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[submodule "themes/hugo-pathogens-portal"]

	path = themes/hugo-pathogens-portal

	url = https://github.com/sib-swiss/hugo-pathogens-portal

---

title: "Swiss Pathogens Portal: supporting researchers for pandemic preparedness and response"

---

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---

title: About the Swiss Pathogens Portal

menu:

  navbar_top:

    name: About

    weight: 1

  footer_about:

    name:  Overview

    weight: 1

layout: about_navbar

---

## Vision

Rapid and open pathogen data sharing is essential to advance research and drive effective surveillance activities. Access to comprehensive data, including genomic sequences, epidemiological information, and clinical data, empowers researchers to track the spread and evolution of pathogens in real-time. This transparency is particularly critical for studying emerging viruses, food-borne pathogens, and antimicrobial-resistant bacteria, which pose significant and complex threats to public health.

A One Health approach, which integrates human, animal, and environmental health perspectives, is crucial in addressing these challenges. By facilitating the sharing of diverse data types across disciplines, this approach promotes a holistic understanding of pathogen dynamics and fosters coordinated research efforts to develop innovative solutions. Rapid and open data sharing not only enhances our ability to respond swiftly to health crises but also accelerates scientific discovery and strengthens global health security and preparedness.

## Aims

The Swiss Pathogens Portal was developed to support researchers in realizing this vision, by notably:

* Providing a one-stop resource for all Swiss pathogen data and projects.

* Fostering collaborations and synergies by creating a forum for discussion.

* Providing documentation and training material on FAIR research data management, especially for pathogen omics data.

* Showcasing Swiss resources that contribute to pathogen data sharing, access, analysis, and interpretation.

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---

title: Programs and Organizations behind the Portal

menu:

  footer_about:

    name:  Partners

    weight: 3

layout: about_navbar

---

{{< organization img="./pathogens_portal_logo.png" name="Pathogens Portal">}}

The Pathogens Portal, launched in July 2023, is an invaluable resource for researchers, clinicians, and policymakers who need access to the latest and most comprehensive datasets on pathogens. The portal is a collaborative effort between the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and partners. The Pathogens Portal provides a centralised platform for sharing and accessing data on key pathogens, including those that can cause diseases in humans and animals, and on vectors and hosts. By bringing together data from multiple sources, and linking these data where possible, the portal enables researchers to better understand the biology and life cycles of pathogens. These pathogens include both pathogens affecting humans and animals, and on vectors and hosts. It is funded through five European Union projects funded under the Horizon 2020 and Horizon Europe programmes: RECODID, VEO, EOSC-Life, CONVERGE and BY-COVID.

The national Pathogens Portals provide information, guidelines, tools and services to support researchers in creating and sharing research data on all pathogens and diseases. The purpose of the national portals is to showcase and highlight pathogen research data from each of the participating countries. Similar to the Pathogens Portal, the national portals rely on open and fair access of sequence and other omics data. The national portals are regularly updated with new tools, services and data.

{{< /organization >}}

{{< organization img="./swe_pathogens_portal_logo.png" name="The Swedish Pathogens Portal">}}

The Swedish Pathogens Portal provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden.

The Portal is operated by the SciLifeLab Data Centre and partners, who developed an open reference implementation for national data portals using Hugo in combination with Bootstrap for styling, DataTables for tables, and Vega/Vega-Lite and Plotly for interactive graphics. All code used for the Swedish Portal is open source (held under an MIT licence) and is available on GitHub. The Swiss Pathogens Portal reused the code from the Swedish Portal.

{{< /organization >}}

{{< organization img="./elixir_logo.png" name="ELIXIR">}}

ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers. Under Web portals (https://elixir-europe.org/what-we-offer/portals) you will find useful portals to support you in making your data and software FAIR. 

{{< /organization >}}

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