From 14323e6405a19c175988c5d6283dfe74a68167f5 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:55:32 +0200 Subject: [PATCH 01/17] add separator lines (#183) --- _sass/_custom_classes.scss | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss index bca26411..24ffc422 100644 --- a/_sass/_custom_classes.scss +++ b/_sass/_custom_classes.scss @@ -105,6 +105,11 @@ main { border-left-color: $primary; } } + + &.mt-3 { + padding-top: $spacer; + border-top: $border-width $border-style $border-color; + } } } } From b345b90f8b6baed7b9315e4e33a61445cd252f61 Mon Sep 17 00:00:00 2001 From: Patricia Palagi Date: Tue, 19 Sep 2023 08:55:22 +0200 Subject: [PATCH 02/17] Update data-sources.md (#232) * Update data-sources.md I have updated the text of this page to correspond to the modifications in the Google doc as of 18/Sep/2023. * Update data-sources.md added EUI data portal in the new way of tagging tools --------- Co-authored-by: Laura Portell Silva <74184187+lauportell@users.noreply.github.com> --- socioeconomic-data/data-sources.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/socioeconomic-data/data-sources.md b/socioeconomic-data/data-sources.md index 4bb09a2e..24a7b1be 100644 --- a/socioeconomic-data/data-sources.md +++ b/socioeconomic-data/data-sources.md @@ -27,22 +27,22 @@ This page provides an introduction to socioeconomic data for infectious disease Social science research is devoted to studying societal phenomena, social changes and the impact on the individuals. The discipline includes branches such as political science, psychology, economics, and sociology, among several others. All disciplines of social sciences have a common ground of producing knowledge around the study of various aspects of human action and cultural interaction. -Social science data can provide important insights for infectious diseases research, as well as policy for disease preparedness and mitigation. For example, social sciences can help understand +Social science data can provide important insights for infectious diseases research, as well as policy for disease preparedness and mitigation. For example, social sciences can help understand: - how infectious diseases spread among and impact different segments of society such as different socioeconomic groups or economic sectors; - how effective different government strategies are at combating the spread of a virus; - how political and psychological factors can affect vaccine uptake; - provide the socioeconomic elements on which policies and communication actions should focus and/or adapt in order to be more efficient. -For these reasons, the social sciences are considered a crucial aspect to deal with infectious diseases, including COVID-19. To facilitate this effort, social science data is mobilized via the {% tool "covid-19-data-portal" %} to achieve the following objectives: +For these reasons, the social sciences are considered a crucial aspect to deal with infectious diseases, including COVID-19. To facilitate this effort, social science data is mobilised via the {% tool "covid-19-data-portal" %} to achieve the following objectives: - Connect it with other sources of data such as clinical or virological data. -- Standardize social science data. +- Standardise social science data. - Provide methods and protocols for exposing and analysing it. ### Considerations -- **Methodologies**: Social sciences methodologies are quite diverse and complex as they try to investigate complex, changeable, and often intangible social phenomena such as trust, ideology, or socioeconomic status. Thus, social sciences use both quantitative and qualitative research methods, often in combination, ranging from large scale quantitative surveys, to interviews or ethnographic research. As such, socioeconomic research methodologies and data often differs significantly from the those typically used in the life sciences. +- **Methodologies**: Social sciences methodologies are quite diverse and complex as they try to investigate complex, changeable, and often intangible social phenomena such as trust, ideology, or socioeconomic status. Thus, social sciences use both quantitative and qualitative research methods, often in combination, ranging from large scale quantitative surveys, to interviews or ethnographic research. As such, socioeconomic research methodologies and data often differ significantly from those typically used in the life sciences. - **Sensitive data and privacy**: due to the prevalence of sensitive and personal data in socioeconomic research, access to such data is often limited by serious data protection and privacy concerns, often making the use and sharing of such data difficult. Solutions such as pseudonymising data, or providing access via secure environments such as the {% tool "oddisei-secure-analysis-environment" %} can often provide some level of access to sensitive data, yet much of this data is only available on request, or as aggregated data. @@ -58,20 +58,22 @@ From the demography perspective, there have been surveys and related publication - the role of nursing homes, especially during the first wave ([Bernandi et al. 2021](https://doi.org/10.1186/s41118-021-00119-5)); - the role of gender or socioeconomic status ([Horton 2020](https://pubmed.ncbi.nlm.nih.gov/32979964/)). -From the perspective of political science, psychology or sociology sciences’ perspective, surveys that studied the effect of conspiracy theories regarding vaccines, propagation of virus and others, have show clusters of people that relate resistance to vaccines with respect to personal ideology, adherence to conspiracy theories or that lower level of education, religiosity, conspiracy thinking can be an indicator for vaccine resistance. +From the political science, psychology or sociology sciences’ perspective, surveys that studied the effect of conspiracy theories regarding vaccines, propagation of virus and others, have shown clusters of people that relate resistance to vaccines with respect to personal ideology, adherence to conspiracy theories or that lower level of education, religiosity, conspiracy thinking can be an indicator for vaccine resistance. Even industrial advanced societies proved that they were not well-prepared to combat the devastated pandemic. Lessons learnt should focus on how to adjust health systems responses but also to find ways to strengthen trust among citizens building on resilience, access to information and services for all. +- Examples of successful uses of social science in infectious diseases research (e.g. ([this](https://madoc.bib.uni-mannheim.de/55629/), or e.g. [papers describing this](https://link.springer.com/content/pdf/10.1007/s13194-021-00416-y.pdf) +- Journals, outlets, platforms, communities etc. for related research - e.g. [BY-COVID Zenodo Community](https://zenodo.org/communities/bycovid/?page=1&size=20), [COVID-19 Social Science working group (who.int)](https://www.who.int/publications/m/item/covid-19-social-science-working-group), relevant [FAIRsharing resources](https://fairsharing.org/3494) -## Relevant data sources -Currently, the COVID-19 Data Portal contains over 537 metadata records from the [Consortium of European Social Science Data Archives' (CESSDA)](https://www.cessda.eu/) {% tool "cessda-data-catalogue" %}, which will soon be joined by data from the [European University Institute's (EUI)](https://www.eui.eu/en/home) {% tool "eui-covid-19-ssh-data-portal" %}. +## Search and discoverability +Currently, the COVID-19 Data Portal contains metadata records from the [Consortium of European Social Science Data Archives' (CESSDA)](https://www.cessda.eu/) {% tool "cessda-data-catalogue" %} and the [European University Institute's](https://www.eui.eu/en/home) (EUI) {% tool "eui-covid-19-ssh-data-portal" %}. For socioeconomics, two primary data sources are considered and are outlined in this section. These data sources provide data that relate to or are relevant for COVID-19 and other infectious disease outbreaks. These data sources are filtered for data relevant to COVID-19, and the resulting metadata is prepared and harmonized via a [harvesting tool](https://t2-4.by-covid.bsc.es/jspui/) before being added to the COVID-19 Data Platform (for more details, see project deliverable [D2.1](https://zenodo.org/record/7017728)). ### Considerations -- **Licenses**: Socio-economic data sources are generally public and accessible, but authorization or licensing agreements may be required to access some datasets. While the complete datasets may not always be openly available, the metadata is typically freely accessible. Socioeconomic data sources also offer programmatic access to their metadata using standards like the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH). This enables the automated harvesting, harmonisation, and transformation of metadata into the OmicsDI format, which can then be used by the COVID-19 Data Portal. +- **Licenses**: Socio-economic data sources are generally public and accessible, but authorisation or licensing agreements may be required to access some datasets. While the complete datasets may not always be openly available, the metadata is typically freely accessible. Socioeconomic data sources also offer programmatic access to their metadata using standards like the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH). This enables the automated harvesting, harmonisation, and transformation of metadata into the OmicsDI format, which can then be used by the COVID-19 Data Portal. ### Existing approaches From 4095ebfdce17f2e58dc584e74d1dee735857b71d Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Tue, 19 Sep 2023 10:57:17 +0200 Subject: [PATCH 03/17] Update CODE_OF_CONDUCT.md (#233) --- CODE_OF_CONDUCT.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 1241f9c8..28b262fb 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -52,7 +52,7 @@ As such, we do not tolerate behaviour that is disrespectful to our community mem We do not tolerate discrimination or harassment based on characteristics that include, but are not limited to: gender identity and expression, sexual orientation, disability, physical appearance, body size, citizenship, nationality, ethnic or social origin, pregnancy, familial status, veteran status, genetic information, religion or belief (or lack thereof), membership of a national minority, property, age, education, socio-economic status, technical choices, and experience level. Everyone who participates in the Infectious Diseases Toolkit activities is required to conform to this Code of Conduct. -This Code of Conduct applies to all spaces managed by the Turing Way project including, but not limited to, in person focus groups and workshops, and communications online via GitHub. +This Code of Conduct applies to all spaces managed by the Infectious Diseases Toolkit including, but not limited to, in person focus groups and workshops, and communications online via GitHub. By participating, contributors indicate their acceptance of the procedures by which the Infectious Diseases Toolkit project core development team resolves any Code of Conduct incidents, which may include storage and processing of their personal information. ### 2.1 Expected behaviour From 57b9985653cc4233134a76804ecb4093acec936f Mon Sep 17 00:00:00 2001 From: Laura Portell Silva <74184187+lauportell@users.noreply.github.com> Date: Tue, 19 Sep 2023 13:26:44 +0200 Subject: [PATCH 04/17] Update human biomolecular data sources page (#155) * Update data sources page * Update data-sources.md * Update data-sources.md (#203) Add of Data Deposition part * adding commit a1609a3 * Update data-sources.md (#205) Put links to data deposition * Update data-sources.md (#206) Update links in data deposition * Update data-sources.md (#207) Removal of Beacon training UI link * Update data-sources.md (#215) * Update tool_and_resource_list.yml * new way of adding tools new way of adding tools * take away full link * Add tools in the yaml Add tools in the yaml * fix in breaking decr * Add missing tools in the new way Add missing tools in the new way --------- Co-authored-by: solcos <92781950+solcos@users.noreply.github.com> Co-authored-by: bedroesb Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> --- _data/tool_and_resource_list.yml | 20 ++- human-biomolecular-data/data-sources.md | 185 ++++++++++++++++++------ 2 files changed, 156 insertions(+), 49 deletions(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 5c97209d..beff00ed 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -10,7 +10,7 @@ registry: tess: ACE Cohort url: https://co-connect.ac.uk/ace-cohort/ -- description: Responsible sharing of biomedical data and biospecimens via the "Automatable Discovery and Access Matrix" (ADA-M). The Automatable Discovery and Access Matrix (ADA-M) provides a standardized way to unambiguously represent the conditions related to data discovery and access. By adopting ADA-M, data custodians can generally describe what their data are (the Header section), who can access them (the Permissions section), terms related to their use (the Terms section), and special conditions (the Meta-Conditions). By doing so, data custodians can participate in data sharing and collaboration by making meta information about their data computer-readable and hence directly available for digital communication, searching and automation activities. +- description: Responsible sharing of biomedical data and biospecimens via the Automatable Discovery and Access Matrix (ADA-M). The Automatable Discovery and Access Matrix (ADA-M) provides a standardized way to unambiguously represent the conditions related to data discovery and access. By adopting ADA-M, data custodians can generally describe what their data are (the Header section), who can access them (the Permissions section), terms related to their use (the Terms section), and special conditions (the Meta-Conditions). By doing so, data custodians can participate in data sharing and collaboration by making meta information about their data computer-readable and hence directly available for digital communication, searching and automation activities. id: ada-m name: ADA-M registry: @@ -709,3 +709,21 @@ id: wfexs name: WfExS url: https://github.com/inab/WfExS-backend +- description: An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. + id: dcat + name: DCAT + url: https://www.w3.org/TR/vocab-dcat-2/ + registry: + fairsharing: h4j3qm +- description: The dutch COVID-19 Data Portal provides researchers with a clear overview of what is available, allow searching for specific data and make access to such data easier when the necessary ethical and legal conditions have been met. + id: dutch-covid19-data-portal + url: https://covid19initiatives.health-ri.nl/p/Dashboard + name: Dutch COVID-19 Data Portal +- description: The Federated EGA is an infrastructure built upon the European Genome-phenome Archive (EGA), an EMBL-EBI and CRG data resource for secure archiving and sharing of human sensitive biomolecular and phenotypic data resulting from biomedical research projects. + id: fega + name: Federated EGA + url: https://www.covid19dataportal.org/federated-ega +- description: Using technology that builds upon existing EMBL-EBI infrastructure, we provide SARS-CoV-2 Data Hubs to those public health agencies and other scientific groups responsible for generating viral sequence data from the outbreak at national or regional levels. + id: sars-cov2-data-hubs + name: SARS-CoV-2 Data Hubs + url: https://www.covid19dataportal.org/data-hubs diff --git a/human-biomolecular-data/data-sources.md b/human-biomolecular-data/data-sources.md index 56766747..29cdf2d9 100644 --- a/human-biomolecular-data/data-sources.md +++ b/human-biomolecular-data/data-sources.md @@ -1,16 +1,21 @@ --- title: Data sources description: Finding and sharing data for human biomolecular related data sources. -contributors: [] -no_robots: true +contributors: [Aina Jené Cortada, Arnau Soler Costa] page_id: hbd_data_sources rdmkit: - - name: - url: + - name: Human Data + url: https://rdmkit.elixir-europe.org/human_data + - name: Sensitive Data + url: https://rdmkit.elixir-europe.org/sensitive_data + - name: Biomolecular simulation data + url: https://rdmkit.elixir-europe.org/biomolecular_simulation_data + - name: Data transfer + url: https://rdmkit.elixir-europe.org/data_transfer related_pages: showcase: [] - human_biomolecular_data: [] - human_clinical_and_health_data: [] + human_biomolecular_data: [hbd_data_description] + human_clinical_and_health_data: [hchd_data_sources, hchd_data_description] socioeconomic_data: [] pathogen_characterisation: [] training: @@ -20,93 +25,177 @@ training: # More information on how to fill in this metadata section can be found here https://www.infectious-diseases-toolkit.org/contribute/page-metadata --- -**We are still working on the content for this page.** If you are interested in adding to the page, then: +## Introduction -[Feel free to contribute](/contribute/){: class="btn btn-primary btn-lg rounded-pill"} +This document aims to serve as a comprehensive resource for anyone interested in the data sources platforms of infectious diseases using human biomolecular data, which have become increasingly important in recent years as a result of advancements in technology and the ever-growing threat of global pandemics. -This is a community-driven website, so contributions are welcome! You will, of course, be listed as a contributor on the page. +By providing this overview of the data sources platforms of infectious diseases using human biomolecular data, this document aims give the user information on where to find these types of data and how to access them (secondary use of the data) and to facilitate the development of new research initiatives and collaborations in the field. -New content is announced on the [home page](/) and [news page](/about/news), so please check for updates there. You can also watch for changes on this page by using a free service like [Visual Ping](https://visualping.io/) or [Distill Web Monitor](https://distill.io/), or by using a [browser add-on](https://chrome.google.com/webstore/detail/distill-web-monitor/inlikjemeeknofckkjolnjbpehgadgge?hl=en). - +### What is human biomolecular data, and why is it important for infectious diseases research? -## Introduction +Human biomolecular data refers to information obtained from the analysis of biological molecules, such as DNA, RNA, proteins, and metabolites. This type of data is used to study the molecular mechanisms underlying disease and to identify potential drug targets. -## What is human biomolecular data, and why is it important for infectious diseases research? +Human clinical data, on the other hand, refers to information obtained from the study of patients, including their medical histories, physical exams, and laboratory tests. This type of data is used to diagnose and treat disease, as well as to evaluate the safety and efficacy of new therapies. -## Topic 1 +While both types of data are important for understanding human health and disease, they are collected and analysed in different ways and for different purposes. - +Human biomolecular data is of great importance in infectious disease research because it plays a critical role in understanding the molecular basis of the disease. By analyzing the biomolecular data, researchers can gain a deeper understanding of the disease's pathogenesis, evolution, and transmission. Personalised medicine is another area where biomolecular data can be applied. By analyzing an individual's biomolecular data, researchers can develop personalised treatment plans that are tailored to the specific needs of the patient. For example, if a patient has a genetic mutation that predisposes them to a particular disease, this information can be used to develop a personalised treatment plan that takes into account the patient's genetic profile. -Short explanation of what this topic is about and why it is important, with an emphasis on infectious diseases and the category that you selected. +Furthermore, its significance extends far beyond disease diagnosis and treatment, encompassing a broader scope of applications. For instance, a secondary use of human biomolecular data becomes vital at the population level, facilitating important policy responses during future infectious disease outbreaks. Additionally, investigating the cost-effectiveness of interventions based on these datasets enables optimal resource allocation for the most impactful healthcare strategies. By analyzing this data, we can make well-informed decisions to protect public health in a long term. -### Considerations +It is important to mention that most analyses of human biomolecular data are complemented by using the clinical data related to them. -Using a bullet point style list format as much as possible, describe the considerations for your topic that are specific to infectious diseases within the category (e.g. pathogen characterisation) that you have selected. + -Please avoid replicating 'generic' guidelines, i.e. those not specific to infectious diseases, here. Add links to RDMkit in the metadata above, if any are needed. + -### Existing approaches + -Mention existing approaches related to the topic. +## Data deposition -## Topic 2 - - - -Short explanation of what this topic is about and why it is important, with an emphasis on infectious diseases and the category that you selected. +For advancing in the understanding of human biomolecular data, data deposition plays a pivotal role. The deposition of this data in publicly accessible databases serves as a valuable resource for scientists and researchers worldwide. It enables the integration and analysis of diverse datasets as well as by sharing and archiving data, researchers can ensure the reproducibility and transparency of their findings, allowing others to validate and build upon their work, encouraging collaboration. +In summary, data deposition not only fuels scientific progress but also empowers the global scientific community to unlock the complexities of human biology, ultimately leading to improved health outcomes and advancements in medical research. ### Considerations -Using a bullet point style list format as much as possible, describe the considerations for your topic that are specific to infectious diseases within the category (e.g. pathogen characterisation) that you have selected. +- Choose a reliable and established public database or repository for data deposition. +- Ensure that the data is properly organized, documented, and annotated for easy understanding and interpretation. +- Adhere to data sharing and privacy regulations to protect sensitive information and maintain data confidentiality. +- Include metadata, such as experimental protocols, sample characteristics, and data processing methods, to provide context and facilitate reproducibility. +- Use standardized data formats and ontologies to enhance interoperability and enable integration with other datasets. +- Use metadata standards (such as {% tool "dcat" %}) to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. It further enables decentralized publishing of catalogs and facilitates federated dataset search across sites. +- Include appropriate quality control measures to ensure data accuracy and reliability. +- Consider data anonymization or de-identification techniques to protect the privacy of individuals involved in the study. +- Provide sufficient data access and sharing permissions, specifying any restrictions or limitations, while ensuring compliance with legal and ethical requirements. +- Consider long-term data preservation strategies to ensure the accessibility and availability of the deposited data for future researchers. +- Promote open and collaborative practices by encouraging data citation and acknowledgement to recognize the contributions of the original data creators. -Please avoid replicating 'generic' guidelines, i.e. those not specific to infectious diseases, here. Add links to RDMkit in the metadata above, if any are needed. +Please note that these considerations are general in nature and may vary depending on the specific requirements and guidelines of the chosen data repository or database. ### Existing approaches -Mention existing approaches related to the topic. +- **Public databases:** Various publicly accessible databases serve as repositories for human biomolecular data, such as the National Center for Biotechnology Information ([NCBI](https://www.ncbi.nlm.nih.gov/)) databases (e.g., {% tool "genbank" %}, {% tool "geo" %}, {% tool "sra" %} and European Bioinformatics Institute ({% tool "ebi" %}) databases (e.g., {% tool "european-nucleotide-archive" %}, {% tool "arrayexpress" %}). +- **Controlled access repositories:** Some data deposition platforms, like dbGaP ({% tool "dbgap" %}) and EGA ({% tool "ega" %}), adopt a controlled access model to protect sensitive human biomolecular data. Researchers interested in accessing the data need to request permission and comply with specific data usage policies. +- **Data integration platforms:** Platforms like the Global Alliance for Genomics and Health ([GA4GH](https://www.ga4gh.org/)) provide frameworks and standards for federated data access and integration across multiple repositories. These initiatives aim to facilitate the aggregation and analysis of human biomolecular data from diverse sources while maintaining data privacy and security. +- **Data citation and DOI assignment:** To acknowledge and promote the contributions of researchers who deposit human biomolecular data, many repositories assign unique digital object identifiers (DOIs) to datasets. This enables proper citation and recognition of the deposited data, enhancing its visibility and impact. +- **Data submission portals:** Some repositories offer user-friendly web portals or submission systems that guide researchers through the process of depositing human biomolecular data. These portals often provide templates, validation checks, and step-by-step instructions to ensure the completeness and quality of the deposited data. +- **Consortium-specific databases:** Collaborative research initiatives often establish dedicated databases for sharing and depositing human biomolecular data, such as The Cancer Genome Atlas ({% tool "tcga" %}) for cancer genomics data or the Genotype-Tissue Expression ({% tool "gtex" %}) project for gene expression data across different tissues. +- **Standardized data formats:** Commonly used data formats like FASTQ, BAM, and VCF facilitate data deposition and sharing by ensuring compatibility and interoperability between different analysis tools and databases. +- **Data publication:** Journals and publishers increasingly require researchers to deposit their human biomolecular data in public repositories as a prerequisite for publication. This promotes data sharing, reproducibility, and transparency in scientific research. +- **Data sharing platforms:** Online platforms like {% tool "figshare" %}, {% tool "zenodo" %}, and {% tool "dryad" %} provide researchers with the means to deposit and share their human biomolecular data, ensuring its long-term accessibility and enabling collaboration. + +## Search and discoverability -## Standards, schemas, ontologies and vocabularies +**Search and discoverability** are crucial for finding and accessing relevant information, resources, and data related to a specific topic or area of interest. Infectious diseases can evolve rapidly and have significant impacts on public health, making it necessary to monitor and respond to outbreaks effectively. This requires access to up-to-date information on disease prevalence, transmission patterns, and clinical outcomes, which can come from various sources, such as clinical data, biomolecular data, public health reports, and social media. - +**Standardised terminology and data formats** are also essential for effective search and discoverability in infectious disease surveillance. The use of common disease codes and data structures can facilitate the integration and analysis of data from multiple sources, making it easier to identify trends and patterns. This can improve the ability to identify emerging disease threats and develop effective disease control measures. See [Data harmonisation](#data-harmonisation) section. -List of standards, schemas, ontologies and/or vocabularies that are relevant to the resources in this category. Consider having links to the "Data description" page. -When applicable, consider adding the appropriate FAIRsharing entry to the tools and resources spreadsheet so that they can be listed and appropriately tagged at the end of the page +**Biomolecular data sources** can be facilitated through the use of standardised data formats and data sharing platforms, allowing the development of effective diagnostic and treatment strategies of infectious diseases data. + +Overall, search and discoverability are essential for effective infectious disease surveillance and response. By ensuring that relevant data sources are easily accessible and usable, public health professionals can more effectively monitor and control the spread of infectious diseases, ultimately protecting public health. ### Considerations -Using a bullet point style list format as much as possible, describe the considerations for your topic that are specific to infectious diseases within the category (e.g. pathogen characterisation) that you have selected. +Despite the growing amount of infectious disease data stored in various sources, finding and analyzing this data can be challenging for the scientific community. There is a clear need for a user-friendly and efficient way to discover and analyse this data. -Please avoid replicating 'generic' guidelines, i.e. those not specific to infectious diseases, here. Add links to RDMkit in the metadata above, if any are needed. +- **Data sharing platforms**: Access to data sharing platforms can facilitate the discovery and sharing of biomolecular data related to infectious diseases. Such as the {% tool "covid-19-data-portal" %}. +- **Data privacy and security**: Privacy and security protocols must be in place to protect sensitive biomolecular data from unauthorised access. +- **National regulations**: Taking into account the National regulations and the General Data Protection Regulation ([GDPR](https://gdpr-info.eu/)) rules. +- **Data quality**: High-quality biomolecular data is critical for accurate disease surveillance, diagnosis, and analysis. Efforts should be made to ensure that data quality is maintained throughout the data lifecycle. See [Human biomolecular data - Quality control](/human-biomolecular-data/quality-control) page. +- **Data storage and management**: Proper data storage and management practices must be followed to ensure that biomolecular data is organised and easily accessible to relevant parties. +- **Metadata**: Metadata should be included with biomolecular data to provide context and facilitate search and discoverability. +- **Collaboration**: Collaboration between data producers, curators, and users can promote effective search and discoverability of biomolecular data related to infectious diseases. +- **Data standardization**: Standardised data formats and common disease codes are essential for integrating and analyzing biomolecular data from different sources. ### Existing approaches -Mention existing approaches related to the topic. +Consequently, we have compiled some of the main tools, portals, and data sharing platforms that allow for searching and discovering biomolecular data related to infectious diseases from various sources with the next considerations. + +- Beacon: {% tool "beacon" %} is an API (usually extended with a user interface) that allows for data discovery of phenoclinic and biomolecular data. The version 2 (v2) of the Beacon protocol has been accepted as GA4GH standard in Spring 2022. It includes, among other changes: + - Query options for biological or technical metadata using filters defined through CURIEs (e.g. phenotypes, disease codes, sex or age). + - An option to trigger the next step in the data access process (e.g. who to contact or which are the data use conditions). + - An option to jump to another system where the data could be accessed (e.g. if the Beacon is for internal use of the hospital, to provide the Id of the EHR of the patients having the mutation of interest). + - Annotations about the variants found, among which the expert/clinician conclusion about the pathogenicity of a given mutation in a given individual or its role in producing a given phenotype. + - Information about cohorts. -### Licenses + Useful links related to Beacon v2: + - [Beacon v2 Website](https://beacon-project.io) + - [Beacon v2 Models](https://docs.genomebeacons.org/models/) + - [Beacon v2 GitHub](https://github.com/ga4gh-beacon/beacon-v2/) + - [Beacon v2 GitHub API](https://github.com/EGA-archive/beacon2-ri-api) + - [Beacon v2 Reference Implementation paper](https://academic.oup.com/bioinformatics/article/38/19/4656/6671215) - + Example of Beacon v2 with synthetic data: + - [Synthetic data (CINECA)](https://ega-archive.org/studies/EGAS00001002472) + - [CINECA Beacon v2 API](https://ega-archive.org/beacon-apis/cineca/) -Under what licenses do the data sources work? +- Biosamples: {% tool "biosamples" %} stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. For example it stores data from infectious diseases such as COVID-19. +- COVID-19 DataPortal: The {% tool "covid-19-data-portal" %} facilitates data sharing and analysis in order to accelerate coronavirus research and acts as a Data sharing platform. The European COVID-19 Data Platform consists of three connected components: + - {% tool "sars-cov2-data-hubs" %}, which organise the flow of SARS-CoV-2 outbreak sequence data and provide comprehensive open data sharing for the European and global research communities. + - {% tool "fega" %}, which provides secure controlled access sharing of sensitive patient and research subject data sets relating to COVID-19 while complying with