Close #44 (#45)

* Close #44 * Build csv, jsonld --------- Co-authored-by: github-actions <[email protected]>
gf-dcc · Jun 22, 2023 · 901e099 · 901e099
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commit 901e099
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diff --git a/GF.csv b/GF.csv
@@ -94,6 +94,7 @@ scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File
 Cell Median Number Reads,Median number of reads per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","",""
 Cell Median Number Genes,Median number of genes detected per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","",""
 Cell Total,Number of sequenced  cells. Applies to raw counts matrix only.,"","","",TRUE,scRNA-seq Level 3,"","",""
+Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those",,"Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality",,FALSE,,Patient,,
 Biospecimen ID, ID associated with a biosample based on  ID SOP (eg x_yyy_zzz),"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""
 Parent ID, ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""
 Parent Biospecimen ID, Biospecimen Identifier (eg x_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""

diff --git a/GF.jsonld b/GF.jsonld
@@ -5098,6 +5098,51 @@
             "sms:required": "sms:true",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Biospecimen",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Biological entity; this can be tissue, blood, analyte and subsamples of those",
+            "rdfs:label": "Biospecimen",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Thing"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Biospecimen",
+            "sms:required": "sms:false",
+            "sms:requiresComponent": [
+                {
+                    "@id": "bts:Patient"
+                }
+            ],
+            "sms:requiresDependency": [
+                {
+                    "@id": "bts:BiospecimenID"
+                },
+                {
+                    "@id": "bts:ParentID"
+                },
+                {
+                    "@id": "bts:ParentBiospecimenID"
+                },
+                {
+                    "@id": "bts:AdjacentBiospecimenIDs"
+                },
+                {
+                    "@id": "bts:BiospecimenType"
+                },
+                {
+                    "@id": "bts:TimepointLabel"
+                },
+                {
+                    "@id": "bts:SpecimenLaterality"
+                }
+            ],
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:BiospecimenID",
             "@type": "rdfs:Class",

diff --git a/modules/Biospecimen/Biospecimen.csv b/modules/Biospecimen/Biospecimen.csv
@@ -1,4 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
+Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those",,"Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality",,FALSE,,Patient,,
 Biospecimen ID, ID associated with a biosample based on  ID SOP (eg x_yyy_zzz),"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""
 Parent ID, ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""
 Parent Biospecimen ID, Biospecimen Identifier (eg x_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,""