REST URLs for fetching XREFs

ENA provides cross-references to external data resources deemed to be important to the user. External resources include services operated by colleagues at the EBI (such as UniProt and Ensembl) and those operated outside the EBI (including SILVA and RFAM). In most cases, we operate a close collaboration with the resources to which we cross-refer, in order to maximise the quality and appropriateness of the cross-references. 

The update frequency of each source is dependent on their own release cycle and/or internal processes, with ENA supporting updates as frequently as once a week.  Cross-references in flat files are still tied to the assembled and annotated release at ENA, so may not display the most recent cross-references for a record.  This REST service provides support for users to obtain the most up-to-date cross-reference mappings, ahead of the next release.

Available cross-reference sources

A list of all cross-reference sources available in this service can be retrieved using the following URL:
http://www.ebi.ac.uk/ena/data/xref/source

The source identifier and description are returned in a tab separated text format. The source identifier should be used when retrieving cross-references using one of the options listed below.

Available ENA targets

A list of all available ENA targets can be retrieved using the following URL:
http://www.ebi.ac.uk/ena/data/xref/target

The target identifier and description are returned in a tab separated text format.  The target identifier should be used when retrieving cross-references using one of the options listed below.  Please note that at this time, not all targets have cross-references.  Most cross-reference sources also have mappings to only one or two ENA targets.

Fetch cross-references

There are three ways to fetch cross-references from this service.  Each of these return the following columns in a tab separated text format: source, source primary accession, source secondary accession, target, target primary accession, target secondary accession.  Not all cross-reference sources have secondary accessions.  Only coding and noncoding targets have secondary accessions (both list the parent sequence accession as the secondary accession).

All cross-references for a single source

All cross-reference mappings for a single source can be fetched.  This can either be all cross-references to a single target type, or all cross-references for the source.  The URL to use for this is:
http://www.ebi.ac.uk/ena/data/xref/search?source=<source>[&target=<target>]

Examples:
http://www.ebi.ac.uk/ena/data/xref/search?source=UniProtKB/Swiss-Prot&target=sequence
http://www.ebi.ac.uk/ena/data/xref/search?source=UniProtKB/Swiss-Prot

All cross-references for a single source ID

All cross-reference mappings for a single source id can be fetched using the following URL. This can either return all mappings between this source record and ENA objects or be restricted to a single target.
http://www.ebi.ac.uk/ena/data/xref/search?source=<source>&source_accession=<source_accession>[&target=<target>]

Examples:
http://www.ebi.ac.uk/ena/data/xref/search?source=PDB&source_accession=1A0N
http://www.ebi.ac.uk/ena/data/xref/search?source=PDB&source_accession=1A0N&target=coding

All cross-references for a single ENA object

All cross-reference mappings available for a single ENA object can be retrieved using the following URL.  This can either return all mappings to this ENA record or it can be restricted to a single cross-reference source.
http://www.ebi.ac.uk/ena/data/xref/search?accession=<accession>[&source=<source>]

Examples:
http://www.ebi.ac.uk/ena/data/xref/search?accession=BN000065
http://www.ebi.ac.uk/ena/data/xref/search?accession=BN000065&source=EuropePMC

Cross-references with attributes

Some cross-reference sources have publicly available attributes, that is additional information about the record other than an ID to an external database source. These can be retrieved using the expanded parameter and setting the value to true.

Examples:
http://www.ebi.ac.uk/ena/data/xref/search?source=COMPARE-RefGenome&expanded=true
http://www.ebi.ac.uk/ena/data/xref/search?source=SILVA-LSU&source_accession=GU926796&expanded=true
http://www.ebi.ac.uk/ena/data/xref/search?source=COMPARE-RefGenome&target=wgsmaster&expanded=true

Each attribute will be provided as additional columns with the names for the attributes supplied in the column headers. If the expanded parameter is used for a cross-reference source without attributes, it will be ignored and the default columns will be returned.

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11 Oct 2017: Read data download issues resolved

Read data download issues previously affecting ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk services now resolved.

06 Oct 2017: ENA read data download issues

Issues with read data download from ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk

04 Oct 2017: ENA Release 133

Release 133 of ENA's assembled/annotated sequences now available