.ebi.ac.uk/biomart |
Not applicable |
www.ebi.ac.uk/biomart/install.html |
www.ebi.ac.uk/biomart/install.html |
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www.ebi.ac.uk/biomart/contact.html |
| Retrieve data from several databases |
SRS |
srs.ebi.ac.uk |
Not applicable |
Not applicable |
srs.ebi.ac.uk/doc |
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www.ebi.ac.uk/support |
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Web services |
www.ebi.ac.uk/Tools/webservices |
Not applicable |
www.ebi.ac.uk/Tools/webservices/download.html |
www.ebi.ac.uk/Tools/webservices/FAQ.html |
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sharmila@ebi.ac.uk |
