diff --git a/script/data-harmonizer/index.js b/script/data-harmonizer/index.js index 14000b31..a348143e 100644 --- a/script/data-harmonizer/index.js +++ b/script/data-harmonizer/index.js @@ -22,7 +22,7 @@ * */ -const VERSION = '1.3.2'; +const VERSION = '1.3.3'; const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION; diff --git a/script/data-harmonizer/validation.js b/script/data-harmonizer/validation.js index 8bf786af..9ea73d06 100644 --- a/script/data-harmonizer/validation.js +++ b/script/data-harmonizer/validation.js @@ -117,6 +117,12 @@ Object.assign(DataHarmonizer, { // Default: any token is valid. valid = true; break; + + case 'Provenance': + // Any provenance string is valid. + valid = true; + break; + } // End switch diff --git a/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx b/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx deleted file mode 100644 index b81121bf..00000000 Binary files a/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx and /dev/null differ diff --git a/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx b/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx new file mode 100644 index 00000000..c7a6fbc3 Binary files /dev/null and b/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx differ diff --git a/template/monkeypox/exampleInput/README.md b/template/monkeypox/exampleInput/README.md index c05b9632..045697ff 100644 --- a/template/monkeypox/exampleInput/README.md +++ b/template/monkeypox/exampleInput/README.md @@ -1,7 +1,7 @@ # Monkeypox Example Input Data This directory contains example input/test data for the Canadian Network for Public Health Intelligence (CNPHI) DataHarmonizer application template: `Monkeypox`. This data is appropriate for testing up to the version appended to the end of the file name, for example: -- `DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx` is _valid_ for version `1-3-2` of the DataHarmonizer. +- `DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx` is _valid_ for version `1-3-3` of the DataHarmonizer. ## Valid Test Data diff --git a/template/monkeypox/export.js b/template/monkeypox/export.js index 653ba6c7..47c8f885 100644 --- a/template/monkeypox/export.js +++ b/template/monkeypox/export.js @@ -242,7 +242,7 @@ var EXPORT_FORMATS = { ['TEXT_ID', []], //['HC_TEXT5', []], //['PH_ID_NUMBER_PRIMARY', []], - //['PH_CASE_ID', []], + ['PH_CASE_ID', []], ['PH_RELATED_PRIMARY_ID', []], ['CUSTOMER', []], @@ -279,28 +279,28 @@ var EXPORT_FORMATS = { ['PH_SPECIMEN_TYPE_ORIG', []], ['COLLECTION_METHOD', []], - //['PH_ANIMAL_TYPE', []], - //['PH_HOST_HEALTH', []], - //['PH_HOST_HEALTH_DETAILS', []], - //['PH_HOST_HEALTH_OUTCOME', []], + ['PH_ANIMAL_TYPE', []], + ['PH_HOST_HEALTH', []], + ['PH_HOST_HEALTH_DETAILS', []], + ['PH_HOST_HEALTH_OUTCOME', []], ['PH_HOST_DISEASE', []], - //['PH_AGE', []], - //['PH_AGE_UNIT', []], - //['PH_AGE_GROUP', []], - //['VD_SEX', []], - //['PH_HOST_COUNTRY', []], - //['PH_HOST_PROVINCE', []], - //['HC_ONSET_DATE', []], - //['HC_SYMPTOMS', []], - //['PH_VACCINATION_HISTORY', []], - //['VE_SYMP_AVAIL', []], // Calculated field (not in import) - //['PH_EXPOSURE_COUNTRY', []], + ['PH_AGE', []], + ['PH_AGE_UNIT', []], + ['PH_AGE_GROUP', []], + ['VD_SEX', []], + ['PH_HOST_COUNTRY', []], + ['PH_HOST_PROVINCE', []], + ['HC_ONSET_DATE', []], + ['HC_SYMPTOMS', []], + ['PH_VACCINATION_HISTORY', []], + ['VE_SYMP_AVAIL', []], // Calculated field (not in import) + ['PH_EXPOSURE_COUNTRY', []], ['PH_TRAVEL', []], //['PH_POINT_OF_ENTRY', []], //['PH_DAY', []], - //['PH_EXPOSURE', []], - //['PH_EXPOSURE_DETAILS', []], - //['PH_HOST_ROLE', []], + ['PH_EXPOSURE', []], + ['PH_EXPOSURE_DETAILS', []], + ['PH_HOST_ROLE', []], ['PH_REASON_FOR_SEQUENCING',[]], ['PH_REASON_FOR_SEQUENCING_DETAILS', []], diff --git a/template/monkeypox/schema.js b/template/monkeypox/schema.js index 353b9158..07c2901e 100644 --- a/template/monkeypox/schema.js +++ b/template/monkeypox/schema.js @@ -1421,6 +1421,62 @@ var SCHEMA = { } } }, + "specimen processing menu": { + "name": "specimen processing menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Virus passage": { + "text": "Virus passage", + "meaning": "GENEPIO:0100039" + }, + "RNA re-extraction (post RT-PCR)": { + "text": "RNA re-extraction (post RT-PCR)", + "meaning": "GENEPIO:0100040" + }, + "Specimens pooled": { + "text": "Specimens pooled", + "meaning": "OBI:0600016" + } + } + }, + "specimen processing international menu": { + "name": "specimen processing international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Virus passage [GENEPIO:0100039]": { + "text": "Virus passage [GENEPIO:0100039]", + "meaning": "GENEPIO:0100039" + }, + "RNA re-extraction (post RT-PCR) [GENEPIO:0100040]": { + "text": "RNA re-extraction (post RT-PCR) [GENEPIO:0100040]", + "meaning": "GENEPIO:0100040" + }, + "Specimens pooled [OBI:0600016]": { + "text": "Specimens pooled [OBI:0600016]", + "meaning": "OBI:0600016" + } + } + }, + "host (common name) menu": { + "name": "host (common name) menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Human": { + "text": "Human", + "meaning": "NCBITaxon:9606" + } + } + }, + "host (common name) international menu": { + "name": "host (common name) international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Human [NCBITaxon:9606]": { + "text": "Human [NCBITaxon:9606]", + "meaning": "NCBITaxon:9606" + } + } + }, "host (scientific name) menu": { "name": "host (scientific name) menu", "from_schema": "https://example.com/monkeypox", @@ -1447,6 +1503,32 @@ var SCHEMA = { } } }, + "host health state menu": { + "name": "host health state menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Asymptomatic": { + "text": "Asymptomatic", + "meaning": "NCIT:C3833" + }, + "Deceased": { + "text": "Deceased", + "meaning": "NCIT:C28554" + }, + "Healthy": { + "text": "Healthy", + "meaning": "NCIT:C115935" + }, + "Recovered": { + "text": "Recovered", + "meaning": "NCIT:C49498" + }, + "Symptomatic": { + "text": "Symptomatic", + "meaning": "NCIT:C25269" + } + } + }, "host health state international menu": { "name": "host health state international menu", "from_schema": "https://example.com/monkeypox", @@ -1473,6 +1555,94 @@ var SCHEMA = { } } }, + "host health status details menu": { + "name": "host health status details menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Hospitalized": { + "text": "Hospitalized", + "meaning": "NCIT:C25179" + }, + "Hospitalized (Non-ICU)": { + "text": "Hospitalized (Non-ICU)", + "meaning": "GENEPIO:0100045", + "is_a": "Hospitalized" + }, + "Hospitalized (ICU)": { + "text": "Hospitalized (ICU)", + "meaning": "GENEPIO:0100046", + "is_a": "Hospitalized" + }, + "Medically Isolated": { + "text": "Medically Isolated", + "meaning": "GENEPIO:0100047" + }, + "Medically Isolated (Negative Pressure)": { + "text": "Medically Isolated (Negative Pressure)", + "meaning": "GENEPIO:0100048", + "is_a": "Medically Isolated" + }, + "Self-quarantining": { + "text": "Self-quarantining", + "meaning": "NCIT:C173768" + } + } + }, + "host health status details international menu": { + "name": "host health status details international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Hospitalized [NCIT:C25179]": { + "text": "Hospitalized [NCIT:C25179]", + "meaning": "NCIT:C25179" + }, + "Hospitalized (Non-ICU) [GENEPIO:0100045]": { + "text": "Hospitalized (Non-ICU) [GENEPIO:0100045]", + "meaning": "GENEPIO:0100045", + "is_a": "Hospitalized [NCIT:C25179]" + }, + "Hospitalized (ICU) [GENEPIO:0100046]": { + "text": "Hospitalized (ICU) [GENEPIO:0100046]", + "meaning": "GENEPIO:0100046", + "is_a": "Hospitalized [NCIT:C25179]" + }, + "Medically Isolated [GENEPIO:0100047]": { + "text": "Medically Isolated [GENEPIO:0100047]", + "meaning": "GENEPIO:0100047" + }, + "Medically Isolated (Negative Pressure) [GENEPIO:0100048]": { + "text": "Medically Isolated (Negative Pressure) [GENEPIO:0100048]", + "meaning": "GENEPIO:0100048", + "is_a": "Medically Isolated [GENEPIO:0100047]" + }, + "Self-quarantining [NCIT:C173768]": { + "text": "Self-quarantining [NCIT:C173768]", + "meaning": "NCIT:C173768" + } + } + }, + "host health outcome menu": { + "name": "host health outcome menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Deceased": { + "text": "Deceased", + "meaning": "NCIT:C28554" + }, + "Deteriorating": { + "text": "Deteriorating", + "meaning": "NCIT:C25254" + }, + "Recovered": { + "text": "Recovered", + "meaning": "NCIT:C49498" + }, + "Stable": { + "text": "Stable", + "meaning": "NCIT:C30103" + } + } + }, "host health outcome international menu": { "name": "host health outcome international menu", "from_schema": "https://example.com/monkeypox", @@ -1495,6 +1665,20 @@ var SCHEMA = { } } }, + "host age unit menu": { + "name": "host age unit menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "month": { + "text": "month", + "meaning": "UO:0000035" + }, + "year": { + "text": "year", + "meaning": "UO:0000036" + } + } + }, "host age unit international menu": { "name": "host age unit international menu", "from_schema": "https://example.com/monkeypox", @@ -1509,6 +1693,56 @@ var SCHEMA = { } } }, + "host age bin menu": { + "name": "host age bin menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "0 - 9": { + "text": "0 - 9", + "meaning": "GENEPIO:0100049" + }, + "10 - 19": { + "text": "10 - 19", + "meaning": "GENEPIO:0100050" + }, + "20 - 29": { + "text": "20 - 29", + "meaning": "GENEPIO:0100051" + }, + "30 - 39": { + "text": "30 - 39", + "meaning": "GENEPIO:0100052" + }, + "40 - 49": { + "text": "40 - 49", + "meaning": "GENEPIO:0100053" + }, + "50 - 59": { + "text": "50 - 59", + "meaning": "GENEPIO:0100054" + }, + "60 - 69": { + "text": "60 - 69", + "meaning": "GENEPIO:0100055" + }, + "70 - 79": { + "text": "70 - 79", + "meaning": "GENEPIO:0100056" + }, + "80 - 89": { + "text": "80 - 89", + "meaning": "GENEPIO:0100057" + }, + "90 - 99": { + "text": "90 - 99", + "meaning": "GENEPIO:0100058" + }, + "100+": { + "text": "100+", + "meaning": "GENEPIO:0100059" + } + } + }, "host age bin international menu": { "name": "host age bin international menu", "from_schema": "https://example.com/monkeypox", @@ -1559,6 +1793,36 @@ var SCHEMA = { } } }, + "host gender menu": { + "name": "host gender menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Female": { + "text": "Female", + "meaning": "NCIT:C46110" + }, + "Male": { + "text": "Male", + "meaning": "NCIT:C46109" + }, + "Non-binary gender": { + "text": "Non-binary gender", + "meaning": "GSSO:000132" + }, + "Transgender (assigned male at birth)": { + "text": "Transgender (assigned male at birth)", + "meaning": "GSSO:004004" + }, + "Transgender (assigned female at birth)": { + "text": "Transgender (assigned female at birth)", + "meaning": "GSSO:004005" + }, + "Undeclared": { + "text": "Undeclared", + "meaning": "NCIT:C110959" + } + } + }, "host gender international menu": { "name": "host gender international menu", "from_schema": "https://example.com/monkeypox", @@ -1592,6 +1856,114 @@ var SCHEMA = { "signs and symptoms menu": { "name": "signs and symptoms menu", "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Chills (sudden cold sensation)": { + "text": "Chills (sudden cold sensation)", + "description": "A sudden sensation of feeling cold.", + "meaning": "HP:0025143" + }, + "Conjunctivitis (pink eye)": { + "text": "Conjunctivitis (pink eye)", + "description": "Inflammation of the conjunctiva.", + "meaning": "HP:0000509" + }, + "Cough": { + "text": "Cough", + "description": "A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.", + "meaning": "HP:0012735" + }, + "Fatigue (tiredness)": { + "text": "Fatigue (tiredness)", + "description": "A subjective feeling of tiredness characterized by a lack of energy and motivation.", + "meaning": "HP:0012378" + }, + "Fever": { + "text": "Fever", + "description": "Body temperature elevated above the normal range.", + "meaning": "HP:0001945" + }, + "Headache": { + "text": "Headache", + "description": "Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.", + "meaning": "HP:0002315" + }, + "Lesion": { + "text": "Lesion", + "meaning": "NCIT:C3824" + }, + "Lesion (Macule)": { + "text": "Lesion (Macule)", + "meaning": "NCIT:C43278", + "is_a": "Lesion" + }, + "Lesion (Papule)": { + "text": "Lesion (Papule)", + "meaning": "NCIT:C39690", + "is_a": "Lesion" + }, + "Lesion (Pustule)": { + "text": "Lesion (Pustule)", + "meaning": "NCIT:C78582", + "is_a": "Lesion" + }, + "Lesion (Scab)": { + "text": "Lesion (Scab)", + "meaning": "GENEPIO:0100490", + "is_a": "Lesion" + }, + "Lesion (Vesicle)": { + "text": "Lesion (Vesicle)", + "meaning": "GENEPIO:0100491", + "is_a": "Lesion" + }, + "Myalgia (muscle pain)": { + "text": "Myalgia (muscle pain)", + "description": "Pain in muscle.", + "meaning": "HP:0003326" + }, + "Back pain": { + "text": "Back pain", + "meaning": "HP:0003418", + "is_a": "Myalgia (muscle pain)" + }, + "Nausea": { + "text": "Nausea", + "description": "A sensation of unease in the stomach together with an urge to vomit.", + "meaning": "HP:0002018" + }, + "Rash": { + "text": "Rash", + "description": "A red eruption of the skin.", + "meaning": "HP:0000988" + }, + "Sore throat": { + "text": "Sore throat", + "description": "Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing.", + "meaning": "NCIT:C50747" + }, + "Sweating": { + "text": "Sweating", + "meaning": "NCIT:C36172" + }, + "Swollen Lymph Nodes": { + "text": "Swollen Lymph Nodes", + "description": "Enlargment (swelling) of a lymph node.", + "meaning": "HP:0002716" + }, + "Ulcer": { + "text": "Ulcer", + "meaning": "NCIT:C3426" + }, + "Vomiting (throwing up)": { + "text": "Vomiting (throwing up)", + "description": "Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.", + "meaning": "HP:0002013" + } + } + }, + "signs and symptoms international menu": { + "name": "signs and symptoms international menu", + "from_schema": "https://example.com/monkeypox", "permissible_values": { "Chills (sudden cold sensation) [HP:0025143]": { "text": "Chills (sudden cold sensation) [HP:0025143]", @@ -1657,6 +2029,11 @@ var SCHEMA = { "description": "Pain in muscle.", "meaning": "HP:0003326" }, + "Back pain [HP:0003418]": { + "text": "Back pain [HP:0003418]", + "meaning": "HP:0003418", + "is_a": "Myalgia (muscle pain) [HP:0003326]" + }, "Nausea [HP:0002018]": { "text": "Nausea [HP:0002018]", "description": "A sensation of unease in the stomach together with an urge to vomit.", @@ -1672,11 +2049,19 @@ var SCHEMA = { "description": "Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing.", "meaning": "NCIT:C50747" }, + "Sweating [NCIT:C36172]": { + "text": "Sweating [NCIT:C36172]", + "meaning": "NCIT:C36172" + }, "Swollen Lymph Nodes [HP:0002716]": { "text": "Swollen Lymph Nodes [HP:0002716]", "description": "Enlargment (swelling) of a lymph node.", "meaning": "HP:0002716" }, + "Ulcer [NCIT:C3426]": { + "text": "Ulcer [NCIT:C3426]", + "meaning": "NCIT:C3426" + }, "Vomiting (throwing up) [HP:0002013]": { "text": "Vomiting (throwing up) [HP:0002013]", "description": "Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.", @@ -1688,36 +2073,386 @@ var SCHEMA = { "name": "pre-existing conditions and risk factors menu", "from_schema": "https://example.com/monkeypox", "permissible_values": { + "Cancer": { + "text": "Cancer", + "meaning": "MONDO:0004992" + }, + "Diabetes mellitus (diabetes)": { + "text": "Diabetes mellitus (diabetes)", + "meaning": "HP:0000819" + }, + "Type I diabetes mellitus (T1D)": { + "text": "Type I diabetes mellitus (T1D)", + "meaning": "HP:0100651", + "is_a": "Diabetes mellitus (diabetes)" + }, + "Type II diabetes mellitus (T2D)": { + "text": "Type II diabetes mellitus (T2D)", + "meaning": "HP:0005978", + "is_a": "Diabetes mellitus (diabetes)" + }, + "Immunocompromised": { + "text": "Immunocompromised", + "meaning": "NCIT:C14139" + }, + "Infectious disorder": { + "text": "Infectious disorder", + "meaning": "NCIT:C26726" + }, + "Chancroid (Haemophilus ducreyi)": { + "text": "Chancroid (Haemophilus ducreyi)", + "meaning": "DOID:13778", + "is_a": "Infectious disorder" + }, + "Chlamydia": { + "text": "Chlamydia", + "meaning": "DOID:11263", + "is_a": "Infectious disorder" + }, + "Gonorrhea": { + "text": "Gonorrhea", + "meaning": "DOID:7551", + "is_a": "Infectious disorder" + }, + "Herpes Simplex Virus infection (HSV)": { + "text": "Herpes Simplex Virus infection (HSV)", + "meaning": "NCIT:C155871", + "is_a": "Infectious disorder" + }, + "Human immunodeficiency virus (HIV)": { + "text": "Human immunodeficiency virus (HIV)", + "meaning": "MONDO:0005109", + "is_a": "Infectious disorder" + }, + "Acquired immunodeficiency syndrome (AIDS)": { + "text": "Acquired immunodeficiency syndrome (AIDS)", + "meaning": "MONDO:0012268", + "is_a": "Human immunodeficiency virus (HIV)" + }, + "Human papilloma virus infection (HPV)": { + "text": "Human papilloma virus infection (HPV)", + "meaning": "MONDO:0005161", + "is_a": "Infectious disorder" + }, + "Lymphogranuloma venereum": { + "text": "Lymphogranuloma venereum", + "meaning": "DOID:13819", + "is_a": "Infectious disorder" + }, + "Mycoplsma genitalium": { + "text": "Mycoplsma genitalium", + "meaning": "NCBITaxon:2097", + "is_a": "Infectious disorder" + }, + "Syphilis": { + "text": "Syphilis", + "meaning": "DOID:4166", + "is_a": "Infectious disorder" + }, + "Trichomoniasis": { + "text": "Trichomoniasis", + "meaning": "DOID:1947", + "is_a": "Infectious disorder" + }, + "Lupus": { + "text": "Lupus", + "meaning": "MONDO:0004670" + }, + "Pregnancy": { + "text": "Pregnancy", + "meaning": "NCIT:C25742" + }, + "Prior therapy": { + "text": "Prior therapy", + "meaning": "NCIT:C16124" + }, + "Cancer treatment": { + "text": "Cancer treatment", + "meaning": "NCIT:C16212", + "is_a": "Prior therapy" + }, + "Chemotherapy": { + "text": "Chemotherapy", + "meaning": "NCIT:C15632", + "is_a": "Cancer treatment" + }, + "HIV and Antiretroviral therapy (ART)": { + "text": "HIV and Antiretroviral therapy (ART)", + "meaning": "NCIT:C16118", + "is_a": "Prior therapy" + }, + "Steroid": { + "text": "Steroid", + "meaning": "CHEBI:35341", + "is_a": "Prior therapy" + }, + "Transplant": { + "text": "Transplant", + "meaning": "NCIT:C159659" + } + } + }, + "pre-existing conditions and risk factors international menu": { + "name": "pre-existing conditions and risk factors international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Cancer [MONDO:0004992]": { + "text": "Cancer [MONDO:0004992]", + "meaning": "MONDO:0004992" + }, + "Diabetes mellitus (diabetes) [HP:0000819]": { + "text": "Diabetes mellitus (diabetes) [HP:0000819]", + "meaning": "HP:0000819" + }, + "Type I diabetes mellitus (T1D) [HP:0100651]": { + "text": "Type I diabetes mellitus (T1D) [HP:0100651]", + "meaning": "HP:0100651", + "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" + }, + "Type II diabetes mellitus (T2D) [HP:0005978]": { + "text": "Type II diabetes mellitus (T2D) [HP:0005978]", + "meaning": "HP:0005978", + "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" + }, + "Immunocompromised [NCIT:C14139]": { + "text": "Immunocompromised [NCIT:C14139]", + "meaning": "NCIT:C14139" + }, + "Infectious disorder [NCIT:C26726]": { + "text": "Infectious disorder [NCIT:C26726]", + "meaning": "NCIT:C26726" + }, + "Chancroid (Haemophilus ducreyi) [DOID:13778]": { + "text": "Chancroid (Haemophilus ducreyi) [DOID:13778]", + "meaning": "DOID:13778", + "is_a": "Infectious disorder [NCIT:C26726]" + }, + "Chlamydia [DOID:11263]": { + "text": "Chlamydia [DOID:11263]", + "meaning": "DOID:11263", + "is_a": "Infectious disorder [NCIT:C26726]" + }, + "Gonorrhea [DOID:7551]": { + "text": "Gonorrhea [DOID:7551]", + "meaning": "DOID:7551", + "is_a": "Infectious disorder [NCIT:C26726]" + }, + "Herpes Simplex Virus infection (HSV) [NCIT:C155871]": { + "text": "Herpes Simplex Virus infection (HSV) [NCIT:C155871]", + "meaning": "NCIT:C155871", + "is_a": "Infectious disorder [NCIT:C26726]" + }, "Human immunodeficiency virus (HIV) [MONDO:0005109]": { "text": "Human immunodeficiency virus (HIV) [MONDO:0005109]", - "meaning": "MONDO:0005109" + "meaning": "MONDO:0005109", + "is_a": "Infectious disorder [NCIT:C26726]" }, "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]": { "text": "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]", "meaning": "MONDO:0012268", "is_a": "Human immunodeficiency virus (HIV) [MONDO:0005109]" }, - "HIV and antiretroviral therapy (ART) [NCIT:C16118]": { - "text": "HIV and antiretroviral therapy (ART) [NCIT:C16118]", - "meaning": "NCIT:C16118", - "is_a": "Human immunodeficiency virus (HIV) [MONDO:0005109]" + "Human papilloma virus infection (HPV) [MONDO:0005161]": { + "text": "Human papilloma virus infection (HPV) [MONDO:0005161]", + "meaning": "MONDO:0005161", + "is_a": "Infectious disorder [NCIT:C26726]" }, - "Immunocompromised [NCIT:C14139]": { - "text": "Immunocompromised [NCIT:C14139]", - "meaning": "NCIT:C14139" + "Lymphogranuloma venereum [DOID:13819]": { + "text": "Lymphogranuloma venereum [DOID:13819]", + "meaning": "DOID:13819", + "is_a": "Infectious disorder [NCIT:C26726]" + }, + "Mycoplsma genitalium [NCBITaxon:2097]": { + "text": "Mycoplsma genitalium [NCBITaxon:2097]", + "meaning": "NCBITaxon:2097", + "is_a": "Infectious disorder [NCIT:C26726]" + }, + "Syphilis [DOID:4166]": { + "text": "Syphilis [DOID:4166]", + "meaning": "DOID:4166", + "is_a": "Infectious disorder [NCIT:C26726]" + }, + "Trichomoniasis [DOID:1947]": { + "text": "Trichomoniasis [DOID:1947]", + "meaning": "DOID:1947", + "is_a": "Infectious disorder [NCIT:C26726]" + }, + "Lupus [MONDO:0004670]": { + "text": "Lupus [MONDO:0004670]", + "meaning": "MONDO:0004670" }, "Pregnancy [NCIT:C25742]": { "text": "Pregnancy [NCIT:C25742]", "meaning": "NCIT:C25742" + }, + "Prior therapy [NCIT:C16124]": { + "text": "Prior therapy [NCIT:C16124]", + "meaning": "NCIT:C16124" + }, + "Cancer treatment [NCIT:C16212]": { + "text": "Cancer treatment [NCIT:C16212]", + "meaning": "NCIT:C16212", + "is_a": "Prior therapy [NCIT:C16124]" + }, + "Chemotherapy [NCIT:C15632]": { + "text": "Chemotherapy [NCIT:C15632]", + "meaning": "NCIT:C15632", + "is_a": "Cancer treatment [NCIT:C16212]" + }, + "HIV and Antiretroviral therapy (ART) [NCIT:C16118]": { + "text": "HIV and Antiretroviral therapy (ART) [NCIT:C16118]", + "meaning": "NCIT:C16118", + "is_a": "Prior therapy [NCIT:C16124]" + }, + "Steroid [CHEBI:35341]": { + "text": "Steroid [CHEBI:35341]", + "meaning": "CHEBI:35341", + "is_a": "Prior therapy [NCIT:C16124]" + }, + "Transplant [NCIT:C159659]": { + "text": "Transplant [NCIT:C159659]", + "meaning": "NCIT:C159659" } } }, - "exposure event menu": { - "name": "exposure event menu", + "complications menu": { + "name": "complications menu", "from_schema": "https://example.com/monkeypox", "permissible_values": { - "Mass Gathering [GENEPIO:0100237]": { - "text": "Mass Gathering [GENEPIO:0100237]", + "Bronchopneumonia": { + "text": "Bronchopneumonia", + "meaning": "MONDO:0005682" + }, + "Corneal infection": { + "text": "Corneal infection", + "meaning": "MONDO:0023865" + }, + "Delayed wound healing (lesion healing)": { + "text": "Delayed wound healing (lesion healing)", + "meaning": "MP:0002908" + }, + "Encephalitis": { + "text": "Encephalitis", + "meaning": "DOID:9588" + }, + "Myocarditis": { + "text": "Myocarditis", + "meaning": "DOID:820" + }, + "Secondary infection": { + "text": "Secondary infection", + "meaning": "IDO:0000567" + }, + "Sepsis": { + "text": "Sepsis", + "meaning": "HP:0100806" + } + } + }, + "complications international menu": { + "name": "complications international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Bronchopneumonia [MONDO:0005682]": { + "text": "Bronchopneumonia [MONDO:0005682]", + "meaning": "MONDO:0005682" + }, + "Corneal infection [MONDO:0023865]": { + "text": "Corneal infection [MONDO:0023865]", + "meaning": "MONDO:0023865" + }, + "Delayed wound healing (lesion healing) [MP:0002908]": { + "text": "Delayed wound healing (lesion healing) [MP:0002908]", + "meaning": "MP:0002908" + }, + "Encephalitis [DOID:9588]": { + "text": "Encephalitis [DOID:9588]", + "meaning": "DOID:9588" + }, + "Myocarditis [DOID:820]": { + "text": "Myocarditis [DOID:820]", + "meaning": "DOID:820" + }, + "Secondary infection [IDO:0000567]": { + "text": "Secondary infection [IDO:0000567]", + "meaning": "IDO:0000567" + }, + "Sepsis [HP:0100806]": { + "text": "Sepsis [HP:0100806]", + "meaning": "HP:0100806" + } + } + }, + "host vaccination status menu": { + "name": "host vaccination status menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Fully Vaccinated": { + "text": "Fully Vaccinated", + "meaning": "GENEPIO:0100100" + }, + "Not Vaccinated": { + "text": "Not Vaccinated", + "meaning": "GENEPIO:0100102" + } + } + }, + "host vaccination status international menu": { + "name": "host vaccination status international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Fully Vaccinated [GENEPIO:0100100]": { + "text": "Fully Vaccinated [GENEPIO:0100100]", + "meaning": "GENEPIO:0100100" + }, + "Not Vaccinated [GENEPIO:0100102]": { + "text": "Not Vaccinated [GENEPIO:0100102]", + "meaning": "GENEPIO:0100102" + } + } + }, + "exposure event menu": { + "name": "exposure event menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Mass Gathering": { + "text": "Mass Gathering", + "meaning": "GENEPIO:0100237" + }, + "Convention (conference)": { + "text": "Convention (conference)", + "meaning": "GENEPIO:0100238" + }, + "Agricultural Event": { + "text": "Agricultural Event", + "meaning": "GENEPIO:0100240", + "is_a": "Convention (conference)" + }, + "Social Gathering": { + "text": "Social Gathering", + "meaning": "PCO:0000033" + }, + "Community Event": { + "text": "Community Event", + "meaning": "PCO:0000034", + "is_a": "Social Gathering" + }, + "Party": { + "text": "Party", + "meaning": "PCO:0000035", + "is_a": "Social Gathering" + }, + "Other exposure event": { + "text": "Other exposure event" + } + } + }, + "exposure event international menu": { + "name": "exposure event international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Mass Gathering [GENEPIO:0100237]": { + "text": "Mass Gathering [GENEPIO:0100237]", "description": "A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held.", "meaning": "GENEPIO:0100237" }, @@ -1758,6 +2493,73 @@ var SCHEMA = { "exposure contact level menu": { "name": "exposure contact level menu", "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Contact with animal": { + "text": "Contact with animal", + "meaning": "GENEPIO:0100494" + }, + "Contact with rodent": { + "text": "Contact with rodent", + "meaning": "GENEPIO:0100495", + "is_a": "Contact with animal" + }, + "Contact with fomite": { + "text": "Contact with fomite", + "meaning": "GENEPIO:0100496" + }, + "Contact with infected individual": { + "text": "Contact with infected individual", + "meaning": "GENEPIO:0100357" + }, + "Direct (human-to-human contact)": { + "text": "Direct (human-to-human contact)", + "meaning": "TRANS:0000001", + "is_a": "Contact with infected individual" + }, + "Mother-to-child transmission": { + "text": "Mother-to-child transmission", + "meaning": "TRANS:0000006", + "is_a": "Direct (human-to-human contact)" + }, + "Sexual transmission": { + "text": "Sexual transmission", + "meaning": "NCIT:C19085", + "is_a": "Direct (human-to-human contact)" + }, + "Indirect contact": { + "text": "Indirect contact", + "meaning": "GENEPIO:0100246", + "is_a": "Contact with infected individual" + }, + "Close contact (face-to-face contact)": { + "text": "Close contact (face-to-face contact)", + "meaning": "GENEPIO:0100247", + "is_a": "Indirect contact" + }, + "Casual contact": { + "text": "Casual contact", + "meaning": "GENEPIO:0100248", + "is_a": "Indirect contact" + }, + "Workplace associated transmission": { + "text": "Workplace associated transmission", + "meaning": "GENEPIO:0100497" + }, + "Healthcare associated transmission": { + "text": "Healthcare associated transmission", + "meaning": "GENEPIO:0100498", + "is_a": "Workplace associated transmission" + }, + "Laboratory associated transmission": { + "text": "Laboratory associated transmission", + "meaning": "GENEPIO:0100499", + "is_a": "Workplace associated transmission" + } + } + }, + "exposure contact level international menu": { + "name": "exposure contact level international menu", + "from_schema": "https://example.com/monkeypox", "permissible_values": { "Contact with animal [GENEPIO:0100494]": { "text": "Contact with animal [GENEPIO:0100494]", @@ -1772,29 +2574,29 @@ var SCHEMA = { "text": "Contact with fomite [GENEPIO:0100496]", "meaning": "GENEPIO:0100496" }, - "Contact with infected individual": { - "text": "Contact with infected individual", + "Contact with infected individual [GENEPIO:0100357]": { + "text": "Contact with infected individual [GENEPIO:0100357]", "meaning": "GENEPIO:0100357" }, "Direct (human-to-human contact) [TRANS:0000001]": { "text": "Direct (human-to-human contact) [TRANS:0000001]", "meaning": "TRANS:0000001", - "is_a": "Contact with infected individual" + "is_a": "Contact with infected individual [GENEPIO:0100357]" }, "Mother-to-child transmission [TRANS:0000006]": { "text": "Mother-to-child transmission [TRANS:0000006]", "meaning": "TRANS:0000006", "is_a": "Direct (human-to-human contact) [TRANS:0000001]" }, - "Sexual transmission[NCIT:C19085]": { - "text": "Sexual transmission[NCIT:C19085]", + "Sexual transmission [NCIT:C19085]": { + "text": "Sexual transmission [NCIT:C19085]", "meaning": "NCIT:C19085", "is_a": "Direct (human-to-human contact) [TRANS:0000001]" }, "Indirect contact [GENEPIO:0100246]": { "text": "Indirect contact [GENEPIO:0100246]", "meaning": "GENEPIO:0100246", - "is_a": "Contact with infected individual" + "is_a": "Contact with infected individual [GENEPIO:0100357]" }, "Close contact (face-to-face contact) [GENEPIO:0100247]": { "text": "Close contact (face-to-face contact) [GENEPIO:0100247]", @@ -1825,6 +2627,177 @@ var SCHEMA = { "host role menu": { "name": "host role menu", "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Attendee": { + "text": "Attendee", + "meaning": "GENEPIO:0100249" + }, + "Student": { + "text": "Student", + "meaning": "OMRSE:00000058", + "is_a": "Attendee" + }, + "Patient": { + "text": "Patient", + "meaning": "OMRSE:00000030" + }, + "Inpatient": { + "text": "Inpatient", + "meaning": "NCIT:C25182", + "is_a": "Patient" + }, + "Outpatient": { + "text": "Outpatient", + "meaning": "NCIT:C28293", + "is_a": "Patient" + }, + "Passenger": { + "text": "Passenger", + "meaning": "GENEPIO:0100250" + }, + "Resident": { + "text": "Resident", + "meaning": "GENEPIO:0100251" + }, + "Visitor": { + "text": "Visitor", + "meaning": "GENEPIO:0100252" + }, + "Volunteer": { + "text": "Volunteer", + "meaning": "GENEPIO:0100253" + }, + "Work": { + "text": "Work", + "meaning": "GENEPIO:0100254" + }, + "Administrator": { + "text": "Administrator", + "meaning": "GENEPIO:0100255", + "is_a": "Work" + }, + "First Responder": { + "text": "First Responder", + "meaning": "GENEPIO:0100256", + "is_a": "Work" + }, + "Housekeeper": { + "text": "Housekeeper", + "meaning": "GENEPIO:0100260", + "is_a": "Work" + }, + "Kitchen Worker": { + "text": "Kitchen Worker", + "meaning": "GENEPIO:0100261", + "is_a": "Work" + }, + "Healthcare Worker": { + "text": "Healthcare Worker", + "meaning": "GENEPIO:0100334", + "is_a": "Work" + }, + "Community Healthcare Worker": { + "text": "Community Healthcare Worker", + "meaning": "GENEPIO:0100420", + "is_a": "Healthcare Worker" + }, + "Laboratory Worker": { + "text": "Laboratory Worker", + "meaning": "GENEPIO:0100262", + "is_a": "Healthcare Worker" + }, + "Nurse": { + "text": "Nurse", + "meaning": "OMRSE:00000014", + "is_a": "Healthcare Worker" + }, + "Personal Care Aid": { + "text": "Personal Care Aid", + "meaning": "GENEPIO:0100263", + "is_a": "Healthcare Worker" + }, + "Pharmacist": { + "text": "Pharmacist", + "meaning": "GENEPIO:0100264", + "is_a": "Healthcare Worker" + }, + "Physician": { + "text": "Physician", + "meaning": "OMRSE:00000013", + "is_a": "Healthcare Worker" + }, + "Rotational Worker": { + "text": "Rotational Worker", + "meaning": "GENEPIO:0100354", + "is_a": "Work" + }, + "Seasonal Worker": { + "text": "Seasonal Worker", + "meaning": "GENEPIO:0100355", + "is_a": "Work" + }, + "Sex Worker": { + "text": "Sex Worker", + "meaning": "GSSO:005831", + "is_a": "Work" + }, + "Veterinarian": { + "text": "Veterinarian", + "meaning": "GENEPIO:0100265", + "is_a": "Work" + }, + "Social role": { + "text": "Social role", + "meaning": "OMRSE:00000001" + }, + "Acquaintance of case": { + "text": "Acquaintance of case", + "meaning": "GENEPIO:0100266", + "is_a": "Social role" + }, + "Relative of case": { + "text": "Relative of case", + "meaning": "GENEPIO:0100267", + "is_a": "Social role" + }, + "Child of case": { + "text": "Child of case", + "meaning": "GENEPIO:0100268", + "is_a": "Relative of case" + }, + "Parent of case": { + "text": "Parent of case", + "meaning": "GENEPIO:0100269", + "is_a": "Relative of case" + }, + "Father of case": { + "text": "Father of case", + "meaning": "GENEPIO:0100270", + "is_a": "Parent of case" + }, + "Mother of case": { + "text": "Mother of case", + "meaning": "GENEPIO:0100271", + "is_a": "Parent of case" + }, + "Sexual partner of case": { + "text": "Sexual partner of case", + "meaning": "GENEPIO:0100500", + "is_a": "Social role" + }, + "Spouse of case": { + "text": "Spouse of case", + "meaning": "GENEPIO:0100272", + "is_a": "Social role" + }, + "Other Host Role": { + "text": "Other Host Role" + } + } + }, + "host role international menu": { + "name": "host role international menu", + "from_schema": "https://example.com/monkeypox", "permissible_values": { "Attendee [GENEPIO:0100249]": { "text": "Attendee [GENEPIO:0100249]", @@ -1934,6 +2907,11 @@ var SCHEMA = { "meaning": "GENEPIO:0100355", "is_a": "Work [GENEPIO:0100254]" }, + "Sex Worker [GSSO:005831]": { + "text": "Sex Worker [GSSO:005831]", + "meaning": "GSSO:005831", + "is_a": "Work [GENEPIO:0100254]" + }, "Veterinarian [GENEPIO:0100265]": { "text": "Veterinarian [GENEPIO:0100265]", "meaning": "GENEPIO:0100265", @@ -1992,133 +2970,435 @@ var SCHEMA = { "name": "exposure setting menu", "from_schema": "https://example.com/monkeypox", "permissible_values": { - "Human Exposure [ECTO:3000005]": { - "text": "Human Exposure [ECTO:3000005]", + "Human Exposure": { + "text": "Human Exposure", "meaning": "ECTO:3000005" }, - "Contact with Known Monkeypox Case [GENEPIO:0100501]": { - "text": "Contact with Known Monkeypox Case [GENEPIO:0100501]", + "Contact with Known Monkeypox Case": { + "text": "Contact with Known Monkeypox Case", "meaning": "GENEPIO:0100501", - "is_a": "Human Exposure [ECTO:3000005]" + "is_a": "Human Exposure" }, - "Contact with Patient [GENEPIO:0100185]": { - "text": "Contact with Patient [GENEPIO:0100185]", + "Contact with Patient": { + "text": "Contact with Patient", "meaning": "GENEPIO:0100185", - "is_a": "Human Exposure [ECTO:3000005]" + "is_a": "Human Exposure" }, - "Contact with Probable Monkeypox Case [GENEPIO:0100502]": { - "text": "Contact with Probable Monkeypox Case [GENEPIO:0100502]", + "Contact with Probable Monkeypox Case": { + "text": "Contact with Probable Monkeypox Case", "meaning": "GENEPIO:0100502", - "is_a": "Human Exposure [ECTO:3000005]" + "is_a": "Human Exposure" }, - "Contact with Person who Recently Travelled [GENEPIO:0100189]": { - "text": "Contact with Person who Recently Travelled [GENEPIO:0100189]", + "Contact with Person who Recently Travelled": { + "text": "Contact with Person who Recently Travelled", "meaning": "GENEPIO:0100189", - "is_a": "Human Exposure [ECTO:3000005]" + "is_a": "Human Exposure" }, - "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]": { - "text": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]", + "Occupational, Residency or Patronage Exposure": { + "text": "Occupational, Residency or Patronage Exposure", "meaning": "GENEPIO:0100190" }, - "Abbatoir [ECTO:1000033]": { - "text": "Abbatoir [ECTO:1000033]", + "Abbatoir": { + "text": "Abbatoir", "meaning": "ECTO:1000033", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Animal Rescue [GENEPIO:0100191]": { - "text": "Animal Rescue [GENEPIO:0100191]", + "Animal Rescue": { + "text": "Animal Rescue", "meaning": "GENEPIO:0100191", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Bar (pub) [GENEPIO:0100503]": { - "text": "Bar (pub) [GENEPIO:0100503]", + "Bar (pub)": { + "text": "Bar (pub)", "meaning": "GENEPIO:0100503", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Childcare [GENEPIO:0100192]": { - "text": "Childcare [GENEPIO:0100192]", + "Childcare": { + "text": "Childcare", "meaning": "GENEPIO:0100192", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Daycare [GENEPIO:0100193]": { - "text": "Daycare [GENEPIO:0100193]", + "Daycare": { + "text": "Daycare", "meaning": "GENEPIO:0100193", - "is_a": "Childcare [GENEPIO:0100192]" + "is_a": "Childcare" }, - "Nursery [GENEPIO:0100194]": { - "text": "Nursery [GENEPIO:0100194]", + "Nursery": { + "text": "Nursery", "meaning": "GENEPIO:0100194", - "is_a": "Childcare [GENEPIO:0100192]" + "is_a": "Childcare" }, - "Community Service Centre [GENEPIO:0100195]": { - "text": "Community Service Centre [GENEPIO:0100195]", + "Community Service Centre": { + "text": "Community Service Centre", "meaning": "GENEPIO:0100195", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Correctional Facility [GENEPIO:0100196]": { - "text": "Correctional Facility [GENEPIO:0100196]", + "Correctional Facility": { + "text": "Correctional Facility", "meaning": "GENEPIO:0100196", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Dormitory [GENEPIO:0100197]": { - "text": "Dormitory [GENEPIO:0100197]", + "Dormitory": { + "text": "Dormitory", "meaning": "GENEPIO:0100197", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Farm [ECTO:1000034]": { - "text": "Farm [ECTO:1000034]", + "Farm": { + "text": "Farm", "meaning": "ECTO:1000034", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "First Nations Reserve [GENEPIO:0100198]": { - "text": "First Nations Reserve [GENEPIO:0100198]", + "First Nations Reserve": { + "text": "First Nations Reserve", "meaning": "GENEPIO:0100198", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Funeral Home [GENEPIO:0100199]": { - "text": "Funeral Home [GENEPIO:0100199]", + "Funeral Home": { + "text": "Funeral Home", "meaning": "GENEPIO:0100199", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Group Home [GENEPIO:0100200]": { - "text": "Group Home [GENEPIO:0100200]", + "Group Home": { + "text": "Group Home", "meaning": "GENEPIO:0100200", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Healthcare Setting [GENEPIO:0100201]": { - "text": "Healthcare Setting [GENEPIO:0100201]", + "Healthcare Setting": { + "text": "Healthcare Setting", "meaning": "GENEPIO:0100201", - "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + "is_a": "Occupational, Residency or Patronage Exposure" }, - "Ambulance [GENEPIO:0100202]": { - "text": "Ambulance [GENEPIO:0100202]", + "Ambulance": { + "text": "Ambulance", "meaning": "GENEPIO:0100202", - "is_a": "Healthcare Setting [GENEPIO:0100201]" + "is_a": "Healthcare Setting" }, - "Acute Care Facility [GENEPIO:0100203]": { - "text": "Acute Care Facility [GENEPIO:0100203]", + "Acute Care Facility": { + "text": "Acute Care Facility", "meaning": "GENEPIO:0100203", - "is_a": "Healthcare Setting [GENEPIO:0100201]" + "is_a": "Healthcare Setting" }, - "Clinic [GENEPIO:0100204]": { - "text": "Clinic [GENEPIO:0100204]", + "Clinic": { + "text": "Clinic", "meaning": "GENEPIO:0100204", - "is_a": "Healthcare Setting [GENEPIO:0100201]" + "is_a": "Healthcare Setting" }, - "Community Healthcare (At-Home) Setting [GENEPIO:0100415]": { - "text": "Community Healthcare (At-Home) Setting [GENEPIO:0100415]", + "Community Healthcare (At-Home) Setting": { + "text": "Community Healthcare (At-Home) Setting", "meaning": "GENEPIO:0100415", - "is_a": "Healthcare Setting [GENEPIO:0100201]" + "is_a": "Healthcare Setting" }, - "Community Health Centre [GENEPIO:0100205]": { - "text": "Community Health Centre [GENEPIO:0100205]", + "Community Health Centre": { + "text": "Community Health Centre", "meaning": "GENEPIO:0100205", - "is_a": "Healthcare Setting [GENEPIO:0100201]" + "is_a": "Healthcare Setting" }, - "Hospital [ECTO:1000035]": { - "text": "Hospital [ECTO:1000035]", + "Hospital": { + "text": "Hospital", "meaning": "ECTO:1000035", - "is_a": "Healthcare Setting [GENEPIO:0100201]" + "is_a": "Healthcare Setting" + }, + "Emergency Department": { + "text": "Emergency Department", + "meaning": "GENEPIO:0100206", + "is_a": "Hospital" + }, + "ICU": { + "text": "ICU", + "meaning": "GENEPIO:0100207", + "is_a": "Hospital" + }, + "Ward": { + "text": "Ward", + "meaning": "GENEPIO:0100208", + "is_a": "Hospital" + }, + "Laboratory": { + "text": "Laboratory", + "meaning": "ECTO:1000036", + "is_a": "Healthcare Setting" + }, + "Long-Term Care Facility": { + "text": "Long-Term Care Facility", + "meaning": "GENEPIO:0100209", + "is_a": "Healthcare Setting" + }, + "Pharmacy": { + "text": "Pharmacy", + "meaning": "GENEPIO:0100210", + "is_a": "Healthcare Setting" + }, + "Physician's Office": { + "text": "Physician's Office", + "meaning": "GENEPIO:0100211", + "is_a": "Healthcare Setting" + }, + "Household": { + "text": "Household", + "meaning": "GENEPIO:0100212", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Insecure Housing (Homeless)": { + "text": "Insecure Housing (Homeless)", + "meaning": "GENEPIO:0100213", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Occupational Exposure": { + "text": "Occupational Exposure", + "meaning": "GENEPIO:0100214", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Worksite": { + "text": "Worksite", + "meaning": "GENEPIO:0100215", + "is_a": "Occupational Exposure" + }, + "Office": { + "text": "Office", + "meaning": "ECTO:1000037", + "is_a": "Worksite" + }, + "Outdoors": { + "text": "Outdoors", + "meaning": "GENEPIO:0100216", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Camp/camping": { + "text": "Camp/camping", + "meaning": "ECTO:5000009", + "is_a": "Outdoors" + }, + "Hiking Trail": { + "text": "Hiking Trail", + "meaning": "GENEPIO:0100217", + "is_a": "Outdoors" + }, + "Hunting Ground": { + "text": "Hunting Ground", + "meaning": "ECTO:6000030", + "is_a": "Outdoors" + }, + "Ski Resort": { + "text": "Ski Resort", + "meaning": "GENEPIO:0100218", + "is_a": "Outdoors" + }, + "Petting zoo": { + "text": "Petting zoo", + "meaning": "ECTO:5000008", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Place of Worship": { + "text": "Place of Worship", + "meaning": "GENEPIO:0100220", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Church": { + "text": "Church", + "meaning": "GENEPIO:0100221", + "is_a": "Place of Worship" + }, + "Mosque": { + "text": "Mosque", + "meaning": "GENEPIO:0100222", + "is_a": "Place of Worship" + }, + "Temple": { + "text": "Temple", + "meaning": "GENEPIO:0100223", + "is_a": "Place of Worship" + }, + "Restaurant": { + "text": "Restaurant", + "meaning": "ECTO:1000040", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Retail Store": { + "text": "Retail Store", + "meaning": "ECTO:1000041", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "School": { + "text": "School", + "meaning": "GENEPIO:0100224", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Temporary Residence": { + "text": "Temporary Residence", + "meaning": "GENEPIO:0100225", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Homeless Shelter": { + "text": "Homeless Shelter", + "meaning": "GENEPIO:0100226", + "is_a": "Temporary Residence" + }, + "Hotel": { + "text": "Hotel", + "meaning": "GENEPIO:0100227", + "is_a": "Temporary Residence" + }, + "Veterinary Care Clinic": { + "text": "Veterinary Care Clinic", + "meaning": "GENEPIO:0100228", + "is_a": "Occupational, Residency or Patronage Exposure" + }, + "Travel Exposure": { + "text": "Travel Exposure", + "meaning": "GENEPIO:0100229" + }, + "Travelled on a Cruise Ship": { + "text": "Travelled on a Cruise Ship", + "meaning": "GENEPIO:0100230", + "is_a": "Travel Exposure" + }, + "Travelled on a Plane": { + "text": "Travelled on a Plane", + "meaning": "GENEPIO:0100231", + "is_a": "Travel Exposure" + }, + "Travelled on Ground Transport": { + "text": "Travelled on Ground Transport", + "meaning": "GENEPIO:0100232", + "is_a": "Travel Exposure" + }, + "Other Exposure Setting": { + "text": "Other Exposure Setting", + "meaning": "GENEPIO:0100235" + } + } + }, + "exposure setting international menu": { + "name": "exposure setting international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Human Exposure [ECTO:3000005]": { + "text": "Human Exposure [ECTO:3000005]", + "meaning": "ECTO:3000005" + }, + "Contact with Known Monkeypox Case [GENEPIO:0100501]": { + "text": "Contact with Known Monkeypox Case [GENEPIO:0100501]", + "meaning": "GENEPIO:0100501", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Contact with Patient [GENEPIO:0100185]": { + "text": "Contact with Patient [GENEPIO:0100185]", + "meaning": "GENEPIO:0100185", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Contact with Probable Monkeypox Case [GENEPIO:0100502]": { + "text": "Contact with Probable Monkeypox Case [GENEPIO:0100502]", + "meaning": "GENEPIO:0100502", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Contact with Person who Recently Travelled [GENEPIO:0100189]": { + "text": "Contact with Person who Recently Travelled [GENEPIO:0100189]", + "meaning": "GENEPIO:0100189", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]": { + "text": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]", + "meaning": "GENEPIO:0100190" + }, + "Abbatoir [ECTO:1000033]": { + "text": "Abbatoir [ECTO:1000033]", + "meaning": "ECTO:1000033", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Animal Rescue [GENEPIO:0100191]": { + "text": "Animal Rescue [GENEPIO:0100191]", + "meaning": "GENEPIO:0100191", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Bar (pub) [GENEPIO:0100503]": { + "text": "Bar (pub) [GENEPIO:0100503]", + "meaning": "GENEPIO:0100503", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Childcare [GENEPIO:0100192]": { + "text": "Childcare [GENEPIO:0100192]", + "meaning": "GENEPIO:0100192", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Daycare [GENEPIO:0100193]": { + "text": "Daycare [GENEPIO:0100193]", + "meaning": "GENEPIO:0100193", + "is_a": "Childcare [GENEPIO:0100192]" + }, + "Nursery [GENEPIO:0100194]": { + "text": "Nursery [GENEPIO:0100194]", + "meaning": "GENEPIO:0100194", + "is_a": "Childcare [GENEPIO:0100192]" + }, + "Community Service Centre [GENEPIO:0100195]": { + "text": "Community Service Centre [GENEPIO:0100195]", + "meaning": "GENEPIO:0100195", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Correctional Facility [GENEPIO:0100196]": { + "text": "Correctional Facility [GENEPIO:0100196]", + "meaning": "GENEPIO:0100196", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Dormitory [GENEPIO:0100197]": { + "text": "Dormitory [GENEPIO:0100197]", + "meaning": "GENEPIO:0100197", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Farm [ECTO:1000034]": { + "text": "Farm [ECTO:1000034]", + "meaning": "ECTO:1000034", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "First Nations Reserve [GENEPIO:0100198]": { + "text": "First Nations Reserve [GENEPIO:0100198]", + "meaning": "GENEPIO:0100198", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Funeral Home [GENEPIO:0100199]": { + "text": "Funeral Home [GENEPIO:0100199]", + "meaning": "GENEPIO:0100199", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Group Home [GENEPIO:0100200]": { + "text": "Group Home [GENEPIO:0100200]", + "meaning": "GENEPIO:0100200", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Healthcare Setting [GENEPIO:0100201]": { + "text": "Healthcare Setting [GENEPIO:0100201]", + "meaning": "GENEPIO:0100201", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Ambulance [GENEPIO:0100202]": { + "text": "Ambulance [GENEPIO:0100202]", + "meaning": "GENEPIO:0100202", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Acute Care Facility [GENEPIO:0100203]": { + "text": "Acute Care Facility [GENEPIO:0100203]", + "meaning": "GENEPIO:0100203", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Clinic [GENEPIO:0100204]": { + "text": "Clinic [GENEPIO:0100204]", + "meaning": "GENEPIO:0100204", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Community Healthcare (At-Home) Setting [GENEPIO:0100415]": { + "text": "Community Healthcare (At-Home) Setting [GENEPIO:0100415]", + "meaning": "GENEPIO:0100415", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Community Health Centre [GENEPIO:0100205]": { + "text": "Community Health Centre [GENEPIO:0100205]", + "meaning": "GENEPIO:0100205", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Hospital [ECTO:1000035]": { + "text": "Hospital [ECTO:1000035]", + "meaning": "ECTO:1000035", + "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Emergency Department [GENEPIO:0100206]": { "text": "Emergency Department [GENEPIO:0100206]", @@ -2290,17 +3570,59 @@ var SCHEMA = { } } }, - "host vaccination status menu": { - "name": "host vaccination status menu", + "prior Monkeypox infection menu": { + "name": "prior Monkeypox infection menu", "from_schema": "https://example.com/monkeypox", "permissible_values": { - "Fully Vaccinated [GENEPIO:0100100]": { - "text": "Fully Vaccinated [GENEPIO:0100100]", - "meaning": "GENEPIO:0100100" + "Prior infection": { + "text": "Prior infection", + "meaning": "GENEPIO:0100037" }, - "Not Vaccinated [GENEPIO:0100102]": { - "text": "Not Vaccinated [GENEPIO:0100102]", - "meaning": "GENEPIO:0100102" + "No prior infection": { + "text": "No prior infection", + "meaning": "GENEPIO:0100233" + } + } + }, + "prior Monkeypox infection international menu": { + "name": "prior Monkeypox infection international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Prior infection [GENEPIO:0100037]": { + "text": "Prior infection [GENEPIO:0100037]", + "meaning": "GENEPIO:0100037" + }, + "No prior infection [GENEPIO:0100233]": { + "text": "No prior infection [GENEPIO:0100233]", + "meaning": "GENEPIO:0100233" + } + } + }, + "prior Monkeypox antiviral treatment menu": { + "name": "prior Monkeypox antiviral treatment menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Prior antiviral treatment": { + "text": "Prior antiviral treatment", + "meaning": "GENEPIO:0100037" + }, + "No prior antiviral treatment": { + "text": "No prior antiviral treatment", + "meaning": "GENEPIO:0100233" + } + } + }, + "prior Monkeypox antiviral treatment international menu": { + "name": "prior Monkeypox antiviral treatment international menu", + "from_schema": "https://example.com/monkeypox", + "permissible_values": { + "Prior antiviral treatment [GENEPIO:0100037]": { + "text": "Prior antiviral treatment [GENEPIO:0100037]", + "meaning": "GENEPIO:0100037" + }, + "No prior antiviral treatment [GENEPIO:0100233]": { + "text": "No prior antiviral treatment [GENEPIO:0100233]", + "meaning": "GENEPIO:0100233" } } }, @@ -5589,6 +6911,25 @@ var SCHEMA = { } ] }, + "case ID": { + "name": "case ID", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:PH_CASE_ID" + ], + "slot_uri": "GENEPIO:0100281", + "range": "WhitespaceMinimizedString" + }, "bioproject accession": { "name": "bioproject accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", @@ -5964,6 +7305,10 @@ var SCHEMA = { "name": "sample received date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." ], @@ -6284,46 +7629,67 @@ var SCHEMA = { "slot_uri": "GENEPIO:0001241", "multivalued": true }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", + "specimen processing": { + "name": "specimen processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen processing", "comments": [ - "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + "Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"." ], "from_schema": "https://example.com/monkeypox", - "exact_mappings": [ - "GISAID:Host", - "NML_LIMS:host (scientific name)", - "BIOSAMPLE:host", - "VirusSeq_Portal:host (scientific name)" - ], - "slot_uri": "GENEPIO:0001387", - "required": true + "slot_uri": "GENEPIO:0001253", + "multivalued": true }, - "host disease": { - "name": "host disease", - "description": "The name of the disease experienced by the host.", - "title": "host disease", + "specimen processing details": { + "name": "specimen processing details", + "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", + "title": "specimen processing details", "comments": [ - "Select \"Monkeypox\" from the pick list provided in the template." + "Provide a free text description of any processing details applied to a sample." + ], + "examples": [ + { + "value": "5 swabs from different body sites were pooled and further prepared as a single sample during library prep." + } ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "CNPHI:Host Disease", - "NML_LIMS:PH_HOST_DISEASE", - "BIOSAMPLE:host_disease", - "VirusSeq_Portal:host disease" + "NML_LIMS:specimen processing details" ], - "slot_uri": "GENEPIO:0001391", - "required": true + "slot_uri": "GENEPIO:0100311", + "range": "WhitespaceMinimizedString" }, - "host subject ID": { - "name": "host subject ID", - "title": "host subject ID", + "host (common name)": { + "name": "host (common name)", + "description": "The commonly used name of the host.", + "title": "host (common name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human." + ], + "examples": [ + { + "value": "Human" + } + ], "from_schema": "https://example.com/monkeypox", - "slot_uri": "GENEPIO:0001398", - "range": "WhitespaceMinimizedString" + "slot_uri": "GENEPIO:0001386" + }, + "host (scientific name)": { + "name": "host (scientific name)", + "description": "The taxonomic, or scientific name of the host.", + "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "GISAID:Host", + "NML_LIMS:host (scientific name)", + "BIOSAMPLE:host", + "VirusSeq_Portal:host (scientific name)" + ], + "slot_uri": "GENEPIO:0001387", + "required": true }, "host health state": { "name": "host health state", @@ -6332,25 +7698,18 @@ var SCHEMA = { "comments": [ "If known, select a value from the pick list." ], - "examples": [ - { - "value": "Asymptomatic [NCIT:C3833]" - } - ], "from_schema": "https://example.com/monkeypox", - "exact_mappings": [ - "GISAID:Patient status", - "BIOSAMPLE:host_health_state" + "slot_uri": "GENEPIO:0001388" + }, + "host health status details": { + "name": "host health status details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host health status details", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." ], - "slot_uri": "GENEPIO:0001388", - "any_of": [ - { - "range": "host health state international menu" - }, - { - "range": "null value menu" - } - ] + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001389" }, "host health outcome": { "name": "host health outcome", @@ -6359,24 +7718,32 @@ var SCHEMA = { "comments": [ "If known, select a value from the pick list." ], - "examples": [ - { - "value": "Recovered [NCIT:C49498]" - } + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001389" + }, + "host disease": { + "name": "host disease", + "description": "The name of the disease experienced by the host.", + "title": "host disease", + "comments": [ + "Select \"Monkeypox\" from the pick list provided in the template." ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "BIOSAMPLE:host_health_outcome" + "CNPHI:Host Disease", + "NML_LIMS:PH_HOST_DISEASE", + "BIOSAMPLE:host_disease", + "VirusSeq_Portal:host disease" ], - "slot_uri": "GENEPIO:0001389", - "any_of": [ - { - "range": "host health outcome international menu" - }, - { - "range": "null value menu" - } - ] + "slot_uri": "GENEPIO:0001391", + "required": true + }, + "host subject ID": { + "name": "host subject ID", + "title": "host subject ID", + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001398", + "range": "WhitespaceMinimizedString" }, "host age": { "name": "host age", @@ -6391,12 +7758,9 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "exact_mappings": [ - "GISAID:Patient age", - "BIOSAMPLE:host_age" - ], "slot_uri": "GENEPIO:0001392", - "recommended": true, + "minimum_value": 0, + "maximum_value": 130, "any_of": [ { "range": "decimal" @@ -6413,25 +7777,8 @@ var SCHEMA = { "comments": [ "If known, provide the age units used to measure the host's age from the pick list." ], - "examples": [ - { - "value": "year [UO:0000036]" - } - ], "from_schema": "https://example.com/monkeypox", - "exact_mappings": [ - "BIOSAMPLE:host_age_unit" - ], - "slot_uri": "GENEPIO:0001393", - "recommended": true, - "any_of": [ - { - "range": "host age unit international menu" - }, - { - "range": "null value menu" - } - ] + "slot_uri": "GENEPIO:0001393" }, "host age bin": { "name": "host age bin", @@ -6440,25 +7787,8 @@ var SCHEMA = { "comments": [ "Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative." ], - "examples": [ - { - "value": "50 - 59 [GENEPIO:0100054]" - } - ], "from_schema": "https://example.com/monkeypox", - "exact_mappings": [ - "BIOSAMPLE:host_age_bin" - ], - "slot_uri": "GENEPIO:0001394", - "recommended": true, - "any_of": [ - { - "range": "host age bin international menu" - }, - { - "range": "null value menu" - } - ] + "slot_uri": "GENEPIO:0001394" }, "host gender": { "name": "host gender", @@ -6467,21 +7797,44 @@ var SCHEMA = { "comments": [ "If known, select a value from the pick list." ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001395", + "structured_pattern": { + "syntax": "{Title_Case}", + "interpolated": true, + "partial_match": false + } + }, + "host residence geo_loc name (country)": { + "name": "host residence geo_loc name (country)", + "description": "The country of residence of the host.", + "title": "host residence geo_loc name (country)", + "comments": [ + "Select the country name from pick list provided in the template." + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001396" + }, + "host residence geo_loc name (state/province/territory)": { + "name": "host residence geo_loc name (state/province/territory)", + "description": "The state/province/territory of residence of the host.", + "title": "host residence geo_loc name (state/province/territory)", + "comments": [ + "Select the province/territory name from pick list provided in the template." + ], "examples": [ { - "value": "Male [NCIT:C46109]" + "value": "Quebec" } ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "GISAID:Gender", - "BIOSAMPLE:host_sex" + "NML_LIMS:PH_HOST_PROVINCE" ], - "slot_uri": "GENEPIO:0001395", - "recommended": true, + "slot_uri": "GENEPIO:0001397", "any_of": [ { - "range": "host gender international menu" + "range": "geo_loc_name (state/province/territory) menu" }, { "range": "null value menu" @@ -6492,6 +7845,10 @@ var SCHEMA = { "name": "symptom onset date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], "comments": [ "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -6501,6 +7858,9 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:HC_ONSET_DATE" + ], "slot_uri": "GENEPIO:0001399", "any_of": [ { @@ -6518,22 +7878,9 @@ var SCHEMA = { "comments": [ "Select all of the symptoms experienced by the host from the pick list." ], - "examples": [ - { - "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" - } - ], "from_schema": "https://example.com/monkeypox", "slot_uri": "GENEPIO:0001400", - "multivalued": true, - "any_of": [ - { - "range": "signs and symptoms menu" - }, - { - "range": "null value menu" - } - ] + "multivalued": true }, "pre-existing conditions and risk factors": { "name": "pre-existing conditions and risk factors", @@ -6542,31 +7889,45 @@ var SCHEMA = { "comments": [ "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." ], - "examples": [ - { - "value": "Asthma" - }, - { - "value": "Pregnancy" - }, - { - "value": "Smoking" - } - ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ "NML_LIMS:pre-existing conditions and risk factors" ], "slot_uri": "GENEPIO:0001401", - "multivalued": true, - "any_of": [ + "multivalued": true + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001402", + "multivalued": true + }, + "antiviral therapy": { + "name": "antiviral therapy", + "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", + "title": "antiviral therapy", + "comments": [ + "Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information." + ], + "examples": [ { - "range": "pre-existing conditions and risk factors menu" + "value": "Tecovirimat used to treat current Monkeypox infection" }, { - "range": "null value menu" + "value": "AZT administered for concurrent HIV infection" } - ] + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:antiviral therapy" + ], + "slot_uri": "NCIT:C16119", + "range": "WhitespaceMinimizedString" }, "host vaccination status": { "name": "host vaccination status", @@ -6575,24 +7936,11 @@ var SCHEMA = { "comments": [ "Select the vaccination status of the host from the pick list." ], - "examples": [ - { - "value": "Fully Vaccinated" - } - ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ "NML_LIMS:PH_VACCINATION_HISTORY" ], - "slot_uri": "GENEPIO:0001404", - "any_of": [ - { - "range": "host vaccination status menu" - }, - { - "range": "null value menu" - } - ] + "slot_uri": "GENEPIO:0001404" }, "number of vaccine doses received": { "name": "number of vaccine doses received", @@ -6607,6 +7955,9 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:number of vaccine doses received" + ], "slot_uri": "GENEPIO:0001406", "range": "integer" }, @@ -6640,6 +7991,10 @@ var SCHEMA = { "name": "vaccination dose 1 vaccination date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination dose 1 vaccination date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], "comments": [ "Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -6684,124 +8039,184 @@ var SCHEMA = { "slot_uri": "GENEPIO:0100321", "range": "WhitespaceMinimizedString" }, - "travel history": { - "name": "travel history", - "description": "Travel history in last six months.", - "title": "travel history", + "location of exposure geo_loc name (country)": { + "name": "location of exposure geo_loc name (country)", + "description": "The country where the host was likely exposed to the causative agent of the illness.", + "title": "location of exposure geo_loc name (country)", "comments": [ - "Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first." + "Select the country name from the pick list provided in the template." + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001410" + }, + "destination of most recent travel (city)": { + "name": "destination of most recent travel (city)", + "description": "The name of the city that was the destination of most recent travel.", + "title": "destination of most recent travel (city)", + "comments": [ + "Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" ], "examples": [ { - "value": "Canada, Vancouver" - }, - { - "value": "USA, Seattle" - }, - { - "value": "Italy, Milan" + "value": "New York City" } ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ "NML_LIMS:PH_TRAVEL" ], - "slot_uri": "GENEPIO:0001416", + "slot_uri": "GENEPIO:0001411", "range": "WhitespaceMinimizedString" }, - "exposure event": { - "name": "exposure event", - "description": "Event leading to exposure.", - "title": "exposure event", + "destination of most recent travel (state/province/territory)": { + "name": "destination of most recent travel (state/province/territory)", + "description": "The name of the state/province/territory that was the destination of most recent travel.", + "title": "destination of most recent travel (state/province/territory)", + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001412" + }, + "destination of most recent travel (country)": { + "name": "destination of most recent travel (country)", + "description": "The name of the country that was the destination of most recent travel.", + "title": "destination of most recent travel (country)", + "comments": [ + "Select the country name from the pick list provided in the template." + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001413" + }, + "most recent travel departure date": { + "name": "most recent travel departure date", + "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", + "title": "most recent travel departure date", "comments": [ - "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + "Provide the travel departure date." ], "examples": [ { - "value": "Party [PCO:0000035]" + "value": "2020-03-16" } ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "GISAID:Additional location information", - "CNPHI:Exposure Event", - "NML_LIMS:PH_EXPOSURE" + "NML_LIMS:PH_TRAVEL" ], - "slot_uri": "GENEPIO:0001417", + "slot_uri": "GENEPIO:0001414", "any_of": [ { - "range": "exposure event menu" + "range": "date" }, { "range": "null value menu" } ] }, - "exposure contact level": { - "name": "exposure contact level", - "description": "The exposure transmission contact type.", - "title": "exposure contact level", + "most recent travel return date": { + "name": "most recent travel return date", + "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", + "title": "most recent travel return date", "comments": [ - "Select direct or indirect exposure from the pick-list." + "Provide the travel return date." ], "examples": [ { - "value": "Contact with infected individual [GENEPIO:0100357]" + "value": "2020-04-26" } ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "NML_LIMS:exposure contact level" + "NML_LIMS:PH_TRAVEL" ], - "slot_uri": "GENEPIO:0001418", + "slot_uri": "GENEPIO:0001415", "any_of": [ { - "range": "exposure contact level menu" + "range": "date" }, { "range": "null value menu" } ] }, - "host role": { - "name": "host role", - "description": "The role of the host in relation to the exposure setting.", - "title": "host role", + "travel history": { + "name": "travel history", + "description": "Travel history in last six months.", + "title": "travel history", "comments": [ - "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + "Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first." ], "examples": [ { - "value": "Acquaintance of case [GENEPIO:0100266]" + "value": "Canada, Vancouver" + }, + { + "value": "USA, Seattle" + }, + { + "value": "Italy, Milan" } ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "NML_LIMS:PH_HOST_ROLE" + "NML_LIMS:PH_TRAVEL" ], - "slot_uri": "GENEPIO:0001419", - "multivalued": true, - "range": "host role menu" + "slot_uri": "GENEPIO:0001416", + "range": "WhitespaceMinimizedString" + }, + "exposure event": { + "name": "exposure event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team." + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "GISAID:Additional location information", + "CNPHI:Exposure Event", + "NML_LIMS:PH_EXPOSURE" + ], + "slot_uri": "GENEPIO:0001417" + }, + "exposure contact level": { + "name": "exposure contact level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select exposure contact level from the pick-list." + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:exposure contact level" + ], + "slot_uri": "GENEPIO:0001418" + }, + "host role": { + "name": "host role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team." + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "slot_uri": "GENEPIO:0001419", + "multivalued": true }, "exposure setting": { "name": "exposure setting", "description": "The setting leading to exposure.", "title": "exposure setting", "comments": [ - "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." - ], - "examples": [ - { - "value": "Healthcare Setting [GENEPIO:0100201]" - } + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team." ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ "NML_LIMS:PH_EXPOSURE" ], "slot_uri": "GENEPIO:0001428", - "multivalued": true, - "range": "exposure setting menu" + "multivalued": true }, "exposure details": { "name": "exposure details", @@ -6822,6 +8237,71 @@ var SCHEMA = { "slot_uri": "GENEPIO:0001431", "range": "WhitespaceMinimizedString" }, + "prior Monkeypox infection": { + "name": "prior Monkeypox infection", + "description": "The absence or presence of a prior Monkeypox infection.", + "title": "prior Monkeypox infection", + "comments": [ + "If known, provide information about whether the individual had a previous Monkeypox infection. Select a value from the pick list." + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0100532" + }, + "prior Monkeypox infection date": { + "name": "prior Monkeypox infection date", + "description": "The date of diagnosis of the prior Monkeypox infection.", + "title": "prior Monkeypox infection date", + "comments": [ + "Provide the date that the most recent prior infection was diagnosed. Provide the prior Monkeypox infection date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2022-06-20" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:prior Monkeypox infection date" + ], + "slot_uri": "GENEPIO:0100533", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "prior Monkeypox antiviral treatment": { + "name": "prior Monkeypox antiviral treatment", + "description": "The absence or presence of antiviral treatment for a prior Monkeypox infection.", + "title": "prior Monkeypox antiviral treatment", + "comments": [ + "If known, provide information about whether the individual had a previous Monkeypox antiviral treatment. Select a value from the pick list." + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0100534" + }, + "prior antiviral treatment during prior Monkeypox infection": { + "name": "prior antiviral treatment during prior Monkeypox infection", + "description": "Antiviral treatment for any infection during the prior Moneypox infection period.", + "title": "prior antiviral treatment during prior Monkeypox infection", + "comments": [ + "Provide a description of any antiviral treatment administered for viral infections (not including Monkeypox treatment) during the prior Monkeypox infection period. This field is meant to capture concurrent treatment information." + ], + "examples": [ + { + "value": "AZT was administered for HIV infection during the prior Monkeypox infection." + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:prior antiviral treatment during Monkeypox infection" + ], + "slot_uri": "GENEPIO:0100535", + "range": "WhitespaceMinimizedString" + }, "purpose of sequencing": { "name": "purpose of sequencing", "description": "The reason that the sample was sequenced.", @@ -6899,6 +8379,45 @@ var SCHEMA = { } ] }, + "library ID": { + "name": "library ID", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:library ID" + ], + "slot_uri": "GENEPIO:0001448", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "amplicon size": { + "name": "amplicon size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", + "comments": [ + "Provide the amplicon size, including the units." + ], + "examples": [ + { + "value": "300bp" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:amplicon size" + ], + "slot_uri": "GENEPIO:0001449", + "range": "WhitespaceMinimizedString" + }, "library preparation kit": { "name": "library preparation kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", @@ -6941,11 +8460,11 @@ var SCHEMA = { "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ - "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" + "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" ], "examples": [ { - "value": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + "value": "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." } ], "from_schema": "https://example.com/monkeypox", @@ -6956,6 +8475,44 @@ var SCHEMA = { "slot_uri": "GENEPIO:0001454", "range": "WhitespaceMinimizedString" }, + "sequencing kit number": { + "name": "sequencing kit number", + "description": "The manufacturer's kit number.", + "title": "sequencing kit number", + "comments": [ + "Alphanumeric value." + ], + "examples": [ + { + "value": "AB456XYZ789" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:sequencing kit number" + ], + "slot_uri": "GENEPIO:0001455", + "range": "WhitespaceMinimizedString" + }, + "amplicon pcr primer scheme": { + "name": "amplicon pcr primer scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "MPXV Sunrise 3.1" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:amplicon pcr primer scheme" + ], + "slot_uri": "GENEPIO:0001456", + "range": "WhitespaceMinimizedString" + }, "raw sequence data processing method": { "name": "raw sequence data processing method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", @@ -6996,6 +8553,63 @@ var SCHEMA = { "slot_uri": "GENEPIO:0001459", "range": "WhitespaceMinimizedString" }, + "consensus sequence name": { + "name": "consensus sequence name", + "description": "The name of the consensus sequence.", + "title": "consensus sequence name", + "comments": [ + "Provide the name and version number of the consensus sequence." + ], + "examples": [ + { + "value": "mpxvassembly3" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:consensus sequence name" + ], + "slot_uri": "GENEPIO:0001460", + "range": "WhitespaceMinimizedString" + }, + "consensus sequence filename": { + "name": "consensus sequence filename", + "description": "The name of the consensus sequence file.", + "title": "consensus sequence filename", + "comments": [ + "Provide the name and version number of the consensus sequence FASTA file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:consensus sequence filename" + ], + "slot_uri": "GENEPIO:0001461", + "range": "WhitespaceMinimizedString" + }, + "consensus sequence filepath": { + "name": "consensus sequence filepath", + "description": "The filepath of the consesnsus sequence file.", + "title": "consensus sequence filepath", + "comments": [ + "Provide the filepath of the consensus sequence FASTA file." + ], + "examples": [ + { + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:consensus sequence filepath" + ], + "slot_uri": "GENEPIO:0001462", + "range": "WhitespaceMinimizedString" + }, "consensus sequence software name": { "name": "consensus sequence software name", "description": "The name of software used to generate the consensus sequence.", @@ -7102,6 +8716,104 @@ var SCHEMA = { "slot_uri": "GENEPIO:0001475", "range": "WhitespaceMinimizedString" }, + "r1 fastq filename": { + "name": "r1 fastq filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1 fastq filename", + "comments": [ + "Provide the r1 FASTQ filename. This information aids in data management." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001476", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "r2 fastq filename": { + "name": "r2 fastq filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2 fastq filename", + "comments": [ + "Provide the r2 FASTQ filename. This information aids in data management." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001477", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "r1 fastq filepath": { + "name": "r1 fastq filepath", + "description": "The location of the r1 FASTQ file within a user's file system.", + "title": "r1 fastq filepath", + "comments": [ + "Provide the filepath for the r1 FASTQ file. This information aids in data management." + ], + "examples": [ + { + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001478", + "range": "WhitespaceMinimizedString" + }, + "r2 fastq filepath": { + "name": "r2 fastq filepath", + "description": "The location of the r2 FASTQ file within a user's file system.", + "title": "r2 fastq filepath", + "comments": [ + "Provide the filepath for the r2 FASTQ file. This information aids in data management." + ], + "examples": [ + { + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001479", + "range": "WhitespaceMinimizedString" + }, + "fast5 filename": { + "name": "fast5 filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5 filename", + "comments": [ + "Provide the FAST5 filename. This information aids in data management." + ], + "examples": [ + { + "value": "mpxv123seq.fast5" + } + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001480", + "range": "WhitespaceMinimizedString" + }, + "fast5 filepath": { + "name": "fast5 filepath", + "description": "The location of the FAST5 file within a user's file system.", + "title": "fast5 filepath", + "comments": [ + "Provide the filepath for the FAST5 file. This information aids in data management." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/mpxv123seq.fast5" + } + ], + "from_schema": "https://example.com/monkeypox", + "slot_uri": "GENEPIO:0001481", + "range": "WhitespaceMinimizedString" + }, "number of base pairs sequenced": { "name": "number of base pairs sequenced", "description": "The number of total base pairs generated by the sequencing process.", @@ -7142,6 +8854,25 @@ var SCHEMA = { "range": "integer", "minimum_value": 0 }, + "reference genome accession": { + "name": "reference genome accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_063383.1" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:reference genome accession" + ], + "slot_uri": "GENEPIO:0001485", + "range": "WhitespaceMinimizedString" + }, "bioinformatics protocol": { "name": "bioinformatics protocol", "description": "A description of the overall bioinformatics strategy used.", @@ -7151,7 +8882,7 @@ var SCHEMA = { ], "examples": [ { - "value": "https://github.com/phac-nml/ncov2019-artic-nf" + "value": "https://github.com/phac-nml/monkeypox-nf" } ], "from_schema": "https://example.com/monkeypox", @@ -7476,29 +9207,34 @@ var SCHEMA = { "rank": 2, "slot_group": "Database Identifiers" }, + "case ID": { + "name": "case ID", + "rank": 3, + "slot_group": "Database Identifiers" + }, "bioproject accession": { "name": "bioproject accession", - "rank": 3, + "rank": 4, "slot_group": "Database Identifiers" }, "biosample accession": { "name": "biosample accession", - "rank": 4, + "rank": 5, "slot_group": "Database Identifiers" }, "SRA accession": { "name": "SRA accession", - "rank": 5, + "rank": 6, "slot_group": "Database Identifiers" }, "GenBank accession": { "name": "GenBank accession", - "rank": 6, + "rank": 7, "slot_group": "Database Identifiers" }, "GISAID accession": { "name": "GISAID accession", - "rank": 7, + "rank": 8, "slot_group": "Database Identifiers" }, "sample collected by": { @@ -7510,7 +9246,7 @@ var SCHEMA = { "BIOSAMPLE:collected_by", "VirusSeq_Portal:sample collected by" ], - "rank": 8, + "rank": 9, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7523,12 +9259,12 @@ var SCHEMA = { }, "sample collector contact email": { "name": "sample collector contact email", - "rank": 9, + "rank": 10, "slot_group": "Sample collection and processing" }, "sample collector contact address": { "name": "sample collector contact address", - "rank": 10, + "rank": 11, "slot_group": "Sample collection and processing" }, "sequenced by": { @@ -7537,7 +9273,7 @@ var SCHEMA = { "NML_LIMS:PH_SEQUENCING_CENTRE", "BIOSAMPLE:sequenced_by" ], - "rank": 11, + "rank": 12, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7550,12 +9286,12 @@ var SCHEMA = { }, "sequenced by contact email": { "name": "sequenced by contact email", - "rank": 12, + "rank": 13, "slot_group": "Sample collection and processing" }, "sequenced by contact address": { "name": "sequenced by contact address", - "rank": 13, + "rank": 14, "slot_group": "Sample collection and processing" }, "sequence submitted by": { @@ -7567,7 +9303,7 @@ var SCHEMA = { "BIOSAMPLE:sequence_submitted_by", "VirusSeq_Portal:sequence submitted by" ], - "rank": 14, + "rank": 15, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7580,27 +9316,27 @@ var SCHEMA = { }, "sequence submitter contact email": { "name": "sequence submitter contact email", - "rank": 15, + "rank": 16, "slot_group": "Sample collection and processing" }, "sequence submitter contact address": { "name": "sequence submitter contact address", - "rank": 16, + "rank": 17, "slot_group": "Sample collection and processing" }, "sample collection date": { "name": "sample collection date", - "rank": 17, + "rank": 18, "slot_group": "Sample collection and processing" }, "sample collection date precision": { "name": "sample collection date precision", - "rank": 18, + "rank": 19, "slot_group": "Sample collection and processing" }, "sample received date": { "name": "sample received date", - "rank": 19, + "rank": 20, "slot_group": "Sample collection and processing" }, "geo_loc_name (country)": { @@ -7610,7 +9346,7 @@ var SCHEMA = { "value": "Canada" } ], - "rank": 20, + "rank": 21, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7626,7 +9362,7 @@ var SCHEMA = { "comments": [ "Provide the province/territory name from the controlled vocabulary provided." ], - "rank": 21, + "rank": 22, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7644,7 +9380,7 @@ var SCHEMA = { "value": "Monkeypox virus" } ], - "rank": 22, + "rank": 23, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7674,7 +9410,7 @@ var SCHEMA = { "VirusSeq_Portal:isolate", "VirusSeq_Portal:fasta header name" ], - "rank": 23, + "rank": 24, "slot_uri": "GENEPIO:0001195", "slot_group": "Sample collection and processing" }, @@ -7685,7 +9421,7 @@ var SCHEMA = { "value": "Diagnostic testing" } ], - "rank": 24, + "rank": 25, "slot_group": "Sample collection and processing", "any_of": [ { @@ -7698,17 +9434,17 @@ var SCHEMA = { }, "purpose of sampling details": { "name": "purpose of sampling details", - "rank": 25, + "rank": 26, "slot_group": "Sample collection and processing" }, "NML submitted specimen type": { "name": "NML submitted specimen type", - "rank": 26, + "rank": 27, "slot_group": "Sample collection and processing" }, "Related specimen relationship type": { "name": "Related specimen relationship type", - "rank": 27, + "rank": 28, "slot_group": "Sample collection and processing" }, "anatomical material": { @@ -7718,7 +9454,7 @@ var SCHEMA = { "value": "Lesion (Pustule)" } ], - "rank": 28, + "rank": 29, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7737,7 +9473,7 @@ var SCHEMA = { "value": "Genital area" } ], - "rank": 29, + "rank": 30, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7756,7 +9492,7 @@ var SCHEMA = { "value": "Pus" } ], - "rank": 30, + "rank": 31, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7775,7 +9511,7 @@ var SCHEMA = { "value": "Swab" } ], - "rank": 31, + "rank": 32, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7794,7 +9530,7 @@ var SCHEMA = { "value": "Biopsy" } ], - "rank": 32, + "rank": 33, "slot_group": "Sample collection and processing", "required": true, "any_of": [ @@ -7806,924 +9542,2271 @@ var SCHEMA = { } ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "specimen processing": { + "name": "specimen processing", "examples": [ { - "value": "Homo sapiens" + "value": "Specimens pooled" } ], - "rank": 33, + "exact_mappings": [ + "NML_LIMS:specimen processing" + ], + "rank": 34, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "specimen processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen processing details": { + "name": "specimen processing details", + "rank": 35, + "slot_group": "Sample collection and processing" + }, + "host (common name)": { + "name": "host (common name)", + "exact_mappings": [ + "NML_LIMS:PH_ANIMAL_TYPE" + ], + "rank": 36, "slot_group": "Host Information", "any_of": [ { - "range": "host (scientific name) menu" + "range": "host (common name) menu" }, { "range": "null value menu" } ] }, - "host disease": { - "name": "host disease", + "host (scientific name)": { + "name": "host (scientific name)", "examples": [ { - "value": "Monkeypox" + "value": "Homo sapiens" } ], - "rank": 34, + "rank": 37, "slot_group": "Host Information", "any_of": [ { - "range": "host disease menu" + "range": "host (scientific name) menu" }, { "range": "null value menu" } ] }, - "travel history": { - "name": "travel history", - "rank": 35, - "slot_group": "Host exposure information" - }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "host health state": { + "name": "host health state", "examples": [ { - "value": "Specimens attributed to individuals with no known intimate contacts to positive cases", - "description": "Select \"Targeted surveillance (non-random sampling)\" if the specimen fits any of the following criteria" - }, - { - "value": "Specimens attributed to youth/minors <18 yrs." - }, - { - "value": "Specimens attributed to vulnerable persons living in transient shelters or congregant settings" - }, + "value": "Asymptomatic" + } + ], + "exact_mappings": [ + "GISAID:Patient status", + "NML_LIMS:PH_HOST_HEALTH", + "BIOSAMPLE:host_health_state" + ], + "rank": 38, + "slot_group": "Host Information", + "any_of": [ { - "value": "Specimens attributed to individuals self-identifying as “female”" + "range": "host health state menu" }, { - "value": "Domestic travel surveillance", - "description": "For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options" - }, + "range": "null value menu" + } + ] + }, + "host health status details": { + "name": "host health status details", + "examples": [ { - "value": "International travel surveillance" - }, + "value": "Hospitalized" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_DETAILS" + ], + "rank": 39, + "slot_group": "Host Information", + "any_of": [ { - "value": "Travel-associated surveillance" + "range": "host health status details menu" }, { - "value": "Cluster/Outbreak investigation", - "description": "For specimens targeted for sequencing as part of an outbreak investigation, please select" - }, + "range": "null value menu" + } + ] + }, + "host health outcome": { + "name": "host health outcome", + "examples": [ { - "value": "Baseline surveillance (random sampling).", - "description": "In all other cases use" + "value": "Recovered" } ], - "rank": 36, - "slot_group": "Sequencing", + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_OUTCOME", + "BIOSAMPLE:host_health_outcome" + ], + "rank": 40, + "slot_group": "Host Information", "any_of": [ { - "range": "purpose of sequencing menu" + "range": "host health outcome menu" }, { "range": "null value menu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "rank": 37, - "slot_group": "Sequencing" - }, - "sequencing date": { - "name": "sequencing date", - "rank": 38, - "slot_group": "Sequencing", - "required": true - }, - "library preparation kit": { - "name": "library preparation kit", - "rank": 39, - "slot_group": "Sequencing" - }, - "sequencing instrument": { - "name": "sequencing instrument", + "host disease": { + "name": "host disease", "examples": [ { - "value": "Oxford Nanopore MinION" + "value": "Monkeypox" } ], - "rank": 40, - "slot_group": "Sequencing", + "rank": 41, + "slot_group": "Host Information", "any_of": [ { - "range": "sequencing instrument menu" + "range": "host disease menu" }, { "range": "null value menu" } ] }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "rank": 41, - "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "dehosting method": { - "name": "dehosting method", + "host age": { + "name": "host age", + "exact_mappings": [ + "GISAID:Patient age", + "NML_LIMS:PH_AGE", + "BIOSAMPLE:host_age" + ], "rank": 42, - "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "rank": 43, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "rank": 44, - "slot_group": "Bioinformatics and QC metrics" - }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "rank": 45, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth of coverage value": { - "name": "depth of coverage value", - "rank": 46, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "rank": 47, - "slot_group": "Bioinformatics and QC metrics" - }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "rank": 48, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus genome length": { - "name": "consensus genome length", - "rank": 49, - "slot_group": "Bioinformatics and QC metrics" - }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "rank": 50, - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Host Information", "required": true }, - "gene name 