teamds.yaml

study_id: TEAM-DS
study_accession:  
study_title: TBD
study_desc: TBD
url: TBD
identifier_prefix: https://includedcc.org/fhir/teamds
dd_prefix: https://includedcc.org/fhir
output_filename: teamds
id_colname: Participant ID
whistle_src: _entry.wstl
annotations:
  virtual_biorepository:
    email: TBD
    url: TBD
    readme: TBD
code_harmonization_dir: harmony/teamds
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
projector_lib: projector
env:
  local: dev0
  dev: dev0
  qa: qa-kf2-inc
  prod: prod-kf2-inc
dataset:
  study_meta: 
    filename: data/tables/TEAM-DS/study.csv
    data_dictionary:
      filename: data/dd/study.csv
    code_harmonization: harmony/teamds/data-harmony.csv
  dataset_meta:
    filename: data/tables/TEAM-DS/datasets.csv
    data_dictionary: 
      filename: data/dd/dataset_meta.csv
    code_harmonization: harmony/teamds/data-harmony.csv
    embed:
      dataset: study_meta
      colname: Study Code
  study_contacts:
    hidden: true
    filename: data/tables/TEAM-DS/contacts.csv
    data_dictionary: 
      filename: data/dd/contacts.csv
    code_harmonization: harmony/teamds/data-harmony.csv
    embed:
      dataset: study_meta
      colname: Study Code
  participant:
    filename: data/tables/TEAM-DS/teamds_participant_harmonized_2024-04-12.csv
    data_dictionary: 
      filename: data/dd/participant.csv
    code_harmonization: harmony/teamds/data-harmony.csv
  condition:
    filename: data/tables/TEAM-DS/teamds_structured_conditions_bmi_2024-04-23.csv
    embed:
      dataset: participant
      colname: Participant External ID
    data_dictionary: 
      filename: data/dd/condition.csv
    code_harmonization: harmony/teamds/data-harmony.csv
  encounter:
    hidden: true
    filename: data/tables/TEAM-DS/encounter.csv
    data_dictionary: 
      filename: data/dd/encounter.csv
    code_harmonization: harmony/teamds/data-harmony.csv
  family:
    hidden: true
    #group_by: Family ID,Family Type
    filename: data/tables/TEAM-DS/family.csv  
    data_dictionary: 
      filename: data/dd/family.csv
    code_harmonization: harmony/teamds/data-harmony.csv