Merge pull request #413 from ncihtan/412-add-option-unfixed-for-fixat…

…ive-type Add unfixed for Fixative type
ncihtan · May 30, 2024 · 70e9fd6 · 70e9fd6
2 parents 6a0d1ed + 4a6bfe9
commit 70e9fd6
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Showing 2 changed files with 21 additions and 1 deletion.
diff --git a/HTAN.model.csv b/HTAN.model.csv
@@ -455,7 +455,7 @@ Acquisition Method Type,Records the method of acquisition or source for the spec
 Other Acquisition Method,A custom acquisition method,,Acquisition Method Other Specify,,FALSE,Biospecimen,,,
 Acquisition Method Other Specify,A custom acquisition method [Text - max length 100 characters],,,,TRUE,Biospecimen,,,
 Preservation Method,Text term that represents the method used to preserve the sample.,"Cryopreserved, Cryopreservation in liquid nitrogen - dead tissue, Cryopreservation in dry ice - dead tissue, Cryopreservation in liquid nitrogen - live cells, Formalin fixed paraffin embedded - FFPE, Formalin fixed-unbuffered, Formalin fixed-buffered, Fresh, Fresh dissociated and single cell sorted into plates in NP40 buffer, OCT, Snap Frozen, Frozen, Negative 80 Deg C, Liquid Nitrogen, Fresh dissociated, Fresh dissociated and single cell sorted, Fresh dissociated and single cell sorted into plates, Methacarn fixed paraffin embedded - MFPE, unknown, Not Reported",,,TRUE,Biospecimen,,,
-Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Carnoy's Fixative, Polaxamer, Other, None, unknown",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=65078&version=3.0,
+Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Carnoy's Fixative, Polaxamer, Other, None, unknown, Unfixed",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=65078&version=3.0,
 Fixation Duration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5230144&version=1.0,
 Ischemic Time,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",,,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,
 Ischemic Temperature,Specify whether specimen experienced warm or cold ischemia.,"Warm Ischemia, Cold Ischemia, Ambient air, 4C wet ice, Negative -20C, Dry Ice, Liquid Nitrogen, unknown",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,

diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld
@@ -27693,6 +27693,9 @@
                 },
                 {
                     "@id": "bts:Unknown"
+                },
+                {
+                    "@id": "bts:Unfixed"
                 }
             ],
             "sms:displayName": "Fixative Type",
@@ -57110,6 +57113,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Unfixed",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Unfixed",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:FixativeType"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Unfixed",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:WarmIschemia",
             "@type": "rdfs:Class",