Abstract
Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses. Tools need to accommodate the workflows that scientists actually perform for specific translational research questions. To understand and model one of these workflows, we conducted a case-based, cognitive task analysis of a biomedical specialist’s exploratory workflow for the question: What functional interactions among gene products of high throughput expression data suggest previously unknown mechanisms of a disease? From our cognitive task analysis four complementary representations of the targeted workflow were developed. They include: usage scenarios, flow diagrams, a cognitive task taxonomy, and a mapping between cognitive tasks and user-centered visualization requirements. The representations capture the flows of cognitive tasks that led a biomedical specialist to inferences critical to hypothesizing. We created representations at levels of detail that could strategically guide visualization development, and we confirmed this by making a trial prototype based on user requirements for a small portion of the workflow. Our results imply that visualizations should make available to scientific users “bundles of features†consonant with the compositional cognitive tasks purposefully enacted at specific points in the workflow. We also highlight certain aspects of visualizations that: (a) need more built-in flexibility; (b) are critical for negotiating meaning; and (c) are necessary for essential metacognitive support.
Highlights
Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses
Our results imply that visualizations should make available to scientific users “bundles of features” consonant with the compositional cognitive tasks purposefully enacted at specific points in the workflow
Our cognitive task analysis shows this flow performed in different tools, but our findings suggest that visualization tools could be designed to include affordances for more parts of the flow or to better integrate work across tools if they were more attuned to scientists’ actual compositional reasoning and actions
Summary
Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses. Payne et al argue that despite a general availability of applications the “absence of sufficiently robust analytical tools capable of addressing the requirements of specific research questions” significantly impedes translational research [1, 137]. One reason for this problem is a paucity of knowledge about “the requirements of specific research questions” from the analytical perspectives of biomedical specialists. We conducted a case‐based, cognitive task analysis of a specialist’s workflow for functionally analyzing expression data in molecular interaction networks for hypothesizing purposes. The workflow includes drawing relationships between molecular‐based insights from network analysis and phenotype data
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