uw-ds-ep.yaml

study_id: UW-CMG
study_accession:  phs000693
study_title: University of Washington Center for Mendelian Genomics (UW-CMG)
study_desc: The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.
url: https://uwcmg.org
identifier_prefix: https://uwcmg.org/fhir/ds-ep
dd_prefix: http://mendelian.org/fhir
output_filename: uwcmg-ds-ep
id_colname: ParticipantID
whistle_src: _cmg.wstl
code_harmonization_dir: harmony/uw
study_sponsor:
  id: nhgri
  name: National Human Genome Research Institute (NHGRI)
consent_group: 
  code: DS-EP
  name: Epileptic Encephalopathy
  description: Use of the data must be related to [disease]. (Programmer's note, the disease should be confirmed by someone in the know)
env:
  local: dev
  dev: dev
  qa: anvil-demo
  prod: anvil-demo
require_official: True
curies:
  http://purl.obolibrary.org/obo/hp.owl_: HP
  http://purl.obolibrary.org/obo/mondo.owl: MONDO
projector_lib: projector
dataset:
  subject: 
    filename: data/uw/dw-ep/uw_phs000693_ds-ep_subject_2021-04-22_y9q6.csv
    data_dictionary: 
      filename:  data/subject-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/uw/cmg-harmony.csv
  sample: 
    filename: data/uw/dw-ep/uw_phs000693_ds-ep_sample_2021-04-22_y9q6.csv
    data_dictionary: 
      filename:  data/sample-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/uw/cmg-harmony.csv
  sequencing: 
    filename: data/uw/dw-ep/uw_phs000693_ds-ep_sequencing_2021-04-22_y9q6.csv
    embed:
      dataset: sample
      colname: sample_id
    data_dictionary: 
      filename:  data/sequencing-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/uw/cmg-harmony.csv
  family:
    filename: data/uw/dw-ep/uw_phs000693_ds-ep_family_2021-04-22_y9q6.csv
    data_dictionary: 
      filename:  data/family-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/uw/cmg-harmony.csv
  conditions:
    filename: data/uw/dw-ep/conditions-dw-ep.csv
    data_dictionary: 
      filename: data/conditions-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/uw/cmg-harmony.csv
  diseases:
    filename: data/uw/dw-ep/diseases-dw-ep.csv
    data_dictionary: 
      filename: data/disease-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/uw/cmg-harmony.csv
active_tables:
  ALL: true