stringent privacy national laws. + - {% tool "covid-19-data-portal" %}, which brings together and continuously updates relevant COVID-19 datasets and tools, will host sequence data sharing and will facilitate access to other SARS-CoV-2 resources. + + You can find further information about the Covid-19 Data Portal in the link [here](https://rdmkit.elixir-europe.org/covid19_data_portal). + +## Data access and transfer + +Sharing genetic and molecular information between researchers and institutions is essential for gaining a better understanding of human biology and disease. This is especially important when it comes to infectious diseases. By studying the genetic makeup of pathogens and how they interact with human cells, researchers can identify new targets for treatments and vaccines. They can also develop strategies to prevent or contain potential outbreaks before they occur. + +Of course, sharing this kind of sensitive information comes with challenges. Privacy, security, and ethical considerations must be taken into account. Researchers need to handle this information responsibly and with respect for individuals' rights. Legal and regulatory barriers can also impede data sharing and collaboration. + +However, the benefits of sharing human biomolecular data outweigh the risks. Access to this data is crucial for scientific progress and medical advancements. It's important for us to continue finding ways to responsibly and securely share this valuable resource. ### Considerations -Using a bullet point style list format as much as possible, describe the considerations for your topic that are specific to infectious diseases within the category (e.g. pathogen characterisation) that you have selected. +When looking for solutions to human biomolecular data access, you should consider the following aspects: + +- **Data Security and Privacy:** Prioritize solutions that ensure strict data security and compliance with ethical guidelines, protecting sensitive biomolecular information and adhering to regulatory requirements. +- **Interoperability and Data Sharing:** Choose solutions that seamlessly integrate with existing biomolecular research platforms and data repositories, facilitating secure data sharing and collaboration among researchers. +- **Data Reproducibility and Transparency:** Choose solutions that promote data reproducibility by providing transparent methodologies, making it easier for researchers to validate and build upon previous findings. +- **Data Quality and Standardization:** Verify that the solution provides reliable and accurate data, while supporting data standardization and metadata organization for consistent data exchange and improved research outcomes. +- **Data Integration Capabilities:** Depending on you study, prioritize solutions that can seamlessly integrate diverse biomolecular data types, such as genomics, proteomics, and metabolomics, for comprehensive analysis and insights. +- **Data structure:** Choose a database with a defined data structure, enabling homogeneity of the data and facilitating standardized and consistent data storage, retrieval and usability. +- **Scalability and Performance:** Look for solutions capable of efficiently handling large-scale biomolecular data sets while maintaining optimal performance, supporting advanced analysis tools for meaningful insights. +- **User-Friendly Interface:** Opt for solutions with intuitive interfaces and flexible access controls, enabling researchers of varying technical backgrounds to access, analyze, and interpret data effectively. -Please avoid replicating 'generic' guidelines, i.e. those not specific to infectious diseases, here. Add links to RDMkit in the metadata above, if any are needed. +When looking for solutions to data transfer, you can check [this](https://rdmkit.elixir-europe.org/data_transfer) documentation. ### Existing approaches -Mention existing approaches related to the topic. +- You can check a list of existing controlled access repositories: + - {% tool "ega" %} + - {% tool "estonian-biobank" %} + - {% tool "dutch-covid19-data-portal" %} + - {% tool "panther" %} + - {% tool "ace-cohort" %} +- You can use one of these standards to make your data use conditions publicly available to possible data requesters. + - The {% tool "the-data-use-ontology" %} is an international standard, which provides codes to represent data use restrictions for controlled access datasets. + - The {% tool "ada-m" %} provides a standardised way to unambiguously represent the conditions related to data discovery and access. + - By depositing your data to one of the existing controlled access repositories, they will already show the data use conditions (e.g. [EGAD00001007777](https://ega-archive.org/datasets/EGAD00001007777)) +- A data access committee (DAC) is a group responsible for reviewing and approving requests for access to sensitive data, such as human biomolecular data. Its role is to ensure that requests are in compliance with relevant laws and regulations, that data is being used for legitimate scientific purposes, and that privacy and security are being maintained. To know more about what is a DAC and how to become one, you can check the [European Genome-phenome Archive - Data Access Committee](https://ega-archive.org/submission/data_access_committee) website. -## Existing data sources +You can find further information about sharing human data [here](https://rdmkit.elixir-europe.org/human_data#sharing-and-reusing-of-human-data). -Using bullet point list style as much as possible, describe when, why and for what purpose a specific data source should be used. +## Data harmonisation -Please avoid replicating 'generic' guidelines, i.e. those not specific to infectious diseases, here. +To ensure that researchers can effectively utilise data, it is essential that it be collected and stored in a standardised manner. Using standardised formats and databases facilitates data sharing across research groups, enabling more efficient and effective analysis. This approach not only saves time, but also yields more accurate results. -Avoid making long lists of links to data sources. +Thanks to the Sars-CoV-2 outbreak, the scientific community has established standards, schemes, and data models with controlled vocabularies and ontologies explained in detail in the Human Clinical and Health Data section. One example could be the [Developing a standardized but extendable framework to increase the findability of infectious disease datasets](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9950378/) paper from February of 2023. + +### Considerations + +- Looking for an existing standardised metadata schema for human biomolecular data, like {% tool "miabis" %} or [EGA](https://ega-archive.org/submission/sequence/programmatic_submissions) schemas. +- Incorporating key data elements such as patient demographics, clinical features, and laboratory test results in the metadata schema +- Ensuring interoperability with other existing metadata schemas to facilitate data sharing and integration +- Including metadata fields for sample collection, processing, and storage information to ensure data quality and reproducibility +- Implementing controlled vocabularies and ontologies for standardised annotation and data integration +- Enabling data harmonisation across different studies to facilitate meta-analyses and systematic reviews +- Seek input and feedback from stakeholders across the research and public health communities to ensure that the schema meets the needs of diverse users and supports a range of research questions and applications. +- Regularly updating and refining the metadata schema to accommodate new data types and emerging research needs. + +### Existing approaches -The data sources inserted in this section do not have to be considered a 'final' or 'perfect' solution, but should be something that is used by the wider community working in this area or topic. +* When looking for solutions to standards, schemas, ontologies and vocabularies, you can check [this](https://rdmkit.elixir-europe.org/metadata_management#how-do-you-find-appropriate-standard-metadata-for-datasets-or-samples) documentation. +* {% tool "fairsharing" %} is also a good resources to find metadata standards that be useful for your research. -Make sure to add the data sources mentioned in the text in the main "tools and resources" table. From 5d9a857980ccf9434399ef6e94ee26ad9cefe3bd Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Wed, 20 Sep 2023 10:30:32 +0200 Subject: [PATCH 05/17] Update news.yml (#234) * Update news.yml * Update _data/news.yml Co-authored-by: rafael buono <77321541+rabuono@users.noreply.github.com> --------- Co-authored-by: rafael buono <77321541+rabuono@users.noreply.github.com> --- _data/news.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/_data/news.yml b/_data/news.yml index 80f30456..c825d1ec 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -57,5 +57,8 @@ - name: "All tools and resources are now described in the page text" date: 2023-08-24 linked_pr: 214 - description: "All items in the 'Relevant tools and resources' tables are now mentioned in the text. This means you have context of when it is appropriate to use each one. Tools and resources in the text will also feature a popup providing extra information about them. These changes means there is a new way to contribute tools: see our [new guidelines](/contribute/tool_resource_update)!" - + description: "All items in the 'Relevant tools and resources' tables are now mentioned in the text. This means you have context of when it is appropriate to use each one. Tools and resources in the text will also feature a popup providing extra information about them. These changes means there is a new way to contribute tools: see our [new guidelines](/contribute/tool-resource-update)!" +- name: "New page: Human Biomolecular data sources" + description: Content was added to the Data sources page in the Human Biomolecular data section. [Discover the page here](/human-biomolecular-data/data-sources) + date: 2023-09-19 + linked_pr: 155 From 2dc7d19d67316c862455becc81535723b1a93da2 Mon Sep 17 00:00:00 2001 From: rafael buono <77321541+rabuono@users.noreply.github.com> Date: Wed, 20 Sep 2023 10:31:07 +0200 Subject: [PATCH 06/17] Update support.md (#236) closes #235 To better reflect the projects/funders displayed --- about/support.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/about/support.md b/about/support.md index ce2291d9..8c3b6a1d 100644 --- a/about/support.md +++ b/about/support.md @@ -8,6 +8,6 @@ The Infectious Diseases Toolkit is developed in [BY-COVID](https://by-covid.org The Infectious Diseases Toolkit is built based on the experience and ways of working of the [RDMkit](https://rdmkit.elixir-europe.org/) and also makes use of the [ELIXIR Toolkit Theme](https://elixir-belgium.github.io/elixir-toolkit-theme/) for deployment. -Additionally we thank the funders that supported some of our contributors. +Additionally we thank the funders that supported the work on the framework used by the Infectious Diseases Toolkit. {% include affiliation-tiles-selection.html type="funder" %} From cd82b6624687f4308e6456a8ab1c9e9615a106a2 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Wed, 20 Sep 2023 14:20:07 +0200 Subject: [PATCH 07/17] Capital --- _data/news.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_data/news.yml b/_data/news.yml index c825d1ec..3e5ddfb6 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -58,7 +58,7 @@ date: 2023-08-24 linked_pr: 214 description: "All items in the 'Relevant tools and resources' tables are now mentioned in the text. This means you have context of when it is appropriate to use each one. Tools and resources in the text will also feature a popup providing extra information about them. These changes means there is a new way to contribute tools: see our [new guidelines](/contribute/tool-resource-update)!" -- name: "New page: Human Biomolecular data sources" - description: Content was added to the Data sources page in the Human Biomolecular data section. [Discover the page here](/human-biomolecular-data/data-sources) +- name: "New page: Human biomolecular data sources" + description: Content was added to the Data sources page in the Human biomolecular data section. [Discover the page here](/human-biomolecular-data/data-sources) date: 2023-09-19 linked_pr: 155 From 84fe3264c67c83266daed5afe45e0b1739478596 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 25 Sep 2023 15:25:59 +0200 Subject: [PATCH 08/17] Update tool/resource_list.yaml (#237) Co-authored-by: bedroesb --- _data/tool_and_resource_list.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index beff00ed..51a0ef12 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -712,16 +712,18 @@ - description: An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. id: dcat name: DCAT - url: https://www.w3.org/TR/vocab-dcat-2/ registry: fairsharing: h4j3qm -- description: The dutch COVID-19 Data Portal provides researchers with a clear overview of what is available, allow searching for specific data and make access to such data easier when the necessary ethical and legal conditions have been met. + url: https://www.w3.org/TR/vocab-dcat-2/ +- description: The dutch COVID-19 Data Portal provides researchers with a clear overview of what is available, allow searching for specific data and make access to such data easier when the necessary ethical and legal conditions have been met. id: dutch-covid19-data-portal - url: https://covid19initiatives.health-ri.nl/p/Dashboard name: Dutch COVID-19 Data Portal + url: https://covid19initiatives.health-ri.nl/p/Dashboard - description: The Federated EGA is an infrastructure built upon the European Genome-phenome Archive (EGA), an EMBL-EBI and CRG data resource for secure archiving and sharing of human sensitive biomolecular and phenotypic data resulting from biomedical research projects. id: fega name: Federated EGA + registry: + tess: Federated EGA url: https://www.covid19dataportal.org/federated-ega - description: Using technology that builds upon existing EMBL-EBI infrastructure, we provide SARS-CoV-2 Data Hubs to those public health agencies and other scientific groups responsible for generating viral sequence data from the outbreak at national or regional levels. id: sars-cov2-data-hubs From 464e3dfc58ffbf76ba1639f3fef517c1160d9dfe Mon Sep 17 00:00:00 2001 From: bedroesb Date: Mon, 25 Sep 2023 15:35:41 +0200 Subject: [PATCH 09/17] update PR text --- .github/workflows/tool_list_conversion.