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‎template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx ‎template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-2-1_July212022.xlsx

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‎template/monkeypox/exampleInput/README.md

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@@ -1,7 +1,7 @@
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# Monkeypox Example Input Data
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This directory contains example input/test data for the Canadian Network for Public Health Intelligence (CNPHI) DataHarmonizer application template: `Monkeypox`. This data is appropriate for testing up to the version appended to the end of the file name, for example:
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4-
- `DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx` is _valid_ for version `1-3-3` of the DataHarmonizer.
4+
- `DH_Canadian_MPX_validTestDataset_2-2-1_July212022.xlsx` is _valid_ for version `1-3-4` of the DataHarmonizer.
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## Valid Test Data
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‎template/monkeypox/schema.js

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@@ -78,7 +78,7 @@ var SCHEMA = {
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"name": "time",
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"description": "A time object represents a (local) time of day, independent of any particular day",
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"notes": [
81-
"URI is dateTime because OWL reasoners don't work with straight date or time"
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"URI is dateTime because OWL reasoners do not work with straight date or time"
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],
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"base": "XSDTime",
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"uri": "xsd:dateTime",
@@ -645,6 +645,11 @@ var SCHEMA = {
645645
"meaning": "UBERON:0006956",
646646
"is_a": "Head"
647647
},
648+
"Cheek": {
649+
"text": "Cheek",
650+
"meaning": "UBERON:0001567",
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"is_a": "Head"
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},
648653
"Ear": {
649654
"text": "Ear",
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"meaning": "UBERON:0001690",
@@ -877,6 +882,11 @@ var SCHEMA = {
877882
"meaning": "UBERON:0006956",
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"is_a": "Head [UBERON:0000033]"
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},
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"Cheek [UBERON:0001567]": {
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"text": "Cheek [UBERON:0001567]",
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"meaning": "UBERON:0001567",
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"is_a": "Head [UBERON:0000033]"
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},
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"Ear [UBERON:0001690]": {
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"text": "Ear [UBERON:0001690]",
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"meaning": "UBERON:0001690",
@@ -4625,50 +4635,29 @@ var SCHEMA = {
46254635
}
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}
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},
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"gene name 1 menu": {
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"name": "gene name 1 menu",
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"gene name menu": {
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"name": "gene name menu",
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"from_schema": "https://example.com/monkeypox",
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"permissible_values": {
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"MPX (orf B6R)": {
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"text": "MPX (orf B6R)",
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"meaning": "GENEPIO:0100505"
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}
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}
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},
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"gene name 2 menu": {
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"name": "gene name 2 menu",
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"from_schema": "https://example.com/monkeypox",
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"permissible_values": {
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},
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"OVP (orf 17L)": {
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"text": "OVP (orf 17L)",
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"meaning": "GENEPIO:0100506"
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}
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}
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},
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"gene name 3 menu": {
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"name": "gene name 3 menu",
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"from_schema": "https://example.com/monkeypox",
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"permissible_values": {
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},
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"OPHA (orf B2R)": {
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"text": "OPHA (orf B2R)",
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"meaning": "GENEPIO:0100507"
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}
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}
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},
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"gene name 4 menu": {
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"name": "gene name 4 menu",
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"from_schema": "https://example.com/monkeypox",
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"permissible_values": {
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},
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"G2R_G (TNFR)": {
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"text": "G2R_G (TNFR)",
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"meaning": "GENEPIO:0100510"
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}
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}
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},
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"gene name 5 menu": {
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"name": "gene name 5 menu",
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"from_schema": "https://example.com/monkeypox",
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"permissible_values": {
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},
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"G2R_G (WA)": {
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"text": "G2R_G (WA)"
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},
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"RNAse P gene (RNP)": {
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"text": "RNAse P gene (RNP)",
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"meaning": "GENEPIO:0100508"
@@ -9051,7 +9040,7 @@ var SCHEMA = {
90519040
],
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"any_of": [
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{
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"range": "gene name 4 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"
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],
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"any_of": [
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{
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"range": "gene name 5 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"
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"slot_group": "Pathogen diagnostic testing",
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"any_of": [
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{
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"range": "gene name 1 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"
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"slot_group": "Pathogen diagnostic testing",
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"any_of": [
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{
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"range": "gene name 2 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"
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"slot_group": "Pathogen diagnostic testing",
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"any_of": [
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{
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"range": "gene name 3 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"
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"slot_group": "Pathogen diagnostic testing",
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"any_of": [
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{
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"range": "gene name 1 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"
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"slot_group": "Pathogen diagnostic testing",
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"any_of": [
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{
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"range": "gene name 2 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"
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"slot_group": "Pathogen diagnostic testing",
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"any_of": [
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{
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"range": "gene name 3 menu"
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"range": "gene name menu"
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},
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{
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"range": "null value menu"

