gregor-dd.yaml

study_id: GREGoR_DD
study_accession:  
study_title: GREGoR Data Model 
study_desc: Data model for the GREGoR consortium
url: https://gregorconsortium.org/
identifier_prefix: https://gregorconsortium.org/fhir
output_filename: gregor
id_colname: subject_id
whistle_src: _cmg.wstl
study_sponsor:
  id: nhgri
  name: National Human Genome Research Institute (NHGRI)
code_harmonization_dir: harmony/gregor
require_official: True
curies:
  http://purl.obolibrary.org/obo/hp.owl: HP
  http://purl.obolibrary.org/obo/mondo.owl: MONDO
projector_lib: projector
env:
  local: dev
  dev: dev
  qa: google
  prod: google
dataset:
  participant: 
    filename: None
    data_dictionary: 
      filename:  data/dd/gregor_data_model/participant.csv
      colnames:
        variable_name: varname
        description: desc
        data_type: type
        enumerations: values
    code_harmonization: harmony/gregor/data-harmony.csv
  analyte: 
    filename: None
    data_dictionary: 
      filename:  data/dd/gregor_data_model/analyte.csv
      colnames:
        variable_name: varname
        description: desc
        data_type: type
        enumerations: values
    code_harmonization: harmony/gregor/data-harmony.csv
  aligned_dna_short_read_set: 
    filename: None
    data_dictionary: 
      filename:  data/dd/gregor_data_model/aligned_dna_short_read_set.csv
      colnames:
        variable_name: varname
        description: desc
        data_type: type
        enumerations: values
    code_harmonization: harmony/gregor/data-harmony.csv
  called_variants_dna_short_read: 
    filename: None
    data_dictionary: 
      filename:  data/dd/gregor_data_model/called_variants_dna_short_read.csv
      colnames:
        variable_name: varname
        description: desc
        data_type: type
        enumerations: values
    code_harmonization: harmony/gregor/data-harmony.csv
  experiment_dna_short_read: 
    filename: None
    data_dictionary: 
      filename:  data/dd/gregor_data_model/experiment_dna_short_read.csv
      colnames:
        variable_name: varname
        description: desc
        data_type: type
        enumerations: values
    code_harmonization: harmony/gregor/data-harmony.csv
  family:
    filename: None
    data_dictionary: 
      filename:  data/dd/gregor_data_model/family.csv
      key_columns: family_id
      colnames:
        variable_name: varname
        description: desc
        data_type: type
        enumerations: values
    code_harmonization: harmony/gregor/data-harmony.csv
  phenotype:
    filename: None
    data_dictionary: 
      filename:  data/dd/gregor_data_model/phenotype.csv
      colnames:
        variable_name: varname
        description: desc
        data_type: type
        enumerations: values
    code_harmonization: harmony/gregor/data-harmony.csv
active_tables:
  ALL: true