Taxon portal

The taxon portal refers to two things:

  1. Performing taxonomic searches; and
  2. Accessing all information about a given taxon including all public data associated with the organism.

Both of these aspects of the taxon portal are described here.

Taxonomic searches

To perform a search for taxa, please go directly to the Taxon Portal (http://www.ebi.ac.uk/ena/data/warehouse/search?portal=taxon) or select the taxon domain from Advanced Search.

Please type in the taxon of interest. A suggestion box will pop up so that you could also select it from the list. The “Search query” (grey box) will be automatically populated (and is not editable).

If you wish to search taxa over a lineage of the taxonomic tree, please tick the “Include subordinate taxa” box and hit the “Search” button. Expanding the “Taxon” results will show a selection of two different types of results: records and report.

After clicking the “Search” button, you will get an onward access into the molecular records themselves as well as information regarding the lineage, common name(s), synonym(s) and rank of the selected taxon.

Records tab

The records tab provides the traditional list of ENA accessions and descriptions, with links to each record page in the browser. There are also options to display or download the full (or partial) list of sequences in text, XML or FASTA formats.

Report tab

The report tab shows a table of metadata for each record. A subset of the available metadata columns is displayed by default and this can be altered by choosing “Select columns”. The selected columns can also be displayed or downloaded in tab separated text format.

Taxon Portal content

The main browser page for every taxon contains a Portal tab.  This portal provides access to all public ENA data that are classified as belonging to the taxa being viewed, or to the full taxonomic subtree starting from the node in question.  With the portal table, the number of objects are listed and these are linked to search result-like listings of all data that can be browsed, viewed or downloaded.

Catalogue of Life

The Taxon Portal provides users with a taxonomic entry point into molecular data and taxonomic exit point for users approaching from molecular data. The two taxonomic systems included in the system, the Catalogue of Life (CoL) and the NCBI Taxonomy (Federhen et al., 2011) are routinely cross-mapped using a cross-mapping tool developed at the University of Cardiff under the European Commission; i4Life FP7 project. The mapping relationships provided by this tool are shown in the figure below; please note that only "corresponds" relationships are currently covered in the Taxon Portal.

cross-mapper relationships

NCBI taxa mapped to CoL records presented as hyperlinks to CoL (via the CoL logo on results pages where there is coverage in CoL). See, for example, http://www.ebi.ac.uk/ena/data/view/Taxon:9689). NCBI taxa which do not contain a CoL logo can be explained by one of the following:

  • The ENA taxon is not in CoL (relationship “not found in”)
  • The ENA taxon refers to >1 taxa in CoL (especially in the case of synonyms conflicts across the 2 systems) (relationship “includes”)
  • The ENA taxon refers to >1 taxa in CoL which in return refer to >1 taxa in ENA (relationship “overlaps”)

While search is currently limited to NCBI taxonomic names, synonyms and IDs, future developments will include support for CoL name searches.

Reference

Federhen S (2011). The NCBI Taxonomy database Nucleic Acids Research, 2011, 1–8.

Latest ENA news

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