Data capture in bioinformatics: requirements and experiences with Pedro.

BMC Bioinformatics
Daniel JamesonNorman W Paton

Abstract

The systematic capture of appropriately annotated experimental data is a prerequisite for most bioinformatics analyses. Data capture is required not only for submission of data to public repositories, but also to underpin integrated analysis, archiving, and sharing - both within laboratories and in collaborative projects. The widespread requirement to capture data means that data capture and annotation are taking place at many sites, but the small scale of the literature on tools, techniques and experiences suggests that there is work to be done to identify good practice and reduce duplication of effort. This paper reports on experience gained in the deployment of the Pedro data capture tool in a range of representative bioinformatics applications. The paper makes explicit the requirements that have recurred when capturing data in different contexts, indicates how these requirements are addressed in Pedro, and describes case studies that illustrate where the requirements have arisen in practice. Data capture is a fundamental activity for bioinformatics; all biological data resources build on some form of data capture activity, and many require a blend of import, analysis and annotation. Recurring requirements in data capture su...Continue Reading

References

Sep 13, 2002·Genome Biology·Paul T SpellmanAlvis Brazma
Mar 1, 2003·Nature Biotechnology·Chris F TaylorStephen G Oliver
Apr 10, 2004·Bioinformatics·Kevin L GarwoodNorman W Paton
Jul 21, 2004·Bioinformatics·R D StevensM Tassabehji
Dec 31, 2005·Nucleic Acids Research·Robert D FinnAlex Bateman
Aug 31, 2006·Methods in Enzymology·Tanya Barrett, Ron Edgar
Oct 4, 2006·Journal of the Royal Society, Interface·Hailin ShenDouglas B Kell
Nov 8, 2006·BMC Bioinformatics·Tim F RaynerAlvis Brazma
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Feb 14, 2007·Nature Reviews. Genetics·Morris A Swertz, Ritsert C Jansen

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Citations

Jul 23, 2009·BMC Bioinformatics·Daniel JamesonNorman W Paton
Jan 19, 2011·BMC Bioinformatics·Morris A SwertzHelen Parkinson
Jun 25, 2014·BMC Bioinformatics·Daniel ArendUwe Scholz

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Software Mentioned

TaxInspector
Proteome Harvest Spreadsheet
Proteome Harvest
MAGE
maxdLoad2
Pedro Grid
- XML
Windows
proteomics
- Tracker

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