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A review of standards for data exchange within systems biology
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology. (IDA/ADIT)ORCID iD: 0000-0002-9084-0470
2007 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 7, no 6, 857-867 p.Article in journal (Refereed) Published
Abstract [en]

The rapid increase in experimental data within systems biology has increased the need for exchange of data to allow analysis and comparison of larger datasets. This has resulted in a need for standardized formats for representation of such results and currently many formats for representation of data have been developed or are under development. In this paper, we give an overview of the current state of available standards and ontologies within systems biology. We focus on XML-based standards for exchange of data and give a thorough description of similarities and differences of currently available formats. For each of these, we discuss how the important concepts such as substances, interactions, and experimental data can be represented. In particular, we note that the purpose of a standard is often visible in the structures it provides for the representation of data. A clear purpose is also crucial for the success of a standard. Moreover, we note that the development of representation formats is parallel to the development of ontologies and the recent trend is that representation formats make more and more use of available ontologies.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2007. Vol. 7, no 6, 857-867 p.
National Category
Computer Science
Identifiers
URN: urn:nbn:se:liu:diva-37738DOI: 10.1002/pmic.200600438ISI: :000245331000005PubMedID: 17370264Local ID: 38205OAI: oai:DiVA.org:liu-37738DiVA: diva2:258587
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13Bibliographically approved

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Strömbäck, LenaHall, DavidLambrix, Patrick

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