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BIOMAP Data Platform

BIOMAP data platform is developed to establish, populate and maintain a robust and secure data management and analysis system in WP2 - Task 2.2. The data platform provides an easy and robust interface for uploading and accessing the 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.

flowchart LR
up[fa:fa-user-circle<br />Data<br />uploader]
user[fa:fa-user-astronaut<br />Data<br />explorer]
    cohort[Cohort<br />metadata]
    dish[fa:fa-file-excel DISH or <br />Appendix B]
    data[fa:fa-file-archive Clinical <br />& omics<br />data]
    meta[fa:fa-file-excel Omics<br />metadata]
    vbb[fa:fa-file-excel Sample<br />metadata]
  subgraph DU[ ]
    DYD([Data capture & upload])
    RC(fa:fa-cubes Cohort<br />REDCap EDC)
    LFT(fa:fa-coins Data<br />storage)
    VB(fa:fa-cubes Virtual<br />biobank<br/>REDCap EDC)
  subgraph DCZ[ ]
    DCZZ([Data access])
    catalog[fa:fa-database<br />Cohort catalog]
    tm[fa:fa-desktop<br />tranSMART]
    ada[fa:fa-desktop<br />Ada]
up --> cohort
up --> dish
up --> data
up --> meta
up --> vbb
cohort --> |"fa:fa-hands-helping<br />----"| RC
dish --> |"fa:fa-upload<br />----"| RC
data --> |"fa:fa-link<br />----"|LFT
meta --> |"fa:fa-link<br />----"|LFT
vbb --> |"fa:fa-hands-helping<br />----"| VB
RC --> catalog
LFT --> catalog
LFT --> tm
LFT --> ada
VB --> ada
catalog -.- |"fa:fa-hands-helping<br />----"| user
tm -.- |"fa:fa-hands-helping<br />----"| user
ada -.- |"fa:fa-hands-helping<br />----"| user

: Login with LUMS is required
: File upload from web-browser
: Upload through LFT Link

Table of contents

  1. BIOMAP-LUMS account
  2. BIOMAP data capture and upload
  3. BIOMAP data access


LUMS is LCSB’s User Management System for accessing the BIOMAP data platform services including the cohort catalog, REDCap, GitLab, Ada and tranSMART. BIOMAP members can make a request for a LUMS account using the following link. Account holders can use the same link for their account reactivation or password change request.

Create ticket

BIOMAP data capture and upload

“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 summarised in this section.

Data and metadata upload

Data owners will upload their data to UL’s data platform using encrypted transfer through the LCSB File Transfer (LFT) service at UL. LFT can be accessed through a web-browser or a command line interface. To upload data please follow the detailed instruction below.

Data upload

BIOMAP Virtual Biobank

To develop a common standard in the BIOMAP Consortium for biobanks’ biospecimen summary data, collectively known as sample-metadata, a catalog solution has been created for sample-metadata and a generic workflow for sample requests will be added shortly.

Biobanking metadata

BIOMAP data access

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

BIOMAP cohort catalog


BIOMAP cohort catalog displays summary cohort information and enables consortium members to download raw and processed data where available. Consortium members can search, filter, and select datasets based on various parameters.

Cohort catalog Login with LUMS


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

tranSMART Login with LUMS


coming soon

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

Ada Login with LUMS

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This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 821511. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA.