sex, again

progenetix · Jun 19, 2024 · 8848da4 · 8848da4
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diff --git a/docs/changelog.md b/docs/changelog.md
@@ -4,6 +4,28 @@ This page lists changes for the [Beacon+](http://beacon.progenetix.org/ui/)
 implementation of the ["Beacon" genomics API](http://beacon-project.io), as well
 as related updates for the [Progenetix](http://progenetix.org) front-end.
 
+## 2024-06-18 Switching ontology use for `individual.sex`
+
+While we had previously used the PATO terms for `genotypic sex` (PATO:0020001 
+or PATO:0020002) we have now recoded those to `"NCIT:C16576": "female" and "NCIT:C20197": "male"`
+to stay in line with the Beacon v2 documentation examples (which will probably drive implementations).
+
+```
+  sex:
+    label: Genotypic Sex
+    infoText: |
+      Genotypic sex of the individual.
+    defaultValue: ""
+    isHidden: true
+    options:
+      - value: ""
+        label: "(no selection)"
+      - value: NCIT:C16576
+        label: female
+      - value: NCIT:C20197
+        label: male
+```
+
 ## 2024-02-24 Adding `analysis_operation` to `analyses`
 
 This new parameter with its (so far) values

diff --git a/docs/common/beacon-api.md b/docs/common/beacon-api.md
@@ -163,8 +163,8 @@ The root path provides the standard `BeaconInfoResponse`.
 * [/individuals/?filters=NCIT:C7541]({{config.api_web_root}}/beacon/individuals/?filters=NCIT:C7541)
     - this example retrieves all individuals having an annotation associated with _NCIT:C7541_ (retinoblastoma)
     - in Progenetix, this particular code will be part of the annotation for the _biosample(s)_ associated with the returned individual
-* [/individuals/?filters=PATO:0020001,NCIT:C9291]({{config.api_web_root}}/beacon/individuals/?filters=PATO:0020001,NCIT:C9291)
-    - this query returns information about individuals with an anal carcinoma (**NCIT:C9291**) and a known male genotypic sex (**PATO:0020001**)
+* [/individuals/?filters=NCIT:C20197,NCIT:C9291]({{config.api_web_root}}/beacon/individuals/?filters=NCIT:C20197,NCIT:C9291)
+    - this query returns information about individuals with an anal carcinoma (**NCIT:C9291**) and a known male genotypic sex (**NCIT:C20197**)
     - in Progenetix, the information about its sex is associated with the _Individual_ object
       (stored in _individuals_), whereas the cancer type is a property of the _Biosample_.
       However, cross entity queries are supported through full aggregation across the different entities.