From bdb2cebfd07a4ab16db19bb4292fe66c5abdda23 Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Tue, 7 Nov 2023 10:45:54 -0800
Subject: [PATCH 1/8] Updated Covid19 spec; fixed paste on date fields

---
 lib/DataHarmonizer.js                         | 33 +++++++++++++++----
 web/templates/canada_covid19/schema.json      |  8 ++++-
 web/templates/canada_covid19/schema.yaml      |  6 +++-
 web/templates/canada_covid19/schema_core.yaml |  2 +-
 web/templates/canada_covid19/schema_enums.tsv |  6 ++--
 web/templates/canada_covid19/schema_slots.tsv |  3 +-
 6 files changed, 44 insertions(+), 14 deletions(-)

diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
index 67a2b36f..d3252473 100644
--- a/lib/DataHarmonizer.js
+++ b/lib/DataHarmonizer.js
@@ -486,7 +486,11 @@ class DataHarmonizer {
         rowHeaders: true,
         copyPaste: true,
         manualColumnResize: true,
+
         //colWidths: [100], //Just fixes first column width
+        beforePaste: (data, coords) => {
+          //data is a 2d array of rows and columns
+        },
         afterCopy: function (changes) {
           self.clipboardCache = self.sheetclip.stringify(changes);
         },
@@ -504,17 +508,32 @@ class DataHarmonizer {
             key: 'paste',
             name: 'Paste',
             disabled: function () {
-              return self.clipboardCache.length === 0;
+              // The only easy way to get system cut+copy buffer contents into
+              // handsontable is to go query the system cut paste buffer every
+              // time the right-click menu is presented, and "Paste" option
+              // enabled.
+              setTimeout(async () => {
+                const text = await navigator.clipboard.readText();
+                if (text && text.length) {
+                  self.clipboardCache = text;
+                }
+              }); 
+
+              return false; // For now always on, even if cut/copy buffer is empty.
             },
             callback: function () {
               var plugin = this.getPlugin('copyPaste');
-
               this.listen();
-              // BUG: It seems like extra lf is added by sheetclip, causing
-              // empty last row to be added and pasted. Exception is pasting
-              // of single empty cell
-              if (self.clipboardCache.length > 0)
+              // An odd issue that with handsontable Paste menu item,
+              // targeted paste area gets extended a row on each subsequent
+              // Paste request.  This doesn't happen if one uses CTRL-V 
+              // instead (but that doesn't work on FlatpickrEditor fields). 
+              // See https://github.com/handsontable/handsontable/issues/1930
+              // Solution is to test for and clear out trailing newline.
+              if (self.clipboardCache && self.clipboardCache.length && self.clipboardCache.substr(-1,1) == "\n") {
                 self.clipboardCache = self.clipboardCache.slice(0, -1);
+              }
+
               plugin.paste(self.clipboardCache);
             },
           },
@@ -907,6 +926,8 @@ class DataHarmonizer {
     return;
   }
 
+
+
   /***************************** PRIVATE functions *************************/
 
   loadSpreadsheetData(data) {
diff --git a/web/templates/canada_covid19/schema.json b/web/templates/canada_covid19/schema.json
index a1a15d4a..6c5b7cd9 100644
--- a/web/templates/canada_covid19/schema.json
+++ b/web/templates/canada_covid19/schema.json
@@ -2,7 +2,7 @@
   "name": "CanCOGeN_Covid-19",
   "description": "",
   "id": "https://example.com/CanCOGeN_Covid-19",
-  "version": "2.1.3",
+  "version": "2.2.3",
   "prefixes": {
     "linkml": {
       "prefix_prefix": "linkml",
@@ -4128,6 +4128,9 @@
         "Newfoundland and Labrador - Eastern Health": {
           "text": "Newfoundland and Labrador - Eastern Health"
         },
+        "Newfoundland and Labrador - Newfoundland and Labrador Health Services": {
+          "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services"
+        },
         "Nova Scotia Health Authority": {
           "text": "Nova Scotia Health Authority"
         },
@@ -4220,6 +4223,9 @@
         "Newfoundland and Labrador - Eastern Health": {
           "text": "Newfoundland and Labrador - Eastern Health"
         },
+        "Newfoundland and Labrador - Newfoundland and Labrador Health Services": {
+          "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services"
+        },
         "Nova Scotia Health Authority": {
           "text": "Nova Scotia Health Authority"
         },
diff --git a/web/templates/canada_covid19/schema.yaml b/web/templates/canada_covid19/schema.yaml
index 59b4b556..88487fa1 100644
--- a/web/templates/canada_covid19/schema.yaml
+++ b/web/templates/canada_covid19/schema.yaml
@@ -1,7 +1,7 @@
 id: https://example.com/CanCOGeN_Covid-19
 name: CanCOGeN_Covid-19
 description: ''
-version: 2.1.3
+version: 2.2.3
 imports:
 - linkml:types
 prefixes:
@@ -5762,6 +5762,8 @@ enums:
         text: "New Brunswick - Vitalit\xE9 Health Network"
       Newfoundland and Labrador - Eastern Health:
         text: Newfoundland and Labrador - Eastern Health
+      Newfoundland and Labrador - Newfoundland and Labrador Health Services:
+        text: Newfoundland and Labrador - Newfoundland and Labrador Health Services
       Nova Scotia Health Authority:
         text: Nova Scotia Health Authority
       Ontario Institute for Cancer Research (OICR):
@@ -5823,6 +5825,8 @@ enums:
         text: "New Brunswick - Vitalit\xE9 Health Network"
       Newfoundland and Labrador - Eastern Health:
         text: Newfoundland and Labrador - Eastern Health
+      Newfoundland and Labrador - Newfoundland and Labrador Health Services:
+        text: Newfoundland and Labrador - Newfoundland and Labrador Health Services
       Nova Scotia Health Authority:
         text: Nova Scotia Health Authority
       Nunavut:
diff --git a/web/templates/canada_covid19/schema_core.yaml b/web/templates/canada_covid19/schema_core.yaml
index a48c372d..997f9180 100644
--- a/web/templates/canada_covid19/schema_core.yaml
+++ b/web/templates/canada_covid19/schema_core.yaml
@@ -1,7 +1,7 @@
 id: https://example.com/CanCOGeN_Covid-19
 name: CanCOGeN_Covid-19
 description: ""
-version: 2.1.3
+version: 2.2.3
 imports:
 - 'linkml:types'
 prefixes:
diff --git a/web/templates/canada_covid19/schema_enums.tsv b/web/templates/canada_covid19/schema_enums.tsv
index a191c2e4..9831e6de 100644
--- a/web/templates/canada_covid19/schema_enums.tsv
+++ b/web/templates/canada_covid19/schema_enums.tsv
@@ -887,6 +887,7 @@ sequence submitted by menu		Alberta Precision Labs (APL)
 		National Microbiology Laboratory (NML)										
 		New Brunswick - Vitalité Health Network										
 		Newfoundland and Labrador - Eastern Health										
+		Newfoundland and Labrador - Newfoundland and Labrador Health Services										
 		Nova Scotia Health Authority										
 		Ontario Institute for Cancer Research (OICR)										
 		Prince Edward Island - Health PEI										
@@ -917,6 +918,7 @@ sequence submitted by menu		Alberta Precision Labs (APL)
 		National Microbiology Laboratory (NML)										
 		New Brunswick - Vitalité Health Network										
 		Newfoundland and Labrador - Eastern Health										
+		Newfoundland and Labrador - Newfoundland and Labrador Health Services										
 		Nova Scotia Health Authority										
 		Nunavut										
 		Ontario Institute for Cancer Research (OICR)										
@@ -1202,6 +1204,4 @@ geo_loc_name (country) menu	GAZ:00006882	Afghanistan
 	GAZ:00000564	Western Sahara										
 	GAZ:00005284	Yemen										
 	GAZ:00001107	Zambia										
-	GAZ:00001106	Zimbabwe										
-												
-												
\ No newline at end of file
+	GAZ:00001106	Zimbabwe										
\ No newline at end of file
diff --git a/web/templates/canada_covid19/schema_slots.tsv b/web/templates/canada_covid19/schema_slots.tsv
index 5ebd5fa2..8bbc11e0 100644
--- a/web/templates/canada_covid19/schema_slots.tsv
+++ b/web/templates/canada_covid19/schema_slots.tsv
@@ -158,5 +158,4 @@ CanCOGeN Covid-19		GENEPIO:0001122	Database Identifiers
 																						
 		GENEPIO:0001516	Contributor acknowledgement																			
 	Contributor acknowledgement	GENEPIO:0001517	authors		WhitespaceMinimizedString					TRUE					Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.	Include the first and last names of all individuals that should be attributed, separated by a comma.	Tejinder Singh, Fei Hu, Joe Blogs	Authors	Authors	PH_CANCOGEN_AUTHORS		
-	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS		
-																						
\ No newline at end of file
+	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS		
\ No newline at end of file

From 7730d57515793fc3914844d067e628c391513f6f Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Tue, 7 Nov 2023 10:55:38 -0800
Subject: [PATCH 2/8] version bump

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 3be3de63..0137606a 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "data-harmonizer",
-  "version": "1.6.0",
+  "version": "1.6.1",
   "description": "A standardized spreadsheet editor and validator that can be run offline and locally",
   "repository": "git@github.com:cidgoh/DataHarmonizer.git",
   "license": "MIT",

From e5550a93e4640f31552db75252ff49c63aa2406d Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Tue, 7 Nov 2023 10:57:55 -0800
Subject: [PATCH 3/8] yarn format

---
 lib/DataHarmonizer.js | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
index 09bce95e..c5fae033 100644
--- a/lib/DataHarmonizer.js
+++ b/lib/DataHarmonizer.js
@@ -520,7 +520,7 @@ class DataHarmonizer {
                 if (text && text.length) {
                   self.clipboardCache = text;
                 }
-              }); 
+              });
 
               return false; // For now always on, even if cut/copy buffer is empty.
             },
@@ -529,11 +529,15 @@ class DataHarmonizer {
               this.listen();
               // An odd issue that with handsontable Paste menu item,
               // targeted paste area gets extended a row on each subsequent
-              // Paste request.  This doesn't happen if one uses CTRL-V 
-              // instead (but that doesn't work on FlatpickrEditor fields). 
+              // Paste request.  This doesn't happen if one uses CTRL-V
+              // instead (but that doesn't work on FlatpickrEditor fields).
               // See https://github.com/handsontable/handsontable/issues/1930
               // Solution is to test for and clear out trailing newline.
-              if (self.clipboardCache && self.clipboardCache.length && self.clipboardCache.substr(-1,1) == "\n") {
+              if (
+                self.clipboardCache &&
+                self.clipboardCache.length &&
+                self.clipboardCache.substr(-1, 1) == '\n'
+              ) {
                 self.clipboardCache = self.clipboardCache.slice(0, -1);
               }
 
@@ -929,8 +933,6 @@ class DataHarmonizer {
     return;
   }
 
-
-
   /***************************** PRIVATE functions *************************/
 
   loadSpreadsheetData(data) {

From a6c4fef60159687101d051fa7d63b3c5aebb4732 Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Tue, 7 Nov 2023 12:18:00 -0800
Subject: [PATCH 4/8] simplification of paste fix for date fields

No need for self.clipboardCache update, that seems to be done elsewhere.
---
 lib/DataHarmonizer.js | 43 +++++++++++++++++++++++++++----------------
 1 file changed, 27 insertions(+), 16 deletions(-)

diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
index c5fae033..e8cb2706 100644
--- a/lib/DataHarmonizer.js
+++ b/lib/DataHarmonizer.js
@@ -511,28 +511,38 @@ class DataHarmonizer {
             key: 'paste',
             name: 'Paste',
             disabled: function () {
-              // The only easy way to get system cut+copy buffer contents into
-              // handsontable is to go query the system cut paste buffer every
-              // time the right-click menu is presented, and "Paste" option
-              // enabled.
+              // For now always on, since we can't query whether something is
+              // in system cut/paste buffer without prompting user for ok.
+              return false; 
+            },
+            callback: function () {
+              var plugin = this.getPlugin('copyPaste');
+              this.listen();
+
+              // Due to asynchronous clipboard calls, this has to be in an 
+              // immediate setTimeout()
               setTimeout(async () => {
                 const text = await navigator.clipboard.readText();
                 if (text && text.length) {
-                  self.clipboardCache = text;
+
+                  // An odd issue that with handsontable Paste menu item,
+                  // targeted paste area gets extended a row on each 
+                  // subsequent Paste request.  This doesn't happen if one
+                  // uses CTRL-V instead (but that doesn't work on
+                  // FlatpickrEditor fields unless they are towards end
+                  // of multi-column paste). 
+                  // See https://github.com/handsontable/handsontable/issues/1930
+                  // Solution is to test for and clear out trailing newline.
+
+                  if (text.substr(-1, 1) == '\n')
+                    text = text.slice(0, -1);
+                  //self.clipboardCache = text;
+                  plugin.paste(text);  
                 }
+
               });
 
-              return false; // For now always on, even if cut/copy buffer is empty.
-            },
-            callback: function () {
-              var plugin = this.getPlugin('copyPaste');
-              this.listen();
-              // An odd issue that with handsontable Paste menu item,
-              // targeted paste area gets extended a row on each subsequent
-              // Paste request.  This doesn't happen if one uses CTRL-V
-              // instead (but that doesn't work on FlatpickrEditor fields).
-              // See https://github.com/handsontable/handsontable/issues/1930
-              // Solution is to test for and clear out trailing newline.
+              /*
               if (
                 self.clipboardCache &&
                 self.clipboardCache.length &&
@@ -542,6 +552,7 @@ class DataHarmonizer {
               }
 
               plugin.paste(self.clipboardCache);
+              */
             },
           },
           'remove_row',

From 75ad0ffada201ec5405e8b9d4c3012514fb4a7c2 Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Tue, 7 Nov 2023 15:59:14 -0800
Subject: [PATCH 5/8] doc tweak

---
 lib/DataHarmonizer.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
index e8cb2706..9f6f071d 100644
--- a/lib/DataHarmonizer.js
+++ b/lib/DataHarmonizer.js
@@ -529,8 +529,8 @@ class DataHarmonizer {
                   // targeted paste area gets extended a row on each 
                   // subsequent Paste request.  This doesn't happen if one
                   // uses CTRL-V instead (but that doesn't work on
-                  // FlatpickrEditor fields unless they are towards end
-                  // of multi-column paste). 
+                  // FlatpickrEditor fields unless they are later in
+                  // multi-column paste). 
                   // See https://github.com/handsontable/handsontable/issues/1930
                   // Solution is to test for and clear out trailing newline.
 

