Update faq.md Add Missing Data FAQ by DeondeJager · Pull Request #15 · MIxS-MInAS/MIxS-MInAS.github.io

DeondeJager · 2025-11-03T10:51:43Z

Added section: How to fill in missing data.
Populated the new section with information.
Fixed a small typo.

- Added section: How to fill in missing data. - Populated the new section with information. - Fixed a small typo.

jfy133 · 2025-11-17T09:16:08Z

+  - it can not be shared due to data agreement restrictions;
+  - it is not applicable to that particular field (e.g. it is a negative control and the field does not apply)
+- Missing data should only be reported for **mandatory** fields, not for **recommended** or **optional** fields. For the latter two, simply leave the field blank if the (meta)data are missing.
+- There are three levels at which you can report missing data, with an increasing amount of specificity for each: _**top level**_, _**lower level**_, and _**reporting level**_. Be as specific/granular as possible when reporting missing values. The _top level_ indicates that the data are missing, while the _lower-_ and _reporting_ levels give a reason (from the [controlled vocabulary](https://www.insdc.org/technical-specifications/missing-value-reporting/)) why the data are missing.


I would break up the three level descriptions into bullets

jfy133 · 2025-11-17T09:20:24Z

+- If using terms from the most granular level (_reporting level_), then exclude the _lower level_ term, as each _reporting level_ term is a "child" of the _lower level_, which can then be inferred based on the [table](https://www.insdc.org/technical-specifications/missing-value-reporting/).
+
+### Examples
+- missing


And let's provide context for each example:

How to encode missing info for a negative control (not applicable)

How to encode missing info because the infromation was not collected during a historical sampling event, or the collection records burnt down

How to encode missing information because native/indigenous groups do not permit sharing of this information

jfy133 · 2025-11-17T09:23:54Z

+  - it can not be shared for privacy reasons;
+  - it can not be shared due to data agreement restrictions;
+  - it is not applicable to that particular field (e.g. it is a negative control and the field does not apply)
+- Missing data should only be reported for **mandatory** fields, not for **recommended** or **optional** fields. For the latter two, simply leave the field blank if the (meta)data are missing.


I think the mandatory fields sentence should go at the beginning of this section in a preamble paragraph and say more along the lines of:

Fields in MIxS that are mandatory always require something filled into the given metadata entry. If you do not have this information, you must encode this using the specific 'missing information' categories as below.

While optional fields in MIxS can be left blank, if you have a specific reason the information will never be able to be reported (see examples below), then it is good to use these missing data categories there also.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

DeondeJager

Made several changes based on feedback from @jfy133.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: Deon de Jager <dejager4@gmail.com>

Move missing data explanation to top.

Delete here. Text moved to top of FAQ.

Add link to MIxS enum for missing values.

DeondeJager

Implemented various changes suggested by @jfy133.

Also made some edits to align with v7.0.0 of MIxS, such as referring to the MIxS missing values enum.

DeondeJager · 2026-08-03T09:14:39Z

@jfy133 Can we merge and close this branch?

If there are more changes to be made, I'd prefer for them to be done in a new issue & branch, as this one is getting a bit messy and difficult to follow (for me at least).

DeondeJager · 2026-08-03T10:11:39Z

Closes #19

Update faq.md Add Missing Data FAQ

dfb665d

- Added section: How to fill in missing data. - Populated the new section with information. - Fixed a small typo.

DeondeJager requested a review from jfy133 November 3, 2025 10:51

DeondeJager mentioned this pull request Nov 3, 2025

Extra guidance sections to add (FAQ) #9

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DeondeJager commented Feb 23, 2026

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Add context for "missing: not collected"

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DeondeJager requested a review from vicyklee August 10, 2026 08:52

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DeondeJager merged commit e33867d into master Aug 10, 2026

DeondeJager deleted the Update-FAQs-20251103 branch August 10, 2026 09:02

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