diff --git a/docs/changelog.md b/docs/changelog.md index 5a535f9c..8f2ed084 100644 --- 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 index 768f702a..9f4863e7 100644 --- 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.