title: Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases.
abstract: Electronic access to multiple data types, from generic information on biological systems at different functional and cellular levels to high-throughput molecular data from human patients, is a prerequisite of successful systems medicine research. However, scientists often encounter technical and conceptual difficulties that forestall the efficient and effective use of these resources. We summarize and discuss some of these obstacles, and suggest ways to avoid or evade them.The methodological gap between data capturing and data analysis is huge in human medical research. Primary data producers often do not fully apprehend the scientific value of their data, whereas data analysts maybe ignorant of the circumstances under which the data were collected. Therefore, the provision of easy-to-use data access tools not only helps to improve data quality on the part of the data producers but also is likely to foster an informed dialogue with the data analysts.We propose a means to integrate phenotypic data, questionnaire data and microbiome data with a user-friendly Systems Medicine toolbox embedded into i2b2/tranSMART. Our approach is exemplified by the integration of a basic outlier detection tool and a more advanced microbiome analysis (alpha diversity) script. Continuous discussion with clinicians, data managers, biostatisticians and systems medicine experts should serve to enrich even further the functionality of toolboxes like ours, being geared to be used by 'informed non-experts' but at the same time attuned to existing, more sophisticated analysis tools.
authors.forename: Christian R
authors.initials: CR
authors.lastname: Bauer
authors.forename: Carolin
authors.initials: C
authors.lastname: Knecht
authors.forename: Christoph
authors.initials: C
authors.lastname: Fretter
authors.forename: Benjamin
authors.initials: B
authors.lastname: Baum
authors.forename: Sandra
authors.initials: S
authors.lastname: Jendrossek
authors.forename: Malte
authors.initials: M
authors.lastname: Rühlemann
authors.forename: Femke-Anouska
authors.initials: FA
authors.lastname: Heinsen
authors.forename: Nadine
authors.initials: N
authors.lastname: Umbach
authors.forename: Bodo
authors.initials: B
authors.lastname: Grimbacher
authors.forename: Andre
authors.initials: A
authors.lastname: Franke
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Lieb
authors.forename: Michael
authors.initials: M
authors.lastname: Krawczak
authors.forename: Marc-Thorsten
authors.initials: MT
authors.lastname: Hütt
authors.forename: Ulrich
authors.initials: U
authors.lastname: Sax
mesh_terms: D035843:Biomedical Research; D006801:Humans; D007249:Inflammation; D013597:Systems Analysis
keywords: data analysis; data integration; genomics; inflammation; microbiome; systems medicine