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Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
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2019 (English)In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, article id 813Article, review/survey (Refereed) Published
Abstract [en]

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019. Vol. 10, article id 813
Keywords [en]
database, content management system, forest tree, bioinformatics, web services
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-161586DOI: 10.3389/fpls.2019.00813ISI: 000473047200001OAI: oai:DiVA.org:umu-161586DiVA, id: diva2:1338360
Available from: 2019-07-22 Created: 2019-07-22 Last updated: 2020-05-05Bibliographically approved
In thesis
1. Human-computer interaction principles for developing web-based genomics resources
Open this publication in new window or tab >>Human-computer interaction principles for developing web-based genomics resources
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Mänskliga-datorinteraktion principer för utveckling av webb-baserade resurser för genomik
Abstract [en]

Genomics projects, including genome sequencing, transcriptomics, genome-wide association mapping and epigenetics assays, producevast quantities of data. Extracting the required information from such complex datasets is a significant challenge and even where software tools do exist, these are often not intuitive or designed fornon-specialist users. This dissertation details how I have applied design principles from the field of Human-Computer Interaction (HCI) to the development of intuitive bioinformatics web-based resources for exploring genomics data. In the first part of the thesis I detail the development of a specialised genomics resource that enables non specialists who lack bioinformatics skills to access, explore and extract new knowledge from a variety of genomics data types. These tools were developed in collaboration with wet lab biologists and bioinformaticians who represent typical end-users. The tools developed have been integrated within the PlantGenIE (Plant Genome IntegrativeExplorer) web resource, which has been established as a platform for exploring genomics data for Populus, conifer, Eucalyptus and Arabidopsisgenomics data. Even though the ability to collect, store and manage data is increasing faster due to new technologies and science, our ability to understand it remains constant. To help address this, in the second part of this dissertation I focus on the usability enhancement of tools based on the HCI and User Experience (UX) practices. To achieve this, I utilised visualisation techniques and design principles in the design process for the improvement of the PlantGenIEUser Interface (UI), and applied usability methods to evaluate the UX of PlantGenIE tools. These results were then used to inform adaptations and fine-tuning of those. I show that utilisation of these research methods and practices with the development life cycle represents a framework for designing usable bioinformatics tools. Wider-scale use of these methods by future designers and developers will enable the creation of more usable bioinformatics resources.

Place, publisher, year, edition, pages
Umeå: Umeå Universitet, 2020. p. 62
National Category
Bioinformatics and Systems Biology Genetics Human Computer Interaction
Identifiers
urn:nbn:se:umu:diva-170109 (URN)978-91-7855-284-9 (ISBN)978-91-7855-285-6 (ISBN)
Public defence
2020-06-11, Stora hörsalen (KB3B1), KBC-huset, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2020-05-20 Created: 2020-04-27 Last updated: 2020-05-25Bibliographically approved

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Mannapperuma, Chanaka
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Department of Plant PhysiologyUmeå Plant Science Centre (UPSC)
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