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 |
|---|---|---|---|
| FAIR data | fd_data_description | Apply the FAIR principles to infectious disease research data, emphasizing documentation, accessibility, metadata standards, and interoperability to promote transparency, collaboration, and reuse. | /data-description/fair-data |
| 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 |
|---|---|---|---|
| General guidelines | general_provenance | General considerations and approaches related to provenance | /provenance/general-guidelines |
| 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 |