Merge pull request #415 from ncihtan/406-add-permissible-value-to-bio…

…specimen-storage-method Add Frozen at -20C as valid value for Storage method
ncihtan · May 30, 2024 · f8798bf · f8798bf
2 parents 70e9fd6 + c868e7c
commit f8798bf
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Showing 2 changed files with 24 additions and 4 deletions.
diff --git a/HTAN.model.csv b/HTAN.model.csv
@@ -470,7 +470,7 @@ Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology
 Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5227611&version=1.0,
 Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3024951&version=1.0,
 Sectioning Days from Index,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',,,,TRUE,Biospecimen,,,regex match \d+$|Not\sApplicable$|unknown$
-Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, 4C in vacuum chamber, Desiccant at 4C, Not Applicable, unknown",,,TRUE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method,
+Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -20C, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, 4C in vacuum chamber, Desiccant at 4C, Not Applicable, unknown",,,TRUE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method,
 Processing Days from Index,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',,,,TRUE,Biospecimen,,,regex match \d+$|Not\sApplicable$|unknown$
 Shipping Condition Type,Text descriptor of the shipping environment of a biospecimen.,"Ambient Pack, Cold Pack, Dry Ice, Ice Pack, Liquid Nitrogen, Specimen at Room Temperature, Other Shipping Environment, Not Shipped",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5495533&version=1.0,
 Site Data Source,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",,,,FALSE,Biospecimen,,,

diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld
@@ -27725,6 +27725,9 @@
                 {
                     "@id": "bts:Fresh"
                 },
+                {
+                    "@id": "bts:Frozenat-20C"
+                },
                 {
                     "@id": "bts:Frozenat-70C"
                 },
@@ -51339,15 +51342,15 @@
                 {
                     "@id": "bts:LungAdjacentHistologyType"
                 },
-                {
-                    "@id": "bts:StorageMethod"
-                },
                 {
                     "@id": "bts:HistoneVariant"
                 },
                 {
                     "@id": "bts:PreservationMethod"
                 },
+                {
+                    "@id": "bts:StorageMethod"
+                },
                 {
                     "@id": "bts:MolecularAnalysisMethod"
                 },
@@ -58448,6 +58451,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Frozenat-20C",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Frozenat-20C",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:StorageMethod"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Frozen at -20C",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Frozenat-70C",
             "@type": "rdfs:Class",