Get started
Work

BY-COVID D1.4 The repurposing of 2 national SARS-CoV-2 data portals towards national pathogen portals

Year: 2024
Type: article
Abstract: This deliverable summarises the creation of two new national pathogen data portals for Switzerland and Norway. These portals were inspired by the Swedish Pathogens Portal, launched in September 2023 by SciLifeLab, and are part of a growing network of national COVID-19/Pathogen Data Portals. National pathogen portals are web sites that serve as community hubs for pathogen related information, guidelines, and light-weight data services and resources. Their content is relevant to, and often developed and operated by, users or organisations in the local country, while also providing a bridge to international resources such as the EMBL-EBI Pathogens Portal and other national data portals. The Swiss Pathogens Portal, launched on 29 August 2024, was developed by SIB, the Swiss ELIXIR node, who already runs and hosts the Swiss Pathogen Surveillance Platform (SPSP.ch) enabling near real-time controlled access of pathogen sequencing data and their associated clinical/epidemiological metadata. SIB created a HUGO official template theme to assist the development of other local Pathogens Portals; this is publicly available on the GitHub repository and includes many advantages outlined in the report below. The Swiss Pathogens Portal includes pathogen and infectious disease dashboards, FAIR data sharing guidelines, Swiss pathogen data catalogues hosted within national data hubs and bioinformatics resources, among others. Its goal is to better support research data management practices in the infectious diseases domain and foster collaborations and synergies. The creation of the Swiss Pathogens portal will enable capturing and highlighting existing efforts, for example, by connecting the SPSP data catalogue to the Pathogens Portal hosted by EMBL-EBI. The Norwegian Pathogens Portal, launched on 9 September 2024, developed by the Arctic University of Norway (UiT), a partner of ELIXIR Norway, aims to cover the need for an infrastructure that supports systematic and FAIR sharing of pathogen data and contextual metadata in Norway. The portal includes national resources related to pathogen research with a focus on human pathogens, but it also links to food, water and vector borne diseases and non-human related pathogens. The Norwegian Pathogens Portal uses a powerful React framework, NextJS, for frontend development, while Notion is used for content management, providing thus a user-friendly interface. Many of the functionalities of the portal are aligned with those of the Swedish and the Swiss portals. The different technological frameworks chosen by the two portals showcased in this deliverable underline the importance of flexibility and adaptability in any framework or template to reflect and meet the needs of each country and community facing unique challenges, be it cultural, technological or related to infrastructure availability.
DOI: 10.5281/zenodo.13946602
Language: English
Open Access status: green
OpenAlex ID: W6930618914
FWCI:
Cites:
Cited by:
Related to: