tranSMART

Mariska Bierkens<fnref n="1" />*, Wim van der Linden², Kees van Bochove³, Ward Weistra³, Remond J.A. Fijneman<fnref n="1" />, Rita Azevedo⁴, Jan-Willem Boiten⁵, Jeroen Beliën<fnref n="1" />, Gerrit A. Meijer<fnref n="1" />

From 1st Clinical Research Informatics (CRI) Solutions Day
Duesseldorf, Germany. 26-27 May 2014

**Characterisation**

Open source data integration platform for translational
research.

**Description**

Translational researchers investigate how molecular
alterations correlate to specific disease phenotypes and
whether these alterations could be used in a diagnostic
or therapeutic manner. In order to allow researchers to

(re)examine previously generated molecular data, a solu-
tion for sustainable management of this data in an
accessible manner is crucial. In the Netherlands, the
Translational Research IT (TraIT) project initiated by
the Center for Translational Molecular Medicine
(CTMM) aims to provide end-to-end solutions for sus-
tainable management and analysis of data by establish-
ing a long-lasting IT infrastructure. The tranSMART
platform is a cornerstone of its infrastructure, in which

<figure><img src="image_1.png" /></figure>

<footnote>* Correspondence: m.bierkens@vumc.nl</footnote>

<footnote n="1">¹Tumor Profiling Unit – VUmc Cancer Center, Amsterdam, the Netherlands
Full list of author information is available at the end of the article</footnote>
processed ‘final’ data of various domains become avail-
able for data-integration, querying, visualisation and
analysis.

tranSMART [1] was developed by Johnson & Johnson
and initially served as an internal research data ware-
house. Made open source in 2012, projects and institu-
tions such as IMI eTRIKS, Janssen, Pfizer, Sanofi, the
tranSMART Foundation and CTMM-TraIT have since
contributed to its further development [2]. Connections
between tranSMART and tools such as OpenClinica
(clinical information), XNAT (imaging), Molgenis Cata-
logue (biobanking), Galaxy (processing pipelines, experi-
mental data) and Phenotype Database (experimental
data) are being established. Per domain, users will be
able to turn raw data obtained from patient samples
into processed data for export into tranSMART, while
from tranSMART it will be possible to trace back the
original raw data and processing pipelines.

Via tranSMART users may explore data (Figure 1) at
various levels without needing to become domain experts
to interpret the data. Data-type experts however will be
capable of examining data in more detail using tools they
are familiar with, or ones provided by CTMM-TraIT. In
summary, tranSMART creates a window to complex
bioinformatics data sets for disease experts with only lim-
ited understanding of specific bioinformatics pipelines.

Status of development

tranSMART1.2 release in deployment “start of 2015”.

Users

CTMM-TraIT, IMI eTRIKS, Janssen, Pfizer, Sanofi, the
tranSMART Foundation, and many others.

Link

http://transmartfoundation.org/

Authors’ details

Published: 22 May 2015

References

1. Perakslis ED, van Dam J, Szalma S: How Informatics Can Potentiate Precompetitive Open-Source Collaboration to Jump-Start Drug Discovery and Development. *Clinical pharmacology & Therapeutics* 2010, 87(5):614-616.

2. Athey BD, Braxenthaler M, Haas M, Guo Y: tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research. *AMIA Jt Summits Transl Sci Proc* 2013, 18:6-8.

doi:10.1186/2043-9113-5-S1-S9

Cite this article as: Bierkens et al.: tranSMART. Journal of Clinical Bioinformatics 2015 5(Suppl 1):S9.

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<footnote n="1">¹Tumor Profiling Unit - VUmc Cancer Center, Amsterdam, the Netherlands.</footnote>

<footnote n="2">²Philips Research, Eindhoven, the Netherlands. ³The Hyve, Utrecht, the Netherlands. ⁴eScience Center, Amsterdam, the Netherlands. ⁵Center for Translational Molecular Medicine, Eindhoven, the Netherlands.</footnote>