add new cohorts

_posts/2024-10-02-ag3-cohorts-v20240924.md

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+---
+layout: post
+title:  "Ag3 cohorts analysis version 20240924"
+tags: data
+---
+
+A new cohorts analysis version `20240924` has been released for the
+Ag3 data resource. This is now the default cohorts analysis version
+when using the `malariagen_data` [Ag3
+API](https://malariagen.github.io/malariagen-data-python/latest/Ag3.html). This
+cohorts analysis is available for datasets up to and including Ag3.11.
+
+Please note that the new cohorts analysis may change the values of
+sample metadata columns including `taxon`, `admin1_iso`,
+`admin1_name`, `admin2_name`, and derived columns beginning `cohorts_`
+relative to previous cohorts analysis versions.
+
+To pin this cohorts analysis when accessing data:
+
+{% highlight python %}
+import malariagen_data
+
+ag3 = malariagen_data.Ag3(
+    cohorts_analysis="20240924",
+)
+{% endhighlight %}
+
+This new version introduces some key changes: 
+
+- Samples that were previously assigned  as `gcx1`, have been renamed as `bissau`:
+    - `gcx` stands for `genetic cryptic species`, we use these labels as name placeholders for groups that fall outside our usual taxonomic assignment 
+    - In line with [Caputo et al. (2024)](https://malariagen.github.io/vobs-updates/2024/09/10/caputo.html), which characterises the `gcx1` group, we have updated its proposed name to `Bissau molecular form`
+    - 291 samples that were previously assigned to the `gcx1` group, are now relabeled as `bissau`.
+    - 5 samples samples that were previously `unassigned`, are now relabeled as `bissau`.
+    - these changes also affect cohort names, e.g. `GM-M_gcx1_2019` has now been relabeled to `GM-M_biss_2019`
+
+- 36 samples that were previously `unassigned`, have been renamed as (32) `melas`, (2)`gambiae`, (1) `fontenillei`, (1) `arabiensis`.
+
+- An error on the administrative region 1 metadata has been fixed, affecting 119 samples. Tor these:
+    -  `admin1_iso` has been relabeled from  `UG-E` to `KE-04` 
+    -  `admin1_name` has been relabeled from  `Eastern Region` to `Busia`
+    - these changes also affect cohort names, e.g. `UG-E_arab_2013` has now been relabeled to `KE-04_arab_2013`
+
+If you need to access the previous version of the cohorts analysis, you can use pin it using the code in [here](https://malariagen.github.io/vobs-updates/2024/07/24/ag3-cohorts-v20240717.html).