From 3df25f40bbf462555926e321f447825d096b5db1 Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Tue, 7 Nov 2023 21:36:29 -0800
Subject: [PATCH 6/8] GRDI template update

---
 web/templates/grdi/schema_core.yaml |   2 +-
 web/templates/grdi/schema_enums.tsv | 144 ++++++++++++++--------------
 web/templates/grdi/schema_slots.tsv |  15 +--
 3 files changed, 75 insertions(+), 86 deletions(-)

diff --git a/web/templates/grdi/schema_core.yaml b/web/templates/grdi/schema_core.yaml
index 16e9df79..7b9f70dd 100644
--- a/web/templates/grdi/schema_core.yaml
+++ b/web/templates/grdi/schema_core.yaml
@@ -1,7 +1,7 @@
 id: https://example.com/GRDI
 name: "GRDI"
 description: ""
-version: 7.7.6
+version: 8.8.4
 imports:
   - 'linkml:types'
 prefixes:
diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv
index 18e58872..d7c8affa 100644
--- a/web/templates/grdi/schema_enums.tsv
+++ b/web/templates/grdi/schema_enums.tsv
@@ -2,11 +2,12 @@ title	meaning	menu_1	menu_2	menu_3	menu_4	menu_5	description
 							
 sample_collected_by menu		Public Health Agency of Canada (PHAC) [GENEPIO:0100551]					
 		Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]					
-		Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100552]	GENEPIO:0100553				
+		Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]					
 		Health Canada (HC) [GENEPIO:0100554]					
 		Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]					
 		Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]					
-		University of Manitoba (UM)					
+		University of Manitoba (UM) [GENEPIO:0004434]					
+							
 							
 purpose_of_sampling menu		Cluster/Outbreak investigation [GENEPIO:0100001]					
 		Diagnostic testing [GENEPIO:0100002]					
@@ -18,14 +19,12 @@ purpose_of_sampling menu		Cluster/Outbreak investigation [GENEPIO:0100001]
 		Surveillance [GENEPIO:0100004]					
 							
 							
-							
-							
 presampling_activity menu		Addition of substances to food/water [GENEPIO:0100536]					
 		Antimicrobial pre-treatment [GENEPIO:0100537]					
 		Certified animal husbandry practices [GENEPIO:0100538]					
-			Certified humane animal husbandry practices				
+			Certified humane animal husbandry practices [GENEPIO:0100894]				
 		Certified organic farming practices [GENEPIO:0100539]					
-		Conventional farming practices					
+		Conventional farming practices [GENEPIO:0100895]					
 		Change in storage conditions [GENEPIO:0100540]					
 		Cleaning/disinfection [GENEPIO:0100541]					
 		Extended downtime between activities [GENEPIO:0100542]					
@@ -37,11 +36,12 @@ presampling_activity menu		Addition of substances to food/water [GENEPIO:0100536
 		Vaccination [NCIT:C15346]					
 							
 							
-specimen_processing menu		Biological replicate					
+specimen_processing menu		Biological replicate [OBI:0000198]					
 		Samples pooled [OBI:0600016]					
-		Technical replicate					
+		Technical replicate [OBI:0000249]					
 		Isolated from single source					
 							
+							
 geo_loc_name (country) menu		Afghanistan [GAZ:00006882]					
 		Albania [GAZ:00002953]					
 		Algeria [GAZ:00000563]					
@@ -315,21 +315,21 @@ geo_loc_name (country) menu		Afghanistan [GAZ:00006882]
 		Zimbabwe [GAZ:00001106]					
 							
 							
-geo_loc_name (state/province/region) menu		Atlantic region (Canada)					
+geo_loc_name (state/province/region) menu		Atlantic region (Canada) [wikidata:Q246972]					
 			     New Brunswick [GAZ:00002570]				
 			     Newfoundland & Labrador [GAZ:00002567]				
 			     Nova Scotia [GAZ:00002565]				
 			     Prince Edward Island [GAZ:00002572]				
-		Central region (Canada)					
+		Central region (Canada) [wikidata:Q1048064]					
 			     Ontario [GAZ:00002563]				
 			     Quebec [GAZ:00002569]				
-		Northern region (Canada)					
+		Northern region (Canada) [wikidata:Q764146]					
 			     Northwest Territories [GAZ:00002575]				
 			     Nunuvut [GAZ:00002574]				
 			     Yukon [GAZ:00002576]				
-		Pacific region (Canada)					
+		Pacific region (Canada) [wikidata:Q122953299]					
 			     British Columbia [GAZ:00002562]				
-		Prairie region (Canada)					
+		Prairie region (Canada) [wikidata:Q1364746]					
 			     Alberta [GAZ:00002566]				
 			     Manitoba [GAZ:00002571]				
 			     Saskatchewan [GAZ:00002564]				
@@ -357,7 +357,7 @@ environmental_site menu		Abattoir [ENVO:01000925]
 			Dairy [ENVO:00003862]				
 			Hospital [ENVO:00002173]				
 			Laboratory facility [ENVO:01001406]				
-			Pigsty				
+			Pigsty [ENVO:03501413]				
 		Building part (organizational term)					
 			Air intake [ENVO:03501380]				
 			Animal pen [ENVO:03501387]				
@@ -371,7 +371,7 @@ environmental_site menu		Abattoir [ENVO:01000925]
 		Farm [ENVO:00000078]					
 			Beef farm				
 			Breeder farm [ENVO:03501384]				
-			Dairy farm				
+			Dairy farm [ENVO:03501416]				
 			Feedlot [ENVO:01000627]				
 				Beef cattle feedlot			
 			Fish farm [ENVO:00000294]				
@@ -486,10 +486,10 @@ animal_or_plant_population menu		Algae [FOODON:03411301]
 			Mollusc [FOODON:03412112]				
 		Tropical fish [FOODON:00004283]					
 		Turkey [NCBITaxon:9103]					
-		Wildlife					
-			Wild bird				
-				Seabird			
-		Turkey					
+		Wildlife [FOODON:00004503]					
+			Wild bird [FOODON:00004505]				
+				Seabird [FOODON:00004504]			
+							
 							
 							
 environmental_material menu		Air [ENVO:00002005]					
@@ -500,21 +500,21 @@ environmental_material menu		Air [ENVO:00002005]
 			Feed pan [AGRO:00000676]				
 			Watering bowl [AGRO:00000677]				
 		Animal transportation equipment [AGRO:00000671]					
-			Dead haul trailer				
+			Dead haul trailer [GENEPIO:0100896]				
 			Dead haul truck [AGRO:00000673]				
-			Live haul trailer				
+			Live haul trailer [GENEPIO:0100897]				
 			Live haul truck [AGRO:00000674]				
 		Belt [NCIT:C49844]					
 		Biosolids [ENVO:00002059]					
 		Boot [GSSO:012935]					
 			Boot cover [OBI:0002806]				
 		Broom [ENVO:03501377]					
-		Bulk tank					
+		Bulk tank [ENVO:03501379]					
 		Chick box [AGRO:00000678]					
 		Chick pad [AGRO:00000672]					
 		Cleaning equipment [ENVO:03501376]					
 		Compost [ENVO:00002170]					
-		Contaminated water (organizational term) [ENVO:00002186]					
+		Contaminated water [ENVO:00002186]					
 			Fecal slurry				
 			Fluid from meat rinse [GENEPIO:0004323]				
 			Effluent [ENVO:03501407]				
@@ -534,7 +534,7 @@ environmental_material menu		Air [ENVO:00002005]
 			Animal manure [AGRO:00000079]				
 				Pig manure [AGRO:00000080]			
 		Manure digester equipment [ENVO:03501424]					
-		Nest					
+		Nest [ENVO:03501432]					
 			Bird's nest [ENVO:00005805]				
 		Permafrost [ENVO:00000134]					
 		Plucking belt [AGRO:00000669]					
@@ -561,10 +561,10 @@ anatomical_material menu		Blood [UBERON:0000178]
 		Tissue [UBERON:0000479]					
 							
 							
-body_product menu		Digestive organ content					
-			Caecal content				
-			Intestinal content				
-			Stomach content				
+body_product menu		Digestive organ content [GENEPIO:0100898]					
+			Caecal content [GENEPIO:0100899]				
+			Intestinal content [GENEPIO:0100900]				
+			Stomach content [GENEPIO:0100901]				
 		Feces [UBERON:0001988]					
 			Fecal composite				
 			Feces (fresh)				
@@ -658,13 +658,13 @@ anatomical_part menu		Carcass [UBERON:0008979]
 			Lung [UBERON:0002048]				
 			Pericardium [UBERON:0002407]				
 		Vent (anatomical) [UBERON:2000298]					
-			Bird vent				
-			Fish vent				
+			Bird vent [UBERON:0012464]				
+			Fish vent [GENEPIO:0100902]				
 							
 							
 anatomical_region menu		Dorso-lateral region [BSPO:0000080]					
-		Exterior anatomical region					
-		Interior anatomical region					
+		Exterior anatomical region [BSPO:0000034]					
+		Interior anatomical region [BSPO:0000033]					
 							
 							
 food_product menu		Animal feed [ENVO:02000047]					
@@ -672,8 +672,8 @@ food_product menu		Animal feed [ENVO:02000047]
 			Bone meal [ENVO:02000054]				
 			Brassica carinata meal [FOODON:00004310]				
 			Canola meal [FOODON:00002694]				
-			Compound feed premix				
-				Compound feed premix (medicated)			
+			Compound feed premix [FOODON:00004323]				
+				Compound feed premix (medicated) [FOODON:00004324]			
 			Feather meal [FOODON:00003927]				
 			Fish meal [FOODON:03301620]				
 			Lay ration [FOODON:00004286]				
@@ -681,7 +681,7 @@ food_product menu		Animal feed [ENVO:02000047]
 			Meat meal [FOODON:00004282]				
 			Pet food [FOODON:00002682]				
 			Soybean meal [FOODON:03302757]				
-		Animal feed ingredient					
+		Animal feed ingredient [FOODON:00004322]					
 		Dairy food product [FOODON:00001256]					
 			Cheese block (whole or parts) [FOODON:03000287]				
 			Cow skim milk (powdered) [FOODON:03310016]				
@@ -748,17 +748,18 @@ food_product menu		Animal feed [ENVO:02000047]
 			Chicken nugget [FOODON:00002672]				
 			Chicken thigh				
 				Chicken thigh (skinless) [FOODON:00003331]			
+				Chicken thigh (skinless, with bone)			
 				Chicken thigh (skinless, boneless) [FOODON:03000417]			
+					Chicken upper thigh [FOODON:03000381]		
+						Chicken upper thigh (with skin) [FOODON:03000383]	
 				Chicken thigh (with skin) [FOODON:00003330]			
 				Chicken thigh (with skin, with bone) [FOODON_00003363]			
-			Chicken upper thigh [FOODON:03000381]				
-				Chicken upper thigh (with skin) [FOODON:03000383]			
 			Chicken wing [FOODON:00002674]				
 			Fish food product [FOODON:00001248]				
 				Fish steak [FOODON:00002986]			
 			Ham food product [FOODON:00002502]				
 			Head cheese [FOODON:03315658]				
-			Lamb				
+			Lamb [FOODON:03411669]				
 			Meat strip [FOODON:00004285]				
 			Mutton [FOODON:00002912]				
 			Pork chop [FOODON:00001049]				
@@ -832,14 +833,14 @@ food_product menu		Animal feed [ENVO:02000047]
 			Apple (whole or parts) [FOODON:03310788]				
 				Apple (whole) [FOODON:00002473]			
 			Arugula greens (raw) [FOODON:00002426]				
-			Avocado				
+			Avocado [FOODON:00003600]				
 			Cantaloupe (whole or parts) [FOODON:03000243]				
 			Chili pepper [FOODON:03315873]				
 			Coconut (whole or parts) [FOODON:03309861]				
 			Corn cob (whole or parts) [FOODON:03310791]				
 			Cucumber (whole or parts) [FOODON:03000229]				
 			Fruit [PO:0009001]				
-			Goji berry				
+			Goji berry [FOODON:00004360]				
 			Greens (raw) [FOODON:03310765]				
 			Kale leaf (whole or parts) [FOODON:03000236]				
 			Lettuce head (whole or parts) [FOODON:03000239]				
@@ -849,7 +850,7 @@ food_product menu		Animal feed [ENVO:02000047]
 			Pattypan squash (whole or parts) [FOODON:03000232]				
 			Peach [FOODON:00002485]				
 			Pepper (whole or parts) [FOODON:03000249]				
-			Potato				
+			Potato [FOODON:03315354]				
 			Salad [FOODON:03316042]				
 			Scallion (whole or parts) [FOODON:03000250]				
 			Spinach (whole or parts) [FOODON:03000221]				
@@ -891,7 +892,7 @@ food_product menu		Animal feed [ENVO:02000047]
 							
 							
 food_product_properties menu		Food (canned) [FOODON:00002418]					
-		Food (cooked)					
+		Food (cooked) [FOODON:00001181]					
 		Food (cut) [FOODON:00004291]					
 			Food (chopped) [FOODON:00002777]				
 			Food (cubed) [FOODON:00004278]				
@@ -903,8 +904,8 @@ food_product_properties menu		Food (canned) [FOODON:00002418]
 		Italian-style food product [FOODON:00004321]					
 		Meat (boneless) [FOODON:00003467]					
 		Meat (skinless) [FOODON:00003468]					
-		Meat (with bone)					
-		Meat (with skin)					
+		Meat (with bone) [FOODON:02010116]					
+		Meat (with skin) [FOODON:02010111]					
 		Organic food claim or use [FOODON:03510128]					
 		Ready-to-eat (RTE) [FOODON:03316636]					
 		Soft [PATO:0000387]					
@@ -919,16 +920,14 @@ animal_source_of_food menu		Cow [NCBITaxon:9913]
 		Sheep [NCBITaxon:9940]					
 							
