start adding tools (#1527)

elixir-europe · Sep 13, 2024 · 9de9889 · 9de9889
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diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
@@ -2265,12 +2265,12 @@
     fairsharing: f5zx00
     tess: Expression Atlas
   url: https://www.ebi.ac.uk/gxa/home
-- description: Accessible database designed by scientist for scientist, to improve the sharing of influenza data.
+- 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: GISAID
+  name: Global Initiative on Sharing All Influenza Data (GISAID)
   registry:
-    fairsharing: ba6a09
-  url: https://www.gisaid.org
+    fairsharing: 2f7f9f
+  url: https://gisaid.org
 - description: Protein Data Bank in Europe Knowledge Base
   id: pdbe-kb
   name: PDBe-KB
@@ -2660,3 +2660,48 @@
   id: better-bibtex
   name: Better BibTeX (BBT)
   url: https://retorque.re/zotero-better-bibtex/
+- description: GA4GH frames policy and builds standards to meet the real-world needs of the global genomics and health community.
+  id: ga4gh
+  name: Global Alliance for Genomics and Health (GA4GH)
+  url: https://www.ga4gh.org
+  registry:
+    biotools: ga4gh
+    fairsharing: 2tpx4v
+    tess: GA4GH
+- description: Discover tools and best practices for working with infectious disease data. IDTk provides general guidance as well as specific information for pathogen characterisation, socioeconomic data, human biomolecular data, and human clinical and health data.
+  id: idtk
+  name: Infectious Diseases Toolkit (IDTk)
+  url: https://www.infectious-diseases-toolkit.org/
+- description: The Beyond 1 Million Genomes (B1MG) project is helping to create a network of genetic and clinical data across Europe. The project provides coordination and support to the 1+ Million Genomes Initiative (1+MG). This initiative is a commitment of 24 EU countries, the UK and Norway to give cross-border access to one million sequenced genomes by 2022.
+  id: beyond-1-million-genomes
+  name: Beyond 1 Million Genomes (B1MG)
+  url: https://b1mg-project.eu/
+- 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://ega-archive.org/about/projects-and-funders/federated-ega/
+- description: The Pathogens Portal aims to provide access to data and tools relating to pathogens, their human and animal hosts and their vectors. Current content spans bacterial, viral and eukaryotic parasite lineages alongside human host data.
+  id: pathogens-portal
+  name: Pathogens Portal
+  registry:
+    fairsharing: a085b2
+    tess: Pathogens Portal
+  url: https://www.pathogensportal.org/
+- description: NCBI Pathogen Detection integrates bacterial and fungal pathogen genomic sequences from numerous ongoing surveillance and research efforts whose sources include food, environmental sources such as water or production facilities, and patient samples. Foodborne, hospital-acquired, and other clinically infectious pathogens are included.
+  id: pathogen-detection
+  name: Pathogen Detection
+  url: https://www.ncbi.nlm.nih.gov/pathogens/
+- description: The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. The portal includes relevant datasets submitted to EMBL-EBI as well as other major centres for biomedical data. The COVID-19 Data Portal is the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.
+  id: covid-19-data-portal
+  name: COVID-19 Data Portal
+  registry:
+    biotools: covid-19-data-portal
+    fairsharing: f3b7a9
+    tess: COVID-19 Data Portal
+  url: https://www.covid19dataportal.org/
+- description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics, underlying mechanisms and related medical vocabulary disease concepts.
+  name: Disease Ontology (DOID)
+  id: doid
+  url: http://www.disease-ontology.org
diff --git a/pages/your_domain/human_pathogen_genomics.md b/pages/your_domain/human_pathogen_genomics.md
@@ -104,18 +104,18 @@ While the objects of interest in this domain are pathogens, the data is usually
 
