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Update human_pathogen_genomics.md
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Genepio moved to tool syntax
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bianchini88 authored Oct 10, 2024
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Expand Up @@ -66,7 +66,7 @@ While the objects of interest in this domain are pathogens, the data is usually
* Refer to general guidance on how to provide [documentation and metadata](metadata_management) during your project.
* Adopt standards, conventions and robust protocols to maximise the reuse potential of the data in parallel initiatives and your future projects.
* The Genomic Standards Consortium (GSC) develops and maintains the {% tool "mixs" %} and the {% tool "migs-mims" %}set of core and extended descriptors for genomes and metagenomes with associated samples and their environment to guide scientists on how to capture the metadata essential for high-quality research.
* The GenEpiO Consortium develops and maintains the [Genomic Epidemiology Application Ontology (GenEpiO)](https://doi.org/10.25504/FAIRsharing.y1mmbv) to support data sharing and integration specifically for foodborne infectious disease surveillance and outbreak investigations.
* The GenEpiO Consortium develops and maintains the {% tool "genepio" %} to support data sharing and integration specifically for foodborne infectious disease surveillance and outbreak investigations.
* The [Public Health Alliance for Genomic Epidemiology (PHA4GE)](https://pha4ge.org/) supports openness and interoperability in public health bioinformatics. The [Data Structures working group](https://pha4ge.org/working-groups/) develops, adapts and standardises data models for microbial sequence data, contextual metadata, results and workflow metrics, such as the [SARS-CoV-2 contextual data specification](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification).
* ISO (the International Organization for Standardization) has issued standards that can be referenced when designing or commissioning genomic sequencing and informatics services, such as
* [ISO 20397-1:2022 Biotechnology — Massively parallel sequencing — Part 1: Nucleic acid and library preparation](https://www.iso.org/standard/74054.html)
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