Integration and visualization of host–pathogen data related to infectious diseases

Driscoll, Timothy; Gabbard, Joseph L.; Mao, Chunhong; Dalay, Oral; Shukla, Maulik; Freifeld, Clark C.; Hoen, Anne G.; Brownstein, John S.; Sobral, Bruno W. S.

doi:10.1093/bioinformatics/btr391

Cited by 17 publications

(20 citation statements)

References 22 publications

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“…Additionally, analysis of a survey conducted by Bassil and Keller [67] indicated that users in academic settings are nearly twice as sensitive to the cost of a new tool as are users in industry. This finding is consistent with many studies exploring or advocating for open-source and web-based infectious disease visualization tools to overcoming cost and resource barriers [62, 70, 73, 77, 79, 84-86]. Moreover, these preferences mirror key themes from Section 3.1, namely user trust, tool credibility and transparency.…”

Section: Resultssupporting

confidence: 88%

“…Cognitive overload, wherein a user is presented with more information than they are able to successfully process, was addressed in several studies. This highlights the unique challenge of displaying complex and large datasets without reducing usability reaching the technical limits of the platform or the cognitive limits of the user [69, 70]. Strategies to minimize cognitive overload were less defined, although Herman [69] suggested human-centered design as a means of improving data visualization interpretation.…”

Section: Resultsmentioning

confidence: 99%

“…Web-based systems, or systems having some web accessible components, were the delivery platform of choice in many cases [28, 29, 46, 70, 72, 74, 77-79, 81-86]. These were often intended to permit distributed access by public health staff, reduce software implementation costs, or expose public health information for public dissemination.…”

Section: Resultsmentioning

confidence: 99%

“…In molecular epidemiology, relationships between isolates are often calculated and conveyed through phylogenetic trees or dendrograms (Figure 4). Visualization tools for molecular epidemiology often included phylogenetic analysis and visualization capabilities [113-115] and visualization of contextual data using connected graphs [70, 113]. The tools we reviewed were primarily designed to be accessed through the internet [70, 113, 114, 116].…”

Section: Resultsmentioning

confidence: 99%

“…Visualization tools for molecular epidemiology often included phylogenetic analysis and visualization capabilities [113-115] and visualization of contextual data using connected graphs [70, 113]. The tools we reviewed were primarily designed to be accessed through the internet [70, 113, 114, 116]. Most studies in our review included the capability to integrate GIS or location-based data with genetic or serotype visualizations [11, 70, 84, 113-117].…”

Section: Resultsmentioning

confidence: 99%

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Visualization and analytics tools for infectious disease epidemiology: A systematic review

Carroll

Detwiler

et al. 2014

Journal of Biomedical Informatics

210

171

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Background A myriad of new tools and algorithms have been developed to help public health professionals analyze and visualize the complex data used in infectious disease control. To better understand approaches to meet these users' information needs, we conducted a systematic literature review focused on the landscape of infectious disease visualization tools for public health professionals, with a special emphasis on geographic information systems (GIS), molecular epidemiology, and social network analysis. The objectives of this review are to: (1) Identify public health user needs and preferences for infectious disease information visualization tools; (2) Identify existing infectious disease information visualization tools and characterize their architecture and features; (3) Identify commonalities among approaches applied to different data types; and (4) Describe tool usability evaluation efforts and barriers to the adoption of such tools. Methods We identified articles published in English from January 1, 1980 to June 30, 2013 from five bibliographic databases. Articles with a primary focus on infectious disease visualization tools, needs of public health users, or usability of information visualizations were included in the review. Results A total of 88 articles met our inclusion criteria. Users were found to have diverse needs, preferences and uses for infectious disease visualization tools, and the existing tools are correspondingly diverse. The architecture of the tools was inconsistently described, and few tools in the review discussed the incorporation of usability studies or plans for dissemination. Many studies identified concerns regarding data sharing, confidentiality and quality. Existing tools offer a range of features and functions that allow users to explore, analyze, and visualize their data, but the tools are often for siloed applications. Commonly cited barriers to widespread adoption included lack of organizational support, access issues, and misconceptions about tool use. Discussion and Conclusion As the volume and complexity of infectious disease data increases, public health professionals must synthesize highly disparate data to facilitate communication with the public and inform decisions regarding measures to protect the public's health. Our review identified several themes: consideration of users' needs, preferences, and computer literacy; integration of tools into routine workflow; complications associated with understanding and use of visualizations; and the role of user trust and organizational support in the adoption of these tools. Interoperability also emerged as a prominent theme, highlighting challenges associated with the increasingly collaborative and interdisciplinary nature of infectious disease control and prevention. Future work should address methods for representing uncertainty and missing data to avoid misleading users as well as strategies to minimize cognitive overload.

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Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 3 more Smart Citations

Visualization and analytics tools for infectious disease epidemiology: A systematic review

Carroll

Detwiler

et al. 2014

Journal of Biomedical Informatics

210

171

View full text Add to dashboard Cite

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Metagenomic Analysis Reveals a Possible Association Between Respiratory Infection and Periodontitis

Liu

Zhang

Wu³

et al. 2021

Genomics, Proteomics &Amp; Bioinformatics

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Periodontitis is an inflammatory disease that is characterized by progressive destruction of the periodontium and causes tooth loss in adults. Periodontitis is known to be associated with dysbiosis of the oral microflora, which is often linked to various diseases. However, the complexity of plaque microbial communities of periodontitis, antibiotic resistance, and enhanced virulence make this disease difficult to treat. In this study, using metagenomic shotgun sequencing, we investigated the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. We revealed a significant shift in the composition of oral microbiota as well as several functional pathways that were represented significantly more abundantly in periodontitis patients than in controls. In addition, we observed several positively selected ARGs and VirGs with the Ka/Ks ratio > 1 by analyzing our data and a previous periodontitis dataset, indicating that ARGs and VirGs in oral microbiota may be subjected to positive selection. Moreover, 5 of 12 positively selected ARGs and VirGs in periodontitis patients were found in the genomes of respiratory tract pathogens. Of note, 91.8% of the background VirGs with at least one non-synonymous single-nucleotide polymorphism for natural selection were also from respiratory tract pathogens. These observations suggest a potential association between periodontitis and respiratory infection at the gene level. Our study enriches the knowledge of pathogens and functional pathways as well as the positive selection of antibiotic resistance and pathogen virulence in periodontitis patients, and provides evidence at the gene level for an association between periodontitis and respiratory infection.

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Protein arrays as tool for studies at the host–pathogen interface

Manzano-Román

Dasilva

Díez

et al. 2013

Journal of Proteomics

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Integration and visualization of host–pathogen data related to infectious diseases

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 17 publications

References 22 publications

Visualization and analytics tools for infectious disease epidemiology: A systematic review

Visualization and analytics tools for infectious disease epidemiology: A systematic review

Metagenomic Analysis Reveals a Possible Association Between Respiratory Infection and Periodontitis

Protein arrays as tool for studies at the host–pathogen interface

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