 * Information about the host phenotype, context and disease is often necessary to answer questions in a research study or policy perspective. Other contextual information can include non-host related environmental factors, such as interactions with other pathogens, drugs and geographic proliferation. It can also include information about the sampled material and how it was processed for sequencing.
 * Adopt common reporting checklists, data dictionaries, terms and vocabularies to simplify data sharing across initiatives.
-  * ENA hosts a selection of [sample checklists](https://www.ebi.ac.uk/ena/browser/checklists) that can be used to annotate sequencing experiements, including checklists derived from the [MIxS consortium](http://w3id.org/mixs). The [ENA virus pathogen reporting standard checklist](https://www.ebi.ac.uk/ena/browser/view/ERC000033) has been widely used for SARS-CoV-2 genomic studies.
-  * Reuse terms and definitions from existing vocabularies, such as the [Phenotypic QualiTy Ontology](https://www.ebi.ac.uk/ols4/ontologies/pato), [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy), [Disease Ontology](https://disease-ontology.org),  [Chemical Entities of Biological Interest](https://bioportal.bioontology.org/ontologies/CHEBI/?p=summary), and [UBER anatomy ONtology](https://bioportal.bioontology.org/ontologies/UBERON).
+  * {% tool "european-nucleotide-archive" %} hosts a selection of [sample checklists](https://www.ebi.ac.uk/ena/browser/checklists) that can be used to annotate sequencing experiements, including checklists derived from the [MIxS consortium](http://w3id.org/mixs). The [ENA virus pathogen reporting standard checklist](https://www.ebi.ac.uk/ena/browser/view/ERC000033) has been widely used for SARS-CoV-2 genomic studies.
+  * Reuse terms and definitions from existing vocabularies, such as the [Phenotypic QualiTy Ontology](https://www.ebi.ac.uk/ols4/ontologies/pato), {% tool "ncbi-taxonomy" %}, {% tool "doid" %},  [Chemical Entities of Biological Interest](https://bioportal.bioontology.org/ontologies/CHEBI/?p=summary), and [UBER anatomy ONtology](https://bioportal.bioontology.org/ontologies/UBERON).
   * The [PHA4GE SARS-CoV-2 contextual data specification](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification) is a comprehensive example including a reporting checklist, related protocols, and mappings to relevant vocabularies and data sharing platforms.
 
 #### Generating genomic data
 * Establish protocols and document the steps taken in the lab to process the sample and in the computational workflow to prepare the resulting data. Make sure to keep information from quality assurance procedures and strive to make your labwork and computational process as reproducible as possible.
     * [High-Throughput Sequencing \| LifeScienceRDMLookUp](https://elixir.no/rdm-lookup/sequencing)
-    * [The Beyond One Million Genomes (B1MG)](https://b1mg-project.eu) project provides guidelines that cover the minimum [quality requirements](https://zenodo.org/record/5018495) for the generation of genome sequencing data.
+    * {% tool"beyond-1-million-genomes" %} project provides guidelines that cover the minimum [quality requirements](https://zenodo.org/record/5018495) for the generation of genome sequencing data.
     * Data repositories generally have information about recommended [data file formats](data_publication) and [metadata](metadata_management)
-    * The [FAIR Cookbook](https://faircookbook.elixir-europe.org/content/home.html) provides instructions on [validation of file formats](https://faircookbook.elixir-europe.org/content/recipes/interoperability/fastq-file-format-validators.html)
+    * The {% tool "fair-cookbook" %} provides instructions on [validation of file formats](https://faircookbook.elixir-europe.org/content/recipes/interoperability/fastq-file-format-validators.html)
     * A good place to look for scientific and technical information about data quality validation software tools for pathogenomics is  [Bio.Tools](https://bio.tools/t?page=1&q=validation&sort=score&topicID=%22topic_3168%22).
-  * The [Infectious Diseases Toolkit (IDTk)](https://www.infectious-diseases-toolkit.org/) has a showcase on [An automated SARS-CoV-2 genome surveillance system built around Galaxy](https://www.infectious-diseases-toolkit.org/showcase/covid19-galaxy)
+  * The {% tool "idtk" %} has a showcase on [An automated SARS-CoV-2 genome surveillance system built around Galaxy](https://www.infectious-diseases-toolkit.org/showcase/covid19-galaxy)
   * The Galaxy Training Network provides free on-line [training materials on quality control](https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html).
 
