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public repo for issues related to NMDC work
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Milestone - Define the outline and deliverables of a partnership with ICTV for implementing viral taxonomy into a robust, reproducible, and machine-readable framework (2.20) #520

Closed ssarrafan closed 5 months ago

ssarrafan commented 9 months ago

Because of the large diversity of viral genome types, complexity, and recombination/mutation rates across the virosphere, different taxonomic classification methods and criteria are used across different taxa and ranks, including gene(s) phylogeny, shared gene content, or genome-wide sequence similarity. These different criteria are still being refined and/or established for many taxa, and are currently stored as part of taxonomic proposals (“TaxoProp”), technical reports available on the ICTV website (https://talk.ictvonline.org/taxonomy/). To help standardize virus taxonomy analyses, particularly for metagenomic data, we propose to partner with ICTV, where NMDC would provide expertise in standardized data analysis and bioinformatic workflow management to translate the current and future demarcation criteria described in several dozens of ICTV TaxoProps into a single computational and actionable workflow (Milestone 2.20). By following the best practices established for NMDC workflow development, ICTV will ensure that taxonomic classification of new viruses can be achieved through portable and reproducible pipelines. This would in turn enable standard metagenomic analyses to not only include virus sequence detection, but also taxonomic classification following the latest ICTV guidelines. Page 35

ssarrafan commented 8 months ago

Update from quarterly report: Discussions were started with the ICTV Bioinformatics Study group about the needs of the viral taxonomy community and the support provided by the NMDC. The exact scope and deliverables still need to be determined in upcoming meetings, and should be finalized by the end of FY24 Q2.

ssarrafan commented 6 months ago

@emileyfadrosh any update on this milestone? Any blockers to this getting done by the end of March 2024?

simroux commented 6 months ago

I think last time we chatted with Emiley, we said we could consider this as done, but to be confirmed by @emileyfadrosh

ssarrafan commented 5 months ago

Updated from DOE QUarterly: Discussions were conducted with the ICTV Bioinformatics Study group about the needs of the viral taxonomy community and the support provided by the NMDC. The NMDC will share high-quality viral genomes identified via the NMDC metagenome annotation pipeline, for potential integration as new species exemplar in the ICTV taxonomy (to be evaluated by ICTV Study groups). In addition, the NMDC will work with the ICTV Bioinformatics Study group to provide documentation and tools for researchers to include metadata from the GSC MIUViG checklist with their viral MAG submission, as recommended by the ICTV (doi: 10.1038/s41587-023-01844-2).