diff --git a/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx b/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-2-1_July212022.xlsx similarity index 83% rename from template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx rename to template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-2-1_July212022.xlsx index c7a6fbc3..350cb7fd 100644 Binary files a/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx and b/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-2-1_July212022.xlsx differ diff --git a/template/monkeypox/exampleInput/README.md b/template/monkeypox/exampleInput/README.md index 045697ff..9b2f256d 100644 --- a/template/monkeypox/exampleInput/README.md +++ b/template/monkeypox/exampleInput/README.md @@ -1,7 +1,7 @@ # Monkeypox Example Input Data 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: -- `DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx` is _valid_ for version `1-3-3` of the DataHarmonizer. +- `DH_Canadian_MPX_validTestDataset_2-2-1_July212022.xlsx` is _valid_ for version `1-3-4` of the DataHarmonizer. ## Valid Test Data diff --git a/template/monkeypox/schema.js b/template/monkeypox/schema.js index 07c2901e..d06648e7 100644 --- a/template/monkeypox/schema.js +++ b/template/monkeypox/schema.js @@ -78,7 +78,7 @@ var SCHEMA = { "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time" ], "base": "XSDTime", "uri": "xsd:dateTime", @@ -645,6 +645,11 @@ var SCHEMA = { "meaning": "UBERON:0006956", "is_a": "Head" }, + "Cheek": { + "text": "Cheek", + "meaning": "UBERON:0001567", + "is_a": "Head" + }, "Ear": { "text": "Ear", "meaning": "UBERON:0001690", @@ -877,6 +882,11 @@ var SCHEMA = { "meaning": "UBERON:0006956", "is_a": "Head [UBERON:0000033]" }, + "Cheek [UBERON:0001567]": { + "text": "Cheek [UBERON:0001567]", + "meaning": "UBERON:0001567", + "is_a": "Head [UBERON:0000033]" + }, "Ear [UBERON:0001690]": { "text": "Ear [UBERON:0001690]", "meaning": "UBERON:0001690", @@ -4625,50 +4635,29 @@ var SCHEMA = { } } }, - "gene name 1 menu": { - "name": "gene name 1 menu", + "gene name menu": { + "name": "gene name menu", "from_schema": "https://example.com/monkeypox", "permissible_values": { "MPX (orf B6R)": { "text": "MPX (orf B6R)", "meaning": "GENEPIO:0100505" - } - } - }, - "gene name 2 menu": { - "name": "gene name 2 menu", - "from_schema": "https://example.com/monkeypox", - "permissible_values": { + }, "OVP (orf 17L)": { "text": "OVP (orf 17L)", "meaning": "GENEPIO:0100506" - } - } - }, - "gene name 3 menu": { - "name": "gene name 3 menu", - "from_schema": "https://example.com/monkeypox", - "permissible_values": { + }, "OPHA (orf B2R)": { "text": "OPHA (orf B2R)", "meaning": "GENEPIO:0100507" - } - } - }, - "gene name 4 menu": { - "name": "gene name 4 menu", - "from_schema": "https://example.com/monkeypox", - "permissible_values": { + }, "G2R_G (TNFR)": { "text": "G2R_G (TNFR)", "meaning": "GENEPIO:0100510" - } - } - }, - "gene name 5 menu": { - "name": "gene name 5 menu", - "from_schema": "https://example.com/monkeypox", - "permissible_values": { + }, + "G2R_G (WA)": { + "text": "G2R_G (WA)" + }, "RNAse P gene (RNP)": { "text": "RNAse P gene (RNP)", "meaning": "GENEPIO:0100508" @@ -9051,7 +9040,7 @@ var SCHEMA = { ], "any_of": [ { - "range": "gene name 4 menu" + "range": "gene name menu" }, { "range": "null value menu" @@ -9105,7 +9094,7 @@ var SCHEMA = { ], "any_of": [ { - "range": "gene name 5 menu" + "range": "gene name menu" }, { "range": "null value menu" @@ -10309,7 +10298,7 @@ var SCHEMA = { "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name 1 menu" + "range": "gene name menu" }, { "range": "null value menu" @@ -10330,7 +10319,7 @@ var SCHEMA = { "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name 2 menu" + "range": "gene name menu" }, { "range": "null value menu" @@ -10351,7 +10340,7 @@ var SCHEMA = { "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name 3 menu" + "range": "gene name menu" }, { "range": "null value menu" @@ -12250,7 +12239,7 @@ var SCHEMA = { "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name 1 menu" + "range": "gene name menu" }, { "range": "null value menu" @@ -12283,7 +12272,7 @@ var SCHEMA = { "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name 2 menu" + "range": "gene name menu" }, { "range": "null value menu" @@ -12316,7 +12305,7 @@ var SCHEMA = { "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name 3 menu" + "range": "gene name menu" }, { "range": "null value menu" diff --git a/template/monkeypox/schema.yaml b/template/monkeypox/schema.yaml index fe851669..81199a28 100644 --- a/template/monkeypox/schema.yaml +++ b/template/monkeypox/schema.yaml @@ -729,7 +729,7 @@ classes: comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. any_of: - - range: gene name 1 menu + - range: gene name menu - range: null value menu diagnostic pcr Ct value 1: rank: 105 @@ -740,7 +740,7 @@ classes: comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. any_of: - - range: gene name 2 menu + - range: gene name menu - range: null value menu diagnostic pcr Ct value 2: rank: 107 @@ -751,7 +751,7 @@ classes: comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. any_of: - - range: gene name 3 menu + - range: gene name menu - range: null value menu diagnostic pcr Ct value 3: rank: 109 @@ -2953,7 +2953,7 @@ slots: examples: - value: G2R_G (TNFR) any_of: - - range: gene name 4 menu + - range: gene name menu - range: null value menu exact_mappings: - CNPHI:Gene Target 4 @@ -2983,7 +2983,7 @@ slots: examples: - value: RNAse P any_of: - - range: gene name 5 menu + - range: gene name menu - range: null value menu exact_mappings: - CNPHI:Gene Target 5 @@ -3407,6 +3407,10 @@ enums: text: Buccal mucosa meaning: UBERON:0006956 is_a: Head + Cheek: + text: Cheek + meaning: UBERON:0001567 + is_a: Head Ear: text: Ear meaning: UBERON:0001690 @@ -3587,6 +3591,10 @@ enums: text: Buccal mucosa [UBERON:0006956] meaning: UBERON:0006956 is_a: Head [UBERON:0000033] + Cheek [UBERON:0001567]: + text: Cheek [UBERON:0001567] + meaning: UBERON:0001567 + is_a: Head [UBERON:0000033] Ear [UBERON:0001690]: text: Ear [UBERON:0001690] meaning: UBERON:0001690 @@ -6417,33 +6425,23 @@ enums: text: Unity Health Toronto William Osler Health System: text: William Osler Health System - gene name 1 menu: - name: gene name 1 menu + gene name menu: + name: gene name menu permissible_values: MPX (orf B6R): text: MPX (orf B6R) meaning: GENEPIO:0100505 - gene name 2 menu: - name: gene name 2 menu - permissible_values: OVP (orf 17L): text: OVP (orf 17L) meaning: GENEPIO:0100506 - gene name 3 menu: - name: gene name 3 menu - permissible_values: OPHA (orf B2R): text: OPHA (orf B2R) meaning: GENEPIO:0100507 - gene name 4 menu: - name: gene name 4 menu - permissible_values: G2R_G (TNFR): text: G2R_G (TNFR) meaning: GENEPIO:0100510 - gene name 5 menu: - name: gene name 5 menu - permissible_values: + G2R_G (WA): + text: G2R_G (WA) RNAse P gene (RNP): text: RNAse P gene (RNP) meaning: GENEPIO:0100508 diff --git a/template/monkeypox/schema_enums.tsv b/template/monkeypox/schema_enums.tsv index 608a1c35..88e14627 100644 --- a/template/monkeypox/schema_enums.tsv +++ b/template/monkeypox/schema_enums.tsv @@ -115,6 +115,7 @@ anatomical part menu UBERON:0001245 Anus FMA:24920 Hand (palm) UBERON:0000033 Head UBERON:0006956 Buccal mucosa + UBERON:0001567 Cheek UBERON:0001690 Ear NCIT:C103848 Preauricular region UBERON:0000970 Eye @@ -168,6 +169,7 @@ anatomical part international menu UBERON:0001245 Anus [UBERON:0001245] FMA:24920 Hand (palm) [FMA:24920] UBERON:0000033 Head [UBERON:0000033] UBERON:0006956 Buccal mucosa [UBERON:0006956] + UBERON:0001567 Cheek [UBERON:0001567] UBERON:0001690 Ear [UBERON:0001690] NCIT:C103848 Preauricular region [NCIT:C103848] UBERON:0000970 Eye [UBERON:0000970] @@ -1006,15 +1008,13 @@ sequenced by menu Alberta Precision Labs (APL) Unity Health Toronto William Osler Health System -gene name 1 menu GENEPIO:0100505 MPX (orf B6R) +gene name menu GENEPIO:0100505 MPX (orf B6R) + GENEPIO:0100506 OVP (orf 17L) + GENEPIO:0100507 OPHA (orf B2R) + GENEPIO:0100510 G2R_G (TNFR) + G2R_G (WA) + GENEPIO:0100508 RNAse P gene (RNP) -gene name 2 menu GENEPIO:0100506 OVP (orf 17L) - -gene name 3 menu GENEPIO:0100507 OPHA (orf B2R) - -gene name 4 menu GENEPIO:0100510 G2R_G (TNFR) - -gene name 5 menu GENEPIO:0100508 RNAse P gene (RNP) geo_loc_name (country) menu GAZ:00006882 Afghanistan GAZ:00002953 Albania diff --git a/template/monkeypox/schema_slots.tsv b/template/monkeypox/schema_slots.tsv index 2d6bcb19..d77c5b2c 100644 --- a/template/monkeypox/schema_slots.tsv +++ b/template/monkeypox/schema_slots.tsv @@ -168,18 +168,18 @@ Monkeypox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol 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 Monkeypox;Monkeypox_international GENEPIO:0001506 Pathogen diagnostic testing -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 +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 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 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 -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 +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 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 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 -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 +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 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 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 -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 +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 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 -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 +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 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 GENEPIO:0001516 Contributor acknowledgement