Introduction of omics metadata into biobanking ontology
department or school: Science, Faculty of
data provider: DSpace
degree campus: UBCV
creator: Alghamdi, Dalia
issued: 2025-11-24T09:02:06Z
issued: 2025
related degree: Doctor of Philosophy - PhD
degree grantor: University of British Columbia
description: Specimens and data sharing through biobanking activities has become increasingly important in global biomedical research. These practices offer the potential to accelerate scientific discovery by enabling the reuse of biospecimens and associated data. However, the benefits of data sharing can only be realized when data are findable, accessible, interoperable, and reusable (FAIR). Biobanks remain fragmented—each operating with different standards, data formats, access policies, and query interfaces—making it difficult for researchers to locate and integrate specimen-derived data. This thesis explores the application of semantic web technologies (e.g., RDF, SPARQL, and ontologies) to improve the discovery and integration of biobank data, particularly omics-derived datasets. In Chapter 1, I provide an overview of the evolution and significance of biobanks in biomedical research, highlighting their transition from physical repositories to data-centric infrastructures, and discuss the persistent challenges researchers encounter in locating, accessing, and integrating fragmented and non-standardized specimen-derived data. In Chapter 2, I examine the current challenges in biobank data discovery and integration, including the lack of standardized contextual metadata, inconsistent identifiers, and insufficient support for automated data reuse. I propose semantic web approaches as a viable solution to these problems by enabling machine-readable, interoperable metadata and flexible, federated querying. In Chapter 3, I present the development of the Next-Generation Biobanking Ontology (NGBO), an open-source application ontology designed to represent omics contextual metadata. It provides persistent identifiers and semantically rich metadata to support both human understanding and computational reasoning. Chapter 4 describes a proof-of-concept implementation of a semantic web application that enables federated querying of biobank metadata across multiple SPARQL endpoints. Chapte…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/92976
note: Introduction of omics metadata into biobanking ontology by Dalia Alghamdi B.Sc., King Abdulaziz University, 2013 M.Sc., University of Leicester, 2014 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Doctor of Philosophy in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) November 2025 © Dalia Alghamdi, 2025 ii The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Introduction of omics metadata into biobanking ontology submitted by Dalia Alghamdi in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Bioinformatics Examining Committee: Dr. William Hsiao, Clinical Associate Professor, Dept of Pathology & Laboratory Medicine, UBC Supervisor Dr. Mel Krajden, Professor, Dept of Pathology & Laboratory Medicine, UBC Supervisory Committee Member Dr. Rachel Pottinger, Professor, Dept of Computer Science, UBC Supervisory Committee Member Dr. Patrick Tang, Clinical Professor, Dept of Pathology & Laboratory Medicine, UBC University Examiner Dr. Steven Jones, Professor, Dept of Medical Genetics, UBC University Examiner Additional Supervisory Committee Members: Dr. Elodie Portales-Casamar, Clinical Associate Professor, Department of Pediatrics, Université de Montréal Supervisory Committee Member iii Abstract Specimens and data sharing through biobanking activities has become increasingly important in global biomedical research. These practices offer the potential to accelerate scientific discovery by enabling the reuse of biospecimens and associated data. However, the benefits of data sharing can only be realized when data are findable, accessible, interoperable, and reusable (FAIR). Biobanks remain fragmented—each operating with different standards, data formats, access policies, and query interfaces—making it difficult for researchers to locate and…
has type: Thesis/Dissertation
date issued: 2026-05
is shown at: 10.14288/1.0450814
language: eng
degree discipline: Bioinformatics
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivatives 4.0 International
rights URI: http://creativecommons.org/licenses/by-nc-nd/4.0/
scholar level: Graduate
contributor: Hsiao, Will
type: Text
identifier URI: http://hdl.handle.net/2429/92976