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Branch improve missing values#200

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Woolly-at-EBI wants to merge 8 commits intomasterfrom
branch_improve_missing_values
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Branch improve missing values#200
Woolly-at-EBI wants to merge 8 commits intomasterfrom
branch_improve_missing_values

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This is an improvement to make the missing value table clearer as requested by

https://ncbijira.ncbi.nlm.nih.gov/browse/INSDC-2063

It is not perfect, but it increases clarity significantly over the original. Can then be re-visited and iterated on from there.

@Woolly-at-EBI Woolly-at-EBI self-assigned this Nov 12, 2024
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I recommend some significant changes to the INSDC Missing Value Reporting Vocabulary:
(1) Flattening the table so that users can pick the exact reporting term without any ambiguity and without having to read the instructions to understand that they need to sometimes append the prefix "missing:"
(2) The "top level", "lower level" and "reporting level" nomenclature is not intuitive and could be replaced by three levels of granularity (low, medium, high). We would recommend using the highest possible level of granularity in order to better contextualise the data.
(3) The vocabulary should be used with mandatory, recommended or optional metadata fields, which simplifies its usage. In the case of batch submissions, any metadata field (mandatory, recommended or optional) may have values for some samples and missing values for other samples.
(4) The vocabulary should become an ontology so that a lookup service can be used to validate Missing Value Reporting terms on any field.
The proposed changes are shared here: https://docs.google.com/spreadsheets/d/13Az7f191RGfavYC1-8BCTOQy9uzZiY6Fy6Cy0R01Py8/edit?gid=2059784181#gid=2059784181
INSDC missing value vocabulary - INSDC missing value terms.pdf

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