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tool_list_conversion.yml b/.github/workflows/tool_list_conversion.yml index 9786ed4f..e7fce1cd 100644 --- a/.github/workflows/tool_list_conversion.yml +++ b/.github/workflows/tool_list_conversion.yml @@ -71,7 +71,7 @@ jobs: commit-message: Update tool/resource_list.yaml title: 'Automatic tool/resource-list update' body: | - This PR is automatically generated based on changes in the main_tool_and_resource_list.csv file or based on new links made between the tool table and TeSS. + This PR is automatically generated based on new links made between the tools and the registries: TeSS, Bio.tools and FAIRsharing. Please verify if these changes are valid. labels: | From fd8b8685bb20f9c27ccac1a9bb3386105bf234e8 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Fri, 20 Oct 2023 06:45:53 +0200 Subject: [PATCH 10/17] hide pages (#242) --- contribute/editorial-board-guide.md | 1 + contribute/editors-checklist.md | 1 + contribute/github-way.md | 1 + contribute/google-doc-way.md | 1 + contribute/index.md | 1 + contribute/page-metadata.md | 1 + contribute/preview-changes.md | 1 + contribute/style-guide.md | 1 + contribute/tool-resource-update.md | 1 + contribute/website-overview.md | 1 + contribute/working-with-git.md | 1 + human-biomolecular-data/attributing-credit.md | 1 + human-biomolecular-data/data-communication.md | 1 + human-biomolecular-data/data-description.md | 1 + human-biomolecular-data/ethical-legal-and-social-issues.md | 1 + human-biomolecular-data/provenance.md | 1 + human-biomolecular-data/quality-control.md | 1 + human-clinical-and-health-data/attributing-credit.md | 1 + human-clinical-and-health-data/data-analysis.md | 1 + human-clinical-and-health-data/data-communication.md | 1 + human-clinical-and-health-data/data-description.md | 1 + human-clinical-and-health-data/data-sources.md | 1 + .../ethical-legal-and-social-issues.md | 1 + human-clinical-and-health-data/quality-control.md | 1 + pathogen-characterisation/attributing-credit.md | 1 + pathogen-characterisation/data-analysis.md | 1 + pathogen-characterisation/data-communication.md | 1 + pathogen-characterisation/data-description.md | 1 + pathogen-characterisation/data-sources.md | 1 + pathogen-characterisation/ethical-legal-and-social-issues.md | 1 + pathogen-characterisation/provenance.md | 1 + pathogen-characterisation/quality-control.md | 1 + socioeconomic-data/attributing-credit.md | 1 + socioeconomic-data/data-analysis.md | 1 + socioeconomic-data/data-communication.md | 1 + socioeconomic-data/data-description.md | 1 + socioeconomic-data/ethical-legal-and-social-issues.md | 1 + socioeconomic-data/provenance.md | 1 + socioeconomic-data/quality-control.md | 1 + 39 files changed, 39 insertions(+) diff --git a/contribute/editorial-board-guide.md b/contribute/editorial-board-guide.md index 0a5d0682..39dd8396 100644 --- a/contribute/editorial-board-guide.md +++ b/contribute/editorial-board-guide.md @@ -1,6 +1,7 @@ --- title: Editorial board guide summary: This guide is there to help editors. +search_exclude: true --- ## All you need to know about this GitHub repository diff --git a/contribute/editors-checklist.md b/contribute/editors-checklist.md index c8b3088a..d371a646 100644 --- a/contribute/editors-checklist.md +++ b/contribute/editors-checklist.md @@ -1,6 +1,7 @@ --- title: Editors checklist summary: Checklist for editors before approving and merging a pull request (PR). +search_exclude: true --- ## Before approving and merging a pull request (PR), the editors must check that diff --git a/contribute/github-way.md b/contribute/github-way.md index ce585ea9..6b609e77 100644 --- a/contribute/github-way.md +++ b/contribute/github-way.md @@ -1,5 +1,6 @@ --- title: GitHub way +search_exclude: true --- diff --git a/contribute/google-doc-way.md b/contribute/google-doc-way.md index 4fa34f1a..ec036a65 100644 --- a/contribute/google-doc-way.md +++ b/contribute/google-doc-way.md @@ -1,5 +1,6 @@ --- title: Google doc way +search_exclude: true --- diff --git a/contribute/index.md b/contribute/index.md index e645e4b3..dbd79560 100644 --- a/contribute/index.md +++ b/contribute/index.md @@ -1,5 +1,6 @@ --- title: How to contribute to the Infectious Diseases Toolkit website +search_exclude: true --- diff --git a/contribute/page-metadata.md b/contribute/page-metadata.md index 5c27d8eb..a9b3eb87 100644 --- a/contribute/page-metadata.md +++ b/contribute/page-metadata.md @@ -1,5 +1,6 @@ --- title: Page metadata +search_exclude: true --- diff --git a/contribute/preview-changes.md b/contribute/preview-changes.md index 1c5fcb4b..ea728c73 100644 --- a/contribute/preview-changes.md +++ b/contribute/preview-changes.md @@ -1,6 +1,7 @@ --- title: Preview changes summary: Use your own fork to preview changes on the website. +search_exclude: true --- ## Introduction diff --git a/contribute/style-guide.md b/contribute/style-guide.md index 38a92a90..1d4819f6 100644 --- a/contribute/style-guide.md +++ b/contribute/style-guide.md @@ -1,5 +1,6 @@ --- title: Style guide +search_exclude: true --- In general, we follow the European Commission's [Web Writing Style Guide](https://wikis.ec.europa.eu/display/WEBGUIDE/02.+Web+writing+guidelines), and the more detailed [English Style Guide](https://commission.europa.eu/system/files/2023-01/styleguide_english_dgt_en.pdf). Below are the points that you might find most useful, though, and that relate particularly to the Infectious Diseases Toolkit. diff --git a/contribute/tool-resource-update.md b/contribute/tool-resource-update.md index 512dea5a..ae936571 100644 --- a/contribute/tool-resource-update.md +++ b/contribute/tool-resource-update.md @@ -1,6 +1,7 @@ --- title: Add new tool or resource summary: How to add a tool or resource to Infectious diseases toolkit +search_exclude: true --- ## Way of working diff --git a/contribute/website-overview.md b/contribute/website-overview.md index ac23dc07..34fc3a7f 100644 --- a/contribute/website-overview.md +++ b/contribute/website-overview.md @@ -1,5 +1,6 @@ --- title: List of page IDs +search_exclude: true --- {% include pageids-overview.html sidebar="main" %} \ No newline at end of file diff --git a/contribute/working-with-git.md b/contribute/working-with-git.md index 4875efb8..f9a75a97 100644 --- a/contribute/working-with-git.md +++ b/contribute/working-with-git.md @@ -1,5 +1,6 @@ --- title: Working with git +search_exclude: true --- diff --git a/human-biomolecular-data/attributing-credit.md b/human-biomolecular-data/attributing-credit.md index 68528794..e40d2348 100644 --- a/human-biomolecular-data/attributing-credit.md +++ b/human-biomolecular-data/attributing-credit.md @@ -3,6 +3,7 @@ title: Attributing credit description: Referencing your sources (citations and recognition of contributions) contributors: [] no_robots: true +search_exclude: true page_id: hbd_provenance rdmkit: - name: diff --git a/human-biomolecular-data/data-communication.md b/human-biomolecular-data/data-communication.md index b8c9b61b..9eabc307 100644 --- a/human-biomolecular-data/data-communication.md +++ b/human-biomolecular-data/data-communication.md @@ -3,6 +3,7 @@ title: Data communication description: Producing visualisations and reports contributors: [] no_robots: true +search_exclude: true page_id: hbd_data_communication rdmkit: - name: diff --git a/human-biomolecular-data/data-description.md b/human-biomolecular-data/data-description.md index 03bf5ba2..931f256d 100644 --- a/human-biomolecular-data/data-description.md +++ b/human-biomolecular-data/data-description.md @@ -3,6 +3,7 @@ title: Data description description: Finding (meta)data standards and documentation contributors: [] no_robots: true +search_exclude: true page_id: hbd_data_description rdmkit: - name: diff --git a/human-biomolecular-data/ethical-legal-and-social-issues.md b/human-biomolecular-data/ethical-legal-and-social-issues.md index 47a649c0..c3723a7e 100644 --- a/human-biomolecular-data/ethical-legal-and-social-issues.md +++ b/human-biomolecular-data/ethical-legal-and-social-issues.md @@ -3,6 +3,7 @@ title: Ethical Legal and Social Issues description: Legal and ethical aspects and how to deal with them contributors: [] no_robots: true +search_exclude: true page_id: hbd_elsi rdmkit: - name: diff --git a/human-biomolecular-data/provenance.md b/human-biomolecular-data/provenance.md index 44e333cd..15e883dd 100644 --- a/human-biomolecular-data/provenance.md +++ b/human-biomolecular-data/provenance.md @@ -3,6 +3,7 @@ title: Provenance description: Tracking data and analysis steps contributors: [] no_robots: true +search_exclude: true page_id: hbd_provenance rdmkit: - name: diff --git a/human-biomolecular-data/quality-control.md b/human-biomolecular-data/quality-control.md index e2e472a4..2b209ba2 100644 --- a/human-biomolecular-data/quality-control.md +++ b/human-biomolecular-data/quality-control.md @@ -3,6 +3,7 @@ title: Quality control description: Tools and methods to assess quality contributors: [] no_robots: true +search_exclude: true page_id: hbd_quality_control rdmkit: - name: diff --git a/human-clinical-and-health-data/attributing-credit.md b/human-clinical-and-health-data/attributing-credit.md index e34989ef..eb5feb71 100644 --- a/human-clinical-and-health-data/attributing-credit.md +++ b/human-clinical-and-health-data/attributing-credit.md @@ -3,6 +3,7 @@ title: Attributing credit description: Referencing your sources (citations and recognition of contributions) contributors: [] no_robots: true +search_exclude: true page_id: hchd_attributing_credit rdmkit: - name: diff --git a/human-clinical-and-health-data/data-analysis.md b/human-clinical-and-health-data/data-analysis.md index 3f618b96..1605ab5f 100644 --- a/human-clinical-and-health-data/data-analysis.md +++ b/human-clinical-and-health-data/data-analysis.md @@ -3,6 +3,7 @@ title: Data analysis description: Generic workflows for different data types contributors: [] no_robots: true +search_exclude: true page_id: hchd_data_analysis rdmkit: - name: diff --git a/human-clinical-and-health-data/data-communication.md b/human-clinical-and-health-data/data-communication.md index f950cd36..485b4e1a 100644 --- a/human-clinical-and-health-data/data-communication.md +++ b/human-clinical-and-health-data/data-communication.md @@ -3,6 +3,7 @@ title: Data communication description: Producing visualisations and reports contributors: [] no_robots: true +search_exclude: true page_id: hchd_data_communication rdmkit: - name: diff --git a/human-clinical-and-health-data/data-description.md b/human-clinical-and-health-data/data-description.md index 154bfd54..a678715d 100644 --- a/human-clinical-and-health-data/data-description.md +++ b/human-clinical-and-health-data/data-description.md @@ -3,6 +3,7 @@ title: Data description description: Finding (meta)data standards and documentation contributors: [] no_robots: true +search_exclude: true page_id: hchd_data_description rdmkit: - name: diff --git a/human-clinical-and-health-data/data-sources.md b/human-clinical-and-health-data/data-sources.md index f904b197..42bc8ae0 100644 --- a/human-clinical-and-health-data/data-sources.md +++ b/human-clinical-and-health-data/data-sources.md @@ -3,6 +3,7 @@ title: Data sources description: Finding and sharing data for human clinical and health data related data sources. contributors: [] no_robots: true +search_exclude: true page_id: hchd_data_sources rdmkit: - name: diff --git a/human-clinical-and-health-data/ethical-legal-and-social-issues.md b/human-clinical-and-health-data/ethical-legal-and-social-issues.md index cd810cff..225b9adc 100644 --- a/human-clinical-and-health-data/ethical-legal-and-social-issues.md +++ b/human-clinical-and-health-data/ethical-legal-and-social-issues.md @@ -3,6 +3,7 @@ title: Ethical Legal and Social Issues description: Legal and ethical aspects and how to deal with them contributors: [] no_robots: true +search_exclude: true page_id: hchd_elsi rdmkit: - name: diff --git a/human-clinical-and-health-data/quality-control.md b/human-clinical-and-health-data/quality-control.md index 8f637844..5a9d024e 100644 --- a/human-clinical-and-health-data/quality-control.md +++ b/human-clinical-and-health-data/quality-control.md @@ -3,6 +3,7 @@ title: Quality control description: Tools and methods to assess quality contributors: [] no_robots: true +search_exclude: true page_id: hchd_quality_control rdmkit: - name: diff --git a/pathogen-characterisation/attributing-credit.md b/pathogen-characterisation/attributing-credit.md index 720d8179..a1233189 100644 --- a/pathogen-characterisation/attributing-credit.md +++ b/pathogen-characterisation/attributing-credit.md @@ -3,6 +3,7 @@ title: Attributing credit description: Referencing your sources (citations and recognition of contributions) contributors: [] no_robots: true +search_exclude: true page_id: pc_attributing_credit rdmkit: - name: diff --git a/pathogen-characterisation/data-analysis.md b/pathogen-characterisation/data-analysis.md index 67b984a9..b0452fa8 100644 --- a/pathogen-characterisation/data-analysis.md +++ b/pathogen-characterisation/data-analysis.md @@ -3,6 +3,7 @@ title: Data analysis description: Generic workflows for different data types contributors: [] no_robots: true +search_exclude: true page_id: pc_data_analysis rdmkit: - name: diff --git a/pathogen-characterisation/data-communication.md b/pathogen-characterisation/data-communication.md index 09618ddf..867cdb7f 100644 --- a/pathogen-characterisation/data-communication.md +++ b/pathogen-characterisation/data-communication.md @@ -3,6 +3,7 @@ title: Data communication description: Producing visualisations and reports contributors: [] no_robots: true +search_exclude: true page_id: pc_data_communication rdmkit: - name: diff --git a/pathogen-characterisation/data-description.md b/pathogen-characterisation/data-description.md index 8752b3fd..07e7e567 100644 --- a/pathogen-characterisation/data-description.md +++ b/pathogen-characterisation/data-description.md @@ -3,6 +3,7 @@ title: Data description description: Finding (meta)data standards and documentation contributors: [] no_robots: true +search_exclude: true page_id: pc_data_description rdmkit: - name: diff --git a/pathogen-characterisation/data-sources.md b/pathogen-characterisation/data-sources.md index 4c7ddb8f..ecab441c 100644 --- a/pathogen-characterisation/data-sources.md +++ b/pathogen-characterisation/data-sources.md @@ -3,6 +3,7 @@ title: Data sources description: Finding and sharing data for pathogen characterisation related data sources. contributors: [] no_robots: true +search_exclude: true page_id: pc_data_sources rdmkit: - name: diff --git a/pathogen-characterisation/ethical-legal-and-social-issues.md b/pathogen-characterisation/ethical-legal-and-social-issues.md index 00b8978a..92da0b17 100644 --- a/pathogen-characterisation/ethical-legal-and-social-issues.md +++ b/pathogen-characterisation/ethical-legal-and-social-issues.md @@ -3,6 +3,7 @@ title: Ethical Legal and Social Issues description: Legal and ethical aspects and how to deal with them contributors: [] no_robots: true +search_exclude: true page_id: pc_elsi rdmkit: - name: diff --git a/pathogen-characterisation/provenance.md b/pathogen-characterisation/provenance.md index ffa177fe..9c0d0a4f 100644 --- a/pathogen-characterisation/provenance.md +++ b/pathogen-characterisation/provenance.md @@ -3,6 +3,7 @@ title: Provenance description: Tracking data and analysis steps contributors: [] no_robots: true +search_exclude: true page_id: pc_provenance rdmkit: - name: diff --git a/pathogen-characterisation/quality-control.md b/pathogen-characterisation/quality-control.md index 3cb0b277..8394f8f8 100644 --- a/pathogen-characterisation/quality-control.md +++ b/pathogen-characterisation/quality-control.md @@ -3,6 +3,7 @@ title: Quality control description: Tools and methods to assess quality contributors: [] no_robots: true +search_exclude: true page_id: pc_quality_control rdmkit: - name: diff --git a/socioeconomic-data/attributing-credit.md b/socioeconomic-data/attributing-credit.md index 4f8f9737..80e49f23 100644 --- a/socioeconomic-data/attributing-credit.md +++ b/socioeconomic-data/attributing-credit.md @@ -3,6 +3,7 @@ title: Attributing credit description: Referencing your sources (citations and recognition of contributions) contributors: [] no_robots: true +search_exclude: true page_id: sed_attributing_credit rdmkit: - name: diff --git a/socioeconomic-data/data-analysis.md b/socioeconomic-data/data-analysis.md index 59687c07..4c5af6e2 100644 --- a/socioeconomic-data/data-analysis.md +++ b/socioeconomic-data/data-analysis.md @@ -3,6 +3,7 @@ title: Data analysis description: Generic workflows for different data types contributors: [] no_robots: true +search_exclude: true page_id: sed_data_analysis rdmkit: - name: diff --git a/socioeconomic-data/data-communication.md b/socioeconomic-data/data-communication.md index 31a8bb34..47f5884c 100644 --- a/socioeconomic-data/data-communication.md +++ b/socioeconomic-data/data-communication.md @@ -3,6 +3,7 @@ title: Data communication description: Producing visualisations and reports contributors: [] no_robots: true +search_exclude: true page_id: sed_data_communication rdmkit: - name: diff --git a/socioeconomic-data/data-description.md b/socioeconomic-data/data-description.md index c31bbbf5..da704742 100644 --- a/socioeconomic-data/data-description.md +++ b/socioeconomic-data/data-description.md @@ -3,6 +3,7 @@ title: Data description description: Finding (meta)data standards and documentation contributors: [] no_robots: true +search_exclude: true page_id: sed_data_description rdmkit: - name: diff --git a/socioeconomic-data/ethical-legal-and-social-issues.md b/socioeconomic-data/ethical-legal-and-social-issues.md index 5609475d..52aae0c4 100644 --- a/socioeconomic-data/ethical-legal-and-social-issues.md +++ b/socioeconomic-data/ethical-legal-and-social-issues.md @@ -3,6 +3,7 @@ title: Ethical Legal and Social Issues description: Legal and ethical aspects and how to deal with them contributors: [] no_robots: true +search_exclude: true page_id: sed_elsi rdmkit: - name: diff --git a/socioeconomic-data/provenance.md b/socioeconomic-data/provenance.md index 60d41334..92ee50ca 100644 --- a/socioeconomic-data/provenance.md +++ b/socioeconomic-data/provenance.md @@ -3,6 +3,7 @@ title: Provenance description: Tracking data and analysis steps contributors: [] no_robots: true +search_exclude: true page_id: sed_provenance rdmkit: - name: diff --git a/socioeconomic-data/quality-control.md b/socioeconomic-data/quality-control.md index 226441dd..982248d6 100644 --- a/socioeconomic-data/quality-control.md +++ b/socioeconomic-data/quality-control.md @@ -3,6 +3,7 @@ title: Quality control description: Tools and methods to assess quality contributors: [] no_robots: true +search_exclude: true page_id: sed_quality_control rdmkit: - name: From 7c880766e98fcfffe650ba49dc8c030c1c5acf49 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 26 Oct 2023 11:39:50 +0200 Subject: [PATCH 11/17] fix box landing page --- index.html | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/index.html b/index.html index b1fdb8d2..1fbcb371 100644 --- a/index.html +++ b/index.html @@ -10,15 +10,15 @@ {% if jekyll.environment == "development" %}{% include dev-info.html %}{% endif %} {% include topnav.html search=false %} -
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This website is under construction
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Don't hesitate to open an issue or to contact us by mail using idtk-editors@elixir-europe.org to give some early feedback.

