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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CanCOGeN template: refresh values, change order of fields in the LIMS export, refresh reference guide #220
I recently made some additional fields required, and tweaked the definition and guidance for "bioinformatics protocol".
Can we do a vocab refresh? And since I updated the ref guide, can we generate a new version for the Help section of the DH? I think we generate those on the fly from the DH template, correct?
And we received some additional LIMS terms for some fields so that they can be integrated into NML LIMS.
To prioritize those fields when NML curators are adding data to their DB, we have been clustering the LIMS fields (i.e. the capitalized output) together at the beginning of the output right before the DH provenance field.
Can we make sure PH_SEQUENCING_DATE outputs after
PH_REASON_FOR_SEQUENCING_DETAILS
And please move
PH_RAW_SEQUENCE_METHOD
PH_DEHOSTING_METHOD
to output right after PH_TESTING_PROTOCOL
and move PH_BIOINFORMATICS_PROTOCOL
after PH_CONSENSUS_SEQUENCE_VERSION?
Also HC_TEXT5 (which is new, and replaces VD_LAB_NUMBER which has been removed) should output after TEXT_ID.
PH_ID_NUMBER_PRIMARY (which is new) should output after HC_TEXT5.
ddooley
commented
3 years ago
I recently made some additional fields required, and tweaked the definition and guidance for "bioinformatics protocol". Can we do a vocab refresh? And since I updated the ref guide, can we generate a new version for the Help section of the DH? I think we generate those on the fly from the DH template, correct?
And we received some additional LIMS terms for some fields so that they can be integrated into NML LIMS. To prioritize those fields when NML curators are adding data to their DB, we have been clustering the LIMS fields (i.e. the capitalized output) together at the beginning of the output right before the DH provenance field.
Can we make sure PH_SEQUENCING_DATE outputs after PH_REASON_FOR_SEQUENCING_DETAILS
And please move PH_RAW_SEQUENCE_METHOD PH_DEHOSTING_METHOD to output right after PH_TESTING_PROTOCOL
and move PH_BIOINFORMATICS_PROTOCOL after PH_CONSENSUS_SEQUENCE_VERSION?
Also HC_TEXT5 (which is new, and replaces VD_LAB_NUMBER which has been removed) should output after TEXT_ID. PH_ID_NUMBER_PRIMARY (which is new) should output after HC_TEXT5.
Thanks!