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Review
. 2015 Sep 2;22(1):9.
doi: 10.1186/s40709-015-0032-5. eCollection 2015 Dec.

Data integration in biological research: an overview

Vasileios Lapatas  1 , Michalis Stefanidakis  1 , Rafael C Jimenez  2 , Allegra Via  3 , Maria Victoria Schneider  4
Affiliations
Review

Data integration in biological research: an overview

Vasileios Lapatas et al. J Biol Res (Thessalon). .

Abstract

Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

Keywords: Bioinformatics; Data driven; Data integration; Open sciences; Standards.

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Figures

Fig. 1
Fig. 1
Data integration methodologies. This figure illustrates six major types of data integration methodologies in biology
Fig. 2
Fig. 2
Current state. This figure illustrates a simplified view of the current state of biological data and tools
Fig. 3
Fig. 3
Ideal state. This figure illustrates a simplified view of an ideal state of biological data and tools
Fig. 4
Fig. 4
Selected parts of a FASTQ file. In this format declaration lines start with two different characters (“@” and “+”) corresponding to different data types (the raw sequence and the sequence quality values, respectively)
Fig. 5
Fig. 5
Selected parts of the GenBank entry DQ408531. The complete entry can be found at http://www.ncbi. nlm.nih.gov/nuccore/DQ408531
Fig. 6
Fig. 6
Selected parts of the Uniprot entry P01308 in XML format - The complete entry can be found at http://www.uniprot.org/uniprot/P01308.xml
Fig. 7
Fig. 7
Selected parts of a SAM file
See this image and copyright information in PMC

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