From 133917dc57c99012e7ec9f887aa3109461db89e5 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Thu, 30 Nov 2023 16:20:19 +0300
Subject: Add a phenotype's chromosome location to the Phenotype fetch.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 gn3/api/metadata.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

(limited to 'gn3/api')

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index d67fcbd..86112f6 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -121,6 +121,9 @@ PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | {
     "sequence": "gnt:sequence",
     "prefLabel": "skos:prefLabel",
     "identifier": "dct:identifier",
+    "chromosome": "gnt:chr",
+    "mb": "gnt:mb",
+    "peakLocation": "gnt:locus",
     "species": "gnt:belongsToSpecies",
     "group": "gnt:belongsToGroup",
 }
@@ -430,11 +433,15 @@ CONSTRUCT {
         ?phenotype ?predicate ?object ;
                    gnt:belongsToSpecies ?speciesName ;
                    dcat:Distribution ?dataset ;
-                   gnt:belongsToGroup ?inbredSetName .
+                   gnt:belongsToGroup ?inbredSetName ;
+                   gnt:locus ?geno .
         ?dataset skos:prefLabel ?datasetName ;
                  dct:identifier ?datasetLabel ;
                  rdf:type dcat:Dataset .
         ?publication ?pubPredicate ?pubObject .
+        ?geno rdfs:label ?locus ;
+              gnt:chr ?chr ;
+              gnt:mb ?mb .
 } WHERE {
         ?phenotype skos:altLabel "$name" ;
                    xkos:classifiedUnder ?inbredSet ;
@@ -450,6 +457,13 @@ CONSTRUCT {
                      ?pubPredicate ?pubObject .
         FILTER (!regex(str(?pubPredicate), '(hasPubMedId|type)', 'i')) .
         } .
+        OPTIONAL {
+        ?geno ^gnt:locus ?phenotype ;
+              rdf:type gnc:Genotype ;
+              rdfs:label ?locus ;
+              gnt:chr ?chr ;
+              gnt:mb ?mb .
+        } .
 	OPTIONAL {
 	?dataset rdf:type dcat:Dataset ;
                  xkos:classifiedUnder  ?inbredSet ;
-- 
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