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cidgoh / DataHarmonizer

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.
MIT License
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SOPs of GISAID template is missing and not able to transform it into GeneBank or any other format #332

Closed mibtisamnasar closed 2 years ago

mibtisamnasar commented 2 years ago

Hi, I am facing conversion issues from GISAID template to any other template. SOPs of this template is also not present. Both images are attached.

Any guidance is highly appreciated. Thanks!

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ddooley commented 2 years ago

I believe Emma communicated that GISAID format currently doesn't have any export formats set up for it, or an SOP, hence the experience you encountered there. I'll close this unless I hear there is some action to extend GISAID that way.

griffie commented 1 year ago

Hi Ibtisam, thanks for trying out the DH! It's true, the GISAID template currently doesn't transform to any other template and is more of an endpoint.

The other templates (PHA4GE, international MPXV) can transform TO the GISAID template but not vice versa.

If you are looking for scripts to transform GISAID records into other formats such as ENA/NCBI, you can try multiSub and also the GISAID-to-ENA script that ENA offers.

If you need more info, let me know.