Annotations

The auxiliary genomic regions data is organized as Annotations in DeepBlue. Each Annotation is composed by a region set, a name, genome, and user attributes.

Annotations are used to store genomic regions that do not come from an epigenomic experiment, but contain other (epi-)genetic information. Examples of annotations are: CpG islands and genes. It is possible to list all available annotations using the list_annotations command. The list_annotations command has two parameters: Genome and user_key.

The following source code demonstrates how to list all available annotations for the genome assembly hg19:

import xmlrpclib
user_key = "anonymous_key"
url = "http://deepblue.mpi-inf.mpg.de/xmlrpc"

server = xmlrpclib.Server(url, encoding='UTF-8', allow_none=True)

hg19_annotations = server.list_annotations("hg19", user_key)