‎template/monkeypox/schema.yaml

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@@ -729,7 +729,7 @@ classes:
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comments: Select the name of the gene used for the diagnostic PCR from the
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standardized pick list.
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any_of:
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- range: gene name 1 menu
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- range: gene name menu
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- range: null value menu
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diagnostic pcr Ct value 1:
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rank: 105
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comments: Select the name of the gene used for the diagnostic PCR from the
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standardized pick list.
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any_of:
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- range: gene name 2 menu
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- range: gene name menu
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- range: null value menu
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diagnostic pcr Ct value 2:
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rank: 107
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comments: Select the name of the gene used for the diagnostic PCR from the
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standardized pick list.
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any_of:
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- range: gene name 3 menu
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- range: gene name menu
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- range: null value menu
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diagnostic pcr Ct value 3:
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rank: 109
@@ -2953,7 +2953,7 @@ slots:
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examples:
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- value: G2R_G (TNFR)
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any_of:
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- range: gene name 4 menu
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- range: gene name menu
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- range: null value menu
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exact_mappings:
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- CNPHI:Gene Target 4
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examples:
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- value: RNAse P
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any_of:
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- range: gene name 5 menu
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- range: gene name menu
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- range: null value menu
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exact_mappings:
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- CNPHI:Gene Target 5
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text: Buccal mucosa
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meaning: UBERON:0006956
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is_a: Head
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Cheek:
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text: Cheek
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meaning: UBERON:0001567
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is_a: Head
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Ear:
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text: Ear
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meaning: UBERON:0001690
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text: Buccal mucosa [UBERON:0006956]
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meaning: UBERON:0006956
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is_a: Head [UBERON:0000033]
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Cheek [UBERON:0001567]:
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text: Cheek [UBERON:0001567]
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meaning: UBERON:0001567
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is_a: Head [UBERON:0000033]
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Ear [UBERON:0001690]:
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text: Ear [UBERON:0001690]
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meaning: UBERON:0001690
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text: Unity Health Toronto
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William Osler Health System:
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text: William Osler Health System
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gene name 1 menu:
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name: gene name 1 menu
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gene name menu:
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name: gene name menu
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permissible_values:
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MPX (orf B6R):
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text: MPX (orf B6R)
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meaning: GENEPIO:0100505
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gene name 2 menu:
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name: gene name 2 menu
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permissible_values:
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OVP (orf 17L):
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text: OVP (orf 17L)
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meaning: GENEPIO:0100506
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gene name 3 menu:
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name: gene name 3 menu
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permissible_values:
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OPHA (orf B2R):
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text: OPHA (orf B2R)
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meaning: GENEPIO:0100507
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gene name 4 menu:
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name: gene name 4 menu
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permissible_values:
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G2R_G (TNFR):
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text: G2R_G (TNFR)
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meaning: GENEPIO:0100510
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gene name 5 menu:
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name: gene name 5 menu
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permissible_values:
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G2R_G (WA):
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text: G2R_G (WA)
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RNAse P gene (RNP):
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text: RNAse P gene (RNP)
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meaning: GENEPIO:0100508

