Merge pull request #13 from microbiomedata/1550-Update-Enum-Extractio…

…nTargetEnum remove phenol/chloroform extraction from ExtractionTargetEnum
microbiomedata · Dec 14, 2023 · b7cd5d4 · b7cd5d4
2 parents 93c71d3 + f840d36
commit b7cd5d4
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Showing 6 changed files with 9 additions and 8 deletions.
diff --git a/src/data/valid/Biosample-exhasutive.yaml b/src/data/valid/Biosample-exhasutive.yaml
@@ -391,7 +391,7 @@ dna_concentration: 100
 #dna_cont_well: C2
 dna_container_id: Pond_MT_041618
 dna_dnase: 'yes'
-dna_isolate_meth: phenol/chloroform extraction
+dna_isolate_meth: DNA
 dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
   (1%)
 dna_project_contact: John Jones
@@ -782,7 +782,7 @@ rna_concentration: 100
 #rna_cont_type: plate
 #rna_cont_well: C2
 rna_container_id: Pond_MT_041618
-rna_isolate_meth: phenol/chloroform extraction
+rna_isolate_meth: RNA
 rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
   (1%)
 rna_project_contact: John Jones

diff --git a/src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml b/src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml
@@ -322,7 +322,7 @@ dna_container_id: Pond_MT_041618
 # dna_dnase expects a yes or no enumerated string. unquoated yes gets converted into Boolean True, whcih isn't acceptable in this case
 dna_dnase: 'yes'
 
-dna_isolate_meth: phenol/chloroform extraction
+dna_isolate_meth: DNA
 dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
   (1%)
 dna_project_contact: John Jones
@@ -343,7 +343,7 @@ rna_concentration: 100
 rna_cont_type: plate
 rna_cont_well: C2
 rna_container_id: Pond_MT_041618
-rna_isolate_meth: phenol/chloroform extraction
+rna_isolate_meth: RNA
 rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
   (1%)
 rna_project_contact: John Jones

diff --git a/src/data/valid/Database-biosample-exhasutive.yaml b/src/data/valid/Database-biosample-exhasutive.yaml
@@ -391,7 +391,7 @@ biosample_set:
     #dna_cont_well: C2
     dna_container_id: Pond_MT_041618
     dna_dnase: 'yes'
-    dna_isolate_meth: phenol/chloroform extraction
+    dna_isolate_meth: DNA
     dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
       (1%)
     dna_project_contact: John Jones
@@ -782,7 +782,7 @@ biosample_set:
     #rna_cont_type: plate
     #rna_cont_well: C2
     rna_container_id: Pond_MT_041618
-    rna_isolate_meth: phenol/chloroform extraction
+    rna_isolate_meth: RNA
     rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
       (1%)
     rna_project_contact: John Jones

diff --git a/src/data/valid/Database-extraction_set-exhaustive.yaml b/src/data/valid/Database-extraction_set-exhaustive.yaml
@@ -31,10 +31,11 @@ extraction_set:
       status: pass
     #leaving as extraction_method to make the model generic, other option considered was 'Nucleic Acid Extraction Method' http://purl.obolibrary.org/obo/NCIT_C177560
     # extraction_method: phenol/chloroform extraction # instantiate in ProtocolExtraction class
+
     #extraction_type should have range of dna_extraction_enum with possible values of 'DNA extraction', 'RNA extraction', 'protein extraction'
     #http://purl.obolibrary.org/obo/OBI_0000257
     extraction_target: DNA
     #not needed at this time
     #protocol_materials:
     #  - { material_name : DNeasy 96 PowerSoil Pro Kit, material_vendor: Qiagen, catalog_number: 47017 }
-    #  - { material_name : X-Pierce Film, material_vendor: Sigma Aldrich, catalog_number: Z722502-100EA }
+    #  - { material_name : X-Pierce Film, material_vendor: Sigma Aldrich, catalog_number: Z722502-100EA }
diff --git a/src/data/valid/Database-nucleic-extraction.yaml b/src/data/valid/Database-nucleic-extraction.yaml
@@ -44,6 +44,7 @@ extraction_set:
     #leaving as extraction_method to make the model generic, other option considered was 'Nucleic Acid Extraction Method' http://purl.obolibrary.org/obo/NCIT_C177560
     # extraction_method: phenol/chloroform extraction #instantiate in ProtocolExtraction class
 
+
     #extraction_type should have range of dna_extraction_enum with possible values of 'DNA extraction', 'RNA extraction', 'protein extraction'
     #http://purl.obolibrary.org/obo/OBI_0000257
     extraction_target: DNA

diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml
@@ -1841,7 +1841,6 @@ enums:
       RNA: { }
       metabolite: { }
       protein: { }
-      phenol/chloroform extraction: { }
 
   LibraryTypeEnum:
     # start using the right case for enum names