1": { - "name": "gene name 1", - "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "host age unit": { + "name": "host age unit", + "examples": [ + { + "value": "year" + } ], - "rank": 51, - "slot_group": "Pathogen diagnostic testing", + "exact_mappings": [ + "NML_LIMS:PH_AGE_UNIT", + "BIOSAMPLE:host_age_unit" + ], + "rank": 43, + "slot_group": "Host Information", + "required": true, "any_of": [ { - "range": "gene name 1 menu" + "range": "host age unit menu" }, { "range": "null value menu" } ] }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", - "rank": 52, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 2": { - "name": "gene name 2", - "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "host age bin": { + "name": "host age bin", + "examples": [ + { + "value": "50 - 59" + } ], - "rank": 53, - "slot_group": "Pathogen diagnostic testing", + "exact_mappings": [ + "NML_LIMS:PH_AGE_GROUP", + "BIOSAMPLE:host_age_bin" + ], + "rank": 44, + "slot_group": "Host Information", + "required": true, "any_of": [ { - "range": "gene name 2 menu" + "range": "host age bin menu" }, { "range": "null value menu" } ] }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "rank": 54, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 3": { + "host gender": { + "name": "host gender", + "examples": [ + { + "value": "Male" + } + ], + "exact_mappings": [ + "GISAID:Gender", + "NML_LIMS:VD_SEX", + "BIOSAMPLE:host_sex" + ], + "rank": 45, + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "host gender menu" + }, + { + "range": "null value menu" + } + ] + }, + "host residence geo_loc name (country)": { + "name": "host residence geo_loc name (country)", + "examples": [ + { + "value": "Canada" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_HOST_COUNTRY" + ], + "rank": 46, + "slot_group": "Host Information", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host residence geo_loc name (state/province/territory)": { + "name": "host residence geo_loc name (state/province/territory)", + "rank": 47, + "slot_group": "Host Information" + }, + "symptom onset date": { + "name": "symptom onset date", + "rank": 48, + "slot_group": "Host Information" + }, + "signs and symptoms": { + "name": "signs and symptoms", + "examples": [ + { + "value": "Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain)" + } + ], + "exact_mappings": [ + "NML_LIMS:HC_SYMPTOMS" + ], + "rank": 49, + "slot_group": "Host Information", + "any_of": [ + { + "range": "signs and symptoms menu" + }, + { + "range": "null value menu" + } + ] + }, + "pre-existing conditions and risk factors": { + "name": "pre-existing conditions and risk factors", + "rank": 50, + "slot_group": "Host Information", + "any_of": [ + { + "range": "pre-existing conditions and risk factors menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "examples": [ + { + "value": "Delayed wound healing (lesion healing)" + } + ], + "exact_mappings": [ + "NML_LIMS:complications" + ], + "rank": 51, + "slot_group": "Host Information", + "any_of": [ + { + "range": "complications menu" + }, + { + "range": "null value menu" + } + ] + }, + "antiviral therapy": { + "name": "antiviral therapy", + "rank": 52, + "slot_group": "Host Information" + }, + "host vaccination status": { + "name": "host vaccination status", + "examples": [ + { + "value": "Not Vaccinated" + } + ], + "rank": 53, + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host vaccination status menu" + }, + { + "range": "null value menu" + } + ] + }, + "number of vaccine doses received": { + "name": "number of vaccine doses received", + "rank": 54, + "slot_group": "Host vaccination information" + }, + "vaccination dose 1 vaccine name": { + "name": "vaccination dose 1 vaccine name", + "rank": 55, + "slot_group": "Host vaccination information" + }, + "vaccination dose 1 vaccination date": { + "name": "vaccination dose 1 vaccination date", + "rank": 56, + "slot_group": "Host vaccination information" + }, + "vaccination history": { + "name": "vaccination history", + "rank": 57, + "slot_group": "Host vaccination information" + }, + "location of exposure geo_loc name (country)": { + "name": "location of exposure geo_loc name (country)", + "examples": [ + { + "value": "Canada" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_COUNTRY" + ], + "rank": 58, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "destination of most recent travel (city)": { + "name": "destination of most recent travel (city)", + "rank": 59, + "slot_group": "Host exposure information" + }, + "destination of most recent travel (state/province/territory)": { + "name": "destination of most recent travel (state/province/territory)", + "comments": [ + "Select the province name from the pick list provided in the template." + ], + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 60, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (state/province/territory) menu" + }, + { + "range": "null value menu" + } + ] + }, + "destination of most recent travel (country)": { + "name": "destination of most recent travel (country)", + "examples": [ + { + "value": "Canada" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 61, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "most recent travel departure date": { + "name": "most recent travel departure date", + "rank": 62, + "slot_group": "Host exposure information" + }, + "most recent travel return date": { + "name": "most recent travel return date", + "rank": 63, + "slot_group": "Host exposure information" + }, + "travel history": { + "name": "travel history", + "rank": 64, + "slot_group": "Host exposure information" + }, + "exposure event": { + "name": "exposure event", + "examples": [ + { + "value": "Party" + } + ], + "rank": 65, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure event menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure contact level": { + "name": "exposure contact level", + "examples": [ + { + "value": "Contact with infected individual" + } + ], + "rank": 66, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure contact level menu" + }, + { + "range": "null value menu" + } + ] + }, + "host role": { + "name": "host role", + "examples": [ + { + "value": "Acquaintance of case" + } + ], + "rank": 67, + "slot_group": "Host exposure information", + "range": "host role menu" + }, + "exposure setting": { + "name": "exposure setting", + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "rank": 68, + "slot_group": "Host exposure information", + "range": "exposure setting menu" + }, + "exposure details": { + "name": "exposure details", + "rank": 69, + "slot_group": "Host exposure information" + }, + "prior Monkeypox infection": { + "name": "prior Monkeypox infection", + "examples": [ + { + "value": "Prior infection" + } + ], + "exact_mappings": [ + "NML_LIMS:prior Monkeypox infection" + ], + "rank": 70, + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "prior Monkeypox infection menu" + }, + { + "range": "null value menu" + } + ] + }, + "prior Monkeypox infection date": { + "name": "prior Monkeypox infection date", + "rank": 71, + "slot_group": "Host reinfection information" + }, + "prior Monkeypox antiviral treatment": { + "name": "prior Monkeypox antiviral treatment", + "examples": [ + { + "value": "Prior antiviral treatment" + } + ], + "exact_mappings": [ + "NML_LIMS:prior Monkeypox antiviral treatment" + ], + "rank": 72, + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "prior Monkeypox antiviral treatment menu" + }, + { + "range": "null value menu" + } + ] + }, + "prior antiviral treatment during prior Monkeypox infection": { + "name": "prior antiviral treatment during prior Monkeypox infection", + "rank": 73, + "slot_group": "Host reinfection information" + }, + "purpose of sequencing": { + "name": "purpose of sequencing", + "examples": [ + { + "value": "Specimens attributed to individuals with no known intimate contacts to positive cases", + "description": "Select \"Targeted surveillance (non-random sampling)\" if the specimen fits any of the following criteria" + }, + { + "value": "Specimens attributed to youth/minors <18 yrs." + }, + { + "value": "Specimens attributed to vulnerable persons living in transient shelters or congregant settings" + }, + { + "value": "Specimens attributed to individuals self-identifying as “female”" + }, + { + "value": "Domestic travel surveillance", + "description": "For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options" + }, + { + "value": "International travel surveillance" + }, + { + "value": "Travel-associated surveillance" + }, + { + "value": "Cluster/Outbreak investigation", + "description": "For specimens targeted for sequencing as part of an outbreak investigation, please select" + }, + { + "value": "Baseline surveillance (random sampling).", + "description": "In all other cases use" + } + ], + "rank": 74, + "slot_group": "Sequencing", + "any_of": [ + { + "range": "purpose of sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose of sequencing details": { + "name": "purpose of sequencing details", + "rank": 75, + "slot_group": "Sequencing" + }, + "sequencing date": { + "name": "sequencing date", + "rank": 76, + "slot_group": "Sequencing", + "required": true + }, + "library ID": { + "name": "library ID", + "rank": 77, + "slot_group": "Sequencing" + }, + "amplicon size": { + "name": "amplicon size", + "rank": 78, + "slot_group": "Sequencing" + }, + "library preparation kit": { + "name": "library preparation kit", + "rank": 79, + "slot_group": "Sequencing" + }, + "sequencing instrument": { + "name": "sequencing instrument", + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], + "rank": 80, + "slot_group": "Sequencing", + "any_of": [ + { + "range": "sequencing instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing protocol": { + "name": "sequencing protocol", + "rank": 81, + "slot_group": "Sequencing" + }, + "sequencing kit number": { + "name": "sequencing kit number", + "rank": 82, + "slot_group": "Sequencing" + }, + "amplicon pcr primer scheme": { + "name": "amplicon pcr primer scheme", + "rank": 83, + "slot_group": "Sequencing" + }, + "raw sequence data processing method": { + "name": "raw sequence data processing method", + "rank": 84, + "slot_group": "Bioinformatics and QC metrics", + "required": true + }, + "dehosting method": { + "name": "dehosting method", + "rank": 85, + "slot_group": "Bioinformatics and QC metrics", + "required": true + }, + "consensus sequence name": { + "name": "consensus sequence name", + "rank": 86, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus sequence filename": { + "name": "consensus sequence filename", + "rank": 87, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus sequence filepath": { + "name": "consensus sequence filepath", + "rank": 88, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus sequence software name": { + "name": "consensus sequence software name", + "rank": 89, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus sequence software version": { + "name": "consensus sequence software version", + "rank": 90, + "slot_group": "Bioinformatics and QC metrics" + }, + "breadth of coverage value": { + "name": "breadth of coverage value", + "rank": 91, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth of coverage value": { + "name": "depth of coverage value", + "rank": 92, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth of coverage threshold": { + "name": "depth of coverage threshold", + "rank": 93, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1 fastq filename": { + "name": "r1 fastq filename", + "rank": 94, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2 fastq filename": { + "name": "r2 fastq filename", + "rank": 95, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1 fastq filepath": { + "name": "r1 fastq filepath", + "rank": 96, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2 fastq filepath": { + "name": "r2 fastq filepath", + "rank": 97, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5 filename": { + "name": "fast5 filename", + "rank": 98, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5 filepath": { + "name": "fast5 filepath", + "rank": 99, + "slot_group": "Bioinformatics and QC metrics" + }, + "number of base pairs sequenced": { + "name": "number of base pairs sequenced", + "rank": 100, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus genome length": { + "name": "consensus genome length", + "rank": 101, + "slot_group": "Bioinformatics and QC metrics" + }, + "reference genome accession": { + "name": "reference genome accession", + "rank": 102, + "slot_group": "Bioinformatics and QC metrics" + }, + "bioinformatics protocol": { + "name": "bioinformatics protocol", + "rank": 103, + "slot_group": "Bioinformatics and QC metrics", + "required": true + }, + "gene name 1": { + "name": "gene name 1", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "rank": 104, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "gene name 1 menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic pcr Ct value 1": { + "name": "diagnostic pcr Ct value 1", + "rank": 105, + "slot_group": "Pathogen diagnostic testing" + }, + "gene name 2": { + "name": "gene name 2", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "rank": 106, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "gene name 2 menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic pcr Ct value 2": { + "name": "diagnostic pcr Ct value 2", + "rank": 107, + "slot_group": "Pathogen diagnostic testing" + }, + "gene name 3": { "name": "gene name 3", "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "rank": 108, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "gene name 3 menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic pcr Ct value 3": { + "name": "diagnostic pcr Ct value 3", + "rank": 109, + "slot_group": "Pathogen diagnostic testing" + }, + "gene name 4": { + "name": "gene name 4", + "rank": 110, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic pcr Ct value 4": { + "name": "diagnostic pcr Ct value 4", + "rank": 111, + "slot_group": "Pathogen diagnostic testing" + }, + "gene name 5": { + "name": "gene name 5", + "rank": 112, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic pcr Ct value 5": { + "name": "diagnostic pcr Ct value 5", + "rank": 113, + "slot_group": "Pathogen diagnostic testing" + }, + "authors": { + "name": "authors", + "rank": 114, + "slot_group": "Contributor acknowledgement" + }, + "DataHarmonizer provenance": { + "name": "DataHarmonizer provenance", + "rank": 115, + "slot_group": "Contributor acknowledgement" + } + }, + "attributes": { + "specimen collector sample ID": { + "name": "specimen collector sample ID", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "from_schema": "https://example.com/monkeypox", + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_ID", + "owner": "Monkeypox", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "Related specimen primary ID": { + "name": "Related specimen primary ID", + "description": "The primary ID of a related specimen previously submitted to the repository.", + "title": "Related specimen primary ID", + "from_schema": "https://example.com/monkeypox", + "rank": 2, + "slot_uri": "GENEPIO:0001128", + "alias": "Related_specimen_primary_ID", + "owner": "Monkeypox", + "slot_group": "Database Identifiers" + }, + "case ID": { + "name": "case ID", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case ID", + "from_schema": "https://example.com/monkeypox", + "rank": 3, + "slot_uri": "GENEPIO:0100281", + "alias": "case_ID", + "owner": "Monkeypox", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString" + }, + "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": 4, + "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": 5, + "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": 6, + "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": 7, + "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": 8, + "slot_uri": "GENEPIO:0001147", + "alias": "GISAID_accession", + "owner": "Monkeypox", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample collected by": { + "name": "sample collected by", + "description": "The name of the agency that collected the original sample.", + "title": "sample collected by", + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "GISAID:Originating lab", + "CNPHI:Lab Name", + "NML_LIMS:CUSTOMER", + "BIOSAMPLE:collected_by", + "VirusSeq_Portal:sample collected by" + ], + "rank": 9, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "sample collected by menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample collector contact email": { + "name": "sample collector contact email", + "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": 10, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "sample collector contact address": { + "name": "sample collector contact address", + "description": "The mailing address of the agency submitting the sample.", + "title": "sample collector contact address", + "from_schema": "https://example.com/monkeypox", + "rank": 11, + "slot_uri": "GENEPIO:0001158", + "alias": "sample_collector_contact_address", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sequenced by": { + "name": "sequenced by", + "description": "The name of the agency that generated the sequence.", + "title": "sequenced by", + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "sequence submitted by menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced by contact email": { + "name": "sequenced by contact email", + "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": 13, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sequenced by contact address": { + "name": "sequenced by contact address", + "description": "The mailing address of the agency submitting the sequence.", + "title": "sequenced by contact address", + "from_schema": "https://example.com/monkeypox", + "rank": 14, + "slot_uri": "GENEPIO:0100423", + "alias": "sequenced_by_contact_address", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sequence submitted by": { + "name": "sequence submitted by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence submitted by", + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "GISAID:Submitting lab", + "CNPHI:Sequencing Centre", + "NML_LIMS:PH_SEQUENCING_SUBMITTER", + "BIOSAMPLE:sequence_submitted_by", + "VirusSeq_Portal:sequence submitted by" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "sequence submitted by menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequence submitter contact email": { + "name": "sequence submitter contact email", + "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": 16, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sequence submitter contact address": { + "name": "sequence submitter contact address", + "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": 17, + "slot_uri": "GENEPIO:0001167", + "alias": "sequence_submitter_contact_address", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample collection date": { + "name": "sample collection date", + "description": "The date on which the sample was collected.", + "title": "sample collection date", + "from_schema": "https://example.com/monkeypox", + "rank": 18, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true + }, + "sample collection date precision": { + "name": "sample collection date precision", + "description": "The precision to which the \"sample collection date\" was provided.", + "title": "sample collection date precision", + "from_schema": "https://example.com/monkeypox", + "rank": 19, + "slot_uri": "GENEPIO:0001177", + "alias": "sample_collection_date_precision", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true + }, + "sample received date": { + "name": "sample received date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "from_schema": "https://example.com/monkeypox", + "rank": 20, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing" + }, + "geo_loc_name (country)": { + "name": "geo_loc_name (country)", + "description": "The country where the sample was collected.", + "title": "geo_loc_name (country)", + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 21, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_(country)", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name (state/province/territory)": { + "name": "geo_loc_name (state/province/territory)", + "description": "The state/province/territory where the sample was collected.", + "title": "geo_loc_name (state/province/territory)", + "comments": [ + "Provide the province/territory name from the controlled vocabulary provided." ], - "rank": 55, - "slot_group": "Pathogen diagnostic testing", + "from_schema": "https://example.com/monkeypox", + "rank": 22, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_(state/province/territory)", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name (state/province/territory) menu" + }, + { + "range": "null value menu" + } + ] + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "examples": [ + { + "value": "Monkeypox virus" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 23, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "isolate": { + "name": "isolate", + "description": "Identifier of the specific isolate.", + "title": "isolate", + "comments": [ + "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\"." + ], + "examples": [ + { + "value": "hMpxV/Canada/UN-NML-12345/2022" + } + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "GISAID:Virus name", + "CNPHI:GISAID Virus Name", + "NML_LIMS:SUBMISSIONS - GISAID Virus Name", + "BIOSAMPLE:isolate", + "BIOSAMPLE:GISAID_virus_name", + "VirusSeq_Portal:isolate", + "VirusSeq_Portal:fasta header name" + ], + "rank": 24, + "slot_uri": "GENEPIO:0001195", + "alias": "isolate", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true + }, + "purpose of sampling": { + "name": "purpose of sampling", + "description": "The reason that the sample was collected.", + "title": "purpose of sampling", + "examples": [ + { + "value": "Diagnostic testing" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 25, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "purpose of sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose of sampling details": { + "name": "purpose of sampling details", + "description": "The description of why the sample was collected, providing specific details.", + "title": "purpose of sampling details", + "from_schema": "https://example.com/monkeypox", + "rank": 26, + "slot_uri": "GENEPIO:0001200", + "alias": "purpose_of_sampling_details", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true + }, + "NML submitted specimen type": { + "name": "NML submitted specimen type", + "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": 27, + "slot_uri": "GENEPIO:0001204", + "alias": "NML_submitted_specimen_type", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "range": "NML submitted specimen type menu", + "required": true + }, + "Related specimen relationship type": { + "name": "Related specimen relationship type", + "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": 28, + "slot_uri": "GENEPIO:0001209", + "alias": "Related_specimen_relationship_type", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing" + }, + "anatomical material": { + "name": "anatomical material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical material", + "examples": [ + { + "value": "Lesion (Pustule)" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 29, + "slot_uri": "GENEPIO:0001211", + "multivalued": true, + "alias": "anatomical_material", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "anatomical material menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical part": { + "name": "anatomical part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical part", + "examples": [ + { + "value": "Genital area" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 30, + "slot_uri": "GENEPIO:0001214", + "multivalued": true, + "alias": "anatomical_part", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "anatomical part menu" + }, + { + "range": "null value menu" + } + ] + }, + "body product": { + "name": "body product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body product", + "examples": [ + { + "value": "Pus" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 31, + "slot_uri": "GENEPIO:0001216", + "multivalued": true, + "alias": "body_product", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "body product menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection device": { + "name": "collection device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection device", + "examples": [ + { + "value": "Swab" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 32, + "slot_uri": "GENEPIO:0001234", + "multivalued": true, + "alias": "collection_device", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "collection device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection method": { + "name": "collection method", + "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", + "title": "collection method", + "examples": [ + { + "value": "Biopsy" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 33, + "slot_uri": "GENEPIO:0001241", + "multivalued": true, + "alias": "collection_method", + "owner": "Monkeypox", + "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { - "range": "gene name 3 menu" + "range": "collection method menu" }, { "range": "null value menu" } ] }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", - "rank": 56, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 4": { - "name": "gene name 4", - "rank": 57, - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic pcr Ct value 4": { - "name": "diagnostic pcr Ct value 4", - "rank": 58, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 5": { - "name": "gene name 5", - "rank": 59, - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic pcr Ct value 5": { - "name": "diagnostic pcr Ct value 5", - "rank": 60, - "slot_group": "Pathogen diagnostic testing" - }, - "authors": { - "name": "authors", - "rank": 61, - "slot_group": "Contributor acknowledgement" - }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "rank": 62, - "slot_group": "Contributor acknowledgement" - } - }, - "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "The user-defined name for the sample.", - "title": "specimen collector sample ID", + "specimen processing": { + "name": "specimen processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen processing", + "examples": [ + { + "value": "Specimens pooled" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "specimen_collector_sample_ID", + "exact_mappings": [ + "NML_LIMS:specimen processing" + ], + "rank": 34, + "slot_uri": "GENEPIO:0001253", + "multivalued": true, + "alias": "specimen_processing", "owner": "Monkeypox", - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "required": true + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "specimen processing menu" + }, + { + "range": "null value menu" + } + ] }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", - "description": "The primary ID of a related specimen previously submitted to the repository.", - "title": "Related specimen primary ID", + "specimen processing details": { + "name": "specimen processing details", + "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", + "title": "specimen processing details", "from_schema": "https://example.com/monkeypox", - "rank": 2, - "slot_uri": "GENEPIO:0001128", - "alias": "Related_specimen_primary_ID", + "rank": 35, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", "owner": "Monkeypox", - "slot_group": "Database Identifiers" + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "bioproject accession": { - "name": "bioproject accession", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "title": "bioproject accession", + "host (common name)": { + "name": "host (common name)", + "description": "The commonly used name of the host.", + "title": "host (common name)", "from_schema": "https://example.com/monkeypox", - "rank": 3, - "slot_uri": "GENEPIO:0001136", - "alias": "bioproject_accession", + "exact_mappings": [ + "NML_LIMS:PH_ANIMAL_TYPE" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001386", + "alias": "host_(common_name)", "owner": "Monkeypox", - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Host Information", + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] }, - "biosample accession": { - "name": "biosample accession", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "title": "biosample accession", + "host (scientific name)": { + "name": "host (scientific name)", + "description": "The taxonomic, or scientific name of the host.", + "title": "host (scientific name)", + "examples": [ + { + "value": "Homo sapiens" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 4, - "slot_uri": "GENEPIO:0001139", - "alias": "biosample_accession", + "rank": 37, + "slot_uri": "GENEPIO:0001387", + "alias": "host_(scientific_name)", "owner": "Monkeypox", - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] }, - "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", + "host health state": { + "name": "host health state", + "description": "Health status of the host at the time of sample collection.", + "title": "host health state", + "examples": [ + { + "value": "Asymptomatic" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 5, - "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", + "exact_mappings": [ + "GISAID:Patient status", + "NML_LIMS:PH_HOST_HEALTH", + "BIOSAMPLE:host_health_state" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", "owner": "Monkeypox", - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Host Information", + "any_of": [ + { + "range": "host health state menu" + }, + { + "range": "null value menu" + } + ] }, - "GenBank accession": { - "name": "GenBank accession", - "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", - "title": "GenBank accession", + "host health status details": { + "name": "host health status details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host health status details", + "examples": [ + { + "value": "Hospitalized" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 6, - "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_DETAILS" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", "owner": "Monkeypox", - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Host Information", + "any_of": [ + { + "range": "host health status details menu" + }, + { + "range": "null value menu" + } + ] }, - "GISAID accession": { - "name": "GISAID accession", - "description": "The GISAID accession number assigned to the sequence.", - "title": "GISAID accession", + "host health outcome": { + "name": "host health outcome", + "description": "Disease outcome in the host.", + "title": "host health outcome", + "examples": [ + { + "value": "Recovered" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 7, - "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_OUTCOME", + "BIOSAMPLE:host_health_outcome" + ], + "rank": 40, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_outcome", "owner": "Monkeypox", - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Host Information", + "any_of": [ + { + "range": "host health outcome menu" + }, + { + "range": "null value menu" + } + ] }, - "sample collected by": { - "name": "sample collected by", - "description": "The name of the agency that collected the original sample.", - "title": "sample collected by", - "from_schema": "https://example.com/monkeypox", - "exact_mappings": [ - "GISAID:Originating lab", - "CNPHI:Lab Name", - "NML_LIMS:CUSTOMER", - "BIOSAMPLE:collected_by", - "VirusSeq_Portal:sample collected by" + "host disease": { + "name": "host disease", + "description": "The name of the disease experienced by the host.", + "title": "host disease", + "examples": [ + { + "value": "Monkeypox" + } ], - "rank": 8, - "slot_uri": "GENEPIO:0001153", - "alias": "sample_collected_by", + "from_schema": "https://example.com/monkeypox", + "rank": 41, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", + "slot_group": "Host Information", "required": true, "any_of": [ { - "range": "sample collected by menu" + "range": "host disease menu" }, { "range": "null value menu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", - "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": 9, - "slot_uri": "GENEPIO:0001156", - "alias": "sample_collector_contact_email", - "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "pattern": "^\\S+@\\S+\\.\\S+$" - }, - "sample collector contact address": { - "name": "sample collector contact address", - "description": "The mailing address of the agency submitting the sample.", - "title": "sample collector contact address", + "host age": { + "name": "host age", + "description": "Age of host at the time of sampling.", + "title": "host age", "from_schema": "https://example.com/monkeypox", - "rank": 10, - "slot_uri": "GENEPIO:0001158", - "alias": "sample_collector_contact_address", + "exact_mappings": [ + "GISAID:Patient age", + "NML_LIMS:PH_AGE", + "BIOSAMPLE:host_age" + ], + "rank": 42, + "slot_uri": "GENEPIO:0001392", + "alias": "host_age", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Host Information", + "required": true, + "minimum_value": 0, + "maximum_value": 130 }, - "sequenced by": { - "name": "sequenced by", - "description": "The name of the agency that generated the sequence.", - "title": "sequenced by", + "host age unit": { + "name": "host age unit", + "description": "The units used to measure the host's age.", + "title": "host age unit", + "examples": [ + { + "value": "year" + } + ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "NML_LIMS:PH_SEQUENCING_CENTRE", - "BIOSAMPLE:sequenced_by" + "NML_LIMS:PH_AGE_UNIT", + "BIOSAMPLE:host_age_unit" ], - "rank": 11, - "slot_uri": "GENEPIO:0100416", - "alias": "sequenced_by", + "rank": 43, + "slot_uri": "GENEPIO:0001393", + "alias": "host_age_unit", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", + "slot_group": "Host Information", "required": true, "any_of": [ { - "range": "sequence submitted by menu" + "range": "host age unit menu" }, { "range": "null value menu" } ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", - "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": 12, - "slot_uri": "GENEPIO:0100422", - "alias": "sequenced_by_contact_email", - "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sequenced by contact address": { - "name": "sequenced by contact address", - "description": "The mailing address of the agency submitting the sequence.", - "title": "sequenced by contact address", - "from_schema": "https://example.com/monkeypox", - "rank": 13, - "slot_uri": "GENEPIO:0100423", - "alias": "sequenced_by_contact_address", - "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sequence submitted by": { - "name": "sequence submitted by", - "description": "The name of the agency that submitted the sequence to a database.", - "title": "sequence submitted by", + "host age bin": { + "name": "host age bin", + "description": "The age category of the host at the time of sampling.", + "title": "host age bin", + "examples": [ + { + "value": "50 - 59" + } + ], "from_schema": "https://example.com/monkeypox", "exact_mappings": [ - "GISAID:Submitting lab", - "CNPHI:Sequencing Centre", - "NML_LIMS:PH_SEQUENCING_SUBMITTER", - "BIOSAMPLE:sequence_submitted_by", - "VirusSeq_Portal:sequence submitted by" + "NML_LIMS:PH_AGE_GROUP", + "BIOSAMPLE:host_age_bin" ], - "rank": 14, - "slot_uri": "GENEPIO:0001159", - "alias": "sequence_submitted_by", + "rank": 44, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", + "slot_group": "Host Information", "required": true, "any_of": [ { - "range": "sequence submitted by menu" + "range": "host age bin menu" }, { "range": "null value menu" } ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "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": 15, - "slot_uri": "GENEPIO:0001165", - "alias": "sequence_submitter_contact_email", - "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "description": "The mailing address of the agency responsible for submission of the sequence.", - "title": "sequence submitter contact address", + "host gender": { + "name": "host gender", + "description": "The gender of the host at the time of sample collection.", + "title": "host gender", + "examples": [ + { + "value": "Male" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 16, - "slot_uri": "GENEPIO:0001167", - "alias": "sequence_submitter_contact_address", + "exact_mappings": [ + "GISAID:Gender", + "NML_LIMS:VD_SEX", + "BIOSAMPLE:host_sex" + ], + "rank": 45, + "slot_uri": "GENEPIO:0001395", + "alias": "host_gender", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Host Information", + "required": true, + "structured_pattern": { + "syntax": "{Title_Case}", + "interpolated": true, + "partial_match": false + }, + "any_of": [ + { + "range": "host gender menu" + }, + { + "range": "null value menu" + } + ] }, - "sample collection date": { - "name": "sample collection date", - "description": "The date on which the sample was collected.", - "title": "sample collection date", + "host residence geo_loc name (country)": { + "name": "host residence geo_loc name (country)", + "description": "The country of residence of the host.", + "title": "host residence geo_loc name (country)", + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 17, - "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", + "exact_mappings": [ + "NML_LIMS:PH_HOST_COUNTRY" + ], + "rank": 46, + "slot_uri": "GENEPIO:0001396", + "alias": "host_residence_geo_loc_name_(country)", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Host Information", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] }, - "sample collection date precision": { - "name": "sample collection date precision", - "description": "The precision to which the \"sample collection date\" was provided.", - "title": "sample collection date precision", + "host residence geo_loc name (state/province/territory)": { + "name": "host residence geo_loc name (state/province/territory)", + "description": "The state/province/territory of residence of the host.", + "title": "host residence geo_loc name (state/province/territory)", "from_schema": "https://example.com/monkeypox", - "rank": 18, - "slot_uri": "GENEPIO:0001177", - "alias": "sample_collection_date_precision", + "rank": 47, + "slot_uri": "GENEPIO:0001397", + "alias": "host_residence_geo_loc_name_(state/province/territory)", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Host Information" }, - "sample received date": { - "name": "sample received date", - "description": "The date on which the sample was received.", - "title": "sample received date", + "symptom onset date": { + "name": "symptom onset date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom onset date", "from_schema": "https://example.com/monkeypox", - "rank": 19, - "slot_uri": "GENEPIO:0001179", - "alias": "sample_received_date", + "rank": 48, + "slot_uri": "GENEPIO:0001399", + "alias": "symptom_onset_date", "owner": "Monkeypox", - "slot_group": "Sample collection and processing" + "slot_group": "Host Information" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", - "description": "The country where the sample was collected.", - "title": "geo_loc_name (country)", + "signs and symptoms": { + "name": "signs and symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs and symptoms", "examples": [ { - "value": "Canada" + "value": "Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain)" } ], "from_schema": "https://example.com/monkeypox", - "rank": 20, - "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "exact_mappings": [ + "NML_LIMS:HC_SYMPTOMS" + ], + "rank": 49, + "slot_uri": "GENEPIO:0001400", + "multivalued": true, + "alias": "signs_and_symptoms", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host Information", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "signs and symptoms menu" }, { "range": "null value menu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", - "description": "The state/province/territory where the sample was collected.", - "title": "geo_loc_name (state/province/territory)", - "comments": [ - "Provide the province/territory name from the controlled vocabulary provided." - ], + "pre-existing conditions and risk factors": { + "name": "pre-existing conditions and risk factors", + "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": 21, - "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", + "rank": 50, + "slot_uri": "GENEPIO:0001401", + "multivalued": true, + "alias": "pre_existing_conditions_and_risk_factors", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host Information", "any_of": [ { - "range": "geo_loc_name (state/province/territory) menu" + "range": "pre-existing conditions and risk factors menu" }, { "range": "null value menu" } ] }, - "organism": { - "name": "organism", - "description": "Taxonomic name of the organism.", - "title": "organism", + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", "examples": [ { - "value": "Monkeypox virus" + "value": "Delayed wound healing (lesion healing)" } ], "from_schema": "https://example.com/monkeypox", - "rank": 22, - "slot_uri": "GENEPIO:0001191", - "alias": "organism", + "exact_mappings": [ + "NML_LIMS:complications" + ], + "rank": 51, + "slot_uri": "GENEPIO:0001402", + "multivalued": true, + "alias": "complications", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host Information", "any_of": [ { - "range": "organism menu" + "range": "complications menu" }, { "range": "null value menu" } ] }, - "isolate": { - "name": "isolate", - "description": "Identifier of the specific isolate.", - "title": "isolate", - "comments": [ - "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\"." - ], - "examples": [ - { - "value": "hMpxV/Canada/UN-NML-12345/2022" - } - ], + "antiviral therapy": { + "name": "antiviral therapy", + "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", + "title": "antiviral therapy", "from_schema": "https://example.com/monkeypox", - "exact_mappings": [ - "GISAID:Virus name", - "CNPHI:GISAID Virus Name", - "NML_LIMS:SUBMISSIONS - GISAID Virus Name", - "BIOSAMPLE:isolate", - "BIOSAMPLE:GISAID_virus_name", - "VirusSeq_Portal:isolate", - "VirusSeq_Portal:fasta header name" - ], - "rank": 23, - "slot_uri": "GENEPIO:0001195", - "alias": "isolate", + "rank": 52, + "slot_uri": "NCIT:C16119", + "alias": "antiviral_therapy", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" }, - "purpose of sampling": { - "name": "purpose of sampling", - "description": "The reason that the sample was collected.", - "title": "purpose of sampling", + "host vaccination status": { + "name": "host vaccination status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host vaccination status", "examples": [ { - "value": "Diagnostic testing" + "value": "Not Vaccinated" } ], "from_schema": "https://example.com/monkeypox", - "rank": 24, - "slot_uri": "GENEPIO:0001198", - "alias": "purpose_of_sampling", + "rank": 53, + "slot_uri": "GENEPIO:0001404", + "alias": "host_vaccination_status", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host vaccination information", "any_of": [ { - "range": "purpose of sampling menu" + "range": "host vaccination status menu" }, { "range": "null value menu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", - "description": "The description of why the sample was collected, providing specific details.", - "title": "purpose of sampling details", + "number of vaccine doses received": { + "name": "number of vaccine doses received", + "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": 25, - "slot_uri": "GENEPIO:0001200", - "alias": "purpose_of_sampling_details", + "rank": 54, + "slot_uri": "GENEPIO:0001406", + "alias": "number_of_vaccine_doses_received", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Host