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Update human_pathogen_genomics.md #1526

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6f8b8bc
Update human_pathogen_genomics.md
bianchini88 Sep 13, 2024
9de9889
start adding tools (#1527)
bedroesb Sep 13, 2024
7897af7
Update tool_and_resource_list.yml
bianchini88 Oct 10, 2024
daddbed
Update tool_and_resource_list.yml
bianchini88 Oct 10, 2024
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Update human_pathogen_genomics.md
bianchini88 Oct 10, 2024
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Update human_pathogen_genomics.md
bianchini88 Oct 11, 2024
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62 changes: 58 additions & 4 deletions _data/tool_and_resource_list.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -2660,3 +2660,57 @@
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 standardised ontology for human disease to provide 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
registry:
fairsharing: 8b6wfq
- description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research food-borne pathogens, infectious disease surveillance and outbreak investigations.
name: Genomic Epidemiology Ontology (GenEpiO)
id: genepio
url: https://genepio.org/
registry:
fairsharing: y1mmbv

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