Dataset Information

GlycanFormatConverter: A conversion tool for translating the complexities of glycans.

ABSTRACT: Motivation:Glycans are biomolecules that take an important role in the biological processes of living organisms. They form diverse, complicated structures such as branched and cyclic forms. Web3 Unique Representation of Carbohydrate Structures (WURCS) was proposed as a new linear notation for uniquely representing glycans during the GlyTouCan project. WURCS defines rules for complex glycan structures that other text formats did not support, and so it is possible to represent a wide variety glycans. However, WURCS uses a complicated nomenclature, so it is not human-readable. Therefore, we aimed to support the interpretation of WURCS by converting WURCS to the most basic and widely used format IUPAC. Results:In this study, we developed GlycanFormatConverter and succeeded in converting WURCS to the three kinds of IUPAC formats (IUPAC-Extended, IUPAC-Condensed, and IUPAC-Short). Furthermore, we have implemented functionality to import IUPAC-Extended, KEGG Chemical Function (KCF) and LinearCode formats and to export WURCS. We have thoroughly tested our GlycanFormatConverter and were able to show that it was possible to convert all the glycans registered in the GlyTouCan repository, with exceptions owing only to the limitations of the original format. The source code for this conversion tool has been released as an open source tool. Availability:https://github.com/glycoinfo/GlycanFormatConverter.git. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Tsuchiya S

PROVIDER: S-EPMC6612873 | biostudies-other | 2018 Dec

REPOSITORIES: biostudies-other

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GlycanFormatConverter: a conversion tool for translating the complexities of glycans.

Tsuchiya Shinichiro S Yamada Issaku I Aoki-Kinoshita Kiyoko F KF

Bioinformatics (Oxford, England) 20190701 14

<h4>Motivation</h4>Glycans are biomolecules that take an important role in the biological processes of living organisms. They form diverse, complicated structures such as branched and cyclic forms. Web3 Unique Representation of Carbohydrate Structures (WURCS) was proposed as a new linear notation for uniquely representing glycans during the GlyTouCan project. WURCS defines rules for complex glycan structures that other text formats did not support, and so it is possible to represent a wide varie ...[more]

PMID: 30535258

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Project description:IntroductionAlthough family members of incapacitated, critically ill patients often struggle in the role of surrogate decision maker, there are no low-cost, easily-scaled interventions to address this problem.Aim of the studyTo develop and pilot-test the Family Support Tool, an interactive, web-based tool to help individuals navigate the complexities of surrogate decision making in ICUs.Material and methodsWe used a mixed methods, user-centered process to create the Family Support Tool, including: 1) creation of a preliminary design by an expert panel; 2) engagement of a key stakeholder panel to iteratively refine the preliminary design; 3) user testing of a low-fidelity prototype of the tool by 6 former ICU surrogates; 4) creation of a web-based prototype; and 5) user testing of the web-based prototype with 14 surrogates and ICU physicians, including semi-structured interviews and quantitative measurement of usability, acceptability, and perceived effectiveness.ResultsThe initial design contained a collection of videos and exercises designed to help individuals understand the surrogate's role and think through the patient's values and preferences. Based on family stakeholders' feedback about the emotional overwhelm they experience early in an ICU stay, we redesigned the tool to be viewed in sections, with the first section focused on decreasing surrogates' emotional distress, and later sections focused on helping surrogates prepare for family meetings. Surrogates actively making decisions in the ICU judged the final tool to be highly usable (mean summary score 83.5, correlating to 95th percentile when normalized to devices of its type), acceptable (mean 4.2 +/- 0.5 out of 5), and effective (mean 4.3 +/- 0.6 out of 5). All surrogates reported the tool helped them consider goals of care and all indicated they would recommend the tool to a friend.ConclusionsWe successfully developed a web-based tool to help individuals navigate the complexities of surrogate decision making in ICUs that has high potential for scalability. Surrogates judged the tool to be usable, acceptable, and effective. These data support proceeding to test the tool in a pilot randomized clinical trial.

Project description:Background. The complexity of decision science models may prevent their use to assist in decision making. User-centered design (UCD) principles provide an opportunity to engage end users in model development and refinement, potentially reducing complexity and increasing model utilization in a practical setting. We report our experiences with UCD to develop a modeling tool for cancer control planners evaluating cancer survivorship interventions. Design. Using UCD principles (described in the article), we developed a dynamic cohort model of cancer survivorship for individuals with female breast, colorectal, lung, and prostate cancer over 10 y. Parameters were obtained from the National Program of Cancer Registries and peer-reviewed literature, with model outcomes captured in quality-adjusted life-years and net monetary benefit. Prototyping and iteration were conducted with structured focus groups involving state cancer control planners and staff from the Centers for Disease Control and Prevention and the American Public Health Association. Results. Initial feedback highlighted model complexity and unclear purpose as barriers to end user uptake. Revisions addressed complexity by simplifying model input requirements, providing clear examples of input types, and reducing complex language. Wording was added to the results page to explain the interpretation of results. After these updates, feedback demonstrated that end users more clearly understood how to use and apply the model for cancer survivorship resource allocation tasks. Conclusions. A UCD approach identified challenges faced by end users in integrating a decision aid into their workflow. This approach created collaboration between modelers and end users, tailoring revisions to meet the needs of the users. Future models developed for individuals without a decision science background could leverage UCD to ensure the model meets the needs of the intended audience.HighlightsModel complexity and unclear purpose are 2 barriers that prevent lay users from integrating decision science tools into their workflow.Modelers could integrate the user-centered design framework when developing a model for lay users to reduce complexity and ensure the model meets the needs of the users.

Dataset Information

GlycanFormatConverter: A conversion tool for translating the complexities of glycans.

Publications

GlycanFormatConverter: a conversion tool for translating the complexities of glycans.

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