config.yaml

output:
  name: test.db
  type: sqlite
  env: .env

dataset: hsapiens_gene_ensembl
host: http://grch37.ensembl.org
error: ignore

# these can be an arbitrary # of columns but keep in mind if you want to download the
# whole ensembl database there is an easier way, just select the ones you think you will need
# you should keep the first columns as they describe the relationship between the gene/transcript
# coordinate table and the annotation table
gene_annotations:
  ensembl_gene_id: #this is mandatory
     type: fk
     index: true
     fk:
       table: genes
       column: id
  external_gene_name:
     type: str
     index: false
  description:
    type: str
    index: false
  gene_biotype:
    type: str
    index: false
  hgnc_id:
    type: str
    index: false
  hgnc_symbol:
    type: str
    index: false
  ucsc:
    type: str
    index: false
  wikigene_name:
    type: str
    index: false
  wikigene_description:
    type: str
    index: false
  external_synonym:
    type: str
    index: false


transcript_annotations:
  ensembl_transcript_id: #this is mandatory
    type: fk
    index: true
    fk:
      table: transcripts
      column: id
  transcript_biotype:
    type: str
    index: false
  external_transcript_name:
    type: str
    index: false
  transcript_is_cannonical:
    type: str
    index: false