From 584836b3e356857bb923eb4dc3e3041f05f28d4a Mon Sep 17 00:00:00 2001
From: Aly Khalifa <87331842+khalifa-aly@users.noreply.github.com>
Date: Tue, 28 Jul 2026 10:40:34 -0500
Subject: [PATCH 1/5] Add SpecimenAssessedReference extension

Added a new extension for referencing assessed specimens.
---
 input/fsh/CGExtensions.fsh | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/input/fsh/CGExtensions.fsh b/input/fsh/CGExtensions.fsh
index 1044ae0..b344225 100644
--- a/input/fsh/CGExtensions.fsh
+++ b/input/fsh/CGExtensions.fsh
@@ -66,3 +66,9 @@ Description: "Used to identify the sample ancestry group using terms obtained fr
 * ^context[+].type = #element
 * ^context[=].expression = "Observation.component"
 * value[x] only CodeableConcept
+
+Extension:   SpecimenAssessedReference
+Id:          specimen-assessed-reference
+Title:       "Specimen Assessed reference to a FHIR resource"
+Description: "Used to reference a specific specimen that was assessed and/or related to the FHIR resource."
+* value[x] only Reference(Specimen)

From 59432941597cc312af52da66eca3168adc708b2e Mon Sep 17 00:00:00 2001
From: Aly Khalifa <87331842+khalifa-aly@users.noreply.github.com>
Date: Tue, 28 Jul 2026 10:44:08 -0500
Subject: [PATCH 2/5] Add specimen reference to genomic data file profile

---
 input/fsh/CGGeneral.fsh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/input/fsh/CGGeneral.fsh b/input/fsh/CGGeneral.fsh
index 11842bc..b744d39 100644
--- a/input/fsh/CGGeneral.fsh
+++ b/input/fsh/CGGeneral.fsh
@@ -149,3 +149,4 @@ Title:          "Genomic Data File"
 Description:    "A profile of DocumentReference used to represent a genomics file."
 * context.related only Reference(GenomicReport)
 * description ^short = "Human-readable description to provide guidance on how the file was generated"
+* extension contains SpecimenAssessedReference named specimen 0..*

From af6cee708edbd77db6b76c90f97227abef9f5c15 Mon Sep 17 00:00:00 2001
From: Aly Khalifa <87331842+khalifa-aly@users.noreply.github.com>
Date: Fri, 21 Aug 2026 08:04:21 +0000
Subject: [PATCH 3/5] removing the specimen extension

---
 input/fsh/CGGeneral.fsh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/input/fsh/CGGeneral.fsh b/input/fsh/CGGeneral.fsh
index b744d39..7c040d2 100644
--- a/input/fsh/CGGeneral.fsh
+++ b/input/fsh/CGGeneral.fsh
@@ -149,4 +149,4 @@ Title:          "Genomic Data File"
 Description:    "A profile of DocumentReference used to represent a genomics file."
 * context.related only Reference(GenomicReport)
 * description ^short = "Human-readable description to provide guidance on how the file was generated"
-* extension contains SpecimenAssessedReference named specimen 0..*
+

From 01cc1737ef4cd69f08a7f016b73598f8adba0d53 Mon Sep 17 00:00:00 2001
From: Aly Khalifa <87331842+khalifa-aly@users.noreply.github.com>
Date: Fri, 21 Aug 2026 08:05:12 +0000
Subject: [PATCH 4/5] removing SpecimenAssessedReference extension

---
 input/fsh/CGExtensions.fsh | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/input/fsh/CGExtensions.fsh b/input/fsh/CGExtensions.fsh
index b344225..501ffef 100644
--- a/input/fsh/CGExtensions.fsh
+++ b/input/fsh/CGExtensions.fsh
@@ -67,8 +67,3 @@ Description: "Used to identify the sample ancestry group using terms obtained fr
 * ^context[=].expression = "Observation.component"
 * value[x] only CodeableConcept
 
-Extension:   SpecimenAssessedReference
-Id:          specimen-assessed-reference
-Title:       "Specimen Assessed reference to a FHIR resource"
-Description: "Used to reference a specific specimen that was assessed and/or related to the FHIR resource."
-* value[x] only Reference(Specimen)

From b3e938fc3ef5036a88dea62bee8889ef7fdfdd48 Mon Sep 17 00:00:00 2001
From: Aly Khalifa <87331842+khalifa-aly@users.noreply.github.com>
Date: Fri, 21 Aug 2026 10:20:02 +0000
Subject: [PATCH 5/5] adding Speciment to related context

---
 input/fsh/CGGeneral.fsh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/input/fsh/CGGeneral.fsh b/input/fsh/CGGeneral.fsh
index 7c040d2..011420d 100644
--- a/input/fsh/CGGeneral.fsh
+++ b/input/fsh/CGGeneral.fsh
@@ -147,6 +147,6 @@ Parent:         DocumentReference
 Id:             genomic-data-file
 Title:          "Genomic Data File"
 Description:    "A profile of DocumentReference used to represent a genomics file."
-* context.related only Reference(GenomicReport)
+* context.related only Reference(GenomicReport or Specimen)
 * description ^short = "Human-readable description to provide guidance on how the file was generated"