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This website is under construction
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Don't hesitate to open an issue or to contact us by mail using idtk-editors@elixir-europe.org to give some early feedback.

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Find tools and guidelines to help you access, analyse and share infectious disease data, and respond quickly to disease outbreaks. From 52b39f11a819182b1899bec397c44cd2f0363032 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 6 Nov 2023 14:19:01 +0100 Subject: [PATCH 12/17] Update tool/resource_list.yaml (#243) Co-authored-by: bedroesb --- _data/tool_and_resource_list.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 51a0ef12..01ad146b 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -105,6 +105,7 @@ name: ClustalW registry: biotools: clustalw + tess: ClustalW url: https://github.com/coldfunction/CUDA-clustalW - description: An open standard for describing workflows that are build from command line tools id: common-workflow-language @@ -493,6 +494,7 @@ name: MUSCLE registry: biotools: muscle + tess: MUSCLE url: https://github.com/rcedgar/muscle - description: MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. id: mzmine From 645498f67ca4a8e85946369b392fba24350d4b97 Mon Sep 17 00:00:00 2001 From: LianeHughes Date: Thu, 9 Nov 2023 14:16:53 +0100 Subject: [PATCH 13/17] Updates after 6 month review of Swedish page (#241) * Sweden 6mo update * minor adjustments * finalise pathogens data description * Update PR following comments * reset data description --- _data/CONTRIBUTORS.yaml | 299 +++++++++--------- _data/tool_and_resource_list.yml | 15 +- national-resources/sweden.md | 116 ++++--- pathogen-characterisation/data-description.md | 2 +- 4 files changed, 234 insertions(+), 198 deletions(-) mode change 100644 => 100755 national-resources/sweden.md diff --git a/_data/CONTRIBUTORS.yaml b/_data/CONTRIBUTORS.yaml index dc12cc2c..d0655555 100644 --- a/_data/CONTRIBUTORS.yaml +++ b/_data/CONTRIBUTORS.yaml @@ -11,187 +11,192 @@ # image_url: absolute path to image (default image from github) Rudolf Wittner: - git: RudoWittner - email: rudolf.wittner@bbmri-eric.eu - orcid: 0000-0002-0003-2024 - role: editor - affiliation: BBMRI-ERIC + git: RudoWittner + email: rudolf.wittner@bbmri-eric.eu + orcid: 0000-0002-0003-2024 + role: editor + affiliation: BBMRI-ERIC Bert Droesbeke: - git: bedroesb - email: bedro@psb.ugent.be - orcid: 0000-0003-0522-5674 - role: editor - affiliation: VIB-UGent / ELIXIR-BE + git: bedroesb + email: bedro@psb.ugent.be + orcid: 0000-0003-0522-5674 + role: editor + affiliation: VIB-UGent / ELIXIR-BE Hedi Peterson: - git: hedi-ee - email: hedi.peterson@gmail.com - orcid: 0000-0001-9951-5116 - role: editor - affiliation: UTARTU / ELIXIR-EE + git: hedi-ee + email: hedi.peterson@gmail.com + orcid: 0000-0001-9951-5116 + role: editor + affiliation: UTARTU / ELIXIR-EE Stian Soiland-Reyes: - git: stain - email: soiland-reyes@manchester.ac.uk - orcid: 0000-0001-9842-9718 - role: editor - affiliation: The University of Manchester / ELIXIR-UK + git: stain + email: soiland-reyes@manchester.ac.uk + orcid: 0000-0001-9842-9718 + role: editor + affiliation: The University of Manchester / ELIXIR-UK Patricia Palagi: - git: ppalagi - email: patricia.palagi@sib.swiss - orcid: 0000-0001-9062-6303 - role: editor - affiliation: SIB Swiss Institute of Bioinformatics / ELIXIR-CH + git: ppalagi + email: patricia.palagi@sib.swiss + orcid: 0000-0001-9062-6303 + role: editor + affiliation: SIB Swiss Institute of Bioinformatics / ELIXIR-CH Liane Hughes: - git: LianeHughes - email: liane.hughes@scilifelab.uu.se - orcid: 0000-0002-4784-5436 - role: editor - affiliation: SciLifeLab / Uppsala University + git: LianeHughes + email: liane.hughes@scilifelab.uu.se + orcid: 0000-0002-4784-5436 + role: editor + affiliation: SciLifeLab / Uppsala University Eva Garcia Alvarez: - git: EvaGarciaAlvarez - email: eva.garcia-alvarez@bbmri-eric.eu - orcid: 0000-0002-3522-5088 - role: editor - affiliation: BBMRI-ERIC + git: EvaGarciaAlvarez + email: eva.garcia-alvarez@bbmri-eric.eu + orcid: 0000-0002-3522-5088 + role: editor + affiliation: BBMRI-ERIC Laura Portell Silva: - git: lauportell - email: laura.portell@bsc.es - orcid: 0000-0003-0390-3208 - role: editor - affiliation: Barcelona Supercomputing Center / ELIXIR-ES + git: lauportell + email: laura.portell@bsc.es + orcid: 0000-0003-0390-3208 + role: editor + affiliation: Barcelona Supercomputing Center / ELIXIR-ES Rafael Andrade Buono: - orcid: 0000-0002-6675-3836 - git: rabuono - affiliation: VIB-UGent / ELIXIR-BE - role: editor + orcid: 0000-0002-6675-3836 + git: rabuono + affiliation: VIB-UGent / ELIXIR-BE + role: editor Shona Cosgrove: - orcid: 0000-0003-3273-9013 - git: ShonaCosgrove - email: shona.cosgrove@sciensano.be - affiliation: Sciensano - role: editor + orcid: 0000-0003-3273-9013 + git: ShonaCosgrove + email: shona.cosgrove@sciensano.be + affiliation: Sciensano + role: editor Iris Van Dam: - orcid: 0000-0002-3965-6184 - git: IrisVanDam - email: iris.vandam@sciensano.be - affiliation: Sciensano - role: editor + orcid: 0000-0002-3965-6184 + git: IrisVanDam + email: iris.vandam@sciensano.be + affiliation: Sciensano + role: editor Katharina Lauer: - orcid: 0000-0002-4347-7525 - git: klauer2207 - email: katharina@airfinity.com - affiliation: Airfinity Ltd. - role: editor + orcid: 0000-0002-4347-7525 + git: klauer2207 + email: katharina@airfinity.com + affiliation: Airfinity Ltd. + role: editor Romain David: - orcid: 0000-0003-4073-7456 - git: RomainDavid24 - email: romain.david@erinha.eu - affiliation: ERINHA - role: editor + orcid: 0000-0003-4073-7456 + git: RomainDavid24 + email: romain.david@erinha.eu + affiliation: ERINHA + role: editor Simone Leo: - orcid: 0000-0001-8271-5429 - git: simleo - affiliation: CRS4, IT + orcid: 0000-0001-8271-5429 + git: simleo + affiliation: CRS4, IT Martin Cook: - git: martin-nc - email: martin.cook@elixir-europe.org - role: editor - affiliation: ELIXIR Hub + git: martin-nc + email: martin.cook@elixir-europe.org + role: editor + affiliation: ELIXIR Hub Erin Calhoun: - orcid: 0009-0003-3752-7156 - git: erincalhoun - email: erin.calhoun@uit.no - role: - affiliation: ELIXIR Norway + orcid: 0009-0003-3752-7156 + git: erincalhoun + email: erin.calhoun@uit.no + role: + affiliation: ELIXIR Norway Nazeefa Fatima: - orcid: 0000-0001-7791-4984 - git: Nazeeefa - email: nazeefaf@uio.no - role: - affiliation: ELIXIR Norway + orcid: 0000-0001-7791-4984 + git: Nazeeefa + email: nazeefaf@uio.no + role: + affiliation: ELIXIR Norway Aina Jené Cortada: - git: ainajene - email: aina.jene@crg.eu - orcid: 0000-0001-7721-7097 - affiliation: European Genome-phenome Archive (EGA) / CRG + git: ainajene + email: aina.jene@crg.eu + orcid: 0000-0001-7721-7097 + affiliation: European Genome-phenome Archive (EGA) / CRG Marcos Casado Barbero: - git: M-casado - email: mcasado@ebi.ac.uk - orcid: 0000-0002-7747-6256 - affiliation: European Genome-phenome Archive (EGA) / EMBL-EBI + git: M-casado + email: mcasado@ebi.ac.uk + orcid: 0000-0002-7747-6256 + affiliation: European Genome-phenome Archive (EGA) / EMBL-EBI Arnau Soler Costa: - git: solcos - email: arnau.soler@crg.eu - orcid: 0000-0002-2853-6742 - affiliation: European Genome-phenome Archive (EGA) / CRG + git: solcos + email: arnau.soler@crg.eu + orcid: 0000-0002-2853-6742 + affiliation: European Genome-phenome Archive (EGA) / CRG Ruben Brondeel: - orcid: 0000-0002-9876-4150 - git: RubenBrondeel - affiliation: Sciensano + orcid: 0000-0002-9876-4150 + git: RubenBrondeel + affiliation: Sciensano Koen Blot: - orcid: 0000-0002-0847-0133 - affiliation: Sciensano + orcid: 0000-0002-0847-0133 + affiliation: Sciensano Nina Van Goethem: - orcid: 0000-0001-7316-6990 - affiliation: Sciensano + orcid: 0000-0001-7316-6990 + affiliation: Sciensano Miriam Saso: - orcid: 0000-0002-1888-1913 - affiliation: Sciensano + orcid: 0000-0002-1888-1913 + affiliation: Sciensano Wolfgang Maier: - git: wm75 - email: maierw@informatik.uni-freiburg.de - orcid: 0000-0002-9464-6640 - affiliation: University of Freiburg / ELIXIR-DE -Anna Asklöf: - git: annaasklof - affiliation: SciLifeLab / Uppsala University + git: wm75 + email: maierw@informatik.uni-freiburg.de + orcid: 0000-0002-9464-6640 + affiliation: University of Freiburg / ELIXIR-DE +Anna Asklöf: + git: annaasklof + affiliation: SciLifeLab / Uppsala University Katarina Öjefors Stark: - orcid: 0000-0001-7970-7778 - git: KatarinaOjeforsStark - affiliation: SciLifeLab / Uppsala University + orcid: 0000-0001-7970-7778 + git: KatarinaOjeforsStark + affiliation: SciLifeLab / Uppsala University Diana Pilvar: - git: diana-pilvar - email: diana.pilvar@ut.ee - orcid: 0000-0002-5788-2687 - affiliation: University of Tartu / ELIXIR-Estonia + git: diana-pilvar + email: diana.pilvar@ut.ee + orcid: 0000-0002-5788-2687 + affiliation: University of Tartu / ELIXIR-Estonia Robin Navest: - orcid: 0000-0002-0152-2092 - git: rnavest - affiliation: Lygature + orcid: 0000-0002-0152-2092 + git: rnavest + affiliation: Lygature Julia Lischke: - orcid: 0000-0002-5524-2838 - git: - affiliation: Lygature + orcid: 0000-0002-5524-2838 + git: + affiliation: Lygature Jan-Willem Boiten: - orcid: 0000-0003-0327-638X - git: + orcid: 0000-0003-0327-638X + git: Jeroen Belien: - orcid: 0000-0002-7160-5942 - git: jambelien - affiliation: Health-RI + orcid: 0000-0002-7160-5942 + git: jambelien + affiliation: Health-RI Clara Amid: - orcid: 0000-0001-6534-7425 - git: - affiliation: Erasmus Medical Center + orcid: 0000-0001-6534-7425 + git: + affiliation: Erasmus Medical Center Angelica Maineri: - orcid: 0000-0002-6978-5278 - git: AngelicaMaineri - affiliation: ODISSEI + orcid: 0000-0002-6978-5278 + git: AngelicaMaineri + affiliation: ODISSEI Ricarda Braukmann: - orcid: 0000-0001-6383-7148 - git: Ruecue - affiliation: DANS + orcid: 0000-0001-6383-7148 + git: Ruecue + affiliation: DANS Simon Saldner: - git: ssaldner - email: simon.saldner@dans.knaw.nl - affiliation: DANS-KNAW - orcid: 0000-0002-1145-7829 + git: ssaldner + email: simon.saldner@dans.knaw.nl + affiliation: DANS-KNAW + orcid: 0000-0002-1145-7829 Dimitra Kondyli: - email: dkondyli@ekke.gr - affiliation: EKKE + email: dkondyli@ekke.gr + affiliation: EKKE Markus Tuominen: - email: markus.tuominen@tuni.fi - affiliation: CESSDA ERIC / TAU-FSD + email: markus.tuominen@tuni.fi + affiliation: CESSDA ERIC / TAU-FSD Vasso Kalaitzi: - email: vasso.kalaitzi@dans.knaw.nl - affiliation: DANS-KNAW - orcid: 0000-0001-8337-120X + email: vasso.kalaitzi@dans.knaw.nl + affiliation: DANS-KNAW + orcid: 0000-0001-8337-120X +Wolmar Nyberg Åkerström: + git: wna-se + email: wolmar.n.akerstrom@nbis.se + orcid: 0000-0002-3890-6620 + affiliation: NBIS / ELIXIR-SE diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 01ad146b..6b70fd30 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -205,8 +205,9 @@ id: dragen-gatk name: Dragen-GATK url: https://gatk.broadinstitute.org/hc/en-us/articles/360045944831 -- description: 'Dryad is an open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data. Dryad has a long-term data preservation strategy, and is a Core Trust Seal Certified Merritt repository with storage in US and EU at the San Diego Supercomputing Center, DANS, and Zenodo. While data is undergoing peer review, it is embargoed if the related journal requires / allows this. Dryad is an independent non-profit that works directly with: researchers to publish datasets utilising best practices for discovery and reuse; publishers to support the integration of data availability statements and data citations into their workflows; and institutions to enable scalable campus support for research data management best practices at low cost. Costs are covered by institutional, publisher, and funder members, otherwise a one-time fee of $120 for authors to cover cost of curation and preservation. Dryad also receives direct funder support through - grants.' +- description: + "Dryad is an open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data. Dryad has a long-term data preservation strategy, and is a Core Trust Seal Certified Merritt repository with storage in US and EU at the San Diego Supercomputing Center, DANS, and Zenodo. While data is undergoing peer review, it is embargoed if the related journal requires / allows this. Dryad is an independent non-profit that works directly with: researchers to publish datasets utilising best practices for discovery and reuse; publishers to support the integration of data availability statements and data citations into their workflows; and institutions to enable scalable campus support for research data management best practices at low cost. Costs are covered by institutional, publisher, and funder members, otherwise a one-time fee of $120 for authors to cover cost of curation and preservation. Dryad also receives direct funder support through + grants." id: dryad name: Dryad registry: @@ -233,7 +234,7 @@ fairsharing: mya1ff tess: European Genome-phenome Archive (EGA) url: https://ega-archive.org/ -- description: 'The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,300 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information, communication technology, and environmental science. ELSST is used for data discovery within CESSDA and facilitates access to data resources across Europe, independent of domain, resource, language, or vocabulary. ELSST is currently available in 16 languages: Danish, Dutch, Czech, English, Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian, Slovenian, Spanish, and Swedish' +- description: "The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,300 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information, communication technology, and environmental science. ELSST is used for data discovery within CESSDA and facilitates access to data resources across Europe, independent of domain, resource, language, or vocabulary. ELSST is currently available in 16 languages: Danish, Dutch, Czech, English, Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian, Slovenian, Spanish, and Swedish" id: european-language-social-science-thesaurus name: European Language Social Science Thesaurus (ELSST) registry: @@ -361,7 +362,7 @@ id: gitlab name: GitLab registry: - fairsharing: '530e61' + fairsharing: 530e61 tess: GitLab url: https://about.gitlab.com/ - description: GO is to perform enrichment analysis on gene sets. @@ -731,3 +732,9 @@ id: sars-cov2-data-hubs name: SARS-CoV-2 Data Hubs url: https://www.covid19dataportal.org/data-hubs +- description: A web-based platform for sharing viral sequence data, initially for influenza data, and now for other pathogens (including SARS-CoV-2). + name: Global Initiative on Sharing All Influenza Data (GISAID) + registry: + fairsharing: 2f7f9f + id: gisaid + url: https://gisaid.org diff --git a/national-resources/sweden.md b/national-resources/sweden.md old mode 100644 new mode 100755 index e1a91c60..6090289e --- a/national-resources/sweden.md +++ b/national-resources/sweden.md @@ -1,12 +1,13 @@ --- title: Sweden country_code: SE -contributors: [Anna Asklöf, Katarina Öjefors Stark, Liane Hughes] +contributors: + [Anna Asklöf, Katarina Öjefors Stark, Liane Hughes, Elisabeth Sundström] coordinators: [Liane Hughes] # Link to other pages in the showcase section on the IDTk by listing the page_id. -# More information on which page_id you can use can be found at https://www.infectious-diseases-toolkit.org/contribute/website-overview +# More information on which page_id you can use can be found at https://www.infectious-diseases-toolkit.org/contribute/website-overview related_pages: - showcase: [] + showcase: [] # List the training resources produced by the specific country in the following spreadsheet: training: @@ -14,43 +15,44 @@ training: registry: GitHub url: https://github.com/mhoehle/mt3002-summer2020 +# Refer to entries of the "main_tool_and_resource_table" if institutions, organizations and projects from the country contribute to the development of international tools and resources. -# Refer to entries of the "main_tool_and_resource_table" if institutions, organizations and projects from the country contribute to the development of international tools and resources. - -national_resources: - - name: COVID-19 & Pandemic Preparedness Data Portal Sweden - description: The Swedish COVID-19 & Pandemic Preparedness Data Portal is a hub for data, tools, services, and other resources centred around COVID-19 and pandemic preparedness in Sweden. - how_to_access: - instance_of: +national_resources: + - name: Swedish Pathogens Portal + description: The Swedish Pathogens Portal is a hub for data, tools, services, and other resources centred around pathogens, such as SARS-CoV-2, and pandemic preparedness in Sweden. + how_to_access: + instance_of: related_pages: - # More information on which page_id you can use can be found at https://www.infectious-diseases-toolkit.org/contribute/website_overview - human_biomolecular_data: [] - human_clinical_and_health_data: [] - socioeconomic_data: [] - pathogen_characterisation: [] - showcase: [] + # More information on which page_id you can use can be found at https://www.infectious-diseases-toolkit.org/contribute/website_overview + human_biomolecular_data: [] + human_clinical_and_health_data: [] + socioeconomic_data: [] + pathogen_characterisation: [] + showcase: [] url: http://pandemicpreparednessportal.se/ registry: biotools: fairsharing: tess: - --- -## Introduction +## Introduction + This page provides a general overview of resources, tools, and data related to infectious disease data management in Sweden. The practices, regulations, and other resources listed here may have originally been developed for use with a specific pathogen, but can be repurposed for more general use. -Support for research data management (RDM), both for infectious disease data and more generally, can be obtained from [National Bioinformatics Infrastructure Sweden (NBIS)](https://nbis.se/) and Science for Life Laboratory (SciLifeLab) [Data Centre](https://www.scilifelab.se/data/). The two have a [shared data management helpdesk](mailto:data-management@scilifelab.se) for providing direct support. In addition, [research data offices (RDO) or Data Access Unit (DAU)](https://data-guidelines.scilifelab.se/topics/university-rdm-resources/) situated at most Swedish universities offer general RDM support. +Support for research data management (RDM), both for infectious disease data and more generally, can be obtained from [National Bioinformatics Infrastructure Sweden (NBIS)](https://nbis.se/) and [Science for Life Laboratory (SciLifeLab) Data Centre](https://www.scilifelab.se/data/). The two have a [shared data management helpdesk](mailto:data-management@scilifelab.se) for providing direct support. In addition, [research data offices (RDO) or Data Access Unit (DAU)](https://data-guidelines.scilifelab.se/topics/university-rdm-resources/) situated at most Swedish universities offer general RDM support. ## Health authorities + There are multiple authorities in Sweden that determine public health policy and the measures that should be taken to protect public health. All are government authorities with different responsibilities. + - **[The Swedish Medical Products Agency (Läkemedelsverket)](https://www.lakemedelsverket.se/en)** is responsible for the approval of prescription medications and vaccinations, as well as for monitoring their efficacy and safety after approval. It also approves and controls clinical trials. - **[The Public Health Agency of Sweden (Folkhälsomyndigheten, FoHM)](https://www.folkhalsomyndigheten.se/the-public-health-agency-of-sweden/)** is responsible for monitoring public health issues in Sweden. It collects and aggregates statistics related to the effect of infectious diseases on public health (e.g. the number of cases and hospitalisations related to infection with a given pathogen). It is possible to search for statistics on many diseases by locating the pathogen in their [statistics directory](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistik-a-o/sjukdomsstatistik/). -- **[The National Board for Health and Welfare (Socialstyrelsen)](https://www.socialstyrelsen.se/en/)** is responsible for issuing guidelines and regulations related to public health. It also maintains multiple [clinical registers](https://www.socialstyrelsen.se/en/statistics-and-data/registers/) and [statistics on health and medical care](https://www.socialstyrelsen.se/en/statistics-and-data/statistics/), including COVID-19. +- **[The National Board for Health and Welfare (Socialstyrelsen)](https://www.socialstyrelsen.se/en/)** is responsible for issuing guidelines and regulations related to public health. It also maintains multiple [clinical registers](https://www.socialstyrelsen.se/en/statistics-and-data/registers/) and [statistics on health and medical care](https://www.socialstyrelsen.se/en/statistics-and-data/statistics/), including COVID-19. ## Disease surveillance initiatives @@ -58,64 +60,86 @@ Multiple initiatives have been established for disease surveillance in Sweden. B ### Wastewater surveillance -Wastewater surveillance has proven to be an effective means of predicting outbreaks, with peaks in viral genome content shown to precede increases in cases and hopitalisations. This is also true of Swedish wastewater surveillance efforts, with e.g. [Wang *et al.* (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/) showing that peaks in viral genome content preceded increases in cases by two weeks. +Wastewater surveillance has proven to be an effective means of predicting outbreaks, with peaks in viral genome content shown to precede increases in cases and hospitalisations. This is also true of Swedish wastewater surveillance efforts, with e.g. [Wang _et al._ (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/) showing that peaks in viral genome content preceded increases in cases by two weeks. -Multiple research groups across Sweden have monitored viral genome content in wastewater, including groups at the [University of Gothenburg](https://www.gu.se/en), [KTH Royal Institute of Technology](https://www.kth.se/en), and [Swedish University of Agricultural Sciences (SLU)](https://www.slu.se/en/). Throughout the COVID-19 pandemic these efforts largely focused on monitoring SARS-CoV-2, but the scope has expanded to include other pathogens. More information on the work by these groups is on the [Swedish COVID-19 and Pandemic Preparedness Portal](https://www.covid19dataportal.se/dashboards/wastewater/). +Multiple research groups across Sweden have monitored viral genome content in wastewater, including groups at the [University of Gothenburg (GU)](https://www.gu.se/en), [KTH Royal Institute of Technology (KTH)](https://www.kth.se/en), and [Swedish University of Agricultural Sciences (SLU)](https://www.slu.se/en/). More information on the work by these groups, including the data collected, is on the [Swedish Pathogens Portal](https://pathogens.se/dashboards/wastewater/). Throughout the COVID-19 pandemic, each of these groups quantified the levels of SARS-CoV-2 in wastewater (see SARS-CoV-2 data from [GU](https://pathogens.se/dashboards/wastewater/covid_quantification/covid_quant_gu/), [KTH](https://pathogens.se/dashboards/wastewater/covid_quantification/covid_quant_kth/), and [SLU](https://pathogens.se/dashboards/wastewater/covid_quantification/covid_quant_slu/)). The groups also monitor other pathogens in wastewater, and share this data on the Swedish Pathogens Portal. For example, see the dashboards related to [monitoring enteric viruses by GU](https://pathogens.se/dashboards/wastewater/enteric_quantification/) and [monitoring influenza by SLU](https://pathogens.se/dashboards/wastewater/influenza_quantification/). ### Sentinel monitoring in healthcare -The [Swedish Public Health Agency](https://www.folkhalsomyndigheten.se/the-public-health-agency-of-sweden/) coordinates [sentinel monitoring (information only available in Swedish)](https://www.folkhalsomyndigheten.se/mikrobiologi-laboratorieanalyser/mikrobiella-och-immunologiska-overvakningsprogram/sentinelovervakning/) for COVID-19 and influenza. In sentinel monitoring, samples are taken from patients with symptoms of influenza or acute respiratory infections. These samples are analysed by The Swedish Public Health Agency. The data is then used to inform national policy decisions, and is presented to the public in regular reports (see the 'Hur presenteras data?' (In English: 'How is the data presented?') section of the [sentinel monitoring page (information only available in Swedish)](https://www.folkhalsomyndigheten.se/mikrobiologi-laboratorieanalyser/mikrobiella-och-immunologiska-overvakningsprogram/sentinelovervakning/) to access the public reports. The data is subsequently reported to the [European Centre for Disease Prevention and Control (ECDC)](https://www.ecdc.europa.eu/en), who then reports the data to the [World Health Organisation (WHO)](https://www.who.int/). + +The [Swedish Public Health Agency](https://www.folkhalsomyndigheten.se/the-public-health-agency-of-sweden/) coordinates [sentinel monitoring (information only available in Swedish)](https://www.folkhalsomyndigheten.se/mikrobiologi-laboratorieanalyser/mikrobiella-och-immunologiska-overvakningsprogram/sentinelovervakning/) for COVID-19 and influenza. In sentinel monitoring, samples are taken from patients with symptoms of influenza or acute respiratory infections. These samples are analysed by The Swedish Public Health Agency. The data is then used to inform national policy decisions, and is presented to the public in regular reports (see the 'Hur presenteras data?' (In English: 'How is the data presented?') section of the [sentinel monitoring page (information only available in Swedish)](https://www.folkhalsomyndigheten.se/mikrobiologi-laboratorieanalyser/mikrobiella-och-immunologiska-overvakningsprogram/sentinelovervakning/) to access the public reports). The data is subsequently reported to the [European Centre for Disease Prevention and Control (ECDC)](https://www.ecdc.europa.eu/en), who then reports the data to the [World Health Organisation (WHO)](https://www.who.int/). ## Dashboards and visualisation platforms -- [SARS-CoV-2 antibody tests conducted by the SciLifeLab Autoimmunity and Serology profiling facility](https://www.covid19dataportal.se/dashboards/serology-statistics/): shows the total number of tests conducted, as well as the number of positive and negative tests over time. -- [Wastewater monitoring by research groups in Sweden](https://www.covid19dataportal.se/dashboards/wastewater/): shows data about the levels of viral genome in wastewater in multiple Swedish cities over time. -- [Administration of COVID-19 vaccinations in Sweden](https://www.covid19dataportal.se/dashboards/vaccines/): shows vaccine coverage in terms of different doses, different regions, and different age groups. -- [Register-based large-scale national population study to monitor COVID-19 vaccination effectiveness and safety](https://www.covid19dataportal.se/dashboards/recovac/): uses registry based data to examine how the number of vaccine doses differs across age ranges and how this relates to ICU admissions for the general population. Also examines dose level among people in specific risk categories in general and when infected with COVID-19. -- [Post COVID-19 condition/long COVID in Sweden](https://www.covid19dataportal.se/dashboards/post_covid/): shows the distribution of patients diagnosed with post COVID-19 condition in Sweden, in terms of age, sex, geography, as well as contacts with healthcare and secondary diagnoses. -- [Swedish COVID-19 Publications](https://www.covid19dataportal.se/dashboards/covid_publications/): shows information about publications related to COVID-19/SARS-CoV-2 that involve at least person affiliated with a Swedish institution. -- [CRUSH Covid project dashboard](https://www.covid19dataportal.se/dashboards/crush_covid/): a compilation of resources related to the outcomes of the CRUSH Covid project, which mapped outbreaks of COVID-19 in Uppsala and issued reports targeted at minimising the impact on public health (no longer updated as of September 2022). -- [COVID symptom study Sweden](https://www.covid19dataportal.se/dashboards/symptom_study_sweden/): a compilation of resources related to the COVID symptom study Sweden project, which monitored the occurrence of COVID-19 symptoms across different regions of Sweden to estimate the prevalence and distribution of symptomatic cases (no longer updated as of July 2022). -- [COVID-19 test statistics from the National Pandemic Centre](https://www.covid19dataportal.se/dashboards/npc-statistics/): shows the number of tests conducted each week, and the relative proportions of positive, negative, and inconclusive results over time (no longer updated as of December 2020). -- [The Swedish Public Health Agency’s COVID-19 statistics ](https://experience.arcgis.com/experience/09f821667ce64bf7be6f9f87457ed9aa): shows data on the number of cases, admissions to intensive care, and mortality related to COVID-19 over time (only available in Swedish). -- [The Swedish Public Health Agency’s information on COVID-19 PCR tests ](https://www.folkhalsomyndigheten.se/PCR-covid-19/): shows the number of PCR