A knowledge-based decision support system in bioinformatics: an application to protein complex extraction

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Research areas:
  • Uncategorized
Year:
2013
Type of Publication:
Article
Authors:
  • Antonino Fiannaca
  • Massimo LaRosa
  • Alfonso Urso
  • Riccardo Rizzo
  • Salvatore Gaglio
Journal:
BMC Bioinformatics
Volume:
14
Number:
Supp1
ISSN:
1471-2105
Abstract:
BACKGROUND:We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for the current experiment and furthermore it offers support in the configuration and running of every processing component of that workflow. This last feature makes our system a crossover between classical DSS and Workflow Management Systems.RESULTS:We briefly present the KDSS' architecture and basic concepts used in the design of the knowledge base and the reasoning component. The system is then tested using a subset of Saccharomyces cerevisiae Protein-Protein interaction dataset. We used this subset because it has been well studied in literature by several research groups in the field of complex extraction: in this way we could easily compare the results obtained through our KDSS with theirs. Our system suggests both a preprocessing and a clustering strategy, and for each of them it proposes and eventually runs suited algorithms. Our system's final results are then composed of a workflow of tasks, that can be reused for other experiments, and the specific numerical results for that particular trial.CONCLUSIONS:The proposed approach, using the KDSS' knowledge base, provides a novel workflow that gives the best results with regard to the other workflows produced by the system. This workflow and its numeric results have been compared with other approaches about PPI network analysis found in literature, offering similar results.