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Update Somatic template #34

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Update Somatic template #34

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d435cd7
changed Catalogue IDs to comments
sellth Oct 25, 2023
8ef2fbe
Ontology updates
sellth Oct 25, 2023
4142df2
finalise ontology update
sellth Oct 26, 2023
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4 changes: 4 additions & 0 deletions cubi_isa_templates/isatab-somatic/cookiecutter.json
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Expand Up @@ -23,6 +23,10 @@
"exome sequencing",
"genome sequencing"
],
"_measurement_type_terms": {
"exome sequencing": "http://purl.obolibrary.org/obo/OBI_0002118",
"genome sequencing": "http://purl.obolibrary.org/obo/OBI_0002117"
},
"lib_kit": [
"Agilent SureSelect Human All Exon V8",
"Agilent SureSelect Human All Exon V7",
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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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Is there a reason why you don't want to use the UO units of measurement ontology?

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Because I don't think it is necessary to define these Units using UO, it is not supported by SODAR anyway, and therefore I removed this complexity.

Original file line number Diff line number Diff line change
@@ -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] Parameter Value[Library strand specificity] Comment[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[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[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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Is there a reason why you don't want to use the UO units of measurement ontology?

Original file line number Diff line number Diff line change
@@ -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] Parameter Value[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[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 %}
10 changes: 5 additions & 5 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 {{cookiecutter._measurement_type_terms[cookiecutter.measurement_type]}}{% 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 %}
Expand All @@ -74,9 +74,9 @@ Study Protocol Type Term Source REF "" "" "" ""
Study Protocol Description "" "" "" ""
Study Protocol URI "" "" "" ""
Study Protocol Version "" "" "" ""
Study Protocol Parameters Name "Conservation method" Concentration measurement "Provider project ID;Library source;Library selection;Library layout;Barcode sequence;Wet-lab insert size;Requestor contact;Library kit;Library kit catalogue ID;{% if cookiecutter.is_triplet == True %}Library strand specificity;{% endif %}Provider contact;Concentration measurement;Provider sample ID;Target insert size;Provider name;Requestor project;Requestor sample ID;Barcode kit;Barcode kit catalogue ID;Barcode name;Provider QC status;Library strategy" "Base quality encoding;Platform;Center contact;Target read length;Target read length (mate 2);Instrument model;Center name"
Study Protocol Parameters Name Term Accession Number "" "" ";;;;;;;;;;;;;;;;;;;;{% if cookiecutter.is_triplet == True %};{% endif %}" ";;;;;;"
Study Protocol Parameters Name Term Source REF "" "" ";;;;;;;;;;;;;;;;;;;;{% if cookiecutter.is_triplet == True %};{% endif %}" ";;;;;;"
Study Protocol Parameters Name "Conservation method" Concentration measurement "Provider project ID;Library source;Library selection;Library layout;Barcode sequence;Wet-lab insert size;Requestor contact;Library kit;{% if cookiecutter.is_triplet == True %}Library strand specificity;{% endif %}Provider contact;Concentration measurement;Provider sample ID;Target insert size;Provider name;Requestor project;Requestor sample ID;Barcode kit;Barcode name;Provider QC status;Library strategy" "Base quality encoding;Platform;Center contact;Target read length;Target read length (mate 2);Instrument model;Center name"
Study Protocol Parameters Name Term Accession Number "" "" ";;;;;;;;;;;;;;;;;;{% if cookiecutter.is_triplet == True %};{% endif %}" ";;;;;;"
Study Protocol Parameters Name Term Source REF "" "" ";;;;;;;;;;;;;;;;;;{% if cookiecutter.is_triplet == True %};{% endif %}" ";;;;;;"
Study Protocol Components Name "" "" "" ""
Study Protocol Components Type "" "" "" ""
Study Protocol Components Type Term Accession Number "" "" "" ""
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