SEEK : a systems biology data and model management platform

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dc.contributor.authorWolstencroft, Katherineen_ZA
dc.contributor.authorOwen, Stuarten_ZA
dc.contributor.authorKrebs, Olgaen_ZA
dc.contributor.authorNguyen, Quyenen_ZA
dc.contributor.authorStanford, Natalie J.en_ZA
dc.contributor.authorGolebiewski, Martinen_ZA
dc.contributor.authorWeidemann, Andreasen_ZA
dc.contributor.authorBittkowski, Meiken_ZA
dc.contributor.authorAn, Lihuaen_ZA
dc.contributor.authorShockley, Daviden_ZA
dc.contributor.authorSnoep, Jacky L.en_ZA
dc.contributor.authorMueller, Wolfgangen_ZA
dc.contributor.authorGoble, Caroleen_ZA
dc.date.accessioned2016-11-02T10:31:23Z
dc.date.available2016-11-02T10:31:23Z
dc.date.issued2015-07-11
dc.descriptionCITATION: Wolstencroft, K. et al. 2015. SEEK : a systems biology data and model management platform. BMC Systems Biology, 9:33, doi:10.1186/s12918-015-0174-y.
dc.descriptionThe original publication is available at http://bmcsystbiol.biomedcentral.com
dc.description.abstractBackground: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. Results: The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. Conclusion: The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.en_ZA
dc.description.urihttp://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-015-0174-y
dc.description.versionPublisher's version
dc.format.extent12 pages : illustrations
dc.identifier.citationWolstencroft, K. et al. 2015. SEEK : a systems biology data and model management platform. BMC Systems Biology, 9:33, doi:10.1186/s12918-015-0174-y.
dc.identifier.issn1752-0509 (online)
dc.identifier.otherdoi:10.1186/s12918-015-0174-y
dc.identifier.urihttp://hdl.handle.net/10019.1/99810
dc.language.isoen_ZAen_ZA
dc.publisherBioMed Central
dc.rights.holderAuthors retain copyright
dc.subjectSystems biology dataen_ZA
dc.subjectData managementen_ZA
dc.subjectModel managementen_ZA
dc.subjectData sharingen_ZA
dc.subjectSemantic data integrationen_ZA
dc.subjectMetadata standardsen_ZA
dc.titleSEEK : a systems biology data and model management platformen_ZA
dc.typeArticleen_ZA
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