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Contents
Part I Introduction of Integrative Bioinformatics
1 Integrative Bioinformatics: History and Perspective ................... 3
Ming Chen, Ralf Hofestädt, and Jan Taubert
2 From Genotypes to Phenotypes: A Plant Perspective
on Current Developments in Data Management and Data
Publication .................................................................. 11
Daniel Arend, Sebastian Beier, Patrick König, Matthias Lange,
Junaid A. Memon, Markus Oppermann, Uwe Scholz,
and Stephan Weise
Part II Data/Database Integration
3 Research Data Resources for Epidemiology ............................. 47
Louise Corti and Deborah Wiltshire
4 Data Warehousing of Life Science Data.................................. 85
Benjamin Kormeier and Klaus Hippe
5 Automation in Graph-Based Data Integration and Mapping ......... 97
Marcel Friedrichs
6 DaTo: An Integrative Web Portal for Biological Databases
and Tools..................................................................... 111
Yincong Zhou, Ralf Hofestädt, and Ming Chen
7 The Use of Data Integration and Knowledge Graphs
in Modern Molecular Plant Breeding .................................... 121
Bjoern Oest Hansen, Jan Taubert, and Thomas Thiel
Part III Integrative Data Analysis
8 Integrative Data Analysis and Exploratory Data Mining
in Biological Knowledge Graphs .......................................... 147
Marco Brandizi, Ajit Singh, Jeremy Parsons, Christopher Rawlings,
and Keywan Hassani-Pak
9 Exploring Plant Transcription Factor Regulatory Networks .......... 171
Ranran Yu and Dijun Chen
10 Microbiome and Big-Data Mining ........................................ 197
Kang Ning
11 Data Integration Applications in Medical Information Systems ...... 223
Marcel Friedrichs
Part IV Network Modeling and Simulation
12 Visualising Metabolic Pathways and Networks: Past,
Present, Future.............................................................. 237
Falk Schreiber, Eva Grafahrend-Belau, Oliver Kohlbacher,
and Huaiyu Mi
13 Comprehensive Open-Source Petri Net Toolchain for
Modeling and Simulation in Systems Biology ........................... 269
Christoph Brinkrolf and Lennart Ochel
14 Immersive Exploration of Cell Localization Scenarios Using
VR, Spatialized Video Communication, and Integrative
Bioinformatics .............................................................. 291
Bjorn Sommer, Ayn Sayuti, Chang Hee Lee, Zidong Lin, Jenny Hu,
and Ashley Hall
Part V Integrative Tools and Workflow
15 IoS: A Needed Platform for Scientific Workflow Management ....... 313
Savas Takan, Visam Gültekin, and Jens Allmer
16 Revealing Genotype–Phenotype Interactions: The AgroLD
Experience and Challenges ................................................ 321
Pierre Larmande and Konstantin Todorov
17 Interactive Data Analyses Using TBtools ................................ 343
Chengjie Chen and Rui Xia
18 Analyzing Multi-Omic Data with Integrative Platforms ............... 377
Yan Zou
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