Browsing by Author "Keppo, Stella"

Now showing 1 - 2 of 2

The endpoint tree: Designing an explorative data visualization tool for genetic research
(2022) Keppo, Stella
School of Arts, Design and Architecture | Master's thesis
This thesis is done in collaboration with FinnGen, a global research project aiming at better understanding the relationship of human genome and health. FinnGen is utilizing vast amounts and varieties of data and is thus using scientific data visualization tools and collaborating with designers in order to remodel, design and implement these tools. This study explores user-centered data visualization practices in the context of browsing phenotypic data within FinnGen. Phenotypic data in this case refers to indicators of health events or outcomes defined using different data from health registries. These indicators in FinnGen are referred to as endpoints, and they are accessed through a phenotype-level data exploration system Risteys. Risteys is a public online platform where researchers acquire information about different endpoints including facts and figures about their definitions, statistics and their relationships with other endpoints. This study asks what kind of challenges users are experiencing while exploring phenotypic data in Risteys, and how these challenges could be answered by data visualization. An understanding of best practises related to scientific data visualization tools within the topic of the study was formed through a literature review. A compact review of limits relating to reading and using data visualization tools imposed by cognitive attributes was also made. After acquiring this knowledge base, a small-scale user study was conducted with a pool of expert researchers to gather information on possible challenges relating to phenotype browsing in Risteys. Based on key findings from the user study, an interactive prototype was designed and produced to answer some of the challenges that the users were found to share. This study establishes a targeted knowledge base on designing and producing an exploratory scientific data visualization tool from a visual communication design standpoint, and contributes to the ongoing discussion about data visualization processes within the confluence of the scientific community and the visual communication design field.
LAVAA: A lightweight association viewer across ailments
(2023) Fauman, Eric B; Keppo, Stella; Cerioli, Nicola; Vyas, Rupesh; Kurki, Mitja; Daly, Mark J.; Reeve, Mary Pat
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Motivation: Biobank scale genetic associations results over thousands of traits can be difficult to visualize and navigate. Results: We have created LAVAA, a visualization web-application to generate genetic volcano plots for simultaneously considering the P-value, effect size, case counts, trait class and fine-mapping posterior probability at a singlenucleotide polymorphism (SNP) across a range of traits from a large set of genome-wide association study. We find that user interaction with association results in LAVAA can enrich and enhance the biological interpretation of individual loci. Availability and implementation: LAVAA is available as a stand-alone web service (https://geneviz.aalto.fi/LAVAA/) and will be available in future releases of the finngen.fi website starting with release 10 in late 2023.