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Ontology updates
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@sellth
sellth committed Oct 25, 2023
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4 changes: 2 additions & 2 deletions .../{{cookiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt
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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 %}
6 changes: 3 additions & 3 deletions ...kiecutter.__output_dir}}/a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt
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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 %}
4 changes: 2 additions & 2 deletions cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt
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Expand Up @@ -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 %}
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