diff --git a/src/data/valid/Biosample-exhasutive.yaml b/src/data/valid/Biosample-exhasutive.yaml index 1b2474390a..e58423c29c 100644 --- 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 index 9b205e3778..93bfe7f906 100644 --- 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 index e3b318c298..694fae6fc2 100644 --- 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 index ba63dfe2a4..cde09d99f3 100644 --- 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 } \ No newline at end of file diff --git a/src/data/valid/Database-nucleic-extraction.yaml b/src/data/valid/Database-nucleic-extraction.yaml index b1af38e4e0..a7b7bb9ca2 100644 --- 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 index 34d6ed9cdb..14c1718147 100644 --- 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