From 8ef2fbe7be2ffa1eddb5fb766e98138ac6ef5f95 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Wed, 25 Oct 2023 17:52:47 +0200 Subject: [PATCH] Ontology updates --- ...{{cookiecutter.s_file_name}}_transcriptome_profiling.txt | 4 ++-- ...iecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt | 6 +++--- .../{{cookiecutter.__output_dir}}/i_Investigation.txt | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt index d3022bd..e6668ff 100644 --- a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt +++ b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt @@ -1,5 +1,5 @@ -Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Comment[Library kit catalogue ID] Parameter Value[Library strand specificity] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Comment[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Target read length] Parameter Value[Target read length (mate 1)] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date +Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Comment[Library kit catalogue ID] Parameter Value[Library strand specificity] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Comment[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Extract Name Characteristics[Concentration] Unit Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Target read length] Parameter Value[Target read length (mate 1)] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date {% set source_names = cookiecutter.source_names.split(",") -%} {%- for source_name in source_names -%} -{{source_name|replace("-", "_")}}-T1 Nucleic acid extraction {{source_name|replace("-", "_")}}-T1-RNA1 Library construction TRANSCRIPTOMIC RNA-Seq PolyA SINGLE Illumina TruSeq Stranded mRNA REVERSE {{source_name|replace("-", "_")}}-T1-RNA1-mRNA_seq1 Nucleic acid sequencing ILLUMINA {{cookiecutter.instrument}} Phred+33 +{{source_name|replace("-", "_")}}-T1 Nucleic acid extraction {{source_name|replace("-", "_")}}-T1-RNA1 Library construction TRANSCRIPTOMIC RNA-Seq PolyA SINGLE Illumina TruSeq Stranded mRNA REVERSE {{source_name|replace("-", "_")}}-T1-RNA1-mRNA_seq1 Nucleic acid sequencing ILLUMINA {{cookiecutter.instrument}} Phred+33 {% endfor %} diff --git a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt index e502e09..26ba9c3 100644 --- a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt +++ b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt @@ -1,6 +1,6 @@ -Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Comment[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Comment[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Target read length] Parameter Value[Target read length (mate 2)] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date +Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Comment[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Comment[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Extract Name Characteristics[Concentration] Unit Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Target read length] Parameter Value[Target read length (mate 2)] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date {% set source_names = cookiecutter.source_names.split(",") -%} {%- for source_name in source_names -%} -{{source_name|replace("-", "_")}}-N1 Nucleic acid extraction {{source_name|replace("-", "_")}}-N1-DNA1 Library construction GENOMIC {{cookiecutter.__lib_strategy}} {{cookiecutter.__lib_selection}} {{cookiecutter.lib_layout}} {{cookiecutter.lib_kit}} {{cookiecutter._lib_kit_cat_ids[cookiecutter.lib_kit]}} {{source_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.__measurement_abbreviation}}1 Nucleic acid sequencing ILLUMINA {{cookiecutter.instrument}} Phred+33 -{{source_name|replace("-", "_")}}-T1 Nucleic acid extraction {{source_name|replace("-", "_")}}-T1-DNA1 Library construction GENOMIC {{cookiecutter.__lib_strategy}} {{cookiecutter.__lib_selection}} {{cookiecutter.lib_layout}} {{cookiecutter.lib_kit}} {{cookiecutter._lib_kit_cat_ids[cookiecutter.lib_kit]}} {{source_name|replace("-", "_")}}-T1-DNA1-{{cookiecutter.__measurement_abbreviation}}1 Nucleic acid sequencing ILLUMINA {{cookiecutter.instrument}} Phred+33 +{{source_name|replace("-", "_")}}-N1 Nucleic acid extraction {{source_name|replace("-", "_")}}-N1-DNA1 Library construction GENOMIC {{cookiecutter.__lib_strategy}} {{cookiecutter.__lib_selection}} {{cookiecutter.lib_layout}} {{cookiecutter.lib_kit}} {{cookiecutter._lib_kit_cat_ids[cookiecutter.lib_kit]}} {{source_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.__measurement_abbreviation}}1 Nucleic acid sequencing ILLUMINA {{cookiecutter.instrument}} Phred+33 +{{source_name|replace("-", "_")}}-T1 Nucleic acid extraction {{source_name|replace("-", "_")}}-T1-DNA1 Library construction GENOMIC {{cookiecutter.__lib_strategy}} {{cookiecutter.__lib_selection}} {{cookiecutter.lib_layout}} {{cookiecutter.lib_kit}} {{cookiecutter._lib_kit_cat_ids[cookiecutter.lib_kit]}} {{source_name|replace("-", "_")}}-T1-DNA1-{{cookiecutter.__measurement_abbreviation}}1 Nucleic acid sequencing ILLUMINA {{cookiecutter.instrument}} Phred+33 {% endfor %} diff --git a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt index 5f0b9c0..06c780c 100644 --- a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt @@ -60,8 +60,8 @@ Study Factor Type Term Source REF STUDY ASSAYS Study Assay File Name a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt{% if cookiecutter.is_triplet == True %} a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt{% endif %} Study Assay Measurement Type {{cookiecutter.measurement_type}}{% if cookiecutter.is_triplet == True %} transcriptome profiling{% endif %} -Study Assay Measurement Type Term Accession Number ""{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000424{% endif %} -Study Assay Measurement Type Term Source REF ""{% if cookiecutter.is_triplet == True %} OBI{% endif %} +Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0002118{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000424{% endif %} +Study Assay Measurement Type Term Source REF OBI{% if cookiecutter.is_triplet == True %} OBI{% endif %} Study Assay Technology Type nucleotide sequencing{% if cookiecutter.is_triplet == True %} nucleotide sequencing{% endif %} Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000626{% endif %} Study Assay Technology Type Term Source REF OBI{% if cookiecutter.is_triplet == True %} OBI{% endif %}