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vocab update
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Fix to male/female NML_LIMS conversion.
Adding Gene Target 3 fields
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Damion Dooley committed Mar 26, 2021
1 parent 9e1a162 commit 5ab9bb2
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Showing 2 changed files with 24 additions and 12 deletions.
14 changes: 12 additions & 2 deletions template/canada_covid19/data.js
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Original file line number Diff line number Diff line change
Expand Up @@ -3978,7 +3978,7 @@ var DATA = [
"exportField": {
"NML_LIMS": [
{
"value": "MALE"
"value": "FEMALE"
}
]
}
Expand All @@ -3987,7 +3987,7 @@ var DATA = [
"exportField": {
"NML_LIMS": [
{
"value": "FEMALE"
"value": "MALE"
}
]
}
Expand Down Expand Up @@ -6916,6 +6916,11 @@ var DATA = [
{
"field": "Gene Target 3"
}
],
"NML_LIMS": [
{
"field": "RESULT - CANCOGEN_SUBMITTED_RESLT_3"
}
]
},
"schema:ItemList": {}
Expand Down Expand Up @@ -6952,6 +6957,11 @@ var DATA = [
{
"field": "Gene Target 3 CT Value"
}
],
"NML_LIMS": [
{
"field": "RESULT - CANCOGEN_SUBMITTED_RESLT_3CT"
}
]
}
}
Expand Down
22 changes: 12 additions & 10 deletions template/canada_covid19/data.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -142,9 +142,9 @@ ID SC %
Pathogen diagnostic testing gene name 2 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) Gene Target 2 RESULT - CANCOGEN_SUBMITTED_RESLT_2 gene_name_2
Pathogen diagnostic testing diagnostic pcr protocol 2 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3
Pathogen diagnostic testing diagnostic pcr Ct value 2 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value RESULT - CANCOGEN_SUBMITTED_RESLT_2CT diagnostic_PCR_CT_value_2
Pathogen diagnostic testing gene name 3 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) Gene Target 3
Pathogen diagnostic testing gene name 3 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) Gene Target 3 RESULT - CANCOGEN_SUBMITTED_RESLT_3
Pathogen diagnostic testing diagnostic pcr protocol 3 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3
Pathogen diagnostic testing diagnostic pcr Ct value 3 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 3 CT Value
Pathogen diagnostic testing diagnostic pcr Ct value 3 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 3 CT Value RESULT - CANCOGEN_SUBMITTED_RESLT_3CT
Contributor acknowledgement
Contributor acknowledgement authors xs:token recommended Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS
Contributor acknowledgement DataHarmonizer provenance provenance DataHarmonizer provenance Additional Comments HC_COMMENTS
Expand Down Expand Up @@ -753,8 +753,8 @@ BTO:0004755 lab host Vero E6 cell line
host age bin 90 - 99
host age bin 100+

OMRSE:00000009? host gender Female MALE
OMRSE:00000008? host gender Male FEMALE
OMRSE:00000009? host gender Female FEMALE
OMRSE:00000008? host gender Male MALE
host gender Non-binary gender NON_BINARY_GENDER
host gender Transgender (Male to Female) TRANSGENDER
host gender Transgender (Female to Male) TRANSGENDER
Expand Down Expand Up @@ -829,7 +829,7 @@ OMRSE:00000008? host gender Male FEMALE
Human Exposure Person with Fever and/or Cough
Human Exposure Person who Recently Travelled
exposure setting Occupational or Residency Exposure
Occupational or Residency Exposure Abbatoir
ECTO_1000033 Occupational or Residency Exposure Abbatoir
Occupational or Residency Exposure Animal Rescue
Occupational or Residency Exposure Childcare
Childcare Daycare
Expand All @@ -843,10 +843,10 @@ OMRSE:00000008? host gender Male FEMALE
Occupational or Residency Exposure Community Service Centre
Occupational or Residency Exposure Correctional Facility
Occupational or Residency Exposure Dormitory
Occupational or Residency Exposure Farm
ECTO_1000034 Occupational or Residency Exposure Farm
Occupational or Residency Exposure First Nations Reserve
Occupational or Residency Exposure Group Home
Occupational or Residency Exposure Healthcare Setting
ECTO_1000035 Occupational or Residency Exposure Healthcare Setting
Healthcare Setting Ambulance
Healthcare Setting Acute Care Facility
Healthcare Setting Clinic
Expand All @@ -855,12 +855,12 @@ OMRSE:00000008? host gender Male FEMALE
Hospital Emergency Department
Hospital ICU
Hospital Ward
Healthcare Setting Laboratory
ECTO_1000036 Healthcare Setting Laboratory
Healthcare Setting Long-Term Care Facility
Healthcare Setting Pharmacy
Healthcare Setting Physician's Office
Occupational or Residency Exposure Insecure Housing (Homeless)
Occupational or Residency Exposure Office
ECTO:1000037 Occupational or Residency Exposure Office
Occupational or Residency Exposure Outdoors
Outdoors Camp/camping
Outdoors Hiking
Expand Down Expand Up @@ -1261,4 +1261,6 @@ GAZ_00009572 geo_loc_name (country) West Bank
GAZ_00000564 geo_loc_name (country) Western Sahara
GAZ_00005284 geo_loc_name (country) Yemen
GAZ_00001107 geo_loc_name (country) Zambia
GAZ_00001106 geo_loc_name (country) Zimbabwe
GAZ_00001106 geo_loc_name (country) Zimbabwe


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