bh-hmb-npu.yaml

study_id: BHCMG
study_accession:  phs000744
study_title: Baylor-Hopkins Center for Mendelian Genomics (BHCMG)
study_desc: Johns Hopkins and Baylor College of Medicine have received NIH-NHGRI grant support for the creation of a Center for Mendelian Genomics (CMG) to help “solve” Mendelian disorders for which the genetic etiology is presently unknown.
url: https://mendeliangenomics.org/
identifier_prefix: https://mendeliangenomics.org/fhir/bh-hmb-npu
dd_prefix: http://mendelian.org/fhir
output_filename: bhcmg-hmb-npu
id_colname: ParticipantID
whistle_src: _cmg.wstl
study_sponsor:
  id: nhgri
  name: National Human Genome Research Institute (NHGRI)
consent_group: 
  code: HMB-NPU
  name: https://omim.org/
  description: For health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.
code_harmonization_dir: harmony/bh
require_official: True
curies:
  http://purl.obolibrary.org/obo/hp.owl: HP
  http://purl.obolibrary.org/obo/mondo.owl: MONDO
env:
  local: dev
  dev: dev
  qa: anvil-demo
  prod: anvil-demo
projector_lib: projector
dataset:
  subject: 
    filename: data/bh/hmb-npu/hmb-npu-subject.csv.dupes-removed
    data_dictionary: 
      filename:  data/subject-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/bh/cmg-harmony.csv
  sample: 
    filename: data/bh/hmb-npu/hmb-npu-sample.csv.dupes-removed
    data_dictionary: 
      filename:  data/sample-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/bh/cmg-harmony.csv
  sequencing: 
    filename: data/bh/hmb-npu/hmb-npu-sequencing.csv.dupes-removed
    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/bh/cmg-harmony.csv
  family:
    filename: data/bh/hmb-npu/hmb-npu-family.csv
    data_dictionary: 
      filename:  data/family-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/bh/cmg-harmony.csv
  discovery:
    filename: data/bh/hmb-npu/hmb-npu-discovery.csv
    data_dictionary: 
      filename:  data/discovery-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/bh/cmg-harmony.csv
  conditions:
    filename: data/bh/hmb-npu/conditions-bh-hmb-npu.csv
    data_dictionary: 
      filename: data/conditions-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/bh/cmg-harmony.csv
  diseases:
    filename: data/bh/hmb-npu/diseases-bh-hmb-npu.csv
    data_dictionary: 
      filename: data/disease-dd.csv
      colnames:
        varname: variable_name
        desc: description
        type: data_type
        values: enumerations
    code_harmonization: harmony/bh/cmg-harmony.csv
active_tables:
  ALL: true