template vocabulary update

cidgoh · Oct 22, 2024 · beedd57 · beedd57
1 parent fdd2166
commit beedd57
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Showing 12 changed files with 4,634 additions and 2,500 deletions.
diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json
diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml
diff --git a/web/templates/hpai/schema_enums.tsv b/web/templates/hpai/schema_enums.tsv
diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv
diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json
@@ -1573,6 +1573,11 @@
           "meaning": "GENEPIO:0100031",
           "is_a": "Filtration"
         },
+        "Finger Prick": {
+          "text": "Finger Prick",
+          "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.",
+          "meaning": "GENEPIO:0100036"
+        },
         "Lavage": {
           "text": "Lavage",
           "description": "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid",
@@ -1626,12 +1631,6 @@
           "description": "The process of collecting specimen material using a swab collection device.",
           "meaning": "GENEPIO:0002117"
         },
-        "Finger Prick": {
-          "text": "Finger Prick",
-          "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.",
-          "meaning": "GENEPIO:0100036",
-          "is_a": "Swabbing"
-        },
         "Thoracentesis (chest tap)": {
           "text": "Thoracentesis (chest tap)",
           "description": "The removal of excess fluid via needle puncture from the thoracic cavity.",
@@ -14465,7 +14464,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxInfectionMenu"
+              "range": "PriorMpoxInfectionMenu"
             },
             {
               "range": "NullValueMenu"
@@ -14491,7 +14490,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxAntiviralTreatmentMenu"
+              "range": "PriorMpoxAntiviralTreatmentMenu"
             },
             {
               "range": "NullValueMenu"
@@ -17261,7 +17260,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxInfectionMenu"
+              "range": "PriorMpoxInfectionMenu"
             },
             {
               "range": "NullValueMenu"
@@ -17329,7 +17328,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxAntiviralTreatmentMenu"
+              "range": "PriorMpoxAntiviralTreatmentMenu"
             },
             {
               "range": "NullValueMenu"
@@ -20256,7 +20255,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxInfectionInternationalMenu"
+              "range": "PriorMpoxInfectionInternationalMenu"
             },
             {
               "range": "NullValueMenu"
@@ -20279,7 +20278,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu"
+              "range": "PriorMpoxAntiviralTreatmentInternationalMenu"
             },
             {
               "range": "NullValueMenu"
@@ -23066,7 +23065,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxInfectionInternationalMenu"
+              "range": "PriorMpoxInfectionInternationalMenu"
             },
             {
               "range": "NullValueMenu"
@@ -23131,7 +23130,7 @@
           "slot_group": "Host reinfection information",
           "any_of": [
             {
-              "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu"
+              "range": "PriorMpoxAntiviralTreatmentInternationalMenu"
             },
             {
               "range": "NullValueMenu"

diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml
@@ -591,7 +591,7 @@ classes:
         examples:
         - value: Prior infection
         any_of:
-        - range: PriorMonkeypoxInfectionMenu
+        - range: PriorMpoxInfectionMenu
         - range: NullValueMenu
         exact_mappings:
         - NML_LIMS:prior%20Monkeypox%20infection
@@ -604,7 +604,7 @@ classes:
         examples:
         - value: Prior antiviral treatment
         any_of:
-        - range: PriorMonkeypoxAntiviralTreatmentMenu
+        - range: PriorMpoxAntiviralTreatmentMenu
         - range: NullValueMenu
         exact_mappings:
         - NML_LIMS:prior%20Monkeypox%20antiviral%20treatment
@@ -1476,7 +1476,7 @@ classes:
         examples:
         - value: Prior infection [GENEPIO:0100037]
         any_of:
-        - range: PriorMonkeypoxInfectionInternationalMenu
+        - range: PriorMpoxInfectionInternationalMenu
         - range: NullValueMenu
       prior_mpox_infection_date:
         rank: 70
@@ -1487,7 +1487,7 @@ classes:
         examples:
         - value: Prior antiviral treatment [GENEPIO:0100037]
         any_of:
-        - range: PriorMonkeypoxAntiviralTreatmentInternationalMenu
+        - range: PriorMpoxAntiviralTreatmentInternationalMenu
         - range: NullValueMenu
       prior_antiviral_treatment_during_prior_mpox_infection:
         rank: 72
@@ -5293,6 +5293,12 @@ enums:
           air via an air filtration device.
         meaning: GENEPIO:0100031
         is_a: Filtration
+      Finger Prick:
+        text: Finger Prick
+        description: A collecting specimen from organism process in which a skin site
+          free of surface arterial flow is pierced with a sterile lancet, after a
+          capillary blood droplet is formed a sample is captured in a capillary tupe.
+        meaning: GENEPIO:0100036
       Lavage:
         text: Lavage
         description: A protocol application to separate cells and/or cellular secretions
@@ -5348,13 +5354,6 @@ enums:
         description: The process of collecting specimen material using a swab collection
           device.
         meaning: GENEPIO:0002117
-      Finger Prick:
-        text: Finger Prick
-        description: A collecting specimen from organism process in which a skin site
-          free of surface arterial flow is pierced with a sterile lancet, after a
-          capillary blood droplet is formed a sample is captured in a capillary tupe.
-        meaning: GENEPIO:0100036
-        is_a: Swabbing
       Thoracentesis (chest tap):
         text: Thoracentesis (chest tap)
         description: The removal of excess fluid via needle puncture from the thoracic

