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The Swedish Reference Genome Portal: A new service facilitating access and discovery of genome data studied in Sweden

Version 2 2024-11-13, 11:13
Version 1 2024-09-13, 06:45
poster
posted on 2024-11-13, 11:13 authored by Daniel BrinkDaniel Brink, Rory Crean, Angela P. Fuentes-PardoAngela P. Fuentes-Pardo, Quentin Ågren, Arnold KochariArnold Kochari, Henrik Lantz, Hanna KultimaHanna Kultima, Bengt Persson, Johan RungJohan Rung

This poster describes the scope, structure, and benefits of the Swedish Reference Genome Portal, a new service facilitating access and discovery of genome data studied in Sweden (https://genomes.scilifelab.se).

The poster was a contribution to the DDLS Annual Conference that took place on November 13-14, 2024 in Stockholm, Sweden.

The Swedish Reference Genome Portal is developed and maintained by the DDLS Data Science Node in Evolution and Biodiversity (DSN-EB) team as part of the SciLifeLab Data Platform, operated by the SciLifeLab Data Centre. Members of the DSN-EB team are affiliated with SciLifeLab Data Centre and the National Bioinformatics Infrastructure Sweden (NBIS), based at Uppsala University and the Swedish Museum of Natural History. This service is supported by SciLifeLab and the Knut and Alice Wallenberg foundation through the Data-Driven Life Science (DDLS) program, as well as by the Swedish Foundation for Strategic Research (SSF).

Abstract:

The Data Science Node in Evolution and Biodiversity (DSN-EB) is part of the SciLifeLab and Wallenberg National Program for Data-Driven Life Science. The node aims to create an environment where users can easily find, access, and utilize resources such as data, tools, and e-infrastructure that are essential for Swedish data-driven research in evolution and biodiversity. The first service that we will offer is a national genome portal that showcases genomic data from non-model eukaryotic species studied in Sweden. Each species will have a dedicated webpage with taxonomic, biological, and genome assembly information, as well as links to external resources such as the Swedish Biodiversity Data Infrastructure (SBDI), the European Nucleotide Archive (ENA), among others. The genome sequence and associated genomic data will be displayed in an embedded JBrowse genome browser, facilitating the visual representation of a variety of data types, session sharing, and export of publication-ready figures. Another important purpose of the genome portal is to promote and facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) sharing of valuable data files produced during genomics data analysis that rarely get published. Examples of these include assembled transcripts, and annotation of features such as methylation patterns, non-coding RNA, and repetitive elements, to name a few. The poster will introduce key features of the genome portal and illustrate what researchers need to consider when submitting genomic data to the portal. With this service, we aim to make genomics data more accessible for all users regardless of their prior level of bioinformatics knowledge. We want more additions to the portal! If you are interested, please contact us at dsn-eb@scilifelab.se.

Funding

SciLifeLab

Knut and Alice Wallenberg Foundation

Swedish Foundation for Strategic Research

History

Publisher

SciLifeLab Data Centre, National Bioinformatics Infrastructure Sweden

SciLifeLab acknowledgement

  • SciLifeLab Data Centre

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