tests performed over time in Sweden (only available in Swedish). -- [The National Board for Health and Welfare’s dashboard on COVID-19 statistics](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/): shows information on the number of COVID-19 cases, and survival rates, as well as information on post COVID-19 condition/longcovid both for different regions and over time (only available in Swedish). -- [The National Board for Health and Welfare’s dashboard on data indirectly related to COVID-19](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/statistik-relaterad-till-covid-19/): shows information related to the number of influenza cases over time, as well as general mortality rates in Sweden (only available in Swedish and no longer updated as of January 2022). +- [SARS-CoV-2 antibody tests conducted by the SciLifeLab Autoimmunity and Serology profiling facility](https://pathogens.se/dashboards/serology-statistics/): shows the total number of tests conducted, as well as the number of positive and negative tests over time. +- [Wastewater monitoring by research groups in Sweden](https://pathogens.se/dashboards/wastewater/): shows data about the levels of viral genomes (e.g. SARS-CoV-2, influenza, enteric viruses) in wastewater in multiple Swedish cities over time. +- [Register-based large-scale national population study to monitor COVID-19 vaccination effectiveness and safety](https://pathogens.se/dashboards/recovac/): uses registry based data to examine how the number of vaccine doses differs across age ranges and how this relates to ICU admissions for the general population. The resource also examines dose level among people in specific risk categories, both in general and when infected with COVID-19. +- [Post COVID-19 condition/long COVID in Sweden](https://pathogens.se/dashboards/post_covid/): shows the distribution of patients diagnosed with post COVID-19 condition in Sweden, in terms of age, sex, geography, as well as contacts with healthcare and secondary diagnoses. +- [Swedish COVID-19 Publications](https://pathogens.se/dashboards/covid_publications/): shows information about publications related to COVID-19/SARS-CoV-2 that involve at least one person affiliated with a Swedish institution. +- [Administration of COVID-19 vaccinations in Sweden](https://pathogens.se/dashboards/vaccines/): shows vaccine coverage in terms of different doses, different regions, and different age groups (no longer updated as of April 2023). +- [CRUSH Covid project dashboard](https://pathogens.se/dashboards/crush_covid/): a compilation of resources related to the outcomes of the CRUSH Covid project, which mapped outbreaks of COVID-19 in Uppsala and issued reports targeted at minimising the impact on public health (no longer updated as of September 2022). +- [COVID symptom study Sweden](https://pathogens.se/dashboards/symptom_study_sweden/): a compilation of resources related to the COVID symptom study Sweden project, which monitored the occurrence of COVID-19 symptoms across different regions of Sweden to estimate the prevalence and distribution of symptomatic cases (no longer updated as of July 2022). +- [COVID-19 test statistics from the National Pandemic Centre](https://pathogens.se/dashboards/npc-statistics/): shows the number of tests conducted each week, and the relative proportions of positive, negative, and inconclusive results over time (no longer updated as of December 2020). +- [The Swedish Public Health Agency’s information on COVID-19 PCR tests ](https://www.folkhalsomyndigheten.se/PCR-covid-19/): shows the number of PCR tests performed over time in Sweden (only available in Swedish). +- [The National Board for Health and Welfare’s dashboard on COVID-19 statistics](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/): shows information on the number of COVID-19 cases, and survival rates, as well as information on post COVID-19 condition/longcovid both for different regions and over time (only available in Swedish). +- [The National Board for Health and Welfare’s dashboard on data indirectly related to COVID-19](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/statistik-relaterad-till-covid-19/): shows information related to the number of influenza cases over time, as well as general mortality rates in Sweden (only available in Swedish and no longer updated as of January 2022). +- [The Swedish Public Health Agency’s information on influenza and RS virus](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistik-a-o/sjukdomsstatistik/influensa-veckorapporter/aktuell-veckorapport-om-influensa/): shows the number of cases in Sweden during the winter season (only available in Swedish). ## National data sources + -- [Database of Swedish COVID-19 publications that make data available](https://www.covid19dataportal.se/datasets/all/). This resource lists all publications on COVID-19 that involve at least one researcher affiliated with a Swedish research institution and make their data openly available. The data has been categorised according to data type (e.g. social and humanities data, genomics data) to aid users (data is openly available). + +- [Database of Swedish COVID-19 publications that make data available](https://pathogens.se/datasets/all/) (data is openly available). This resource lists all publications on COVID-19 that involve at least one researcher affiliated with a Swedish research institution and make their data openly available. The data has been categorised according to data type (e.g. social and humanities data, genomics data) to aid users. - [Data on infectious diseases from The Public Health Agency of Sweden](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistik-a-o/sjukdomsstatistik/) (data is openly available). This resource is a directory of statistics (e.g. the number of cases detected, and the number of resulting hospitalisations) collected by the Public Health Agency of Sweden on multiple diseases. The statistics for each pathogen/disease can be accessed by locating a given pathogen in the directory (sorted alphabetically). -- [COVID-19 data sources from The National Board for Health and Welfare](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/) (data is openly available). This resource includes data on post COVID-19 condition (or long COVID), as well as other information on the length of care required after infection with COVID-19. -- [Infectious diseases data sources published on the SciLifeLab Data Repository](https://figshare.scilifelab.se/categories/Biomedical_and_clinical_sciences/24457?categories=24508) (some data is openly available, otherwise access to data is restricted). The SciLifeLab Data Repository includes multiple different types of data (e.g. image data), the information found at the link shows only the data related to infectious disease, regardless of data type. +- [COVID-19 data sources from The National Board for Health and Welfare](https://www.socialstyrelsen.se/statistik-och-data/statistik/statistik-om-covid-19/) (data is openly available). This resource includes data on post COVID-19 condition (or long COVID), as well as other information on the length of care required after infection with COVID-19. +- [Infectious diseases data sources published on the SciLifeLab Data Repository](https://figshare.scilifelab.se/categories/Biomedical_and_clinical_sciences/24457?categories=24508) (some data is openly available, otherwise access to data is restricted). The SciLifeLab Data Repository includes multiple different types of data (e.g. image data), the information found at the link shows only the data related to infectious disease, regardless of data type. - [National Patient Register](https://www.socialstyrelsen.se/en/statistics-and-data/registers/national-patient-register/) (access to data is restricted). This resource includes four different types of data about patients; basic patient data (e.g. age), geographic data (e.g. hospital department), administrative data (e.g. data of inpatient check in), and medical data (e.g. main diagnosis). - [National Prescribed Drug Register](https://www.socialstyrelsen.se/en/statistics-and-data/registers/national-prescribed-drug-register/) (access to data is restricted). This resource provides official statistics related to drugs prescribed in Sweden. It is used to increase patient safety in relation to prescribed drugs. - [Quality Registry for SARS-CoV-2 data](https://covid19register.se/) (only available in Swedish) (access to data is restricted). This resource provides quality indicators related to SARS-CoV-2 (e.g. the number or PCR tests done overall, and percentage of the population tested). ## Regulations + + In Sweden, ethical reviews, biobanks and the processing of patient data within the healthcare system data is regulated by law. The [Swedish Ethical Review Authority](https://etikprovningsmyndigheten.se/en/) is the Swedish authority performing ethical reviews. Sweden follows European [General Data Protection Regulations (GDPR)](https://eur-lex.europa.eu/legal-content/SV/TXT/?uri=celex%3A32016R0679). - [The Ethics Review Act](https://www.riksdagen.se/sv/dokument-lagar/dokument/svensk-forfattningssamling/lag-2003460-om-etikprovning-av-forskning-som_sfs-2003-460) (only available in Swedish) - [The Patient Data Act](https://www.riksdagen.se/sv/dokument-lagar/dokument/svensk-forfattningssamling/patientdatalag-2008355_sfs-2008-355) (only available in Swedish) - [The Biobank Act](https://www.riksdagen.se/sv/dokument-lagar/dokument/svensk-forfattningssamling/biobankslag-202338_sfs-2023-38) (only available in Swedish) -## Domain-specific infrastructures or resources +## Domain-specific infrastructures or resources + + Below is a list of national infrastructures and resources that are associated with infectious disease data. They are involved in different stages of the data life cycle. - -### National Pandemic Centre -The [National Pandemic Centre (NPC)](https://ki.se/en/mtc/national-pandemic-centre-npc) is a research facility located at [Karolinska Institute](https://ki.se/en)/[SciLifeLab](https://www.scilifelab.se/). It is responsible for sequencing SARS-CoV-2 variants in Sweden, and collaborates with multiple Swedish regional health agencies and the Swedish Public Health Agency to collect samples and distribute data accordingly. + +### National Pandemic Centre + +The [National Pandemic Centre (NPC)](https://ki.se/en/mtc/national-pandemic-centre-npc) is a research facility located at [Karolinska Institutet](https://ki.se/en)/[SciLifeLab](https://www.scilifelab.se/). It is responsible for sequencing SARS-CoV-2 variants in Sweden, and collaborates with multiple Swedish regional health agencies and the Swedish Public Health Agency to collect samples and distribute data accordingly. ### Biobank Sweden -[Biobank Sweden](https://biobanksverige.se/en/home/) is the Swedish node of the European biobanking research infrastructure [BBMRI-ERIC](https://www.bbmri-eric.eu/). It facilitates, and promotes collaborations between healthcare, academia, industry, and patient organisations. It develops and maintains the [COVID-19 sample collections database](https://biobanks.covid19dataportal.se/) in collaboration with the Swedish COVID-19 and Pandemic Preparedness Portal. The database shows which biobanks collections are available across Sweden, and provides details about the collections (e.g. the size and conditions for access). + +[Biobank Sweden](https://biobanksverige.se/en/home/) is the Swedish node of the European biobanking research infrastructure [BBMRI-ERIC](https://www.bbmri-eric.eu/). It facilitates, and promotes collaborations between healthcare, academia, industry, and patient organisations. It develops and maintains the [COVID-19 sample collections database](https://pathogens.se/biobanks/) in collaboration with the Swedish Pathogens Portal. The database shows which biobanks collections are available across Sweden, and provides details about the collections (e.g. the size of the collection and conditions for access). ### Genomic Medicine Sweden + [Genomic Medicine Sweden (GMS)](https://genomicmedicine.se/), is a collaboration founded in 2018. It aims to enable genomic innovation to be translated into clinical practice, and to provide a sustainable precision medicine infrastructure. [Infectious disease](https://genomicmedicine.se/en/infectious-diseases/) is one of the seven disease areas covered by GMS. In late 2022 the fourteen partners involved in GMS signed an [agreement for data sharing](https://genomicmedicine.se/en/2022/12/07/national-it-infrastructure-in-operation-to-share-genomics-data-across-healthcare-regions-in-sweden/). It represents the first agreement enabling healthcare data, including genomics data, to be shared throughout Sweden. -### Pandemic Laboratory Preparedness program +### Pandemic Laboratory Preparedness Program -The [Pandemic Laboratory Preparedness (PLP) program](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/) is a SciLifeLab research program commissioned by the Swedish government. It aims to build laboratory capacity to ensure future laboratory preparedness through the development of research, competence, and technology. Information about the projects (including research and development projects), and collaborations with infrastructure and government agencies can be found on [The Swedish COVID-19 and Pandemic Preparedness Data Portal](https://pandemicpreparednessportal.se). +The [Pandemic Laboratory Preparedness (PLP) program](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/) is a SciLifeLab research program commissioned by the Swedish government. It aims to build laboratory capacity to ensure future laboratory preparedness through the development of research, competence, and technology. Information about the projects (including research and development projects), and collaborations with infrastructure and government agencies can be found on the [Swedish Pathogens Portal](https://pathogens.se). ### Chemical Biology Consortium Sweden [Chemical Biology Consortium Sweden (CBCS)](http://www.cbcs.se/) is a SciLifeLab national research infrastructure (i.e. a national infrastructure unit that is funded by SciLifelab). The CBCS enables researchers to find and develop small molecules to understand and decipher the function of biological pathways, including those associated with infectious disease. + +### Data-driven Life Science Data Science Nodes + +Four national Data Science Nodes (DSNs) have been established as part of the [SciLifeLab and Wallenberg Program for Data-Driven Life Science (DDLS)](https://scilifelab.se/data-driven) initiative. The DSN for the [Epidemiology and Biology of Infection](https://www.scilifelab.se/data-driven/ddls-research/ddls-epidemiology-and-biology-of-infection-ra/), hosted at Umeå University, will coordinate and develop national services for databases and data support as well as bioinformatics support to the Swedish research community focused on infectious diseases. The node will work closely with the [Swedish Pathogens Portal](https://pathogens.se). + +### Centre for Health Crisis + +[The Centre for Health Crisis](https://ki.se/en/collaboration/centre-for-health-crises) has been established at Karolinska Institutet and aims to contribute to building better preparedness for health crises in society, through research, education, and interdisciplinary collaboration. + +### Laboratory for Molecular Infection Medicine Sweden + +The [Laboratory for Molecular Infection Medicine Sweden (MIMS)](https://www.umu.se/en/mims/) in Umeå is the Nordic EMBL Partnership, a major strategic player in Europe’s molecular understanding of disease mechanisms. MIMS is the focus for basic and translational research in molecular infection medicine. diff --git a/pathogen-characterisation/data-description.md b/pathogen-characterisation/data-description.md index 07e7e567..82a9b0e2 100644 --- a/pathogen-characterisation/data-description.md +++ b/pathogen-characterisation/data-description.md @@ -8,7 +8,7 @@ page_id: pc_data_description rdmkit: - name: url: -related_pages: +related_pages: showcase: [] human_biomolecular_data: [] human_clinical_and_health_data: [] From 2116065484fa1741ffdee2457eceff1ff6b667d2 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 16 Nov 2023 15:17:13 +0100 Subject: [PATCH 14/17] keep id as string --- var/tools_validator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/tools_validator.py b/var/tools_validator.py index 91cadbba..52b21775 100644 --- a/var/tools_validator.py +++ b/var/tools_validator.py @@ -128,7 +128,7 @@ def fairsharing_available(query, token): if len(output) >= 1: for fairsharing_obj in output: if query.lower() in fairsharing_obj['attributes']['name'].lower() and fairsharing_obj['attributes']['doi']: - return fairsharing_obj['attributes']['url'].split(".")