 							
-production_stream menu		Food animal production stream					
-			Beef cattle production stream				
-			Broiler chicken production stream				
-			Dairy cattle production stream				
-			Layer chicken production stream				
-		Food product production stream					
-			Egg production stream				
-			Meat production stream				
-				Veal production stream			
-			Milk production stream				
+food_product_production_stream menu		Beef cattle production stream [FOODON:03000452]					
+		Broiler chicken production stream [FOODON:03000455]					
+		Dairy cattle production stream [FOODON:03000453]					
+		Egg production stream [FOODON:03000458]					
+		Layer chicken production stream [FOODON:03000456]					
+		Meat production stream [FOODON:03000460]					
+			Veal meat production stream [FOODON:03000461]				
+		Milk production stream [FOODON:03000459]					
 							
 							
 collection_device menu		Auger (earth auger) [AGRO:00000405]					
@@ -942,9 +941,9 @@ collection_device menu		Auger (earth auger) [AGRO:00000405]
 			Petri dish [NCIT:C96141]				
 		Filter [GENEPIO:0100103]					
 		PONAR grab sampler					
-		Scoop					
+		Scoop [GENEPIO:0002125]					
 		Soil sample probe					
-		Spatula					
+		Spatula [NCIT:C149941]					
 		Sponge [OBI:0002819]					
 			Swab [GENEPIO:0100027]				
 				Drag swab [OBI:0002822]			
@@ -973,7 +972,7 @@ collection_method menu		Aspiration [HP:0002835]
 							
 food_packaging menu		Bag, sack or pouch [FOODON:03490197]					
 			Paper bag, sack or pouch [FOODON:03490120]				
-			Plastic bag, sack or pouch				
+			Plastic bag, sack or pouch [FOODON:03490166]				
 				Plastic shrink wrap [FOODON:03490137]			
 				Plastic wrapper [FOODON:03490128]			
 		Bottle or jar [FOODON:03490203]					
@@ -983,9 +982,9 @@ food_packaging menu		Bag, sack or pouch [FOODON:03490197]
 		Plastic tray or pan [FOODON:03490126]					
 							
 							
-host (common name) menu		Bird					
+host (common name) menu		Bird [NCBITaxon:8782]					
 			Chicken [NCBITaxon:9031]				
-			Seabird				
+			Seabird [FOODON:00004504]				
 				Cormorant [NCBITaxon:9206]			
 					Double Crested Cormorant [NCBITaxon:56069]		
 				Crane [NCBITaxon:9109]			
@@ -1025,7 +1024,6 @@ host (scientific name) menu		Bos taurus [NCBITaxon:9913]
 		Larus delawarensis [NCBITaxon:126683]					
 		Larus glaucescens [NCBITaxon:119606]					
 		Larus marinus [NCBITaxon:8912]					
-		Larus sp.					
 		Meleagris gallopavo [NCBITaxon:9103]					
 		Mytilus edulis [NCBITaxon:6550]					
 		Oncorhynchus mykiss [NCBITaxon:8022]					
@@ -1202,6 +1200,12 @@ organism menu		Acinetobacter [NCBITaxon:469]
 			Vibrio cholerae [NCBITaxon:666]				
 							
 							
+taxonomic_identification_process menu		Whole genome sequencing assay [OBI:0002117]					
+		16S ribosomal gene sequencing assay [OBI:0002763]					
+		PCR assay [OBI:0002740]					
+		Comparative phenotypic assessment [OBI:0001546]					
+							
+							
 sequenced_by menu		Public Health Agency of Canada (PHAC) [GENEPIO:0100551]					
 		Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]					
 		Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]					
@@ -1210,11 +1214,6 @@ sequenced_by menu		Public Health Agency of Canada (PHAC) [GENEPIO:0100551]
 		Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]					
 							
 							
-taxonomic_identification_process menu		Whole genome sequencing assay [OBI:0002117]					
-		16S ribosomal gene sequencing assay [OBI:0002763]					
-		PCR assay [OBI:0002740]					
-		Comparative phenotypic assessment [OBI:0001546]					
-							
 purpose_of_sequencing menu		Cluster/Outbreak investigation [GENEPIO:0100001]					
 		Diagnostic testing [GENEPIO:0100001]	GENEPIO:0100002				
 		Environmental testing [GENEPIO:0100548]					
@@ -1323,12 +1322,12 @@ antimicrobial_phenotype menu		Antibiotic resistance not defined [GENEPIO:0002040
 		Susceptible dose dependent antimicrobial phenotype [ARO:3004304]					
 							
 							
-antimicrobial_measurement_units menu		mg/L [UO:0000273]					
-		mm [UO:0000016]					
-		ug/mL [UO:0000274]					
+antimicrobial_measurement_units menu		milligram per litre (mg/L) [UO:0000273]					
+		millimetre (mm) [UO:0000016]					
+		microgram per millilitre (ug/mL) [UO:0000274]					
 							
 							
-antimicrobial_measurement_sign menu		less than  (<) [GENEPIO:0001002]					
+antimicrobial_measurement_sign menu		less than (<) [GENEPIO:0001002]					
 		less than or equal to (<=) [GENEPIO:0001003]					
 		equal to (==) [GENEPIO:0001004]					
 		greater than (>) [GENEPIO:0001006]					
@@ -1336,7 +1335,7 @@ antimicrobial_measurement_sign menu		less than  (<) [GENEPIO:0001002]
 							
 							
 antimicrobial_laboratory_typing_method menu		Agar diffusion [NCIT:85595]					
-		Antimicrobial gradient (E-test) [NCIT:85596]					
+			Antimicrobial gradient (E-test) [NCIT:85596]				
 		Agar dilution [ARO:3004411]					
 		Broth dilution [ARO:3004397]					
 							
@@ -1347,6 +1346,7 @@ antimicrobial_laboratory_typing_platform menu		BIOMIC Microbiology System
 		Sensititre [ARO:3004402]					
 		Vitek System [ARO:3004403]					
 							
+							
 antimicrobial_vendor_name		Becton Dickinson [ARO:3004405]					
 		bioMérieux [ARO:3004406]					
 		Omron [ARO:3004408]					
@@ -1361,8 +1361,8 @@ antimicrobial_testing_standard menu		British Society for Antimicrobial Chemother
 		National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]					
 		National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]					
 		Société Française de Microbiologie (SFM) [ARO:3004369]					
-							
-							
+		Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]					
+		Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]					
 							
 							
 							
\ No newline at end of file
diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv
index fbc3c6f4..06ed026c 100644
--- a/web/templates/grdi/schema_slots.tsv
+++ b/web/templates/grdi/schema_slots.tsv
@@ -47,7 +47,7 @@ Multiple identifiers can be provided and separated by semi-colons. If the inform
 	Sample collection and processing	GENEPIO:0100444	food_product		food_product menu	null value menu		TRUE		TRUE					A material consumed and digested for nutritional value or enjoyment.	This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon.	Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703]	isolation_source;food_product
 	Sample collection and processing	GENEPIO:0100445	food_product_properties		food_product_properties menu	null value menu		TRUE		TRUE					Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.	Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free).	Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636]	isolation_source;food_product_properties
 	Sample collection and processing	GENEPIO:0100446	animal_source_of_food		animal_source_of_food menu	null value menu		TRUE		TRUE					The animal from which the food product was derived.	Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma.	Chicken [NCBITaxon:9031]	
-	Sample collection and processing	GENEPIO:0100699	production_stream		production_stream menu	null value menu									A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a particular commodity.	Provide the name of the agricultural production stream from the picklist.		
+	Sample collection and processing	GENEPIO:0100699	food_product_production_stream		food_product_production_stream menu	null value menu									A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity.	Provide the name of the agricultural production stream from the picklist.	Beef cattle production stream [FOODON:03000452]	
 	Sample collection and processing	GENEPIO:0100447	sample_storage_method		WhitespaceMinimizedString										The type of packaging used to contain a food product.	If known, provide information regarding how the food product was packaged.	Plastic tray or pan [FOODON:03490126]	
 	Sample collection and processing	GENEPIO:0100448	sample_storage_medium		WhitespaceMinimizedString										A specification of the way that a specimen is or was stored.	Provide a description of how the same was stored.	Frozen at -20C	
 	Sample collection and processing	GENEPIO:0001234	collection_device		collection_device menu	null value menu				TRUE					The instrument or container used to collect the sample e.g. swab.	This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon.	PBS + 20% glycerol	isolation_source;collection_device
@@ -733,15 +733,4 @@ Multiple alternative isolate IDs can be provided, separated by semi-colons."	GHI
 	Antimicrobial resistance		trimethoprim-sulfamethoxazole_resistant_breakpoint		WhitespaceMinimizedString										The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.	This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied.	32	
 		GENEPIO:0001516	Contributor acknowledgement															
 	Contributor acknowledgement	GENEPIO:0001517	authors		WhitespaceMinimizedString					TRUE					Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.	Include the first and last names of all individuals that should be attributed, separated by a comma.	Tejinder Singh, Fei Hu, Joe Blogs	
-	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, GRDI v1.0.0	
-																		
-																		
-																		
-																		
-																		
-																		
-																		
-																		
-																		
-																		
-																		
\ No newline at end of file
+	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, GRDI v1.0.0	
\ No newline at end of file

From 1008caddf288f60981c888362600d5ff6249a5fe Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Wed, 8 Nov 2023 08:13:42 -0800
Subject: [PATCH 7/8] grdi tweaks

---
 web/templates/grdi/schema.json | 419 ++++++++++++++++-----------------
 web/templates/grdi/schema.yaml | 379 +++++++++++++++--------------
 2 files changed, 395 insertions(+), 403 deletions(-)

diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json
index dd6bb8ca..44845652 100644
--- a/web/templates/grdi/schema.json
+++ b/web/templates/grdi/schema.json
@@ -2,7 +2,7 @@
   "name": "GRDI",
   "description": "",
   "id": "https://example.com/GRDI",
-  "version": "7.7.6",
+  "version": "8.8.4",
   "prefixes": {
     "linkml": {
       "prefix_prefix": "linkml",
@@ -226,8 +226,8 @@
         "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]": {
           "text": "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]"
         },
-        "Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100552]": {
-          "text": "Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100552]"
+        "Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]": {
+          "text": "Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]"
         },
         "Health Canada (HC) [GENEPIO:0100554]": {
           "text": "Health Canada (HC) [GENEPIO:0100554]"
@@ -238,8 +238,8 @@
         "Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]": {
           "text": "Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]"
         },
-        "University of Manitoba (UM)": {
-          "text": "University of Manitoba (UM)"
+        "University of Manitoba (UM) [GENEPIO:0004434]": {
+          "text": "University of Manitoba (UM) [GENEPIO:0004434]"
         }
       }
     },
@@ -289,15 +289,15 @@
         "Certified animal husbandry practices [GENEPIO:0100538]": {
           "text": "Certified animal husbandry practices [GENEPIO:0100538]"
         },
-        "Certified humane animal husbandry practices": {
-          "text": "Certified humane animal husbandry practices",
+        "Certified humane animal husbandry practices [GENEPIO:0100894]": {
+          "text": "Certified humane animal husbandry practices [GENEPIO:0100894]",
           "is_a": "Certified animal husbandry practices [GENEPIO:0100538]"
         },
         "Certified organic farming practices [GENEPIO:0100539]": {
           "text": "Certified organic farming practices [GENEPIO:0100539]"
         },
-        "Conventional farming practices": {
-          "text": "Conventional farming practices"
+        "Conventional farming practices [GENEPIO:0100895]": {
+          "text": "Conventional farming practices [GENEPIO:0100895]"
         },
         "Change in storage conditions [GENEPIO:0100540]": {
           "text": "Change in storage conditions [GENEPIO:0100540]"
@@ -332,14 +332,14 @@
       "name": "specimen_processing menu",
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
-        "Biological replicate": {
-          "text": "Biological replicate"
+        "Biological replicate [OBI:0000198]": {
+          "text": "Biological replicate [OBI:0000198]"
         },
         "Samples pooled [OBI:0600016]": {
           "text": "Samples pooled [OBI:0600016]"
         },
-        "Technical replicate": {
-          "text": "Technical replicate"
+        "Technical replicate [OBI:0000249]": {
+          "text": "Technical replicate [OBI:0000249]"
         },
         "Isolated from single source": {
           "text": "Isolated from single source"
@@ -1169,72 +1169,72 @@
       "name": "geo_loc_name (state/province/region) menu",
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
-        "Atlantic region (Canada)": {
-          "text": "Atlantic region (Canada)"
+        "Atlantic region (Canada) [wikidata:Q246972]": {
+          "text": "Atlantic region (Canada) [wikidata:Q246972]"
         },
         "New Brunswick [GAZ:00002570]": {
           "text": "New Brunswick [GAZ:00002570]",
-          "is_a": "Atlantic region (Canada)"
+          "is_a": "Atlantic region (Canada) [wikidata:Q246972]"
         },
         "Newfoundland & Labrador [GAZ:00002567]": {
           "text": "Newfoundland & Labrador [GAZ:00002567]",
-          "is_a": "Atlantic region (Canada)"
+          "is_a": "Atlantic region (Canada) [wikidata:Q246972]"
         },
         "Nova Scotia [GAZ:00002565]": {
           "text": "Nova Scotia [GAZ:00002565]",
-          "is_a": "Atlantic region (Canada)"
+          "is_a": "Atlantic region (Canada) [wikidata:Q246972]"
         },
         "Prince Edward Island [GAZ:00002572]": {
           "text": "Prince Edward Island [GAZ:00002572]",
-          "is_a": "Atlantic region (Canada)"
+          "is_a": "Atlantic region (Canada) [wikidata:Q246972]"
         },
-        "Central region (Canada)": {
-          "text": "Central region (Canada)"
+        "Central region (Canada) [wikidata:Q1048064]": {
+          "text": "Central region (Canada) [wikidata:Q1048064]"
         },
         "Ontario [GAZ:00002563]": {
           "text": "Ontario [GAZ:00002563]",
-          "is_a": "Central region (Canada)"
+          "is_a": "Central region (Canada) [wikidata:Q1048064]"
         },
         "Quebec [GAZ:00002569]": {
           "text": "Quebec [GAZ:00002569]",
-          "is_a": "Central region (Canada)"
+          "is_a": "Central region (Canada) [wikidata:Q1048064]"
         },
-        "Northern region (Canada)": {
-          "text": "Northern region (Canada)"
+        "Northern region (Canada) [wikidata:Q764146]": {
+          "text": "Northern region (Canada) [wikidata:Q764146]"
         },
         "Northwest Territories [GAZ:00002575]": {
           "text": "Northwest Territories [GAZ:00002575]",
-          "is_a": "Northern region (Canada)"
+          "is_a": "Northern region (Canada) [wikidata:Q764146]"
         },
         "Nunuvut [GAZ:00002574]": {
           "text": "Nunuvut [GAZ:00002574]",
-          "is_a": "Northern region (Canada)"
+          "is_a": "Northern region (Canada) [wikidata:Q764146]"
         },
         "Yukon [GAZ:00002576]": {
           "text": "Yukon [GAZ:00002576]",
-          "is_a": "Northern region (Canada)"
+          "is_a": "Northern region (Canada) [wikidata:Q764146]"
         },
-        "Pacific region (Canada)": {
-          "text": "Pacific region (Canada)"
+        "Pacific region (Canada) [wikidata:Q122953299]": {
+          "text": "Pacific region (Canada) [wikidata:Q122953299]"
         },
         "British Columbia [GAZ:00002562]": {
           "text": "British Columbia [GAZ:00002562]",
-          "is_a": "Pacific region (Canada)"
+          "is_a": "Pacific region (Canada) [wikidata:Q122953299]"
         },
-        "Prairie region (Canada)": {
-          "text": "Prairie region (Canada)"
+        "Prairie region (Canada) [wikidata:Q1364746]": {
+          "text": "Prairie region (Canada) [wikidata:Q1364746]"
         },
         "Alberta [GAZ:00002566]": {
           "text": "Alberta [GAZ:00002566]",
-          "is_a": "Prairie region (Canada)"
+          "is_a": "Prairie region (Canada) [wikidata:Q1364746]"
         },
         "Manitoba [GAZ:00002571]": {
           "text": "Manitoba [GAZ:00002571]",
-          "is_a": "Prairie region (Canada)"
+          "is_a": "Prairie region (Canada) [wikidata:Q1364746]"
         },
         "Saskatchewan [GAZ:00002564]": {
           "text": "Saskatchewan [GAZ:00002564]",
-          "is_a": "Prairie region (Canada)"
+          "is_a": "Prairie region (Canada) [wikidata:Q1364746]"
         }
       }
     },
@@ -1317,8 +1317,8 @@
           "text": "Laboratory facility [ENVO:01001406]",
           "is_a": "Building [ENVO:00000073]"
         },
-        "Pigsty": {
-          "text": "Pigsty",
+        "Pigsty [ENVO:03501413]": {
+          "text": "Pigsty [ENVO:03501413]",
           "is_a": "Building [ENVO:00000073]"
         },
         "Building part (organizational term)": {
@@ -1370,8 +1370,8 @@
           "text": "Breeder farm [ENVO:03501384]",
           "is_a": "Farm [ENVO:00000078]"
         },
-        "Dairy farm": {
-          "text": "Dairy farm",
+        "Dairy farm [ENVO:03501416]": {
+          "text": "Dairy farm [ENVO:03501416]",
           "is_a": "Farm [ENVO:00000078]"
         },
         "Feedlot [ENVO:01000627]": {
@@ -1776,19 +1776,16 @@
         "Turkey [NCBITaxon:9103]": {
           "text": "Turkey [NCBITaxon:9103]"
         },
-        "Wildlife": {
-          "text": "Wildlife"
-        },
-        "Wild bird": {
-          "text": "Wild bird",
-          "is_a": "Wildlife"
+        "Wildlife [FOODON:00004503]": {
+          "text": "Wildlife [FOODON:00004503]"
         },
-        "Seabird": {
-          "text": "Seabird",
-          "is_a": "Wild bird"
+        "Wild bird [FOODON:00004505]": {
+          "text": "Wild bird [FOODON:00004505]",
+          "is_a": "Wildlife [FOODON:00004503]"
         },
-        "Turkey": {
-          "text": "Turkey"
+        "Seabird [FOODON:00004504]": {
+          "text": "Seabird [FOODON:00004504]",
+          "is_a": "Wild bird [FOODON:00004505]"
         }
       }
     },
@@ -1824,16 +1821,16 @@
         "Animal transportation equipment [AGRO:00000671]": {
           "text": "Animal transportation equipment [AGRO:00000671]"
         },
-        "Dead haul trailer": {
-          "text": "Dead haul trailer",
+        "Dead haul trailer [GENEPIO:0100896]": {
+          "text": "Dead haul trailer [GENEPIO:0100896]",
           "is_a": "Animal transportation equipment [AGRO:00000671]"
         },
         "Dead haul truck [AGRO:00000673]": {
           "text": "Dead haul truck [AGRO:00000673]",
           "is_a": "Animal transportation equipment [AGRO:00000671]"
         },
-        "Live haul trailer": {
-          "text": "Live haul trailer",
+        "Live haul trailer [GENEPIO:0100897]": {
+          "text": "Live haul trailer [GENEPIO:0100897]",
           "is_a": "Animal transportation equipment [AGRO:00000671]"
         },
         "Live haul truck [AGRO:00000674]": {
@@ -1856,8 +1853,8 @@
         "Broom [ENVO:03501377]": {
           "text": "Broom [ENVO:03501377]"
         },
-        "Bulk tank": {
-          "text": "Bulk tank"
+        "Bulk tank [ENVO:03501379]": {
+          "text": "Bulk tank [ENVO:03501379]"
         },
         "Chick box [AGRO:00000678]": {
           "text": "Chick box [AGRO:00000678]"
@@ -1871,40 +1868,40 @@
         "Compost [ENVO:00002170]": {
           "text": "Compost [ENVO:00002170]"
         },
-        "Contaminated water (organizational term) [ENVO:00002186]": {
-          "text": "Contaminated water (organizational term) [ENVO:00002186]"
+        "Contaminated water [ENVO:00002186]": {
+          "text": "Contaminated water [ENVO:00002186]"
         },
         "Fecal slurry": {
           "text": "Fecal slurry",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Fluid from meat rinse [GENEPIO:0004323]": {
           "text": "Fluid from meat rinse [GENEPIO:0004323]",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Effluent [ENVO:03501407]": {
           "text": "Effluent [ENVO:03501407]",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Influent": {
           "text": "Influent",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Surface runoff [ENVO:03501408]": {
           "text": "Surface runoff [ENVO:03501408]",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Poultry plucking water [AGRO_00000693]": {
           "text": "Poultry plucking water [AGRO_00000693]",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Wastewater [ENVO:00002001]": {
           "text": "Wastewater [ENVO:00002001]",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Weep fluid [AGRO_00000692]": {
           "text": "Weep fluid [AGRO_00000692]",
-          "is_a": "Contaminated water (organizational term) [ENVO:00002186]"
+          "is_a": "Contaminated water [ENVO:00002186]"
         },
         "Crate [ENVO:03501372]": {
           "text": "Crate [ENVO:03501372]"
@@ -1942,12 +1939,12 @@
         "Manure digester equipment [ENVO:03501424]": {
           "text": "Manure digester equipment [ENVO:03501424]"
         },
-        "Nest": {
-          "text": "Nest"
+        "Nest [ENVO:03501432]": {
+          "text": "Nest [ENVO:03501432]"
         },
         "Bird's nest [ENVO:00005805]": {
           "text": "Bird's nest [ENVO:00005805]",
-          "is_a": "Nest"
+          "is_a": "Nest [ENVO:03501432]"
         },
         "Permafrost [ENVO:00000134]": {
           "text": "Permafrost [ENVO:00000134]"
@@ -2034,20 +2031,20 @@
       "name": "body_product menu",
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
-        "Digestive organ content": {
-          "text": "Digestive organ content"
+        "Digestive organ content [GENEPIO:0100898]": {
+          "text": "Digestive organ content [GENEPIO:0100898]"
         },
-        "Caecal content": {
-          "text": "Caecal content",
-          "is_a": "Digestive organ content"
+        "Caecal content [GENEPIO:0100899]": {
+          "text": "Caecal content [GENEPIO:0100899]",
+          "is_a": "Digestive organ content [GENEPIO:0100898]"
         },
-        "Intestinal content": {
-          "text": "Intestinal content",
-          "is_a": "Digestive organ content"
+        "Intestinal content [GENEPIO:0100900]": {
+          "text": "Intestinal content [GENEPIO:0100900]",
+          "is_a": "Digestive organ content [GENEPIO:0100898]"
         },
-        "Stomach content": {
-          "text": "Stomach content",
-          "is_a": "Digestive organ content"
+        "Stomach content [GENEPIO:0100901]": {
+          "text": "Stomach content [GENEPIO:0100901]",
+          "is_a": "Digestive organ content [GENEPIO:0100898]"
         },
         "Feces [UBERON:0001988]": {
           "text": "Feces [UBERON:0001988]"
@@ -2397,12 +2394,12 @@
         "Vent (anatomical) [UBERON:2000298]": {
           "text": "Vent (anatomical) [UBERON:2000298]"
         },
-        "Bird vent": {
-          "text": "Bird vent",
+        "Bird vent [UBERON:0012464]": {
+          "text": "Bird vent [UBERON:0012464]",
           "is_a": "Vent (anatomical) [UBERON:2000298]"
         },
-        "Fish vent": {
-          "text": "Fish vent",
+        "Fish vent [GENEPIO:0100902]": {
+          "text": "Fish vent [GENEPIO:0100902]",
           "is_a": "Vent (anatomical) [UBERON:2000298]"
         }
       }
@@ -2414,11 +2411,11 @@
         "Dorso-lateral region [BSPO:0000080]": {
           "text": "Dorso-lateral region [BSPO:0000080]"
         },
-        "Exterior anatomical region": {
-          "text": "Exterior anatomical region"
+        "Exterior anatomical region [BSPO:0000034]": {
+          "text": "Exterior anatomical region [BSPO:0000034]"
         },
-        "Interior anatomical region": {
-          "text": "Interior anatomical region"
+        "Interior anatomical region [BSPO:0000033]": {
+          "text": "Interior anatomical region [BSPO:0000033]"
         }
       }
     },
@@ -2445,13 +2442,13 @@
           "text": "Canola meal [FOODON:00002694]",
           "is_a": "Animal feed [ENVO:02000047]"
         },
-        "Compound feed premix": {
-          "text": "Compound feed premix",
+        "Compound feed premix [FOODON:00004323]": {
+          "text": "Compound feed premix [FOODON:00004323]",
           "is_a": "Animal feed [ENVO:02000047]"
         },
-        "Compound feed premix (medicated)": {
-          "text": "Compound feed premix (medicated)",
-          "is_a": "Compound feed premix"
+        "Compound feed premix (medicated) [FOODON:00004324]": {
+          "text": "Compound feed premix (medicated) [FOODON:00004324]",
+          "is_a": "Compound feed premix [FOODON:00004323]"
         },
         "Feather meal [FOODON:00003927]": {
           "text": "Feather meal [FOODON:00003927]",
@@ -2481,8 +2478,8 @@
           "text": "Soybean meal [FOODON:03302757]",
           "is_a": "Animal feed [ENVO:02000047]"
         },
-        "Animal feed ingredient": {
-          "text": "Animal feed ingredient"
+        "Animal feed ingredient [FOODON:00004322]": {
+          "text": "Animal feed ingredient [FOODON:00004322]"
         },
         "Dairy food product [FOODON:00001256]": {
           "text": "Dairy food product [FOODON:00001256]"
@@ -2739,10 +2736,22 @@
           "text": "Chicken thigh (skinless) [FOODON:00003331]",
           "is_a": "Chicken thigh"
         },
+        "Chicken thigh (skinless, with bone)": {
+          "text": "Chicken thigh (skinless, with bone)",
+          "is_a": "Chicken thigh"
+        },
         "Chicken thigh (skinless, boneless) [FOODON:03000417]": {
           "text": "Chicken thigh (skinless, boneless) [FOODON:03000417]",
           "is_a": "Chicken thigh"
         },
+        "Chicken upper thigh [FOODON:03000381]": {
+          "text": "Chicken upper thigh [FOODON:03000381]",
+          "is_a": "Chicken thigh (skinless, boneless) [FOODON:03000417]"
+        },
+        "Chicken upper thigh (with skin) [FOODON:03000383]": {
+          "text": "Chicken upper thigh (with skin) [FOODON:03000383]",
+          "is_a": "Chicken upper thigh [FOODON:03000381]"
+        },
         "Chicken thigh (with skin) [FOODON:00003330]": {
           "text": "Chicken thigh (with skin) [FOODON:00003330]",
           "is_a": "Chicken thigh"
@@ -2751,14 +2760,6 @@
           "text": "Chicken thigh (with skin, with bone) [FOODON_00003363]",
           "is_a": "Chicken thigh"
         },
-        "Chicken upper thigh [FOODON:03000381]": {
-          "text": "Chicken upper thigh [FOODON:03000381]",
-          "is_a": "Meat, poultry and fish (organizational term)"
-        },
-        "Chicken upper thigh (with skin) [FOODON:03000383]": {
-          "text": "Chicken upper thigh (with skin) [FOODON:03000383]",
-          "is_a": "Chicken upper thigh [FOODON:03000381]"
-        },
         "Chicken wing [FOODON:00002674]": {
           "text": "Chicken wing [FOODON:00002674]",
           "is_a": "Meat, poultry and fish (organizational term)"
@@ -2779,8 +2780,8 @@
           "text": "Head cheese [FOODON:03315658]",
           "is_a": "Meat, poultry and fish (organizational term)"
         },
-        "Lamb": {
-          "text": "Lamb",
+        "Lamb [FOODON:03411669]": {
+          "text": "Lamb [FOODON:03411669]",
           "is_a": "Meat, poultry and fish (organizational term)"
         },
         "Meat strip [FOODON:00004285]": {
@@ -3071,8 +3072,8 @@
           "text": "Arugula greens (raw) [FOODON:00002426]",
           "is_a": "Produce [FOODON:03305145]"
         },
-        "Avocado": {
-          "text": "Avocado",
+        "Avocado [FOODON:00003600]": {
+          "text": "Avocado [FOODON:00003600]",
           "is_a": "Produce [FOODON:03305145]"
         },
         "Cantaloupe (whole or parts) [FOODON:03000243]": {
@@ -3099,8 +3100,8 @@
           "text": "Fruit [PO:0009001]",
           "is_a": "Produce [FOODON:03305145]"
         },
-        "Goji berry": {
-          "text": "Goji berry",
+        "Goji berry [FOODON:00004360]": {
+          "text": "Goji berry [FOODON:00004360]",
           "is_a": "Produce [FOODON:03305145]"
         },
         "Greens (raw) [FOODON:03310765]": {
@@ -3139,8 +3140,8 @@
           "text": "Pepper (whole or parts) [FOODON:03000249]",
           "is_a": "Produce [FOODON:03305145]"
         },
-        "Potato": {
-          "text": "Potato",
+        "Potato [FOODON:03315354]": {
+          "text": "Potato [FOODON:03315354]",
           "is_a": "Produce [FOODON:03305145]"
         },
         "Salad [FOODON:03316042]": {
@@ -3303,8 +3304,8 @@
         "Food (canned) [FOODON:00002418]": {
           "text": "Food (canned) [FOODON:00002418]"
         },
-        "Food (cooked)": {
-          "text": "Food (cooked)"
+        "Food (cooked) [FOODON:00001181]": {
+          "text": "Food (cooked) [FOODON:00001181]"
         },
         "Food (cut) [FOODON:00004291]": {
           "text": "Food (cut) [FOODON:00004291]"
@@ -3341,11 +3342,11 @@
         "Meat (skinless) [FOODON:00003468]": {
           "text": "Meat (skinless) [FOODON:00003468]"
         },
-        "Meat (with bone)": {
-          "text": "Meat (with bone)"
+        "Meat (with bone) [FOODON:02010116]": {
+          "text": "Meat (with bone) [FOODON:02010116]"
         },
-        "Meat (with skin)": {
-          "text": "Meat (with skin)"
+        "Meat (with skin) [FOODON:02010111]": {
+          "text": "Meat (with skin) [FOODON:02010111]"
         },
         "Organic food claim or use [FOODON:03510128]": {
           "text": "Organic food claim or use [FOODON:03510128]"
@@ -3387,47 +3388,34 @@
         }
       }
     },
-    "production_stream menu": {
-      "name": "production_stream menu",
+    "food_product_production_stream menu": {
+      "name": "food_product_production_stream menu",
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
-        "Food animal production stream": {
-          "text": "Food animal production stream"
+        "Beef cattle production stream [FOODON:03000452]": {
+          "text": "Beef cattle production stream [FOODON:03000452]"
         },
-        "Beef cattle production stream": {
-          "text": "Beef cattle production stream",
-          "is_a": "Food animal production stream"
+        "Broiler chicken production stream [FOODON:03000455]": {
+          "text": "Broiler chicken production stream [FOODON:03000455]"
         },
-        "Broiler chicken production stream": {
-          "text": "Broiler chicken production stream",
-          "is_a": "Food animal production stream"
+        "Dairy cattle production stream [FOODON:03000453]": {
+          "text": "Dairy cattle production stream [FOODON:03000453]"
         },
-        "Dairy cattle production stream": {
-          "text": "Dairy cattle production stream",
-          "is_a": "Food animal production stream"
+        "Egg production stream [FOODON:03000458]": {
+          "text": "Egg production stream [FOODON:03000458]"
         },
-        "Layer chicken production stream": {
-          "text": "Layer chicken production stream",
-          "is_a": "Food animal production stream"
+        "Layer chicken production stream [FOODON:03000456]": {
+          "text": "Layer chicken production stream [FOODON:03000456]"
         },
-        "Food product production stream": {
-          "text": "Food product production stream"
+        "Meat production stream [FOODON:03000460]": {
+          "text": "Meat production stream [FOODON:03000460]"
         },
-        "Egg production stream": {
-          "text": "Egg production stream",
-          "is_a": "Food product production stream"
+        "Veal meat production stream [FOODON:03000461]": {
+          "text": "Veal meat production stream [FOODON:03000461]",
+          "is_a": "Meat production stream [FOODON:03000460]"
         },
-        "Meat production stream": {
-          "text": "Meat production stream",
-          "is_a": "Food product production stream"
-        },
-        "Veal production stream": {
-          "text": "Veal production stream",
-          "is_a": "Meat production stream"
-        },
-        "Milk production stream": {
-          "text": "Milk production stream",
-          "is_a": "Food product production stream"
+        "Milk production stream [FOODON:03000459]": {
+          "text": "Milk production stream [FOODON:03000459]"
         }
       }
     },
@@ -3473,14 +3461,14 @@
         "PONAR grab sampler": {
           "text": "PONAR grab sampler"
         },
-        "Scoop": {
-          "text": "Scoop"
+        "Scoop [GENEPIO:0002125]": {
+          "text": "Scoop [GENEPIO:0002125]"
         },
         "Soil sample probe": {
           "text": "Soil sample probe"
         },
-        "Spatula": {
-          "text": "Spatula"
+        "Spatula [NCIT:C149941]": {
+          "text": "Spatula [NCIT:C149941]"
         },
         "Sponge [OBI:0002819]": {
           "text": "Sponge [OBI:0002819]"
@@ -3575,17 +3563,17 @@
           "text": "Paper bag, sack or pouch [FOODON:03490120]",
           "is_a": "Bag, sack or pouch [FOODON:03490197]"
         },
-        "Plastic bag, sack or pouch": {
-          "text": "Plastic bag, sack or pouch",
+        "Plastic bag, sack or pouch [FOODON:03490166]": {
+          "text": "Plastic bag, sack or pouch [FOODON:03490166]",
           "is_a": "Bag, sack or pouch [FOODON:03490197]"
         },
         "Plastic shrink wrap [FOODON:03490137]": {
           "text": "Plastic shrink wrap [FOODON:03490137]",
-          "is_a": "Plastic bag, sack or pouch"
+          "is_a": "Plastic bag, sack or pouch [FOODON:03490166]"
         },
         "Plastic wrapper [FOODON:03490128]": {
           "text": "Plastic wrapper [FOODON:03490128]",
-          "is_a": "Plastic bag, sack or pouch"
+          "is_a": "Plastic bag, sack or pouch [FOODON:03490166]"
         },
         "Bottle or jar [FOODON:03490203]": {
           "text": "Bottle or jar [FOODON:03490203]"
@@ -3608,20 +3596,20 @@
       "name": "host (common name) menu",
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
-        "Bird": {
-          "text": "Bird"
+        "Bird [NCBITaxon:8782]": {
+          "text": "Bird [NCBITaxon:8782]"
         },
         "Chicken [NCBITaxon:9031]": {
           "text": "Chicken [NCBITaxon:9031]",
-          "is_a": "Bird"
+          "is_a": "Bird [NCBITaxon:8782]"
         },
-        "Seabird": {
-          "text": "Seabird",
-          "is_a": "Bird"
+        "Seabird [FOODON:00004504]": {
+          "text": "Seabird [FOODON:00004504]",
+          "is_a": "Bird [NCBITaxon:8782]"
         },
         "Cormorant [NCBITaxon:9206]": {
           "text": "Cormorant [NCBITaxon:9206]",
-          "is_a": "Seabird"
+          "is_a": "Seabird [FOODON:00004504]"
         },
         "Double Crested Cormorant [NCBITaxon:56069]": {
           "text": "Double Crested Cormorant [NCBITaxon:56069]",
@@ -3629,7 +3617,7 @@
         },
         "Crane [NCBITaxon:9109]": {
           "text": "Crane [NCBITaxon:9109]",
-          "is_a": "Seabird"
+          "is_a": "Seabird [FOODON:00004504]"
         },
         "Whooping Crane [NCBITaxon:9117]": {
           "text": "Whooping Crane [NCBITaxon:9117]",
@@ -3637,7 +3625,7 @@
         },
         "Gull (Seagull) [NCBITaxon:8911]": {
           "text": "Gull (Seagull) [NCBITaxon:8911]",
-          "is_a": "Seabird"
+          "is_a": "Seabird [FOODON:00004504]"
         },
         "Glaucous-winged Gull [NCBITaxon:119606]": {
           "text": "Glaucous-winged Gull [NCBITaxon:119606]",
@@ -3657,7 +3645,7 @@
         },
         "Eider [NCBITaxon:50366]": {
           "text": "Eider [NCBITaxon:50366]",
-          "is_a": "Seabird"
+          "is_a": "Seabird [FOODON:00004504]"
         },
         "Common Eider [NCBITaxon:76058]": {
           "text": "Common Eider [NCBITaxon:76058]",
@@ -3665,7 +3653,7 @@
         },
         "Turkey [NCBITaxon:9103]": {
           "text": "Turkey [NCBITaxon:9103]",
-          "is_a": "Bird"
+          "is_a": "Bird [NCBITaxon:8782]"
         },
         "Fish [FOODON:03411222]": {
           "text": "Fish [FOODON:03411222]"
@@ -3760,9 +3748,6 @@
         "Larus marinus [NCBITaxon:8912]": {
           "text": "Larus marinus [NCBITaxon:8912]"
         },
-        "Larus sp.": {
-          "text": "Larus sp."
-        },
         "Meleagris gallopavo [NCBITaxon:9103]": {
           "text": "Meleagris gallopavo [NCBITaxon:9103]"
         },
@@ -4400,6 +4385,24 @@
         }
       }
     },
+    "taxonomic_identification_process menu": {
+      "name": "taxonomic_identification_process menu",
+      "from_schema": "https://example.com/GRDI",
+      "permissible_values": {
+        "Whole genome sequencing assay [OBI:0002117]": {
+          "text": "Whole genome sequencing assay [OBI:0002117]"
+        },
+        "16S ribosomal gene sequencing assay [OBI:0002763]": {
+          "text": "16S ribosomal gene sequencing assay [OBI:0002763]"
+        },
+        "PCR assay [OBI:0002740]": {
+          "text": "PCR assay [OBI:0002740]"
+        },
+        "Comparative phenotypic assessment [OBI:0001546]": {
+          "text": "Comparative phenotypic assessment [OBI:0001546]"
+        }
+      }
+    },
     "sequenced_by menu": {
       "name": "sequenced_by menu",
       "from_schema": "https://example.com/GRDI",
@@ -4424,24 +4427,6 @@
         }
       }
     },
-    "taxonomic_identification_process menu": {
-      "name": "taxonomic_identification_process menu",
-      "from_schema": "https://example.com/GRDI",
-      "permissible_values": {
-        "Whole genome sequencing assay [OBI:0002117]": {
-          "text": "Whole genome sequencing assay [OBI:0002117]"
-        },
-        "16S ribosomal gene sequencing assay [OBI:0002763]": {
-          "text": "16S ribosomal gene sequencing assay [OBI:0002763]"
-        },
-        "PCR assay [OBI:0002740]": {
-          "text": "PCR assay [OBI:0002740]"
-        },
-        "Comparative phenotypic assessment [OBI:0001546]": {
-          "text": "Comparative phenotypic assessment [OBI:0001546]"
-        }
-      }
-    },
     "purpose_of_sequencing menu": {
       "name": "purpose_of_sequencing menu",
       "from_schema": "https://example.com/GRDI",
@@ -4814,14 +4799,14 @@
       "name": "antimicrobial_measurement_units menu",
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
-        "mg/L [UO:0000273]": {
-          "text": "mg/L [UO:0000273]"
+        "milligram per litre (mg/L) [UO:0000273]": {
+          "text": "milligram per litre (mg/L) [UO:0000273]"
         },
-        "mm [UO:0000016]": {
-          "text": "mm [UO:0000016]"
+        "millimetre (mm) [UO:0000016]": {
+          "text": "millimetre (mm) [UO:0000016]"
         },
-        "ug/mL [UO:0000274]": {
-          "text": "ug/mL [UO:0000274]"
+        "microgram per millilitre (ug/mL) [UO:0000274]": {
+          "text": "microgram per millilitre (ug/mL) [UO:0000274]"
         }
       }
     },
@@ -4829,8 +4814,8 @@
       "name": "antimicrobial_measurement_sign menu",
       "from_schema": "https://example.com/GRDI",
       "permissible_values": {
-        "less than  (<) [GENEPIO:0001002]": {
-          "text": "less than  (<) [GENEPIO:0001002]"
+        "less than (<) [GENEPIO:0001002]": {
+          "text": "less than (<) [GENEPIO:0001002]"
         },
         "less than or equal to (<=) [GENEPIO:0001003]": {
           "text": "less than or equal to (<=) [GENEPIO:0001003]"
@@ -4854,7 +4839,8 @@
           "text": "Agar diffusion [NCIT:85595]"
         },
         "Antimicrobial gradient (E-test) [NCIT:85596]": {
-          "text": "Antimicrobial gradient (E-test) [NCIT:85596]"
+          "text": "Antimicrobial gradient (E-test) [NCIT:85596]",
+          "is_a": "Agar diffusion [NCIT:85595]"
         },
         "Agar dilution [ARO:3004411]": {
           "text": "Agar dilution [ARO:3004411]"
@@ -4930,6 +4916,12 @@
         },
         "Société Française de Microbiologie (SFM) [ARO:3004369]": {
           "text": "Société Française de Microbiologie (SFM) [ARO:3004369]"
+        },
+        "Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]": {
+          "text": "Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]"
+        },
+        "Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]": {
+          "text": "Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]"
         }
       }
     }
@@ -5825,18 +5817,23 @@
         }
       ]
     },
-    "production_stream": {
-      "name": "production_stream",
-      "description": "A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a particular commodity.",
-      "title": "production_stream",
+    "food_product_production_stream": {
+      "name": "food_product_production_stream",
+      "description": "A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity.",
+      "title": "food_product_production_stream",
       "comments": [
         "Provide the name of the agricultural production stream from the picklist."
       ],
+      "examples": [
+        {
+          "value": "Beef cattle production stream [FOODON:03000452]"
+        }
+      ],
       "from_schema": "https://example.com/GRDI",
       "slot_uri": "GENEPIO:0100699",
       "any_of": [
         {
-          "range": "production_stream menu"
+          "range": "food_product_production_stream menu"
