| Autor: |
Monzón Fernández, Sara, Nyberg Åkerström, Wolmar, Lara, María, Cuesta de la Plaza, Isabel, Neves, Aitana, Mohamed, Anliat, Salgado, David, Pilvar, Diana, Inno, Heleri, Messak, Imane, van Helden, Jacques, Willassen, Nils-Peder, Denecker, Thomas, Pergl, Robert, Suchánek, Marek |
| Jazyk: |
angličtina |
| Rok vydání: |
2023 |
| Předmět: |
|
| DOI: |
10.5281/zenodo.8177166 |
| Popis: |
This deliverable pertains to task 9.3, which is dedicated to the establishment of data standards for SARS-CoV-2 variants and lineages. It plays a crucial role in the development of a network of specialised data experts in SARS-CoV-2 genomic surveillance, contributing to the objectives of WP1 and WP8. Furthermore, it aligns with WP2, focusing on training and capacity building initiatives. The accomplished work encompasses a workshop centred around the Fair Data Point concept, exploring its potential in advancing the goals of WP9. Additionally, a workshop addressing SARS-CoV-2 data standards was conducted, covering essential aspects such as metadata standards and variant/lineage nomenclature. A dedicated data standards task force was formed, which conducted a comprehensive survey to gauge the adoption of the proposed standards among participating countries within CONVERGE WP9. Furthermore, a separate task force dedicated to pathogen genomics data management collaborated with other projects, contributing to the development of valuable resources aimed at facilitating efficient data sharing. Overall, these endeavours represent significant progress in the establishment of robust data standards and effective data management practices within the project, ultimately contributing to enhanced genomic surveillance of SARS-CoV-2. Regarding variant and lineage nomenclature, Nextclade and Pangolin are widely adopted tools for variant classification. Integrating both tools in a comprehensive data hub allows for a thorough understanding of the genetic diversity of SARS-CoV-2. The data standards task force compared the metadata requirements of GISAID, ENA, and PHA4GE, revealing differences in the number and specificity of fields. The comparison showed that PHA4GE had the most comprehensive set of fields, while GISAID and ENA had unique fields specific to their databases. Harmonising metadata specifications and promoting interoperability remain essential challenges. The survey on metadata availability and public accessibility highlighted disparities among countries, emphasising the need for standardised metadata across the network. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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