1 of 3

Data Loading

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).

Pre-Requisite: Download test data

From the medco-deployment folder, execute the resources/data/download.sh script to download the test datasets.

cd ${MEDCO_SETUP_DIR}/resources/data
bash download.sh

Dummy Generation

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.

v0 (Genomic Data)

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.

How to use

Ensure you have 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.

Examples

Loading the three nodes on the dev-local-3nodes profile

Loading one node on a network-test profile

Explanation of the command's arguments

Test that the loading was successful

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).

v1 (I2B2 Demodata)

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

How to use

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.

Examples

Loading the three nodes on the dev-local-3nodes profile

export MEDCO_SETUP_DIR=~/medco-deployment \
    MEDCO_DEPLOYMENT_PROFILE=dev-local-3nodes
cd "${MEDCO_SETUP_DIR}/compose-profiles/${MEDCO_DEPLOYMENT_PROFILE}"
docker-compose -f docker-compose.tools.yml run medco-loader-srv0 v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml
docker-compose -f docker-compose.tools.yml run medco-loader-srv1 v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml
docker-compose -f docker-compose.tools.yml run medco-loader-srv2 v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml

Loading one node on a network-test profile

export MEDCO_SETUP_DIR=~/medco-deployment \
    MEDCO_DEPLOYMENT_PROFILE=test-network-xxx-node0
cd "${MEDCO_SETUP_DIR}/compose-profiles/${MEDCO_DEPLOYMENT_PROFILE}"
docker-compose -f docker-compose.tools.yml run medco-loader v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml

Explanation of the command's arguments

NAME:
    medco-loader v1 - Convert existing i2b2 data model

USAGE:
    medco-loader v1 [command options] [arguments...]

OPTIONS:
    --group value, -g value               UnLynx group definition file
    --entryPointIdx value, --entry value  Index (relative to the group definition file) of the collective authority server to load the data
    --sensitive value, --sen value        File containing a list of sensitive concepts
    --dbHost value, --dbH value           Database hostname
    --dbPort value, --dbP value           Database port (default: 0)
    --dbName value, --dbN value           Database name
    --dbUser value, --dbU value           Database user
    --dbPassword value, --dbPw value      Database password
    --files value, -f value               Configuration toml with the path of the all the necessary i2b2 files
    --empty, -e                           Empty patient and visit dimension tables (y/n)

Test that the loading was successful

To check that it is working you can query for:

-> Diagnoses -> Neoplasm -> Benign neoplasm -> Benign neoplasm of breast

You should obtain 2 matching subjects.

v1 (I2B2 Demodata)

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

How to use

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.

Examples

Loading the three nodes on the dev-local-3nodes profile

export MEDCO_SETUP_DIR=~/medco-deployment \
    MEDCO_DEPLOYMENT_PROFILE=dev-local-3nodes
cd "${MEDCO_SETUP_DIR}/compose-profiles/${MEDCO_DEPLOYMENT_PROFILE}"
docker-compose -f docker-compose.tools.yml run medco-loader-srv0 v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml
docker-compose -f docker-compose.tools.yml run medco-loader-srv1 v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml
docker-compose -f docker-compose.tools.yml run medco-loader-srv2 v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml

Loading one node on a network-test profile

export MEDCO_SETUP_DIR=~/medco-deployment \
    MEDCO_DEPLOYMENT_PROFILE=test-network-xxx-node0
cd "${MEDCO_SETUP_DIR}/compose-profiles/${MEDCO_DEPLOYMENT_PROFILE}"
docker-compose -f docker-compose.tools.yml run medco-loader v1 \
    --sen /data/i2b2/sensitive.txt \
    --files /data/i2b2/files.toml

Explanation of the command's arguments

NAME:
    medco-loader v1 - Convert existing i2b2 data model

USAGE:
    medco-loader v1 [command options] [arguments...]

OPTIONS:
    --group value, -g value               UnLynx group definition file
    --entryPointIdx value, --entry value  Index (relative to the group definition file) of the collective authority server to load the data
    --sensitive value, --sen value        File containing a list of sensitive concepts
    --dbHost value, --dbH value           Database hostname
    --dbPort value, --dbP value           Database port (default: 0)
    --dbName value, --dbN value           Database name
    --dbUser value, --dbU value           Database user
    --dbPassword value, --dbPw value      Database password
    --files value, -f value               Configuration toml with the path of the all the necessary i2b2 files
    --empty, -e                           Empty patient and visit dimension tables (y/n)

Test that the loading was successful

To check that it is working you can query for:

-> Diagnoses -> Neoplasm -> Benign neoplasm -> Benign neoplasm of breast

You should obtain 2 matching subjects.

v0 (Genomic Data)

How to use

Ensure you have 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.

Examples

Loading the three nodes on the dev-local-3nodes profile

Loading one node on a network-test profile

export MEDCO_SETUP_DIR=~/medco-deployment \
    MEDCO_DEPLOYMENT_PROFILE=test-network-xxx-node0
cd "${MEDCO_SETUP_DIR}/compose-profiles/${MEDCO_DEPLOYMENT_PROFILE}"
docker-compose -f docker-compose.tools.yml run medco-loader v0 \
    --ont_clinical /data/genomic/tcga_cbio/8_clinical_data.csv \
    --sen /data/genomic/sensitive.txt \
    --ont_genomic /data/genomic/tcga_cbio/8_mutation_data.csv \
    --clinical /data/genomic/tcga_cbio/8_clinical_data.csv \
    --genomic /data/genomic/tcga_cbio/8_mutation_data.csv \
    --output /data/

Explanation of the command's arguments

NAME:
    medco-loader v0 - Load genomic data (e.g. tcga_bio dataset)

USAGE:
    medco-loader v0 [command options] [arguments...]

OPTIONS:
    --group value, -g value               UnLynx group definition file
    --entryPointIdx value, --entry value  Index (relative to the group definition file) of the collective authority server to load the data
    --sensitive value, --sen value        File containing a list of sensitive concepts
    --dbHost value, --dbH value           Database hostname
    --dbPort value, --dbP value           Database port (default: 0)
    --dbName value, --dbN value           Database name
    --dbUser value, --dbU value           Database user
    --dbPassword value, --dbPw value      Database password
    --ont_clinical value, --oc value      Clinical ontology to load
    --ont_genomic value, --og value       Genomic ontology to load
    --clinical value, --cl value          Clinical file to load
    --genomic value, --gen value          Genomic file to load
    --output value, -o value              Output path to the .csv files

Test that the loading was successful

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).