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remove phenol/chloroform extraction from ExtractionTargetEnum #13

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merged 8 commits into from
Dec 14, 2023
Merged

remove phenol/chloroform extraction from ExtractionTargetEnum #13

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e33bca7
remove phenol/chloroform extraction from ExtractionTargetEnum
mslarae13 Dec 13, 2023
164e581
removed references to Phenol/chloroform extraction
Dec 13, 2023
3ff95b4
Merge branch 'main' into 1550-Update-Enum-ExtractionTargetEnum
Dec 13, 2023
1de9689
remove reference to phenol/chloroform
Dec 13, 2023
ec48453
Merge branch 'main' into 1550-Update-Enum-ExtractionTargetEnum
JamesTessmer Dec 13, 2023
6599d34
Merge branch 'main' into 1550-Update-Enum-ExtractionTargetEnum
Dec 14, 2023
9678e3f
catch rna_isolate_meth having DNA
Dec 14, 2023
f840d36
fix RNA typo
Dec 14, 2023
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4 changes: 2 additions & 2 deletions src/data/valid/Biosample-exhasutive.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml
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Expand Up @@ -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
Expand All @@ -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
Expand Down
4 changes: 2 additions & 2 deletions src/data/valid/Database-biosample-exhasutive.yaml
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
3 changes: 2 additions & 1 deletion src/data/valid/Database-extraction_set-exhaustive.yaml
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Expand Up @@ -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 }
1 change: 1 addition & 0 deletions src/data/valid/Database-nucleic-extraction.yaml
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Expand Up @@ -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
Expand Down
1 change: 0 additions & 1 deletion src/schema/nmdc.yaml
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Expand Up @@ -1841,7 +1841,6 @@ enums:
RNA: { }
metabolite: { }
protein: { }
phenol/chloroform extraction: { }

LibraryTypeEnum:
# start using the right case for enum names
Expand Down
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