The current version of the loader offers two different loading alternatives: (v0) loading of clinical and genomic data based on MAF datasets; and (v1) loading of generic i2b2 data. Currently these two loaders support each one dataset:
v0: a genomic dataset (tcga_cbio publicly available in cBioPortal)
v1: the i2b2 demodata.
Future releases of this software will allow for other arbitrary data sources, given that they follow a specific structure (e.g. BAM format).
From the medco-deployment folder, execute the resources/data/download.sh script to download the test datasets.
The provided example data set files come with dummy data pre-generated. Those data are random dummy entries whose purpose is to prevent frequency attacks. In a future release, the generation will be done dynamically by the loader.
The v0 loader expects an ontology, with mutation and clinical data in the MAF format. As the ontology data you must use ${MEDCO_SETUP_DIR}/resources/data/genomic/tcga_cbio/clinical_data.csv and ${MEDCO_SETUP_DIR}/resources/data/genomic/tcga_cbio/mutation_data.csv. For clinical data you can keep using the same two files or a subset of the data (e.g. 8_clinical_data.csv). More information about how to generate sample data files can be found below. After the following script is executed all the data is encrypted and deterministically tagged in compliance with the MedCo data model.
Ensure you have downloaded the data before proceeding to the loading.
The following examples show you how to load data into a running MedCo deployment. Adapt accordingly the commands your use-case.
To check that it is working you can query for:
-> MedCo Gemomic Ontology -> Gene Name -> BRPF3
For the small dataset 8_xxxx you should obtain 3 matching subjects (one at each site).
The v1 loader expects an already existing i2b2 database (in .csv format) that will be converted in a way that is compliant with the MedCo data model. This involves encrypting and deterministically tagging some of the data.
List of input (‘original’) files:
all i2b2metadata files (e.g. i2b2.csv)
dummy_to_patient.csv
patient_dimension.csv
visit_dimension.csv
concept_dimension.csv
modifier_dimension.csv
observation_fact.csv
table_access.csv
Ensure you have downloaded the data before proceeding to the loading.
The following examples show you how to load data into a running MedCo deployment. Adapt accordingly the commands your use-case.
To check that it is working you can query for:
-> Diagnoses -> Neoplasm -> Benign neoplasm -> Benign neoplasm of breast
You should obtain 2 matching subjects.