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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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MPX international template: adjust order of NCBI Biosample export field output #325

Closed griffie closed 2 years ago

griffie commented 2 years ago

Can we tweak the order of the field output in the NCBI Biosample export?

The preferred output order would be: sample_name bioproject_accession attribute_package GISAID_accession GISAID_virus_name collection_date collected_by sequenced_by sequence_submitted_by geo_loc_name organism isolate Isolation_source anatomical_material anatomical_part body_product environmental_material environmental_site collection_device collection_method lab_host passage_history passage_method host host_disease host_health_state host_disease_outcome host_age host_age_unit host_age_bin host_sex host_subject_id purpose_of_sampling purpose_of_sequencing gene_name_1 diagnostic_PCR_CT_value_1 gene_name_2 diagnostic_PCR_CT_value_2 description

attribute_package will need to be added to the output and filled by the user, it won't come from any information supplied in the MPX template.

ddooley commented 2 years ago

Done in latest Monkeypox_international commit. Should a similar reorder happen in CanCoGen?

Collection_date seems to be a new field? "sample collection date" is removed? host_age_unit added? host_age_bin added?

griffie commented 2 years ago

I think I reviewed the CanCOGeN Biosample export a few months ago and was ok. Let's leave it for now. :)