vaccination information", + "range": "integer" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", - "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", - "title": "NML submitted specimen type", + "vaccination dose 1 vaccine name": { + "name": "vaccination dose 1 vaccine name", + "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": 26, - "slot_uri": "GENEPIO:0001204", - "alias": "NML_submitted_specimen_type", + "rank": 55, + "slot_uri": "GENEPIO:0100313", + "alias": "vaccination_dose_1_vaccine_name", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "range": "NML submitted specimen type menu", - "required": true + "slot_group": "Host vaccination information" }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", - "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", - "title": "Related specimen relationship type", + "vaccination dose 1 vaccination date": { + "name": "vaccination dose 1 vaccination date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination dose 1 vaccination date", "from_schema": "https://example.com/monkeypox", - "rank": 27, - "slot_uri": "GENEPIO:0001209", - "alias": "Related_specimen_relationship_type", + "rank": 56, + "slot_uri": "GENEPIO:0100314", + "alias": "vaccination_dose_1_vaccination_date", "owner": "Monkeypox", - "slot_group": "Sample collection and processing" + "slot_group": "Host vaccination information" }, - "anatomical material": { - "name": "anatomical material", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "title": "anatomical material", + "vaccination history": { + "name": "vaccination history", + "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": 57, + "slot_uri": "GENEPIO:0100321", + "alias": "vaccination_history", + "owner": "Monkeypox", + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "location of exposure geo_loc name (country)": { + "name": "location of exposure geo_loc name (country)", + "description": "The country where the host was likely exposed to the causative agent of the illness.", + "title": "location of exposure geo_loc name (country)", "examples": [ { - "value": "Lesion (Pustule)" + "value": "Canada" } ], "from_schema": "https://example.com/monkeypox", - "rank": 28, - "slot_uri": "GENEPIO:0001211", - "multivalued": true, - "alias": "anatomical_material", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_COUNTRY" + ], + "rank": 58, + "slot_uri": "GENEPIO:0001410", + "alias": "location_of_exposure_geo_loc_name_(country)", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "anatomical material menu" + "range": "geo_loc_name (country) menu" }, { "range": "null value menu" } ] }, - "anatomical part": { - "name": "anatomical part", - "description": "An anatomical part of an organism e.g. oropharynx.", - "title": "anatomical part", + "destination of most recent travel (city)": { + "name": "destination of most recent travel (city)", + "description": "The name of the city that was the destination of most recent travel.", + "title": "destination of most recent travel (city)", + "from_schema": "https://example.com/monkeypox", + "rank": 59, + "slot_uri": "GENEPIO:0001411", + "alias": "destination_of_most_recent_travel_(city)", + "owner": "Monkeypox", + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "destination of most recent travel (state/province/territory)": { + "name": "destination of most recent travel (state/province/territory)", + "description": "The name of the state/province/territory that was the destination of most recent travel.", + "title": "destination of most recent travel (state/province/territory)", + "comments": [ + "Select the province name from the pick list provided in the template." + ], + "from_schema": "https://example.com/monkeypox", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 60, + "slot_uri": "GENEPIO:0001412", + "alias": "destination_of_most_recent_travel_(state/province/territory)", + "owner": "Monkeypox", + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (state/province/territory) menu" + }, + { + "range": "null value menu" + } + ] + }, + "destination of most recent travel (country)": { + "name": "destination of most recent travel (country)", + "description": "The name of the country that was the destination of most recent travel.", + "title": "destination of most recent travel (country)", "examples": [ { - "value": "Genital area" + "value": "Canada" } ], "from_schema": "https://example.com/monkeypox", - "rank": 29, - "slot_uri": "GENEPIO:0001214", - "multivalued": true, - "alias": "anatomical_part", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 61, + "slot_uri": "GENEPIO:0001413", + "alias": "destination_of_most_recent_travel_(country)", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "anatomical part menu" + "range": "geo_loc_name (country) menu" }, { "range": "null value menu" } ] }, - "body product": { - "name": "body product", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "title": "body product", + "most recent travel departure date": { + "name": "most recent travel departure date", + "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", + "title": "most recent travel departure date", + "from_schema": "https://example.com/monkeypox", + "rank": 62, + "slot_uri": "GENEPIO:0001414", + "alias": "most_recent_travel_departure_date", + "owner": "Monkeypox", + "slot_group": "Host exposure information" + }, + "most recent travel return date": { + "name": "most recent travel return date", + "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", + "title": "most recent travel return date", + "from_schema": "https://example.com/monkeypox", + "rank": 63, + "slot_uri": "GENEPIO:0001415", + "alias": "most_recent_travel_return_date", + "owner": "Monkeypox", + "slot_group": "Host exposure information" + }, + "travel history": { + "name": "travel history", + "description": "Travel history in last six months.", + "title": "travel history", + "from_schema": "https://example.com/monkeypox", + "rank": 64, + "slot_uri": "GENEPIO:0001416", + "alias": "travel_history", + "owner": "Monkeypox", + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "exposure event": { + "name": "exposure event", + "description": "Event leading to exposure.", + "title": "exposure event", "examples": [ { - "value": "Pus" + "value": "Party" } ], "from_schema": "https://example.com/monkeypox", - "rank": 30, - "slot_uri": "GENEPIO:0001216", - "multivalued": true, - "alias": "body_product", + "rank": 65, + "slot_uri": "GENEPIO:0001417", + "alias": "exposure_event", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "body product menu" + "range": "exposure event menu" }, { "range": "null value menu" } ] }, - "collection device": { - "name": "collection device", - "description": "The instrument or container used to collect the sample e.g. swab.", - "title": "collection device", + "exposure contact level": { + "name": "exposure contact level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", "examples": [ { - "value": "Swab" + "value": "Contact with infected individual" } - ], - "from_schema": "https://example.com/monkeypox", - "rank": 31, - "slot_uri": "GENEPIO:0001234", - "multivalued": true, - "alias": "collection_device", + ], + "from_schema": "https://example.com/monkeypox", + "rank": 66, + "slot_uri": "GENEPIO:0001418", + "alias": "exposure_contact_level", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "collection device menu" + "range": "exposure contact level menu" }, { "range": "null value menu" } ] }, - "collection method": { - "name": "collection method", - "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", - "title": "collection method", + "host role": { + "name": "host role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", "examples": [ { - "value": "Biopsy" + "value": "Acquaintance of case" } ], "from_schema": "https://example.com/monkeypox", - "rank": 32, - "slot_uri": "GENEPIO:0001241", + "rank": 67, + "slot_uri": "GENEPIO:0001419", "multivalued": true, - "alias": "collection_method", + "alias": "host_role", "owner": "Monkeypox", - "slot_group": "Sample collection and processing", - "required": true, - "any_of": [ - { - "range": "collection method menu" - }, + "slot_group": "Host exposure information", + "range": "host role menu" + }, + "exposure setting": { + "name": "exposure setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "examples": [ { - "range": "null value menu" + "value": "Healthcare Setting" } - ] + ], + "from_schema": "https://example.com/monkeypox", + "rank": 68, + "slot_uri": "GENEPIO:0001428", + "multivalued": true, + "alias": "exposure_setting", + "owner": "Monkeypox", + "slot_group": "Host exposure information", + "range": "exposure setting menu" }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", + "exposure details": { + "name": "exposure details", + "description": "Additional host exposure information.", + "title": "exposure details", + "from_schema": "https://example.com/monkeypox", + "rank": 69, + "slot_uri": "GENEPIO:0001431", + "alias": "exposure_details", + "owner": "Monkeypox", + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "prior Monkeypox infection": { + "name": "prior Monkeypox infection", + "description": "The absence or presence of a prior Monkeypox infection.", + "title": "prior Monkeypox infection", "examples": [ { - "value": "Homo sapiens" + "value": "Prior infection" } ], "from_schema": "https://example.com/monkeypox", - "rank": 33, - "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", + "exact_mappings": [ + "NML_LIMS:prior Monkeypox infection" + ], + "rank": 70, + "slot_uri": "GENEPIO:0100532", + "alias": "prior_Monkeypox_infection", "owner": "Monkeypox", - "slot_group": "Host Information", - "required": true, + "slot_group": "Host reinfection information", "any_of": [ { - "range": "host (scientific name) menu" + "range": "prior Monkeypox infection menu" }, { "range": "null value menu" } ] }, - "host disease": { - "name": "host disease", - "description": "The name of the disease experienced by the host.", - "title": "host disease", + "prior Monkeypox infection date": { + "name": "prior Monkeypox infection date", + "description": "The date of diagnosis of the prior Monkeypox infection.", + "title": "prior Monkeypox infection date", + "from_schema": "https://example.com/monkeypox", + "rank": 71, + "slot_uri": "GENEPIO:0100533", + "alias": "prior_Monkeypox_infection_date", + "owner": "Monkeypox", + "slot_group": "Host reinfection information" + }, + "prior Monkeypox antiviral treatment": { + "name": "prior Monkeypox antiviral treatment", + "description": "The absence or presence of antiviral treatment for a prior Monkeypox infection.", + "title": "prior Monkeypox antiviral treatment", "examples": [ { - "value": "Monkeypox" + "value": "Prior antiviral treatment" } ], "from_schema": "https://example.com/monkeypox", - "rank": 34, - "slot_uri": "GENEPIO:0001391", - "alias": "host_disease", + "exact_mappings": [ + "NML_LIMS:prior Monkeypox antiviral treatment" + ], + "rank": 72, + "slot_uri": "GENEPIO:0100534", + "alias": "prior_Monkeypox_antiviral_treatment", "owner": "Monkeypox", - "slot_group": "Host Information", - "required": true, + "slot_group": "Host reinfection information", "any_of": [ { - "range": "host disease menu" + "range": "prior Monkeypox antiviral treatment menu" }, { "range": "null value menu" } ] }, - "travel history": { - "name": "travel history", - "description": "Travel history in last six months.", - "title": "travel history", + "prior antiviral treatment during prior Monkeypox infection": { + "name": "prior antiviral treatment during prior Monkeypox infection", + "description": "Antiviral treatment for any infection during the prior Moneypox infection period.", + "title": "prior antiviral treatment during prior Monkeypox infection", "from_schema": "https://example.com/monkeypox", - "rank": 35, - "slot_uri": "GENEPIO:0001416", - "alias": "travel_history", + "rank": 73, + "slot_uri": "GENEPIO:0100535", + "alias": "prior_antiviral_treatment_during_prior_Monkeypox_infection", "owner": "Monkeypox", - "slot_group": "Host exposure information", + "slot_group": "Host reinfection information", "range": "WhitespaceMinimizedString" }, "purpose of sequencing": { @@ -8764,7 +11847,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 36, + "rank": 74, "slot_uri": "GENEPIO:0001445", "multivalued": true, "alias": "purpose_of_sequencing", @@ -8785,7 +11868,7 @@ 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": 37, + "rank": 75, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "Monkeypox", @@ -8797,19 +11880,44 @@ var SCHEMA = { "description": "The date the sample was sequenced.", "title": "sequencing date", "from_schema": "https://example.com/monkeypox", - "rank": 38, + "rank": 76, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "Monkeypox", "slot_group": "Sequencing", "required": true }, + "library ID": { + "name": "library ID", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library ID", + "from_schema": "https://example.com/monkeypox", + "rank": 77, + "slot_uri": "GENEPIO:0001448", + "alias": "library_ID", + "owner": "Monkeypox", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "amplicon size": { + "name": "amplicon size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", + "from_schema": "https://example.com/monkeypox", + "rank": 78, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "Monkeypox", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, "library preparation kit": { "name": "library preparation kit", "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": 39, + "rank": 79, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "Monkeypox", @@ -8826,7 +11934,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 40, + "rank": 80, "slot_uri": "GENEPIO:0001452", "multivalued": true, "alias": "sequencing_instrument", @@ -8842,12 +11950,48 @@ var SCHEMA = { } ] }, + "sequencing protocol": { + "name": "sequencing protocol", + "description": "The protocol used to generate the sequence.", + "title": "sequencing protocol", + "from_schema": "https://example.com/monkeypox", + "rank": 81, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "Monkeypox", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "sequencing kit number": { + "name": "sequencing kit number", + "description": "The manufacturer's kit number.", + "title": "sequencing kit number", + "from_schema": "https://example.com/monkeypox", + "rank": 82, + "slot_uri": "GENEPIO:0001455", + "alias": "sequencing_kit_number", + "owner": "Monkeypox", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "amplicon pcr primer scheme": { + "name": "amplicon pcr primer scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", + "from_schema": "https://example.com/monkeypox", + "rank": 83, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "Monkeypox", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, "raw sequence data processing method": { "name": "raw sequence data processing method", "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": 41, + "rank": 84, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "Monkeypox", @@ -8860,7 +12004,7 @@ var SCHEMA = { "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "from_schema": "https://example.com/monkeypox", - "rank": 42, + "rank": 85, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "Monkeypox", @@ -8868,12 +12012,48 @@ var SCHEMA = { "range": "WhitespaceMinimizedString", "required": true }, + "consensus sequence name": { + "name": "consensus sequence name", + "description": "The name of the consensus sequence.", + "title": "consensus sequence name", + "from_schema": "https://example.com/monkeypox", + "rank": 86, + "slot_uri": "GENEPIO:0001460", + "alias": "consensus_sequence_name", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "consensus sequence filename": { + "name": "consensus sequence filename", + "description": "The name of the consensus sequence file.", + "title": "consensus sequence filename", + "from_schema": "https://example.com/monkeypox", + "rank": 87, + "slot_uri": "GENEPIO:0001461", + "alias": "consensus_sequence_filename", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "consensus sequence filepath": { + "name": "consensus sequence filepath", + "description": "The filepath of the consesnsus sequence file.", + "title": "consensus sequence filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 88, + "slot_uri": "GENEPIO:0001462", + "alias": "consensus_sequence_filepath", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, "consensus sequence software name": { "name": "consensus sequence software name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", "from_schema": "https://example.com/monkeypox", - "rank": 43, + "rank": 89, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "Monkeypox", @@ -8886,7 +12066,7 @@ 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": 44, + "rank": 90, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "Monkeypox", @@ -8899,7 +12079,7 @@ 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": 45, + "rank": 91, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "Monkeypox", @@ -8911,7 +12091,7 @@ 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": 46, + "rank": 92, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "Monkeypox", @@ -8923,19 +12103,93 @@ 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": 47, + "rank": 93, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "Monkeypox", "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, + "r1 fastq filename": { + "name": "r1 fastq filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1 fastq filename", + "from_schema": "https://example.com/monkeypox", + "rank": 94, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "r2 fastq filename": { + "name": "r2 fastq filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2 fastq filename", + "from_schema": "https://example.com/monkeypox", + "rank": 95, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "r1 fastq filepath": { + "name": "r1 fastq filepath", + "description": "The location of the r1 FASTQ file within a user's file system.", + "title": "r1 fastq filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 96, + "slot_uri": "GENEPIO:0001478", + "alias": "r1_fastq_filepath", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "r2 fastq filepath": { + "name": "r2 fastq filepath", + "description": "The location of the r2 FASTQ file within a user's file system.", + "title": "r2 fastq filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 97, + "slot_uri": "GENEPIO:0001479", + "alias": "r2_fastq_filepath", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "fast5 filename": { + "name": "fast5 filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5 filename", + "from_schema": "https://example.com/monkeypox", + "rank": 98, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "fast5 filepath": { + "name": "fast5 filepath", + "description": "The location of the FAST5 file within a user's file system.", + "title": "fast5 filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 99, + "slot_uri": "GENEPIO:0001481", + "alias": "fast5_filepath", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, "number of base pairs sequenced": { "name": "number of base pairs sequenced", "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": 48, + "rank": 100, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "Monkeypox", @@ -8948,7 +12202,7 @@ 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": 49, + "rank": 101, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "Monkeypox", @@ -8956,12 +12210,24 @@ var SCHEMA = { "range": "integer", "minimum_value": 0 }, + "reference genome accession": { + "name": "reference genome accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "from_schema": "https://example.com/monkeypox", + "rank": 102, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "Monkeypox", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, "bioinformatics protocol": { "name": "bioinformatics protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "from_schema": "https://example.com/monkeypox", - "rank": 50, + "rank": 103, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "Monkeypox", @@ -8977,7 +12243,7 @@ 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": 104, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", "owner": "Monkeypox", @@ -8996,7 +12262,7 @@ 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": 52, + "rank": 105, "slot_uri": "GENEPIO:0001509", "alias": "diagnostic_pcr_Ct_value_1", "owner": "Monkeypox", @@ -9010,7 +12276,7 @@ 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": 53, + "rank": 106, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", "owner": "Monkeypox", @@ -9029,7 +12295,7 @@ 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": 54, + "rank": 107, "slot_uri": "GENEPIO:0001512", "alias": "diagnostic_pcr_Ct_value_2", "owner": "Monkeypox", @@ -9043,7 +12309,7 @@ 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": 55, + "rank": 108, "slot_uri": "GENEPIO:0001513", "alias": "gene_name_3", "owner": "Monkeypox", @@ -9062,7 +12328,7 @@ 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": 56, + "rank": 109, "slot_uri": "GENEPIO:0001515", "alias": "diagnostic_pcr_Ct_value_3", "owner": "Monkeypox", @@ -9073,7 +12339,7 @@ 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": 57, + "rank": 110, "alias": "gene_name_4", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -9083,7 +12349,7 @@ 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": 58, + "rank": 111, "alias": "diagnostic_pcr_Ct_value_4", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -9093,7 +12359,7 @@ 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": 59, + "rank": 112, "alias": "gene_name_5", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -9103,7 +12369,7 @@ 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": 60, + "rank": 113, "alias": "diagnostic_pcr_Ct_value_5", "owner": "Monkeypox", "slot_group": "Pathogen diagnostic testing" @@ -9113,7 +12379,7 @@ 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": 61, + "rank": 114, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "Monkeypox", @@ -9126,7 +12392,7 @@ var SCHEMA = { "description": "The DataHarmonizer software version provenance.", "title": "DataHarmonizer provenance", "from_schema": "https://example.com/monkeypox", - "rank": 62, + "rank": 115, "slot_uri": "GENEPIO:0001518", "alias": "DataHarmonizer_provenance", "owner": "Monkeypox", @@ -9149,34 +12415,39 @@ var SCHEMA = { "rank": 1, "slot_group": "Database Identifiers" }, + "case ID": { + "name": "case ID", + "rank": 2, + "slot_group": "Database Identifiers" + }, "bioproject accession": { "name": "bioproject accession", - "rank": 2, + "rank": 3, "slot_group": "Database Identifiers" }, "biosample accession": { "name": "biosample accession", - "rank": 3, + "rank": 4, "slot_group": "Database Identifiers" }, "SRA accession": { "name": "SRA accession", - "rank": 4, + "rank": 5, "slot_group": "Database Identifiers" }, "GenBank accession": { "name": "GenBank accession", - "rank": 5, + "rank": 6, "slot_group": "Database Identifiers" }, "GISAID virus name": { "name": "GISAID virus name", - "rank": 6, + "rank": 7, "slot_group": "Database Identifiers" }, "GISAID accession": { "name": "GISAID accession", - "rank": 7, + "rank": 8, "slot_group": "Database Identifiers" }, "sample collected by": { @@ -9185,7 +12456,7 @@ var SCHEMA = { "GISAID:Originating lab", "BIOSAMPLE:collected_by" ], - "rank": 8, + "rank": 9, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9198,12 +12469,12 @@ var SCHEMA = { }, "sample collector contact email": { "name": "sample collector contact email", - "rank": 9, + "rank": 10, "slot_group": "Sample collection and processing" }, "sample collector contact address": { "name": "sample collector contact address", - "rank": 10, + "rank": 11, "slot_group": "Sample collection and processing" }, "sequenced by": { @@ -9211,7 +12482,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:sequenced_by" ], - "rank": 11, + "rank": 12, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9224,12 +12495,12 @@ var SCHEMA = { }, "sequenced by contact email": { "name": "sequenced by contact email", - "rank": 12, + "rank": 13, "slot_group": "Sample collection and processing" }, "sequenced by contact address": { "name": "sequenced by contact address", - "rank": 13, + "rank": 14, "slot_group": "Sample collection and processing" }, "sequence submitted by": { @@ -9238,7 +12509,7 @@ var SCHEMA = { "GISAID:Submitting lab", "BIOSAMPLE:sequence_submitted_by" ], - "rank": 14, + "rank": 15, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9251,22 +12522,22 @@ var SCHEMA = { }, "sequence submitter contact email": { "name": "sequence submitter contact email", - "rank": 15, + "rank": 16, "slot_group": "Sample collection and processing" }, "sequence submitter contact address": { "name": "sequence submitter contact address", - "rank": 16, + "rank": 17, "slot_group": "Sample collection and processing" }, "sample collection date": { "name": "sample collection date", - "rank": 17, + "rank": 18, "slot_group": "Sample collection and processing" }, "sample received date": { "name": "sample received date", - "rank": 18, + "rank": 19, "slot_group": "Sample collection and processing" }, "geo_loc_name (country)": { @@ -9276,7 +12547,7 @@ var SCHEMA = { "value": "United States of America [GAZ:00002459]" } ], - "rank": 19, + "rank": 20, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9292,7 +12563,7 @@ var SCHEMA = { "comments": [ "Provide the state/province/territory name from the controlled vocabulary provided." ], - "rank": 21, + "rank": 22, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9305,12 +12576,12 @@ var SCHEMA = { }, "geo_loc latitude": { "name": "geo_loc latitude", - "rank": 22, + "rank": 23, "slot_group": "Sample collection and processing" }, "geo_loc longitude": { "name": "geo_loc longitude", - "rank": 23, + "rank": 24, "slot_group": "Sample collection and processing" }, "organism": { @@ -9320,7 +12591,7 @@ var SCHEMA = { "value": "Monkeypox virus [NCBITaxon:10244]" } ], - "rank": 24, + "rank": 25, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9344,7 +12615,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:isolate" ], - "rank": 25, + "rank": 26, "slot_uri": "GENEPIO:0001644", "slot_group": "Sample collection and processing" }, @@ -9355,7 +12626,7 @@ var SCHEMA = { "value": "Diagnostic testing [GENEPIO:0100002]" } ], - "rank": 26, + "rank": 27, "slot_group": "Sample collection and processing", "any_of": [ { @@ -9368,7 +12639,7 @@ var SCHEMA = { }, "purpose of sampling details": { "name": "purpose of sampling details", - "rank": 27, + "rank": 28, "slot_group": "Sample collection and processing" }, "anatomical material": { @@ -9378,7 +12649,7 @@ var SCHEMA = { "value": "Lesion (Pustule) [NCIT:C78582]" } ], - "rank": 28, + "rank": 29, "slot_group": "Sample collection and processing", "recommended": true, "any_of": [ @@ -9397,228 +12668,596 @@ var SCHEMA = { "value": "Genital area [BTO:0003358]" } ], - "rank": 29, + "rank": 30, + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "anatomical part international menu" + }, + { + "range": "null value menu" + } + ] + }, + "body product": { + "name": "body product", + "examples": [ + { + "value": "Pus [UBERON:0000177]" + } + ], + "rank": 31, + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "body product international menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection device": { + "name": "collection device", + "examples": [ + { + "value": "Swab [GENEPIO:0100027]" + } + ], + "rank": 32, + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection device international menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection method": { + "name": "collection method", + "examples": [ + { + "value": "Biopsy [OBI:0002650]" + } + ], + "rank": 33, + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection method international menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen processing": { + "name": "specimen processing", + "examples": [ + { + "value": "Specimens pooled [OBI:0600016]" + } + ], + "rank": 34, "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "specimen processing international menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen processing details": { + "name": "specimen processing details", + "rank": 35, + "slot_group": "Sample collection and processing" + }, + "host (common name)": { + "name": "host (common name)", + "rank": 36, + "slot_group": "Host Information", + "any_of": [ + { + "range": "host (common name) international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host (scientific name)": { + "name": "host (scientific name)", + "examples": [ + { + "value": "Homo sapiens [NCBITaxon:9606]" + } + ], + "rank": 37, + "slot_group": "Host Information", + "any_of": [ + { + "range": "host (scientific name) international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host health state": { + "name": "host health state", + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "exact_mappings": [ + "GISAID:Patient status", + "BIOSAMPLE:host_health_state" + ], + "rank": 38, + "slot_group": "Host Information", + "any_of": [ + { + "range": "host health state international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host health status details": { + "name": "host health status details", + "examples": [ + { + "value": "Hospitalized [NCIT:C25179]" + } + ], + "rank": 39, + "slot_group": "Host Information", + "any_of": [ + { + "range": "host health status details international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host health outcome": { + "name": "host health outcome", + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], + "exact_mappings": [ + "BIOSAMPLE:host_health_outcome" + ], + "rank": 40, + "slot_group": "Host Information", + "any_of": [ + { + "range": "host health outcome international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host disease": { + "name": "host disease", + "examples": [ + { + "value": "Monkeypox [MONDO:0002594]" + } + ], + "rank": 41, + "slot_group": "Host Information", + "any_of": [ + { + "range": "host disease international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host subject ID": { + "name": "host subject ID", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "comments": [ + "Provide the host identifier. Should be a unique, user-defined identifier." + ], + "examples": [ + { + "value": "BCxy123" + } + ], + "exact_mappings": [ + "NML_LIMS:host subject ID", + "BIOSAMPLE:host_subject_id" + ], + "rank": 47, + "slot_group": "Host Information" + }, + "host age": { + "name": "host age", + "exact_mappings": [ + "GISAID:Patient age", + "BIOSAMPLE:host_age" + ], + "rank": 43, + "slot_group": "Host Information", + "recommended": true + }, + "host age unit": { + "name": "host age unit", + "examples": [ + { + "value": "year [UO:0000036]" + } + ], + "exact_mappings": [ + "BIOSAMPLE:host_age_unit" + ], + "rank": 44, + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "host age unit international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host age bin": { + "name": "host age bin", + "examples": [ + { + "value": "50 - 59 [GENEPIO:0100054]" + } + ], + "exact_mappings": [ + "BIOSAMPLE:host_age_bin" + ], + "rank": 45, + "slot_group": "Host Information", "recommended": true, "any_of": [ { - "range": "anatomical part international menu" + "range": "host age bin international menu" }, { "range": "null value menu" } ] }, - "body product": { - "name": "body product", + "host gender": { + "name": "host gender", "examples": [ { - "value": "Pus [UBERON:0000177]" + "value": "Male [NCIT:C46109]" } ], - "rank": 30, - "slot_group": "Sample collection and processing", + "exact_mappings": [ + "GISAID:Gender", + "BIOSAMPLE:host_sex" + ], + "rank": 46, + "slot_group": "Host Information", "recommended": true, "any_of": [ { - "range": "body product international menu" + "range": "host gender international menu" }, { "range": "null value menu" } ] }, - "collection device": { - "name": "collection device", + "host residence geo_loc name (country)": { + "name": "host residence geo_loc name (country)", "examples": [ { - "value": "Swab [GENEPIO:0100027]" + "value": "Canada [GAZ:00002560]" } ], - "rank": 31, - "slot_group": "Sample collection and processing", - "recommended": true, + "rank": 48, + "slot_group": "Host Information", "any_of": [ { - "range": "collection device international menu" + "range": "geo_loc_name (country) international menu" }, { "range": "null value menu" } ] }, - "collection method": { - "name": "collection method", + "symptom onset date": { + "name": "symptom onset date", + "rank": 49, + "slot_group": "Host Information" + }, + "signs and symptoms": { + "name": "signs and symptoms", "examples": [ { - "value": "Biopsy [OBI:0002650]" + "value": "Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326]" } ], - "rank": 32, - "slot_group": "Sample collection and processing", - "recommended": true, + "rank": 50, + "slot_group": "Host Information", "any_of": [ { - "range": "collection method international menu" + "range": "signs and symptoms international menu" }, { "range": "null value menu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", - "examples": [ - { - "value": "Homo sapiens [NCBITaxon:9606]" - } - ], - "rank": 33, + "pre-existing conditions and risk factors": { + "name": "pre-existing conditions and risk factors", + "rank": 51, "slot_group": "Host Information", "any_of": [ { - "range": "host (scientific name) international menu" + "range": "pre-existing conditions and risk factors international menu" }, { "range": "null value menu" } ] }, - "host disease": { - "name": "host disease", + "complications": { + "name": "complications", "examples": [ { - "value": "Monkeypox [MONDO:0002594]" + "value": "Delayed wound healing (lesion healing) [MP:0002908]" } ], - "rank": 34, + "rank": 52, "slot_group": "Host Information", "any_of": [ { - "range": "host disease international menu" + "range": "complications international menu" }, { "range": "null value menu" } ] }, - "host subject ID": { - "name": "host subject ID", - "description": "A unique identifier by which each host can be referred to e.g. #131", - "comments": [ - "Provide the host identifier. Should be a unique, user-defined identifier." - ], - "examples": [ - { - "value": "BCxy123" - } - ], - "exact_mappings": [ - "NML_LIMS:host subject ID", - "BIOSAMPLE:host_subject_id" - ], - "rank": 42, - "slot_group": "Host Information" - }, - "host health state": { - "name": "host health state", - "rank": 36, - "slot_group": "Host Information" - }, - "host health outcome": { - "name": "host health outcome", - "rank": 37, - "slot_group": "Host Information" - }, - "host age": { - "name": "host age", - "rank": 38, - "slot_group": "Host Information" - }, - "host age unit": { - "name": "host age unit", - "rank": 39, - "slot_group": "Host Information" - }, - "host age bin": { - "name": "host age bin", - "rank": 40, - "slot_group": "Host Information" - }, - "host gender": { - "name": "host gender", - "rank": 41, - "slot_group": "Host Information" - }, - "symptom onset date": { - "name": "symptom onset date", - "rank": 43, - "slot_group": "Host Information" - }, - "signs and symptoms": { - "name": "signs and symptoms", - "rank": 44, - "slot_group": "Host Information" - }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", - "rank": 45, + "antiviral therapy": { + "name": "antiviral therapy", + "rank": 53, "slot_group": "Host Information" }, "host vaccination status": { "name": "host vaccination status", - "rank": 46, - "slot_group": "Host vaccination information" + "examples": [ + { + "value": "Not Vaccinated [GENEPIO:0100102]" + } + ], + "rank": 54, + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host vaccination status international menu" + }, + { + "range": "null value menu" + } + ] }, "number of vaccine doses received": { "name": "number of vaccine doses received", - "rank": 47, + "rank": 55, "slot_group": "Host vaccination information" }, "vaccination dose 1 vaccine name": { "name": "vaccination dose 1 vaccine name", - "rank": 48, + "rank": 56, "slot_group": "Host vaccination information" }, "vaccination dose 1 vaccination date": { "name": "vaccination dose 1 vaccination date", - "rank": 49, + "rank": 57, "slot_group": "Host vaccination information" }, "vaccination history": { "name": "vaccination history", - "rank": 50, + "rank": 58, "slot_group": "Host vaccination information" }, + "location of exposure geo_loc name (country)": { + "name": "location of exposure geo_loc name (country)", + "examples": [ + { + "value": "Canada [GAZ:00002560]" + } + ], + "rank": 59, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (country) international menu" + }, + { + "range": "null value menu" + } + ] + }, + "destination of most recent travel (city)": { + "name": "destination of most recent travel (city)", + "rank": 60, + "slot_group": "Host exposure information" + }, + "destination of most recent travel (state/province/territory)": { + "name": "destination of most recent travel (state/province/territory)", + "comments": [ + "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "California" + } + ], + "rank": 61, + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "destination of most recent travel (country)": { + "name": "destination of most recent travel (country)", + "examples": [ + { + "value": "United Kingdom [GAZ:00002637]" + } + ], + "rank": 62, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (country) international menu" + }, + { + "range": "null value menu" + } + ] + }, + "most recent travel departure date": { + "name": "most recent travel departure date", + "rank": 63, + "slot_group": "Host exposure information" + }, + "most recent travel return date": { + "name": "most recent travel return date", + "rank": 64, + "slot_group": "Host exposure information" + }, "travel history": { "name": "travel history", - "rank": 51, + "rank": 65, "slot_group": "Host exposure information" }, "exposure event": { "name": "exposure event", - "rank": 52, - "slot_group": "Host exposure information" + "examples": [ + { + "value": "Party [PCO:0000035]" + } + ], + "rank": 66, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure event international menu" + }, + { + "range": "null value menu" + } + ] }, "exposure contact level": { "name": "exposure contact level", - "rank": 53, - "slot_group": "Host exposure information" + "examples": [ + { + "value": "Contact with infected individual [GENEPIO:0100357]" + } + ], + "rank": 67, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure contact level international menu" + }, + { + "range": "null value menu" + } + ] }, "host role": { "name": "host role", - "rank": 54, + "examples": [ + { + "value": "Acquaintance of case [GENEPIO:0100266]" + } + ], + "rank": 68, + "slot_group": "Host exposure information", + "range": "host role international menu" + }, + "exposure setting": { + "name": "exposure setting", + "examples": [ + { + "value": "Healthcare Setting [GENEPIO:0100201]" + } + ], + "rank": 69, + "slot_group": "Host exposure information", + "range": "exposure setting international menu" + }, + "exposure details": { + "name": "exposure details", + "rank": 70, "slot_group": "Host exposure information" }, - "exposure setting": { - "name": "exposure setting", - "rank": 55, - "slot_group": "Host exposure information" + "prior Monkeypox infection": { + "name": "prior Monkeypox infection", + "examples": [ + { + "value": "Prior infection [GENEPIO:0100037]" + } + ], + "rank": 71, + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "prior Monkeypox infection international menu" + }, + { + "range": "null value menu" + } + ] + }, + "prior Monkeypox infection date": { + "name": "prior Monkeypox infection date", + "rank": 72, + "slot_group": "Host reinfection information" }, - "exposure details": { - "name": "exposure details", - "rank": 56, - "slot_group": "Host exposure information" + "prior Monkeypox antiviral treatment": { + "name": "prior Monkeypox antiviral treatment", + "examples": [ + { + "value": "Prior antiviral treatment [GENEPIO:0100037]" + } + ], + "rank": 73, + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "prior Monkeypox antiviral treatment international menu" + }, + { + "range": "null value menu" + } + ] + }, + "prior antiviral treatment during prior Monkeypox infection": { + "name": "prior antiviral treatment during prior Monkeypox infection", + "rank": 74, + "slot_group": "Host reinfection information" }, "purpose of sequencing": { "name": "purpose of sequencing", @@ -9627,7 +13266,7 @@ var SCHEMA = { "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" } ], - "rank": 57, + "rank": 75, "slot_group": "Sequencing", "any_of": [ { @@ -9640,17 +13279,27 @@ var SCHEMA = { }, "purpose of sequencing details": { "name": "purpose of sequencing details", - "rank": 58, + "rank": 76, "slot_group": "Sequencing" }, "sequencing date": { "name": "sequencing date", - "rank": 59, + "rank": 77, + "slot_group": "Sequencing" + }, + "library ID": { + "name": "library ID", + "rank": 78, + "slot_group": "Sequencing" + }, + "amplicon size": { + "name": "amplicon size", + "rank": 79, "slot_group": "Sequencing" }, "library preparation kit": { "name": "library preparation kit", - "rank": 60, + "rank": 80, "slot_group": "Sequencing" }, "sequencing instrument": { @@ -9660,7 +13309,7 @@ var SCHEMA = { "value": "Oxford Nanopore MinION [GENEPIO:0100142]" } ], - "rank": 61, + "rank": 81, "slot_group": "Sequencing", "any_of": [ { @@ -9673,57 +13322,117 @@ var SCHEMA = { }, "sequencing protocol": { "name": "sequencing protocol", - "rank": 62, + "rank": 82, + "slot_group": "Sequencing" + }, + "sequencing kit number": { + "name": "sequencing kit number", + "rank": 83, + "slot_group": "Sequencing" + }, + "amplicon pcr primer scheme": { + "name": "amplicon pcr primer scheme", + "rank": 84, "slot_group": "Sequencing" }, "raw sequence data processing method": { "name": "raw sequence data processing method", - "rank": 63, + "rank": 85, "slot_group": "Bioinformatics and QC metrics" }, "dehosting method": { "name": "dehosting method", - "rank": 64, + "rank": 86, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus sequence name": { + "name": "consensus sequence name", + "rank": 87, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus sequence filename": { + "name": "consensus sequence filename", + "rank": 88, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus sequence filepath": { + "name": "consensus sequence filepath", + "rank": 89, "slot_group": "Bioinformatics and QC metrics" }, "consensus sequence software name": { "name": "consensus sequence software name", - "rank": 65, + "rank": 90, "slot_group": "Bioinformatics and QC metrics" }, "consensus sequence software version": { "name": "consensus sequence software version", - "rank": 66, + "rank": 91, "slot_group": "Bioinformatics and QC metrics" }, "breadth of coverage value": { "name": "breadth of coverage value", - "rank": 67, + "rank": 92, "slot_group": "Bioinformatics and QC metrics" }, "depth of coverage value": { "name": "depth of coverage value", - "rank": 68, + "rank": 93, "slot_group": "Bioinformatics and QC metrics" }, "depth of coverage threshold": { "name": "depth of coverage threshold", - "rank": 69, + "rank": 94, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1 fastq filename": { + "name": "r1 fastq filename", + "rank": 95, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2 fastq filename": { + "name": "r2 fastq filename", + "rank": 96, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1 fastq filepath": { + "name": "r1 fastq filepath", + "rank": 97, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2 fastq filepath": { + "name": "r2 fastq filepath", + "rank": 98, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5 filename": { + "name": "fast5 filename", + "rank": 99, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5 