dsc.yaml

study_id: DSC
study_accession:  
study_title: DS-Connect-The Down Syndrome Registry
study_desc: The Down Syndrome Registry are to better understand the health of people with Down syndrome and to inform eligible participants who, based on their health history, may be a match for research studies or new clinical trials.
url: https://includedcc.org/studies/ds-connect
identifier_prefix: https://includedcc.org/fhir/dsc
dd_prefix: https://includedcc.org/fhir
output_filename: dsc
id_colname: Participant ID

projection_version: current
whistle_src: _entry.wstl

# This is where the harmony file will be written 
code_harmonization_dir: harmony/dsc

# This is the prefix associated with the final study harmony file
# This must match whatever is used in the whistle code (which is data-harmony
# at this time)
harmony_prefix: data-harmony

# List each file required to support the level of harmonized terms required
# by this project. 
code_harmonization: 
 - harmony/study.csv
 - harmony/dataset.csv
 - harmony/demographics.csv
 - harmony/encounter.csv
 - harmony/misc.csv
 - harmony/specimen.csv
 - harmony/dsc-conditions.csv
projections: 
  study: projector/study_only
  dataset: projector/dataset
  harmonized: projector/harmonized

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
env:
  local: dev
  dev: dev
  qa: qa-kf2-inc
  prod: prod-kf2-inc
dataset:
  study_meta: 
    filename: data/tables/DSC/study.csv
    data_dictionary:
      filename: data/dd/study.csv
  study_contacts:
    hidden: true
    filename: data/tables/DSC/contacts.csv
    data_dictionary: 
      filename: data/dd/contacts.csv
    embed:
      dataset: study_meta
      colname: Study Code
  dataset_manifest:
    filename: data/tables/DSC/dsc_unharmonized_clinical_dataset_manifest_2024-10-08.csv
    data_dictionary: 
      filename: data/dd/dataset_manifest.csv
    embed:
      dataset: dataset_meta
      colname: Dataset External ID
  dataset_meta:
    filename: data/tables/DSC/datasets.csv
    data_dictionary:
      filename: data/dd/dataset_meta.csv
  dataset_file_manifest:
    filename: data/tables/DSC/dsc_unharmonized_clinical_datafiles_2024-10-08.csv
    data_dictionary:
      filename: data/dd/datafile.csv
  participant:
    filename: data/tables/DSC/dsc_participant_harmonized_2024-04-12.csv
    data_dictionary: 
      filename: data/dd/participant.csv
  condition:
    filename: data/tables/DSC/dsc_condition_harmonized_2024-04-12.csv
    embed:
      dataset: participant
      colname: Participant External ID
    data_dictionary: 
      filename: data/dd/condition.csv
  encounter:
    hidden: true
    filename: data/tables/DSC/encounter.csv    
    data_dictionary: 
      filename: data/dd/encounter.csv
  family:
    hidden: true
    #group_by: Family ID,Family Type
    filename: data/tables/DSC/family.csv    
    data_dictionary: 
      filename: data/dd/family.csv
  specimen:
    filename: None
    data_dictionary:
      filename: data/dd/specimen.csv
  file_manifest:
    filename: None
    data_dictionary:
      filename: data/dd/datafile.csv
active_tables:
  ALL: true
#  family: true