Pidò S, Crovari P, Garzotto F. Modelling the bioinformatics tertiary analysis research process.
BMC Bioinformatics 2021;
22:452. [PMID:
34592928 PMCID:
PMC8482564 DOI:
10.1186/s12859-021-04310-5]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background
With 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.
Methods
To 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.
Results
The 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.
Conclusions
To 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.
Supplementary Information
The online version contains supplementary material available at 10.1186/s12859-021-04310-5.
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