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x01-hakon.yaml
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x01-hakon.yaml
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study_id: X01-Hakonarson
study_accession: phs002983
study_title: Genetic Underpinnings of the Multifactorial Phenotype of Trisomy 21 Patients Unveiled by Multi-Omics Approaches
study_desc:
url:
identifier_prefix: https://includedcc.org/fhir/x01-hakon
dd_prefix: https://includedcc.org/fhir
output_filename: x01-hakon
id_colname: Participant ID
whistle_src: _entry.wstl
annotations:
virtual_biorepository:
email: [email protected]
code_harmonization_dir: harmony/x01-hakon
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/X01-Hakon/study.csv
data_dictionary:
filename: data/dd/study.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
dataset_meta:
filename: data/tables/X01-Hakon/datasets.csv
data_dictionary:
filename: data/dd/dataset_meta.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
embed:
dataset: study_meta
colname: Study Code
study_contacts:
hidden: true
filename: data/tables/X01-Hakon/contacts.csv
data_dictionary:
filename: data/dd/contacts.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
embed:
dataset: study_meta
colname: Study Code
participant:
filename: data/tables/X01-Hakon/participant.csv
data_dictionary:
filename: data/dd/participant.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
condition:
filename: data/tables/X01-Hakon/condition.csv
embed:
dataset: participant
colname: Participant External ID
data_dictionary:
filename: data/dd/condition.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
encounter:
hidden: true
filename: data/tables/X01-Hakon/encounter.csv
data_dictionary:
filename: data/dd/encounter.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
family:
hidden: true
#group_by: Family ID,Family Type
filename: data/tables/X01-Hakon/family.csv
data_dictionary:
filename: data/dd/family.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
specimen:
filename: data/tables/X01-Hakon/FV_CFPDTD0T_hakon_biospecimen_manifest.csv
# group_by: Participant External ID, Sample External ID
embed:
dataset: participant
colname: Participant External ID
data_dictionary:
filename: data/dd/specimen.csv
code_harmonization: harmony/x01-hakon/data-harmony.csv
file_manifest:
#filename: data/tables/X01-Hakon/final_hakon_datafile_manfiest_w_controlled_and_registered_data_v2.csv
filename: data/tables/X01-Hakon/hakon_file_manifest_controlled-20240314.csv,data/tables/X01-Hakon/hakon_file_manifest_registered-20240314.csv
# filename: data/tables/X01-Hakon/hakon_file_manifest_registered-20240314.csv
data_dictionary:
filename: data/dd/datafile.csv
group_by: File External ID
code_harmonization: harmony/x01-hakon/data-harmony.csv
active_tables:
ALL: true
#only_study:
# study_meta: true
# study_contacts: true
# ALL: true
# family: true