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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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CanCOGeN template - LIMS export change to Specimen source field label #148

Closed griffie closed 3 years ago

griffie commented 3 years ago

Currently the CNPHI export from the CanCOGeN template outputs an extra field not in the template called "Specimen Type" where the sample is classified using hard coded logic as Human, Environmental or Animal. In the NML LIMS export, this field should be renamed as "PH_SPECIMEN_SOURCE" and the values tweaked to HUMAN, ENVIRO and ANIMAL.

ddooley commented 3 years ago

This is included in Cancogen nml lims v0.1 #155 pull request.