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List of page IDs

Data analysis

title page_id description url
Human biomolecular data hbd_data_analysis Analysing Human biomolecular related data. /data-analysis/human-biomolecular-data
Pathogen characterisation pc_data_analysis Analysing Pathogen related data. /data-analysis/pathogen-characterisation
Socioeconomic data sed_data_analysis Generic workflows for different data types. /data-analysis/socioeconomic-data

Data communication

title page_id description url
Data communication data_communication Producing visualisations and reports /data-communication/

Data description

title page_id description url
Human clinical and health data hchd_data_description Guidance in describing human clinical and health data. /data-description/human-clinical-and-health-data
Pathogen characterisation pc_data_description Finding (meta)data standards and documentation. /data-description/pathogen-characterisation

Data sources

title page_id description url
Human biomolecular data hbd_data_sources Finding and sharing data for human biomolecular related data sources. /data-sources/human-biomolecular-data
Human clinical and health data hchd_data_sources Finding and sharing data from human clinical and health data related data sources. /data-sources/human-clinical-and-health-data
Socioeconomic data sed_data_sources Finding and sharing data for socioeconomic related data sources. /data-sources/socioeconomic-data

Ethical, Legal, and Social Issues

title page_id description url
Ethical, Legal, and Social Issues ethical_legal_and_social_issues This page offers guidance on how to comprehensively assess the ELSI aspects of your work throughout all stages of data management, from study planning and data collection to processing, analysis, sharing, and archiving. /ethical-legal-and-social-issues/

Provenance

title page_id description url
Human clinical and health data hchd_provenance Tracking data and analysis steps. /provenance/human-clinical-and-health-data
Socioeconomic data sed_provenance Tracking socioeconomic data and documenting the analysis steps applied to it. /provenance/socioeconomic-data

Quality control

title page_id description url
Human biomolecular data hbd_quality_control This page explains in detail the importance of quality control for human biomolecular data in the context of infectious diseases, as well as explains the steps to follow. /quality-control/human-biomolecular-data
Human clinical and health data hchd_quality_control General considerations for human clinical and health data quality control. /quality-control/human-clinical-and-health-data
Pathogen characterisation pc_quality_control General considerations for pathogen characterization quality control. /quality-control/pathogen-characterisation
Socioeconomic data sed_quality_control Tools and methods to assess quality of socio-economics data. /quality-control/socioeconomic-data

Showcase

title page_id description url
An automated pipeline for analysing brain autoradiography images brain_autoradiography Development of an open source, semi-automated processing pipeline for aligning autoradiography images from mouse brain tissue to study infection-induced neuroinflammation funded by the ISIDORe project. /showcase/brain-autoradiography
An automated SARS-CoV-2 genome surveillance system built around Galaxy covid19_galaxy_project An automated, modular system for large-scale FAIR analysis of SARS-CoV-2 sequencing data analysis powered by the Galaxy platform. /showcase/covid19-galaxy
Using the ENA data submission toolbox for SARS-CoV-2 data ena_upload High scale publishing of infectious diseases data to ENA using easy to use metadata templates. /showcase/ena-data-submission-toolbox
Prevalence study of SARS-CoV-2 in Estonia: lessons learned prevalence_est Insights and practical guidelines from the SARS-CoV-2 prevalence study in Estonia (2020-2023). /showcase/estonian-prevalence-study
Knowledge Graph Generator (KGG) - A fully automated workflow for creating disease-specific KGs knowledge_graph_generator Open source workflow integrating biological databases for FAIR data compliant Knowledge Graphs /showcase/knowledge-graph-generator
SARS-CoV-2 sequencing in Estonia 2021-2022 korogenoest Full-genomic sequencing and analysis of SARS-CoV-2 strains in Estonia during 2021-2022. /showcase/korogenoest
Linked pathogen and host data across archives - a multi-omics, SARS-CoV-2 cohort case study linked_cohort_data Here we describe the first example of linking and sharing a COVID-19, multi-omics cohort data set via the EMBL-EBI infrastructure. /showcase/linked-cohort-data
Prototyping federated causal research questions reusing sensitive health data prototyping_research_questions Methodological framework for causal federated research based on real-world observational data sources across national borders /showcase/prototyping-research-questions
The Swedish Pathogens Portal swedish_pathogens_portal A web portal that provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden. We offer support to all those involved in pandemic preparedness research that are affiliated with a Swedish research institution or university. /showcase/swedish-pathogens-portal