update to Cancogen vocabulary

And marking PHAC Dexa, GRDI and GISAID templates as published.
cidgoh · May 3, 2022 · c4f78db · c4f78db
1 parent 6d7a25f
commit c4f78db
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Showing 3 changed files with 9 additions and 6 deletions.
diff --git a/script/main.js b/script/main.js
@@ -11,13 +11,13 @@
  * main.html?template=test_template
  *
  */
-const VERSION = '0.15.4';
+const VERSION = '0.15.5';
 const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION;
 const TEMPLATES = {
   'CanCOGeN Covid-19': {'folder': 'canada_covid19', 'status': 'published'},
-  'PHAC Dexa (ALPHA)': {'folder': 'phac_dexa', 'status': 'draft'},
-  'GRDI (ALPHA)':      {'folder': 'grdi', 'status': 'draft'},
-  'GISAID (ALPHA)':    {'folder': 'gisaid', 'status': 'draft'},
+  'PHAC Dexa': {'folder': 'phac_dexa', 'status': 'published'},
+  'GRDI':      {'folder': 'grdi', 'status': 'published'},
+  'GISAID':    {'folder': 'gisaid', 'status': 'published'},
   'PHA4GE':    {'folder': 'pha4ge', 'status': 'published'}
 };
 // Currently selected cell range[row,col,row2,col2]

diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js
@@ -418,6 +418,7 @@ var DATA = [
           "Public Health Ontario (PHO)": {},
           "Queen's University / Kingston Health Sciences Centre": {},
           "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)": {},
+          "Shared Hospital Laboratory": {},
           "St. John's Rehab at Sunnybrook Hospital": {},
           "Switch Health": {},
           "Sunnybrook Health Sciences Centre": {},

diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv
@@ -1,5 +1,4 @@
 Ontology ID	Meaning (LinkML)	parent class	label	datatype	source	data status	requirement	min value	max value	capitalize	pattern	description	guidance	examples	EXPORT_GISAID	EXPORT_CNPHI	EXPORT_NML_LIMS	EXPORT_BIOSAMPLE	EXPORT_VirusSeq_Portal
-ID		SC %																	
 GENEPIO:0001122			Database Identifiers																
 GENEPIO:0001123		Database Identifiers	specimen collector sample ID	xs:unique		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required					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_rona_99	Sample ID given by the sample provider	Primary Specimen ID	TEXT_ID	sample_name	specimen collector sample ID
 GENEPIO:0001202		Database Identifiers	third party lab service provider name	xs:token								The name of the third party company or laboratory that provided services.	Provide the full, unabbreviated name of the company or laboratory.	Switch Health			HC_TEXT5		
@@ -1075,6 +1074,7 @@ GENEPIO:0100183		gene name 1	SARS-COV-2 5' UTR
 		 sample collected by	Public Health Ontario (PHO)																
 		 sample collected by	Queen's University / Kingston Health Sciences Centre																
 		 sample collected by	Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)																
+		 sample collected by	Shared Hospital Laboratory																
 		 sample collected by	St. John's Rehab at Sunnybrook Hospital																
 		 sample collected by	Switch Health																
 		 sample collected by	Sunnybrook Health Sciences Centre																
@@ -1352,4 +1352,6 @@ 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																
+
+