ENA data formats

ENA data tiers

Data tiers within ENA provide a level of abstraction from the underlying infrastructure that has resulted from the integration of three databases: the EMBL Nucleotide Sequence Database (EMBL-Bank), the Trace Archive and the Sequence Read Archive (SRA). The three ENA data tiers are:

• Reads: sequencing machine output including base and colour calls, call qualities and signals. Next generation sequencing reads are submitted to the Sequence Read Archive (SRA).

• Assembly: information relating overlapping fragmented sequence reads to contigs and higher order structures representing complete biological molecules, such as chromosomes.

• Annotation: interpretations of biological function projected onto coordinate-defined regions of assembled sequence in the form of annotation.

ENA data types

Data from the ENA tiers are organised into data types which are further subdivided into data classes. Each data class typically belongs to a single data tier but some data classes are included into multiple tiers. Also associated with the data tiers are a number of auxiliary data types that provide integration across ENA and serve to expand the information content of their particular parts. These auxiliary data types are:

• Sample: information relating to the biological sample studied in the sequencing experiment.

• Taxon: information relating to the organism that was the source of the sequenced biological sample.

• Project: information relating to the scope of the sequencing effort. The primary use of the projects is to unite content otherwise dispersed across the ENA data classes.

ENA data classes

Data is presented uniformly within each ENA data class. Please refer to the table below for a summary of ENA data classes and supported formats. The 'Example' column contains example entries retrieved from the ENA Browser in HTML, XML, Fasta, Fastq and flatfile formats. The ENA Browser provides retrieval and visualisation functionality over ENA data and metadata and uses REST URLs to support both interactive and programmatic access. The 'Schema' column points to the XML Schemas that describe the data class specific XML formats. Please note that all XML documents returned by the ENA Browser are included in and validate against the ENA.root.xsd XML Schema.