Output formats

Types

Ensembl REST supports a number of standard language formats such as JSON but also a number of bioinformatical formats e.g. FASTA. Specifying the value depends heavily on your client and the type of operation you are executing. GET requests support 3 ways of specifying the format. POST only supports one.

• GET
  • Accept or Content-type HTTP header
  • content-type HTTP parameter e.g. /info/ping?content-type=application/json
  • File extension e.g. /info/ping.json
• POST
  • Accept HTTP header only

Be aware that some characters such as + can be interpreted incorrectly when given as a parameter rather than a header; instead use the URL encoded version of the character e.g. instead of + use %2B.

Structure of a MIME Type

Mime types are constructed of 2 portions separated by a /. The first describes the media type and the second part gives the name of said media with an optional suffix. text indicates the content is human readable. application indicates a multipurpose file but most likely not for direct human consumption. Names of media can be prefixed with a x- stating that the MIME type is not part of the official IANA list of MIME types. Finally the name can have a suffix when a MIME type is actually another format.

For example PhyloXML's type is text/x-phyloxml+xml. This indicates that the content could be suitable for human reading, it is a non-standard MIME type and is actually XML and should be handled as such. More advanced clients can look at these values and pass back appropriate data structures depending on the value. Both browsers and libraries like jQuery do this.

Supported MIME Types

Format	Content-type	Extension	Notes
FASTA	text/x-fasta	.fasta	Sequence serialisation format. Only supported on the /sequence endpoint.
GFF3	text/x-gff3	.gff3	Genomic feature serialisation format. Only supported on the /feature endpoint.
BED	text/x-bed	.bed	Browser Extensible Data format as defined by UCSC. Only supported on the /feature endpoint.
JSON	application/json	.json	JavaScript compatible generic text based serialisation format. Supported by most programming languages and the recommended consumption format
JSONP	text/javascript	.jsonp	Extension of JSON to avoid issues of web browser same origin policy. Commonly used by JavaScript plugins like jQuery.
Newick (New Hampshire) format	text/x-nh`	.nh	Phylogenetic serialisation format. Used in /genetree end points
SeqXML	text/x-seqxml+xml	.seqxml	XML schema used to hold sequence information
PhyloXML	text/x-phyloxml+xml	.phyloxml	XML phylogenetic serialisation format. Used in /genetree end points
XML	text/xml	.xml	-
YAML	text/x-yaml	.yaml	-