Open Access Methodology article

Identifying elemental genomic track types and representing them uniformly

Sveinung Gundersen1, Matúš Kalaš23, Osman Abul4, Arnoldo Frigessi56, Eivind Hovig178 and Geir Kjetil Sandve8*

Author Affiliations

1 Department of Tumor Biology, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0310 Oslo, Norway

2 Computational Biology Unit, Uni Computing, Thormøhlensgate 55, 5008 Bergen, Norway

3 Department of Informatics, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway

4 TOBB University of Economics and Technology, Ankara, Turkey

5 Statistics For Innovation, Norwegian Computing Center, 0314 Oslo, Norway

6 Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Blindern, 0317 Oslo, Norway

7 Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0310 Oslo, Norway

8 Department of Informatics, University of Oslo, Blindern, 0316 Oslo, Norway

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BMC Bioinformatics 2011, 12:494  doi:10.1186/1471-2105-12-494

Published: 30 December 2011

Abstract

Background

With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, are rapidly being generated in an increasing number of laboratories. The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that are easy to parse. A host of alternative formats are currently available and in use, complicating analysis and tool development. The issue of whether and how the multitude of formats reflects varying underlying characteristics of data has to our knowledge not previously been systematically treated.

Results

We here identify intrinsic distinctions between genomic features, and argue that the distinctions imply that a certain variation in the representation of features as genomic tracks is warranted. Four core informational properties of tracks are discussed: gaps, lengths, values and interconnections. From this we delineate fifteen generic track types. Based on the track type distinctions, we characterize major existing representational formats and find that the track types are not adequately supported by any single format. We also find, in contrast to the XML formats, that none of the existing tabular formats are conveniently extendable to support all track types. We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0.

Conclusions

The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience.