Epigenetic Marks

The Epigenetic Marks controlled vocabulary contains epigenetic modifications and variations. Examples of epigenetic marks are DNA methylation, DNaseI hypersensitive sites, mRNA, histone variants and post-translational modification. We also included chromatin state segmentation as an epigenetic mark.

The command list_epigenetic_marks is used to list all epigenetic marks included in DeepBlue:

print server.list_epigenetic_marks(user_key)

Insert new epigenetic marks by using the add_epigenetic_mark command:

print server.add_epigenetic_mark("Epigenetic Mark Example",
                                 "A example of epigenetic mark", user_key)

Before inserting a new epigenetic mark, please check if a similar name already exists in order to avoid data duplication. Use list_similar_epigenetic_marks:

print server.list_similar_epigenetic_marks("methylation", user_key)

This command will return the most similar epigenetic mark names:

['okay', ['Methylation', 'mRNA-seq', 'PAX5-N19', 'H4K12bio', 'eGFP-FOS']]