         },
         {
           "range": "null value menu"
@@ -19009,8 +19006,8 @@
           "rank": 40,
           "slot_group": "Sample collection and processing"
         },
-        "production_stream": {
-          "name": "production_stream",
+        "food_product_production_stream": {
+          "name": "food_product_production_stream",
           "rank": 41,
           "slot_group": "Sample collection and processing"
         },
@@ -22982,14 +22979,14 @@
           "slot_group": "Sample collection and processing",
           "recommended": true
         },
-        "production_stream": {
-          "name": "production_stream",
-          "description": "A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a particular commodity.",
-          "title": "production_stream",
+        "food_product_production_stream": {
+          "name": "food_product_production_stream",
+          "description": "A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity.",
+          "title": "food_product_production_stream",
           "from_schema": "https://example.com/GRDI",
           "rank": 41,
           "slot_uri": "GENEPIO:0100699",
-          "alias": "production_stream",
+          "alias": "food_product_production_stream",
           "owner": "GRDI",
           "domain_of": [
             "GRDI"
diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml
index de08e6c0..a618c6c8 100644
--- a/web/templates/grdi/schema.yaml
+++ b/web/templates/grdi/schema.yaml
@@ -1,7 +1,7 @@
 id: https://example.com/GRDI
 name: GRDI
 description: ''
-version: 7.7.6
+version: 8.8.4
 imports:
 - linkml:types
 prefixes:
@@ -57,7 +57,7 @@ classes:
     - food_product
     - food_product_properties
     - animal_source_of_food
-    - production_stream
+    - food_product_production_stream
     - sample_storage_method
     - sample_storage_medium
     - collection_device
@@ -850,7 +850,7 @@ classes:
       animal_source_of_food:
         rank: 40
         slot_group: Sample collection and processing
-      production_stream:
+      food_product_production_stream:
         rank: 41
         slot_group: Sample collection and processing
       sample_storage_method:
@@ -3458,16 +3458,18 @@ slots:
     - range: null value menu
     multivalued: true
     recommended: true
-  production_stream:
-    name: production_stream
-    title: production_stream
+  food_product_production_stream:
+    name: food_product_production_stream
+    title: food_product_production_stream
     description: A production pathway incorporating the processes, material entities
       (e.g. equipment, animals, locations), and conditions that participate in the
-      generation of a particular commodity.
+      generation of a food commodity.
     comments: Provide the name of the agricultural production stream from the picklist.
+    examples:
+    - value: Beef cattle production stream [FOODON:03000452]
     slot_uri: GENEPIO:0100699
     any_of:
-    - range: production_stream menu
+    - range: food_product_production_stream menu
     - range: null value menu
   sample_storage_method:
     name: sample_storage_method
@@ -10840,16 +10842,16 @@ enums:
         text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551]
       Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]:
         text: Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]
-      Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100552]:
-        text: Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100552]
+      Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]:
+        text: Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]
       Health Canada (HC) [GENEPIO:0100554]:
         text: Health Canada (HC) [GENEPIO:0100554]
       Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]:
         text: Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]
       Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]:
         text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]
-      University of Manitoba (UM):
-        text: University of Manitoba (UM)
+      University of Manitoba (UM) [GENEPIO:0004434]:
+        text: University of Manitoba (UM) [GENEPIO:0004434]
   purpose_of_sampling menu:
     name: purpose_of_sampling menu
     permissible_values:
@@ -10881,13 +10883,13 @@ enums:
         text: Antimicrobial pre-treatment [GENEPIO:0100537]
       Certified animal husbandry practices [GENEPIO:0100538]:
         text: Certified animal husbandry practices [GENEPIO:0100538]
-      Certified humane animal husbandry practices:
-        text: Certified humane animal husbandry practices
+      Certified humane animal husbandry practices [GENEPIO:0100894]:
+        text: Certified humane animal husbandry practices [GENEPIO:0100894]
         is_a: Certified animal husbandry practices [GENEPIO:0100538]
       Certified organic farming practices [GENEPIO:0100539]:
         text: Certified organic farming practices [GENEPIO:0100539]
-      Conventional farming practices:
-        text: Conventional farming practices
+      Conventional farming practices [GENEPIO:0100895]:
+        text: Conventional farming practices [GENEPIO:0100895]
       Change in storage conditions [GENEPIO:0100540]:
         text: Change in storage conditions [GENEPIO:0100540]
       Cleaning/disinfection [GENEPIO:0100541]:
@@ -10909,12 +10911,12 @@ enums:
   specimen_processing menu:
     name: specimen_processing menu
     permissible_values:
-      Biological replicate:
-        text: Biological replicate
+      Biological replicate [OBI:0000198]:
+        text: Biological replicate [OBI:0000198]
       Samples pooled [OBI:0600016]:
         text: Samples pooled [OBI:0600016]
-      Technical replicate:
-        text: Technical replicate
+      Technical replicate [OBI:0000249]:
+        text: Technical replicate [OBI:0000249]
       Isolated from single source:
         text: Isolated from single source
   geo_loc_name (country) menu:
@@ -11465,55 +11467,55 @@ enums:
   geo_loc_name (state/province/region) menu:
     name: geo_loc_name (state/province/region) menu
     permissible_values:
-      Atlantic region (Canada):
-        text: Atlantic region (Canada)
+      Atlantic region (Canada) [wikidata:Q246972]:
+        text: Atlantic region (Canada) [wikidata:Q246972]
       New Brunswick [GAZ:00002570]:
         text: New Brunswick [GAZ:00002570]
-        is_a: Atlantic region (Canada)
+        is_a: Atlantic region (Canada) [wikidata:Q246972]
       Newfoundland & Labrador [GAZ:00002567]:
         text: Newfoundland & Labrador [GAZ:00002567]
-        is_a: Atlantic region (Canada)
+        is_a: Atlantic region (Canada) [wikidata:Q246972]
       Nova Scotia [GAZ:00002565]:
         text: Nova Scotia [GAZ:00002565]
-        is_a: Atlantic region (Canada)
+        is_a: Atlantic region (Canada) [wikidata:Q246972]
       Prince Edward Island [GAZ:00002572]:
         text: Prince Edward Island [GAZ:00002572]
-        is_a: Atlantic region (Canada)
-      Central region (Canada):
-        text: Central region (Canada)
+        is_a: Atlantic region (Canada) [wikidata:Q246972]
+      Central region (Canada) [wikidata:Q1048064]:
+        text: Central region (Canada) [wikidata:Q1048064]
       Ontario [GAZ:00002563]:
         text: Ontario [GAZ:00002563]
-        is_a: Central region (Canada)
+        is_a: Central region (Canada) [wikidata:Q1048064]
       Quebec [GAZ:00002569]:
         text: Quebec [GAZ:00002569]
-        is_a: Central region (Canada)
-      Northern region (Canada):
-        text: Northern region (Canada)
+        is_a: Central region (Canada) [wikidata:Q1048064]
+      Northern region (Canada) [wikidata:Q764146]:
+        text: Northern region (Canada) [wikidata:Q764146]
       Northwest Territories [GAZ:00002575]:
         text: Northwest Territories [GAZ:00002575]
-        is_a: Northern region (Canada)
+        is_a: Northern region (Canada) [wikidata:Q764146]
       Nunuvut [GAZ:00002574]:
         text: Nunuvut [GAZ:00002574]
-        is_a: Northern region (Canada)
+        is_a: Northern region (Canada) [wikidata:Q764146]
       Yukon [GAZ:00002576]:
         text: Yukon [GAZ:00002576]
-        is_a: Northern region (Canada)
-      Pacific region (Canada):
-        text: Pacific region (Canada)
+        is_a: Northern region (Canada) [wikidata:Q764146]
+      Pacific region (Canada) [wikidata:Q122953299]:
+        text: Pacific region (Canada) [wikidata:Q122953299]
       British Columbia [GAZ:00002562]:
         text: British Columbia [GAZ:00002562]
-        is_a: Pacific region (Canada)
-      Prairie region (Canada):
-        text: Prairie region (Canada)
+        is_a: Pacific region (Canada) [wikidata:Q122953299]
+      Prairie region (Canada) [wikidata:Q1364746]:
+        text: Prairie region (Canada) [wikidata:Q1364746]
       Alberta [GAZ:00002566]:
         text: Alberta [GAZ:00002566]
-        is_a: Prairie region (Canada)
+        is_a: Prairie region (Canada) [wikidata:Q1364746]
       Manitoba [GAZ:00002571]:
         text: Manitoba [GAZ:00002571]
-        is_a: Prairie region (Canada)
+        is_a: Prairie region (Canada) [wikidata:Q1364746]
       Saskatchewan [GAZ:00002564]:
         text: Saskatchewan [GAZ:00002564]
-        is_a: Prairie region (Canada)
+        is_a: Prairie region (Canada) [wikidata:Q1364746]
   sample_collection_date_precision menu:
     name: sample_collection_date_precision menu
     permissible_values:
@@ -11569,8 +11571,8 @@ enums:
       Laboratory facility [ENVO:01001406]:
         text: Laboratory facility [ENVO:01001406]
         is_a: Building [ENVO:00000073]
-      Pigsty:
-        text: Pigsty
+      Pigsty [ENVO:03501413]:
+        text: Pigsty [ENVO:03501413]
         is_a: Building [ENVO:00000073]
       Building part (organizational term):
         text: Building part (organizational term)
@@ -11608,8 +11610,8 @@ enums:
       Breeder farm [ENVO:03501384]:
         text: Breeder farm [ENVO:03501384]
         is_a: Farm [ENVO:00000078]
-      Dairy farm:
-        text: Dairy farm
+      Dairy farm [ENVO:03501416]:
+        text: Dairy farm [ENVO:03501416]
         is_a: Farm [ENVO:00000078]
       Feedlot [ENVO:01000627]:
         text: Feedlot [ENVO:01000627]
@@ -11896,16 +11898,14 @@ enums:
         text: Tropical fish [FOODON:00004283]
       Turkey [NCBITaxon:9103]:
         text: Turkey [NCBITaxon:9103]
-      Wildlife:
-        text: Wildlife
-      Wild bird:
-        text: Wild bird
-        is_a: Wildlife
-      Seabird:
-        text: Seabird
-        is_a: Wild bird
-      Turkey:
-        text: Turkey
+      Wildlife [FOODON:00004503]:
+        text: Wildlife [FOODON:00004503]
+      Wild bird [FOODON:00004505]:
+        text: Wild bird [FOODON:00004505]
+        is_a: Wildlife [FOODON:00004503]
+      Seabird [FOODON:00004504]:
+        text: Seabird [FOODON:00004504]
+        is_a: Wild bird [FOODON:00004505]
   environmental_material menu:
     name: environmental_material menu
     permissible_values:
@@ -11929,14 +11929,14 @@ enums:
         is_a: Animal feeding equipment [AGRO:00000675]
       Animal transportation equipment [AGRO:00000671]:
         text: Animal transportation equipment [AGRO:00000671]
-      Dead haul trailer:
-        text: Dead haul trailer
+      Dead haul trailer [GENEPIO:0100896]:
+        text: Dead haul trailer [GENEPIO:0100896]
         is_a: Animal transportation equipment [AGRO:00000671]
       Dead haul truck [AGRO:00000673]:
         text: Dead haul truck [AGRO:00000673]
         is_a: Animal transportation equipment [AGRO:00000671]
-      Live haul trailer:
-        text: Live haul trailer
+      Live haul trailer [GENEPIO:0100897]:
+        text: Live haul trailer [GENEPIO:0100897]
         is_a: Animal transportation equipment [AGRO:00000671]
       Live haul truck [AGRO:00000674]:
         text: Live haul truck [AGRO:00000674]
@@ -11952,8 +11952,8 @@ enums:
         is_a: Boot [GSSO:012935]
       Broom [ENVO:03501377]:
         text: Broom [ENVO:03501377]
-      Bulk tank:
-        text: Bulk tank
+      Bulk tank [ENVO:03501379]:
+        text: Bulk tank [ENVO:03501379]
       Chick box [AGRO:00000678]:
         text: Chick box [AGRO:00000678]
       Chick pad [AGRO:00000672]:
@@ -11962,32 +11962,32 @@ enums:
         text: Cleaning equipment [ENVO:03501376]
       Compost [ENVO:00002170]:
         text: Compost [ENVO:00002170]
-      Contaminated water (organizational term) [ENVO:00002186]:
-        text: Contaminated water (organizational term) [ENVO:00002186]
+      Contaminated water [ENVO:00002186]:
+        text: Contaminated water [ENVO:00002186]
       Fecal slurry:
         text: Fecal slurry
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Fluid from meat rinse [GENEPIO:0004323]:
         text: Fluid from meat rinse [GENEPIO:0004323]
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Effluent [ENVO:03501407]:
         text: Effluent [ENVO:03501407]
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Influent:
         text: Influent
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Surface runoff [ENVO:03501408]:
         text: Surface runoff [ENVO:03501408]
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Poultry plucking water [AGRO_00000693]:
         text: Poultry plucking water [AGRO_00000693]
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Wastewater [ENVO:00002001]:
         text: Wastewater [ENVO:00002001]
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Weep fluid [AGRO_00000692]:
         text: Weep fluid [AGRO_00000692]
-        is_a: Contaminated water (organizational term) [ENVO:00002186]
+        is_a: Contaminated water [ENVO:00002186]
       Crate [ENVO:03501372]:
         text: Crate [ENVO:03501372]
       Dumpster [ENVO:03501400]:
@@ -12013,11 +12013,11 @@ enums:
         is_a: Animal manure [AGRO:00000079]
       Manure digester equipment [ENVO:03501424]:
         text: Manure digester equipment [ENVO:03501424]
-      Nest:
-        text: Nest
+      Nest [ENVO:03501432]:
+        text: Nest [ENVO:03501432]
       Bird's nest [ENVO:00005805]:
         text: Bird's nest [ENVO:00005805]
-        is_a: Nest
+        is_a: Nest [ENVO:03501432]
       Permafrost [ENVO:00000134]:
         text: Permafrost [ENVO:00000134]
       Plucking belt [AGRO:00000669]:
@@ -12076,17 +12076,17 @@ enums:
   body_product menu:
     name: body_product menu
     permissible_values:
-      Digestive organ content:
-        text: Digestive organ content
-      Caecal content:
-        text: Caecal content
-        is_a: Digestive organ content
-      Intestinal content:
-        text: Intestinal content
-        is_a: Digestive organ content
-      Stomach content:
-        text: Stomach content
-        is_a: Digestive organ content
+      Digestive organ content [GENEPIO:0100898]:
+        text: Digestive organ content [GENEPIO:0100898]
+      Caecal content [GENEPIO:0100899]:
+        text: Caecal content [GENEPIO:0100899]
+        is_a: Digestive organ content [GENEPIO:0100898]
+      Intestinal content [GENEPIO:0100900]:
+        text: Intestinal content [GENEPIO:0100900]
+        is_a: Digestive organ content [GENEPIO:0100898]
+      Stomach content [GENEPIO:0100901]:
+        text: Stomach content [GENEPIO:0100901]
+        is_a: Digestive organ content [GENEPIO:0100898]
       Feces [UBERON:0001988]:
         text: Feces [UBERON:0001988]
       Fecal composite:
@@ -12342,21 +12342,21 @@ enums:
         is_a: Vascular system [UBERON:0007798]
       Vent (anatomical) [UBERON:2000298]:
         text: Vent (anatomical) [UBERON:2000298]
-      Bird vent:
-        text: Bird vent
+      Bird vent [UBERON:0012464]:
+        text: Bird vent [UBERON:0012464]
         is_a: Vent (anatomical) [UBERON:2000298]
-      Fish vent:
-        text: Fish vent
+      Fish vent [GENEPIO:0100902]:
+        text: Fish vent [GENEPIO:0100902]
         is_a: Vent (anatomical) [UBERON:2000298]
   anatomical_region menu:
     name: anatomical_region menu
