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Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping / ZAHRA ALMOWIL

Swansea University Author: ZAHRA ALMOWIL

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DOI (Published version): 10.23889/SUthesis.62363

Abstract

Background: Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack...

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Published: Swansea 2023
Institution: Swansea University
Degree level: Doctoral
Degree name: Ph.D
Supervisor: Brophy, Sinead ; Croxall, Jodie
URI: https://cronfa.swan.ac.uk/Record/cronfa62363
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Objective: This thesis aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, for both new and existing data portals for phenotypes (concept libraries). Methods: Exploratory sequential mixed methods were used in this thesis to look at which concept libraries are available, how they are used, what their characteristics are, where there are gaps, and what needs to be done in the future from the point of view of the people who use them. This thesis consists of three phases: 1) two qualitative studies, including one-to-one interviews with researchers, clinicians, machine learning experts, and senior research managers in health data science, as well as focus group discussions with researchers working with the Secured Anonymized Information Linkage databank, 2) the creation of an email survey (i.e., the Concept Library Usability Scale), and 3) a quantitative study with researchers, health professionals, and clinicians. Results: Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would encourage them to: 1) share their work, such as receiving citations from other researchers; and 2) reuse the work of others, such as saving a lot of time and effort, which they frequently spend on creating new code lists from scratch. They also pointed out several barriers that could inhibit them from: 1) sharing their work, such as concerns about intellectual property (e.g., if they shared their methods before publication, other researchers would use them as their own); and 2) reusing others' work, such as a lack of confidence in the quality and validity of their code lists. Participants suggested some developments that they would like to see happen in order to make research that is done with routine data more reproducible, such as the availability of a drive for more transparency in research methods documentation, such as publishing complete phenotype definitions and clear code lists. Conclusions: The findings of this thesis indicated that most participants valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform such as the CALIBER research platform. Analysis of interviews, focus group discussions, and qualitative studies revealed that different users have different requirements, facilitators, barriers, and concerns about concept libraries. This work was to investigate if we should develop concept libraries in Kuwait to facilitate the development of improved data sharing. 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spelling 2023-01-18T13:45:23.5271505 v2 62363 2023-01-18 Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping 2fae47dc8567b17441bdbd5927c6ad28 ZAHRA ALMOWIL ZAHRA ALMOWIL true false 2023-01-18 Background: Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it hard to compare different study findings and hinders the ability to conduct repeatable and reusable research. Objective: This thesis aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, for both new and existing data portals for phenotypes (concept libraries). Methods: Exploratory sequential mixed methods were used in this thesis to look at which concept libraries are available, how they are used, what their characteristics are, where there are gaps, and what needs to be done in the future from the point of view of the people who use them. This thesis consists of three phases: 1) two qualitative studies, including one-to-one interviews with researchers, clinicians, machine learning experts, and senior research managers in health data science, as well as focus group discussions with researchers working with the Secured Anonymized Information Linkage databank, 2) the creation of an email survey (i.e., the Concept Library Usability Scale), and 3) a quantitative study with researchers, health professionals, and clinicians. Results: Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would encourage them to: 1) share their work, such as receiving citations from other researchers; and 2) reuse the work of others, such as saving a lot of time and effort, which they frequently spend on creating new code lists from scratch. They also pointed out several barriers that could inhibit them from: 1) sharing their work, such as concerns about intellectual property (e.g., if they shared their methods before publication, other researchers would use them as their own); and 2) reusing others' work, such as a lack of confidence in the quality and validity of their code lists. Participants suggested some developments that they would like to see happen in order to make research that is done with routine data more reproducible, such as the availability of a drive for more transparency in research methods documentation, such as publishing complete phenotype definitions and clear code lists. Conclusions: The findings of this thesis indicated that most participants valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform such as the CALIBER research platform. Analysis of interviews, focus group discussions, and qualitative studies revealed that different users have different requirements, facilitators, barriers, and concerns about concept libraries. This work was to investigate if we should develop concept libraries in Kuwait to facilitate the development of improved data sharing. However, at the end of this thesis the recommendation is this would be unlikely to be cost effective or highly valued by users and investment in open access research publications may be of more value to the Kuwait research/academic community. E-Thesis Swansea linked Electronic health records, phenotype algorithms, concept libraries, repeatable research 18 1 2023 2023-01-18 10.23889/SUthesis.62363 ORCiD identifier: https://orcid.org/0000-0001-9942-0811 COLLEGE NANME COLLEGE CODE Swansea University Brophy, Sinead ; Croxall, Jodie Doctoral Ph.D Kuwait Culture Office in London 2023-01-18T13:45:23.5271505 2023-01-18T13:16:05.6486672 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine ZAHRA ALMOWIL 1 62363__26328__8b143a6856c6413eb41ba9d44aea5137.pdf Almowil_Zahra_PhD_Thesis_Fina_Redacted_Signature.pdf 2023-01-18T13:35:53.6325159 Output 7379883 application/pdf E-Thesis – open access true Copyright: The author, Zahra A. Almowil, 2023. Released under the terms of a Creative Commons Attribution-Only (CC-BY) License. Third party content is excluded for use under the license terms. true eng https://creativecommons.org/licenses/by/4.0/
title Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping
spellingShingle Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping
ZAHRA ALMOWIL
title_short Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping
title_full Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping
title_fullStr Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping
title_full_unstemmed Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping
title_sort Repeatable and reusable research - Exploring the needs of users for a Data Portal for Disease Phenotyping
author_id_str_mv 2fae47dc8567b17441bdbd5927c6ad28
author_id_fullname_str_mv 2fae47dc8567b17441bdbd5927c6ad28_***_ZAHRA ALMOWIL
author ZAHRA ALMOWIL
author2 ZAHRA ALMOWIL
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publishDate 2023
institution Swansea University
doi_str_mv 10.23889/SUthesis.62363
college_str Faculty of Medicine, Health and Life Sciences
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hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
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description Background: Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it hard to compare different study findings and hinders the ability to conduct repeatable and reusable research. Objective: This thesis aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, for both new and existing data portals for phenotypes (concept libraries). Methods: Exploratory sequential mixed methods were used in this thesis to look at which concept libraries are available, how they are used, what their characteristics are, where there are gaps, and what needs to be done in the future from the point of view of the people who use them. This thesis consists of three phases: 1) two qualitative studies, including one-to-one interviews with researchers, clinicians, machine learning experts, and senior research managers in health data science, as well as focus group discussions with researchers working with the Secured Anonymized Information Linkage databank, 2) the creation of an email survey (i.e., the Concept Library Usability Scale), and 3) a quantitative study with researchers, health professionals, and clinicians. Results: Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would encourage them to: 1) share their work, such as receiving citations from other researchers; and 2) reuse the work of others, such as saving a lot of time and effort, which they frequently spend on creating new code lists from scratch. They also pointed out several barriers that could inhibit them from: 1) sharing their work, such as concerns about intellectual property (e.g., if they shared their methods before publication, other researchers would use them as their own); and 2) reusing others' work, such as a lack of confidence in the quality and validity of their code lists. Participants suggested some developments that they would like to see happen in order to make research that is done with routine data more reproducible, such as the availability of a drive for more transparency in research methods documentation, such as publishing complete phenotype definitions and clear code lists. Conclusions: The findings of this thesis indicated that most participants valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform such as the CALIBER research platform. Analysis of interviews, focus group discussions, and qualitative studies revealed that different users have different requirements, facilitators, barriers, and concerns about concept libraries. This work was to investigate if we should develop concept libraries in Kuwait to facilitate the development of improved data sharing. However, at the end of this thesis the recommendation is this would be unlikely to be cost effective or highly valued by users and investment in open access research publications may be of more value to the Kuwait research/academic community.
published_date 2023-01-18T04:21:55Z
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