gru.yaml

study_id: CMG
study_accession:  phs000744
study_title: Yale Center for Mendelian Genomics (Y 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://medicine.yale.edu/keck/ycga/mendelian/
identifier_prefix: https://ycmg.org/fhir
output_filename: ycmg-gru
id_colname: ParticipantID
whistle_src: _cmg.wstl
study_sponsor:
  id: nhgri
  name: National Human Genome Research Institute (NHGRI)
consent_group: 
  code: GRU
  name: general research use and clinical care
  description: For health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.
code_harmonization_dir: harmony
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/gru/Subject_CMG_Yale_phs000744_GRU_20201218_Y9Q1.csv
    data_dictionary: 
      filename:  data/subject-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/cmg-harmony.csv
  sample: 
    filename: data/gru/Sample_CMG_Yale_phs000744_GRU_20201218_Y9Q1.csv
    data_dictionary: 
      filename:  data/sample-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/cmg-harmony.csv
  sequencing: 
    filename: data/gru/Sequencing_CMG_Yale_phs000744_GRU_20201218_Y9Q1.csv
    embed:
      dataset: sample
      colname: sample_id
    data_dictionary: 
      filename:  data/sequencing-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/cmg-harmony.csv
  family:
    filename: data/gru/Family_CMG_Yale_phs000744_GRU_20201218_Y9Q1.csv
    data_dictionary: 
      filename:  data/family-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/cmg-harmony.csv
  discovery:
    filename: data/gru/Discovery_CMG_Yale_phs000744_GRU_20201218_Y9Q1.csv
    data_dictionary: 
      filename:  data/discovery-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/cmg-harmony.csv
  conditions:
    filename: data/gru/conditions-gru.csv
    data_dictionary: 
      filename: data/conditions-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/cmg-harmony.csv
  diseases:
    filename: data/gru/diseases-gru.csv
    data_dictionary: 
      filename: data/disease-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/cmg-harmony.csv
active_tables:
  ALL: true