Alignment files

Alignment files are elaborated by code system owners. They are simple CSV file, with commas as column separators.

They can be edited with a worksheet editor. In regions where Excel uses the semicolon as the CSV separator, OpenOffice can be used as an alternative.

Columns

The alignment file has 2 to 4 columns:

  • Column 1 is the code in the code system
  • Column 2 is its direct equivalent in NUVA
  • Optional column 3 is the textual description of the code in its code system
  • Optional column 4 is the textual description of the NUVA code

Only columns 1 and 2 are required when importing an alignment table into the editor.

If column 3 is present, it will be reused in the code system reverse map.

Column 4 is automatically filled by the editor when exporting an alignment table.

Headers

THe first row in the table contains titles. The title in the first column is used as the code system identifier.

Conventions

  • To avoid unwanted conversions by worksheet editors from strings to numbers, all codes in column 1 are prefixed with the code system identifier and a dash.
    For example, CVX-56 is used for the CVX 56 code, “Dengue fever, tetravalent”.
  • Code values that should no longer be used are prefixed with a #. This allows to interpret them if they are found into legacy records, but to exclude them from further transcriptions.
    For example, CVX-#15 is a former code for Influenza vaccines.
  • NUVA codes in column 2 are expected to be either:
    • a correctly formed vaccine code VACxxxx (VAC followed by 4 digits).
    • #NA if the concept in the original code system does not belong to the NUVA domain (e.g. CVX-98 is a tuberculin skin test, that is not a vaccine nor an antibody).
    • #MIS if the concept should belong to NUVA, but is missing for now.
  • When exported from the editor, the alignment file is named ident2nuva_YYYY-MM-DD.csv, where ident stands for the code system identifier found in the header and YYYY-MM-DD is the day of the export.

Example

This is an excerpt of the cvx2nuva.csv alignment file.

CVX,NUVA,CVX label, NUVA label
CVX-19,VAC0134,"Bacillus Calmette-Guerin vaccine","BCG vaccine, unspecified"
CVX-27,VAC0909,"botulinum antitoxin","Botulinum antitoxin"
CVX-95,#NA,"tuberculin skin test; old tuberculin, multipuncture device",
CVX-194,#MISS,"influenza, Southern Hemisphere, unspecified formulation",
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