Ensembl REST query examples

%load_ext autoreload
%autoreload 2

from bionty._servers import EnsemblREST

er = EnsemblREST()

ids = ["ENSG00000275717", "ENSG00000248378"]

Check if ids are current

er.archive_ids(ids)

[{'latest': 'ENSG00000275717.5',
  'assembly': 'GRCh38',
  'id': 'ENSG00000275717',
  'peptide': None,
  'is_current': '1',
  'version': 5,
  'release': '106',
  'possible_replacement': [],
  'type': 'Gene'},
 {'latest': 'ENSG00000248378.1',
  'assembly': 'GRCh38',
  'peptide': None,
  'id': 'ENSG00000248378',
  'is_current': '1',
  'version': 1,
  'release': '106',
  'possible_replacement': [],
  'type': 'Gene'}]

Retrieve external references for an id

res = er.xref("ENSG00000275717")

res[:2]

[{'synonyms': [],
  'display_id': 'ENSG00000275717',
  'info_type': 'DIRECT',
  'info_text': '',
  'primary_id': 'ENSG00000275717',
  'description': None,
  'db_display_name': 'Expression Atlas',
  'version': '0',
  'dbname': 'ArrayExpress'},
 {'info_type': 'DEPENDENT',
  'info_text': '',
  'synonyms': [],
  'display_id': 'KIR3DL1',
  'description': 'killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1',
  'primary_id': '3811',
  'db_display_name': 'NCBI gene (formerly Entrezgene)',
  'dbname': 'EntrezGene',
  'version': '0'}]

set([i["dbname"] for i in res])

{'ArrayExpress',
 'EntrezGene',
 'HGNC',
 'MIM_GENE',
 'MIM_MORBID',
 'Uniprot_gn',
 'WikiGene'}

Retrieve external references for multiple ids

res = er.xref(ids)

set([i["dbname"] for i in res[0]])

{'ArrayExpress',
 'EntrezGene',
 'HGNC',
 'MIM_GENE',
 'MIM_MORBID',
 'Uniprot_gn',
 'WikiGene'}