The SEEK: a platform for sharing data and models in systems biology
published: Nov. 23, 2012, recorded: November 2012, views: 4755
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Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be heterogeneous and often involves high-throughput "omics" analyses. Models are developed iteratively from data generated in the projects and from the literature. Consequently, there is a growing requirement for exchanging experimental data, mathematical models, and scientific protocols between consortium members and a necessity to record and share the outcomes of experiments and the links between data and models.
The SEEK is an open-source, web-based platform for the management and exchange of Systems Biology data, models and processes. It was originally developed in the SysMO-DB project (http://www.sysmodb.org) for the pan-European SysMO consortia (Systems Biology of Micro Organisms). However, it is now also being adopted by a large number of other consortia across Europe, for example, the Virtual Liver, EviMalar and Unicellsys. The SysMO-DB solution is being developed in close collaboration with the users, and with a very pragmatic approach, trying to adapt to the common procedures of users and combining this with methods and technologies that allow an effective dissemination, linkage and exchange of data and information.
Underlying the SEEK is the JERM (Just Enough Results Model), which is a minimum information model describing the structure and content of the SEEK assets and relationships between them. A JERM for any one type of data (i.e. microarray data, or metabolomic data) is the minimum data schema that SysMO projects agree to share. This is used to create JERM templates. SysMO-DB leverages these minimum models wherever possible, enabling easy export and publishing of SysMO data to public repositories. In addition, we have developed RightField (the Spreadsheet Ontology Annotation tool) to help researchers to develop templates for experimental data with embedded semantic descriptions. Data can then be consistently annotated with terms from appropriate ontologies and controlled vocabularies consistently. The SEEK provides an access control layer to enable researchers to restrict access to their data to collaborators and colleagues or to share it with the wider community.
Availability: SEEK code is open source and available for download http://code.google.com/p/sysmo-db/. For a demonstration of the SEEK capabilities, and to try out the software, demo SEEK is available here https://demo.sysmo-db.org/. RightField download: http://www.sysmo-db.org/rightfield
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