bri-dsr.yaml

study_id: BRI-DSR
study_accession:  
study_title: Benaroya Research Institute Down Syndrome Registry
study_desc: The Down syndrome registry at Benaroya Research Institute (BRI) builds on institutional expertise to collect and analyze longitudinal biological samples and concomitant clinical metadata across the lifespan of people with Down syndrome. 
url: https://includedcc.org/studies/benaroya-research-institute-bri
identifier_prefix: https://includedcc.org/fhir/bri-dsr
dd_prefix: https://includedcc.org/fhir
output_filename: bri-dsr
id_colname: Participant ID
whistle_src: _entry.wstl
code_harmonization_dir: harmony/bri-dsr
require_official: True
curies:
  http://purl.obolibrary.org/obo/hp.owl: HP
  http://purl.obolibrary.org/obo/mondo.owl: MONDO
  http://purl.obolibrary.org/obo/maxo.owl: MAXO
  http://purl.obolibrary.org/obo/ncit.owl: NCIT
projector_lib: projector
env:
  local: dev0
  dev: dev0
  qa: qa-kf2-inc
  prod: prod-kf2-inc
dataset:
  study_meta: 
    filename: data/tables/BRI-DSR/study.csv
    data_dictionary:
      filename: data/dd/study.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
  dataset_meta:
    filename: data/tables/BRI-DSR/datasets.csv
    data_dictionary: 
      filename: data/dd/dataset_meta.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
    embed:
      dataset: study_meta
      colname: Study Code
  study_contacts:
    hidden: true
    filename: data/tables/BRI-DSR/contacts.csv
    data_dictionary: 
      filename: data/dd/contacts.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
    embed:
      dataset: study_meta
      colname: Study Code
  participant:
    filename: data/tables/BRI-DSR/participant.csv
    data_dictionary: 
      filename: data/dd/participant.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
  condition:
    filename: data/tables/BRI-DSR/condition.csv
    embed:
      dataset: participant
      colname: Participant External ID
    data_dictionary: 
      filename: data/dd/condition.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
  encounter:
    hidden: true
    filename: data/tables/BRI-DSR/encounter.csv    
    data_dictionary: 
      filename: data/dd/encounter.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
  family:
    hidden: true
    #group_by: Family ID,Family Type
    filename: data/tables/BRI-DSR/family.csv    
    data_dictionary: 
      filename: data/dd/family.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
  specimen:
    filename: data/tables/BRI-DSR/FV_DYE2YKY2_FV_8ZY1CTV2_khor_biospecimen_manifest_draft_age_days.csv
    data_dictionary:
      filename: data/dd/specimen.csv
    embed:
      dataset: participant
      colname: Participant External ID
    code_harmonization: harmony/bri-dsr/data-harmony.csv
  file_manifest:
    filename: data/tables/BRI-DSR/FV_XS4Q6649_FV_XAS6JTHQ_brids_data_file_manifest_v3.csv
    group_by: File External ID
    data_dictionary:
      filename: data/dd/datafile.csv
    code_harmonization: harmony/bri-dsr/data-harmony.csv
active_tables:
  ALL: true
#  family: true