htp-filemanifest.yaml

study_id: HTP
study_accession: phs002330 
study_title: Crnic Institute Human Trisome Project
study_desc: TBD
url: https://includedcc.org/studies/human-trisome-project
identifier_prefix: https://include.org/htp/fhir
output_filename: htp-file-manifest
id_colname: ParticipantID
whistle_src: _htp.wstl
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:
  participant:
    filename: data/csv/participant.csv
    data_dictionary: 
      filename: data/csv/dd/participant-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/htp-harmony.csv
  condition: 
    filename: data/csv/condition.csv
    data_dictionary: 
      filename:  data/csv/dd/condition-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/htp-harmony.csv
  ds_condition: 
    filename: data/csv/ds_condition.csv
    data_dictionary: 
      filename:  data/csv/dd/ds_condition-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/htp-harmony.csv
  encounter:
    filename: data/csv/encounter.csv
    data_dictionary: 
      filename:  data/csv/dd/encounter-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/htp-harmony.csv
  additive:
    filename: data/csv/biospecimen-20220303.5/additive.csv
    data_dictionary:
      filename: data/csv/biospecimen-20220303.5/additive-dd.csv
      colnames: 
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/htp-harmony.csv        
  specimen:
    filename: data/csv/biospecimen-20220303.5/htp_sample.csv,data/csv/biospecimen-20220303.5/updated-htp_sample_collection_supplement.csv
    data_dictionary:
      filename: data/csv/biospecimen-20220303.5/htp_sample-dd.csv
      colnames: 
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/htp-harmony.csv        
  aliquot:
    filename: data/csv/biospecimen-20220303.5/aliquot.csv
    group_by: Sample ID
    data_dictionary:
      filename: data/csv/biospecimen-20220303.5/aliquot-dd.csv
      colnames: 
        varname: varname
        desc: vardesc
        type: type
        values: values
    code_harmonization: harmony/htp-harmony.csv  
  kf-manifests:
    filename: data/csv/updated-kf-file-manifests.csv,data/csv/updated-kf-file-manifests-rna.csv,data/csv/updated-kf-omics.csv
    data_dictionary:
      filename: data/csv/updated-kf-file-manifests-dd.csv
      colnames:
        varname: varname
        desc: vardesc
        type: type
        values: values
      code_harmonization: harmony/htp-harmony.csv    
active_tables:
  study: true
  code-systems: false
  data-dictionary: false
  participant: false
  encounter: false
  condition: false
  ds_condition: false
  harmony: false
  additive: false
  specimen: false
  aliquot: false
  kf-manifests: true