CanCOGeN template: "HUMAN" case change in LIMS export

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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CanCOGeN template: "HUMAN" case change in LIMS export #229

Closed griffie closed 2 years ago

griffie commented 2 years ago

Currently the "Homo sapiens" value under Host (scientific name) exports in LIMS format as HUMAN (as a relic of the previous CNPHI requirements). "Homo sapiens" now needs to export as "Human" to be compatible with NML LIMS.

However, the NML LIMS export format didn't originally have any value in it in the DH template so I think 'HUMAN" must be as a result of some specific coding. Can you check and update as necessary, pretty please? I also added "Human" in NML export in the DH template.

Thanks!

ddooley commented 2 years ago

Currently a few values are capitalized ... should they all be title case?

griffie commented 2 years ago

Oh, I think those are relics from the past as well. I doubt we will get many more animal/enviro samples as all the prov stuff is Human. So let's leave the others as-is for the time being.

ddooley commented 2 years ago

Done in "vocabulary update" branch.