Dataset Information

A Comparison of Microbial Genome Web Portals.

ABSTRACT: Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs. We assessed both the bioinformatics tools and the data content of BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC. For each portal, our assessment compared and tallied the available capabilities. The strengths of BioCyc include its genomic and metabolic tools, multi-search capabilities, table-based analysis tools, regulatory network tools and data, omics data analysis tools, breadth of data content, and large amount of curated data. The strengths of KEGG include its genomic and metabolic tools. The strengths of Ensembl Bacteria include its genomic tools and large number of genomes. The strengths of KBase include its genomic tools and metabolic models. The strengths of IMG include its genomic tools, multi-search capabilities, large number of genomes, table-based analysis tools, and breadth of data content. The strengths of PATRIC include its large number of genomes, table-based analysis tools, metabolic models, and breadth of data content.

SUBMITTER: Karp PD

PROVIDER: S-EPMC6395428 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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A Comparison of Microbial Genome Web Portals.

Karp Peter D PD Ivanova Natalia N Krummenacker Markus M Kyrpides Nikos N Latendresse Mario M Midford Peter P Ong Wai Kit WK Paley Suzanne S Seshadri Rekha R

Frontiers in microbiology 20190222

Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs. We assessed both the bioinformatics tools and the data content of BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC. For each portal, our assessment compared and tallied the available capa ...[more]

PMID: 30853946

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Project description:BackgroundA frequently used feature of electronic patient portals is the viewing of test results. Research on patient portals is abundant and offers evidence to help portal implementers make policy and practice decisions. In contrast, no comparable comprehensive summary of research addresses the direct release of and patient access to test results.ObjectiveThis scoping review aims to analyze and synthesize published research focused on patient and health care provider perspectives on the direct release of laboratory, imaging, and radiology results to patients via web portals.MethodsPRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines were followed. Searches were conducted in CINAHL, MEDLINE, and other databases. Citations were screened in Covidence using the inclusion and exclusion criteria. Primary studies that focused on patient and health care provider perspectives on patient access to laboratory and imaging results via web portals were included. An updated search was conducted up to August 2023. Our review included 27 articles-20 examining patient views, 3 examining provider views, and 4 examining both patient and provider views. Data extraction and inductive data analysis were informed by sensitizing concepts from sociomaterial perspectives, and 15 themes were generated.ResultsPatient perspectives (24 papers) were synthesized using nine themes: (1) patterns of use and patient characteristics; (2) emotional response when viewing the results and uncertainty about their implications; (3) understanding test results; (4) preferences for mode and timing of result release; (5). information seeking and patients' actions motivated by viewing results via a portal; (6) contemplating changes in behavior and managing own health; (7) benefits of accessing test results via a portal; (8) limitations of accessing test results via a portal; and (9) suggestions for portal improvement. Health care provider perspectives (7 papers) were synthetized into six themes: (1) providers' view of benefits of patient access to results via the portal; (2) effects on health care provider workload; (3) concerns about patient anxiety; (4) timing of result release into the patient portal; (5) the method of result release into the patient portal: manual versus automatic release; and (6) the effects of hospital health information technology system on patient quality outcomes.ConclusionsThe timing of the release of test results emerged as a particularly important topic. In some countries, the policy context may motivate immediate release of most tests directly into patient portals. However, our findings aim to make policy makers, health administrators, and other stakeholders aware of factors to consider when making decisions about the timing of result release. This review is sensitive to the characteristics of patient populations and portal technology and can inform result release framework policies. The findings are timely, as patient portals have become more common internationally.

Dataset Information

A Comparison of Microbial Genome Web Portals.

Publications

A Comparison of Microbial Genome Web Portals.

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