From 6052953648f7a75f1e9f646556f3710af06a09f1 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 13 Jul 2022 15:03:04 -0700 Subject: [PATCH 1/7] Adding Glans --- script/data-harmonizer/index.js | 2 +- template/monkeypox/schema.js | 12 +++++++++++- template/monkeypox/schema.yaml | 12 +++++++++++- template/monkeypox/schema_core.yaml | 2 +- template/monkeypox/schema_enums.tsv | 2 ++ 5 files changed, 26 insertions(+), 4 deletions(-) diff --git a/script/data-harmonizer/index.js b/script/data-harmonizer/index.js index 329b6686..14000b31 100644 --- a/script/data-harmonizer/index.js +++ b/script/data-harmonizer/index.js @@ -22,7 +22,7 @@ * */ -const VERSION = '1.3.1'; +const VERSION = '1.3.2'; const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION; diff --git a/template/monkeypox/schema.js b/template/monkeypox/schema.js index 24563a83..4030d773 100644 --- a/template/monkeypox/schema.js +++ b/template/monkeypox/schema.js @@ -2,7 +2,7 @@ var SCHEMA = { "name": "Monkeypox", "description": "", "id": "https://example.com/monkeypox", - "version": "1.0.0", + "version": "1.1.0", "prefixes": { "linkml": { "prefix_prefix": "linkml", @@ -593,6 +593,11 @@ var SCHEMA = { "meaning": "UBERON:0000989", "is_a": "Genital area" }, + "Glans (tip of penis)": { + "text": "Glans (tip of penis)", + "meaning": "UBERON:0035651", + "is_a": "Penis" + }, "Prepuce of penis (foreskin)": { "text": "Prepuce of penis (foreskin)", "meaning": "UBERON:0001332", @@ -820,6 +825,11 @@ var SCHEMA = { "meaning": "UBERON:0000989", "is_a": "Genital area [BTO:0003358]" }, + "Glans (tip of penis) [UBERON:0035651]": { + "text": "Glans (tip of penis) [UBERON:0035651]", + "meaning": "UBERON:0035651", + "is_a": "Penis [UBERON:0000989]" + }, "Prepuce of penis (foreskin)": { "text": "Prepuce of penis (foreskin)", "meaning": "UBERON:0001332", diff --git a/template/monkeypox/schema.yaml b/template/monkeypox/schema.yaml index 98e02609..3c034c39 100644 --- a/template/monkeypox/schema.yaml +++ b/template/monkeypox/schema.yaml @@ -1,6 +1,6 @@ id: https://example.com/monkeypox name: Monkeypox -version: 1.0.0 +version: 1.1.0 description: '' imports: - linkml:types @@ -18,6 +18,7 @@ classes: gathering is_a: dh_interface see_also: template/monkeypox/SOP_Monkeypox.pdf + version: 1.1.0 slots: - specimen collector sample ID - Related specimen primary ID @@ -404,6 +405,7 @@ classes: data gathering is_a: dh_interface see_also: template/monkeypox/SOP_Monkeypox_international.pdf + version: 1.1.0 slots: - specimen collector sample ID - bioproject accession @@ -2398,6 +2400,10 @@ enums: text: Penis meaning: UBERON:0000989 is_a: Genital area + Glans (tip of penis): + text: Glans (tip of penis) + meaning: UBERON:0035651 + is_a: Penis Prepuce of penis (foreskin): text: Prepuce of penis (foreskin) meaning: UBERON:0001332 @@ -2574,6 +2580,10 @@ enums: text: Penis [UBERON:0000989] meaning: UBERON:0000989 is_a: Genital area [BTO:0003358] + Glans (tip of penis) [UBERON:0035651]: + text: Glans (tip of penis) [UBERON:0035651] + meaning: UBERON:0035651 + is_a: Penis [UBERON:0000989] Prepuce of penis (foreskin): text: Prepuce of penis (foreskin) meaning: UBERON:0001332 diff --git a/template/monkeypox/schema_core.yaml b/template/monkeypox/schema_core.yaml index 752b5edd..46017e0d 100644 --- a/template/monkeypox/schema_core.yaml +++ b/template/monkeypox/schema_core.yaml @@ -1,6 +1,6 @@ id: https://example.com/monkeypox name: Monkeypox -version: 1.0.0 +version: 1.1.0 description: "" imports: - "linkml:types" diff --git a/template/monkeypox/schema_enums.tsv b/template/monkeypox/schema_enums.tsv index 90fdd22e..b5a863e1 100644 --- a/template/monkeypox/schema_enums.tsv +++ b/template/monkeypox/schema_enums.tsv @@ -104,6 +104,7 @@ anatomical part menu UBERON:0001245 Anus BTO:0000476 Foot BTO:0003358 Genital area UBERON:0000989 Penis + UBERON:0035651 Glans (tip of penis) UBERON:0001332 Prepuce of penis (foreskin) UBERON:0002356 Perineum UBERON:0001300 Scrotum @@ -156,6 +157,7 @@ anatomical part international menu UBERON:0001245 Anus [UBERON:0001245] BTO:0000476 Foot [BTO:0000476] BTO:0003358 Genital area [BTO:0003358] UBERON:0000989 Penis [UBERON:0000989] + UBERON:0035651 Glans (tip of penis) [UBERON:0035651] UBERON:0001332 Prepuce of penis (foreskin) UBERON:0002356 Perineum [UBERON:0002356] UBERON:0001300 Scrotum [UBERON:0001300] From b8764e8ee7972be5d3c40c74fa09075e83d0f9ea Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 13 Jul 2022 15:10:02 -0700 Subject: [PATCH 2/7] NLM LIMS export field reorganization --- template/monkeypox/export.js | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/template/monkeypox/export.js b/template/monkeypox/export.js index 55e38636..850e6be6 100644 --- a/template/monkeypox/export.js +++ b/template/monkeypox/export.js @@ -244,10 +244,7 @@ var EXPORT_FORMATS = { //['PH_ID_NUMBER_PRIMARY', []], //['PH_CASE_ID', []], ['PH_RELATED_PRIMARY_ID', []], - //['PH_BIOPROJECT_ACCESSION', []], - //['PH_BIOSAMPLE_ACCESSION', []], - //['PH_SRA_ACCESSION', []], - ['SUBMISSIONS - GISAID Accession ID', []], + ['CUSTOMER', []], ['PH_SEQUENCING_CENTRE', []], @@ -261,6 +258,15 @@ var EXPORT_FORMATS = { ['HC_PROVINCE', []], ['HC_CURRENT_ID', []], + + ['SUBMISSIONS - BioProject Accession', []], + ['SUBMISSIONS - BioSample Accession', []], + ['SUBMISSIONS - SRA Accession', []], + ['SUBMISSIONS - GenBank Accession', []], + ['SUBMISSIONS - GISAID Virus Name', []], + ['SUBMISSIONS - GISAID Accession', []], + + ['RESULT - CANCOGEN_SUBMISSIONS', []], ['HC_SAMPLE_CATEGORY', []], ['PH_SAMPLING_DETAILS', []], @@ -356,6 +362,7 @@ var EXPORT_FORMATS = { ]); + const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); From 72b80d57918a142746bb4641b3406528934db92c Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 13 Jul 2022 15:36:03 -0700 Subject: [PATCH 3/7] version blip --- template/monkeypox/schema.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/template/monkeypox/schema.yaml b/template/monkeypox/schema.yaml index 3c034c39..86ac5d81 100644 --- a/template/monkeypox/schema.yaml +++ b/template/monkeypox/schema.yaml @@ -18,7 +18,6 @@ classes: gathering is_a: dh_interface see_also: template/monkeypox/SOP_Monkeypox.pdf - version: 1.1.0 slots: - specimen collector sample ID - Related specimen primary ID @@ -405,7 +404,6 @@ classes: data gathering is_a: dh_interface see_also: template/monkeypox/SOP_Monkeypox_international.pdf - version: 1.1.0 slots: - specimen collector sample ID - bioproject accession From da37c9c221fdce58d62db410f3d95b63182c62a1 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 13 Jul 2022 15:38:02 -0700 Subject: [PATCH 4/7] vocab tweak --- template/monkeypox/schema.js | 708 ++++++++++++++++++---------- template/monkeypox/schema.yaml | 323 ++++++++----- template/monkeypox/schema_slots.tsv | 10 +- 3 files changed, 645 insertions(+), 396 deletions(-) diff --git a/template/monkeypox/schema.js b/template/monkeypox/schema.js index 4030d773..353b9158 100644 --- a/template/monkeypox/schema.js +++ b/template/monkeypox/schema.js @@ -5602,6 +5602,9 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS - BioProject Accession" + ], "slot_uri": "GENEPIO:0001136", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -5623,6 +5626,9 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS - BioSample Accession" + ], "slot_uri": "GENEPIO:0001139", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -5631,6 +5637,54 @@ var SCHEMA = { "partial_match": false } }, + "SRA accession": { + "name": "SRA accession", + "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "title": "SRA accession", + "comments": [ + "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR." + ], + "examples": [ + { + "value": "SRR11177792" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS - SRA Accession" + ], + "slot_uri": "GENEPIO:0001142", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "GenBank accession": { + "name": "GenBank accession", + "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", + "title": "GenBank accession", + "comments": [ + "Store the accession returned from a GenBank submission (viral genome assembly)." + ], + "examples": [ + { + "value": "MN908947.3" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS - GenBank Accession" + ], + "slot_uri": "GENEPIO:0001145", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, "GISAID virus name": { "name": "GISAID virus name", "description": "Identifier of the specific isolate.", @@ -5666,7 +5720,7 @@ var SCHEMA = { "from_schema": "https://example.com/monkeypox", "exact_mappings": [ "CNPHI:GISAID Accession (if known)", - "NML_LIMS:SUBMISSIONS - GISAID Accession ID", + "NML_LIMS:SUBMISSIONS - GISAID Accession", "BIOSAMPLE:GISAID_accession", "VirusSeq_Portal:GISAID accession" ], @@ -7422,9 +7476,29 @@ var SCHEMA = { "rank": 2, "slot_group": "Database Identifiers" }, + "bioproject accession": { + "name": "bioproject accession", + "rank": 3, + "slot_group": "Database Identifiers" + }, + "biosample accession": { + "name": "biosample accession", + "rank": 4, + "slot_group": "Database Identifiers" + }, + "SRA accession": { + "name": "SRA accession", + "rank": 5, + "slot_group": "Database Identifiers" + }, + "GenBank accession": { + "name": "GenBank accession", + "rank": 6, + "slot_group": "Database Identifiers" + }, "GISAID accession": { "name": "GISAID accession", - "rank": 3, + "rank": 7, "slot_group": "Database Identifiers" }, "sample collected by": { @@ -7436,7 +7510,7 @@ var SCHEMA = { "BIOSAMPLE:collected_by", "VirusSeq_Portal:sample collected by" ], - "rank": 4, + "rank": 8, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7449,12 +7523,12 @@ var SCHEMA = { }, "sample collector contact email": { "name": "sample collector contact email", - "rank": 5, + "rank": 9, "slot_group": "Sample collection and processing" }, "sample collector contact address": { "name": "sample collector contact address", - "rank": 6, + "rank": 10, "slot_group": "Sample collection and processing" }, "sequenced by": { @@ -7463,7 +7537,7 @@ var SCHEMA = { "NML_LIMS:PH_SEQUENCING_CENTRE", "BIOSAMPLE:sequenced_by" ], - "rank": 7, + "rank": 11, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7476,12 +7550,12 @@ var SCHEMA = { }, "sequenced by contact email": { "name": "sequenced by contact email", - "rank": 8, + "rank": 12, "slot_group": "Sample collection and processing" }, "sequenced by contact address": { "name": "sequenced by contact address", - "rank": 9, + "rank": 13, "slot_group": "Sample collection and processing" }, "sequence submitted by": { @@ -7493,7 +7567,7 @@ var SCHEMA = { "BIOSAMPLE:sequence_submitted_by", "VirusSeq_Portal:sequence submitted by" ], - "rank": 10, + "rank": 14, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7506,27 +7580,27 @@ var SCHEMA = { }, "sequence submitter contact email": { "name": "sequence submitter contact email", - "rank": 11, + "rank": 15, "slot_group": "Sample collection and processing" }, "sequence submitter contact address": { "name": "sequence submitter contact address", - "rank": 12, + "rank": 16, "slot_group": "Sample collection and processing" }, "sample collection date": { "name": "sample collection date", - "rank": 13, + "rank": 17, "slot_group": "Sample collection and processing" }, "sample collection date precision": { "name": "sample collection date precision", - "rank": 14, + "rank": 18, "slot_group": "Sample collection