BIOMAP Data and Analysis Portal


image alt < BIOMAP Data and Analysis Portal is developed to establish, populate and maintain a robust and secure data management and analysis system in WP2 - Task 2.2. The data portal will provide easy and robust interface for the input of new clinical and molecular data. A researcher will be able to perform cross-study comparisons; slice and dice the cohorts based on certain clinical features and run in-built workflows.

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BIOMAP Data Capture and Upload


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"Data and knowledge generated within BIOMAP project [...] will be shared and made accessible through a secure and encrypted channel.” ―(from the BIOMAP proposal).

WP2 has set up a number of services to facilitate providing data in a structured way and complying with legal requirements as identified by WP8. Detailed instructions and access to the upload platforms are summarized in this section.

BIOMAP-LUMS Account


image alt < LUMS is UL’s centralized identity management system for signing into UL hosted BIOMAP services including OwnCloud, REDCap, GitLab, ADA and tranSMART. BIOMAP members can select different services and request for a LUMS account using the following link. You can also request to enable services for your existing LUMS account using the same link.

Legal Agreement


To complete required legal procedures to upload sensitive data, you should consult with the Data Protection Officer (DPO) of your institution. For further clarification please consult BIOMAP Legal Help (UniVie). Please upload the signed Data Protection Sheet and other legal data to BIOMAP’s ownCloud server.

Cohort Metadata


Cohort metadata describing the information that gets collected, such as the clinical variables and their format, OMICS platform types or chip models etc, can be shared with the consortium without the need of a data processing/sharing agreement, since this metadata does not contain information about individuals. This section contains detailed information on providing such metadata.

Data Upload


Data contributors will upload their data to UL’s data provenance using encrypted transfer through Download Upload Manager (DUMA) service at UL. DUMA can be accessed through web-browser or command line interface. To upload data please follow the detailed instruction below.

To upload Biobank Biosample Metadata please follow the instruction below.

BIOMAP Data Management and Access


image alt < BIOMAP Consortium members can access the uploaded datasets and run analysis through web-based interfaces like tranSMART and ADA. They will be able to perform cross-study comparisons; slice and dice the cohorts based on certain clinical features and run in-built workflows. The raw data can also be downloaded locally for analysis.

ADA


Ada is a performant and highly configurable system for secured integration, visualization, and collaborative analysis of heterogeneous data sets.

Ada status

tranSMART


tranSMART is a modular open source software platform for feasibility queries, exploration and analysis of clinical, translational and genomics data.

tranSMART Status

Raw data


Raw datasets (OMICS and Clinical) for offline data-analysis is also available for consortium members on request using encrypted transfer through Download Upload Manager (DUMA) service at UL.

BIOMAP GitLab Code Repository


image alt < BIOMAP Consortium members can share and collaborate on BIOMAP-GitLab Code Repository hosted at UL-R3 GitLab instance.

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