Update faqs 20250922 Geographic metadata FAQ & fix typos by DeondeJager · Pull Request #14 · MIxS-MInAS/MIxS-MInAS.github.io

DeondeJager · 2025-09-22T09:58:23Z

No description provided.

- Filled-in geographic metadata FAQ. - Fixed a couple of typos.

jfy133

Looks good as first pass! Mostly maybe consider removing a bit of the detail that is already in the term itself, and give examples with the aDNA specific implementation

Updated geography FAQ by removing some details and adding an example.

jfy133

Additional minor comments

jfy133 · 2026-01-12T10:13:50Z

 _TODO_

 ## How to fill in geographic metadata
+There are two primary ways of providing the geographic location of a sample with existing MIxS terms: `Geographic location (latitude and longitude)` and `Geographic location (country and/or sea,region)`. Both of these are required fields and we suggest filling in at both terms with as precise information as possible. There is also a third term that is specific to the ancient DNA MInAS checklist, `Name of site or location where sample was originated`, which should be used to record the name of the archaeological/palaeontological site.


Suggested change

There are two primary ways of providing the geographic location of a sample with existing MIxS terms: `Geographic location (latitude and longitude)` and `Geographic location (country and/or sea,region)`. Both of these are required fields and we suggest filling in at both terms with as precise information as possible. There is also a third term that is specific to the ancient DNA MInAS checklist, `Name of site or location where sample was originated`, which should be used to record the name of the archaeological/palaeontological site.

There are two primary ways of providing the geographic location of a sample with existing MIxS terms: `Geographic location (latitude and longitude)` and `Geographic location (country and/or sea,region)`.

Both of these are required fields and we suggest filling in at both terms with as precise information as possible.

There is also a third term that is specific to the ancient DNA MInAS checklist, `Name of site or location where sample was originated`, which should be used to record the name of the archaeological/palaeontological site.

jfy133 · 2026-01-12T10:15:27Z


-_TODO_
+-   **Geographic location (latitude and longitude)**:
+    -  The MIxS term [`Geographic location (latitude and longitude)`](https://genomicsstandardsconsortium.github.io/mixs/0000009/) is used to record the coordinates in decimal degrees, limited to 8 decimal points and separated by a single whitespace (e.g. `-39.27774231 175.61028236`). While limited to 8 decimal points, you will rarely need such precision, unless you've extracted DNA from a [specific grain of sand](https://xkcd.com/2170/). See [here](https://en.wikipedia.org/wiki/Decimal_degrees) to guide your decision on the appropriate level of precision to report.


The grain of sand thing should maybe go as a footnote using [^1] and [^1]: description syntax

Need to rewrite this FAQ once site location terms have been added (see MIxS-MInAS/extension-ancient#45 (comment))

As suggested by James [here](https://github.com/MIxS-MInAS/MIxS-MInAS.github.io/pull/14/changes#r2681621333)

jfy133

I'm still finding this section a bit confusing to follow...

The way I would structure it put it is something more like:

MIxS and MInAS has two ways of representing geographical information about a sample
These two ways cover where the sample normally is based at the time of sampling (e.g. museum), and where the original geographical 'source' the sample was from (the original burial site, or natural location)
For the former, use the MIxS terms XYZ... (with specific guidance for each term, e.g. lat_lon precision)
For the latter, use the MInAS terms orig_... (with specific guidance for each term, e.g. lat_lon precision)
If you directly sampled the ancient material at the burial location, the information will be the same

General thing: try to avoid bullet point lists when you have long text

And I guess now we have the new terms you can add more examples too :)

jfy133 · 2026-03-02T20:21:26Z

+These fields are used to record the museum location if the specimen originated from a museum, because this is where the sampling with intention to sequence occurred (see the ENA [FAQs](https://ena-docs.readthedocs.io/en/latest/faq/spatiotemporal-metadata.html#i-have-an-ancient-dna-sample-how-do-i-provide-the-spatiotemporal-information-for-my-sample-which-location-and-date-should-be-reported)). 
+If the specimen was excavated from an archaeological/palaeontlogical site with the intention to sequence (without first going via a museum) then the site information goes in the above terms.


I would flip this:

By default we assume samples were sampled directly from the environment/burial context

How IF the samples have been removed from their natural environment/burial context and are stored and/or were sampled from a collection or archive, the ENA guidance is that these geographic information terms should represent the collection or archive.

i.e., the collections is the exception not the rule

jfy133 · 2026-03-03T08:11:01Z

+    -    _insert site_lat_lon tarm_
+    -    `Name of site or location where sample was originated`, which should be used to record the name of the archaeological/palaeontological site.
+
+-   **Geographic location (latitude and longitude)**:


OK I'm confused by the order again 😅

DeondeJager · 2026-08-03T09:46:08Z

+-   **Geographic location (country and/or sea,region)**:
+    -   The MIxS term [`Geographic location (country and/or sea,region)`](https://genomicsstandardsconsortium.github.io/mixs/0000010/) is used to record this information in the format `Country:Region, Locality`.
+    -   Country or sea names should be chosen from the [INSDC country list](http://insdc.org/country.html), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ)
+    -   This term is not intended for the archaeological/palaeontological/ecological site name (if relevant). Instead, include the site name under the MInAS-specific term `Name of site or location where sample was originated`.


Suggested change

- This term is not intended for the archaeological/palaeontological/ecological site name (if relevant). Instead, include the site name under the MInAS-specific term `Name of site or location where sample was originated`.

- The term `Geographic location (country and/or sea,region)` is not intended for the archaeological/palaeontological/ecological site name (if relevant). Instead, include the site name under the MInAS-specific term `Name of site or location where sample was originated`.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Deon de Jager <dejager4@gmail.com>

DeondeJager · 2026-08-03T09:58:24Z

@jfy133 Can we merge and close this branch? Any additional edits/updates can be done in a new issue & branch.

DeondeJager · 2026-08-03T10:12:35Z

Closes #23

DeondeJager added 2 commits September 22, 2025 11:54

Update faq.md Geographic metadata & typos

6e0a9a6

- Filled-in geographic metadata FAQ. - Fixed a couple of typos.

Update faq.md Fix ticks around term names.

5229823

DeondeJager requested a review from jfy133 September 22, 2025 09:58

jfy133 reviewed Nov 17, 2025

View reviewed changes

Comment thread docs/documentation/user-documentation/faq.md

Comment thread docs/documentation/user-documentation/faq.md Outdated

Comment thread docs/documentation/user-documentation/faq.md

Update faq.md

9fa52ab

Updated geography FAQ by removing some details and adding an example.

DeondeJager requested a review from jfy133 January 12, 2026 10:11

jfy133 reviewed Jan 12, 2026

View reviewed changes

Update Geographic location faq.md

37bd8db

Need to rewrite this FAQ once site location terms have been added (see MIxS-MInAS/extension-ancient#45 (comment))

DeondeJager commented Feb 23, 2026

View reviewed changes

Comment thread docs/documentation/user-documentation/faq.md Outdated

Move grain of sand to footnote.

c963207

As suggested by James [here](https://github.com/MIxS-MInAS/MIxS-MInAS.github.io/pull/14/changes#r2681621333)

jfy133 reviewed Mar 3, 2026

View reviewed changes