and processing" }, "sample received date": { "name": "sample received date", - "rank": 15, + "rank": 19, "slot_group": "Sample collection and processing" }, "geo_loc_name (country)": { @@ -7536,7 +7610,7 @@ var SCHEMA = { "value": "Canada" } ], - "rank": 16, + "rank": 20, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7552,7 +7626,7 @@ var SCHEMA = { "comments": [ "Provide the province/territory name from the controlled vocabulary provided." ], - "rank": 17, + "rank": 21, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7570,7 +7644,7 @@ var SCHEMA = { "value": "Monkeypox virus" } ], - "rank": 18, + "rank": 22, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7594,13 +7668,13 @@ var SCHEMA = { "exact_mappings": [ "GISAID:Virus name", "CNPHI:GISAID Virus Name", - "NML_LIMS:RESULT - CANCOGEN_SUBMISSIONS", + "NML_LIMS:SUBMISSIONS - GISAID Virus Name", "BIOSAMPLE:isolate", "BIOSAMPLE:GISAID_virus_name", "VirusSeq_Portal:isolate", "VirusSeq_Portal:fasta header name" ], - "rank": 19, + "rank": 23, "slot_uri": "GENEPIO:0001195", "slot_group": "Sample collection and processing" }, @@ -7611,7 +7685,7 @@ var SCHEMA = { "value": "Diagnostic testing" } ], - "rank": 20, + "rank": 24, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7624,17 +7698,17 @@ var SCHEMA = { }, "purpose of sampling details": { "name": "purpose of sampling details", - "rank": 21, + "rank": 25, "slot_group": "Sample collection and processing" }, "NML submitted specimen type": { "name": "NML submitted specimen type", - "rank": 22, + "rank": 26, "slot_group": "Sample collection and processing" }, "Related specimen relationship type": { "name": "Related specimen relationship type", - "rank": 23, + "rank": 27, "slot_group": "Sample collection and processing" }, "anatomical material": { @@ -7644,7 +7718,7 @@ var SCHEMA = { "value": "Lesion (Pustule)" } ], - "rank": 24, + "rank": 28, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7663,7 +7737,7 @@ var SCHEMA = { "value": "Genital area" } ], - "rank": 25, + "rank": 29, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7682,7 +7756,7 @@ var SCHEMA = { "value": "Pus" } ], - "rank": 26, + "rank": 30, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7701,7 +7775,7 @@ var SCHEMA = { "value": "Swab" } ], - "rank": 27, + "rank": 31, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7720,7 +7794,7 @@ var SCHEMA = { "value": "Biopsy" } ], - "rank": 28, + "rank": 32, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7739,7 +7813,7 @@ var SCHEMA = { "value": "Homo sapiens" } ], - "rank": 29, + "rank": 33, "slot_group": "Host Information", "any_of": [ { @@ -7757,7 +7831,7 @@ var SCHEMA = { "value": "Monkeypox" } ], - "rank": 30, + "rank": 34, "slot_group": "Host Information", "any_of": [ { @@ -7770,7 +7844,7 @@ var SCHEMA = { }, "travel history": { "name": "travel history", - "rank": 31, + "rank": 35, "slot_group": "Host exposure information" }, "purpose of sequencing": { @@ -7808,7 +7882,7 @@ var SCHEMA = { "description": "In all other cases use" } ], - "rank": 32, + "rank": 36, "slot_group": "Sequencing", "any_of": [ { @@ -7821,18 +7895,18 @@ var SCHEMA = { }, "purpose of sequencing details": { "name": "purpose of sequencing details", - "rank": 33, + "rank": 37, "slot_group": "Sequencing" }, "sequencing date": { "name": "sequencing date", - "rank": 34, + "rank": 38, "slot_group": "Sequencing", "required": true }, "library preparation kit": { "name": "library preparation kit", - "rank": 35, + "rank": 39, "slot_group": "Sequencing" }, "sequencing instrument": { @@ -7842,7 +7916,7 @@ var SCHEMA = { "value": "Oxford Nanopore MinION" } ], - "rank": 36, + "rank": 40, "slot_group": "Sequencing", "any_of": [ { @@ -7855,54 +7929,54 @@ var SCHEMA = { }, "raw sequence data processing method": { "name": "raw sequence data processing method", - "rank": 37, + "rank": 41, "slot_group": "Bioinformatics and QC metrics", "required": true }, "dehosting method": { "name": "dehosting method", - "rank": 38, + "rank": 42, "slot_group": "Bioinformatics and QC metrics", "required": true }, "consensus sequence software name": { "name": "consensus sequence software name", - "rank": 39, + "rank": 43, "slot_group": "Bioinformatics and QC metrics" }, "consensus sequence software version": { "name": "consensus sequence software version", - "rank": 40, + "rank": 44, "slot_group": "Bioinformatics and QC metrics" }, "breadth of coverage value": { "name": "breadth of coverage value", - "rank": 41, + "rank": 45, "slot_group": "Bioinformatics and QC metrics" }, "depth of coverage value": { "name": "depth of coverage value", - "rank": 42, + "rank": 46, "slot_group": "Bioinformatics and QC metrics" }, "depth of coverage threshold": { "name": "depth of coverage threshold", - "rank": 43, + "rank": 47, "slot_group": "Bioinformatics and QC metrics" }, "number of base pairs sequenced": { "name": "number of base pairs sequenced", - "rank": 44, + "rank": 48, "slot_group": "Bioinformatics and QC metrics" }, "consensus genome length": { "name": "consensus genome length", - "rank": 45, + "rank": 49, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics protocol": { "name": "bioinformatics protocol", - "rank": 46, + "rank": 50, "slot_group": "Bioinformatics and QC metrics", "required": true }, @@ -7911,7 +7985,7 @@ var SCHEMA = { "comments": [ "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], - "rank": 47, + "rank": 51, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -7924,7 +7998,7 @@ var SCHEMA = { }, "diagnostic pcr Ct value 1": { "name": "diagnostic pcr Ct value 1", - "rank": 48, + "rank": 52, "slot_group": "Pathogen diagnostic testing" }, "gene name 2": { @@ -7932,7 +8006,7 @@ var SCHEMA = { "comments": [ "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], - "rank": 49, + "rank": 53, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -7945,7 +8019,7 @@ var SCHEMA = { }, "diagnostic pcr Ct value 2": { "name": "diagnostic pcr Ct value 2", - "rank": 50, + "rank": 54, "slot_group": "Pathogen diagnostic testing" }, "gene name 3": { @@ -7953,7 +8027,7 @@ var SCHEMA = { "comments": [ "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], - "rank": 51, + "rank": 55, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -7966,37 +8040,37 @@ var SCHEMA = { }, "diagnostic pcr Ct value 3": { "name": "diagnostic pcr Ct value 3", - "rank": 52, + "rank": 56, "slot_group": "Pathogen diagnostic testing" }, "gene name 4": { "name": "gene name 4", - "rank": 53, + "rank": 57, "slot_group": "Pathogen diagnostic testing" }, "diagnostic pcr Ct value 4": { "name": "diagnostic pcr Ct value 4", - "rank": 54, + "rank": 58, "slot_group": "Pathogen diagnostic testing" }, "gene name 5": { "name": "gene name 5", - "rank": 55, + "rank": 59, "slot_group": "Pathogen diagnostic testing" }, "diagnostic pcr Ct value 5": { "name": "diagnostic pcr Ct value 5", - "rank": 56, + "rank": 60, "slot_group": "Pathogen diagnostic testing" }, "authors": { "name": "authors", - "rank": 57, + "rank": 61, "slot_group": "Contributor acknowledgement" }, "DataHarmonizer provenance": { "name": "DataHarmonizer provenance", - "rank": 58, + "rank": 62, "slot_group": "Contributor acknowledgement" } }, @@ -8026,12 +8100,80 @@ var SCHEMA = { "owner": "Monkeypox", "slot_group": "Database Identifiers" }, + "bioproject accession": { + "name": "bioproject accession", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "title": "bioproject accession", + "from_schema": "https://example.com/monkeypox", + "rank": 3, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "Monkeypox", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample accession": { + "name": "biosample accession", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "title": "biosample accession", + "from_schema": "https://example.com/monkeypox", + "rank": 4, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "Monkeypox", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "SRA accession": { + "name": "SRA accession", + "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "title": "SRA accession", + "from_schema": "https://example.com/monkeypox", + "rank": 5, + "slot_uri": "GENEPIO:0001142", + "alias": "SRA_accession", + "owner": "Monkeypox", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "GenBank accession": { + "name": "GenBank accession", + "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", + "title": "GenBank accession", + "from_schema": "https://example.com/monkeypox", + "rank": 6, + "slot_uri": "GENEPIO:0001145", + "alias": "GenBank_accession", + "owner": "Monkeypox", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, "GISAID accession": { "name": "GISAID accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", "from_schema": "https://example.com/monkeypox", - "rank": 3, + "rank": 7, "slot_uri": "GENEPIO:0001147", "alias": "GISAID_accession", "owner": "Monkeypox", @@ -8055,7 +8197,7 @@ var SCHEMA = { "BIOSAMPLE:collected_by", "VirusSeq_Portal:sample collected by" ], - "rank": 4, + "rank": 8, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", "owner": "Monkeypox", @@ -8075,7 +8217,7 @@ var SCHEMA = { "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "from_schema": "https://example.com/monkeypox", - "rank": 5, + "rank": 9, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", "owner": "Monkeypox", @@ -8088,7 +8230,7 @@ var SCHEMA = { "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", "from_schema": "https://example.com/monkeypox", - "rank": 6, + "rank": 10, "slot_uri": "GENEPIO:0001158", "alias": "sample_collector_contact_address", "owner": "Monkeypox", @@ -8104,7 +8246,7 @@ var SCHEMA = { "NML_LIMS:PH_SEQUENCING_CENTRE", "BIOSAMPLE:sequenced_by" ], - "rank": 7, + "rank": 11, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "Monkeypox", @@ -8124,7 +8266,7 @@ var SCHEMA = { "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact email", "from_schema": "https://example.com/monkeypox", - "rank": 8, + "rank": 12, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "Monkeypox", @@ -8136,7 +8278,7 @@ var SCHEMA = { "description": "The mailing address of the agency submitting the sequence.", "title": "sequenced by contact address", "from_schema": "https://example.com/monkeypox", - "rank": 9, + "rank": 13, "slot_uri": "GENEPIO:0100423", "alias": "sequenced_by_contact_address", "owner": "Monkeypox", @@ -8155,7 +8297,7 @@ var SCHEMA = { "BIOSAMPLE:sequence_submitted_by", "VirusSeq_Portal:sequence submitted by" ], - "rank": 10, + "rank": 14, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "Monkeypox", @@ -8175,7 +8317,7 @@ var SCHEMA = { "description": "The email address of the agency responsible for submission of the sequence.", "title": "sequence submitter contact email", "from_schema": "https://example.com/monkeypox", - "rank": 11, + "rank": 15, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "Monkeypox", @@ -8187,7 +8329,7 @@ var SCHEMA = { "description": "The mailing address of the agency responsible for submission of the sequence.", "title": "sequence submitter contact address", "from_schema": "https://example.com/monkeypox", - "rank": 12, + "rank": 16, "slot_uri": "GENEPIO:0001167", "alias": "sequence_submitter_contact_address", "owner": "Monkeypox", @@ -8199,7 +8341,7 @@ var SCHEMA = { "description": "The date on which the sample was collected.", "title": "sample collection date", "from_schema": "https://example.com/monkeypox", - "rank": 13, + "rank": 17, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", "owner": "Monkeypox", @@ -8211,7 +8353,7 @@ var SCHEMA = { "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", "from_schema": "https://example.com/monkeypox", - "rank": 14, + "rank": 18, "slot_uri": "GENEPIO:0001177", "alias": "sample_collection_date_precision", "owner": "Monkeypox", @@ -8223,7 +8365,7 @@ var SCHEMA = { "description": "The date on which the sample was received.", "title": "sample received date", "from_schema": "https://example.com/monkeypox", - "rank": 15, + "rank": 19, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "Monkeypox", @@ -8239,7 +8381,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 16, + "rank": 20, "slot_uri": "GENEPIO:0001181", "alias": "geo_loc_name_(country)", "owner": "Monkeypox", @@ -8262,7 +8404,7 @@ var SCHEMA = { "Provide the province/territory name from the controlled vocabulary provided." ], "from_schema": "https://example.com/monkeypox", - "rank": 17, + "rank": 21, "slot_uri": "GENEPIO:0001185", "alias": "geo_loc_name_(state/province/territory)", "owner": "Monkeypox", @@ -8287,7 +8429,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 18, + "rank": 22, "slot_uri": "GENEPIO:0001191", "alias": "organism", "owner": "Monkeypox", @@ -8318,13 +8460,13 @@ var SCHEMA = { "exact_mappings": [ "GISAID:Virus name", "CNPHI:GISAID Virus Name", - "NML_LIMS:RESULT - CANCOGEN_SUBMISSIONS", + "NML_LIMS:SUBMISSIONS - GISAID Virus Name", "BIOSAMPLE:isolate", "BIOSAMPLE:GISAID_virus_name", "VirusSeq_Portal:isolate", "VirusSeq_Portal:fasta header name" ], - "rank": 19, + "rank": 23, "slot_uri": "GENEPIO:0001195", "alias": "isolate", "owner": "Monkeypox", @@ -8341,7 +8483,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 20, + "rank": 24, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", "owner": "Monkeypox", @@ -8361,7 +8503,7 @@ var SCHEMA = { "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", "from_schema": "https://example.com/monkeypox", - "rank": 21, + "rank": 25, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", "owner": "Monkeypox", @@ -8373,7 +8515,7 @@ var SCHEMA = { "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", "from_schema": "https://example.com/monkeypox", - "rank": 22, + "rank": 26, "slot_uri": "GENEPIO:0001204", "alias": "NML_submitted_specimen_type", "owner": "Monkeypox", @@ -8386,7 +8528,7 @@ var SCHEMA = { "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", "title": "Related specimen relationship type", "from_schema": "https://example.com/monkeypox", - "rank": 23, + "rank": 27, "slot_uri": "GENEPIO:0001209", "alias": "Related_specimen_relationship_type", "owner": "Monkeypox", @@ -8402,7 +8544,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 24, + "rank": 28, "slot_uri": "GENEPIO:0001211", "multivalued": true, "alias": "anatomical_material", @@ -8428,7 +8570,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 25, + "rank": 29, "slot_uri": "GENEPIO:0001214", "multivalued": true, "alias": "anatomical_part", @@ -8454,7 +8596,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 26, + "rank": 30, "slot_uri": "GENEPIO:0001216", "multivalued": true, "alias": "body_product", @@ -8480,7 +8622,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 27, + "rank": 31, "slot_uri": "GENEPIO:0001234", "multivalued": true, "alias": "collection_device", @@ -8506,7 +8648,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 28, + "rank": 32, "slot_uri": "GENEPIO:0001241", "multivalued": true, "alias": "collection_method", @@ -8532,7 +8674,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 29, + "rank": 33, "slot_uri": "GENEPIO:0001387", "alias": "host_(scientific_name)", "owner": "Monkeypox", @@ -8557,7 +8699,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 30, + "rank": 34, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", "owner": "Monkeypox", @@ -8577,7 +8719,7 @@ var SCHEMA = { "description": "Travel history in last six months.", "title": "travel history", "from_schema": "https://example.com/monkeypox", - "rank": 31, + "rank": 35, "slot_uri": "GENEPIO:0001416", "alias": "travel_history", "owner": "Monkeypox", @@ -8622,7 +8764,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 32, + "rank": 36, "slot_uri": "GENEPIO:0001445", "multivalued": true, "alias": "purpose_of_sequencing", @@ -8643,7 +8785,7 @@ var SCHEMA = { "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "from_schema": "https://example.com/monkeypox", - "rank": 33, + "rank": 37, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "Monkeypox", @@ -8655,7 +8797,7 @@ var SCHEMA = { "description": "The date the sample was sequenced.", "title": "sequencing date", "from_schema": "https://example.com/monkeypox", - "rank": 34, + "rank": 38, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "Monkeypox", @@ -8667,7 +8809,7 @@ var SCHEMA = { "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", "from_schema": "https://example.com/monkeypox", - "rank": 35, + "rank": 39, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "Monkeypox", @@ -8684,7 +8826,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 36, + "rank": 40, "slot_uri": "GENEPIO:0001452", "multivalued": true, "alias": "sequencing_instrument", @@ -8705,7 +8847,7 @@ var SCHEMA = { "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", "from_schema": "https://example.com/monkeypox", - "rank": 37, + "rank": 41, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "Monkeypox", @@ -8718,7 +8860,7 @@ var SCHEMA = { "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "from_schema": "https://example.com/monkeypox", - "rank": 38, + "rank": 42, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "Monkeypox", @@ -8731,7 +8873,7 @@ var SCHEMA = { "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", "from_schema": "https://example.com/monkeypox", - "rank": 39, + "rank": 43, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "Monkeypox", @@ -8744,7 +8886,7 @@ var SCHEMA = { "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", "from_schema": "https://example.com/monkeypox", - "rank": 40, + "rank": 44, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "Monkeypox", @@ -8757,7 +8899,7 @@ var SCHEMA = { "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", "from_schema": "https://example.com/monkeypox", - "rank": 41, + "rank": 45, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "Monkeypox", @@ -8769,7 +8911,7 @@ var SCHEMA = { "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", "from_schema": "https://example.com/monkeypox", - "rank": 42, + "rank": 46, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "Monkeypox", @@ -8781,7 +8923,7 @@ var SCHEMA = { "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", "from_schema": "https://example.com/monkeypox", - "rank": 43, + "rank": 47, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "Monkeypox", @@ -8793,7 +8935,7 @@ var SCHEMA = { "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", "from_schema": "https://example.com/monkeypox", - "rank": 44, + "rank": 48, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "Monkeypox", @@ -8806,7 +8948,7 @@ var SCHEMA = { "description": "Size of the reconstructed genome described as the number of base pairs.", "title": "consensus genome length", "from_schema": "https://example.com/monkeypox", - "rank": 45, + "rank": 49, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "Monkeypox", @@ -8819,7 +8961,7 @@ var SCHEMA = { "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "from_schema": "https://example.com/monkeypox", - "rank": 46, + "rank": 50, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "Monkeypox", @@ -8835,7 +8977,7 @@ var SCHEMA = { "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], "from_schema": "https://example.com/monkeypox", - "rank": 47, + "rank": 51, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", "owner": "Monkeypox", @@ -8854,7 +8996,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", "from_schema": "https://example.com/monkeypox", - "rank": 48, + "rank": 52, "slot_uri": "GENEPIO:0001509", "alias": "diagnostic_pcr_Ct_value_1", "owner": "Monkeypox", @@ -8868,7 +9010,7 @@ var SCHEMA = { "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], "from_schema": "https://example.com/monkeypox", - "rank": 49, + "rank": 53, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", "owner": "Monkeypox", @@ -8887,7 +9029,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", "from_schema": "https://example.com/monkeypox", - "rank": 50, + "rank": 54, "slot_uri": "GENEPIO:0001512", "alias": "diagnostic_pcr_Ct_value_2", "owner": "Monkeypox", @@ -8901,7 +9043,7 @@ var SCHEMA = { "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], "from_schema": "https://example.com/monkeypox", - "rank": 51, + "rank": 55, "slot_uri": "GENEPIO:0001513", "alias": "gene_name_3", "owner": "Monkeypox", @@ -8920,7 +9062,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 3", "from_schema": "https://example.com/monkeypox", - "rank": 52, + "rank": 56, "slot_uri": "GENEPIO:0001515", "alias": "diagnostic_pcr_Ct_value_3", "owner": "Monkeypox", @@ -8931,7 +9073,7 @@ var SCHEMA = { "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 4", "from_schema": "https://example.com/monkeypox", - "rank": 53, + "rank": 57, "alias": "gene_name_4", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -8941,7 +9083,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 4", "from_schema": "https://example.com/monkeypox", - "rank": 54, + "rank": 58, "alias": "diagnostic_pcr_Ct_value_4", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -8951,7 +9093,7 @@ var SCHEMA = { "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 5", "from_schema": "https://example.com/monkeypox", - "rank": 55, + "rank": 59, "alias": "gene_name_5", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -8961,7 +9103,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 5", "from_schema": "https://example.com/monkeypox", - "rank": 56, + "rank": 60, "alias": "diagnostic_pcr_Ct_value_5", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -8971,7 +9113,7 @@ var SCHEMA = { "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", "from_schema": "https://example.com/monkeypox", - "rank": 57, + "rank": 61, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "Monkeypox", @@ -8984,7 +9126,7 @@ var SCHEMA = { "description": "The DataHarmonizer software version provenance.", "title": "DataHarmonizer provenance", "from_schema": "https://example.com/monkeypox", - "rank": 58, + "rank": 62, "slot_uri": "GENEPIO:0001518", "alias": "DataHarmonizer_provenance", "owner": "Monkeypox", @@ -9017,14 +9159,24 @@ var SCHEMA = { "rank": 3, "slot_group": "Database Identifiers" }, + "SRA accession": { + "name": "SRA accession", + "rank": 4, + "slot_group": "Database Identifiers" + }, + "GenBank accession": { + "name": "GenBank accession", + "rank": 5, + "slot_group": "Database Identifiers" + }, "GISAID virus name": { "name": "GISAID virus name", - "rank": 4, + "rank": 6, "slot_group": "Database Identifiers" }, "GISAID accession": { "name": "GISAID accession", - "rank": 5, + "rank": 7, "slot_group": "Database Identifiers" }, "sample collected by": { @@ -9033,7 +9185,7 @@ var SCHEMA = { "GISAID:Originating lab", "BIOSAMPLE:collected_by" ], - "rank": 6, + "rank": 8, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9046,12 +9198,12 @@ var SCHEMA = { }, "sample collector contact email": { "name": "sample collector contact email", - "rank": 7, + "rank": 9, "slot_group": "Sample collection and processing" }, "sample collector contact address": { "name": "sample collector contact address", - "rank": 8, + "rank": 10, "slot_group": "Sample collection and processing" }, "sequenced by": { @@ -9059,7 +9211,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:sequenced_by" ], - "rank": 9, + "rank": 11, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9072,12 +9224,12 @@ var SCHEMA = { }, "sequenced by contact email": { "name": "sequenced by contact email", - "rank": 10, + "rank": 12, "slot_group": "Sample collection and processing" }, "sequenced by contact address": { "name": "sequenced by contact address", - "rank": 11, + "rank": 13, "slot_group": "Sample collection and processing" }, "sequence submitted by": { @@ -9086,7 +9238,7 @@ var SCHEMA = { "GISAID:Submitting lab", "BIOSAMPLE:sequence_submitted_by" ], - "rank": 12, + "rank": 14, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9099,22 +9251,22 @@ var SCHEMA = { }, "sequence submitter contact email": { "name": "sequence submitter contact email", - "rank": 13, + "rank": 15, "slot_group": "Sample collection and processing" }, "sequence submitter contact address": { "name": "sequence submitter contact address", - "rank": 14, + "rank": 16, "slot_group": "Sample collection and processing" }, "sample collection date": { "name": "sample collection date", - "rank": 15, + "rank": 17, "slot_group": "Sample collection and processing" }, "sample received date": { "name": "sample received date", - "rank": 16, + "rank": 18, "slot_group": "Sample collection and processing" }, "geo_loc_name (country)": { @@ -9124,7 +9276,7 @@ var SCHEMA = { "value": "United States of America [GAZ:00002459]" } ], - "rank": 17, + "rank": 19, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9140,7 +9292,7 @@ var SCHEMA = { "comments": [ "Provide the state/province/territory name from the controlled vocabulary provided." ], - "rank": 19, + "rank": 21, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9153,12 +9305,12 @@ var SCHEMA = { }, "geo_loc latitude": { "name": "geo_loc latitude", - "rank": 20, + "rank": 22, "slot_group": "Sample collection and processing" }, "geo_loc longitude": { "name": "geo_loc longitude", - "rank": 21, + "rank": 23, "slot_group": "Sample collection and processing" }, "organism": { @@ -9168,7 +9320,7 @@ var SCHEMA = { "value": "Monkeypox virus [NCBITaxon:10244]" } ], - "rank": 22, + "rank": 24, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9192,7 +9344,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:isolate" ], - "rank": 23, + "rank": 25, "slot_uri": "GENEPIO:0001644", "slot_group": "Sample collection and processing" }, @@ -9203,7 +9355,7 @@ var SCHEMA = { "value": "Diagnostic testing [GENEPIO:0100002]" } ], - "rank": 24, + "rank": 26, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9216,7 +9368,7 @@ var SCHEMA = { }, "purpose of sampling details": { "name": "purpose of sampling details", - "rank": 25, + "rank": 27, "slot_group": "Sample collection and processing" }, "anatomical material": { @@ -9226,7 +9378,7 @@ var SCHEMA = { "value": "Lesion (Pustule) [NCIT:C78582]" } ], - "rank": 26, + "rank": 28, "slot_group": "Sample collection and processing", "recommended": true, "any_of": [ @@ -9245,7 +9397,7 @@ var SCHEMA = { "value": "Genital area [BTO:0003358]" } ], - "rank": 27, + "rank": 29, "slot_group": "Sample collection and processing", "recommended": true, "any_of": [ @@ -9264,7 +9416,7 @@ var SCHEMA = { "value": "Pus [UBERON:0000177]" } ], - "rank": 28, + "rank": 30, "slot_group": "Sample collection and processing", "recommended": true, "any_of": [ @@ -9283,7 +9435,7 @@ var SCHEMA = { "value": "Swab [GENEPIO:0100027]" } ], - "rank": 29, + "rank": 31, "slot_group": "Sample collection and processing", "recommended": true, "any_of": [ @@ -9302,7 +9454,7 @@ var SCHEMA = { "value": "Biopsy [OBI:0002650]" } ], - "rank": 30, + "rank": 32, "slot_group": "Sample collection and processing", "recommended": true, "any_of": [ @@ -9321,7 +9473,7 @@ var SCHEMA = { "value": "Homo sapiens [NCBITaxon:9606]" } ], - "rank": 31, + "rank": 33, "slot_group": "Host Information", "any_of": [ { @@ -9339,7 +9491,7 @@ var SCHEMA = { "value": "Monkeypox [MONDO:0002594]" } ], - "rank": 32, + "rank": 34, "slot_group": "Host Information", "any_of": [ { @@ -9365,107 +9517,107 @@ var SCHEMA = { "NML_LIMS:host subject ID", "BIOSAMPLE:host_subject_id" ], - "rank": 40, + "rank": 42, "slot_group": "Host Information" }, "host health state": { "name": "host health state", - "rank": 34, + "rank": 36, "slot_group": "Host Information" }, "host health outcome": { "name": "host health outcome", - "rank": 35, + "rank": 37, "slot_group": "Host Information" }, "host age": { "name": "host age", - "rank": 36, + "rank": 38, "slot_group": "Host Information" }, "host age unit": { "name": "host age unit", - "rank": 37, + "rank": 39, "slot_group": "Host Information" }, "host age bin": { "name": "host age bin", - "rank": 38, + "rank": 40, "slot_group": "Host Information" }, "host gender": { "name": "host gender", - "rank": 39, + "rank": 41, "slot_group": "Host Information" }, "symptom onset date": { "name": "symptom onset date", - "rank": 41, + "rank": 43, "slot_group": "Host Information" }, "signs and symptoms": { "name": "signs and symptoms", - "rank": 42, + "rank": 44, "slot_group": "Host Information" }, "pre-existing conditions and risk factors": { "name": "pre-existing conditions and risk factors", - "rank": 43, + "rank": 45, "slot_group": "Host Information" }, "host vaccination status": { "name": "host vaccination status", - "rank": 44, + "rank": 46, "slot_group": "Host vaccination information" }, "number of vaccine doses received": { "name": "number of vaccine doses received", - "rank": 45, + "rank": 47, "slot_group": "Host vaccination information" }, "vaccination dose 1 vaccine name": { "name": "vaccination dose 1 vaccine name", - "rank": 46, + "rank": 48, "slot_group": "Host vaccination information" }, "vaccination dose 1 vaccination date": { "name": "vaccination dose 1 vaccination date", - "rank": 47, + "rank": 49, "slot_group": "Host vaccination information" }, "vaccination history": { "name": "vaccination history", - "rank": 48, + "rank": 50, "slot_group": "Host vaccination information" }, "travel history": { "name": "travel history", - "rank": 49, + "rank": 51, "slot_group": "Host exposure information" }, "exposure event": { "name": "exposure event", - "rank": 50, + "rank": 52, "slot_group": "Host exposure information" }, "exposure contact level": { "name": "exposure contact level", - "rank": 51, + "rank": 53, "slot_group": "Host exposure information" }, "host role": { "name": "host role", - "rank": 52, + "rank": 54, "slot_group": "Host exposure information" }, "exposure setting": { "name": "exposure setting", - "rank": 53, + "rank": 55, "slot_group": "Host exposure information" }, "exposure details": { "name": "exposure details", - "rank": 54, + "rank": 56, "slot_group": "Host exposure information" }, "purpose of sequencing": { @@ -9475,7 +9627,7 @@ var SCHEMA = { "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" } ], - "rank": 55, + "rank": 57, "slot_group": "Sequencing", "any_of": [ { @@ -9488,17 +9640,17 @@ var SCHEMA = { }, "purpose of sequencing details": { "name": "purpose of sequencing details", - "rank": 56, + "rank": 58, "slot_group": "Sequencing" }, "sequencing date": { "name": "sequencing date", - "rank": 57, + "rank": 59, "slot_group": "Sequencing" }, "library preparation kit": { "name": "library preparation kit", - "rank": 58, + "rank": 60, "slot_group": "Sequencing" }, "sequencing instrument": { @@ -9508,7 +9660,7 @@ var SCHEMA = { "value": "Oxford Nanopore MinION [GENEPIO:0100142]" } ], - "rank": 59, + "rank": 61, "slot_group": "Sequencing", "any_of": [ { @@ -9521,57 +9673,57 @@ var SCHEMA = { }, "sequencing protocol": { "name": "sequencing protocol", - "rank": 60, + "rank": 62, "slot_group": "Sequencing" }, "raw sequence data processing method": { "name": "raw sequence data processing method", - "rank": 61, + "rank": 63, "slot_group": "Bioinformatics and QC metrics" }, "dehosting method": { "name": "dehosting method", - "rank": 62, + "rank": 64, "slot_group": "Bioinformatics and QC metrics" }, "consensus sequence software name": { "name": "consensus sequence software name", - "rank": 63, + "rank": 65, "slot_group": "Bioinformatics and QC metrics" }, "consensus sequence software version": { "name": "consensus sequence software version", - "rank": 64, + "rank": 66, "slot_group": "Bioinformatics and QC metrics" }, "breadth of coverage value": { "name": "breadth of coverage value", - "rank": 65, + "rank": 67, "slot_group": "Bioinformatics and QC metrics" }, "depth of coverage value": { "name": "depth of coverage value", - "rank": 66, + "rank": 68, "slot_group": "Bioinformatics and QC metrics" }, "depth of coverage threshold": { "name": "depth of coverage threshold", - "rank": 67, + "rank": 69, "slot_group": "Bioinformatics and QC metrics" }, "number of base pairs sequenced": { "name": "number of base pairs sequenced", - "rank": 68, + "rank": 70, "slot_group": "Bioinformatics and QC metrics" }, "consensus genome length": { "name": "consensus genome length", - "rank": 69, + "rank": 71, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics protocol": { "name": "bioinformatics protocol", - "rank": 70, + "rank": 72, "slot_group": "Bioinformatics and QC metrics" }, "gene name 1": { @@ -9579,7 +9731,7 @@ var SCHEMA = { "comments": [ "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" ], - "rank": 71, + "rank": 73, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -9592,7 +9744,7 @@ var SCHEMA = { }, "diagnostic pcr Ct value 1": { "name": "diagnostic pcr Ct value 1", - "rank": 72, + "rank": 74, "slot_group": "Pathogen diagnostic testing" }, "gene name 2": { @@ -9600,7 +9752,7 @@ var SCHEMA = { "comments": [ "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" ], - "rank": 73, + "rank": 75, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -9613,7 +9765,7 @@ var SCHEMA = { }, "diagnostic pcr Ct value 2": { "name": "diagnostic pcr Ct value 2", - "rank": 74, + "rank": 76, "slot_group": "Pathogen diagnostic testing" }, "gene name 3": { @@ -9621,7 +9773,7 @@ var SCHEMA = { "comments": [ "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" ], - "rank": 75, + "rank": 77, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -9634,17 +9786,17 @@ var SCHEMA = { }, "diagnostic pcr Ct value 3": { "name": "diagnostic pcr Ct value 3", - "rank": 76, + "rank": 78, "slot_group": "Pathogen diagnostic testing" }, "authors": { "name": "authors", - "rank": 77, + "rank": 79, "slot_group": "Contributor acknowledgement" }, "DataHarmonizer provenance": { "name": "DataHarmonizer provenance", - "rank": 78, + "rank": 80, "slot_group": "Contributor acknowledgement" } }, @@ -9697,12 +9849,46 @@ var SCHEMA = { "partial_match": false } }, + "SRA accession": { + "name": "SRA accession", + "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "title": "SRA accession", + "from_schema": "https://example.com/monkeypox", + "rank": 