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htp.yaml
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htp.yaml
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study_id: HTP
study_accession: phs002330
study_title: Crnic Institute Human Trisome Project
study_desc: The Crnic Institute Human Trisome Project® (HTP) is an in-depth study of people with Down syndrome using the latest technologies in precision medicine.
url: https://includedcc.org/studies/human-trisome-project
identifier_prefix: https://includedcc.org/fhir/htp
dd_prefix: https://includedcc.org/fhir
output_filename: htp
id_colname: Participant ID
whistle_src: _entry.wstl
annotations:
virtual_biorepository:
email: [email protected]
url: https://redcap.link/HTPVBRrequest
readme: To request biospecimens from the HTP biobank, please use the request form (https://redcap.link/HTPVBRrequest). General inquiries can be directed to [email protected].
code_harmonization_dir: harmony/htp
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/HTP/study.csv
data_dictionary:
filename: data/dd/study.csv
code_harmonization: harmony/htp/data-harmony.csv
dataset_meta:
filename: data/tables/HTP/datasets.csv
data_dictionary:
filename: data/dd/dataset_meta.csv
code_harmonization: harmony/htp/data-harmony.csv
embed:
dataset: study_meta
colname: Study Code
study_contacts:
hidden: true
filename: data/tables/HTP/contacts.csv
data_dictionary:
filename: data/dd/contacts.csv
code_harmonization: harmony/htp/data-harmony.csv
embed:
dataset: study_meta
colname: Study Code
participant:
#filename: data/tables/HTP/vbr_participants_harmonized_final_na_2023-11-07.csv
filename: data/tables/HTP/htp_v4_participant_updated_2024-06-21.csv
#filename: data/tables/HTP/vbr_participants_harmonized_final.csv
data_dictionary:
filename: data/dd/participant.csv
code_harmonization: harmony/htp/data-harmony.csv
condition:
filename: data/tables/HTP/vbr_participants_conditions.csv
embed:
dataset: participant
colname: Participant External ID
data_dictionary:
filename: data/dd/condition.csv
code_harmonization: harmony/htp/data-harmony.csv
encounter:
hidden: true
filename: data/tables/HTP/encounter.csv
data_dictionary:
filename: data/dd/encounter.csv
code_harmonization: harmony/htp/data-harmony.csv
family:
hidden: true
#group_by: Family ID,Family Type
filename: data/tables/HTP/family.csv
data_dictionary:
filename: data/dd/family.csv
code_harmonization: harmony/htp/data-harmony.csv
additive:
hidden: true
filename: data/tables/HTP/additive.csv
key_columns: Additive ID
data_dictionary:
filename: data/dd/additive.csv
code_harmonization: harmony/htp/data-harmony.csv
specimen:
#filename: data/tables/HTP/vbr_biospecimens_harmonized_2023-10-05.csv
filename: data/tables/HTP/vbr_biospecimens_harmonized_20231116.csv
subject_id: Participant External ID
key_columns: Sample Global ID
group_by: Participant External ID, Sample External ID
data_dictionary:
filename: data/dd/specimen.csv
code_harmonization: harmony/htp/data-harmony.csv
file_manifest:
#filename: data/tables/HTP/htp_v5_datafile_manifest_new_data_updated_descriptors.csv
# The following represents all of the File Manifests, including the one we have loaded and deleted repeatedly
filename: data/tables/HTP/htp_v1_omics_datafiles_2023-10-10.csv,data/tables/HTP/FV_PJ79R4DY_FV_9Q2N4BTN_FV_7MVH1YCE_htp_datafile_manifest_w_crnic_files_v5.csv,data/tables/HTP/htp_v5_datafile_manifest_new_data_controlled_access_only.csv,data/tables/HTP/htp_v5_datafile_manifest_new_data_updated_registered_access_only.csv
# This represents all data that is currently accessible as of Mar 2024
# filename: data/tables/HTP/htp_v1_omics_datafiles_2023-10-10.csv,data/tables/HTP/FV_PJ79R4DY_FV_9Q2N4BTN_FV_7MVH1YCE_htp_datafile_manifest_w_crnic_files_v5.csv,data/tables/HTP/htp_v5_datafile_manifest_new_data_updated_registered_access_only.csv
group_by: File External ID
data_dictionary:
filename: data/dd/datafile.csv
code_harmonization: harmony/htp/data-harmony.csv
active_tables:
ALL: true
# family: true