 
@@ -134,17 +134,17 @@ While the objects of interest in this domain are pathogens, the data is usually
 #### Sharing host related and other contextual information
 * Some host related information can be personal and/or sensitive and care should be taken when storing and sharing it. Apply data masking and aggregation techniques to pseudonymise or anonymise the contextual information and take measures to separate personal and sensitive information from the pathogen data when possible.
 * Adopt solutions for federated analysis to support distributed analyses on information that could otherwise not be shared, such as establishing contractual agreements with suitable regional or international data infrastructures.
-* [GA4GH (Global Alliance for Genomics and Health)](https://www.ga4gh.org/what-we-do/) is a global organisation that frames policy and builds standards to meet the real-world needs of the genomics and health community. Its [GDPR & International Health Data Sharing Forum](https://www.ga4gh.org/product/gdpr-international-health-data-sharing-forum/) shares *GDPR Briefs* that represent a consensus position among its Forum Members (not legal advice) regarding the current understanding of the GDPR and its implications for genomic and health-related research, such as 
+* {% tool "ga4gh" %} is a global organisation that frames policy and builds standards to meet the real-world needs of the genomics and health community. Its [GDPR & International Health Data Sharing Forum](https://www.ga4gh.org/product/gdpr-international-health-data-sharing-forum/) shares *GDPR Briefs* that represent a consensus position among its Forum Members (not legal advice) regarding the current understanding of the GDPR and its implications for genomic and health-related research, such as 
   * [GDPR Brief: data protection implications of publishing metadata to enable discovery](https://www.ga4gh.org/news_item/ga4gh-gdpr-brief-data-protection-implications-of-publishing-metadata-to-enable-discovery/)
   * [GDPR Brief: federated analysis for responsible data sharing under the GDPR](https://www.ga4gh.org/news_item/ga4gh-gdpr-brief-federated-analysis-for-responsible-data-sharing-under-the-gdpr/)
 
 #### Sharing pathogen genomic data
 * You should adopt good practices for [data sharing](sharing) and identify which data sharing platforms to use to reach the relevant stakeholders. You can use more than one platform but care should be taken to make sure that data is interconnected where possible to enable deduplication in downstream analyses.
   * European healthcare surveillance systems is administered and used by public health authorities such as [ECDC’s TESSy/EpiPulse](https://www.ecdc.europa.eu/en/publications-data/epipulse-european-surveillance-portal-infectious-diseases)
-  * International research data exchanges such as [European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena/browser/submit) for non-sensitive genomic data and the [Federated EGA](https://ega-archive.org/federated) network for sensitive data.
-  * There are also pathogen specifc initiatives, such as [EMBL-EBI Pathogens](https://www.ebi.ac.uk/ena/pathogens/home) and [NCBI Pathogen Detection](https://www.ncbi.nlm.nih.gov/pathogens/). And initiatives focusing specifically on viruses, certain pathogens or certain data types, such as [GISAID (Global Initiative on Sharing All Influenza Data)](https://gisaid.org/) for observations and assembled consensus sequences on a selection of pathogens.
+  * International research data exchanges such as {% tool "european-nucleotide-archive" %} for non-sensitive genomic data 
+  * There are also pathogen specific initiatives, such as {% tool "pathogens-portal" %} and {% tool "pathogen-detection" %}. And initiatives focusing specifically on viruses, certain pathogens or certain data types, such as {% tool "gisaid"%} for observations and assembled consensus sequences on a selection of pathogens.
 * Investigate if there are [national resources](national_resources) or a [data brokering](data_brokering) organisation available to facilitate data sharing.
-  * [EBI Pathogens data hubs](https://www.ebi.ac.uk/ena/pathogens/v2/)
-  * [Submit new data \| European COVID-19 platform](https://www.covid19dataportal.org/submit-data)
+  * {% tool "pathogens-portal" %} Data Hubs network for sensitive data.
+  * {% tool "covid-19-data-portal" %}