From 420f676b14335cbdb57d51ba7835ff9749122e4f Mon Sep 17 00:00:00 2001 From: Christian Busse Date: Tue, 14 Nov 2023 03:11:05 +0100 Subject: [PATCH] Add guidelines for geolocation information to the Metadata annotation section of tge Docs --- docs/miairr/metadata_guidelines.rst | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/docs/miairr/metadata_guidelines.rst b/docs/miairr/metadata_guidelines.rst index a8f1280de..a3139b511 100644 --- a/docs/miairr/metadata_guidelines.rst +++ b/docs/miairr/metadata_guidelines.rst @@ -232,3 +232,24 @@ experiments SHOULD be annotated as follows: reliably determined. * ``reverse_pcr_primer_target_location``: Locus and position according to the respective set of reverse primers. + + +Geolocation information +----------------------- + +For questions regarding population genetics, the information about the +membership of a given individual in a (potentially) distinct population +group is of high interest. However, no reasonably complete ontology +exists for the concept of "ethnicity", which in addition is limited +to humans (not to mention the challenge of assigning consistent values +to this property). Therefore, the AIRR Schema uses annotation of the +location of birth of an individual and the location where a given sample +was taken as imperfect but at least operationalizable substitute. + +The respective properties ``Subject``.``location_birth`` and +``Sample``.``collection_location`` are ontology controlled and expect +values that are geographic locations. The provided value SHOULD +allow to resolve at least the country-level information of the annotated +location. Higher granularity SHOULD only be provided, if this does not +exposed the data subject to the risk of being re-identified via based on +or assisted by this information.