Abstract
BackgroundWith the advancements of Next Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods. Bioinformatics Tertiary Analysis is a complex multidisciplinary process that represents the final step of the whole bioinformatics analysis pipeline. Despite the popularity of the subject, the Bioinformatics Tertiary Analysis process has not yet been specified in a systematic way. The lack of a reference model results into a plethora of technological tools that are designed mostly on the data and not on the human process involved in Tertiary Analysis, making such systems difficult to use and to integrate.MethodsTo address this problem, we propose a conceptual model that captures the salient characteristics of the research methods and human tasks involved in Bioinformatics Tertiary Analysis. The model is grounded on a user study that involved bioinformatics specialists for the elicitation of a hierarchical task tree representing the Tertiary Analysis process. The outcome was refined and validated using the results of a vast survey of the literature reporting examples of Bioinformatics Tertiary Analysis activities.ResultsThe final hierarchical task tree was then converted into an ontological representation using an ontology standard formalism. The results of our research provides a reference process model for Tertiary Analysis that can be used both to analyze and to compare existing tools, or to design new tools.ConclusionsTo highlight the potential of our approach and to exemplify its concrete applications, we describe a new bioinformatics tool and how the proposed process model informed its design.
Highlights
With the advancements of Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods
Bioinformatics Tertiary Analysis is defined as the use of complex computer science methods, algorithms and tools to understand and analyze the sequencing results extracted from raw genomic data [1, 2]
With respect to the previous publication, here we present a novel validation of the user study results, mapping more than 35 research works found in the literature on the elicited process model, and describes the translation of the Hierarchical Task Tree into an ontology-based formalism
Summary
With the advancements of Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods. Introduction Bioinformatics Tertiary Analysis is defined as the use of complex computer science methods, algorithms and tools to understand and analyze the sequencing results extracted from raw genomic data [1, 2]. As Bolchini stated in [5], the usability of bioinformatics tools is a severe problem that weakens their power to support bioinformatics research and their potential for adoption Even if these applications were developed to support the bioinformatics activities and mitigate the difficulties that are intrinsic in the subject, many of these tools are perceived as very complex to learn and to use. If the user is not an expert in both biology and computer science, managing them requires a significant cognitive effort which should instead be devoted to answer research questions This problem is more accentuated when biological data and operations increase in complexity. They require advanced algorithms and computer science methods that are often understood only by machine learning engines or data mining experts
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