A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
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MPX export to GISAID: headers of the output file need to be updated, remove one field #321
1. The headers in the GISAID output file from the MPX templates need to be updated.
Currently the DH GISAID export is using the same headers as the GISAID CanCOGeN export but GISAID is using MPX-specific headers in the MPX-specific submission form now.
Can we change the MPX headers please?
Keep them as is in the COVID GISAID export.
2. They have also removed one field for MPX, so we need to remove it too.
The removed field was called "Type" (which was always populated with betacoronavirus in the COVID template).
The header for the Type field was covv_type.
Can we remove this field from the MPX GISAID export please?
Keep it for the COVID GISAID export.
ddooley
commented
2 years ago
1. The headers in the GISAID output file from the MPX templates need to be updated. Currently the DH GISAID export is using the same headers as the GISAID CanCOGeN export but GISAID is using MPX-specific headers in the MPX-specific submission form now. Can we change the MPX headers please? Keep them as is in the COVID GISAID export.
The COVID-to-MPX header mapping can be in the attached sheet. GISAID_covid_to_pox_header_changes_June2022.xls
2. They have also removed one field for MPX, so we need to remove it too. The removed field was called "Type" (which was always populated with betacoronavirus in the COVID template). The header for the Type field was covv_type. Can we remove this field from the MPX GISAID export please? Keep it for the COVID GISAID export.