‎template/monkeypox/schema_enums.tsv

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@@ -115,6 +115,7 @@ anatomical part menu UBERON:0001245 Anus
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FMA:24920 Hand (palm)
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UBERON:0000033 Head
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UBERON:0006956 Buccal mucosa
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UBERON:0001567 Cheek
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UBERON:0001690 Ear
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NCIT:C103848 Preauricular region
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UBERON:0000970 Eye
@@ -168,6 +169,7 @@ anatomical part international menu UBERON:0001245 Anus [UBERON:0001245]
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FMA:24920 Hand (palm) [FMA:24920]
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UBERON:0000033 Head [UBERON:0000033]
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UBERON:0006956 Buccal mucosa [UBERON:0006956]
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UBERON:0001567 Cheek [UBERON:0001567]
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UBERON:0001690 Ear [UBERON:0001690]
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NCIT:C103848 Preauricular region [NCIT:C103848]
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UBERON:0000970 Eye [UBERON:0000970]
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10061008
Unity Health Toronto
10071009
William Osler Health System
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1009-
gene name 1 menu GENEPIO:0100505 MPX (orf B6R)
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gene name menu GENEPIO:0100505 MPX (orf B6R)
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GENEPIO:0100506 OVP (orf 17L)
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GENEPIO:0100507 OPHA (orf B2R)
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GENEPIO:0100510 G2R_G (TNFR)
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G2R_G (WA)
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GENEPIO:0100508 RNAse P gene (RNP)
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1011-
gene name 2 menu GENEPIO:0100506 OVP (orf 17L)
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gene name 3 menu GENEPIO:0100507 OPHA (orf B2R)
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gene name 4 menu GENEPIO:0100510 G2R_G (TNFR)
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gene name 5 menu GENEPIO:0100508 RNAse P gene (RNP)
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10191019
geo_loc_name (country) menu GAZ:00006882 Afghanistan
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GAZ:00002953 Albania

‎template/monkeypox/schema_slots.tsv

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@@ -168,18 +168,18 @@ Monkeypox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol
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Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol
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170170
Monkeypox;Monkeypox_international GENEPIO:0001506 Pathogen diagnostic testing
171-
Monkeypox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene name 1 menu null value menu 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. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name
171+
Monkeypox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene name menu null value menu 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. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name
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Monkeypox_international Pathogen diagnostic testing GENEPIO:0001507 gene name 1 WhitespaceMinimizedString null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name
173173
Monkeypox;Monkeypox_international Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value
174-
Monkeypox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene name 2 menu null value menu 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. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2
174+
Monkeypox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene name menu null value menu 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. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2
175175
Monkeypox_international Pathogen diagnostic testing GENEPIO:0001510 gene name 2 WhitespaceMinimizedString null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2
176176
Monkeypox;Monkeypox_international Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 decimal null value menu 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. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2
177-
Monkeypox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene name 3 menu null value menu 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. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3
177+
Monkeypox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene name menu null value menu 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. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3
178178
Monkeypox_international Pathogen diagnostic testing GENEPIO:0001513 gene name 3 WhitespaceMinimizedString null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3
179179
Monkeypox;Monkeypox_international Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 decimal null value menu 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. 19 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value diagnostic_PCR_CT_value_3
180-
Monkeypox Pathogen diagnostic testing gene name 4 gene name 4 menu null value menu 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. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4
180+
Monkeypox Pathogen diagnostic testing gene name 4 gene name menu null value menu 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. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4
181181
Monkeypox Pathogen diagnostic testing diagnostic pcr Ct value 4 decimal null value menu 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
182-
Monkeypox Pathogen diagnostic testing gene name 5 gene name 5 menu null value menu 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
182+
Monkeypox Pathogen diagnostic testing gene name 5 gene name menu null value menu 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
183183
Monkeypox Pathogen diagnostic testing diagnostic pcr Ct value 5 decimal null value menu 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
184184

185185
GENEPIO:0001516 Contributor acknowledgement

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