     permissible_values:
       Dorso-lateral region [BSPO:0000080]:
         text: Dorso-lateral region [BSPO:0000080]
-      Exterior anatomical region:
-        text: Exterior anatomical region
-      Interior anatomical region:
-        text: Interior anatomical region
+      Exterior anatomical region [BSPO:0000034]:
+        text: Exterior anatomical region [BSPO:0000034]
+      Interior anatomical region [BSPO:0000033]:
+        text: Interior anatomical region [BSPO:0000033]
   food_product menu:
     name: food_product menu
     permissible_values:
@@ -12374,12 +12374,12 @@ enums:
       Canola meal [FOODON:00002694]:
         text: Canola meal [FOODON:00002694]
         is_a: Animal feed [ENVO:02000047]
-      Compound feed premix:
-        text: Compound feed premix
+      Compound feed premix [FOODON:00004323]:
+        text: Compound feed premix [FOODON:00004323]
         is_a: Animal feed [ENVO:02000047]
-      Compound feed premix (medicated):
-        text: Compound feed premix (medicated)
-        is_a: Compound feed premix
+      Compound feed premix (medicated) [FOODON:00004324]:
+        text: Compound feed premix (medicated) [FOODON:00004324]
+        is_a: Compound feed premix [FOODON:00004323]
       Feather meal [FOODON:00003927]:
         text: Feather meal [FOODON:00003927]
         is_a: Animal feed [ENVO:02000047]
@@ -12401,8 +12401,8 @@ enums:
       Soybean meal [FOODON:03302757]:
         text: Soybean meal [FOODON:03302757]
         is_a: Animal feed [ENVO:02000047]
-      Animal feed ingredient:
-        text: Animal feed ingredient
+      Animal feed ingredient [FOODON:00004322]:
+        text: Animal feed ingredient [FOODON:00004322]
       Dairy food product [FOODON:00001256]:
         text: Dairy food product [FOODON:00001256]
       Cheese block (whole or parts) [FOODON:03000287]:
@@ -12592,21 +12592,24 @@ enums:
       Chicken thigh (skinless) [FOODON:00003331]:
         text: Chicken thigh (skinless) [FOODON:00003331]
         is_a: Chicken thigh
+      Chicken thigh (skinless, with bone):
+        text: Chicken thigh (skinless, with bone)
+        is_a: Chicken thigh
       Chicken thigh (skinless, boneless) [FOODON:03000417]:
         text: Chicken thigh (skinless, boneless) [FOODON:03000417]
         is_a: Chicken thigh
+      Chicken upper thigh [FOODON:03000381]:
+        text: Chicken upper thigh [FOODON:03000381]
+        is_a: Chicken thigh (skinless, boneless) [FOODON:03000417]
+      Chicken upper thigh (with skin) [FOODON:03000383]:
+        text: Chicken upper thigh (with skin) [FOODON:03000383]
+        is_a: Chicken upper thigh [FOODON:03000381]
       Chicken thigh (with skin) [FOODON:00003330]:
         text: Chicken thigh (with skin) [FOODON:00003330]
         is_a: Chicken thigh
       Chicken thigh (with skin, with bone) [FOODON_00003363]:
         text: Chicken thigh (with skin, with bone) [FOODON_00003363]
         is_a: Chicken thigh
-      Chicken upper thigh [FOODON:03000381]:
-        text: Chicken upper thigh [FOODON:03000381]
-        is_a: Meat, poultry and fish (organizational term)
-      Chicken upper thigh (with skin) [FOODON:03000383]:
-        text: Chicken upper thigh (with skin) [FOODON:03000383]
-        is_a: Chicken upper thigh [FOODON:03000381]
       Chicken wing [FOODON:00002674]:
         text: Chicken wing [FOODON:00002674]
         is_a: Meat, poultry and fish (organizational term)
@@ -12622,8 +12625,8 @@ enums:
       Head cheese [FOODON:03315658]:
         text: Head cheese [FOODON:03315658]
         is_a: Meat, poultry and fish (organizational term)
-      Lamb:
-        text: Lamb
+      Lamb [FOODON:03411669]:
+        text: Lamb [FOODON:03411669]
         is_a: Meat, poultry and fish (organizational term)
       Meat strip [FOODON:00004285]:
         text: Meat strip [FOODON:00004285]
@@ -12840,8 +12843,8 @@ enums:
       Arugula greens (raw) [FOODON:00002426]:
         text: Arugula greens (raw) [FOODON:00002426]
         is_a: Produce [FOODON:03305145]
-      Avocado:
-        text: Avocado
+      Avocado [FOODON:00003600]:
+        text: Avocado [FOODON:00003600]
         is_a: Produce [FOODON:03305145]
       Cantaloupe (whole or parts) [FOODON:03000243]:
         text: Cantaloupe (whole or parts) [FOODON:03000243]
@@ -12861,8 +12864,8 @@ enums:
       Fruit [PO:0009001]:
         text: Fruit [PO:0009001]
         is_a: Produce [FOODON:03305145]
-      Goji berry:
-        text: Goji berry
+      Goji berry [FOODON:00004360]:
+        text: Goji berry [FOODON:00004360]
         is_a: Produce [FOODON:03305145]
       Greens (raw) [FOODON:03310765]:
         text: Greens (raw) [FOODON:03310765]
@@ -12891,8 +12894,8 @@ enums:
       Pepper (whole or parts) [FOODON:03000249]:
         text: Pepper (whole or parts) [FOODON:03000249]
         is_a: Produce [FOODON:03305145]
-      Potato:
-        text: Potato
+      Potato [FOODON:03315354]:
+        text: Potato [FOODON:03315354]
         is_a: Produce [FOODON:03305145]
       Salad [FOODON:03316042]:
         text: Salad [FOODON:03316042]
@@ -13012,8 +13015,8 @@ enums:
     permissible_values:
       Food (canned) [FOODON:00002418]:
         text: Food (canned) [FOODON:00002418]
-      Food (cooked):
-        text: Food (cooked)
+      Food (cooked) [FOODON:00001181]:
+        text: Food (cooked) [FOODON:00001181]
       Food (cut) [FOODON:00004291]:
         text: Food (cut) [FOODON:00004291]
       Food (chopped) [FOODON:00002777]:
@@ -13038,10 +13041,10 @@ enums:
         text: Meat (boneless) [FOODON:00003467]
       Meat (skinless) [FOODON:00003468]:
         text: Meat (skinless) [FOODON:00003468]
-      Meat (with bone):
-        text: Meat (with bone)
-      Meat (with skin):
-        text: Meat (with skin)
+      Meat (with bone) [FOODON:02010116]:
+        text: Meat (with bone) [FOODON:02010116]
+      Meat (with skin) [FOODON:02010111]:
+        text: Meat (with skin) [FOODON:02010111]
       Organic food claim or use [FOODON:03510128]:
         text: Organic food claim or use [FOODON:03510128]
       Ready-to-eat (RTE) [FOODON:03316636]:
@@ -13067,37 +13070,26 @@ enums:
         is_a: Poultry [FOODON:03411563]
       Sheep [NCBITaxon:9940]:
         text: Sheep [NCBITaxon:9940]
-  production_stream menu:
-    name: production_stream menu
+  food_product_production_stream menu:
+    name: food_product_production_stream menu
     permissible_values:
-      Food animal production stream:
-        text: Food animal production stream
-      Beef cattle production stream:
-        text: Beef cattle production stream
-        is_a: Food animal production stream
-      Broiler chicken production stream:
-        text: Broiler chicken production stream
-        is_a: Food animal production stream
-      Dairy cattle production stream:
-        text: Dairy cattle production stream
-        is_a: Food animal production stream
-      Layer chicken production stream:
-        text: Layer chicken production stream
-        is_a: Food animal production stream
-      Food product production stream:
-        text: Food product production stream
-      Egg production stream:
-        text: Egg production stream
-        is_a: Food product production stream
-      Meat production stream:
-        text: Meat production stream
-        is_a: Food product production stream
-      Veal production stream:
-        text: Veal production stream
-        is_a: Meat production stream
-      Milk production stream:
-        text: Milk production stream
-        is_a: Food product production stream
+      Beef cattle production stream [FOODON:03000452]:
+        text: Beef cattle production stream [FOODON:03000452]
+      Broiler chicken production stream [FOODON:03000455]:
+        text: Broiler chicken production stream [FOODON:03000455]
+      Dairy cattle production stream [FOODON:03000453]:
+        text: Dairy cattle production stream [FOODON:03000453]
+      Egg production stream [FOODON:03000458]:
+        text: Egg production stream [FOODON:03000458]
+      Layer chicken production stream [FOODON:03000456]:
+        text: Layer chicken production stream [FOODON:03000456]
+      Meat production stream [FOODON:03000460]:
+        text: Meat production stream [FOODON:03000460]
+      Veal meat production stream [FOODON:03000461]:
+        text: Veal meat production stream [FOODON:03000461]
+        is_a: Meat production stream [FOODON:03000460]
+      Milk production stream [FOODON:03000459]:
+        text: Milk production stream [FOODON:03000459]
   collection_device menu:
     name: collection_device menu
     permissible_values:
@@ -13128,12 +13120,12 @@ enums:
         text: Filter [GENEPIO:0100103]
       PONAR grab sampler:
         text: PONAR grab sampler
-      Scoop:
-        text: Scoop
+      Scoop [GENEPIO:0002125]:
+        text: Scoop [GENEPIO:0002125]
       Soil sample probe:
         text: Soil sample probe
-      Spatula:
-        text: Spatula
+      Spatula [NCIT:C149941]:
+        text: Spatula [NCIT:C149941]
       Sponge [OBI:0002819]:
         text: Sponge [OBI:0002819]
       Swab [GENEPIO:0100027]:
@@ -13197,15 +13189,15 @@ enums:
       Paper bag, sack or pouch [FOODON:03490120]:
         text: Paper bag, sack or pouch [FOODON:03490120]
         is_a: Bag, sack or pouch [FOODON:03490197]
-      Plastic bag, sack or pouch:
-        text: Plastic bag, sack or pouch
+      Plastic bag, sack or pouch [FOODON:03490166]:
+        text: Plastic bag, sack or pouch [FOODON:03490166]
         is_a: Bag, sack or pouch [FOODON:03490197]
       Plastic shrink wrap [FOODON:03490137]:
         text: Plastic shrink wrap [FOODON:03490137]
-        is_a: Plastic bag, sack or pouch
+        is_a: Plastic bag, sack or pouch [FOODON:03490166]
       Plastic wrapper [FOODON:03490128]:
         text: Plastic wrapper [FOODON:03490128]
-        is_a: Plastic bag, sack or pouch
+        is_a: Plastic bag, sack or pouch [FOODON:03490166]
       Bottle or jar [FOODON:03490203]:
         text: Bottle or jar [FOODON:03490203]
       Can (container) [FOODON:03490204]:
@@ -13219,29 +13211,29 @@ enums:
   host (common name) menu:
     name: host (common name) menu
     permissible_values:
-      Bird:
-        text: Bird
+      Bird [NCBITaxon:8782]:
+        text: Bird [NCBITaxon:8782]
       Chicken [NCBITaxon:9031]:
         text: Chicken [NCBITaxon:9031]
-        is_a: Bird
-      Seabird:
-        text: Seabird
-        is_a: Bird
+        is_a: Bird [NCBITaxon:8782]
+      Seabird [FOODON:00004504]:
+        text: Seabird [FOODON:00004504]
+        is_a: Bird [NCBITaxon:8782]
       Cormorant [NCBITaxon:9206]:
         text: Cormorant [NCBITaxon:9206]
-        is_a: Seabird
+        is_a: Seabird [FOODON:00004504]
       Double Crested Cormorant [NCBITaxon:56069]:
         text: Double Crested Cormorant [NCBITaxon:56069]
         is_a: Cormorant [NCBITaxon:9206]
       Crane [NCBITaxon:9109]:
         text: Crane [NCBITaxon:9109]
-        is_a: Seabird
+        is_a: Seabird [FOODON:00004504]
       Whooping Crane [NCBITaxon:9117]:
         text: Whooping Crane [NCBITaxon:9117]
         is_a: Crane [NCBITaxon:9109]
       Gull (Seagull) [NCBITaxon:8911]:
         text: Gull (Seagull) [NCBITaxon:8911]
-        is_a: Seabird
+        is_a: Seabird [FOODON:00004504]
       Glaucous-winged Gull [NCBITaxon:119606]:
         text: Glaucous-winged Gull [NCBITaxon:119606]
         is_a: Gull (Seagull) [NCBITaxon:8911]
@@ -13256,13 +13248,13 @@ enums:
         is_a: Gull (Seagull) [NCBITaxon:8911]
       Eider [NCBITaxon:50366]:
         text: Eider [NCBITaxon:50366]
-        is_a: Seabird
+        is_a: Seabird [FOODON:00004504]
       Common Eider [NCBITaxon:76058]:
         text: Common Eider [NCBITaxon:76058]
         is_a: Eider [NCBITaxon:50366]
       Turkey [NCBITaxon:9103]:
         text: Turkey [NCBITaxon:9103]
-        is_a: Bird
+        is_a: Bird [NCBITaxon:8782]
       Fish [FOODON:03411222]:
         text: Fish [FOODON:03411222]
       Rainbow Trout [NCBITaxon:8022]:
@@ -13328,8 +13320,6 @@ enums:
         text: Larus glaucescens [NCBITaxon:119606]
       Larus marinus [NCBITaxon:8912]:
         text: Larus marinus [NCBITaxon:8912]
-      Larus sp.:
-        text: Larus sp.
       Meleagris gallopavo [NCBITaxon:9103]:
         text: Meleagris gallopavo [NCBITaxon:9103]
       Mytilus edulis [NCBITaxon:6550]:
@@ -13787,6 +13777,17 @@ enums:
       Vibrio cholerae [NCBITaxon:666]:
         text: Vibrio cholerae [NCBITaxon:666]
         is_a: Vibrio [NCBITaxon:662]
+  taxonomic_identification_process menu:
+    name: taxonomic_identification_process menu
+    permissible_values:
+      Whole genome sequencing assay [OBI:0002117]:
+        text: Whole genome sequencing assay [OBI:0002117]
+      16S ribosomal gene sequencing assay [OBI:0002763]:
+        text: 16S ribosomal gene sequencing assay [OBI:0002763]
+      PCR assay [OBI:0002740]:
+        text: PCR assay [OBI:0002740]
+      Comparative phenotypic assessment [OBI:0001546]:
+        text: Comparative phenotypic assessment [OBI:0001546]
   sequenced_by menu:
     name: sequenced_by menu
     permissible_values:
@@ -13802,17 +13803,6 @@ enums:
         text: Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]
       Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]:
         text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]
-  taxonomic_identification_process menu:
-    name: taxonomic_identification_process menu
-    permissible_values:
-      Whole genome sequencing assay [OBI:0002117]:
-        text: Whole genome sequencing assay [OBI:0002117]
-      16S ribosomal gene sequencing assay [OBI:0002763]:
-        text: 16S ribosomal gene sequencing assay [OBI:0002763]
-      PCR assay [OBI:0002740]:
-        text: PCR assay [OBI:0002740]
-      Comparative phenotypic assessment [OBI:0001546]:
-        text: Comparative phenotypic assessment [OBI:0001546]
   purpose_of_sequencing menu:
     name: purpose_of_sequencing menu
     permissible_values:
@@ -14068,17 +14058,17 @@ enums:
   antimicrobial_measurement_units menu:
     name: antimicrobial_measurement_units menu
     permissible_values:
-      mg/L [UO:0000273]:
-        text: mg/L [UO:0000273]
-      mm [UO:0000016]:
-        text: mm [UO:0000016]
-      ug/mL [UO:0000274]:
-        text: ug/mL [UO:0000274]
+      milligram per litre (mg/L) [UO:0000273]:
+        text: milligram per litre (mg/L) [UO:0000273]
+      millimetre (mm) [UO:0000016]:
+        text: millimetre (mm) [UO:0000016]
+      microgram per millilitre (ug/mL) [UO:0000274]:
+        text: microgram per millilitre (ug/mL) [UO:0000274]
   antimicrobial_measurement_sign menu:
     name: antimicrobial_measurement_sign menu
     permissible_values:
-      less than  (<) [GENEPIO:0001002]:
-        text: less than  (<) [GENEPIO:0001002]
+      less than (<) [GENEPIO:0001002]:
+        text: less than (<) [GENEPIO:0001002]
       less than or equal to (<=) [GENEPIO:0001003]:
         text: less than or equal to (<=) [GENEPIO:0001003]
       equal to (==) [GENEPIO:0001004]:
@@ -14094,6 +14084,7 @@ enums:
         text: Agar diffusion [NCIT:85595]
       Antimicrobial gradient (E-test) [NCIT:85596]:
         text: Antimicrobial gradient (E-test) [NCIT:85596]
+        is_a: Agar diffusion [NCIT:85595]
       Agar dilution [ARO:3004411]:
         text: Agar dilution [ARO:3004411]
       Broth dilution [ARO:3004397]:
@@ -14142,6 +14133,10 @@ enums:
         text: National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]
       "Soci\xE9t\xE9 Fran\xE7aise de Microbiologie (SFM) [ARO:3004369]":
         text: "Soci\xE9t\xE9 Fran\xE7aise de Microbiologie (SFM) [ARO:3004369]"
+      Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]:
+        text: Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]
+      Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]:
+        text: Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]
 types:
   WhitespaceMinimizedString:
     name: WhitespaceMinimizedString

From 3758c9c6eb3c56db97ac2bf1c5df4726d889c020 Mon Sep 17 00:00:00 2001
From: Kenneth Bruskiewicz <kbruskie@sfu.ca>
Date: Wed, 8 Nov 2023 17:31:34 -0800
Subject: [PATCH 8/8] eslint

---
 lib/DataHarmonizer.js | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
index 9f6f071d..b2da29e5 100644
--- a/lib/DataHarmonizer.js
+++ b/lib/DataHarmonizer.js
@@ -491,7 +491,8 @@ class DataHarmonizer {
         manualColumnResize: true,
 
         //colWidths: [100], //Just fixes first column width
-        beforePaste: (data, coords) => {
+        // beforePaste: (data, coords) => { // commented out for eslint
+        beforePaste: () => {
           //data is a 2d array of rows and columns
         },
         afterCopy: function (changes) {
@@ -513,33 +514,30 @@ class DataHarmonizer {
             disabled: function () {
               // For now always on, since we can't query whether something is
               // in system cut/paste buffer without prompting user for ok.
-              return false; 
+              return false;
             },
             callback: function () {
               var plugin = this.getPlugin('copyPaste');
               this.listen();
 
-              // Due to asynchronous clipboard calls, this has to be in an 
+              // Due to asynchronous clipboard calls, this has to be in an
               // immediate setTimeout()
               setTimeout(async () => {
-                const text = await navigator.clipboard.readText();
+                let text = await navigator.clipboard.readText();
                 if (text && text.length) {
-
                   // An odd issue that with handsontable Paste menu item,
-                  // targeted paste area gets extended a row on each 
+                  // targeted paste area gets extended a row on each
                   // subsequent Paste request.  This doesn't happen if one
                   // uses CTRL-V instead (but that doesn't work on
                   // FlatpickrEditor fields unless they are later in
-                  // multi-column paste). 
+                  // multi-column paste).
                   // See https://github.com/handsontable/handsontable/issues/1930
                   // Solution is to test for and clear out trailing newline.
 
-                  if (text.substr(-1, 1) == '\n')
-                    text = text.slice(0, -1);
+                  if (text.substr(-1, 1) == '\n') text = text.slice(0, -1);
                   //self.clipboardCache = text;
-                  plugin.paste(text);  
+                  plugin.paste(text);
                 }
-
               });
 
               /*