diff --git a/web/templates/mpox/schema_enums.tsv b/web/templates/mpox/schema_enums.tsv
@@ -241,6 +241,7 @@ collection method menu	CollectionMethodMenu	NCIT:C52009	Amniocentesis					A pren
 		OBI:0002651		Needle Biopsy				A biopsy that uses a hollow needle to extract cells.																		
 		OBI:0302885	Filtration					Filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device																		
 		GENEPIO:0100031		Air filtration				A filtration process which removes solid particulates from the air via an air filtration device.																		
+		GENEPIO:0100036	Finger Prick					A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.																		
 		OBI:0600044	Lavage					A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid																		
 		GENEPIO:0100032		Bronchoalveolar lavage (BAL)				The collection of bronchoalveolar lavage fluid (BAL) from the lungs.																		
 		GENEPIO:0100033		Gastric Lavage				The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach.																		
@@ -251,7 +252,6 @@ collection method menu	CollectionMethodMenu	NCIT:C52009	Amniocentesis					A pren
 		GENEPIO:0100034		Saline gargle (mouth rinse and gargle)				A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device.																		
 		GENEPIO:0100035	Scraping					A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device.																		
 		GENEPIO:0002117	Swabbing					The process of collecting specimen material using a swab collection device.																		
-		GENEPIO:0100036		Finger Prick				A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.																		
 		NCIT:C15392	Thoracentesis (chest tap)					The removal of excess fluid via needle puncture from the thoracic cavity.																		
 
 collection method international menu	CollectionMethodInternationalMenu	NCIT:C52009	Amniocentesis [NCIT:C52009]					A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus.						Mpox_international												

diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv
@@ -116,11 +116,11 @@ MpoxInternational	Host exposure information	GENEPIO:0001428	exposure setting	exp
 Mpox;MpoxInternational	Host exposure information	GENEPIO:0001431	exposure details	exposure_details	WhitespaceMinimizedString										Additional host exposure information.	Free text description of the exposure.	Large party, many contacts			PH_EXPOSURE_DETAILS			Mpox;MpoxInternational						
 
