Model, Integrate, Search... Repeat: A Sound Approach to Building Integrated Repositories of Genomic Data

Foreword
Preface
Acknowledgements
Contents
Acronyms
Introduction
	Genomic Data Integration
	Thesis Contribution within the GeCo Project
	The Recent COVID-19 Pandemic
	Thesis Structure
Part I Human Genomic Data Integration
Genomic Data Players and Processes
	Technological Pipeline of Genomic Data
		Production
		Integration
		Services and Access
	Taxonomy of Players Involved in Data Production and Integration
	Main Genomic Data Players
		Contributors
		Repository Hosts
		Consortia
		Integrators
Modeling Genomic Data
	The Genomic Data Model
	The Genomic Conceptual Model
		Analysis of Metadata Attributes
		Model Design
		Validation: Source-Specific Views of GCM
	Related Works
Integrating Genomic Data
	Theoretical Rationale
	Approach Overview
	Data Download
	Data Transformation
	Data Cleaning
	Data Mapping
	Data Normalization and Enrichment
		Search Service and Ontology Selection
		Enrichment Process
	Data Constraint Checking
	Architecture Implementation
		Data Persistence
	Architecture Validation
		Lossless Integration
		Semantic Enrichment
		User Evaluation
	Related Works
Snapshot of the Data Repository
	Included Data Sources
	OpenGDC: Integrating Cancer Genomic Data and Metadata
	Towards Automated Integration of Unstructured Metadata
		Experiments
		Related Works
Searching Genomic Data
	Issues in Exploiting Semantic Knowledge in Genomics
	Inference Explanation
	GeKnowGraph: Exploration-Based Interface
		Exploration Interaction
	GenoSurf: a Web-Based Search Server for Genomic Datasets
		Data Search
		Key-Value Search
		Query Sessions
		Result Visualization
		Additional Functionalities
		Use Cases
		Validation of GenoSurf
	Related Works
Future Directions of the Data Repository
	Including New Data Sources
	Improving Genomic Data Quality Dimensions
	Towards Better Interoperability
	Simplifying Data and Tools for End Users
	Monitoring Integration and Search Value
Part II Viral Sequence Data Integration
Viral Sequences Data Management Resources
	Landscape of Data Resources for Viral Sequences
		Fully Open-Source Resources
		GISAID and its Resources
	Integration of Sources of Viral Sequences
		Metadata Integration
		Value Harmonization and Ontological Efforts
		Replicated Sequences in Multiple Sources
	SARS-CoV-2 Search Systems
		Portals to NCBI and GISAID Resources
		Integrative Search Systems
		Comparison
	Discussion
		GISAID Restrictions
		Metadata Quality
		(Un)Willingness to Share Sequence Data
Modeling Viral Sequence Data
	Conceptual Modeling for Viral Genomics
	Answering Complex Biological Queries
	Related Works
Integrating Viral Sequence Data
	Database Content
	Relational Schema
	Data Import
	Annotation and Variant Calling
	Data Curation
Searching Viral Sequence Data
	Requirements Analysis
		Lessons Learnt
	Web Interface
	Example Queries
	Discussion
	Related Works
Future Directions of the Viral Sequence Repository
	Research Agenda
	ViruSurf Extensions
	Visualization Support: VirusViz
	Active Monitoring of SARS-CoV-2 Variations
	Integrating Host-Pathogen Information
		The Virus Genotype – Host Phenotype Connection
		The Host Genotype – Host Phenotype Connection
Part III Epilogue
Conclusions and Vision
	Summary of Thesis Contributions
	Achievements within GeCo Project
	Outlook
META-BASE tool configuration
	User Manual
	Process Configuration
	Mapper Configuration
Experimental setup GEO metadata extraction
Mappings of viral sources attributes into ViruSurf
References