filepath": { + "name": "fast5 filepath", + "rank": 100, "slot_group": "Bioinformatics and QC metrics" }, "number of base pairs sequenced": { "name": "number of base pairs sequenced", - "rank": 70, + "rank": 101, "slot_group": "Bioinformatics and QC metrics" }, "consensus genome length": { "name": "consensus genome length", - "rank": 71, + "rank": 102, + "slot_group": "Bioinformatics and QC metrics" + }, + "reference genome accession": { + "name": "reference genome accession", + "rank": 103, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics protocol": { "name": "bioinformatics protocol", - "rank": 72, + "rank": 104, "slot_group": "Bioinformatics and QC metrics" }, "gene name 1": { @@ -9731,7 +13440,7 @@ 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": 73, + "rank": 105, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -9744,7 +13453,7 @@ var SCHEMA = { }, "diagnostic pcr Ct value 1": { "name": "diagnostic pcr Ct value 1", - "rank": 74, + "rank": 106, "slot_group": "Pathogen diagnostic testing" }, "gene name 2": { @@ -9752,7 +13461,7 @@ 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": 107, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -9765,7 +13474,7 @@ var SCHEMA = { }, "diagnostic pcr Ct value 2": { "name": "diagnostic pcr Ct value 2", - "rank": 76, + "rank": 108, "slot_group": "Pathogen diagnostic testing" }, "gene name 3": { @@ -9773,7 +13482,7 @@ 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": 77, + "rank": 109, "slot_group": "Pathogen diagnostic testing", "any_of": [ { @@ -9786,17 +13495,17 @@ var SCHEMA = { }, "diagnostic pcr Ct value 3": { "name": "diagnostic pcr Ct value 3", - "rank": 78, + "rank": 110, "slot_group": "Pathogen diagnostic testing" }, "authors": { "name": "authors", - "rank": 79, + "rank": 111, "slot_group": "Contributor acknowledgement" }, "DataHarmonizer provenance": { "name": "DataHarmonizer provenance", - "rank": 80, + "rank": 112, "slot_group": "Contributor acknowledgement" } }, @@ -9815,12 +13524,24 @@ var SCHEMA = { "range": "WhitespaceMinimizedString", "required": true }, + "case ID": { + "name": "case ID", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case ID", + "from_schema": "https://example.com/monkeypox", + "rank": 2, + "slot_uri": "GENEPIO:0100281", + "alias": "case_ID", + "owner": "Monkeypox_international", + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString" + }, "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": 2, + "rank": 3, "slot_uri": "GENEPIO:0001136", "alias": "bioproject_accession", "owner": "Monkeypox_international", @@ -9837,7 +13558,7 @@ var SCHEMA = { "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", "from_schema": "https://example.com/monkeypox", - "rank": 3, + "rank": 4, "slot_uri": "GENEPIO:0001139", "alias": "biosample_accession", "owner": "Monkeypox_international", @@ -9854,7 +13575,7 @@ var SCHEMA = { "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, + "rank": 5, "slot_uri": "GENEPIO:0001142", "alias": "SRA_accession", "owner": "Monkeypox_international", @@ -9871,7 +13592,7 @@ var SCHEMA = { "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", "title": "GenBank accession", "from_schema": "https://example.com/monkeypox", - "rank": 5, + "rank": 6, "slot_uri": "GENEPIO:0001145", "alias": "GenBank_accession", "owner": "Monkeypox_international", @@ -9888,7 +13609,7 @@ var SCHEMA = { "description": "Identifier of the specific isolate.", "title": "GISAID virus name", "from_schema": "https://example.com/monkeypox", - "rank": 6, + "rank": 7, "slot_uri": "GENEPIO:0100282", "alias": "GISAID_virus_name", "owner": "Monkeypox_international", @@ -9900,7 +13621,7 @@ var SCHEMA = { "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", "from_schema": "https://example.com/monkeypox", - "rank": 7, + "rank": 8, "slot_uri": "GENEPIO:0001147", "alias": "GISAID_accession", "owner": "Monkeypox_international", @@ -9921,7 +13642,7 @@ var SCHEMA = { "GISAID:Originating lab", "BIOSAMPLE:collected_by" ], - "rank": 8, + "rank": 9, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", "owner": "Monkeypox_international", @@ -9941,7 +13662,7 @@ 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": 9, + "rank": 10, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", "owner": "Monkeypox_international", @@ -9954,7 +13675,7 @@ var SCHEMA = { "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", "from_schema": "https://example.com/monkeypox", - "rank": 10, + "rank": 11, "slot_uri": "GENEPIO:0001158", "alias": "sample_collector_contact_address", "owner": "Monkeypox_international", @@ -9969,7 +13690,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:sequenced_by" ], - "rank": 11, + "rank": 12, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "Monkeypox_international", @@ -9989,7 +13710,7 @@ 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": 12, + "rank": 13, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "Monkeypox_international", @@ -10001,7 +13722,7 @@ var SCHEMA = { "description": "The mailing address of the agency submitting the sequence.", "title": "sequenced by contact address", "from_schema": "https://example.com/monkeypox", - "rank": 13, + "rank": 14, "slot_uri": "GENEPIO:0100423", "alias": "sequenced_by_contact_address", "owner": "Monkeypox_international", @@ -10017,7 +13738,7 @@ var SCHEMA = { "GISAID:Submitting lab", "BIOSAMPLE:sequence_submitted_by" ], - "rank": 14, + "rank": 15, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "Monkeypox_international", @@ -10037,7 +13758,7 @@ 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": 15, + "rank": 16, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "Monkeypox_international", @@ -10049,7 +13770,7 @@ 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": 16, + "rank": 17, "slot_uri": "GENEPIO:0001167", "alias": "sequence_submitter_contact_address", "owner": "Monkeypox_international", @@ -10061,7 +13782,7 @@ var SCHEMA = { "description": "The date on which the sample was collected.", "title": "sample collection date", "from_schema": "https://example.com/monkeypox", - "rank": 17, + "rank": 18, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", "owner": "Monkeypox_international", @@ -10073,7 +13794,7 @@ var SCHEMA = { "description": "The date on which the sample was received.", "title": "sample received date", "from_schema": "https://example.com/monkeypox", - "rank": 18, + "rank": 19, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "Monkeypox_international", @@ -10089,7 +13810,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 19, + "rank": 20, "slot_uri": "GENEPIO:0001181", "alias": "geo_loc_name_(country)", "owner": "Monkeypox_international", @@ -10112,7 +13833,7 @@ var SCHEMA = { "Provide the state/province/territory name from the controlled vocabulary provided." ], "from_schema": "https://example.com/monkeypox", - "rank": 21, + "rank": 22, "slot_uri": "GENEPIO:0001185", "alias": "geo_loc_name_(state/province/territory)", "owner": "Monkeypox_international", @@ -10132,7 +13853,7 @@ var SCHEMA = { "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo_loc latitude", "from_schema": "https://example.com/monkeypox", - "rank": 22, + "rank": 23, "slot_uri": "GENEPIO:0100309", "alias": "geo_loc_latitude", "owner": "Monkeypox_international", @@ -10144,7 +13865,7 @@ var SCHEMA = { "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo_loc longitude", "from_schema": "https://example.com/monkeypox", - "rank": 23, + "rank": 24, "slot_uri": "GENEPIO:0100310", "alias": "geo_loc_longitude", "owner": "Monkeypox_international", @@ -10161,7 +13882,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 24, + "rank": 25, "slot_uri": "GENEPIO:0001191", "alias": "organism", "owner": "Monkeypox_international", @@ -10192,7 +13913,7 @@ var SCHEMA = { "exact_mappings": [ "BIOSAMPLE:isolate" ], - "rank": 25, + "rank": 26, "slot_uri": "GENEPIO:0001644", "alias": "isolate", "owner": "Monkeypox_international", @@ -10209,7 +13930,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 26, + "rank": 27, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", "owner": "Monkeypox_international", @@ -10229,7 +13950,7 @@ 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": 27, + "rank": 28, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", "owner": "Monkeypox_international", @@ -10246,7 +13967,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 28, + "rank": 29, "slot_uri": "GENEPIO:0001211", "multivalued": true, "alias": "anatomical_material", @@ -10272,119 +13993,254 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 29, + "rank": 30, "slot_uri": "GENEPIO:0001214", "multivalued": true, "alias": "anatomical_part", "owner": "Monkeypox_international", - "slot_group": "Sample collection and processing", - "recommended": true, + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "anatomical part international menu" + }, + { + "range": "null value menu" + } + ] + }, + "body product": { + "name": "body product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body product", + "examples": [ + { + "value": "Pus [UBERON:0000177]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 31, + "slot_uri": "GENEPIO:0001216", + "multivalued": true, + "alias": "body_product", + "owner": "Monkeypox_international", + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "body product international menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection device": { + "name": "collection device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection device", + "examples": [ + { + "value": "Swab [GENEPIO:0100027]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 32, + "slot_uri": "GENEPIO:0001234", + "multivalued": true, + "alias": "collection_device", + "owner": "Monkeypox_international", + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection device international menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection method": { + "name": "collection method", + "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", + "title": "collection method", + "examples": [ + { + "value": "Biopsy [OBI:0002650]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 33, + "slot_uri": "GENEPIO:0001241", + "multivalued": true, + "alias": "collection_method", + "owner": "Monkeypox_international", + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection method international menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen processing": { + "name": "specimen processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen processing", + "examples": [ + { + "value": "Specimens pooled [OBI:0600016]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 34, + "slot_uri": "GENEPIO:0001253", + "multivalued": true, + "alias": "specimen_processing", + "owner": "Monkeypox_international", + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "specimen processing international menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen processing details": { + "name": "specimen processing details", + "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", + "title": "specimen processing details", + "from_schema": "https://example.com/monkeypox", + "rank": 35, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "Monkeypox_international", + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "host (common name)": { + "name": "host (common name)", + "description": "The commonly used name of the host.", + "title": "host (common name)", + "from_schema": "https://example.com/monkeypox", + "rank": 36, + "slot_uri": "GENEPIO:0001386", + "alias": "host_(common_name)", + "owner": "Monkeypox_international", + "slot_group": "Host Information", "any_of": [ { - "range": "anatomical part international menu" + "range": "host (common name) international menu" }, { "range": "null value menu" } ] }, - "body product": { - "name": "body product", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "title": "body product", + "host (scientific name)": { + "name": "host (scientific name)", + "description": "The taxonomic, or scientific name of the host.", + "title": "host (scientific name)", "examples": [ { - "value": "Pus [UBERON:0000177]" + "value": "Homo sapiens [NCBITaxon:9606]" } ], "from_schema": "https://example.com/monkeypox", - "rank": 30, - "slot_uri": "GENEPIO:0001216", - "multivalued": true, - "alias": "body_product", + "rank": 37, + "slot_uri": "GENEPIO:0001387", + "alias": "host_(scientific_name)", "owner": "Monkeypox_international", - "slot_group": "Sample collection and processing", - "recommended": true, + "slot_group": "Host Information", + "required": true, "any_of": [ { - "range": "body product international menu" + "range": "host (scientific name) international menu" }, { "range": "null value menu" } ] }, - "collection device": { - "name": "collection device", - "description": "The instrument or container used to collect the sample e.g. swab.", - "title": "collection device", + "host health state": { + "name": "host health state", + "description": "Health status of the host at the time of sample collection.", + "title": "host health state", "examples": [ { - "value": "Swab [GENEPIO:0100027]" + "value": "Asymptomatic [NCIT:C3833]" } ], "from_schema": "https://example.com/monkeypox", - "rank": 31, - "slot_uri": "GENEPIO:0001234", - "multivalued": true, - "alias": "collection_device", + "exact_mappings": [ + "GISAID:Patient status", + "BIOSAMPLE:host_health_state" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", "owner": "Monkeypox_international", - "slot_group": "Sample collection and processing", - "recommended": true, + "slot_group": "Host Information", "any_of": [ { - "range": "collection device international menu" + "range": "host health state international menu" }, { "range": "null value menu" } ] }, - "collection method": { - "name": "collection method", - "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", - "title": "collection method", + "host health status details": { + "name": "host health status details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host health status details", "examples": [ { - "value": "Biopsy [OBI:0002650]" + "value": "Hospitalized [NCIT:C25179]" } ], "from_schema": "https://example.com/monkeypox", - "rank": 32, - "slot_uri": "GENEPIO:0001241", - "multivalued": true, - "alias": "collection_method", + "rank": 39, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", "owner": "Monkeypox_international", - "slot_group": "Sample collection and processing", - "recommended": true, + "slot_group": "Host Information", "any_of": [ { - "range": "collection method international menu" + "range": "host health status details international menu" }, { "range": "null value menu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", + "host health outcome": { + "name": "host health outcome", + "description": "Disease outcome in the host.", + "title": "host health outcome", "examples": [ { - "value": "Homo sapiens [NCBITaxon:9606]" + "value": "Recovered [NCIT:C49498]" } ], "from_schema": "https://example.com/monkeypox", - "rank": 33, - "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", + "exact_mappings": [ + "BIOSAMPLE:host_health_outcome" + ], + "rank": 40, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_outcome", "owner": "Monkeypox_international", "slot_group": "Host Information", - "required": true, "any_of": [ { - "range": "host (scientific name) international menu" + "range": "host health outcome international menu" }, { "range": "null value menu" @@ -10401,7 +14257,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 34, + "rank": 41, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", "owner": "Monkeypox_international", @@ -10433,89 +14289,151 @@ var SCHEMA = { "NML_LIMS:host subject ID", "BIOSAMPLE:host_subject_id" ], - "rank": 42, + "rank": 47, "slot_uri": "GENEPIO:0001398", "alias": "host_subject_ID", "owner": "Monkeypox_international", "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "host health state": { - "name": "host health state", - "description": "Health status of the host at the time of sample collection.", - "title": "host health state", - "from_schema": "https://example.com/monkeypox", - "rank": 36, - "slot_uri": "GENEPIO:0001388", - "alias": "host_health_state", - "owner": "Monkeypox_international", - "slot_group": "Host Information" - }, - "host health outcome": { - "name": "host health outcome", - "description": "Disease outcome in the host.", - "title": "host health outcome", - "from_schema": "https://example.com/monkeypox", - "rank": 37, - "slot_uri": "GENEPIO:0001389", - "alias": "host_health_outcome", - "owner": "Monkeypox_international", - "slot_group": "Host Information" - }, "host age": { "name": "host age", "description": "Age of host at the time of sampling.", "title": "host age", "from_schema": "https://example.com/monkeypox", - "rank": 38, + "exact_mappings": [ + "GISAID:Patient age", + "BIOSAMPLE:host_age" + ], + "rank": 43, "slot_uri": "GENEPIO:0001392", "alias": "host_age", "owner": "Monkeypox_international", "slot_group": "Host Information", - "recommended": true + "recommended": true, + "minimum_value": 0, + "maximum_value": 130 }, "host age unit": { "name": "host age unit", "description": "The units used to measure the host's age.", "title": "host age unit", + "examples": [ + { + "value": "year [UO:0000036]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 39, + "exact_mappings": [ + "BIOSAMPLE:host_age_unit" + ], + "rank": 44, "slot_uri": "GENEPIO:0001393", "alias": "host_age_unit", "owner": "Monkeypox_international", "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "host age unit international menu" + }, + { + "range": "null value menu" + } + ] }, "host age bin": { "name": "host age bin", "description": "The age category of the host at the time of sampling.", "title": "host age bin", + "examples": [ + { + "value": "50 - 59 [GENEPIO:0100054]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 40, + "exact_mappings": [ + "BIOSAMPLE:host_age_bin" + ], + "rank": 45, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", "owner": "Monkeypox_international", "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "host age bin international menu" + }, + { + "range": "null value menu" + } + ] }, "host gender": { "name": "host gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", + "examples": [ + { + "value": "Male [NCIT:C46109]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 41, + "exact_mappings": [ + "GISAID:Gender", + "BIOSAMPLE:host_sex" + ], + "rank": 46, "slot_uri": "GENEPIO:0001395", "alias": "host_gender", "owner": "Monkeypox_international", "slot_group": "Host Information", - "recommended": true + "recommended": true, + "structured_pattern": { + "syntax": "{Title_Case}", + "interpolated": true, + "partial_match": false + }, + "any_of": [ + { + "range": "host gender international menu" + }, + { + "range": "null value menu" + } + ] + }, + "host residence geo_loc name (country)": { + "name": "host residence geo_loc name (country)", + "description": "The country of residence of the host.", + "title": "host residence geo_loc name (country)", + "examples": [ + { + "value": "Canada [GAZ:00002560]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 48, + "slot_uri": "GENEPIO:0001396", + "alias": "host_residence_geo_loc_name_(country)", + "owner": "Monkeypox_international", + "slot_group": "Host Information", + "any_of": [ + { + "range": "geo_loc_name (country) international menu" + }, + { + "range": "null value menu" + } + ] }, "symptom onset date": { "name": "symptom onset date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", "from_schema": "https://example.com/monkeypox", - "rank": 43, + "rank": 49, "slot_uri": "GENEPIO:0001399", "alias": "symptom_onset_date", "owner": "Monkeypox_international", @@ -10525,43 +14443,114 @@ var SCHEMA = { "name": "signs and symptoms", "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", "title": "signs and symptoms", + "examples": [ + { + "value": "Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 44, + "rank": 50, "slot_uri": "GENEPIO:0001400", "multivalued": true, "alias": "signs_and_symptoms", "owner": "Monkeypox_international", - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "signs and symptoms international menu" + }, + { + "range": "null value menu" + } + ] }, "pre-existing conditions and risk factors": { "name": "pre-existing conditions and risk factors", "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": 45, + "rank": 51, "slot_uri": "GENEPIO:0001401", "multivalued": true, "alias": "pre_existing_conditions_and_risk_factors", "owner": "Monkeypox_international", - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "pre-existing conditions and risk factors international menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "examples": [ + { + "value": "Delayed wound healing (lesion healing) [MP:0002908]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 52, + "slot_uri": "GENEPIO:0001402", + "multivalued": true, + "alias": "complications", + "owner": "Monkeypox_international", + "slot_group": "Host Information", + "any_of": [ + { + "range": "complications international menu" + }, + { + "range": "null value menu" + } + ] + }, + "antiviral therapy": { + "name": "antiviral therapy", + "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", + "title": "antiviral therapy", + "from_schema": "https://example.com/monkeypox", + "rank": 53, + "slot_uri": "NCIT:C16119", + "alias": "antiviral_therapy", + "owner": "Monkeypox_international", + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" }, "host vaccination status": { "name": "host vaccination status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", + "examples": [ + { + "value": "Not Vaccinated [GENEPIO:0100102]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 46, + "rank": 54, "slot_uri": "GENEPIO:0001404", "alias": "host_vaccination_status", "owner": "Monkeypox_international", - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host vaccination status international menu" + }, + { + "range": "null value menu" + } + ] }, "number of vaccine doses received": { "name": "number of vaccine doses received", "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": 47, + "rank": 55, "slot_uri": "GENEPIO:0001406", "alias": "number_of_vaccine_doses_received", "owner": "Monkeypox_international", @@ -10573,7 +14562,7 @@ 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": 48, + "rank": 56, "slot_uri": "GENEPIO:0100313", "alias": "vaccination_dose_1_vaccine_name", "owner": "Monkeypox_international", @@ -10584,7 +14573,7 @@ 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": 49, + "rank": 57, "slot_uri": "GENEPIO:0100314", "alias": "vaccination_dose_1_vaccination_date", "owner": "Monkeypox_international", @@ -10595,19 +14584,121 @@ 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": 50, + "rank": 58, "slot_uri": "GENEPIO:0100321", "alias": "vaccination_history", "owner": "Monkeypox_international", "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, + "location of exposure geo_loc name (country)": { + "name": "location of exposure geo_loc name (country)", + "description": "The country where the host was likely exposed to the causative agent of the illness.", + "title": "location of exposure geo_loc name (country)", + "examples": [ + { + "value": "Canada [GAZ:00002560]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 59, + "slot_uri": "GENEPIO:0001410", + "alias": "location_of_exposure_geo_loc_name_(country)", + "owner": "Monkeypox_international", + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (country) international menu" + }, + { + "range": "null value menu" + } + ] + }, + "destination of most recent travel (city)": { + "name": "destination of most recent travel (city)", + "description": "The name of the city that was the destination of most recent travel.", + "title": "destination of most recent travel (city)", + "from_schema": "https://example.com/monkeypox", + "rank": 60, + "slot_uri": "GENEPIO:0001411", + "alias": "destination_of_most_recent_travel_(city)", + "owner": "Monkeypox_international", + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "destination of most recent travel (state/province/territory)": { + "name": "destination of most recent travel (state/province/territory)", + "description": "The name of the state/province/territory that was the destination of most recent travel.", + "title": "destination of most recent travel (state/province/territory)", + "comments": [ + "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "California" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 61, + "slot_uri": "GENEPIO:0001412", + "alias": "destination_of_most_recent_travel_(state/province/territory)", + "owner": "Monkeypox_international", + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "destination of most recent travel (country)": { + "name": "destination of most recent travel (country)", + "description": "The name of the country that was the destination of most recent travel.", + "title": "destination of most recent travel (country)", + "examples": [ + { + "value": "United Kingdom [GAZ:00002637]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 62, + "slot_uri": "GENEPIO:0001413", + "alias": "destination_of_most_recent_travel_(country)", + "owner": "Monkeypox_international", + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "geo_loc_name (country) international menu" + }, + { + "range": "null value menu" + } + ] + }, + "most recent travel departure date": { + "name": "most recent travel departure date", + "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", + "title": "most recent travel departure date", + "from_schema": "https://example.com/monkeypox", + "rank": 63, + "slot_uri": "GENEPIO:0001414", + "alias": "most_recent_travel_departure_date", + "owner": "Monkeypox_international", + "slot_group": "Host exposure information" + }, + "most recent travel return date": { + "name": "most recent travel return date", + "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", + "title": "most recent travel return date", + "from_schema": "https://example.com/monkeypox", + "rank": 64, + "slot_uri": "GENEPIO:0001415", + "alias": "most_recent_travel_return_date", + "owner": "Monkeypox_international", + "slot_group": "Host exposure information" + }, "travel history": { "name": "travel history", "description": "Travel history in last six months.", "title": "travel history", "from_schema": "https://example.com/monkeypox", - "rank": 51, + "rank": 65, "slot_uri": "GENEPIO:0001416", "alias": "travel_history", "owner": "Monkeypox_international", @@ -10618,62 +14709,169 @@ var SCHEMA = { "name": "exposure event", "description": "Event leading to exposure.", "title": "exposure event", + "examples": [ + { + "value": "Party [PCO:0000035]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 52, + "rank": 66, "slot_uri": "GENEPIO:0001417", "alias": "exposure_event", "owner": "Monkeypox_international", - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure event international menu" + }, + { + "range": "null value menu" + } + ] }, "exposure contact level": { "name": "exposure contact level", "description": "The exposure transmission contact type.", "title": "exposure contact level", + "examples": [ + { + "value": "Contact with infected individual [GENEPIO:0100357]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 53, + "rank": 67, "slot_uri": "GENEPIO:0001418", "alias": "exposure_contact_level", "owner": "Monkeypox_international", - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure contact level international menu" + }, + { + "range": "null value menu" + } + ] }, "host role": { "name": "host role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", + "examples": [ + { + "value": "Acquaintance of case [GENEPIO:0100266]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 54, + "rank": 68, "slot_uri": "GENEPIO:0001419", "multivalued": true, "alias": "host_role", "owner": "Monkeypox_international", "slot_group": "Host exposure information", - "range": "host role menu" + "range": "host role international menu" }, "exposure setting": { "name": "exposure setting", "description": "The setting leading to exposure.", "title": "exposure setting", + "examples": [ + { + "value": "Healthcare Setting [GENEPIO:0100201]" + } + ], "from_schema": "https://example.com/monkeypox", - "rank": 55, + "rank": 69, "slot_uri": "GENEPIO:0001428", "multivalued": true, "alias": "exposure_setting", "owner": "Monkeypox_international", "slot_group": "Host exposure information", - "range": "exposure setting menu" + "range": "exposure setting international menu" }, "exposure details": { "name": "exposure details", "description": "Additional host exposure information.", "title": "exposure details", "from_schema": "https://example.com/monkeypox", - "rank": 56, + "rank": 70, "slot_uri": "GENEPIO:0001431", "alias": "exposure_details", "owner": "Monkeypox_international", "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, + "prior Monkeypox infection": { + "name": "prior Monkeypox infection", + "description": "The absence or presence of a prior Monkeypox infection.", + "title": "prior Monkeypox infection", + "examples": [ + { + "value": "Prior infection [GENEPIO:0100037]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 71, + "slot_uri": "GENEPIO:0100532", + "alias": "prior_Monkeypox_infection", + "owner": "Monkeypox_international", + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "prior Monkeypox infection international menu" + }, + { + "range": "null value menu" + } + ] + }, + "prior Monkeypox infection date": { + "name": "prior Monkeypox infection date", + "description": "The date of diagnosis of the prior Monkeypox infection.", + "title": "prior Monkeypox infection date", + "from_schema": "https://example.com/monkeypox", + "rank": 72, + "slot_uri": "GENEPIO:0100533", + "alias": "prior_Monkeypox_infection_date", + "owner": "Monkeypox_international", + "slot_group": "Host reinfection information" + }, + "prior Monkeypox antiviral treatment": { + "name": "prior Monkeypox antiviral treatment", + "description": "The absence or presence of antiviral treatment for a prior Monkeypox infection.", + "title": "prior Monkeypox antiviral treatment", + "examples": [ + { + "value": "Prior antiviral treatment [GENEPIO:0100037]" + } + ], + "from_schema": "https://example.com/monkeypox", + "rank": 73, + "slot_uri": "GENEPIO:0100534", + "alias": "prior_Monkeypox_antiviral_treatment", + "owner": "Monkeypox_international", + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "prior Monkeypox antiviral treatment international menu" + }, + { + "range": "null value menu" + } + ] + }, + "prior antiviral treatment during prior Monkeypox infection": { + "name": "prior antiviral treatment during prior Monkeypox infection", + "description": "Antiviral treatment for any infection during the prior Moneypox infection period.", + "title": "prior antiviral treatment during prior Monkeypox infection", + "from_schema": "https://example.com/monkeypox", + "rank": 74, + "slot_uri": "GENEPIO:0100535", + "alias": "prior_antiviral_treatment_during_prior_Monkeypox_infection", + "owner": "Monkeypox_international", + "slot_group": "Host reinfection information", + "range": "WhitespaceMinimizedString" + }, "purpose of sequencing": { "name": "purpose of sequencing", "description": "The reason that the sample was sequenced.", @@ -10684,7 +14882,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 57, + "rank": 75, "slot_uri": "GENEPIO:0001445", "multivalued": true, "alias": "purpose_of_sequencing", @@ -10705,7 +14903,7 @@ 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": 58, + "rank": 76, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "Monkeypox_international", @@ -10717,18 +14915,43 @@ var SCHEMA = { "description": "The date the sample was sequenced.", "title": "sequencing date", "from_schema": "https://example.com/monkeypox", - "rank": 59, + "rank": 77, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "Monkeypox_international", "slot_group": "Sequencing" }, + "library ID": { + "name": "library ID", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library ID", + "from_schema": "https://example.com/monkeypox", + "rank": 78, + "slot_uri": "GENEPIO:0001448", + "alias": "library_ID", + "owner": "Monkeypox_international", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "amplicon size": { + "name": "amplicon size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", + "from_schema": "https://example.com/monkeypox", + "rank": 79, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "Monkeypox_international", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, "library preparation kit": { "name": "library preparation kit", "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": 60, + "rank": 80, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "Monkeypox_international", @@ -10745,7 +14968,7 @@ var SCHEMA = { } ], "from_schema": "https://example.com/monkeypox", - "rank": 61, + "rank": 81, "slot_uri": "GENEPIO:0001452", "multivalued": true, "alias": "sequencing_instrument", @@ -10766,19 +14989,43 @@ var SCHEMA = { "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "from_schema": "https://example.com/monkeypox", - "rank": 62, + "rank": 82, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "Monkeypox_international", "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, + "sequencing kit number": { + "name": "sequencing kit number", + "description": "The manufacturer's kit number.", + "title": "sequencing kit number", + "from_schema": "https://example.com/monkeypox", + "rank": 83, + "slot_uri": "GENEPIO:0001455", + "alias": "sequencing_kit_number", + "owner": "Monkeypox_international", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "amplicon pcr primer scheme": { + "name": "amplicon pcr primer scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", + "from_schema": "https://example.com/monkeypox", + "rank": 84, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "Monkeypox_international", + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, "raw sequence data processing method": { "name": "raw sequence data processing method", "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": 63, + "rank": 85, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "Monkeypox_international", @@ -10790,19 +15037,55 @@ var SCHEMA = { "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "from_schema": "https://example.com/monkeypox", - "rank": 64, + "rank": 86, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "Monkeypox_international", "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, + "consensus sequence name": { + "name": "consensus sequence name", + "description": "The name of the consensus sequence.", + "title": "consensus sequence name", + "from_schema": "https://example.com/monkeypox", + "rank": 87, + "slot_uri": "GENEPIO:0001460", + "alias": "consensus_sequence_name", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "consensus sequence filename": { + "name": "consensus sequence filename", + "description": "The name of the consensus sequence file.", + "title": "consensus sequence filename", + "from_schema": "https://example.com/monkeypox", + "rank": 88, + "slot_uri": "GENEPIO:0001461", + "alias": "consensus_sequence_filename", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "consensus sequence filepath": { + "name": "consensus sequence filepath", + "description": "The filepath of the consesnsus sequence file.", + "title": "consensus sequence filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 89, + "slot_uri": "GENEPIO:0001462", + "alias": "consensus_sequence_filepath", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, "consensus sequence software name": { "name": "consensus sequence software name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", "from_schema": "https://example.com/monkeypox", - "rank": 65, + "rank": 90, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "Monkeypox_international", @@ -10815,7 +15098,7 @@ 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": 66, + "rank": 91, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "Monkeypox_international", @@ -10828,7 +15111,7 @@ 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": 67, + "rank": 92, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "Monkeypox_international", @@ -10840,7 +15123,7 @@ 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": 68, + "rank": 93, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "Monkeypox_international", @@ -10852,19 +15135,93 @@ 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": 69, + "rank": 94, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "Monkeypox_international", "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, + "r1 fastq filename": { + "name": "r1 fastq filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1 fastq filename", + "from_schema": "https://example.com/monkeypox", + "rank": 95, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "r2 fastq filename": { + "name": "r2 fastq filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2 fastq filename", + "from_schema": "https://example.com/monkeypox", + "rank": 96, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "r1 fastq filepath": { + "name": "r1 fastq filepath", + "description": "The location of the r1 FASTQ file within a user's file system.", + "title": "r1 fastq filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 97, + "slot_uri": "GENEPIO:0001478", + "alias": "r1_fastq_filepath", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "r2 fastq filepath": { + "name": "r2 fastq filepath", + "description": "The location of the r2 FASTQ file within a user's file system.", + "title": "r2 fastq filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 98, + "slot_uri": "GENEPIO:0001479", + "alias": "r2_fastq_filepath", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "fast5 filename": { + "name": "fast5 filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5 filename", + "from_schema": "https://example.com/monkeypox", + "rank": 99, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "fast5 filepath": { + "name": "fast5 filepath", + "description": "The location of the FAST5 file within a user's file system.", + "title": "fast5 filepath", + "from_schema": "https://example.com/monkeypox", + "rank": 100, + "slot_uri": "GENEPIO:0001481", + "alias": "fast5_filepath", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, "number of base pairs sequenced": { "name": "number of base pairs sequenced", "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": 70, + "rank": 101, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "Monkeypox_international", @@ -10877,7 +15234,7 @@ 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": 71, + "rank": 102, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "Monkeypox_international", @@ -10885,12 +15242,24 @@ var SCHEMA = { "range": "integer", "minimum_value": 0 }, + "reference genome accession": { + "name": "reference genome accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "from_schema": "https://example.com/monkeypox", + "rank": 103, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "Monkeypox_international", + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, "bioinformatics protocol": { "name": "bioinformatics protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "from_schema": "https://example.com/monkeypox", - "rank": 72, + "rank": 104, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "Monkeypox_international", @@ -10905,7 +15274,7 @@ 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": 73, + "rank": 105, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", "owner": "Monkeypox_international", @@ -10924,7 +15293,7 @@ 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": 74, + "rank": 106, "slot_uri": "GENEPIO:0001509", "alias": "diagnostic_pcr_Ct_value_1", "owner": "Monkeypox_international", @@ -10938,7 +15307,7 @@ 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": 107, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", "owner": "Monkeypox_international", @@ -10957,7 +15326,7 @@ 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": 76, + "rank": 108, "slot_uri": "GENEPIO:0001512", "alias": "diagnostic_pcr_Ct_value_2", "owner": "Monkeypox_international", @@ -10971,7 +15340,7 @@ 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": 77, + "rank": 109, "slot_uri": "GENEPIO:0001513", "alias": "gene_name_3", "owner": "Monkeypox_international", @@ -10990,7 +15359,7 @@ 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": 78, + "rank": 110, "slot_uri": "GENEPIO:0001515", "alias": "diagnostic_pcr_Ct_value_3", "owner": "Monkeypox_international", @@ -11001,7 +15370,7 @@ 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": 79, + "rank": 111, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "Monkeypox_international", @@ -11014,7 +15383,7 @@ var SCHEMA = { "description": "The DataHarmonizer software version provenance.", "title": "DataHarmonizer provenance", "from_schema": "https://example.com/monkeypox", - "rank": 80, + "rank": 112, "slot_uri": "GENEPIO:0001518", "alias": "DataHarmonizer_provenance", "owner": "Monkeypox_international", diff --git a/template/monkeypox/schema.yaml b/template/monkeypox/schema.yaml index d800a5d8..fe851669 100644 --- a/template/monkeypox/schema.yaml +++ b/template/monkeypox/schema.yaml @@ -21,6 +21,7 @@ classes: slots: - specimen collector sample ID - Related specimen primary ID + - case ID - bioproject accession - biosample accession - SRA accession @@ -51,23 +52,75 @@ classes: - body product - collection device - collection method + - specimen processing + - specimen processing details + - host (common name) - host (scientific name) + - host health state + - host health status details + - host health outcome - host disease + - host age + - host age unit + - host age bin + - host gender + - host residence geo_loc name (country) + - host residence geo_loc name (state/province/territory) + - symptom onset date + - signs and symptoms + - pre-existing conditions and risk factors + - complications + - antiviral therapy + - host vaccination status + - number of vaccine doses received + - vaccination dose 1 vaccine name + - vaccination dose 1 vaccination date + - vaccination history + - location of exposure geo_loc name (country) + - destination of most recent travel (city) + - destination of most recent travel (state/province/territory) + - destination of most recent travel (country) + - most recent travel departure date + - most recent travel return date - travel history + - exposure event + - exposure contact level + - host role + - exposure setting + - exposure details + - prior Monkeypox infection + - prior Monkeypox infection date + - prior Monkeypox antiviral treatment + - prior antiviral treatment during prior Monkeypox infection - purpose of sequencing - purpose of sequencing details - sequencing date + - library ID + - amplicon size - library preparation kit - sequencing instrument + - sequencing protocol + - sequencing kit number + - amplicon pcr primer scheme - raw sequence data processing method - dehosting method + - consensus sequence name + - consensus sequence filename + - consensus sequence filepath - consensus sequence software name - consensus sequence software version - breadth of coverage value - depth of coverage value - depth of coverage threshold + - r1 fastq filename + - r2 fastq filename + - r1 fastq filepath + - r2 fastq filepath + - fast5 filename + - fast5 filepath - number of base pairs sequenced - consensus genome length + - reference genome accession - bioinformatics protocol - gene name 1 - diagnostic pcr Ct value 1 @@ -88,23 +141,26 @@ classes: Related specimen primary ID: rank: 2 slot_group: Database Identifiers - bioproject accession: + case ID: rank: 3 slot_group: Database Identifiers - biosample accession: + bioproject accession: rank: 4 slot_group: Database Identifiers - SRA accession: + biosample accession: rank: 5 slot_group: Database Identifiers - GenBank accession: + SRA accession: rank: 6 slot_group: Database Identifiers - GISAID accession: + GenBank accession: rank: 7 slot_group: Database Identifiers - sample collected by: + GISAID accession: rank: 8 + slot_group: Database Identifiers + sample collected by: + rank: 9 slot_group: Sample collection and processing any_of: - range: sample collected by menu @@ -116,13 +172,13 @@ classes: - BIOSAMPLE:collected_by - VirusSeq_Portal:sample collected by sample collector contact email: - rank: 9 + rank: 10 slot_group: Sample collection and processing sample collector contact address: - rank: 10 + rank: 11 slot_group: Sample collection and processing sequenced by: - rank: 11 + rank: 12 slot_group: Sample collection and processing any_of: - range: sequence submitted by menu @@ -131,13 +187,13 @@ classes: - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by sequenced by contact email: - rank: 12 + rank: 13 slot_group: Sample collection and processing sequenced by contact address: - rank: 13 + rank: 14 slot_group: Sample collection and processing sequence submitted by: - rank: 14 + rank: 15 slot_group: Sample collection and processing any_of: - range: sequence submitted by menu @@ -149,22 +205,22 @@ classes: - BIOSAMPLE:sequence_submitted_by - VirusSeq_Portal:sequence submitted by sequence submitter contact email: - rank: 15 + rank: 16 slot_group: Sample collection and processing sequence submitter contact address: - rank: 16 + rank: 17 slot_group: Sample collection and processing sample collection date: - rank: 17 + rank: 18 slot_group: Sample collection and processing sample collection date precision: - rank: 18 + rank: 19 slot_group: Sample collection and processing sample received date: - rank: 19 + rank: 20 slot_group: Sample collection and processing geo_loc_name (country): - rank: 20 + rank: 21 slot_group: Sample collection and processing examples: - value: Canada @@ -172,7 +228,7 @@ classes: - range: geo_loc_name (country) menu - range: null value menu geo_loc_name (state/province/territory): - rank: 21 + rank: 22 slot_group: Sample collection and processing comments: Provide the province/territory name from the controlled vocabulary provided. @@ -180,7 +236,7 @@ classes: - range: geo_loc_name (state/province/territory) menu - range: null value menu organism: - rank: 22 + rank: 23 slot_group: Sample collection and processing examples: - value: Monkeypox virus @@ -188,7 +244,7 @@ classes: - range: organism menu - range: null value menu isolate: - rank: 23 + rank: 24 slot_group: Sample collection and processing slot_uri: GENEPIO:0001195 comments: "Provide the GISAID EpiPox virus name, which should be written in\ @@ -206,7 +262,7 @@ classes: - VirusSeq_Portal:isolate - VirusSeq_Portal:fasta header name purpose of sampling: - rank: 24 + rank: 25 slot_group: Sample collection and processing examples: - value: Diagnostic testing @@ -214,16 +270,16 @@ classes: - range: purpose of sampling menu - range: null value menu purpose of sampling details: - rank: 25 + rank: 26 slot_group: Sample collection and processing NML submitted specimen type: - rank: 26 + rank: 27 slot_group: Sample collection and processing Related specimen relationship type: - rank: 27 + rank: 28 slot_group: Sample collection and processing anatomical material: - rank: 28 + rank: 29 slot_group: Sample collection and processing required: true examples: @@ -232,7 +288,7 @@ classes: - range: anatomical material menu - range: null value menu anatomical part: - rank: 29 + rank: 30 slot_group: Sample collection and processing required: true examples: @@ -241,7 +297,7 @@ classes: - range: anatomical part menu - range: null value menu body product: - rank: 30 + rank: 31 slot_group: Sample collection and processing required: true examples: @@ -250,7 +306,7 @@ classes: - range: body product menu - range: null value menu collection device: - rank: 31 + rank: 32 slot_group: Sample collection and processing required: true examples: @@ -259,7 +315,7 @@ classes: - range: collection device menu - range: null value menu collection method: - rank: 32 + rank: 33 slot_group: Sample collection and processing required: true examples: @@ -267,27 +323,286 @@ classes: any_of: - range: collection method menu - range: null value menu + specimen processing: + rank: 34 + slot_group: Sample collection and processing + examples: + - value: Specimens pooled + any_of: + - range: specimen processing menu + - range: null value menu + exact_mappings: + - NML_LIMS:specimen processing + specimen processing details: + rank: 35 + slot_group: Sample collection and processing + host (common name): + rank: 36 + slot_group: Host Information + any_of: + - range: host (common name) menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_ANIMAL_TYPE host (scientific name): - rank: 33 + rank: 37 slot_group: Host Information examples: - value: Homo sapiens any_of: - range: host (scientific name) menu - range: null value menu + host health state: + rank: 38 + slot_group: Host Information + examples: + - value: Asymptomatic + any_of: + - range: host health state menu + - range: null value menu + exact_mappings: + - GISAID:Patient status + - NML_LIMS:PH_HOST_HEALTH + - BIOSAMPLE:host_health_state + host health status details: + rank: 39 + slot_group: Host Information + examples: + - value: Hospitalized + any_of: + - range: host health status details menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_HOST_HEALTH_DETAILS + host health outcome: + rank: 40 + slot_group: Host Information + examples: + - value: Recovered + any_of: + - range: host health outcome menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_HOST_HEALTH_OUTCOME + - BIOSAMPLE:host_health_outcome host disease: - rank: 34 + rank: 41 slot_group: Host Information examples: - value: Monkeypox any_of: - range: host disease menu - range: null value menu + host age: + rank: 42 + slot_group: Host Information + required: true + exact_mappings: + - GISAID:Patient age + - NML_LIMS:PH_AGE + - BIOSAMPLE:host_age + host age unit: + rank: 43 + slot_group: Host Information + required: true + examples: + - value: year + any_of: + - range: host age unit menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_AGE_UNIT + - BIOSAMPLE:host_age_unit + host age bin: + rank: 44 + slot_group: Host Information + required: true + examples: + - value: 50 - 59 + any_of: + - range: host age bin menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_AGE_GROUP + - BIOSAMPLE:host_age_bin + host gender: + rank: 45 + slot_group: Host Information + required: true + examples: + - value: Male + any_of: + - range: host gender menu + - range: null value menu + exact_mappings: + - GISAID:Gender + - NML_LIMS:VD_SEX + - BIOSAMPLE:host_sex + host residence geo_loc name (country): + rank: 46 + slot_group: Host Information + examples: + - value: Canada + any_of: + - range: geo_loc_name (country) menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_HOST_COUNTRY + host residence geo_loc name (state/province/territory): + rank: 47 + slot_group: Host Information + symptom onset date: + rank: 48 + slot_group: Host Information + signs and symptoms: + rank: 49 + slot_group: Host Information + examples: + - value: Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) + any_of: + - range: signs and symptoms menu + - range: null value menu + exact_mappings: + - NML_LIMS:HC_SYMPTOMS + pre-existing conditions and risk factors: + rank: 50 + slot_group: Host Information + any_of: + - range: pre-existing conditions and risk factors menu + - range: null value menu + complications: + rank: 51 + slot_group: Host Information + examples: + - value: Delayed wound healing (lesion healing) + any_of: + - range: complications menu + - range: null value menu + exact_mappings: + - NML_LIMS:complications + antiviral therapy: + rank: 52 + slot_group: Host Information + host vaccination status: + rank: 53 + slot_group: Host vaccination information + examples: + - value: Not Vaccinated + any_of: + - range: host vaccination status menu + - range: null value menu + number of vaccine doses received: + rank: 54 + slot_group: Host vaccination information + vaccination dose 1 vaccine name: + rank: 55 + slot_group: Host vaccination information + vaccination dose 1 vaccination date: + rank: 56 + slot_group: Host vaccination information + vaccination history: + rank: 57 + slot_group: Host vaccination information + location of exposure geo_loc name (country): + rank: 58 + slot_group: Host exposure information + examples: + - value: Canada + any_of: + - range: geo_loc_name (country) menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_EXPOSURE_COUNTRY + destination of most recent travel (city): + rank: 59 + slot_group: Host exposure information + destination of most recent travel (state/province/territory): + rank: 60 + slot_group: Host exposure information + comments: Select the province name from the pick list provided in the template. + any_of: + - range: geo_loc_name (state/province/territory) menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_TRAVEL + destination of most recent travel (country): + rank: 61 + slot_group: Host exposure information + examples: + - value: Canada + any_of: + - range: geo_loc_name (country) menu + - range: null value menu + exact_mappings: + - NML_LIMS:PH_TRAVEL + most recent travel departure date: + rank: 62 + slot_group: Host exposure information + most recent travel return date: + rank: 63 + slot_group: Host exposure information travel history: - rank: 35 + rank: 64 + slot_group: Host exposure information + exposure event: + rank: 65 + slot_group: Host exposure information + examples: + - value: Party + any_of: + - range: exposure event menu + - range: null value menu + exposure contact level: + rank: 66 + slot_group: Host exposure information + examples: + - value: Contact with infected individual + any_of: + - range: exposure contact level menu + - range: null value menu + host role: + rank: 67 + slot_group: Host exposure information + range: host role menu + examples: + - value: Acquaintance of case + exposure setting: + rank: 68 + slot_group: Host exposure information + range: exposure setting menu + examples: + - value: Healthcare Setting + exposure details: + rank: 69 slot_group: Host exposure information + prior Monkeypox infection: + rank: 70 + slot_group: Host reinfection information + examples: + - value: Prior infection + any_of: + - range: prior Monkeypox infection menu + - range: null value menu + exact_mappings: + - NML_LIMS:prior Monkeypox infection + prior Monkeypox infection date: + rank: 71 + slot_group: Host reinfection information + prior Monkeypox antiviral treatment: + rank: 72 + slot_group: Host reinfection information + examples: + - value: Prior antiviral treatment + any_of: + - range: prior Monkeypox antiviral treatment menu + - range: null value menu + exact_mappings: + - NML_LIMS:prior Monkeypox antiviral treatment + prior antiviral treatment during prior Monkeypox infection: + rank: 73 + slot_group: Host reinfection information purpose of sequencing: - rank: 36 + rank: 74 slot_group: Sequencing examples: - description: Select "Targeted surveillance (non-random sampling)" if the @@ -313,58 +628,103 @@ classes: - range: purpose of sequencing menu - range: null value menu purpose of sequencing details: - rank: 37 + rank: 75 slot_group: Sequencing sequencing date: - rank: 38 + rank: 76 slot_group: Sequencing required: true + library ID: + rank: 77 + slot_group: Sequencing + amplicon size: + rank: 78 + slot_group: Sequencing library preparation kit: - rank: 39 + rank: 79 slot_group: Sequencing sequencing instrument: - rank: 40 + rank: 80 slot_group: Sequencing examples: - value: Oxford Nanopore MinION any_of: - range: sequencing instrument menu - range: null value menu + sequencing protocol: + rank: 81 + slot_group: Sequencing + sequencing kit number: + rank: 82 + slot_group: Sequencing + amplicon pcr primer scheme: + rank: 83 + slot_group: Sequencing raw sequence data processing method: - rank: 41 + rank: 84 slot_group: Bioinformatics and QC metrics required: true dehosting method: - rank: 42 + rank: 85 slot_group: Bioinformatics and QC metrics required: true + consensus sequence name: + rank: 86 + slot_group: Bioinformatics and QC metrics + consensus sequence filename: + rank: 87 + slot_group: Bioinformatics and QC metrics + consensus sequence filepath: + rank: 88 + slot_group: Bioinformatics and QC metrics consensus sequence software name: - rank: 43 + rank: 89 slot_group: Bioinformatics and QC metrics consensus sequence software version: - rank: 44 + rank: 90 slot_group: Bioinformatics and QC metrics breadth of coverage value: - rank: 45 + rank: 91 slot_group: Bioinformatics and QC metrics depth of coverage value: - rank: 46 + rank: 92 slot_group: Bioinformatics and QC metrics depth of coverage threshold: - rank: 47 + rank: 93 + slot_group: Bioinformatics and QC metrics + r1 fastq filename: + rank: 94 + slot_group: Bioinformatics and QC metrics + r2 fastq filename: + rank: 95 + slot_group: Bioinformatics and QC metrics + r1 fastq filepath: + rank: 96 + slot_group: Bioinformatics and QC metrics + r2 fastq filepath: + rank: 97 + slot_group: Bioinformatics and QC metrics + fast5 filename: + rank: 98 + slot_group: Bioinformatics and QC metrics + fast5 filepath: + rank: 99 slot_group: Bioinformatics and QC metrics number of base pairs sequenced: - rank: 48 + rank: 100 slot_group: Bioinformatics and QC metrics consensus genome length: - rank: 49 + rank: 101 + slot_group: Bioinformatics and QC metrics + reference genome accession: + rank: 102 slot_group: Bioinformatics and QC metrics bioinformatics protocol: - rank: 50 + rank: 103 slot_group: Bioinformatics and QC metrics required: true gene name 1: - rank: 51 + rank: 104 slot_group: Pathogen diagnostic testing comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. @@ -372,10 +732,10 @@ classes: - range: gene name 1 menu - range: null value menu diagnostic pcr Ct value 1: - rank: 52 + rank: 105 slot_group: Pathogen diagnostic testing gene name 2: - rank: 53 + rank: 106 slot_group: Pathogen diagnostic testing comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. @@ -383,10 +743,10 @@ classes: - range: gene name 2 menu - range: null value menu diagnostic pcr Ct value 2: - rank: 54 + rank: 107 slot_group: Pathogen diagnostic testing gene name 3: - rank: 55 + rank: 108 slot_group: Pathogen diagnostic testing comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. @@ -394,25 +754,25 @@ classes: - range: gene name 3 menu - range: null value menu diagnostic pcr Ct value 3: - rank: 56 + rank: 109 slot_group: Pathogen diagnostic testing gene name 4: - rank: 57 + rank: 110 slot_group: Pathogen diagnostic testing diagnostic pcr Ct value 4: - rank: 58 + rank: 111 slot_group: Pathogen diagnostic testing gene name 5: - rank: 59 + rank: 112 slot_group: Pathogen diagnostic testing diagnostic pcr Ct value 5: - rank: 60 + rank: 113 slot_group: Pathogen diagnostic testing authors: - rank: 61 + rank: 114 slot_group: Contributor acknowledgement DataHarmonizer provenance: - rank: 62 + rank: 115 slot_group: Contributor acknowledgement Monkeypox_international: name: Monkeypox_international @@ -422,6 +782,7 @@ classes: see_also: template/monkeypox/SOP_Monkeypox_international.pdf slots: - specimen collector sample ID + - case ID - bioproject accession - biosample accession - SRA accession @@ -453,45 +814,76 @@ classes: - body product - collection device - collection method + - specimen processing + - specimen processing details + - host (common name) - host (scientific name) - - host disease - - host subject ID - host health state + - host health status details - host health outcome + - host disease + - host subject ID - host age - host age unit - host age bin - host gender - host subject ID + - host residence geo_loc name (country) - symptom onset date - signs and symptoms - pre-existing conditions and risk factors + - complications + - antiviral therapy - host vaccination status - number of vaccine doses received - vaccination dose 1 vaccine name - vaccination dose 1 vaccination date - vaccination history + - location of exposure geo_loc name (country) + - destination of most recent travel (city) + - destination of most recent travel (state/province/territory) + - destination of most recent travel (country) + - most recent travel departure date + - most recent travel return date - travel history - exposure event - exposure contact level - host role - exposure setting - exposure details + - prior Monkeypox infection + - prior Monkeypox infection date + - prior Monkeypox antiviral treatment + - prior antiviral treatment during prior Monkeypox infection - purpose of sequencing - purpose of sequencing details - sequencing date + - library ID + - amplicon size - library preparation kit - sequencing instrument - sequencing protocol + - sequencing kit number + - amplicon pcr primer scheme - raw sequence data processing method - dehosting method + - consensus sequence name + - consensus sequence filename + - consensus sequence filepath - consensus sequence software name - consensus sequence software version - breadth of coverage value - depth of coverage value - depth of coverage threshold + - r1 fastq filename + - r2 fastq filename + - r1 fastq filepath + - r2 fastq filepath + - fast5 filename + - fast5 filepath - number of base pairs sequenced - consensus genome length + - reference genome accession - bioinformatics protocol - gene name 1 - diagnostic pcr Ct value 1 @@ -505,26 +897,29 @@ classes: specimen collector sample ID: rank: 1 slot_group: Database Identifiers - bioproject accession: + case ID: rank: 2 slot_group: Database Identifiers - biosample accession: + bioproject accession: rank: 3 slot_group: Database Identifiers - SRA accession: + biosample accession: rank: 4 slot_group: Database Identifiers - GenBank accession: + SRA accession: rank: 5 slot_group: Database Identifiers - GISAID virus name: + GenBank accession: rank: 6 slot_group: Database Identifiers - GISAID accession: + GISAID virus name: rank: 7 slot_group: Database Identifiers - sample collected by: + GISAID accession: rank: 8 + slot_group: Database Identifiers + sample collected by: + rank: 9 slot_group: Sample collection and processing any_of: - range: WhitespaceMinimizedString @@ -533,13 +928,13 @@ classes: - GISAID:Originating lab - BIOSAMPLE:collected_by sample collector contact email: - rank: 9 + rank: 10 slot_group: Sample collection and processing sample collector contact address: - rank: 10 + rank: 11 slot_group: Sample collection and processing sequenced by: - rank: 11 + rank: 12 slot_group: Sample collection and processing any_of: - range: WhitespaceMinimizedString @@ -547,13 +942,13 @@ classes: exact_mappings: - BIOSAMPLE:sequenced_by sequenced by contact email: - rank: 12 + rank: 13 slot_group: Sample collection and processing sequenced by contact address: - rank: 13 + rank: 14 slot_group: Sample collection and processing sequence submitted by: - rank: 14 + rank: 15 slot_group: Sample collection and processing any_of: - range: WhitespaceMinimizedString @@ -562,19 +957,19 @@ classes: - GISAID:Submitting lab - BIOSAMPLE:sequence_submitted_by sequence submitter contact email: - rank: 15 + rank: 16 slot_group: Sample collection and processing sequence submitter contact address: - rank: 16 + rank: 17 slot_group: Sample collection and processing sample collection date: - rank: 17 + rank: 18 slot_group: Sample collection and processing sample received date: - rank: 18 + rank: 19 slot_group: Sample collection and processing geo_loc_name (country): - rank: 19 + rank: 20 slot_group: Sample collection and processing examples: - value: United States of America [GAZ:00002459] @@ -582,7 +977,7 @@ classes: - range: geo_loc_name (country) international menu - range: null value menu geo_loc_name (state/province/territory): - rank: 21 + rank: 22 slot_group: Sample collection and processing comments: Provide the state/province/territory name from the controlled vocabulary provided. @@ -590,13 +985,13 @@ classes: - range: WhitespaceMinimizedString - range: null value menu geo_loc latitude: - rank: 22 + rank: 23 slot_group: Sample collection and processing geo_loc longitude: - rank: 23 + rank: 24 slot_group: Sample collection and processing organism: - rank: 24 + rank: 25 slot_group: Sample collection and processing examples: - value: Monkeypox virus [NCBITaxon:10244] @@ -604,7 +999,7 @@ classes: - range: organism international menu - range: null value menu isolate: - rank: 25 + rank: 26 slot_group: Sample collection and processing slot_uri: GENEPIO:0001644 comments: 'This identifier should be an unique, indexed, alpha-numeric ID @@ -616,7 +1011,7 @@ classes: exact_mappings: - BIOSAMPLE:isolate purpose of sampling: - rank: 26 + rank: 27 slot_group: Sample collection and processing examples: - value: Diagnostic testing [GENEPIO:0100002] @@ -624,10 +1019,10 @@ classes: - range: purpose of sampling international menu - range: null value menu purpose of sampling details: - rank: 27 + rank: 28 slot_group: Sample collection and processing anatomical material: - rank: 28 + rank: 29 slot_group: Sample collection and processing recommended: true examples: @@ -636,7 +1031,7 @@ classes: - range: anatomical material international menu - range: null value menu anatomical part: - rank: 29 + rank: 30 slot_group: Sample collection and processing recommended: true examples: @@ -645,7 +1040,7 @@ classes: - range: anatomical part international menu - range: null value menu body product: - rank: 30 + rank: 31 slot_group: Sample collection and processing recommended: true examples: @@ -654,7 +1049,7 @@ classes: - range: body product international menu - range: null value menu collection device: - rank: 31 + rank: 32 slot_group: Sample collection and processing recommended: true examples: @@ -663,7 +1058,7 @@ classes: - range: collection device international menu - range: null value menu collection method: - rank: 32 + rank: 33 slot_group: Sample collection and processing recommended: true examples: @@ -671,16 +1066,62 @@ classes: any_of: - range: collection method international menu - range: null value menu + specimen processing: + rank: 34 + slot_group: Sample collection and processing + examples: + - value: Specimens pooled [OBI:0600016] + any_of: + - range: specimen processing international menu + - range: null value menu + specimen processing details: + rank: 35 + slot_group: Sample collection and processing + host (common name): + rank: 36 + slot_group: Host Information + any_of: + - range: host (common name) international menu + - range: null value menu host (scientific name): - rank: 33 + rank: 37 slot_group: Host Information examples: - value: Homo sapiens [NCBITaxon:9606] any_of: - range: host (scientific name) international menu - range: null value menu + host health state: + rank: 38 + slot_group: Host Information + examples: + - value: Asymptomatic [NCIT:C3833] + any_of: + - range: host health state international menu + - range: null value menu + exact_mappings: + - GISAID:Patient status + - BIOSAMPLE:host_health_state + host health status details: + rank: 39 + slot_group: Host Information + examples: + - value: Hospitalized [NCIT:C25179] + any_of: + - range: host health status details international menu + - range: null value menu + host health outcome: + rank: 40 + slot_group: Host Information + examples: + - value: Recovered [NCIT:C49498] + any_of: + - range: host health outcome international menu + - range: null value menu + exact_mappings: + - BIOSAMPLE:host_health_outcome host disease: - rank: 34 + rank: 41 slot_group: Host Information examples: - value: Monkeypox [MONDO:0002594] @@ -688,7 +1129,7 @@ classes: - range: host disease international menu - range: null value menu host subject ID: - rank: 42 + rank: 47 slot_group: Host Information description: 'A unique identifier by which each host can be referred to e.g. #131' @@ -698,68 +1139,196 @@ classes: exact_mappings: - NML_LIMS:host subject ID - BIOSAMPLE:host_subject_id - host health state: - rank: 36 - slot_group: Host Information - host health outcome: - rank: 37 - slot_group: Host Information host age: - rank: 38 + rank: 43 slot_group: Host Information + recommended: true + exact_mappings: + - GISAID:Patient age + - BIOSAMPLE:host_age host age unit: - rank: 39 + rank: 44 slot_group: Host Information + recommended: true + examples: + - value: year [UO:0000036] + any_of: + - range: host age unit international menu + - range: null value menu + exact_mappings: + - BIOSAMPLE:host_age_unit host age bin: - rank: 40 + rank: 45 slot_group: Host Information + recommended: true + examples: + - value: 50 - 59 [GENEPIO:0100054] + any_of: + - range: host age bin international menu + - range: null value menu + exact_mappings: + - BIOSAMPLE:host_age_bin host gender: - rank: 41 + rank: 46 + slot_group: Host Information + recommended: true + examples: + - value: Male [NCIT:C46109] + any_of: + - range: host gender international menu + - range: null value menu + exact_mappings: + - GISAID:Gender + - BIOSAMPLE:host_sex + host residence geo_loc name (country): + rank: 48 slot_group: Host Information + examples: + - value: Canada [GAZ:00002560] + any_of: + - range: geo_loc_name (country) international menu + - range: null value menu symptom onset date: - rank: 43 + rank: 49 slot_group: Host Information signs and symptoms: - rank: 44 + rank: 50 slot_group: Host Information + examples: + - value: Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], + Myalgia (muscle pain) [HP:0003326] + any_of: + - range: signs and symptoms international menu + - range: null value menu pre-existing conditions and risk factors: - rank: 45 + rank: 51 + slot_group: Host Information + any_of: + - range: pre-existing conditions and risk factors international menu + - range: null value menu + complications: + rank: 52 + slot_group: Host Information + examples: + - value: Delayed wound healing (lesion healing) [MP:0002908] + any_of: + - range: complications international menu + - range: null value menu + antiviral therapy: + rank: 53 slot_group: Host Information host vaccination status: - rank: 46 + rank: 54 slot_group: Host vaccination information + examples: + - value: Not Vaccinated [GENEPIO:0100102] + any_of: + - range: host vaccination status international menu + - range: null value menu number of vaccine doses received: - rank: 47 + rank: 55 slot_group: Host vaccination information vaccination dose 1 vaccine name: - rank: 48 + rank: 56 slot_group: Host vaccination information vaccination dose 1 vaccination date: - rank: 49 + rank: 57 slot_group: Host vaccination information vaccination history: - rank: 50 + rank: 58 slot_group: Host vaccination information + location of exposure geo_loc name (country): + rank: 59 + slot_group: Host exposure information + examples: + - value: Canada [GAZ:00002560] + any_of: + - range: geo_loc_name (country) international menu + - range: null value menu + destination of most recent travel (city): + rank: 60 + slot_group: Host exposure information + destination of most recent travel (state/province/territory): + rank: 61 + slot_group: Host exposure information + range: WhitespaceMinimizedString + comments: 'Provide the name of the state/province/territory that the host + travelled to. Use this look-up service to identify the standardized term: + https://www.ebi.ac.uk/ols/ontologies/gaz' + examples: + - value: California + destination of most recent travel (country): + rank: 62 + slot_group: Host exposure information + examples: + - value: United Kingdom [GAZ:00002637] + any_of: + - range: geo_loc_name (country) international menu + - range: null value menu + most recent travel departure date: + rank: 63 + slot_group: Host exposure information + most recent travel return date: + rank: 64 + slot_group: Host exposure information travel history: - rank: 51 + rank: 65 slot_group: Host exposure information exposure event: - rank: 52 + rank: 66 slot_group: Host exposure information + examples: + - value: Party [PCO:0000035] + any_of: + - range: exposure event international menu + - range: null value menu exposure contact level: - rank: 53 + rank: 67 slot_group: Host exposure information + examples: + - value: Contact with infected individual [GENEPIO:0100357] + any_of: + - range: exposure contact level international menu + - range: null value menu host role: - rank: 54 + rank: 68 slot_group: Host exposure information + range: host role international menu + examples: + - value: Acquaintance of case [GENEPIO:0100266] exposure setting: - rank: 55 + rank: 69 slot_group: Host exposure information + range: exposure setting international menu + examples: + - value: Healthcare Setting [GENEPIO:0100201] exposure details: - rank: 56 + rank: 70 slot_group: Host exposure information + prior Monkeypox infection: + rank: 71 + slot_group: Host reinfection information + examples: + - value: Prior infection [GENEPIO:0100037] + any_of: + - range: prior Monkeypox infection international menu + - range: null value menu + prior Monkeypox infection date: + rank: 72 + slot_group: Host reinfection information + prior Monkeypox antiviral treatment: + rank: 73 + slot_group: Host reinfection information + examples: + - value: Prior antiviral treatment [GENEPIO:0100037] + any_of: + - range: prior Monkeypox antiviral treatment international menu + - range: null value menu + prior antiviral treatment during prior Monkeypox infection: + rank: 74 + slot_group: Host reinfection information purpose of sequencing: - rank: 57 + rank: 75 slot_group: Sequencing examples: - value: Baseline surveillance (random sampling) [GENEPIO:0100005] @@ -767,16 +1336,22 @@ classes: - range: purpose of sequencing international menu - range: null value menu purpose of sequencing details: - rank: 58 + rank: 76 slot_group: Sequencing sequencing date: - rank: 59 + rank: 77 + slot_group: Sequencing + library ID: + rank: 78 + slot_group: Sequencing + amplicon size: + rank: 79 slot_group: Sequencing library preparation kit: - rank: 60 + rank: 80 slot_group: Sequencing sequencing instrument: - rank: 61 + rank: 81 slot_group: Sequencing examples: - value: Oxford Nanopore MinION [GENEPIO:0100142] @@ -784,40 +1359,76 @@ classes: - range: sequencing instrument international menu - range: null value menu sequencing protocol: - rank: 62 + rank: 82 + slot_group: Sequencing + sequencing kit number: + rank: 83 + slot_group: Sequencing + amplicon pcr primer scheme: + rank: 84 slot_group: Sequencing raw sequence data processing method: - rank: 63 + rank: 85 slot_group: Bioinformatics and QC metrics dehosting method: - rank: 64 + rank: 86 + slot_group: Bioinformatics and QC metrics + consensus sequence name: + rank: 87 + slot_group: Bioinformatics and QC metrics + consensus sequence filename: + rank: 88 + slot_group: Bioinformatics and QC metrics + consensus sequence filepath: + rank: 89 slot_group: Bioinformatics and QC metrics consensus sequence software name: - rank: 65 + rank: 90 slot_group: Bioinformatics and QC metrics consensus sequence software version: - rank: 66 + rank: 91 slot_group: Bioinformatics and QC metrics breadth of coverage value: - rank: 67 + rank: 92 slot_group: Bioinformatics and QC metrics depth of coverage value: - rank: 68 + rank: 93 slot_group: Bioinformatics and QC metrics depth of coverage threshold: - rank: 69 + rank: 94 + slot_group: Bioinformatics and QC metrics + r1 fastq filename: + rank: 95 + slot_group: Bioinformatics and QC metrics + r2 fastq filename: + rank: 96 + slot_group: Bioinformatics and QC metrics + r1 fastq filepath: + rank: 97 + slot_group: Bioinformatics and QC metrics + r2 fastq filepath: + rank: 98 + slot_group: Bioinformatics and QC metrics + fast5 filename: + rank: 99 + slot_group: Bioinformatics and QC metrics + fast5 filepath: + rank: 100 slot_group: Bioinformatics and QC metrics number of base pairs sequenced: - rank: 70 + rank: 101 slot_group: Bioinformatics and QC metrics consensus genome length: - rank: 71 + rank: 102 + slot_group: Bioinformatics and QC metrics + reference genome accession: + rank: 103 slot_group: Bioinformatics and QC metrics bioinformatics protocol: - rank: 72 + rank: 104 slot_group: Bioinformatics and QC metrics gene name 1: - rank: 73 + rank: 105 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 @@ -827,10 +1438,10 @@ classes: - range: WhitespaceMinimizedString - range: null value menu diagnostic pcr Ct value 1: - rank: 74 + rank: 106 slot_group: Pathogen diagnostic testing gene name 2: - rank: 75 + rank: 107 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 @@ -840,10 +1451,10 @@ classes: - range: WhitespaceMinimizedString - range: null value menu diagnostic pcr Ct value 2: - rank: 76 + rank: 108 slot_group: Pathogen diagnostic testing gene name 3: - rank: 77 + rank: 109 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 @@ -853,13 +1464,13 @@ classes: - range: WhitespaceMinimizedString - range: null value menu diagnostic pcr Ct value 3: - rank: 78 + rank: 110 slot_group: Pathogen diagnostic testing authors: - rank: 79 + rank: 111 slot_group: Contributor acknowledgement DataHarmonizer provenance: - rank: 80 + rank: 112 slot_group: Contributor acknowledgement slots: specimen collector sample ID: @@ -903,6 +1514,20 @@ slots: - CNPHI:Related Specimen Relationship Type - NML_LIMS:PH_RELATED_PRIMARY_ID - BIOSAMPLE:host_subject_ID + case ID: + name: case ID + title: case ID + description: The identifier used to specify an epidemiologically detected case + of disease. + comments: Provide the case identifer. The case ID greatly facilitates linkage + between laboratory and epidemiological data. The case ID may be considered identifiable + information. Consult the data steward before sharing. + examples: + - value: ABCD1234 + slot_uri: GENEPIO:0100281 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:PH_CASE_ID bioproject accession: name: bioproject accession title: bioproject accession @@ -1174,6 +1799,9 @@ slots: any_of: - range: date - range: null value menu + todos: + - '>=2019-10-01' + - <={today} exact_mappings: - NML_LIMS:sample received date geo_loc_name (country): @@ -1409,6 +2037,41 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_method - VirusSeq_Portal:collection method + specimen processing: + name: specimen processing + title: specimen processing + description: Any processing applied to the sample during or after receiving the + sample. + comments: Critical for interpreting data. Select all the applicable processes + from the pick list. If virus was passaged, include information in "lab host", + "passage number", and "passage method" fields. If none of the processes in the + pick list apply, put "not applicable". + slot_uri: GENEPIO:0001253 + multivalued: true + specimen processing details: + name: specimen processing details + title: specimen processing details + description: Detailed information regarding the processing applied to a sample + during or after receiving the sample. + comments: Provide a free text description of any processing details applied to + a sample. + examples: + - value: 5 swabs from different body sites were pooled and further prepared as + a single sample during library prep. + slot_uri: GENEPIO:0100311 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:specimen processing details + host (common name): + name: host (common name) + title: host (common name) + description: The commonly used name of the host. + comments: Common name or scientific name are required if there was a host. Both + can be provided, if known. Use terms from the pick lists in the template. Common + name e.g. human. + examples: + - value: Human + slot_uri: GENEPIO:0001386 host (scientific name): name: host (scientific name) title: host (scientific name) @@ -1423,6 +2086,25 @@ slots: - NML_LIMS:host (scientific name) - BIOSAMPLE:host - VirusSeq_Portal:host (scientific name) + host health state: + name: host health state + title: host health state + description: Health status of the host at the time of sample collection. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001388 + host health status details: + name: host health status details + title: host health status details + description: Further details pertaining to the health or disease status of the + host at time of collection. + comments: If known, select a descriptor from the pick list provided in the template. + slot_uri: GENEPIO:0001389 + host health outcome: + name: host health outcome + title: host health outcome + description: Disease outcome in the host. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001389 host disease: name: host disease title: host disease @@ -1440,33 +2122,6 @@ slots: title: host subject ID slot_uri: GENEPIO:0001398 range: WhitespaceMinimizedString - host health state: - name: host health state - title: host health state - description: Health status of the host at the time of sample collection. - comments: If known, select a value from the pick list. - examples: - - value: Asymptomatic [NCIT:C3833] - slot_uri: GENEPIO:0001388 - any_of: - - range: host health state international menu - - range: null value menu - exact_mappings: - - GISAID:Patient status - - BIOSAMPLE:host_health_state - host health outcome: - name: host health outcome - title: host health outcome - description: Disease outcome in the host. - comments: If known, select a value from the pick list. - examples: - - value: Recovered [NCIT:C49498] - slot_uri: GENEPIO:0001389 - any_of: - - range: host health outcome international menu - - range: null value menu - exact_mappings: - - BIOSAMPLE:host_health_outcome host age: name: host age title: host age @@ -1478,55 +2133,51 @@ slots: any_of: - range: decimal - range: null value menu - recommended: true - exact_mappings: - - GISAID:Patient age - - BIOSAMPLE:host_age + minimum_value: '0' + maximum_value: '130' host age unit: name: host age unit title: host age unit description: The units used to measure the host's age. comments: If known, provide the age units used to measure the host's age from the pick list. - examples: - - value: year [UO:0000036] slot_uri: GENEPIO:0001393 - any_of: - - range: host age unit international menu - - range: null value menu - recommended: true - exact_mappings: - - BIOSAMPLE:host_age_unit host age bin: name: host age bin title: host age bin description: The age category of the host at the time of sampling. comments: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. - examples: - - value: 50 - 59 [GENEPIO:0100054] slot_uri: GENEPIO:0001394 - any_of: - - range: host age bin international menu - - range: null value menu - recommended: true - exact_mappings: - - BIOSAMPLE:host_age_bin host gender: name: host gender title: host gender description: The gender of the host at the time of sample collection. comments: If known, select a value from the pick list. - examples: - - value: Male [NCIT:C46109] slot_uri: GENEPIO:0001395 + structured_pattern: + syntax: '{Title_Case}' + partial_match: false + interpolated: true + host residence geo_loc name (country): + name: host residence geo_loc name (country) + title: host residence geo_loc name (country) + description: The country of residence of the host. + comments: Select the country name from pick list provided in the template. + slot_uri: GENEPIO:0001396 + host residence geo_loc name (state/province/territory): + name: host residence geo_loc name (state/province/territory) + title: host residence geo_loc name (state/province/territory) + description: The state/province/territory of residence of the host. + comments: Select the province/territory name from pick list provided in the template. + examples: + - value: Quebec + slot_uri: GENEPIO:0001397 any_of: - - range: host gender international menu + - range: geo_loc_name (state/province/territory) menu - range: null value menu - recommended: true exact_mappings: - - GISAID:Gender - - BIOSAMPLE:host_sex + - NML_LIMS:PH_HOST_PROVINCE symptom onset date: name: symptom onset date title: symptom onset date @@ -1539,18 +2190,18 @@ slots: any_of: - range: date - range: null value menu + todos: + - '>=2019-10-01' + - <={today} + exact_mappings: + - NML_LIMS:HC_ONSET_DATE signs and symptoms: name: signs and symptoms title: signs and symptoms description: A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. comments: Select all of the symptoms experienced by the host from the pick list. - examples: - - value: Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] slot_uri: GENEPIO:0001400 - any_of: - - range: signs and symptoms menu - - range: null value menu multivalued: true pre-existing conditions and risk factors: name: pre-existing conditions and risk factors @@ -1562,29 +2213,41 @@ slots: comments: Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. - examples: - - value: Asthma - - value: Pregnancy - - value: Smoking slot_uri: GENEPIO:0001401 - any_of: - - range: pre-existing conditions and risk factors menu - - range: null value menu multivalued: true exact_mappings: - NML_LIMS:pre-existing conditions and risk factors + complications: + name: complications + title: complications + description: Patient medical complications that are believed to have occurred + as a result of host disease. + comments: Select all of the complications experienced by the host from the pick + list. If the desired term is missing, contact the curation team. + slot_uri: GENEPIO:0001402 + multivalued: true + antiviral therapy: + name: antiviral therapy + title: antiviral therapy + description: Treatment of viral infections with agents that prevent viral replication + in infected cells without impairing the host cell function. + comments: Provide details of all current antiviral treatment during the current + Monkeypox infection period. Consult with the data steward prior to sharing this + information. + examples: + - value: Tecovirimat used to treat current Monkeypox infection + - value: AZT administered for concurrent HIV infection + slot_uri: NCIT:C16119 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:antiviral therapy host vaccination status: name: host vaccination status title: host vaccination status description: The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). comments: Select the vaccination status of the host from the pick list. - examples: - - value: Fully Vaccinated slot_uri: GENEPIO:0001404 - any_of: - - range: host vaccination status menu - - range: null value menu exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY number of vaccine doses received: @@ -1596,6 +2259,8 @@ slots: - value: '1' slot_uri: GENEPIO:0001406 range: integer + exact_mappings: + - NML_LIMS:number of vaccine doses received vaccination dose 1 vaccine name: name: vaccination dose 1 vaccine name title: vaccination dose 1 vaccine name @@ -1623,6 +2288,9 @@ slots: any_of: - range: date - range: null value menu + todos: + - '>=2019-10-01' + - <={today} exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY vaccination history: @@ -1640,6 +2308,65 @@ slots: range: WhitespaceMinimizedString exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY + location of exposure geo_loc name (country): + name: location of exposure geo_loc name (country) + title: location of exposure geo_loc name (country) + description: The country where the host was likely exposed to the causative agent + of the illness. + comments: Select the country name from the pick list provided in the template. + slot_uri: GENEPIO:0001410 + destination of most recent travel (city): + name: destination of most recent travel (city) + title: destination of most recent travel (city) + description: The name of the city that was the destination of most recent travel. + comments: 'Provide the name of the city that the host travelled to. Use this look-up + service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz' + examples: + - value: New York City + slot_uri: GENEPIO:0001411 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:PH_TRAVEL + destination of most recent travel (state/province/territory): + name: destination of most recent travel (state/province/territory) + title: destination of most recent travel (state/province/territory) + description: The name of the state/province/territory that was the destination + of most recent travel. + slot_uri: GENEPIO:0001412 + destination of most recent travel (country): + name: destination of most recent travel (country) + title: destination of most recent travel (country) + description: The name of the country that was the destination of most recent travel. + comments: Select the country name from the pick list provided in the template. + slot_uri: GENEPIO:0001413 + most recent travel departure date: + name: most recent travel departure date + title: most recent travel departure date + description: The date of a person's most recent departure from their primary residence + (at that time) on a journey to one or more other locations. + comments: Provide the travel departure date. + examples: + - value: '2020-03-16' + slot_uri: GENEPIO:0001414 + any_of: + - range: date + - range: null value menu + exact_mappings: + - NML_LIMS:PH_TRAVEL + most recent travel return date: + name: most recent travel return date + title: most recent travel return date + description: The date of a person's most recent return to some residence from + a journey originating at that residence. + comments: Provide the travel return date. + examples: + - value: '2020-04-26' + slot_uri: GENEPIO:0001415 + any_of: + - range: date + - range: null value menu + exact_mappings: + - NML_LIMS:PH_TRAVEL travel history: name: travel history title: travel history @@ -1660,13 +2387,8 @@ slots: title: exposure event description: Event leading to exposure. comments: Select an exposure event from the pick list provided in the template. - If the desired term is missing, contact the curation team. - examples: - - value: Party [PCO:0000035] + If the desired term is missing, contact the DataHarmonizer curation team. slot_uri: GENEPIO:0001417 - any_of: - - range: exposure event menu - - range: null value menu exact_mappings: - GISAID:Additional location information - CNPHI:Exposure Event @@ -1675,13 +2397,8 @@ slots: name: exposure contact level title: exposure contact level description: The exposure transmission contact type. - comments: Select direct or indirect exposure from the pick-list. - examples: - - value: Contact with infected individual [GENEPIO:0100357] + comments: Select exposure contact level from the pick-list. slot_uri: GENEPIO:0001418 - any_of: - - range: exposure contact level menu - - range: null value menu exact_mappings: - NML_LIMS:exposure contact level host role: @@ -1689,11 +2406,9 @@ slots: title: host role description: The role of the host in relation to the exposure setting. comments: Select the host's personal role(s) from the pick list provided in the - template. If the desired term is missing, contact the curation team. - examples: - - value: Acquaintance of case [GENEPIO:0100266] + template. If the desired term is missing, contact the DataHarmonizer curation + team. slot_uri: GENEPIO:0001419 - range: host role menu multivalued: true exact_mappings: - NML_LIMS:PH_HOST_ROLE @@ -1702,11 +2417,9 @@ slots: title: exposure setting description: The setting leading to exposure. comments: Select the host exposure setting(s) from the pick list provided in the - template. If a desired term is missing, contact the curation team. - examples: - - value: Healthcare Setting [GENEPIO:0100201] + template. If a desired term is missing, contact the DataHarmonizer curation + team. slot_uri: GENEPIO:0001428 - range: exposure setting menu multivalued: true exact_mappings: - NML_LIMS:PH_EXPOSURE @@ -1721,6 +2434,49 @@ slots: range: WhitespaceMinimizedString exact_mappings: - NML_LIMS:PH_EXPOSURE_DETAILS + prior Monkeypox infection: + name: prior Monkeypox infection + title: prior Monkeypox infection + description: The absence or presence of a prior Monkeypox infection. + comments: If known, provide information about whether the individual had a previous + Monkeypox infection. Select a value from the pick list. + slot_uri: GENEPIO:0100532 + prior Monkeypox infection date: + name: prior Monkeypox infection date + title: prior Monkeypox infection date + description: The date of diagnosis of the prior Monkeypox infection. + comments: Provide the date that the most recent prior infection was diagnosed. + Provide the prior Monkeypox infection date in ISO 8601 standard format "YYYY-MM-DD". + examples: + - value: '2022-06-20' + slot_uri: GENEPIO:0100533 + any_of: + - range: date + - range: null value menu + exact_mappings: + - NML_LIMS:prior Monkeypox infection date + prior Monkeypox antiviral treatment: + name: prior Monkeypox antiviral treatment + title: prior Monkeypox antiviral treatment + description: The absence or presence of antiviral treatment for a prior Monkeypox + infection. + comments: If known, provide information about whether the individual had a previous + Monkeypox antiviral treatment. Select a value from the pick list. + slot_uri: GENEPIO:0100534 + prior antiviral treatment during prior Monkeypox infection: + name: prior antiviral treatment during prior Monkeypox infection + title: prior antiviral treatment during prior Monkeypox infection + description: Antiviral treatment for any infection during the prior Moneypox infection + period. + comments: Provide a description of any antiviral treatment administered for viral + infections (not including Monkeypox treatment) during the prior Monkeypox infection + period. This field is meant to capture concurrent treatment information. + examples: + - value: AZT was administered for HIV infection during the prior Monkeypox infection. + slot_uri: GENEPIO:0100535 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:prior antiviral treatment during Monkeypox infection purpose of sequencing: name: purpose of sequencing title: purpose of sequencing @@ -1775,6 +2531,30 @@ slots: - '>={sample collection date}' exact_mappings: - NML_LIMS:PH_SEQUENCING_DATE + library ID: + name: library ID + title: library ID + description: The user-specified identifier for the library prepared for sequencing. + comments: The library name should be unique, and can be an autogenerated ID from + your LIMS, or modification of the isolate ID. + examples: + - value: XYZ_123345 + slot_uri: GENEPIO:0001448 + range: WhitespaceMinimizedString + recommended: true + exact_mappings: + - NML_LIMS:library ID + amplicon size: + name: amplicon size + title: amplicon size + description: The length of the amplicon generated by PCR amplification. + comments: Provide the amplicon size, including the units. + examples: + - value: 300bp + slot_uri: GENEPIO:0001449 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:amplicon size library preparation kit: name: library preparation kit title: library preparation kit @@ -1806,19 +2586,42 @@ slots: description: The protocol used to generate the sequence. comments: 'Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: - "Viral sequencing was performed following a tiling amplicon strategy using the - primer scheme. Sequencing was performed using a sequencing - instrument. Libraries were prepared using library kit. "' + "Viral sequencing was performed following a metagenomic shotgun sequencing approach. + Sequencing was performed using a sequencing instrument. Libraries + were prepared using library kit. "' examples: - - value: Genomes were generated through amplicon sequencing of 1200 bp amplicons - with Freed schema primers. Libraries were created using Illumina DNA Prep - kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing - kits. + - value: Viral sequencing was performed following a metagenomic shotgun sequencing + approach. Libraries were created using Illumina DNA Prep kits, and sequence + data was produced using Miseq Micro v2 (500 cycles) sequencing kits. slot_uri: GENEPIO:0001454 range: WhitespaceMinimizedString exact_mappings: - NML_LIMS:PH_TESTING_PROTOCOL - VirusSeq_Portal:sequencing protocol + sequencing kit number: + name: sequencing kit number + title: sequencing kit number + description: The manufacturer's kit number. + comments: Alphanumeric value. + examples: + - value: AB456XYZ789 + slot_uri: GENEPIO:0001455 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:sequencing kit number + amplicon pcr primer scheme: + name: amplicon pcr primer scheme + title: amplicon pcr primer scheme + description: The specifications of the primers (primer sequences, binding positions, + fragment size generated etc) used to generate the amplicons to be sequenced. + comments: Provide the name and version of the primer scheme used to generate the + amplicons for sequencing. + examples: + - value: MPXV Sunrise 3.1 + slot_uri: GENEPIO:0001456 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:amplicon pcr primer scheme raw sequence data processing method: name: raw sequence data processing method title: raw sequence data processing method @@ -1846,6 +2649,40 @@ slots: exact_mappings: - NML_LIMS:PH_DEHOSTING_METHOD - VirusSeq_Portal:dehosting method + consensus sequence name: + name: consensus sequence name + title: consensus sequence name + description: The name of the consensus sequence. + comments: Provide the name and version number of the consensus sequence. + examples: + - value: mpxvassembly3 + slot_uri: GENEPIO:0001460 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:consensus sequence name + consensus sequence filename: + name: consensus sequence filename + title: consensus sequence filename + description: The name of the consensus sequence file. + comments: Provide the name and version number of the consensus sequence FASTA + file. + examples: + - value: mpxvassembly.fasta + slot_uri: GENEPIO:0001461 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:consensus sequence filename + consensus sequence filepath: + name: consensus sequence filepath + title: consensus sequence filepath + description: The filepath of the consesnsus sequence file. + comments: Provide the filepath of the consensus sequence FASTA file. + examples: + - value: /User/Documents/ViralLab/Data/mpxvassembly.fasta + slot_uri: GENEPIO:0001462 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:consensus sequence filepath consensus sequence software name: name: consensus sequence software name title: consensus sequence software name @@ -1914,6 +2751,65 @@ slots: range: WhitespaceMinimizedString exact_mappings: - NML_LIMS:depth of coverage threshold + r1 fastq filename: + name: r1 fastq filename + title: r1 fastq filename + description: The user-specified filename of the r1 FASTQ file. + comments: Provide the r1 FASTQ filename. This information aids in data management. + examples: + - value: ABC123_S1_L001_R1_001.fastq.gz + slot_uri: GENEPIO:0001476 + range: WhitespaceMinimizedString + recommended: true + r2 fastq filename: + name: r2 fastq filename + title: r2 fastq filename + description: The user-specified filename of the r2 FASTQ file. + comments: Provide the r2 FASTQ filename. This information aids in data management. + examples: + - value: ABC123_S1_L001_R2_001.fastq.gz + slot_uri: GENEPIO:0001477 + range: WhitespaceMinimizedString + recommended: true + r1 fastq filepath: + name: r1 fastq filepath + title: r1 fastq filepath + description: The location of the r1 FASTQ file within a user's file system. + comments: Provide the filepath for the r1 FASTQ file. This information aids in + data management. + examples: + - value: /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz + slot_uri: GENEPIO:0001478 + range: WhitespaceMinimizedString + r2 fastq filepath: + name: r2 fastq filepath + title: r2 fastq filepath + description: The location of the r2 FASTQ file within a user's file system. + comments: Provide the filepath for the r2 FASTQ file. This information aids in + data management. + examples: + - value: /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz + slot_uri: GENEPIO:0001479 + range: WhitespaceMinimizedString + fast5 filename: + name: fast5 filename + title: fast5 filename + description: The user-specified filename of the FAST5 file. + comments: Provide the FAST5 filename. This information aids in data management. + examples: + - value: mpxv123seq.fast5 + slot_uri: GENEPIO:0001480 + range: WhitespaceMinimizedString + fast5 filepath: + name: fast5 filepath + title: fast5 filepath + description: The location of the FAST5 file within a user's file system. + comments: Provide the filepath for the FAST5 file. This information aids in data + management. + examples: + - value: /User/Documents/RespLab/Data/mpxv123seq.fast5 + slot_uri: GENEPIO:0001481 + range: WhitespaceMinimizedString number of base pairs sequenced: name: number of base pairs sequenced title: number of base pairs sequenced @@ -1939,6 +2835,17 @@ slots: minimum_value: '0' exact_mappings: - NML_LIMS:consensus genome length + reference genome accession: + name: reference genome accession + title: reference genome accession + description: A persistent, unique identifier of a genome database entry. + comments: Provide the accession number of the reference genome. + examples: + - value: NC_063383.1 + slot_uri: GENEPIO:0001485 + range: WhitespaceMinimizedString + exact_mappings: + - NML_LIMS:reference genome accession bioinformatics protocol: name: bioinformatics protocol title: bioinformatics protocol @@ -1948,7 +2855,7 @@ slots: can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. examples: - - value: https://github.com/phac-nml/ncov2019-artic-nf + - value: https://github.com/phac-nml/monkeypox-nf slot_uri: GENEPIO:0001489 range: WhitespaceMinimizedString exact_mappings: @@ -3088,6 +3995,42 @@ enums: Virus Transport Medium [OBI:0002866]: text: Virus Transport Medium [OBI:0002866] meaning: OBI:0002866 + specimen processing menu: + name: specimen processing menu + permissible_values: + Virus passage: + text: Virus passage + meaning: GENEPIO:0100039 + RNA re-extraction (post RT-PCR): + text: RNA re-extraction (post RT-PCR) + meaning: GENEPIO:0100040 + Specimens pooled: + text: Specimens pooled + meaning: OBI:0600016 + specimen processing international menu: + name: specimen processing international menu + permissible_values: + Virus passage [GENEPIO:0100039]: + text: Virus passage [GENEPIO:0100039] + meaning: GENEPIO:0100039 + RNA re-extraction (post RT-PCR) [GENEPIO:0100040]: + text: RNA re-extraction (post RT-PCR) [GENEPIO:0100040] + meaning: GENEPIO:0100040 + Specimens pooled [OBI:0600016]: + text: Specimens pooled [OBI:0600016] + meaning: OBI:0600016 + host (common name) menu: + name: host (common name) menu + permissible_values: + Human: + text: Human + meaning: NCBITaxon:9606 + host (common name) international menu: + name: host (common name) international menu + permissible_values: + Human [NCBITaxon:9606]: + text: Human [NCBITaxon:9606] + meaning: NCBITaxon:9606 host (scientific name) menu: name: host (scientific name) menu permissible_values: @@ -3104,6 +4047,24 @@ enums: meaning: NCBITaxon:9606 exact_mappings: - NML_LIMS:Human + host health state menu: + name: host health state menu + permissible_values: + Asymptomatic: + text: Asymptomatic + meaning: NCIT:C3833 + Deceased: + text: Deceased + meaning: NCIT:C28554 + Healthy: + text: Healthy + meaning: NCIT:C115935 + Recovered: + text: Recovered + meaning: NCIT:C49498 + Symptomatic: + text: Symptomatic + meaning: NCIT:C25269 host health state international menu: name: host health state international menu permissible_values: @@ -3122,6 +4083,69 @@ enums: Symptomatic [NCIT:C25269]: text: Symptomatic [NCIT:C25269] meaning: NCIT:C25269 + host health status details menu: + name: host health status details menu + permissible_values: + Hospitalized: + text: Hospitalized + meaning: NCIT:C25179 + Hospitalized (Non-ICU): + text: Hospitalized (Non-ICU) + meaning: GENEPIO:0100045 + is_a: Hospitalized + Hospitalized (ICU): + text: Hospitalized (ICU) + meaning: GENEPIO:0100046 + is_a: Hospitalized + Medically Isolated: + text: Medically Isolated + meaning: GENEPIO:0100047 + Medically Isolated (Negative Pressure): + text: Medically Isolated (Negative Pressure) + meaning: GENEPIO:0100048 + is_a: Medically Isolated + Self-quarantining: + text: Self-quarantining + meaning: NCIT:C173768 + host health status details international menu: + name: host health status details international menu + permissible_values: + Hospitalized [NCIT:C25179]: + text: Hospitalized [NCIT:C25179] + meaning: NCIT:C25179 + Hospitalized (Non-ICU) [GENEPIO:0100045]: + text: Hospitalized (Non-ICU) [GENEPIO:0100045] + meaning: GENEPIO:0100045 + is_a: Hospitalized [NCIT:C25179] + Hospitalized (ICU) [GENEPIO:0100046]: + text: Hospitalized (ICU) [GENEPIO:0100046] + meaning: GENEPIO:0100046 + is_a: Hospitalized [NCIT:C25179] + Medically Isolated [GENEPIO:0100047]: + text: Medically Isolated [GENEPIO:0100047] + meaning: GENEPIO:0100047 + Medically Isolated (Negative Pressure) [GENEPIO:0100048]: + text: Medically Isolated (Negative Pressure) [GENEPIO:0100048] + meaning: GENEPIO:0100048 + is_a: Medically Isolated [GENEPIO:0100047] + Self-quarantining [NCIT:C173768]: + text: Self-quarantining [NCIT:C173768] + meaning: NCIT:C173768 + host health outcome menu: + name: host health outcome menu + permissible_values: + Deceased: + text: Deceased + meaning: NCIT:C28554 + Deteriorating: + text: Deteriorating + meaning: NCIT:C25254 + Recovered: + text: Recovered + meaning: NCIT:C49498 + Stable: + text: Stable + meaning: NCIT:C30103 host health outcome international menu: name: host health outcome international menu permissible_values: @@ -3137,6 +4161,15 @@ enums: Stable [NCIT:C30103]: text: Stable [NCIT:C30103] meaning: NCIT:C30103 + host age unit menu: + name: host age unit menu + permissible_values: + month: + text: month + meaning: UO:0000035 + year: + text: year + meaning: UO:0000036 host age unit international menu: name: host age unit international menu permissible_values: @@ -3146,6 +4179,42 @@ enums: year [UO:0000036]: text: year [UO:0000036] meaning: UO:0000036 + host age bin menu: + name: host age bin menu + permissible_values: + 0 - 9: + text: 0 - 9 + meaning: GENEPIO:0100049 + 10 - 19: + text: 10 - 19 + meaning: GENEPIO:0100050 + 20 - 29: + text: 20 - 29 + meaning: GENEPIO:0100051 + 30 - 39: + text: 30 - 39 + meaning: GENEPIO:0100052 + 40 - 49: + text: 40 - 49 + meaning: GENEPIO:0100053 + 50 - 59: + text: 50 - 59 + meaning: GENEPIO:0100054 + 60 - 69: + text: 60 - 69 + meaning: GENEPIO:0100055 + 70 - 79: + text: 70 - 79 + meaning: GENEPIO:0100056 + 80 - 89: + text: 80 - 89 + meaning: GENEPIO:0100057 + 90 - 99: + text: 90 - 99 + meaning: GENEPIO:0100058 + 100+: + text: 100+ + meaning: GENEPIO:0100059 host age bin international menu: name: host age bin international menu permissible_values: @@ -3182,6 +4251,27 @@ enums: 100+ [GENEPIO:0100059]: text: 100+ [GENEPIO:0100059] meaning: GENEPIO:0100059 + host gender menu: + name: host gender menu + permissible_values: + Female: + text: Female + meaning: NCIT:C46110 + Male: + text: Male + meaning: NCIT:C46109 + Non-binary gender: + text: Non-binary gender + meaning: GSSO:000132 + Transgender (assigned male at birth): + text: Transgender (assigned male at birth) + meaning: GSSO:004004 + Transgender (assigned female at birth): + text: Transgender (assigned female at birth) + meaning: GSSO:004005 + Undeclared: + text: Undeclared + meaning: NCIT:C110959 host gender international menu: name: host gender international menu permissible_values: @@ -3205,6 +4295,96 @@ enums: meaning: NCIT:C110959 signs and symptoms menu: name: signs and symptoms menu + permissible_values: + Chills (sudden cold sensation): + text: Chills (sudden cold sensation) + description: A sudden sensation of feeling cold. + meaning: HP:0025143 + Conjunctivitis (pink eye): + text: Conjunctivitis (pink eye) + description: Inflammation of the conjunctiva. + meaning: HP:0000509 + Cough: + text: Cough + description: A sudden, audible expulsion of air from the lungs through a partially + closed glottis, preceded by inhalation. + meaning: HP:0012735 + Fatigue (tiredness): + text: Fatigue (tiredness) + description: A subjective feeling of tiredness characterized by a lack of + energy and motivation. + meaning: HP:0012378 + Fever: + text: Fever + description: Body temperature elevated above the normal range. + meaning: HP:0001945 + Headache: + text: Headache + description: Cephalgia, or pain sensed in various parts of the head, not confined + to the area of distribution of any nerve. + meaning: HP:0002315 + Lesion: + text: Lesion + meaning: NCIT:C3824 + Lesion (Macule): + text: Lesion (Macule) + meaning: NCIT:C43278 + is_a: Lesion + Lesion (Papule): + text: Lesion (Papule) + meaning: NCIT:C39690 + is_a: Lesion + Lesion (Pustule): + text: Lesion (Pustule) + meaning: NCIT:C78582 + is_a: Lesion + Lesion (Scab): + text: Lesion (Scab) + meaning: GENEPIO:0100490 + is_a: Lesion + Lesion (Vesicle): + text: Lesion (Vesicle) + meaning: GENEPIO:0100491 + is_a: Lesion + Myalgia (muscle pain): + text: Myalgia (muscle pain) + description: Pain in muscle. + meaning: HP:0003326 + Back pain: + text: Back pain + meaning: HP:0003418 + is_a: Myalgia (muscle pain) + Nausea: + text: Nausea + description: A sensation of unease in the stomach together with an urge to + vomit. + meaning: HP:0002018 + Rash: + text: Rash + description: A red eruption of the skin. + meaning: HP:0000988 + Sore throat: + text: Sore throat + description: Any kind of inflammatory process of the tonsils, pharynx, or/and + larynx characterized by pain in swallowing. + meaning: NCIT:C50747 + Sweating: + text: Sweating + meaning: NCIT:C36172 + Swollen Lymph Nodes: + text: Swollen Lymph Nodes + description: Enlargment (swelling) of a lymph node. + meaning: HP:0002716 + Ulcer: + text: Ulcer + meaning: NCIT:C3426 + Vomiting (throwing up): + text: Vomiting (throwing up) + description: Forceful ejection of the contents of the stomach through the + mouth by means of a series of involuntary spasmic contractions. + meaning: HP:0002013 + signs and symptoms international menu: + name: signs and symptoms international menu permissible_values: Chills (sudden cold sensation) [HP:0025143]: text: Chills (sudden cold sensation) [HP:0025143] @@ -3260,6 +4440,10 @@ enums: text: Myalgia (muscle pain) [HP:0003326] description: Pain in muscle. meaning: HP:0003326 + Back pain [HP:0003418]: + text: Back pain [HP:0003418] + meaning: HP:0003418 + is_a: Myalgia (muscle pain) [HP:0003326] Nausea [HP:0002018]: text: Nausea [HP:0002018] description: A sensation of unease in the stomach together with an urge to @@ -3274,10 +4458,16 @@ enums: description: Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing. meaning: NCIT:C50747 + Sweating [NCIT:C36172]: + text: Sweating [NCIT:C36172] + meaning: NCIT:C36172 Swollen Lymph Nodes [HP:0002716]: text: Swollen Lymph Nodes [HP:0002716] description: Enlargment (swelling) of a lymph node. meaning: HP:0002716 + Ulcer [NCIT:C3426]: + text: Ulcer [NCIT:C3426] + meaning: NCIT:C3426 Vomiting (throwing up) [HP:0002013]: text: Vomiting (throwing up) [HP:0002013] description: Forceful ejection of the contents of the stomach through the @@ -3286,25 +4476,287 @@ enums: pre-existing conditions and risk factors menu: name: pre-existing conditions and risk factors menu permissible_values: + Cancer: + text: Cancer + meaning: MONDO:0004992 + Diabetes mellitus (diabetes): + text: Diabetes mellitus (diabetes) + meaning: HP:0000819 + Type I diabetes mellitus (T1D): + text: Type I diabetes mellitus (T1D) + meaning: HP:0100651 + is_a: Diabetes mellitus (diabetes) + Type II diabetes mellitus (T2D): + text: Type II diabetes mellitus (T2D) + meaning: HP:0005978 + is_a: Diabetes mellitus (diabetes) + Immunocompromised: + text: Immunocompromised + meaning: NCIT:C14139 + Infectious disorder: + text: Infectious disorder + meaning: NCIT:C26726 + Chancroid (Haemophilus ducreyi): + text: Chancroid (Haemophilus ducreyi) + meaning: DOID:13778 + is_a: Infectious disorder + Chlamydia: + text: Chlamydia + meaning: DOID:11263 + is_a: Infectious disorder + Gonorrhea: + text: Gonorrhea + meaning: DOID:7551 + is_a: Infectious disorder + Herpes Simplex Virus infection (HSV): + text: Herpes Simplex Virus infection (HSV) + meaning: NCIT:C155871 + is_a: Infectious disorder + Human immunodeficiency virus (HIV): + text: Human immunodeficiency virus (HIV) + meaning: MONDO:0005109 + is_a: Infectious disorder + Acquired immunodeficiency syndrome (AIDS): + text: Acquired immunodeficiency syndrome (AIDS) + meaning: MONDO:0012268 + is_a: Human immunodeficiency virus (HIV) + Human papilloma virus infection (HPV): + text: Human papilloma virus infection (HPV) + meaning: MONDO:0005161 + is_a: Infectious disorder + Lymphogranuloma venereum: + text: Lymphogranuloma venereum + meaning: DOID:13819 + is_a: Infectious disorder + Mycoplsma genitalium: + text: Mycoplsma genitalium + meaning: NCBITaxon:2097 + is_a: Infectious disorder + Syphilis: + text: Syphilis + meaning: DOID:4166 + is_a: Infectious disorder + Trichomoniasis: + text: Trichomoniasis + meaning: DOID:1947 + is_a: Infectious disorder + Lupus: + text: Lupus + meaning: MONDO:0004670 + Pregnancy: + text: Pregnancy + meaning: NCIT:C25742 + Prior therapy: + text: Prior therapy + meaning: NCIT:C16124 + Cancer treatment: + text: Cancer treatment + meaning: NCIT:C16212 + is_a: Prior therapy + Chemotherapy: + text: Chemotherapy + meaning: NCIT:C15632 + is_a: Cancer treatment + HIV and Antiretroviral therapy (ART): + text: HIV and Antiretroviral therapy (ART) + meaning: NCIT:C16118 + is_a: Prior therapy + Steroid: + text: Steroid + meaning: CHEBI:35341 + is_a: Prior therapy + Transplant: + text: Transplant + meaning: NCIT:C159659 + pre-existing conditions and risk factors international menu: + name: pre-existing conditions and risk factors international menu + permissible_values: + Cancer [MONDO:0004992]: + text: Cancer [MONDO:0004992] + meaning: MONDO:0004992 + Diabetes mellitus (diabetes) [HP:0000819]: + text: Diabetes mellitus (diabetes) [HP:0000819] + meaning: HP:0000819 + Type I diabetes mellitus (T1D) [HP:0100651]: + text: Type I diabetes mellitus (T1D) [HP:0100651] + meaning: HP:0100651 + is_a: Diabetes mellitus (diabetes) [HP:0000819] + Type II diabetes mellitus (T2D) [HP:0005978]: + text: Type II diabetes mellitus (T2D) [HP:0005978] + meaning: HP:0005978 + is_a: Diabetes mellitus (diabetes) [HP:0000819] + Immunocompromised [NCIT:C14139]: + text: Immunocompromised [NCIT:C14139] + meaning: NCIT:C14139 + Infectious disorder [NCIT:C26726]: + text: Infectious disorder [NCIT:C26726] + meaning: NCIT:C26726 + Chancroid (Haemophilus ducreyi) [DOID:13778]: + text: Chancroid (Haemophilus ducreyi) [DOID:13778] + meaning: DOID:13778 + is_a: Infectious disorder [NCIT:C26726] + Chlamydia [DOID:11263]: + text: Chlamydia [DOID:11263] + meaning: DOID:11263 + is_a: Infectious disorder [NCIT:C26726] + Gonorrhea [DOID:7551]: + text: Gonorrhea [DOID:7551] + meaning: DOID:7551 + is_a: Infectious disorder [NCIT:C26726] + Herpes Simplex Virus infection (HSV) [NCIT:C155871]: + text: Herpes Simplex Virus infection (HSV) [NCIT:C155871] + meaning: NCIT:C155871 + is_a: Infectious disorder [NCIT:C26726] Human immunodeficiency virus (HIV) [MONDO:0005109]: text: Human immunodeficiency virus (HIV) [MONDO:0005109] meaning: MONDO:0005109 + is_a: Infectious disorder [NCIT:C26726] Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]: text: Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] meaning: MONDO:0012268 is_a: Human immunodeficiency virus (HIV) [MONDO:0005109] - HIV and antiretroviral therapy (ART) [NCIT:C16118]: - text: HIV and antiretroviral therapy (ART) [NCIT:C16118] - meaning: NCIT:C16118 - is_a: Human immunodeficiency virus (HIV) [MONDO:0005109] - Immunocompromised [NCIT:C14139]: - text: Immunocompromised [NCIT:C14139] - meaning: NCIT:C14139 + Human papilloma virus infection (HPV) [MONDO:0005161]: + text: Human papilloma virus infection (HPV) [MONDO:0005161] + meaning: MONDO:0005161 + is_a: Infectious disorder [NCIT:C26726] + Lymphogranuloma venereum [DOID:13819]: + text: Lymphogranuloma venereum [DOID:13819] + meaning: DOID:13819 + is_a: Infectious disorder [NCIT:C26726] + Mycoplsma genitalium [NCBITaxon:2097]: + text: Mycoplsma genitalium [NCBITaxon:2097] + meaning: NCBITaxon:2097 + is_a: Infectious disorder [NCIT:C26726] + Syphilis [DOID:4166]: + text: Syphilis [DOID:4166] + meaning: DOID:4166 + is_a: Infectious disorder [NCIT:C26726] + Trichomoniasis [DOID:1947]: + text: Trichomoniasis [DOID:1947] + meaning: DOID:1947 + is_a: Infectious disorder [NCIT:C26726] + Lupus [MONDO:0004670]: + text: Lupus [MONDO:0004670] + meaning: MONDO:0004670 Pregnancy [NCIT:C25742]: text: Pregnancy [NCIT:C25742] meaning: NCIT:C25742 + Prior therapy [NCIT:C16124]: + text: Prior therapy [NCIT:C16124] + meaning: NCIT:C16124 + Cancer treatment [NCIT:C16212]: + text: Cancer treatment [NCIT:C16212] + meaning: NCIT:C16212 + is_a: Prior therapy [NCIT:C16124] + Chemotherapy [NCIT:C15632]: + text: Chemotherapy [NCIT:C15632] + meaning: NCIT:C15632 + is_a: Cancer treatment [NCIT:C16212] + HIV and Antiretroviral therapy (ART) [NCIT:C16118]: + text: HIV and Antiretroviral therapy (ART) [NCIT:C16118] + meaning: NCIT:C16118 + is_a: Prior therapy [NCIT:C16124] + Steroid [CHEBI:35341]: + text: Steroid [CHEBI:35341] + meaning: CHEBI:35341 + is_a: Prior therapy [NCIT:C16124] + Transplant [NCIT:C159659]: + text: Transplant [NCIT:C159659] + meaning: NCIT:C159659 + complications menu: + name: complications menu + permissible_values: + Bronchopneumonia: + text: Bronchopneumonia + meaning: MONDO:0005682 + Corneal infection: + text: Corneal infection + meaning: MONDO:0023865 + Delayed wound healing (lesion healing): + text: Delayed wound healing (lesion healing) + meaning: MP:0002908 + Encephalitis: + text: Encephalitis + meaning: DOID:9588 + Myocarditis: + text: Myocarditis + meaning: DOID:820 + Secondary infection: + text: Secondary infection + meaning: IDO:0000567 + Sepsis: + text: Sepsis + meaning: HP:0100806 + complications international menu: + name: complications international menu + permissible_values: + Bronchopneumonia [MONDO:0005682]: + text: Bronchopneumonia [MONDO:0005682] + meaning: MONDO:0005682 + Corneal infection [MONDO:0023865]: + text: Corneal infection [MONDO:0023865] + meaning: MONDO:0023865 + Delayed wound healing (lesion healing) [MP:0002908]: + text: Delayed wound healing (lesion healing) [MP:0002908] + meaning: MP:0002908 + Encephalitis [DOID:9588]: + text: Encephalitis [DOID:9588] + meaning: DOID:9588 + Myocarditis [DOID:820]: + text: Myocarditis [DOID:820] + meaning: DOID:820 + Secondary infection [IDO:0000567]: + text: Secondary infection [IDO:0000567] + meaning: IDO:0000567 + Sepsis [HP:0100806]: + text: Sepsis [HP:0100806] + meaning: HP:0100806 + host vaccination status menu: + name: host vaccination status menu + permissible_values: + Fully Vaccinated: + text: Fully Vaccinated + meaning: GENEPIO:0100100 + Not Vaccinated: + text: Not Vaccinated + meaning: GENEPIO:0100102 + host vaccination status international menu: + name: host vaccination status international menu + permissible_values: + Fully Vaccinated [GENEPIO:0100100]: + text: Fully Vaccinated [GENEPIO:0100100] + meaning: GENEPIO:0100100 + Not Vaccinated [GENEPIO:0100102]: + text: Not Vaccinated [GENEPIO:0100102] + meaning: GENEPIO:0100102 exposure event menu: name: exposure event menu + permissible_values: + Mass Gathering: + text: Mass Gathering + meaning: GENEPIO:0100237 + Convention (conference): + text: Convention (conference) + meaning: GENEPIO:0100238 + Agricultural Event: + text: Agricultural Event + meaning: GENEPIO:0100240 + is_a: Convention (conference) + Social Gathering: + text: Social Gathering + meaning: PCO:0000033 + Community Event: + text: Community Event + meaning: PCO:0000034 + is_a: Social Gathering + Party: + text: Party + meaning: PCO:0000035 + is_a: Social Gathering + Other exposure event: + text: Other exposure event + exposure event international menu: + name: exposure event international menu permissible_values: Mass Gathering [GENEPIO:0100237]: text: Mass Gathering [GENEPIO:0100237] @@ -3348,6 +4800,57 @@ enums: description: An exposure event not specified in the picklist. exposure contact level menu: name: exposure contact level menu + permissible_values: + Contact with animal: + text: Contact with animal + meaning: GENEPIO:0100494 + Contact with rodent: + text: Contact with rodent + meaning: GENEPIO:0100495 + is_a: Contact with animal + Contact with fomite: + text: Contact with fomite + meaning: GENEPIO:0100496 + Contact with infected individual: + text: Contact with infected individual + meaning: GENEPIO:0100357 + Direct (human-to-human contact): + text: Direct (human-to-human contact) + meaning: TRANS:0000001 + is_a: Contact with infected individual + Mother-to-child transmission: + text: Mother-to-child transmission + meaning: TRANS:0000006 + is_a: Direct (human-to-human contact) + Sexual transmission: + text: Sexual transmission + meaning: NCIT:C19085 + is_a: Direct (human-to-human contact) + Indirect contact: + text: Indirect contact + meaning: GENEPIO:0100246 + is_a: Contact with infected individual + Close contact (face-to-face contact): + text: Close contact (face-to-face contact) + meaning: GENEPIO:0100247 + is_a: Indirect contact + Casual contact: + text: Casual contact + meaning: GENEPIO:0100248 + is_a: Indirect contact + Workplace associated transmission: + text: Workplace associated transmission + meaning: GENEPIO:0100497 + Healthcare associated transmission: + text: Healthcare associated transmission + meaning: GENEPIO:0100498 + is_a: Workplace associated transmission + Laboratory associated transmission: + text: Laboratory associated transmission + meaning: GENEPIO:0100499 + is_a: Workplace associated transmission + exposure contact level international menu: + name: exposure contact level international menu permissible_values: Contact with animal [GENEPIO:0100494]: text: Contact with animal [GENEPIO:0100494] @@ -3359,25 +4862,25 @@ enums: Contact with fomite [GENEPIO:0100496]: text: Contact with fomite [GENEPIO:0100496] meaning: GENEPIO:0100496 - Contact with infected individual: - text: Contact with infected individual + Contact with infected individual [GENEPIO:0100357]: + text: Contact with infected individual [GENEPIO:0100357] meaning: GENEPIO:0100357 Direct (human-to-human contact) [TRANS:0000001]: text: Direct (human-to-human contact) [TRANS:0000001] meaning: TRANS:0000001 - is_a: Contact with infected individual + is_a: Contact with infected individual [GENEPIO:0100357] Mother-to-child transmission [TRANS:0000006]: text: Mother-to-child transmission [TRANS:0000006] meaning: TRANS:0000006 is_a: Direct (human-to-human contact) [TRANS:0000001] - Sexual transmission[NCIT:C19085]: - text: Sexual transmission[NCIT:C19085] + Sexual transmission [NCIT:C19085]: + text: Sexual transmission [NCIT:C19085] meaning: NCIT:C19085 is_a: Direct (human-to-human contact) [TRANS:0000001] Indirect contact [GENEPIO:0100246]: text: Indirect contact [GENEPIO:0100246] meaning: GENEPIO:0100246 - is_a: Contact with infected individual + is_a: Contact with infected individual [GENEPIO:0100357] Close contact (face-to-face contact) [GENEPIO:0100247]: text: Close contact (face-to-face contact) [GENEPIO:0100247] meaning: GENEPIO:0100247 @@ -3399,6 +4902,139 @@ enums: is_a: Workplace associated transmission [GENEPIO:0100497] host role menu: name: host role menu + permissible_values: + Attendee: + text: Attendee + meaning: GENEPIO:0100249 + Student: + text: Student + meaning: OMRSE:00000058 + is_a: Attendee + Patient: + text: Patient + meaning: OMRSE:00000030 + Inpatient: + text: Inpatient + meaning: NCIT:C25182 + is_a: Patient + Outpatient: + text: Outpatient + meaning: NCIT:C28293 + is_a: Patient + Passenger: + text: Passenger + meaning: GENEPIO:0100250 + Resident: + text: Resident + meaning: GENEPIO:0100251 + Visitor: + text: Visitor + meaning: GENEPIO:0100252 + Volunteer: + text: Volunteer + meaning: GENEPIO:0100253 + Work: + text: Work + meaning: GENEPIO:0100254 + Administrator: + text: Administrator + meaning: GENEPIO:0100255 + is_a: Work + First Responder: + text: First Responder + meaning: GENEPIO:0100256 + is_a: Work + Housekeeper: + text: Housekeeper + meaning: GENEPIO:0100260 + is_a: Work + Kitchen Worker: + text: Kitchen Worker + meaning: GENEPIO:0100261 + is_a: Work + Healthcare Worker: + text: Healthcare Worker + meaning: GENEPIO:0100334 + is_a: Work + Community Healthcare Worker: + text: Community Healthcare Worker + meaning: GENEPIO:0100420 + is_a: Healthcare Worker + Laboratory Worker: + text: Laboratory Worker + meaning: GENEPIO:0100262 + is_a: Healthcare Worker + Nurse: + text: Nurse + meaning: OMRSE:00000014 + is_a: Healthcare Worker + Personal Care Aid: + text: Personal Care Aid + meaning: GENEPIO:0100263 + is_a: Healthcare Worker + Pharmacist: + text: Pharmacist + meaning: GENEPIO:0100264 + is_a: Healthcare Worker + Physician: + text: Physician + meaning: OMRSE:00000013 + is_a: Healthcare Worker + Rotational Worker: + text: Rotational Worker + meaning: GENEPIO:0100354 + is_a: Work + Seasonal Worker: + text: Seasonal Worker + meaning: GENEPIO:0100355 + is_a: Work + Sex Worker: + text: Sex Worker + meaning: GSSO:005831 + is_a: Work + Veterinarian: + text: Veterinarian + meaning: GENEPIO:0100265 + is_a: Work + Social role: + text: Social role + meaning: OMRSE:00000001 + Acquaintance of case: + text: Acquaintance of case + meaning: GENEPIO:0100266 + is_a: Social role + Relative of case: + text: Relative of case + meaning: GENEPIO:0100267 + is_a: Social role + Child of case: + text: Child of case + meaning: GENEPIO:0100268 + is_a: Relative of case + Parent of case: + text: Parent of case + meaning: GENEPIO:0100269 + is_a: Relative of case + Father of case: + text: Father of case + meaning: GENEPIO:0100270 + is_a: Parent of case + Mother of case: + text: Mother of case + meaning: GENEPIO:0100271 + is_a: Parent of case + Sexual partner of case: + text: Sexual partner of case + meaning: GENEPIO:0100500 + is_a: Social role + Spouse of case: + text: Spouse of case + meaning: GENEPIO:0100272 + is_a: Social role + Other Host Role: + text: Other Host Role + host role international menu: + name: host role international menu permissible_values: Attendee [GENEPIO:0100249]: text: Attendee [GENEPIO:0100249] @@ -3485,6 +5121,10 @@ enums: text: Seasonal Worker [GENEPIO:0100355] meaning: GENEPIO:0100355 is_a: Work [GENEPIO:0100254] + Sex Worker [GSSO:005831]: + text: Sex Worker [GSSO:005831] + meaning: GSSO:005831 + is_a: Work [GENEPIO:0100254] Veterinarian [GENEPIO:0100265]: text: Veterinarian [GENEPIO:0100265] meaning: GENEPIO:0100265 @@ -3528,6 +5168,245 @@ enums: text: Other Host Role exposure setting menu: name: exposure setting menu + permissible_values: + Human Exposure: + text: Human Exposure + meaning: ECTO:3000005 + Contact with Known Monkeypox Case: + text: Contact with Known Monkeypox Case + meaning: GENEPIO:0100501 + is_a: Human Exposure + Contact with Patient: + text: Contact with Patient + meaning: GENEPIO:0100185 + is_a: Human Exposure + Contact with Probable Monkeypox Case: + text: Contact with Probable Monkeypox Case + meaning: GENEPIO:0100502 + is_a: Human Exposure + Contact with Person who Recently Travelled: + text: Contact with Person who Recently Travelled + meaning: GENEPIO:0100189 + is_a: Human Exposure + Occupational, Residency or Patronage Exposure: + text: Occupational, Residency or Patronage Exposure + meaning: GENEPIO:0100190 + Abbatoir: + text: Abbatoir + meaning: ECTO:1000033 + is_a: Occupational, Residency or Patronage Exposure + Animal Rescue: + text: Animal Rescue + meaning: GENEPIO:0100191 + is_a: Occupational, Residency or Patronage Exposure + Bar (pub): + text: Bar (pub) + meaning: GENEPIO:0100503 + is_a: Occupational, Residency or Patronage Exposure + Childcare: + text: Childcare + meaning: GENEPIO:0100192 + is_a: Occupational, Residency or Patronage Exposure + Daycare: + text: Daycare + meaning: GENEPIO:0100193 + is_a: Childcare + Nursery: + text: Nursery + meaning: GENEPIO:0100194 + is_a: Childcare + Community Service Centre: + text: Community Service Centre + meaning: GENEPIO:0100195 + is_a: Occupational, Residency or Patronage Exposure + Correctional Facility: + text: Correctional Facility + meaning: GENEPIO:0100196 + is_a: Occupational, Residency or Patronage Exposure + Dormitory: + text: Dormitory + meaning: GENEPIO:0100197 + is_a: Occupational, Residency or Patronage Exposure + Farm: + text: Farm + meaning: ECTO:1000034 + is_a: Occupational, Residency or Patronage Exposure + First Nations Reserve: + text: First Nations Reserve + meaning: GENEPIO:0100198 + is_a: Occupational, Residency or Patronage Exposure + Funeral Home: + text: Funeral Home + meaning: GENEPIO:0100199 + is_a: Occupational, Residency or Patronage Exposure + Group Home: + text: Group Home + meaning: GENEPIO:0100200 + is_a: Occupational, Residency or Patronage Exposure + Healthcare Setting: + text: Healthcare Setting + meaning: GENEPIO:0100201 + is_a: Occupational, Residency or Patronage Exposure + Ambulance: + text: Ambulance + meaning: GENEPIO:0100202 + is_a: Healthcare Setting + Acute Care Facility: + text: Acute Care Facility + meaning: GENEPIO:0100203 + is_a: Healthcare Setting + Clinic: + text: Clinic + meaning: GENEPIO:0100204 + is_a: Healthcare Setting + Community Healthcare (At-Home) Setting: + text: Community Healthcare (At-Home) Setting + meaning: GENEPIO:0100415 + is_a: Healthcare Setting + Community Health Centre: + text: Community Health Centre + meaning: GENEPIO:0100205 + is_a: Healthcare Setting + Hospital: + text: Hospital + meaning: ECTO:1000035 + is_a: Healthcare Setting + Emergency Department: + text: Emergency Department + meaning: GENEPIO:0100206 + is_a: Hospital + ICU: + text: ICU + meaning: GENEPIO:0100207 + is_a: Hospital + Ward: + text: Ward + meaning: GENEPIO:0100208 + is_a: Hospital + Laboratory: + text: Laboratory + meaning: ECTO:1000036 + is_a: Healthcare Setting + Long-Term Care Facility: + text: Long-Term Care Facility + meaning: GENEPIO:0100209 + is_a: Healthcare Setting + Pharmacy: + text: Pharmacy + meaning: GENEPIO:0100210 + is_a: Healthcare Setting + Physician's Office: + text: Physician's Office + meaning: GENEPIO:0100211 + is_a: Healthcare Setting + Household: + text: Household + meaning: GENEPIO:0100212 + is_a: Occupational, Residency or Patronage Exposure + Insecure Housing (Homeless): + text: Insecure Housing (Homeless) + meaning: GENEPIO:0100213 + is_a: Occupational, Residency or Patronage Exposure + Occupational Exposure: + text: Occupational Exposure + meaning: GENEPIO:0100214 + is_a: Occupational, Residency or Patronage Exposure + Worksite: + text: Worksite + meaning: GENEPIO:0100215 + is_a: Occupational Exposure + Office: + text: Office + meaning: ECTO:1000037 + is_a: Worksite + Outdoors: + text: Outdoors + meaning: GENEPIO:0100216 + is_a: Occupational, Residency or Patronage Exposure + Camp/camping: + text: Camp/camping + meaning: ECTO:5000009 + is_a: Outdoors + Hiking Trail: + text: Hiking Trail + meaning: GENEPIO:0100217 + is_a: Outdoors + Hunting Ground: + text: Hunting Ground + meaning: ECTO:6000030 + is_a: Outdoors + Ski Resort: + text: Ski Resort + meaning: GENEPIO:0100218 + is_a: Outdoors + Petting zoo: + text: Petting zoo + meaning: ECTO:5000008 + is_a: Occupational, Residency or Patronage Exposure + Place of Worship: + text: Place of Worship + meaning: GENEPIO:0100220 + is_a: Occupational, Residency or Patronage Exposure + Church: + text: Church + meaning: GENEPIO:0100221 + is_a: Place of Worship + Mosque: + text: Mosque + meaning: GENEPIO:0100222 + is_a: Place of Worship + Temple: + text: Temple + meaning: GENEPIO:0100223 + is_a: Place of Worship + Restaurant: + text: Restaurant + meaning: ECTO:1000040 + is_a: Occupational, Residency or Patronage Exposure + Retail Store: + text: Retail Store + meaning: ECTO:1000041 + is_a: Occupational, Residency or Patronage Exposure + School: + text: School + meaning: GENEPIO:0100224 + is_a: Occupational, Residency or Patronage Exposure + Temporary Residence: + text: Temporary Residence + meaning: GENEPIO:0100225 + is_a: Occupational, Residency or Patronage Exposure + Homeless Shelter: + text: Homeless Shelter + meaning: GENEPIO:0100226 + is_a: Temporary Residence + Hotel: + text: Hotel + meaning: GENEPIO:0100227 + is_a: Temporary Residence + Veterinary Care Clinic: + text: Veterinary Care Clinic + meaning: GENEPIO:0100228 + is_a: Occupational, Residency or Patronage Exposure + Travel Exposure: + text: Travel Exposure + meaning: GENEPIO:0100229 + Travelled on a Cruise Ship: + text: Travelled on a Cruise Ship + meaning: GENEPIO:0100230 + is_a: Travel Exposure + Travelled on a Plane: + text: Travelled on a Plane + meaning: GENEPIO:0100231 + is_a: Travel Exposure + Travelled on Ground Transport: + text: Travelled on Ground Transport + meaning: GENEPIO:0100232 + is_a: Travel Exposure + Other Exposure Setting: + text: Other Exposure Setting + meaning: GENEPIO:0100235 + exposure setting international menu: + name: exposure setting international menu permissible_values: Human Exposure [ECTO:3000005]: text: Human Exposure [ECTO:3000005] @@ -3765,15 +5644,42 @@ enums: Other Exposure Setting [GENEPIO:0100235]: text: Other Exposure Setting [GENEPIO:0100235] meaning: GENEPIO:0100235 - host vaccination status menu: - name: host vaccination status menu + prior Monkeypox infection menu: + name: prior Monkeypox infection menu permissible_values: - Fully Vaccinated [GENEPIO:0100100]: - text: Fully Vaccinated [GENEPIO:0100100] - meaning: GENEPIO:0100100 - Not Vaccinated [GENEPIO:0100102]: - text: Not Vaccinated [GENEPIO:0100102] - meaning: GENEPIO:0100102 + Prior infection: + text: Prior infection + meaning: GENEPIO:0100037 + No prior infection: + text: No prior infection + meaning: GENEPIO:0100233 + prior Monkeypox infection international menu: + name: prior Monkeypox infection international menu + permissible_values: + Prior infection [GENEPIO:0100037]: + text: Prior infection [GENEPIO:0100037] + meaning: GENEPIO:0100037 + No prior infection [GENEPIO:0100233]: + text: No prior infection [GENEPIO:0100233] + meaning: GENEPIO:0100233 + prior Monkeypox antiviral treatment menu: + name: prior Monkeypox antiviral treatment menu + permissible_values: + Prior antiviral treatment: + text: Prior antiviral treatment + meaning: GENEPIO:0100037 + No prior antiviral treatment: + text: No prior antiviral treatment + meaning: GENEPIO:0100233 + prior Monkeypox antiviral treatment international menu: + name: prior Monkeypox antiviral treatment international menu + permissible_values: + Prior antiviral treatment [GENEPIO:0100037]: + text: Prior antiviral treatment [GENEPIO:0100037] + meaning: GENEPIO:0100037 + No prior antiviral treatment [GENEPIO:0100233]: + text: No prior antiviral treatment [GENEPIO:0100233] + meaning: GENEPIO:0100233 organism menu: name: organism menu permissible_values: diff --git a/template/monkeypox/schema_enums.tsv b/template/monkeypox/schema_enums.tsv index b5a863e1..608a1c35 100644 --- a/template/monkeypox/schema_enums.tsv +++ b/template/monkeypox/schema_enums.tsv @@ -297,25 +297,78 @@ collection device international menu OBI:0002859 Blood Collection Tube [OBI:0002 OBI:0002866 Virus Transport Medium [OBI:0002866] +specimen processing menu GENEPIO:0100039 Virus passage + GENEPIO:0100040 RNA re-extraction (post RT-PCR) + OBI:0600016 Specimens pooled + +specimen processing international menu GENEPIO:0100039 Virus passage [GENEPIO:0100039] + GENEPIO:0100040 RNA re-extraction (post RT-PCR) [GENEPIO:0100040] + OBI:0600016 Specimens pooled [OBI:0600016] + + +host (common name) menu NCBITaxon:9606 Human + +host (common name) international menu NCBITaxon:9606 Human [NCBITaxon:9606] + host (scientific name) menu NCBITaxon:9606 Homo sapiens Human host (scientific name) international menu NCBITaxon:9606 Homo sapiens [NCBITaxon:9606] Human +host health state menu NCIT:C3833 Asymptomatic + NCIT:C28554 Deceased + NCIT:C115935 Healthy + NCIT:C49498 Recovered + NCIT:C25269 Symptomatic + host health state international menu NCIT:C3833 Asymptomatic [NCIT:C3833] NCIT:C28554 Deceased [NCIT:C28554] NCIT:C115935 Healthy [NCIT:C115935] NCIT:C49498 Recovered [NCIT:C49498] NCIT:C25269 Symptomatic [NCIT:C25269] +host health status details menu NCIT:C25179 Hospitalized + GENEPIO:0100045 Hospitalized (Non-ICU) + GENEPIO:0100046 Hospitalized (ICU) + GENEPIO:0100047 Medically Isolated + GENEPIO:0100048 Medically Isolated (Negative Pressure) + NCIT:C173768 Self-quarantining + +host health status details international menu NCIT:C25179 Hospitalized [NCIT:C25179] + GENEPIO:0100045 Hospitalized (Non-ICU) [GENEPIO:0100045] + GENEPIO:0100046 Hospitalized (ICU) [GENEPIO:0100046] + GENEPIO:0100047 Medically Isolated [GENEPIO:0100047] + GENEPIO:0100048 Medically Isolated (Negative Pressure) [GENEPIO:0100048] + NCIT:C173768 Self-quarantining [NCIT:C173768] + +host health outcome menu NCIT:C28554 Deceased + NCIT:C25254 Deteriorating + NCIT:C49498 Recovered + NCIT:C30103 Stable + host health outcome international menu NCIT:C28554 Deceased [NCIT:C28554] NCIT:C25254 Deteriorating [NCIT:C25254] NCIT:C49498 Recovered [NCIT:C49498] NCIT:C30103 Stable [NCIT:C30103] +host age unit menu UO:0000035 month + UO:0000036 year + host age unit international menu UO:0000035 month [UO:0000035] UO:0000036 year [UO:0000036] +host age bin menu GENEPIO:0100049 0 - 9 + GENEPIO:0100050 10 - 19 + GENEPIO:0100051 20 - 29 + GENEPIO:0100052 30 - 39 + GENEPIO:0100053 40 - 49 + GENEPIO:0100054 50 - 59 + GENEPIO:0100055 60 - 69 + GENEPIO:0100056 70 - 79 + GENEPIO:0100057 80 - 89 + GENEPIO:0100058 90 - 99 + GENEPIO:0100059 100+ + host age bin international menu GENEPIO:0100049 0 - 9 [GENEPIO:0100049] GENEPIO:0100050 10 - 19 [GENEPIO:0100050] GENEPIO:0100051 20 - 29 [GENEPIO:0100051] @@ -328,6 +381,13 @@ host age bin international menu GENEPIO:0100049 0 - 9 [GENEPIO:0100049] GENEPIO:0100058 90 - 99 [GENEPIO:0100058] GENEPIO:0100059 100+ [GENEPIO:0100059] +host gender menu NCIT:C46110 Female + NCIT:C46109 Male + GSSO:000132 Non-binary gender + GSSO:004004 Transgender (assigned male at birth) + GSSO:004005 Transgender (assigned female at birth) + NCIT:C110959 Undeclared + host gender international menu NCIT:C46110 Female [NCIT:C46110] NCIT:C46109 Male [NCIT:C46109] GSSO:000132 Non-binary gender [GSSO:000132] @@ -336,7 +396,30 @@ host gender international menu NCIT:C46110 Female [NCIT:C46110] NCIT:C110959 Undeclared [NCIT:C110959] -signs and symptoms menu HP:0025143 Chills (sudden cold sensation) [HP:0025143] A sudden sensation of feeling cold. +signs and symptoms menu HP:0025143 Chills (sudden cold sensation) A sudden sensation of feeling cold. + HP:0000509 Conjunctivitis (pink eye) Inflammation of the conjunctiva. + HP:0012735 Cough A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. + HP:0012378 Fatigue (tiredness) A subjective feeling of tiredness characterized by a lack of energy and motivation. + HP:0001945 Fever Body temperature elevated above the normal range. + HP:0002315 Headache Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. + NCIT:C3824 Lesion + NCIT:C43278 Lesion (Macule) + NCIT:C39690 Lesion (Papule) + NCIT:C78582 Lesion (Pustule) + GENEPIO:0100490 Lesion (Scab) + GENEPIO:0100491 Lesion (Vesicle) + HP:0003326 Myalgia (muscle pain) Pain in muscle. + HP:0003418 Back pain + HP:0002018 Nausea A sensation of unease in the stomach together with an urge to vomit. + HP:0000988 Rash A red eruption of the skin. + NCIT:C50747 Sore throat Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing. + NCIT:C36172 Sweating + HP:0002716 Swollen Lymph Nodes Enlargment (swelling) of a lymph node. + NCIT:C3426 Ulcer + HP:0002013 Vomiting (throwing up) Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. + + +signs and symptoms international menu HP:0025143 Chills (sudden cold sensation) [HP:0025143] A sudden sensation of feeling cold. HP:0000509 Conjunctivitis (pink eye) [HP:0000509] Inflammation of the conjunctiva. HP:0012735 Cough [HP:0012735] A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. HP:0012378 Fatigue (tiredness) [HP:0012378] A subjective feeling of tiredness characterized by a lack of energy and motivation. @@ -349,21 +432,99 @@ signs and symptoms menu HP:0025143 Chills (sudden cold sensation) [HP:0025143] GENEPIO:0100490 Lesion (Scab) [GENEPIO:0100490] GENEPIO:0100491 Lesion (Vesicle) [GENEPIO:0100491] HP:0003326 Myalgia (muscle pain) [HP:0003326] Pain in muscle. + HP:0003418 Back pain [HP:0003418] HP:0002018 Nausea [HP:0002018] A sensation of unease in the stomach together with an urge to vomit. HP:0000988 Rash [HP:0000988] A red eruption of the skin. NCIT:C50747 Sore throat [NCIT:C50747] Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing. + NCIT:C36172 Sweating [NCIT:C36172] HP:0002716 Swollen Lymph Nodes [HP:0002716] Enlargment (swelling) of a lymph node. + NCIT:C3426 Ulcer [NCIT:C3426] HP:0002013 Vomiting (throwing up) [HP:0002013] Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. -pre-existing conditions and risk factors menu MONDO:0005109 Human immunodeficiency virus (HIV) [MONDO:0005109] - MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] - NCIT:C16118 HIV and antiretroviral therapy (ART) [NCIT:C16118] +pre-existing conditions and risk factors menu MONDO:0004992 Cancer + HP:0000819 Diabetes mellitus (diabetes) + HP:0100651 Type I diabetes mellitus (T1D) + HP:0005978 Type II diabetes mellitus (T2D) + NCIT:C14139 Immunocompromised + NCIT:C26726 Infectious disorder + DOID:13778 Chancroid (Haemophilus ducreyi) + DOID:11263 Chlamydia + DOID:7551 Gonorrhea + NCIT:C155871 Herpes Simplex Virus infection (HSV) + MONDO:0005109 Human immunodeficiency virus (HIV) + MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) + MONDO:0005161 Human papilloma virus infection (HPV) + DOID:13819 Lymphogranuloma venereum + NCBITaxon:2097 Mycoplsma genitalium + DOID:4166 Syphilis + DOID:1947 Trichomoniasis + MONDO:0004670 Lupus + NCIT:C25742 Pregnancy + NCIT:C16124 Prior therapy + NCIT:C16212 Cancer treatment + NCIT:C15632 Chemotherapy + NCIT:C16118 HIV and Antiretroviral therapy (ART) + CHEBI:35341 Steroid + NCIT:C159659 Transplant + +pre-existing conditions and risk factors international menu MONDO:0004992 Cancer [MONDO:0004992] + HP:0000819 Diabetes mellitus (diabetes) [HP:0000819] + HP:0100651 Type I diabetes mellitus (T1D) [HP:0100651] + HP:0005978 Type II diabetes mellitus (T2D) [HP:0005978] NCIT:C14139 Immunocompromised [NCIT:C14139] + NCIT:C26726 Infectious disorder [NCIT:C26726] + DOID:13778 Chancroid (Haemophilus ducreyi) [DOID:13778] + DOID:11263 Chlamydia [DOID:11263] + DOID:7551 Gonorrhea [DOID:7551] + NCIT:C155871 Herpes Simplex Virus infection (HSV) [NCIT:C155871] + MONDO:0005109 Human immunodeficiency virus (HIV) [MONDO:0005109] + MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] + MONDO:0005161 Human papilloma virus infection (HPV) [MONDO:0005161] + DOID:13819 Lymphogranuloma venereum [DOID:13819] + NCBITaxon:2097 Mycoplsma genitalium [NCBITaxon:2097] + DOID:4166 Syphilis [DOID:4166] + DOID:1947 Trichomoniasis [DOID:1947] + MONDO:0004670 Lupus [MONDO:0004670] NCIT:C25742 Pregnancy [NCIT:C25742] + NCIT:C16124 Prior therapy [NCIT:C16124] + NCIT:C16212 Cancer treatment [NCIT:C16212] + NCIT:C15632 Chemotherapy [NCIT:C15632] + NCIT:C16118 HIV and Antiretroviral therapy (ART) [NCIT:C16118] + CHEBI:35341 Steroid [CHEBI:35341] + NCIT:C159659 Transplant [NCIT:C159659] + +complications menu MONDO:0005682 Bronchopneumonia + MONDO:0023865 Corneal infection + MP:0002908 Delayed wound healing (lesion healing) + DOID:9588 Encephalitis + DOID:820 Myocarditis + IDO:0000567 Secondary infection + HP:0100806 Sepsis + +complications international menu MONDO:0005682 Bronchopneumonia [MONDO:0005682] + MONDO:0023865 Corneal infection [MONDO:0023865] + MP:0002908 Delayed wound healing (lesion healing) [MP:0002908] + DOID:9588 Encephalitis [DOID:9588] + DOID:820 Myocarditis [DOID:820] + IDO:0000567 Secondary infection [IDO:0000567] + HP:0100806 Sepsis [HP:0100806] + +host vaccination status menu GENEPIO:0100100 Fully Vaccinated + GENEPIO:0100102 Not Vaccinated + +host vaccination status international menu GENEPIO:0100100 Fully Vaccinated [GENEPIO:0100100] + GENEPIO:0100102 Not Vaccinated [GENEPIO:0100102] +exposure event menu GENEPIO:0100237 Mass Gathering + GENEPIO:0100238 Convention (conference) + GENEPIO:0100240 Agricultural Event + PCO:0000033 Social Gathering + PCO:0000034 Community Event + PCO:0000035 Party + Other exposure event -exposure event menu GENEPIO:0100237 Mass Gathering [GENEPIO:0100237] A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held. +exposure event international menu GENEPIO:0100237 Mass Gathering [GENEPIO:0100237] A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held. GENEPIO:0100238 Convention (conference) [GENEPIO:0100238] A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom. GENEPIO:0100240 Agricultural Event [GENEPIO:0100240] A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry. PCO:0000033 Social Gathering [PCO:0000033] A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. @@ -372,13 +533,27 @@ exposure event menu GENEPIO:0100237 Mass Gathering [GENEPIO:0100237] A gathe Other exposure event An exposure event not specified in the picklist. -exposure contact level menu GENEPIO:0100494 Contact with animal [GENEPIO:0100494] +exposure contact level menu GENEPIO:0100494 Contact with animal + GENEPIO:0100495 Contact with rodent + GENEPIO:0100496 Contact with fomite + GENEPIO:0100357 Contact with infected individual + TRANS:0000001 Direct (human-to-human contact) + TRANS:0000006 Mother-to-child transmission + NCIT:C19085 Sexual transmission + GENEPIO:0100246 Indirect contact + GENEPIO:0100247 Close contact (face-to-face contact) + GENEPIO:0100248 Casual contact + GENEPIO:0100497 Workplace associated transmission + GENEPIO:0100498 Healthcare associated transmission + GENEPIO:0100499 Laboratory associated transmission + +exposure contact level international menu GENEPIO:0100494 Contact with animal [GENEPIO:0100494] GENEPIO:0100495 Contact with rodent [GENEPIO:0100495] GENEPIO:0100496 Contact with fomite [GENEPIO:0100496] - GENEPIO:0100357 Contact with infected individual + GENEPIO:0100357 Contact with infected individual [GENEPIO:0100357] TRANS:0000001 Direct (human-to-human contact) [TRANS:0000001] TRANS:0000006 Mother-to-child transmission [TRANS:0000006] - NCIT:C19085 Sexual transmission[NCIT:C19085] + NCIT:C19085 Sexual transmission [NCIT:C19085] GENEPIO:0100246 Indirect contact [GENEPIO:0100246] GENEPIO:0100247 Close contact (face-to-face contact) [GENEPIO:0100247] GENEPIO:0100248 Casual contact [GENEPIO:0100248] @@ -386,7 +561,43 @@ exposure contact level menu GENEPIO:0100494 Contact with animal [GENEPIO:0100494 GENEPIO:0100498 Healthcare associated transmission [GENEPIO:0100498] GENEPIO:0100499 Laboratory associated transmission [GENEPIO:0100499] -host role menu GENEPIO:0100249 Attendee [GENEPIO:0100249] +host role menu GENEPIO:0100249 Attendee + OMRSE:00000058 Student + OMRSE:00000030 Patient + NCIT:C25182 Inpatient + NCIT:C28293 Outpatient + GENEPIO:0100250 Passenger + GENEPIO:0100251 Resident + GENEPIO:0100252 Visitor + GENEPIO:0100253 Volunteer + GENEPIO:0100254 Work + GENEPIO:0100255 Administrator + GENEPIO:0100256 First Responder + GENEPIO:0100260 Housekeeper + GENEPIO:0100261 Kitchen Worker + GENEPIO:0100334 Healthcare Worker + GENEPIO:0100420 Community Healthcare Worker + GENEPIO:0100262 Laboratory Worker + OMRSE:00000014 Nurse + GENEPIO:0100263 Personal Care Aid + GENEPIO:0100264 Pharmacist + OMRSE:00000013 Physician + GENEPIO:0100354 Rotational Worker + GENEPIO:0100355 Seasonal Worker + GSSO:005831 Sex Worker + GENEPIO:0100265 Veterinarian + OMRSE:00000001 Social role + GENEPIO:0100266 Acquaintance of case + GENEPIO:0100267 Relative of case + GENEPIO:0100268 Child of case + GENEPIO:0100269 Parent of case + GENEPIO:0100270 Father of case + GENEPIO:0100271 Mother of case + GENEPIO:0100500 Sexual partner of case + GENEPIO:0100272 Spouse of case + Other Host Role + +host role international menu GENEPIO:0100249 Attendee [GENEPIO:0100249] OMRSE:00000058 Student [OMRSE:00000058] OMRSE:00000030 Patient [OMRSE:00000030] NCIT:C25182 Inpatient [NCIT:C25182] @@ -409,6 +620,7 @@ host role menu GENEPIO:0100249 Attendee [GENEPIO:0100249] OMRSE:00000013 Physician [OMRSE:00000013] GENEPIO:0100354 Rotational Worker [GENEPIO:0100354] GENEPIO:0100355 Seasonal Worker [GENEPIO:0100355] + GSSO:005831 Sex Worker [GSSO:005831] GENEPIO:0100265 Veterinarian [GENEPIO:0100265] OMRSE:00000001 Social role [OMRSE:00000001] GENEPIO:0100266 Acquaintance of case [GENEPIO:0100266] @@ -421,7 +633,69 @@ host role menu GENEPIO:0100249 Attendee [GENEPIO:0100249] GENEPIO:0100272 Spouse of case [GENEPIO:0100272] Other Host Role -exposure setting menu ECTO:3000005 Human Exposure [ECTO:3000005] +exposure setting menu ECTO:3000005 Human Exposure + GENEPIO:0100501 Contact with Known Monkeypox Case + GENEPIO:0100185 Contact with Patient + GENEPIO:0100502 Contact with Probable Monkeypox Case + GENEPIO:0100189 Contact with Person who Recently Travelled + GENEPIO:0100190 Occupational, Residency or Patronage Exposure + ECTO:1000033 Abbatoir + GENEPIO:0100191 Animal Rescue + GENEPIO:0100503 Bar (pub) + GENEPIO:0100192 Childcare + GENEPIO:0100193 Daycare + GENEPIO:0100194 Nursery + GENEPIO:0100195 Community Service Centre + GENEPIO:0100196 Correctional Facility + GENEPIO:0100197 Dormitory + ECTO:1000034 Farm + GENEPIO:0100198 First Nations Reserve + GENEPIO:0100199 Funeral Home + GENEPIO:0100200 Group Home + GENEPIO:0100201 Healthcare Setting + GENEPIO:0100202 Ambulance + GENEPIO:0100203 Acute Care Facility + GENEPIO:0100204 Clinic + GENEPIO:0100415 Community Healthcare (At-Home) Setting + GENEPIO:0100205 Community Health Centre + ECTO:1000035 Hospital + GENEPIO:0100206 Emergency Department + GENEPIO:0100207 ICU + GENEPIO:0100208 Ward + ECTO:1000036 Laboratory + GENEPIO:0100209 Long-Term Care Facility + GENEPIO:0100210 Pharmacy + GENEPIO:0100211 Physician's Office + GENEPIO:0100212 Household + GENEPIO:0100213 Insecure Housing (Homeless) + GENEPIO:0100214 Occupational Exposure + GENEPIO:0100215 Worksite + ECTO:1000037 Office + GENEPIO:0100216 Outdoors + ECTO:5000009 Camp/camping + GENEPIO:0100217 Hiking Trail + ECTO:6000030 Hunting Ground + GENEPIO:0100218 Ski Resort + ECTO:5000008 Petting zoo + GENEPIO:0100220 Place of Worship + GENEPIO:0100221 Church + GENEPIO:0100222 Mosque + GENEPIO:0100223 Temple + ECTO:1000040 Restaurant + ECTO:1000041 Retail Store + GENEPIO:0100224 School + GENEPIO:0100225 Temporary Residence + GENEPIO:0100226 Homeless Shelter + GENEPIO:0100227 Hotel + GENEPIO:0100228 Veterinary Care Clinic + GENEPIO:0100229 Travel Exposure + GENEPIO:0100230 Travelled on a Cruise Ship + GENEPIO:0100231 Travelled on a Plane + GENEPIO:0100232 Travelled on Ground Transport + GENEPIO:0100235 Other Exposure Setting + + +exposure setting international menu ECTO:3000005 Human Exposure [ECTO:3000005] GENEPIO:0100501 Contact with Known Monkeypox Case [GENEPIO:0100501] GENEPIO:0100185 Contact with Patient [GENEPIO:0100185] GENEPIO:0100502 Contact with Probable Monkeypox Case [GENEPIO:0100502] @@ -482,11 +756,17 @@ exposure setting menu ECTO:3000005 Human Exposure [ECTO:3000005] GENEPIO:0100232 Travelled on Ground Transport [GENEPIO:0100232] GENEPIO:0100235 Other Exposure Setting [GENEPIO:0100235] +prior Monkeypox infection menu GENEPIO:0100037 Prior infection + GENEPIO:0100233 No prior infection +prior Monkeypox infection international menu GENEPIO:0100037 Prior infection [GENEPIO:0100037] + GENEPIO:0100233 No prior infection [GENEPIO:0100233] -host vaccination status menu GENEPIO:0100100 Fully Vaccinated [GENEPIO:0100100] - GENEPIO:0100102 Not Vaccinated [GENEPIO:0100102] +prior Monkeypox antiviral treatment menu GENEPIO:0100037 Prior antiviral treatment + GENEPIO:0100233 No prior antiviral treatment +prior Monkeypox antiviral treatment international menu GENEPIO:0100037 Prior antiviral treatment [GENEPIO:0100037] + GENEPIO:0100233 No prior antiviral treatment [GENEPIO:0100233] organism menu NCBITaxon:10244 Monkeypox virus diff --git a/template/monkeypox/schema_slots.tsv b/template/monkeypox/schema_slots.tsv index 9d1b9371..2d6bcb19 100644 --- a/template/monkeypox/schema_slots.tsv +++ b/template/monkeypox/schema_slots.tsv @@ -2,6 +2,7 @@ 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;Monkeypox_international Database Identifiers GENEPIO:0100281 case ID WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID 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 @@ -23,7 +24,7 @@ Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:00011 Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0001167 sequence submitter contact address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0001174 sample collection date date null value menu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE collection_date sample collection date Monkeypox Sample collection and processing GENEPIO:0001177 sample collection date precision sample collection date precision menu null value menu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 -Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0001179 sample received date date null value menu The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date +Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0001179 sample received date date null value menu 2019-10-01 {today} The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date Monkeypox Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) menu null value menu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) Monkeypox_international Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) international menu null value menu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. United States of America [GAZ:00002459] Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name (state/province/territory) menu null value menu TRUE The state/province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) @@ -49,36 +50,82 @@ Monkeypox Sample collection and processing GENEPIO:0001234 collection device co Monkeypox_international Sample collection and processing GENEPIO:0001234 collection device collection device international menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device Monkeypox Sample collection and processing GENEPIO:0001241 collection method collection method menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method Monkeypox_international Sample collection and processing GENEPIO:0001241 collection method collection method international menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy [OBI:0002650] Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method +Monkeypox Sample collection and processing GENEPIO:0001253 specimen processing specimen processing menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled specimen processing +Monkeypox_international Sample collection and processing GENEPIO:0001253 specimen processing specimen processing international menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled [OBI:0600016] +Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0100311 specimen processing details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 5 swabs from different body sites were pooled and further prepared as a single sample during library prep. specimen processing details Monkeypox;Monkeypox_international GENEPIO:0001268 Host Information +Monkeypox Host Information GENEPIO:0001386 host (common name) host (common name) menu null value menu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human PH_ANIMAL_TYPE +Monkeypox_international Host Information GENEPIO:0001386 host (common name) host (common name) international menu null value menu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human Monkeypox Host Information GENEPIO:0001387 host (scientific name) host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) Monkeypox_international Host Information GENEPIO:0001387 host (scientific name) host (scientific name) international menu null value menu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens [NCBITaxon:9606] Host host (scientific name) host host (scientific name) +Monkeypox Host Information GENEPIO:0001388 host health state host health state menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic Patient status PH_HOST_HEALTH host_health_state +Monkeypox_international Host Information GENEPIO:0001388 host health state host health state international menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state +Monkeypox Host Information GENEPIO:0001389 host health status details host health status details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized PH_HOST_HEALTH_DETAILS +Monkeypox_international Host Information GENEPIO:0001389 host health status details host health status details international menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized [NCIT:C25179] +Monkeypox Host Information GENEPIO:0001389 host health outcome host health outcome menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered PH_HOST_HEALTH_OUTCOME host_health_outcome +Monkeypox_international Host Information GENEPIO:0001389 host health outcome host health outcome international menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome Monkeypox Host Information GENEPIO:0001391 host disease host disease menu null value menu TRUE The name of the disease experienced by the host. Select "Monkeypox" from the pick list provided in the template. Monkeypox Host Disease PH_HOST_DISEASE host_disease host disease Monkeypox_international Host Information GENEPIO:0001391 host disease host disease international menu null value menu TRUE The name of the disease experienced by the host. Select "Monkeypox" from the pick list provided in the template. Monkeypox [MONDO:0002594] Host Disease PH_HOST_DISEASE host_disease host disease Monkeypox_international Host Information GENEPIO:0001398 host subject ID WhitespaceMinimizedString A unique identifier by which each host can be referred to. This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information. 12345B-222 host_subject_id -Monkeypox_international Host Information GENEPIO:0001388 host health state host health state international menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state -Monkeypox_international Host Information GENEPIO:0001389 host health outcome host health outcome international menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome -Monkeypox_international Host Information GENEPIO:0001392 host age decimal null value menu TRUE Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age +Monkeypox Host Information GENEPIO:0001392 host age decimal null value menu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age PH_AGE host_age +Monkeypox_international Host Information GENEPIO:0001392 host age decimal null value menu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age +Monkeypox Host Information GENEPIO:0001393 host age unit host age unit menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year PH_AGE_UNIT host_age_unit Monkeypox_international Host Information GENEPIO:0001393 host age unit host age unit international menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] host_age_unit +Monkeypox Host Information GENEPIO:0001394 host age bin host age bin menu null value menu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 PH_AGE_GROUP host_age_bin Monkeypox_international Host Information GENEPIO:0001394 host age bin host age bin international menu null value menu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] host_age_bin -Monkeypox_international Host Information GENEPIO:0001395 host gender host gender international menu null value menu TRUE The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex +Monkeypox Host Information GENEPIO:0001395 host gender host gender menu null value menu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male Gender VD_SEX host_sex +Monkeypox_international Host Information GENEPIO:0001395 host gender host gender international menu null value menu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex Monkeypox_international Host Information GENEPIO:0001398 host subject ID WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host subject ID host_subject_id -Monkeypox_international Host Information GENEPIO:0001399 symptom onset date date null value menu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 -Monkeypox_international Host Information GENEPIO:0001400 signs and symptoms signs and symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] -Monkeypox_international Host Information GENEPIO:0001401 pre-existing conditions and risk factors pre-existing conditions and risk factors menu null value menu TRUE 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. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma; Pregnancy; Smoking pre-existing conditions and risk factors -Monkeypox_international GENEPIO:0001403 Host vaccination information -Monkeypox_international Host vaccination information GENEPIO:0001404 host vaccination status host vaccination status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated PH_VACCINATION_HISTORY -Monkeypox_international Host vaccination information GENEPIO:0001406 number of vaccine doses received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 -Monkeypox_international Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name WhitespaceMinimizedString null value menu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY -Monkeypox_international Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date date null value menu The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY -Monkeypox_international Host vaccination information GENEPIO:0100321 vaccination history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY +Monkeypox Host Information GENEPIO:0001396 host residence geo_loc name (country) geo_loc_name (country) menu null value menu The country of residence of the host. Select the country name from pick list provided in the template. Canada PH_HOST_COUNTRY +Monkeypox_international Host Information GENEPIO:0001396 host residence geo_loc name (country) geo_loc_name (country) international menu null value menu The country of residence of the host. Select the country name from pick list provided in the template. Canada [GAZ:00002560] +Monkeypox Host Information GENEPIO:0001397 host residence geo_loc name (state/province/territory) geo_loc_name (state/province/territory) menu null value menu The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE +Monkeypox;Monkeypox_international Host Information GENEPIO:0001399 symptom onset date date null value menu 2019-10-01 {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 HC_ONSET_DATE +Monkeypox Host Information GENEPIO:0001400 signs and symptoms signs and symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) HC_SYMPTOMS +Monkeypox_international Host Information GENEPIO:0001400 signs and symptoms signs and symptoms international menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] +Monkeypox Host Information GENEPIO:0001401 pre-existing conditions and risk factors pre-existing conditions and risk factors menu null value menu TRUE 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. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors +Monkeypox_international Host Information GENEPIO:0001401 pre-existing conditions and risk factors pre-existing conditions and risk factors international menu null value menu TRUE 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. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors +Monkeypox Host Information GENEPIO:0001402 complications complications menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) complications +Monkeypox_international Host Information GENEPIO:0001402 complications complications international menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) [MP:0002908] +Monkeypox;Monkeypox_international Host Information NCIT:C16119 antiviral therapy WhitespaceMinimizedString Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection antiviral therapy +Monkeypox;Monkeypox_international GENEPIO:0001403 Host vaccination information +Monkeypox Host vaccination information GENEPIO:0001404 host vaccination status host vaccination status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated PH_VACCINATION_HISTORY +Monkeypox_international Host vaccination information GENEPIO:0001404 host vaccination status host vaccination status international menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated [GENEPIO:0100102] PH_VACCINATION_HISTORY +Monkeypox;Monkeypox_international Host vaccination information GENEPIO:0001406 number of vaccine doses received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 number of vaccine doses received +Monkeypox;Monkeypox_international Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name WhitespaceMinimizedString null value menu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY +Monkeypox;Monkeypox_international Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date date null value menu 2019-10-01 {today} The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY +Monkeypox;Monkeypox_international Host vaccination information GENEPIO:0100321 vaccination history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY Monkeypox;Monkeypox_international GENEPIO:0001409 Host exposure information +Monkeypox Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) geo_loc_name (country) menu null value menu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada PH_EXPOSURE_COUNTRY +Monkeypox_international Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) geo_loc_name (country) international menu null value menu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada [GAZ:00002560] +Monkeypox;Monkeypox_international Host exposure information GENEPIO:0001411 destination of most recent travel (city) WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City PH_TRAVEL +Monkeypox Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) geo_loc_name (state/province/territory) menu null value menu The name of the state/province/territory that was the destination of most recent travel. Select the province name from the pick list provided in the template. PH_TRAVEL +Monkeypox_international Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) WhitespaceMinimizedString The name of the state/province/territory that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California +Monkeypox Host exposure information GENEPIO:0001413 destination of most recent travel (country) geo_loc_name (country) menu null value menu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. Canada PH_TRAVEL +Monkeypox_international Host exposure information GENEPIO:0001413 destination of most recent travel (country) geo_loc_name (country) international menu null value menu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. United Kingdom [GAZ:00002637] +Monkeypox;Monkeypox_international Host exposure information GENEPIO:0001414 most recent travel departure date date null value menu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 PH_TRAVEL +Monkeypox;Monkeypox_international Host exposure information GENEPIO:0001415 most recent travel return date date null value menu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 PH_TRAVEL Monkeypox;Monkeypox_international Host exposure information GENEPIO:0001416 travel history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan PH_TRAVEL -Monkeypox_international Host exposure information GENEPIO:0001417 exposure event exposure event menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE -Monkeypox_international Host exposure information GENEPIO:0001418 exposure contact level exposure contact level menu null value menu The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level -Monkeypox_international Host exposure information GENEPIO:0001419 host role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE -Monkeypox_international Host exposure information GENEPIO:0001428 exposure setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE -Monkeypox_international Host exposure information GENEPIO:0001431 exposure details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS +Monkeypox Host exposure information GENEPIO:0001417 exposure event exposure event menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party Additional location information Exposure Event PH_EXPOSURE +Monkeypox_international Host exposure information GENEPIO:0001417 exposure event exposure event international menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE +Monkeypox Host exposure information GENEPIO:0001418 exposure contact level exposure contact level menu null value menu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual exposure contact level +Monkeypox_international Host exposure information GENEPIO:0001418 exposure contact level exposure contact level international menu null value menu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level +Monkeypox Host exposure information GENEPIO:0001419 host role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case PH_HOST_ROLE +Monkeypox_international Host exposure information GENEPIO:0001419 host role host role international menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE +Monkeypox Host exposure information GENEPIO:0001428 exposure setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting PH_EXPOSURE +Monkeypox_international Host exposure information GENEPIO:0001428 exposure setting exposure setting international menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE +Monkeypox;Monkeypox_international Host exposure information GENEPIO:0001431 exposure details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS + +Monkeypox;Monkeypox_international GENEPIO:0001434 Host reinfection information +Monkeypox Host reinfection information GENEPIO:0100532 prior Monkeypox infection prior Monkeypox infection menu null value menu The absence or presence of a prior Monkeypox infection. If known, provide information about whether the individual had a previous Monkeypox infection. Select a value from the pick list. Prior infection prior Monkeypox infection +Monkeypox_international Host reinfection information GENEPIO:0100532 prior Monkeypox infection prior Monkeypox infection international menu null value menu The absence or presence of a prior Monkeypox infection. If known, provide information about whether the individual had a previous Monkeypox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] +Monkeypox;Monkeypox_international Host reinfection information GENEPIO:0100533 prior Monkeypox infection date date null value menu The date of diagnosis of the prior Monkeypox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Monkeypox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date +Monkeypox Host reinfection information GENEPIO:0100534 prior Monkeypox antiviral treatment prior Monkeypox antiviral treatment menu null value menu The absence or presence of antiviral treatment for a prior Monkeypox infection. If known, provide information about whether the individual had a previous Monkeypox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment +Monkeypox_international Host reinfection information GENEPIO:0100534 prior Monkeypox antiviral treatment prior Monkeypox antiviral treatment international menu null value menu The absence or presence of antiviral treatment for a prior Monkeypox infection. If known, provide information about whether the individual had a previous Monkeypox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] +Monkeypox;Monkeypox_international Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Monkeypox infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Moneypox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Monkeypox treatment) during the prior Monkeypox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Monkeypox infection. prior antiviral treatment during Monkeypox infection + + + Monkeypox;Monkeypox_international GENEPIO:0001441 Sequencing @@ -87,26 +134,38 @@ Monkeypox_international Sequencing GENEPIO:0001445 purpose of sequencing purpos Monkeypox;Monkeypox_international Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details Monkeypox Sequencing GENEPIO:0001447 sequencing date date null value menu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE Monkeypox_international Sequencing GENEPIO:0001447 sequencing date date null value menu {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE +Monkeypox;Monkeypox_international Sequencing GENEPIO:0001448 library ID WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID +Monkeypox;Monkeypox_international Sequencing GENEPIO:0001449 amplicon size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size Monkeypox;Monkeypox_international Sequencing GENEPIO:0001450 library preparation kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT Monkeypox Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument Monkeypox_international Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument international menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument -Monkeypox_international Sequencing GENEPIO:0001454 sequencing protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol - - +Monkeypox;Monkeypox_international Sequencing GENEPIO:0001454 sequencing protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol +Monkeypox;Monkeypox_international Sequencing GENEPIO:0001455 sequencing kit number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number +Monkeypox;Monkeypox_international Sequencing GENEPIO:0001456 amplicon pcr primer scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. MPXV Sunrise 3.1 amplicon pcr primer scheme Monkeypox;Monkeypox_international GENEPIO:0001457 Bioinformatics and QC metrics Monkeypox Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method Monkeypox Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001460 consensus sequence name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. mpxvassembly3 consensus sequence name +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001461 consensus sequence filename WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. mpxvassembly.fasta consensus sequence filename +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001462 consensus sequence filepath WhitespaceMinimizedString The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta consensus sequence filepath Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% breadth of coverage value breadth of coverage value Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Depth of coverage depth of coverage value depth of coverage value Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001480 fast5 filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. This information aids in data management. mpxv123seq.fast5 +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001481 fast5 filepath WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/mpxv123seq.fast5 Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 2639019 number of base pairs sequenced Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 197063 consensus genome length -Monkeypox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol -Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol +Monkeypox;Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_063383.1 reference genome accession +Monkeypox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol +Monkeypox_international Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol Monkeypox;Monkeypox_international GENEPIO:0001506 Pathogen diagnostic testing Monkeypox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene name 1 menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name