 Mpox;MpoxInternational		GENEPIO:0001434	Host reinfection information	host_reinfection_information																			Mpox;MpoxInternational						
-Mpox	Host reinfection information	GENEPIO:0100532	prior Mpox infection	prior_mpox_infection	PriorMonkeypoxInfectionMenu	NullValueMenu									The absence or presence of a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list.	Prior infection 			prior Monkeypox infection			Mpox						
-MpoxInternational	Host reinfection information	GENEPIO:0100532	prior Mpox infection	prior_mpox_infection	PriorMonkeypoxInfectionInternationalMenu	NullValueMenu									The absence or presence of a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list.	Prior infection [GENEPIO:0100037]						MpoxInternational						
+Mpox	Host reinfection information	GENEPIO:0100532	prior Mpox infection	prior_mpox_infection	PriorMpoxInfectionMenu	NullValueMenu									The absence or presence of a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list.	Prior infection 			prior Monkeypox infection			Mpox						
+MpoxInternational	Host reinfection information	GENEPIO:0100532	prior Mpox infection	prior_mpox_infection	PriorMpoxInfectionInternationalMenu	NullValueMenu									The absence or presence of a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list.	Prior infection [GENEPIO:0100037]						MpoxInternational						
 Mpox;MpoxInternational	Host reinfection information	GENEPIO:0100533	prior Mpox infection date	prior_mpox_infection_date	date	NullValueMenu									The date of diagnosis of the prior Mpox infection.	Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD".	2022-06-20			prior Monkeypox infection date			Mpox;MpoxInternational						
-Mpox	Host reinfection information	GENEPIO:0100534	prior Mpox antiviral treatment	prior_mpox_antiviral_treatment	PriorMonkeypoxAntiviralTreatmentMenu	NullValueMenu									The absence or presence of antiviral treatment for a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list.	Prior antiviral treatment 			prior Monkeypox antiviral treatment			Mpox						
-MpoxInternational	Host reinfection information	GENEPIO:0100534	prior Mpox antiviral treatment	prior_mpox_antiviral_treatment	PriorMonkeypoxAntiviralTreatmentInternationalMenu	NullValueMenu									The absence or presence of antiviral treatment for a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list.	Prior antiviral treatment [GENEPIO:0100037]						MpoxInternational						
+Mpox	Host reinfection information	GENEPIO:0100534	prior Mpox antiviral treatment	prior_mpox_antiviral_treatment	PriorMpoxAntiviralTreatmentMenu	NullValueMenu									The absence or presence of antiviral treatment for a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list.	Prior antiviral treatment 			prior Monkeypox antiviral treatment			Mpox						
+MpoxInternational	Host reinfection information	GENEPIO:0100534	prior Mpox antiviral treatment	prior_mpox_antiviral_treatment	PriorMpoxAntiviralTreatmentInternationalMenu	NullValueMenu									The absence or presence of antiviral treatment for a prior Mpox infection.	If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list.	Prior antiviral treatment [GENEPIO:0100037]						MpoxInternational						
 Mpox;MpoxInternational	Host reinfection information	GENEPIO:0100535	prior antiviral treatment during prior Mpox infection	prior_antiviral_treatment_during_prior_mpox_infection	WhitespaceMinimizedString										Antiviral treatment for any infection during the prior Mpox infection period.	Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information.	AZT was administered for HIV infection during the prior Mpox infection.			prior antiviral treatment during Monkeypox infection			Mpox;MpoxInternational						
 
 
@@ -229,7 +229,6 @@ Mpox	Pathogen diagnostic testing	GENEPIO:0100576	gene name 4	gene_name_4	GeneNam
 Mpox	Pathogen diagnostic testing	GENEPIO:0100577	diagnostic pcr Ct value 4	diagnostic_pcr_ct_value_4	decimal	NullValueMenu									The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the second diagnostic RT-PCR test.	27		Gene Target 4 CT Value	SUBMITTED_RESLT - Gene Target #4 CT Value	diagnostic_PCR_CT_value_4		Mpox						
 Mpox	Pathogen diagnostic testing	GENEPIO:0100578	gene name 5	gene_name_5	GeneNameMenu	NullValueMenu									The name of the gene used in the diagnostic RT-PCR test.	Select the name of the gene used for the diagnostic PCR from the standardized pick list.	RNAse P		Gene Target 5	SUBMITTED_RESLT - Gene Target #5	gene_name_5		Mpox						
 Mpox	Pathogen diagnostic testing	GENEPIO:0100579	diagnostic pcr Ct value 5	diagnostic_pcr_ct_value_5	decimal	NullValueMenu									The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.	Provide the CT value of the sample from the second diagnostic RT-PCR test.	30		Gene Target 5 CT Value	SUBMITTED_RESLT - Gene Target #5 CT Value	diagnostic_PCR_CT_value_5		Mpox						
-
 		GENEPIO:0001516	Contributor acknowledgement	contributor_acknowledgement																									
 Mpox;MpoxInternational	Contributor acknowledgement	GENEPIO:0001517	authors	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_SEQUENCING_AUTHORS			Mpox;MpoxInternational						
 Mpox;MpoxInternational	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance	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, Mpox v3.3.1		Additional Comments	HC_COMMENTS			Mpox;MpoxInternational