4, + "slot_uri": "GENEPIO:0001142", + "alias": "SRA_accession", + "owner": "Monkeypox_international", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "GenBank accession": { + "name": "GenBank accession", + "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", + "title": "GenBank accession", + "from_schema": "https://example.com/monkeypox", + "rank": 5, + "slot_uri": "GENEPIO:0001145", + "alias": "GenBank_accession", + "owner": "Monkeypox_international", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, "GISAID virus name": { "name": "GISAID virus name", "description": "Identifier of the specific isolate.", "title": "GISAID virus name", "from_schema": "https://example.com/monkeypox", - "rank": 4, + "rank": 6, "slot_uri": "GENEPIO:0100282", "alias": "GISAID_virus_name", "owner": "Monkeypox_international", @@ -9714,7 +9900,7 @@ var SCHEMA = { "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", "from_schema": "https://example.com/monkeypox", - "rank": 5, + "rank": 7, "slot_uri": "GENEPIO:0001147", "alias": "GISAID_accession", "owner": "Monkeypox_international", @@ -9735,7 +9921,7 @@ var SCHEMA = { "GISAID:Originating lab", "BIOSAMPLE:collected_by" ], - "rank": 6, + "rank": 8, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", "owner": "Monkeypox_international", @@ -9755,7 +9941,7 @@ var SCHEMA = { "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "from_schema": "https://example.com/monkeypox", - "rank": 7, + "rank": 9, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", "owner": "Monkeypox_international", @@ -9768,7 +9954,7 @@ var SCHEMA = { "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", "from_schema": "https://example.com/monkeypox", - "rank": 8, + "rank": 10, "slot_uri": "GENEPIO:0001158", "alias": "sample_collector_contact_address", "owner": "Monkeypox_international", @@ -9783,7 +9969,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:sequenced_by" ], - "rank": 9, + "rank": 11, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "Monkeypox_international", @@ -9803,7 +9989,7 @@ var SCHEMA = { "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact email", "from_schema": "https://example.com/monkeypox", - "rank": 10, + "rank": 12, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "Monkeypox_international", @@ -9815,7 +10001,7 @@ var SCHEMA = { "description": "The mailing address of the agency submitting the sequence.", "title": "sequenced by contact address", "from_schema": "https://example.com/monkeypox", - "rank": 11, + "rank": 13, "slot_uri": "GENEPIO:0100423", "alias": "sequenced_by_contact_address", "owner": "Monkeypox_international", @@ -9831,7 +10017,7 @@ var SCHEMA = { "GISAID:Submitting lab", "BIOSAMPLE:sequence_submitted_by" ], - "rank": 12, + "rank": 14, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "Monkeypox_international", @@ -9851,7 +10037,7 @@ var SCHEMA = { "description": "The email address of the agency responsible for submission of the sequence.", "title": "sequence submitter contact email", "from_schema": "https://example.com/monkeypox", - "rank": 13, + "rank": 15, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "Monkeypox_international", @@ -9863,7 +10049,7 @@ var SCHEMA = { "description": "The mailing address of the agency responsible for submission of the sequence.", "title": "sequence submitter contact address", "from_schema": "https://example.com/monkeypox", - "rank": 14, + "rank": 16, "slot_uri": "GENEPIO:0001167", "alias": "sequence_submitter_contact_address", "owner": "Monkeypox_international", @@ -9875,7 +10061,7 @@ var SCHEMA = { "description": "The date on which the sample was collected.", "title": "sample collection date", "from_schema": "https://example.com/monkeypox", - "rank": 15, + "rank": 17, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", "owner": "Monkeypox_international", @@ -9887,7 +10073,7 @@ var SCHEMA = { "description": "The date on which the sample was received.", "title": "sample received date", "from_schema": "https://example.com/monkeypox", - "rank": 16, + "rank": 18, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "Monkeypox_international", @@ -9903,7 +10089,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 17, + "rank": 19, "slot_uri": "GENEPIO:0001181", "alias": "geo_loc_name_(country)", "owner": "Monkeypox_international", @@ -9926,7 +10112,7 @@ var SCHEMA = { "Provide the state/province/territory name from the controlled vocabulary provided." ], "from_schema": "https://example.com/monkeypox", - "rank": 19, + "rank": 21, "slot_uri": "GENEPIO:0001185", "alias": "geo_loc_name_(state/province/territory)", "owner": "Monkeypox_international", @@ -9946,7 +10132,7 @@ var SCHEMA = { "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo_loc latitude", "from_schema": "https://example.com/monkeypox", - "rank": 20, + "rank": 22, "slot_uri": "GENEPIO:0100309", "alias": "geo_loc_latitude", "owner": "Monkeypox_international", @@ -9958,7 +10144,7 @@ var SCHEMA = { "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo_loc longitude", "from_schema": "https://example.com/monkeypox", - "rank": 21, + "rank": 23, "slot_uri": "GENEPIO:0100310", "alias": "geo_loc_longitude", "owner": "Monkeypox_international", @@ -9975,7 +10161,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 22, + "rank": 24, "slot_uri": "GENEPIO:0001191", "alias": "organism", "owner": "Monkeypox_international", @@ -10006,7 +10192,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:isolate" ], - "rank": 23, + "rank": 25, "slot_uri": "GENEPIO:0001644", "alias": "isolate", "owner": "Monkeypox_international", @@ -10023,7 +10209,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 24, + "rank": 26, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", "owner": "Monkeypox_international", @@ -10043,7 +10229,7 @@ var SCHEMA = { "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", "from_schema": "https://example.com/monkeypox", - "rank": 25, + "rank": 27, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", "owner": "Monkeypox_international", @@ -10060,7 +10246,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 26, + "rank": 28, "slot_uri": "GENEPIO:0001211", "multivalued": true, "alias": "anatomical_material", @@ -10086,7 +10272,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 27, + "rank": 29, "slot_uri": "GENEPIO:0001214", "multivalued": true, "alias": "anatomical_part", @@ -10112,7 +10298,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 28, + "rank": 30, "slot_uri": "GENEPIO:0001216", "multivalued": true, "alias": "body_product", @@ -10138,7 +10324,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 29, + "rank": 31, "slot_uri": "GENEPIO:0001234", "multivalued": true, "alias": "collection_device", @@ -10164,7 +10350,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 30, + "rank": 32, "slot_uri": "GENEPIO:0001241", "multivalued": true, "alias": "collection_method", @@ -10190,7 +10376,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 31, + "rank": 33, "slot_uri": "GENEPIO:0001387", "alias": "host_(scientific_name)", "owner": "Monkeypox_international", @@ -10215,7 +10401,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 32, + "rank": 34, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", "owner": "Monkeypox_international", @@ -10247,7 +10433,7 @@ var SCHEMA = { "NML_LIMS:host subject ID", "BIOSAMPLE:host_subject_id" ], - "rank": 40, + "rank": 42, "slot_uri": "GENEPIO:0001398", "alias": "host_subject_ID", "owner": "Monkeypox_international", @@ -10259,7 +10445,7 @@ var SCHEMA = { "description": "Health status of the host at the time of sample collection.", "title": "host health state", "from_schema": "https://example.com/monkeypox", - "rank": 34, + "rank": 36, "slot_uri": "GENEPIO:0001388", "alias": "host_health_state", "owner": "Monkeypox_international", @@ -10270,7 +10456,7 @@ var SCHEMA = { "description": "Disease outcome in the host.", "title": "host health outcome", "from_schema": "https://example.com/monkeypox", - "rank": 35, + "rank": 37, "slot_uri": "GENEPIO:0001389", "alias": "host_health_outcome", "owner": "Monkeypox_international", @@ -10281,7 +10467,7 @@ var SCHEMA = { "description": "Age of host at the time of sampling.", "title": "host age", "from_schema": "https://example.com/monkeypox", - "rank": 36, + "rank": 38, "slot_uri": "GENEPIO:0001392", "alias": "host_age", "owner": "Monkeypox_international", @@ -10293,7 +10479,7 @@ var SCHEMA = { "description": "The units used to measure the host's age.", "title": "host age unit", "from_schema": "https://example.com/monkeypox", - "rank": 37, + "rank": 39, "slot_uri": "GENEPIO:0001393", "alias": "host_age_unit", "owner": "Monkeypox_international", @@ -10305,7 +10491,7 @@ var SCHEMA = { "description": "The age category of the host at the time of sampling.", "title": "host age bin", "from_schema": "https://example.com/monkeypox", - "rank": 38, + "rank": 40, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", "owner": "Monkeypox_international", @@ -10317,7 +10503,7 @@ var SCHEMA = { "description": "The gender of the host at the time of sample collection.", "title": "host gender", "from_schema": "https://example.com/monkeypox", - "rank": 39, + "rank": 41, "slot_uri": "GENEPIO:0001395", "alias": "host_gender", "owner": "Monkeypox_international", @@ -10329,7 +10515,7 @@ var SCHEMA = { "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", "from_schema": "https://example.com/monkeypox", - "rank": 41, + "rank": 43, "slot_uri": "GENEPIO:0001399", "alias": "symptom_onset_date", "owner": "Monkeypox_international", @@ -10340,7 +10526,7 @@ var SCHEMA = { "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", "title": "signs and symptoms", "from_schema": "https://example.com/monkeypox", - "rank": 42, + "rank": 44, "slot_uri": "GENEPIO:0001400", "multivalued": true, "alias": "signs_and_symptoms", @@ -10352,7 +10538,7 @@ var SCHEMA = { "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", "title": "pre-existing conditions and risk factors", "from_schema": "https://example.com/monkeypox", - "rank": 43, + "rank": 45, "slot_uri": "GENEPIO:0001401", "multivalued": true, "alias": "pre_existing_conditions_and_risk_factors", @@ -10364,7 +10550,7 @@ var SCHEMA = { "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", "from_schema": "https://example.com/monkeypox", - "rank": 44, + "rank": 46, "slot_uri": "GENEPIO:0001404", "alias": "host_vaccination_status", "owner": "Monkeypox_international", @@ -10375,7 +10561,7 @@ var SCHEMA = { "description": "The number of doses of the vaccine recived by the host.", "title": "number of vaccine doses received", "from_schema": "https://example.com/monkeypox", - "rank": 45, + "rank": 47, "slot_uri": "GENEPIO:0001406", "alias": "number_of_vaccine_doses_received", "owner": "Monkeypox_international", @@ -10387,7 +10573,7 @@ var SCHEMA = { "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", "title": "vaccination dose 1 vaccine name", "from_schema": "https://example.com/monkeypox", - "rank": 46, + "rank": 48, "slot_uri": "GENEPIO:0100313", "alias": "vaccination_dose_1_vaccine_name", "owner": "Monkeypox_international", @@ -10398,7 +10584,7 @@ var SCHEMA = { "description": "The date the first dose of a vaccine was administered.", "title": "vaccination dose 1 vaccination date", "from_schema": "https://example.com/monkeypox", - "rank": 47, + "rank": 49, "slot_uri": "GENEPIO:0100314", "alias": "vaccination_dose_1_vaccination_date", "owner": "Monkeypox_international", @@ -10409,7 +10595,7 @@ var SCHEMA = { "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", "from_schema": "https://example.com/monkeypox", - "rank": 48, + "rank": 50, "slot_uri": "GENEPIO:0100321", "alias": "vaccination_history", "owner": "Monkeypox_international", @@ -10421,7 +10607,7 @@ var SCHEMA = { "description": "Travel history in last six months.", "title": "travel history", "from_schema": "https://example.com/monkeypox", - "rank": 49, + "rank": 51, "slot_uri": "GENEPIO:0001416", "alias": "travel_history", "owner": "Monkeypox_international", @@ -10433,7 +10619,7 @@ var SCHEMA = { "description": "Event leading to exposure.", "title": "exposure event", "from_schema": "https://example.com/monkeypox", - "rank": 50, + "rank": 52, "slot_uri": "GENEPIO:0001417", "alias": "exposure_event", "owner": "Monkeypox_international", @@ -10444,7 +10630,7 @@ var SCHEMA = { "description": "The exposure transmission contact type.", "title": "exposure contact level", "from_schema": "https://example.com/monkeypox", - "rank": 51, + "rank": 53, "slot_uri": "GENEPIO:0001418", "alias": "exposure_contact_level", "owner": "Monkeypox_international", @@ -10455,7 +10641,7 @@ var SCHEMA = { "description": "The role of the host in relation to the exposure setting.", "title": "host role", "from_schema": "https://example.com/monkeypox", - "rank": 52, + "rank": 54, "slot_uri": "GENEPIO:0001419", "multivalued": true, "alias": "host_role", @@ -10468,7 +10654,7 @@ var SCHEMA = { "description": "The setting leading to exposure.", "title": "exposure setting", "from_schema": "https://example.com/monkeypox", - "rank": 53, + "rank": 55, "slot_uri": "GENEPIO:0001428", "multivalued": true, "alias": "exposure_setting", @@ -10481,7 +10667,7 @@ var SCHEMA = { "description": "Additional host exposure information.", "title": "exposure details", "from_schema": "https://example.com/monkeypox", - "rank": 54, + "rank": 56, "slot_uri": "GENEPIO:0001431", "alias": "exposure_details", "owner": "Monkeypox_international", @@ -10498,7 +10684,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 55, + "rank": 57, "slot_uri": "GENEPIO:0001445", "multivalued": true, "alias": "purpose_of_sequencing", @@ -10519,7 +10705,7 @@ var SCHEMA = { "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "from_schema": "https://example.com/monkeypox", - "rank": 56, + "rank": 58, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "Monkeypox_international", @@ -10531,7 +10717,7 @@ var SCHEMA = { "description": "The date the sample was sequenced.", "title": "sequencing date", "from_schema": "https://example.com/monkeypox", - "rank": 57, + "rank": 59, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "Monkeypox_international", @@ -10542,7 +10728,7 @@ var SCHEMA = { "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", "from_schema": "https://example.com/monkeypox", - "rank": 58, + "rank": 60, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "Monkeypox_international", @@ -10559,7 +10745,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 59, + "rank": 61, "slot_uri": "GENEPIO:0001452", "multivalued": true, "alias": "sequencing_instrument", @@ -10580,7 +10766,7 @@ var SCHEMA = { "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "from_schema": "https://example.com/monkeypox", - "rank": 60, + "rank": 62, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "Monkeypox_international", @@ -10592,7 +10778,7 @@ var SCHEMA = { "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", "from_schema": "https://example.com/monkeypox", - "rank": 61, + "rank": 63, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "Monkeypox_international", @@ -10604,7 +10790,7 @@ var SCHEMA = { "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "from_schema": "https://example.com/monkeypox", - "rank": 62, + "rank": 64, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "Monkeypox_international", @@ -10616,7 +10802,7 @@ var SCHEMA = { "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", "from_schema": "https://example.com/monkeypox", - "rank": 63, + "rank": 65, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "Monkeypox_international", @@ -10629,7 +10815,7 @@ var SCHEMA = { "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", "from_schema": "https://example.com/monkeypox", - "rank": 64, + "rank": 66, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "Monkeypox_international", @@ -10642,7 +10828,7 @@ var SCHEMA = { "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", "from_schema": "https://example.com/monkeypox", - "rank": 65, + "rank": 67, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "Monkeypox_international", @@ -10654,7 +10840,7 @@ var SCHEMA = { "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", "from_schema": "https://example.com/monkeypox", - "rank": 66, + "rank": 68, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "Monkeypox_international", @@ -10666,7 +10852,7 @@ var SCHEMA = { "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", "from_schema": "https://example.com/monkeypox", - "rank": 67, + "rank": 69, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "Monkeypox_international", @@ -10678,7 +10864,7 @@ var SCHEMA = { "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", "from_schema": "https://example.com/monkeypox", - "rank": 68, + "rank": 70, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "Monkeypox_international", @@ -10691,7 +10877,7 @@ var SCHEMA = { "description": "Size of the reconstructed genome described as the number of base pairs.", "title": "consensus genome length", "from_schema": "https://example.com/monkeypox", - "rank": 69, + "rank": 71, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "Monkeypox_international", @@ -10704,7 +10890,7 @@ var SCHEMA = { "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "from_schema": "https://example.com/monkeypox", - "rank": 70, + "rank": 72, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "Monkeypox_international", @@ -10719,7 +10905,7 @@ var SCHEMA = { "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" ], "from_schema": "https://example.com/monkeypox", - "rank": 71, + "rank": 73, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", "owner": "Monkeypox_international", @@ -10738,7 +10924,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", "from_schema": "https://example.com/monkeypox", - "rank": 72, + "rank": 74, "slot_uri": "GENEPIO:0001509", "alias": "diagnostic_pcr_Ct_value_1", "owner": "Monkeypox_international", @@ -10752,7 +10938,7 @@ var SCHEMA = { "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" ], "from_schema": "https://example.com/monkeypox", - "rank": 73, + "rank": 75, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", "owner": "Monkeypox_international", @@ -10771,7 +10957,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", "from_schema": "https://example.com/monkeypox", - "rank": 74, + "rank": 76, "slot_uri": "GENEPIO:0001512", "alias": "diagnostic_pcr_Ct_value_2", "owner": "Monkeypox_international", @@ -10785,7 +10971,7 @@ var SCHEMA = { "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" ], "from_schema": "https://example.com/monkeypox", - "rank": 75, + "rank": 77, "slot_uri": "GENEPIO:0001513", "alias": "gene_name_3", "owner": "Monkeypox_international", @@ -10804,7 +10990,7 @@ var SCHEMA = { "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 3", "from_schema": "https://example.com/monkeypox", - "rank": 76, + "rank": 78, "slot_uri": "GENEPIO:0001515", "alias": "diagnostic_pcr_Ct_value_3", "owner": "Monkeypox_international", @@ -10815,7 +11001,7 @@ var SCHEMA = { "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", "from_schema": "https://example.com/monkeypox", - "rank": 77, + "rank": 79, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "Monkeypox_international", @@ -10828,7 +11014,7 @@ var SCHEMA = { "description": "The DataHarmonizer software version provenance.", "title": "DataHarmonizer provenance", "from_schema": "https://example.com/monkeypox", - "rank": 78, + "rank": 80, "slot_uri": "GENEPIO:0001518", "alias": "DataHarmonizer_provenance", "owner": "Monkeypox_international", diff --git a/template/monkeypox/schema.yaml b/template/monkeypox/schema.yaml index 86ac5d81..d800a5d8 100644 --- a/template/monkeypox/schema.yaml +++ b/template/monkeypox/schema.yaml @@ -21,6 +21,10 @@ classes: slots: - specimen collector sample ID - Related specimen primary ID + - bioproject accession + - biosample accession + - SRA accession + - GenBank accession - GISAID accession - sample collected by - sample collector contact email @@ -84,11 +88,23 @@ classes: Related specimen primary ID: rank: 2 slot_group: Database Identifiers - GISAID accession: + bioproject accession: rank: 3 slot_group: Database Identifiers - sample collected by: + biosample accession: rank: 4 + slot_group: Database Identifiers + SRA accession: + rank: 5 + slot_group: Database Identifiers + GenBank accession: + rank: 6 + slot_group: Database Identifiers + GISAID accession: + rank: 7 + slot_group: Database Identifiers + sample collected by: + rank: 8 slot_group: Sample collection and processing any_of: - range: sample collected by menu @@ -100,13 +116,13 @@ classes: - BIOSAMPLE:collected_by - VirusSeq_Portal:sample collected by sample collector contact email: - rank: 5 + rank: 9 slot_group: Sample collection and processing sample collector contact address: - rank: 6 + rank: 10 slot_group: Sample collection and processing sequenced by: - rank: 7 + rank: 11 slot_group: Sample collection and processing any_of: - range: sequence submitted by menu @@ -115,13 +131,13 @@ classes: - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by sequenced by contact email: - rank: 8 + rank: 12 slot_group: Sample collection and processing sequenced by contact address: - rank: 9 + rank: 13 slot_group: Sample collection and processing sequence submitted by: - rank: 10 + rank: 14 slot_group: Sample collection and processing any_of: - range: sequence submitted by menu @@ -133,22 +149,22 @@ classes: - BIOSAMPLE:sequence_submitted_by - VirusSeq_Portal:sequence submitted by sequence submitter contact email: - rank: 11 + rank: 15 slot_group: Sample collection and processing sequence submitter contact address: - rank: 12 + rank: 16 slot_group: Sample collection and processing sample collection date: - rank: 13 + rank: 17 slot_group: Sample collection and processing sample collection date precision: - rank: 14 + rank: 18 slot_group: Sample collection and processing sample received date: - rank: 15 + rank: 19 slot_group: Sample collection and processing geo_loc_name (country): - rank: 16 + rank: 20 slot_group: Sample collection and processing examples: - value: Canada @@ -156,7 +172,7 @@ classes: - range: geo_loc_name (country) menu - range: null value menu geo_loc_name (state/province/territory): - rank: 17 + rank: 21 slot_group: Sample collection and processing comments: Provide the province/territory name from the controlled vocabulary provided. @@ -164,7 +180,7 @@ classes: - range: geo_loc_name (state/province/territory) menu - range: null value menu organism: - rank: 18 + rank: 22 slot_group: Sample collection and processing examples: - value: Monkeypox virus @@ -172,7 +188,7 @@ classes: - range: organism menu - range: null value menu isolate: - rank: 19 + rank: 23 slot_group: Sample collection and processing slot_uri: GENEPIO:0001195 comments: "Provide the GISAID EpiPox virus name, which should be written in\ @@ -184,13 +200,13 @@ classes: exact_mappings: - GISAID:Virus name - CNPHI:GISAID Virus Name - - NML_LIMS:RESULT - CANCOGEN_SUBMISSIONS + - NML_LIMS:SUBMISSIONS - GISAID Virus Name - BIOSAMPLE:isolate - BIOSAMPLE:GISAID_virus_name - VirusSeq_Portal:isolate - VirusSeq_Portal:fasta header name purpose of sampling: - rank: 20 + rank: 24 slot_group: Sample collection and processing examples: - value: Diagnostic testing @@ -198,16 +214,16 @@ classes: - range: purpose of sampling menu - range: null value menu purpose of sampling details: - rank: 21 + rank: 25 slot_group: Sample collection and processing NML submitted specimen type: - rank: 22 + rank: 26 slot_group: Sample collection and processing Related specimen relationship type: - rank: 23 + rank: 27 slot_group: Sample collection and processing anatomical material: - rank: 24 + rank: 28 slot_group: Sample collection and processing required: true examples: @@ -216,7 +232,7 @@ classes: - range: anatomical material menu - range: null value menu anatomical part: - rank: 25 + rank: 29 slot_group: Sample collection and processing required: true examples: @@ -225,7 +241,7 @@ classes: - range: anatomical part menu - range: null value menu body product: - rank: 26 + rank: 30 slot_group: Sample collection and processing required: true examples: @@ -234,7 +250,7 @@ classes: - range: body product menu - range: null value menu collection device: - rank: 27 + rank: 31 slot_group: Sample collection and processing required: true examples: @@ -243,7 +259,7 @@ classes: - range: collection device menu - range: null value menu collection method: - rank: 28 + rank: 32 slot_group: Sample collection and processing required: true examples: @@ -252,7 +268,7 @@ classes: - range: collection method menu - range: null value menu host (scientific name): - rank: 29 + rank: 33 slot_group: Host Information examples: - value: Homo sapiens @@ -260,7 +276,7 @@ classes: - range: host (scientific name) menu - range: null value menu host disease: - rank: 30 + rank: 34 slot_group: Host Information examples: - value: Monkeypox @@ -268,10 +284,10 @@ classes: - range: host disease menu - range: null value menu travel history: - rank: 31 + rank: 35 slot_group: Host exposure information purpose of sequencing: - rank: 32 + rank: 36 slot_group: Sequencing examples: - description: Select "Targeted surveillance (non-random sampling)" if the @@ -297,17 +313,17 @@ classes: - range: purpose of sequencing menu - range: null value menu purpose of sequencing details: - rank: 33 + rank: 37 slot_group: Sequencing sequencing date: - rank: 34 + rank: 38 slot_group: Sequencing required: true library preparation kit: - rank: 35 + rank: 39 slot_group: Sequencing sequencing instrument: - rank: 36 + rank: 40 slot_group: Sequencing examples: - value: Oxford Nanopore MinION @@ -315,40 +331,40 @@ classes: - range: sequencing instrument menu - range: null value menu raw sequence data processing method: - rank: 37 + rank: 41 slot_group: Bioinformatics and QC metrics required: true dehosting method: - rank: 38 + rank: 42 slot_group: Bioinformatics and QC metrics required: true consensus sequence software name: - rank: 39 + rank: 43 slot_group: Bioinformatics and QC metrics consensus sequence software version: - rank: 40 + rank: 44 slot_group: Bioinformatics and QC metrics breadth of coverage value: - rank: 41 + rank: 45 slot_group: Bioinformatics and QC metrics depth of coverage value: - rank: 42 + rank: 46 slot_group: Bioinformatics and QC metrics depth of coverage threshold: - rank: 43 + rank: 47 slot_group: Bioinformatics and QC metrics number of base pairs sequenced: - rank: 44 + rank: 48 slot_group: Bioinformatics and QC metrics consensus genome length: - rank: 45 + rank: 49 slot_group: Bioinformatics and QC metrics bioinformatics protocol: - rank: 46 + rank: 50 slot_group: Bioinformatics and QC metrics required: true gene name 1: - rank: 47 + rank: 51 slot_group: Pathogen diagnostic testing comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. @@ -356,10 +372,10 @@ classes: - range: gene name 1 menu - range: null value menu diagnostic pcr Ct value 1: - rank: 48 + rank: 52 slot_group: Pathogen diagnostic testing gene name 2: - rank: 49 + rank: 53 slot_group: Pathogen diagnostic testing comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. @@ -367,10 +383,10 @@ classes: - range: gene name 2 menu - range: null value menu diagnostic pcr Ct value 2: - rank: 50 + rank: 54 slot_group: Pathogen diagnostic testing gene name 3: - rank: 51 + rank: 55 slot_group: Pathogen diagnostic testing comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. @@ -378,25 +394,25 @@ classes: - range: gene name 3 menu - range: null value menu diagnostic pcr Ct value 3: - rank: 52 + rank: 56 slot_group: Pathogen diagnostic testing gene name 4: - rank: 53 + rank: 57 slot_group: Pathogen diagnostic testing diagnostic pcr Ct value 4: - rank: 54 + rank: 58 slot_group: Pathogen diagnostic testing gene name 5: - rank: 55 + rank: 59 slot_group: Pathogen diagnostic testing diagnostic pcr Ct value 5: - rank: 56 + rank: 60 slot_group: Pathogen diagnostic testing authors: - rank: 57 + rank: 61 slot_group: Contributor acknowledgement DataHarmonizer provenance: - rank: 58 + rank: 62 slot_group: Contributor acknowledgement Monkeypox_international: name: Monkeypox_international @@ -408,6 +424,8 @@ classes: - specimen collector sample ID - bioproject accession - biosample accession + - SRA accession + - GenBank accession - GISAID virus name - GISAID accession - sample collected by @@ -493,14 +511,20 @@ classes: biosample accession: rank: 3 slot_group: Database Identifiers - GISAID virus name: + SRA accession: rank: 4 slot_group: Database Identifiers - GISAID accession: + GenBank accession: rank: 5 slot_group: Database Identifiers - sample collected by: + GISAID virus name: rank: 6 + slot_group: Database Identifiers + GISAID accession: + rank: 7 + slot_group: Database Identifiers + sample collected by: + rank: 8 slot_group: Sample collection and processing any_of: - range: WhitespaceMinimizedString @@ -509,13 +533,13 @@ classes: - GISAID:Originating lab - BIOSAMPLE:collected_by sample collector contact email: - rank: 7 + rank: 9 slot_group: Sample collection and processing sample collector contact address: - rank: 8 + rank: 10 slot_group: Sample collection and processing sequenced by: - rank: 9 + rank: 11 slot_group: Sample collection and processing any_of: - range: WhitespaceMinimizedString @@ -523,13 +547,13 @@ classes: exact_mappings: - BIOSAMPLE:sequenced_by sequenced by contact email: - rank: 10 + rank: 12 slot_group: Sample collection and processing sequenced by contact address: - rank: 11 + rank: 13 slot_group: Sample collection and processing sequence submitted by: - rank: 12 + rank: 14 slot_group: Sample collection and processing any_of: - range: WhitespaceMinimizedString @@ -538,19 +562,19 @@ classes: - GISAID:Submitting lab - BIOSAMPLE:sequence_submitted_by sequence submitter contact email: - rank: 13 + rank: 15 slot_group: Sample collection and processing sequence submitter contact address: - rank: 14 + rank: 16 slot_group: Sample collection and processing sample collection date: - rank: 15 + rank: 17 slot_group: Sample collection and processing sample received date: - rank: 16 + rank: 18 slot_group: Sample collection and processing geo_loc_name (country): - rank: 17 + rank: 19 slot_group: Sample collection and processing examples: - value: United States of America [GAZ:00002459] @@ -558,7 +582,7 @@ classes: - range: geo_loc_name (country) international menu - range: null value menu geo_loc_name (state/province/territory): - rank: 19 + rank: 21 slot_group: Sample collection and processing comments: Provide the state/province/territory name from the controlled vocabulary provided. @@ -566,13 +590,13 @@ classes: - range: WhitespaceMinimizedString - range: null value menu geo_loc latitude: - rank: 20 + rank: 22 slot_group: Sample collection and processing geo_loc longitude: - rank: 21 + rank: 23 slot_group: Sample collection and processing organism: - rank: 22 + rank: 24 slot_group: Sample collection and processing examples: - value: Monkeypox virus [NCBITaxon:10244] @@ -580,7 +604,7 @@ classes: - range: organism international menu - range: null value menu isolate: - rank: 23 + rank: 25 slot_group: Sample collection and processing slot_uri: GENEPIO:0001644 comments: 'This identifier should be an unique, indexed, alpha-numeric ID @@ -592,7 +616,7 @@ classes: exact_mappings: - BIOSAMPLE:isolate purpose of sampling: - rank: 24 + rank: 26 slot_group: Sample collection and processing examples: - value: Diagnostic testing [GENEPIO:0100002] @@ -600,10 +624,10 @@ classes: - range: purpose of sampling international menu - range: null value menu purpose of sampling details: - rank: 25 + rank: 27 slot_group: Sample collection and processing anatomical material: - rank: 26 + rank: 28 slot_group: Sample collection and processing recommended: true examples: @@ -612,7 +636,7 @@ classes: - range: anatomical material international menu - range: null value menu anatomical part: - rank: 27 + rank: 29 slot_group: Sample collection and processing recommended: true examples: @@ -621,7 +645,7 @@ classes: - range: anatomical part international menu - range: null value menu body product: - rank: 28 + rank: 30 slot_group: Sample collection and processing recommended: true examples: @@ -630,7 +654,7 @@ classes: - range: body product international menu - range: null value menu collection device: - rank: 29 + rank: 31 slot_group: Sample collection and processing recommended: true examples: @@ -639,7 +663,7 @@ classes: - range: collection device international menu - range: null value menu collection method: - rank: 30 + rank: 32 slot_group: Sample collection and processing recommended: true examples: @@ -648,7 +672,7 @@ classes: - range: collection method international menu - range: null value menu host (scientific name): - rank: 31 + rank: 33 slot_group: Host Information examples: - value: Homo sapiens [NCBITaxon:9606] @@ -656,7 +680,7 @@ classes: - range: host (scientific name) international menu - range: null value menu host disease: - rank: 32 + rank: 34 slot_group: Host Information examples: - value: Monkeypox [MONDO:0002594] @@ -664,7 +688,7 @@ classes: - range: host disease international menu - range: null value menu host subject ID: - rank: 40 + rank: 42 slot_group: Host Information description: 'A unique identifier by which each host can be referred to e.g. #131' @@ -675,67 +699,67 @@ classes: - NML_LIMS:host subject ID - BIOSAMPLE:host_subject_id host health state: - rank: 34 + rank: 36 slot_group: Host Information host health outcome: - rank: 35 + rank: 37 slot_group: Host Information host age: - rank: 36 + rank: 38 slot_group: Host Information host age unit: - rank: 37 + rank: 39 slot_group: Host Information host age bin: - rank: 38 + rank: 40 slot_group: Host Information host gender: - rank: 39 + rank: 41 slot_group: Host Information symptom onset date: - rank: 41 + rank: 43 slot_group: Host Information signs and symptoms: - rank: 42 + rank: 44 slot_group: Host Information pre-existing conditions and risk factors: - rank: 43 + rank: 45 slot_group: Host Information host vaccination status: - rank: 44 + rank: 46 slot_group: Host vaccination information number of vaccine doses received: - rank: 45 + rank: 47 slot_group: Host vaccination information vaccination dose 1 vaccine name: - rank: 46 + rank: 48 slot_group: Host vaccination information vaccination dose 1 vaccination date: - rank: 47 + rank: 49 slot_group: Host vaccination information vaccination history: - rank: 48 + rank: 50 slot_group: Host vaccination information travel history: - rank: 49 + rank: 51 slot_group: Host exposure information exposure event: - rank: 50 + rank: 52 slot_group: Host exposure information exposure contact level: - rank: 51 + rank: 53 slot_group: Host exposure information host role: - rank: 52 + rank: 54 slot_group: Host exposure information exposure setting: - rank: 53 + rank: 55 slot_group: Host exposure information exposure details: - rank: 54 + rank: 56 slot_group: Host exposure information purpose of sequencing: - rank: 55 + rank: 57 slot_group: Sequencing examples: - value: Baseline surveillance (random sampling) [GENEPIO:0100005] @@ -743,16 +767,16 @@ classes: - range: purpose of sequencing international menu - range: null value menu purpose of sequencing details: - rank: 56 + rank: 58 slot_group: Sequencing sequencing date: - rank: 57 + rank: 59 slot_group: Sequencing library preparation kit: - rank: 58 + rank: 60 slot_group: Sequencing sequencing instrument: - rank: 59 + rank: 61 slot_group: Sequencing examples: - value: Oxford Nanopore MinION [GENEPIO:0100142] @@ -760,40 +784,40 @@ classes: - range: sequencing instrument international menu - range: null value menu sequencing protocol: - rank: 60 + rank: 62 slot_group: Sequencing raw sequence data processing method: - rank: 61 + rank: 63 slot_group: Bioinformatics and QC metrics dehosting method: - rank: 62 + rank: 64 slot_group: Bioinformatics and QC metrics consensus sequence software name: - rank: 63 + rank: 65 slot_group: Bioinformatics and QC metrics consensus sequence software version: - rank: 64 + rank: 66 slot_group: Bioinformatics and QC metrics breadth of coverage value: - rank: 65 + rank: 67 slot_group: Bioinformatics and QC metrics depth of coverage value: - rank: 66 + rank: 68 slot_group: Bioinformatics and QC metrics depth of coverage threshold: - rank: 67 + rank: 69 slot_group: Bioinformatics and QC metrics number of base pairs sequenced: - rank: 68 + rank: 70 slot_group: Bioinformatics and QC metrics consensus genome length: - rank: 69 + rank: 71 slot_group: Bioinformatics and QC metrics bioinformatics protocol: - rank: 70 + rank: 72 slot_group: Bioinformatics and QC metrics gene name 1: - rank: 71 + rank: 73 slot_group: Pathogen diagnostic testing comments: '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 @@ -803,10 +827,10 @@ classes: - range: WhitespaceMinimizedString - range: null value menu diagnostic pcr Ct value 1: - rank: 72 + rank: 74 slot_group: Pathogen diagnostic testing gene name 2: - rank: 73 + rank: 75 slot_group: Pathogen diagnostic testing comments: '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 @@ -816,10 +840,10 @@ classes: - range: WhitespaceMinimizedString - range: null value menu diagnostic pcr Ct value 2: - rank: 74 + rank: 76 slot_group: Pathogen diagnostic testing gene name 3: - rank: 75 + rank: 77 slot_group: Pathogen diagnostic testing comments: '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 @@ -829,13 +853,13 @@ classes: - range: WhitespaceMinimizedString - range: null value menu diagnostic pcr Ct value 3: - rank: 76 + rank: 78 slot_group: Pathogen diagnostic testing authors: - rank: 77 + rank: 79 slot_group: Contributor acknowledgement DataHarmonizer provenance: - rank: 78 + rank: 80 slot_group: Contributor acknowledgement slots: specimen collector sample ID: @@ -897,6 +921,8 @@ slots: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + exact_mappings: + - NML_LIMS:SUBMISSIONS - BioProject Accession biosample accession: name: biosample accession title: biosample accession @@ -911,6 +937,41 @@ slots: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + exact_mappings: + - NML_LIMS:SUBMISSIONS - BioSample Accession + SRA accession: + name: SRA accession + title: SRA accession + description: The Sequence Read Archive (SRA) identifier linking raw read data, + methodological metadata and quality control metrics submitted to the INSDC. + comments: Store the accession assigned to the submitted "run". NCBI-SRA accessions + start with SRR. + examples: + - value: SRR11177792 + slot_uri: GENEPIO:0001142 + range: WhitespaceMinimizedString + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + exact_mappings: + - NML_LIMS:SUBMISSIONS - SRA Accession + GenBank accession: + name: GenBank accession + title: GenBank accession + description: The GenBank identifier assigned to the sequence in the INSDC archives. + comments: Store the accession returned from a GenBank submission (viral genome + assembly). + examples: + - value: MN908947.3 + slot_uri: GENEPIO:0001145 + range: WhitespaceMinimizedString + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + exact_mappings: + - NML_LIMS:SUBMISSIONS - GenBank Accession GISAID virus name: name: GISAID virus name title: GISAID virus name @@ -941,7 +1002,7 @@ slots: interpolated: true exact_mappings: - CNPHI:GISAID Accession (if known) - - NML_LIMS:SUBMISSIONS - GISAID Accession ID + - NML_LIMS:SUBMISSIONS - GISAID Accession - BIOSAMPLE:GISAID_accession - VirusSeq_Portal:GISAID accession sample collected by: diff --git a/template/monkeypox/schema_slots.tsv b/template/monkeypox/schema_slots.tsv index 8c5618a5..9d1b9371 100644 --- a/template/monkeypox/schema_slots.tsv +++ b/template/monkeypox/schema_slots.tsv @@ -2,10 +2,12 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued r Monkeypox;Monkeypox_international GENEPIO:0001122 Database Identifiers Monkeypox;Monkeypox_international Database Identifiers GENEPIO:0001123 specimen collector sample ID WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_monkeypox_1234 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID Monkeypox Database Identifiers GENEPIO:0001128 Related specimen primary ID WhitespaceMinimizedString null value menu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID -Monkeypox_international Database Identifiers GENEPIO:0001136 bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 -Monkeypox_international Database Identifiers GENEPIO:0001139 biosample accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 +Monkeypox;Monkeypox_international Database Identifiers GENEPIO:0001136 bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession +Monkeypox;Monkeypox_international Database Identifiers GENEPIO:0001139 biosample accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession +Monkeypox;Monkeypox_international Database Identifiers GENEPIO:0001142 SRA accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SUBMISSIONS - SRA Accession +Monkeypox;Monkeypox_international Database Identifiers GENEPIO:0001145 GenBank accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 SUBMISSIONS - GenBank Accession Monkeypox_international Database Identifiers GENEPIO:0100282 GISAID virus name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name -Monkeypox;Monkeypox_international Database Identifiers GENEPIO:0001147 GISAID accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession +Monkeypox;Monkeypox_international Database Identifiers GENEPIO:0001147 GISAID accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession Monkeypox;Monkeypox_international GENEPIO:0001150 Sample collection and processing Monkeypox Sample collection and processing GENEPIO:0001153 sample collected by sample collected by menu null value menu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by Monkeypox_international Sample collection and processing GENEPIO:0001153 sample collected by WhitespaceMinimizedString null value menu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab collected_by @@ -30,7 +32,7 @@ Monkeypox_international Sample collection and processing GENEPIO:0100309 geo_loc Monkeypox_international Sample collection and processing GENEPIO:0100310 geo_loc longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon Monkeypox Sample collection and processing GENEPIO:0001191 organism organism menu null value menu TRUE Taxonomic name of the organism. Use "Monkeypox virus". This value is provided in the template. Monkeypox virus Pathogen HC_CURRENT_ID organism organism Monkeypox_international Sample collection and processing GENEPIO:0001191 organism organism international menu null value menu TRUE Taxonomic name of the organism. Use "Monkeypox virus". This value is provided in the template. Monkeypox virus [NCBITaxon:10244] Pathogen HC_CURRENT_ID organism organism -Monkeypox Sample collection and processing GENEPIO:0001195 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name +Monkeypox Sample collection and processing GENEPIO:0001195 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name SUBMISSIONS - GISAID Virus Name isolate;GISAID_virus_name isolate;fasta header name Monkeypox_international Sample collection and processing GENEPIO:0001644 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "MpxV/host/country/sampleID/date". MpxV/human/USA/CA-CDPH-001/2020 isolate Monkeypox Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling menu null value menu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling Monkeypox_international Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling international menu null value menu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing [GENEPIO:0100002] Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling From 0f1363968c61584939f9280e5872f77220d79a61 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 13 Jul 2022 17:10:11 -0700 Subject: [PATCH 5/7] remove extraneous field --- template/monkeypox/export.js | 2 -- 1 file changed, 2 deletions(-) diff --git a/template/monkeypox/export.js b/template/monkeypox/export.js index 850e6be6..653ba6c7 100644 --- a/template/monkeypox/export.js +++ b/template/monkeypox/export.js @@ -266,8 +266,6 @@ var EXPORT_FORMATS = { ['SUBMISSIONS - GISAID Virus Name', []], ['SUBMISSIONS - GISAID Accession', []], - - ['RESULT - CANCOGEN_SUBMISSIONS', []], ['HC_SAMPLE_CATEGORY', []], ['PH_SAMPLING_DETAILS', []], ['PH_SPECIMEN_TYPE', []], From de0364ee7ed8a8319d59dab7338e7e4e10b81777 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 13 Jul 2022 17:21:57 -0700 Subject: [PATCH 6/7] add test dataset --- 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z4lqGki}(%XrK8k$X1I3H$=q$6N!;sO)xCIc*NwJ|VA%;K9UT9vle-WL`E)SSp^hDLp0$4o{&p>TCp7=j!S<`*uYEj!iH^S)Jbvlw`BnJu?Gb;80s+;& z5A^@vEb*(JUu))nY1)PT_n-K$3i_{Fey!5{rKJVwA8R(hD)=>#^_PNg@0I-b;rx}> z`c?GTjs0JuAh>^s{<_WoRl~0o^DhmpM8D3#KN8Mg75>WD{!-Wu_+8;IeC;3k+pkLh z9@qa;2?TUZ0tED5QT|u)zdPsu6gPe+mH!t1(^bn!g1=)B2ng=|MfMJ3Ose1R{vVb^ BSu+3t diff --git a/template/monkeypox/exampleInput/README.md b/template/monkeypox/exampleInput/README.md index 23ef31aa..c05b9632 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: -- `validTestData_1-0-0.csv` is _valid_ for version `1-0-0` of the DataHarmonizer. +- `DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx` is _valid_ for version `1-3-2` of the DataHarmonizer. ## Valid Test Data