[-1] + return str(fairsharing_obj['attributes']['url'].split(".")[-1]) except: print(response) sys.exit("Could not connect to FAIRsharing") From 0d84fd32f054137b1f431fe5b65d92ed39e3ce77 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 17 Nov 2023 10:21:03 +0100 Subject: [PATCH 15/17] Automatic tool/resource-list update (#245) * Update tool/resource_list.yaml * Update tool_and_resource_list.yml --------- Co-authored-by: bedroesb Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> --- _data/tool_and_resource_list.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 6b70fd30..e740a0d2 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -205,9 +205,8 @@ id: dragen-gatk name: Dragen-GATK url: https://gatk.broadinstitute.org/hc/en-us/articles/360045944831 -- description: - "Dryad is an open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data. Dryad has a long-term data preservation strategy, and is a Core Trust Seal Certified Merritt repository with storage in US and EU at the San Diego Supercomputing Center, DANS, and Zenodo. While data is undergoing peer review, it is embargoed if the related journal requires / allows this. Dryad is an independent non-profit that works directly with: researchers to publish datasets utilising best practices for discovery and reuse; publishers to support the integration of data availability statements and data citations into their workflows; and institutions to enable scalable campus support for research data management best practices at low cost. Costs are covered by institutional, publisher, and funder members, otherwise a one-time fee of $120 for authors to cover cost of curation and preservation. Dryad also receives direct funder support through - grants." +- description: 'Dryad is an open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data. Dryad has a long-term data preservation strategy, and is a Core Trust Seal Certified Merritt repository with storage in US and EU at the San Diego Supercomputing Center, DANS, and Zenodo. While data is undergoing peer review, it is embargoed if the related journal requires / allows this. Dryad is an independent non-profit that works directly with: researchers to publish datasets utilising best practices for discovery and reuse; publishers to support the integration of data availability statements and data citations into their workflows; and institutions to enable scalable campus support for research data management best practices at low cost. Costs are covered by institutional, publisher, and funder members, otherwise a one-time fee of $120 for authors to cover cost of curation and preservation. Dryad also receives direct funder support through + grants.' id: dryad name: Dryad registry: @@ -234,7 +233,7 @@ fairsharing: mya1ff tess: European Genome-phenome Archive (EGA) url: https://ega-archive.org/ -- description: "The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,300 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information, communication technology, and environmental science. ELSST is used for data discovery within CESSDA and facilitates access to data resources across Europe, independent of domain, resource, language, or vocabulary. ELSST is currently available in 16 languages: Danish, Dutch, Czech, English, Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian, Slovenian, Spanish, and Swedish" +- description: 'The European Language Social Science Thesaurus (ELSST) is a broad-based, multilingual thesaurus for the social sciences. It is owned and published by the Consortium of European Social Science Data Archives (CESSDA) and its national Service Providers. The thesaurus consists of over 3,300 concepts and covers the core social science disciplines: politics, sociology, economics, education, law, crime, demography, health, employment, information, communication technology, and environmental science. ELSST is used for data discovery within CESSDA and facilitates access to data resources across Europe, independent of domain, resource, language, or vocabulary. ELSST is currently available in 16 languages: Danish, Dutch, Czech, English, Finnish, French, German, Greek, Hungarian, Icelandic, Lithuanian, Norwegian, Romanian, Slovenian, Spanish, and Swedish' id: european-language-social-science-thesaurus name: European Language Social Science Thesaurus (ELSST) registry: @@ -733,8 +732,8 @@ name: SARS-CoV-2 Data Hubs url: https://www.covid19dataportal.org/data-hubs - description: A web-based platform for sharing viral sequence data, initially for influenza data, and now for other pathogens (including SARS-CoV-2). + id: gisaid name: Global Initiative on Sharing All Influenza Data (GISAID) registry: fairsharing: 2f7f9f - id: gisaid url: https://gisaid.org From e3bbd66053c1f848153cf9e8b972a6de4af60424 Mon Sep 17 00:00:00 2001 From: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Date: Fri, 17 Nov 2023 13:46:09 +0100 Subject: [PATCH 16/17] no countries (#244) --- .github/workflows/tool_list_conversion.yml | 4 - _data/countries.yml | 250 --------------------- var/country_list.py | 50 ----- 3 files changed, 304 deletions(-) delete mode 100644 _data/countries.yml delete mode 100644 var/country_list.py diff --git a/.github/workflows/tool_list_conversion.yml b/.github/workflows/tool_list_conversion.yml index e7fce1cd..515ec559 100644 --- a/.github/workflows/tool_list_conversion.yml +++ b/.github/workflows/tool_list_conversion.yml @@ -55,10 +55,6 @@ jobs: run: | python var/tools_validator.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}" - - name: Fetch country names with corresponding iso - run: | - python var/country_list.py - - name: Show differences run: | git diff --stat diff --git a/_data/countries.yml b/_data/countries.yml deleted file mode 100644 index 66a54e12..00000000 --- a/_data/countries.yml +++ /dev/null @@ -1,250 +0,0 @@ -AD: Andorra -AE: United Arab Emirates -AF: Afghanistan -AG: Antigua and Barbuda -AI: Anguilla -AL: Albania -AM: Armenia -AO: Angola -AQ: Antarctica -AR: Argentina -AS: American Samoa -AT: Austria -AU: Australia -AW: Aruba -AX: "\xC5land Islands" -AZ: Azerbaijan -BA: Bosnia and Herzegovina -BB: Barbados -BD: Bangladesh -BE: Belgium -BF: Burkina Faso -BG: Bulgaria -BH: Bahrain -BI: Burundi -BJ: Benin -BL: "Saint Barth\xE9lemy" -BM: Bermuda -BN: Brunei Darussalam -BO: Bolivia (Plurinational State of) -BQ: Bonaire, Sint Eustatius and Saba -BR: Brazil -BS: Bahamas -BT: Bhutan -BV: Bouvet Island -BW: Botswana -BY: Belarus -BZ: Belize -CA: Canada -CC: Cocos (Keeling) Islands -CD: Congo (Democratic Republic of the) -CF: Central African Republic -CG: Congo -CH: Switzerland -CI: Ivory Coast -CK: Cook Islands -CL: Chile -CM: Cameroon -CN: China -CO: Colombia -CR: Costa Rica -CU: Cuba -CV: Cabo Verde -CW: "Cura\xE7ao" -CX: Christmas Island -CY: Cyprus -CZ: Czech Republic -DE: Germany -DJ: Djibouti -DK: Denmark -DM: Dominica -DO: Dominican Republic -DZ: Algeria -EC: Ecuador -EE: Estonia -EG: Egypt -EH: Western Sahara -ER: Eritrea -ES: Spain -ET: Ethiopia -FI: Finland -FJ: Fiji -FK: Falkland Islands (Malvinas) -FM: Micronesia (Federated States of) -FO: Faroe Islands -FR: France -GA: Gabon -GB: United Kingdom of Great Britain and Northern Ireland -GD: Grenada -GE: Georgia -GF: French Guiana -GG: Guernsey -GH: Ghana -GI: Gibraltar -GL: Greenland -GM: Gambia -GN: Guinea -GP: Guadeloupe -GQ: Equatorial Guinea -GR: Greece -GS: South Georgia and the South Sandwich Islands -GT: Guatemala -GU: Guam -GW: Guinea-Bissau -GY: Guyana -HK: Hong Kong -HM: Heard Island and McDonald Islands -HN: Honduras -HR: Croatia -HT: Haiti -HU: Hungary -ID: Indonesia -IE: Ireland -IL: Israel -IM: Isle of Man -IN: India -IO: British Indian Ocean Territory -IQ: Iraq -IR: Iran (Islamic Republic of) -IS: Iceland -IT: Italy -JE: Jersey -JM: Jamaica -JO: Jordan -JP: Japan -KE: Kenya -KG: Kyrgyzstan -KH: Cambodia -KI: Kiribati -KM: Comoros -KN: Saint Kitts and Nevis -KP: Korea (Democratic People's Republic of) -KR: Korea (Republic of) -KW: Kuwait -KY: Cayman Islands -KZ: Kazakhstan -LA: Lao People's Democratic Republic -LB: Lebanon -LC: Saint Lucia -LI: Liechtenstein -LK: Sri Lanka -LR: Liberia -LS: Lesotho -LT: Lithuania -LU: Luxembourg -LV: Latvia -LY: Libya -MA: Morocco -MC: Monaco -MD: Moldova (Republic of) -ME: Montenegro -MF: Saint Martin (French part) -MG: Madagascar -MH: Marshall Islands -MK: North Macedonia -ML: Mali -MM: Myanmar -MN: Mongolia -MO: Macao -MP: Northern Mariana Islands -MQ: Martinique -MR: Mauritania -MS: Montserrat -MT: Malta -MU: Mauritius -MV: Maldives -MW: Malawi -MX: Mexico -MY: Malaysia -MZ: Mozambique -NA: Namibia -NC: New Caledonia -NE: Niger -NF: Norfolk Island -NG: Nigeria -NI: Nicaragua -NL: Netherlands -'NO': Norway -NP: Nepal -NR: Nauru -NU: Niue -NZ: New Zealand -OM: Oman -PA: Panama -PE: Peru -PF: French Polynesia -PG: Papua New Guinea -PH: Philippines -PK: Pakistan -PL: Poland -PM: Saint Pierre and Miquelon -PN: Pitcairn -PR: Puerto Rico -PS: Palestine, State of -PT: Portugal -PW: Palau -PY: Paraguay -QA: Qatar -RE: "R\xE9union" -RO: Romania -RS: Serbia -RU: Russian Federation -RW: Rwanda -SA: Saudi Arabia -SB: Solomon Islands -SC: Seychelles -SD: Sudan -SE: Sweden -SG: Singapore -SH: Saint Helena, Ascension and Tristan da Cunha -SI: Slovenia -SJ: Svalbard and Jan Mayen -SK: Slovakia -SL: Sierra Leone -SM: San Marino -SN: Senegal -SO: Somalia -SR: Suriname -SS: South Sudan -ST: Sao Tome and Principe -SV: El Salvador -SX: Sint Maarten (Dutch part) -SY: Syrian Arab Republic -SZ: Swaziland -TC: Turks and Caicos Islands -TD: Chad -TF: French Southern Territories -TG: Togo -TH: Thailand -TJ: Tajikistan -TK: Tokelau -TL: Timor-Leste -TM: Turkmenistan -TN: Tunisia -TO: Tonga -TR: Turkey -TT: Trinidad and Tobago -TV: Tuvalu -TW: Taiwan -TZ: Tanzania, United Republic of -UA: Ukraine -UG: Uganda -UM: United States Minor Outlying Islands -US: United States of America -UY: Uruguay -UZ: Uzbekistan -VA: Vatican City -VC: Saint Vincent and the Grenadines -VE: Venezuela (Bolivarian Republic of) -VG: Virgin Islands (British) -VI: Virgin Islands (U.S.) -VN: Vietnam -VU: Vanuatu -WF: Wallis and Futuna -WS: Samoa -XK: Republic of Kosovo -YE: Yemen -YT: Mayotte -ZA: South Africa -ZM: Zambia -ZW: Zimbabwe diff --git a/var/country_list.py b/var/country_list.py deleted file mode 100644 index 1fb6698b..00000000 --- a/var/country_list.py +++ /dev/null @@ -1,50 +0,0 @@ -import yaml -import requests -from requests.adapters import HTTPAdapter -from urllib3.util.retry import Retry - -def client(url): - """API object fetcher""" - session = requests.Session() - retry = Retry(connect=3, backoff_factor=15) - adapter = HTTPAdapter(max_retries=retry) - session.mount('http://', adapter) - session.mount('https://', adapter) - try: - r = session.get(url) - except: - print("Could not connect") - if r.status_code == requests.codes.ok: - return r.json() - -def fetch_country_list(): - json_output = client( - f"https://restcountries.com/v2/all") - if json_output: - return json_output - else: - print("Country lookup is skipped") - exit() - - -# --------- Variables --------- - -output_path = "_data/countries.yml" - -# --------- Reading out page_ids from pages --------- - -print(f"----> Fetching list of countries") -country_list = fetch_country_list() - -print(f"----> Fetching country name based on country ID") -countries = {} - -for country in country_list: - if country['name'] and country['alpha2Code']: - countries[country['alpha2Code']] = country['name'] - - -with open(output_path, 'w') as yaml_file: - documents = yaml.dump(countries, yaml_file) - -print("----> YAML is dumped successfully") From ec085146b3a373416b5553ccdb047a4214b74a2c Mon Sep 17 00:00:00 2001 From: rafael buono <77321541+rabuono@users.noreply.github.com> Date: Fri, 17 Nov 2023 14:40:15 +0100 Subject: [PATCH 17/17] Update _config.yml (#246) enable data tables --- _config.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/_config.yml b/_config.yml index e51f6280..fe12e567 100644 --- a/_config.yml +++ b/_config.yml @@ -50,6 +50,7 @@ defaults: type: "pages" values: type: pathogen_characterisation + datatable: true - scope: @@ -57,6 +58,7 @@ defaults: type: "pages" values: type: socioeconomic_data + datatable: true - scope: @@ -64,6 +66,7 @@ defaults: type: "pages" values: type: human_clinical_and_health_data + datatable: true - scope: @@ -71,6 +74,7 @@ defaults: type: "pages" values: type: human_biomolecular_data + datatable: true - scope: @@ -78,6 +82,7 @@ defaults: type: "pages" values: type: showcase + datatable: true - scope: @@ -85,6 +90,7 @@ defaults: type: "pages" values: type: national_resources + datatable: true - scope: