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incorporate meta core feedback
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@sellth
sellth committed Dec 12, 2023
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4 changes: 2 additions & 2 deletions ...b-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_FIA.txt
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Sample Name Protocol REF Parameter Value[Derivatization] Parameter Value[Phase] Parameter Value[Kit name] Parameter Value[Kit lot no.] Performer Date Extract Name Characteristics[Batch ID] Characteristics[Well position] Protocol REF Parameter Value[Extract dilution] Unit Parameter Value[Extract dilution solution] Parameter Value[Injection instrument] Parameter Value[Injection volume] Unit Parameter Value[Flow rate] Unit Comment[Injection method file] Parameter Value[Cleaning solution] Comment[Cleaning method file] Performer Date Protocol REF Parameter Value[Scan polarity] Term Source REF Term Accession Number Parameter Value[Scan m/z range] Parameter Value[Instrument model] Term Source REF Term Accession Number Parameter Value[Ionization type] Term Source REF Term Accession Number Parameter Value[Mass analyzer type] Term Source REF Term Accession Number Parameter Value[Detector type] Term Source REF Term Accession Number Parameter Value[Aquisition mode] Term Source REF Term Accession Number Parameter Value[Aquisition software] Term Source REF Term Accession Number Parameter Value[Aquisition software version] Comment[Additional parameters] Comment[Last electrode replacement] Comment[Last deep cleaning] Comment[Last tuning/calibration] Comment[Last vacuum off] Performer Date MS Assay Name Comment[MS assay file] Raw Spectral Data File Comment[Sample type] Comment[Data quality] Protocol REF Parameter Value[Analysis software] Term Source REF Term Accession Number Parameter Value[Analysis software version] Comment[Report file] Comment[Log file] Derived Data File Comment[Data quality] Protocol REF Parameter Value[Software name] Parameter Value[Software version] Comment[Report file] Performer Date Derived Data File Comment[Data quality]
Sample Name Protocol REF Parameter Value[Derivatization] Parameter Value[Phase] Parameter Value[Kit name] Parameter Value[Kit lot no.] Performer Date Comment[Protocol file] Extract Name Characteristics[Batch ID] Characteristics[Well position] Protocol REF Parameter Value[Extract dilution] Unit Parameter Value[Extract dilution solution] Parameter Value[Injection instrument] Parameter Value[Injection volume] Unit Parameter Value[Flow rate] Unit Comment[Injection method file] Parameter Value[Cleaning solution] Comment[Cleaning method file] Performer Date Protocol REF MS Assay Name Parameter Value[Scan polarity] Term Source REF Term Accession Number Parameter Value[Scan m/z range] Parameter Value[Instrument model] Term Source REF Term Accession Number Parameter Value[Ionization type] Term Source REF Term Accession Number Parameter Value[Mass analyzer type] Term Source REF Term Accession Number Parameter Value[Acquisition mode] Term Source REF Term Accession Number Parameter Value[Acquisition software] Term Source REF Term Accession Number Parameter Value[Acquisition software version] Comment[Additional parameters] Comment[MS method file] Performer Date Comment[Protocol file] Comment[Last electrode replacement] Comment[Last deep cleaning] Comment[Last tuning/calibration] Comment[Last vacuum off] Raw Spectral Data File Comment[Data quality] Protocol REF Parameter Value[Analysis software] Term Source REF Term Accession Number Parameter Value[Analysis software version] Comment[Report file] Comment[Log file] Performer Date Derived Data File Comment[Data quality] Protocol REF Parameter Value[Software name] Parameter Value[Software version] Comment[Report file] Performer Date Derived Data File Comment[Data quality]
{% set sample_names = cookiecutter.sample_names.split(",") -%}
{%- for sample_name in sample_names -%}
{{sample_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.biocrates_kit}} {{sample_name|replace("-", "_")}}-N1-Meta1 Injection Mass spectrometry Positive scan MS http://purl.obolibrary.org/obo/MS_1000130 {{cookiecutter._instruments[cookiecutter.instrument].term}} {{cookiecutter._instruments[cookiecutter.instrument].source}} {{cookiecutter._instruments[cookiecutter.instrument].accession}} ESI MS http://purl.obolibrary.org/obo/MS_1000073 Orbitrap MS http://purl.obolibrary.org/obo/MS_1000484 Inductive detector MS http://purl.obolibrary.org/obo/MS_1000624 DDA Xcalibur MS http://purl.obolibrary.org/obo/MS_1000532 {{sample_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_FIA}}1 Data transformation Biocrates MetIDQ {{cookiecutter.biocrates_metidq_version}} Quality Control MeTaQuaC {{cookiecutter.metaquac_version}}
{{sample_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.biocrates_kit}} {{sample_name|replace("-", "_")}}-N1-Meta1 Injection Mass spectrometry Positive scan MS http://purl.obolibrary.org/obo/MS_1000130 {{cookiecutter._instruments[cookiecutter.instrument].term}} {{cookiecutter._instruments[cookiecutter.instrument].source}} {{cookiecutter._instruments[cookiecutter.instrument].accession}} ESI MS http://purl.obolibrary.org/obo/MS_1000073 Orbitrap MS http://purl.obolibrary.org/obo/MS_1000484 DDA Xcalibur MS http://purl.obolibrary.org/obo/MS_1000532 {{sample_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_FIA}}1 Data transformation Biocrates MetIDQ {{cookiecutter.biocrates_metidq_version}} Quality Control MeTaQuaC {{cookiecutter.metaquac_version}}
{% endfor %}
4 changes: 2 additions & 2 deletions ...ab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_LC.txt
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Sample Name Protocol REF Parameter Value[Derivatization] Parameter Value[Phase] Parameter Value[Kit name] Parameter Value[Kit lot no.] Performer Date Extract Name Characteristics[Batch ID] Characteristics[Well position] Protocol REF Parameter Value[Extract dilution] Unit Parameter Value[Extract dilution solution] Parameter Value[Chromatography instrument] Parameter Value[Column type] Term Source REF Term Accession Number Parameter Value[Column model] Parameter Value[Column lot no.] Parameter Value[Running solutions] Parameter Value[Flow rate] Unit Comment[Chromatography method file] Parameter Value[Cleaning solutions] Comment[Cleaning method file] Performer Date Protocol REF Parameter Value[Scan polarity] Term Source REF Term Accession Number Parameter Value[Scan m/z range] Parameter Value[Instrument model] Term Source REF Term Accession Number Parameter Value[Ionization type] Term Source REF Term Accession Number Parameter Value[Mass analyzer type] Term Source REF Term Accession Number Parameter Value[Detector type] Term Source REF Term Accession Number Parameter Value[Aquisition mode] Term Source REF Term Accession Number Parameter Value[Aquisition software] Term Source REF Term Accession Number Parameter Value[Aquisition software version] Comment[Additional parameters] Comment[Aquisition method file] Comment[Last electrode replacement] Comment[Last deep cleaning] Comment[Last tuning/calibration] Comment[Last vacuum off] Comment[Last RT adjustment] Performer Date MS Assay Name Comment[MS assay file] Raw Spectral Data File Comment[Sample type] Comment[Data quality] Protocol REF Parameter Value[Analysis software] Term Source REF Term Accession Number Parameter Value[Analysis software version] Comment[Report file] Comment[Log file] Derived Data File Comment[Data quality] Protocol REF Parameter Value[Software name] Parameter Value[Software version] Comment[Report file] Performer Date Derived Data File Comment[Data quality]
Sample Name Protocol REF Parameter Value[Derivatization] Parameter Value[Phase] Parameter Value[Kit name] Parameter Value[Kit lot no.] Performer Date Comment[Protocol file] Extract Name Characteristics[Batch ID] Characteristics[Well position] Protocol REF Parameter Value[Extract dilution] Unit Parameter Value[Extract dilution solution] Parameter Value[Chromatography instrument] Parameter Value[Column type] Term Source REF Term Accession Number Parameter Value[Column model] Parameter Value[Column lot no.] Parameter Value[Running solutions] Parameter Value[Flow rate] Unit Comment[Chromatography method file] Parameter Value[Cleaning solutions] Comment[Cleaning method file] Performer Date Protocol REF MS Assay Name Parameter Value[Scan polarity] Term Source REF Term Accession Number Parameter Value[Scan m/z range] Parameter Value[Instrument model] Term Source REF Term Accession Number Parameter Value[Ionization type] Term Source REF Term Accession Number Parameter Value[Mass analyzer type] Term Source REF Term Accession Number Parameter Value[Acquisition mode] Term Source REF Term Accession Number Parameter Value[Acquisition software] Term Source REF Term Accession Number Parameter Value[Acquisition software version] Comment[Additional parameters] Comment[MS method file] Performer Date Comment[Protocol file] Comment[Last electrode replacement] Comment[Last deep cleaning] Comment[Last tuning/calibration] Comment[Last vacuum off] Comment[Last RT adjustment] Raw Spectral Data File Comment[Data quality] Protocol REF Parameter Value[Analysis software] Term Source REF Term Accession Number Parameter Value[Analysis software version] Comment[Report file] Comment[Log file] Performer Date Derived Data File Comment[Data quality] Protocol REF Parameter Value[Software name] Parameter Value[Software version] Comment[Report file] Performer Date Derived Data File Comment[Data quality]
{% set sample_names = cookiecutter.sample_names.split(",") -%}
{%- for sample_name in sample_names -%}
{{sample_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.biocrates_kit}} {{sample_name|replace("-", "_")}}-N1-Meta1 Chromatography {{cookiecutter.chromatography_instrument}} Reversed phase column OBI http://purl.obolibrary.org/obo/OBI_0000510 ; ; Mass spectrometry Positive scan MS http://purl.obolibrary.org/obo/MS_1000130 {{cookiecutter._instruments[cookiecutter.instrument].term}} {{cookiecutter._instruments[cookiecutter.instrument].source}} {{cookiecutter._instruments[cookiecutter.instrument].accession}} ESI MS http://purl.obolibrary.org/obo/MS_1000073 Orbitrap MS http://purl.obolibrary.org/obo/MS_1000484 Inductive detector MS http://purl.obolibrary.org/obo/MS_1000624 DDA Xcalibur MS http://purl.obolibrary.org/obo/MS_1000532 {{sample_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_LC}}1 Data transformation Biocrates MetIDQ {{cookiecutter.biocrates_metidq_version}} Quality Control MeTaQuaC {{cookiecutter.metaquac_version}}
{{sample_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.biocrates_kit}} {{sample_name|replace("-", "_")}}-N1-Meta1 Chromatography {{cookiecutter.chromatography_instrument}} Reversed phase column OBI http://purl.obolibrary.org/obo/OBI_0000510 ; ; Mass spectrometry Positive scan MS http://purl.obolibrary.org/obo/MS_1000130 {{cookiecutter._instruments[cookiecutter.instrument].term}} {{cookiecutter._instruments[cookiecutter.instrument].source}} {{cookiecutter._instruments[cookiecutter.instrument].accession}} ESI MS http://purl.obolibrary.org/obo/MS_1000073 Orbitrap MS http://purl.obolibrary.org/obo/MS_1000484 DDA Xcalibur MS http://purl.obolibrary.org/obo/MS_1000532 {{sample_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_LC}}1 Data transformation Biocrates MetIDQ {{cookiecutter.biocrates_metidq_version}} Quality Control MeTaQuaC {{cookiecutter.metaquac_version}}
{% endfor %}
2 changes: 1 addition & 1 deletion ..._isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/i_Investigation.txt
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Expand Up @@ -72,7 +72,7 @@ Study Protocol Type Term Source REF OBI MS MS OBI MS MS
Study Protocol Description
Study Protocol URI
Study Protocol Version
Study Protocol Parameters Name Phase;Derivatization;Kit name;Kit lot no. Extract dilution;Extract dilution solution;Chromatography instrument;Column type;Column model;Column lot no.;Running solutions;Flow rate;Cleaning solutions Scan polarity;Scan m/z range;Instrument model;Ionization type;Mass analyzer type;Detector type;Aquisition mode;Aquisition software;Aquisition software version Analysis software;Analysis software version Software name;Software version Extract dilution;Extract dilution solution;Injection instrument;Injection volume;Flow rate;Cleaning solution
Study Protocol Parameters Name Phase;Derivatization;Kit name;Kit lot no. Extract dilution;Extract dilution solution;Chromatography instrument;Column type;Column model;Column lot no.;Running solutions;Flow rate;Cleaning solutions Scan polarity;Scan m/z range;Instrument model;Ionization type;Mass analyzer type;Detector type;Acquisition mode;Acquisition software;Acquisition software version Analysis software;Analysis software version Software name;Software version Extract dilution;Extract dilution solution;Injection instrument;Injection volume;Flow rate;Cleaning solution
Study Protocol Parameters Name Term Accession Number ;;; ;;http://purl.obolibrary.org/obo/OBI_0000485;;;;;http://purl.obolibrary.org/obo/PATO_0002243; http://purl.obolibrary.org/obo/MS_1000465;;http://purl.obolibrary.org/obo/MS_1000031;http://purl.obolibrary.org/obo/MS_1000008;http://purl.obolibrary.org/obo/MS_1000443;http://purl.obolibrary.org/obo/MS_1000026;;http://purl.obolibrary.org/obo/MS_1001455; http://purl.obolibrary.org/obo/MS_1001456; ; ;;;;http://purl.obolibrary.org/obo/PATO_0002243;
Study Protocol Parameters Name Term Source REF ;;; ;;OBI;;;;;MS; MS;;MS;MS;MS;MS;;MS; MS; ; ;;;;MS;
Study Protocol Components Name
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4 changes: 2 additions & 2 deletions ...ab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt
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Source Name Characteristics[UUID] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Sex] Characteristics[Disease type] Term Source REF Term Accession Number Characteristics[Disease status] Term Source REF Term Accession Number Characteristics[Age] Unit Term Source REF Term Accession Number Characteristics[BMI] Unit Term Source REF Term Accession Number Characteristics[HPO terms] Term Source REF Term Accession Number Comment[Disease notes] Protocol REF Performer Date Sample Name Characteristics[External links] Characteristics[Visit] Characteristics[Visit Centrum] Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number
Source Name Characteristics[UUID] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Sex] Characteristics[Disease type] Term Source REF Term Accession Number Characteristics[Disease status] Term Source REF Term Accession Number Characteristics[Age] Unit Term Source REF Term Accession Number Characteristics[BMI] Unit Term Source REF Term Accession Number Characteristics[HPO terms] Term Source REF Term Accession Number Comment[Disease notes] Protocol REF Performer Date Sample Name Characteristics[Sample type] Characteristics[External links] Characteristics[Visit] Characteristics[Visit Centrum] Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number
{% set sample_names = cookiecutter.sample_names.split(",") -%}
{%- for sample_name in sample_names -%}
{{sample_name|replace("-", "_")}} {{cookiecutter._organisms[cookiecutter.organism].name}} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter._organisms[cookiecutter.organism].taxon}} UNKNOWN UNKNOWN UNKNOWN year UO http://purl.obolibrary.org/obo/UO_0000036 kilogram per square meter UO http://purl.obolibrary.org/obo/UO_0000086 Sample collection {{sample_name|replace("-", "_")}}-N1
{{sample_name|replace("-", "_")}} {{cookiecutter._organisms[cookiecutter.organism].name}} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter._organisms[cookiecutter.organism].taxon}} UNKNOWN UNKNOWN UNKNOWN year UO http://purl.obolibrary.org/obo/UO_0000036 kilogram per square meter UO http://purl.obolibrary.org/obo/UO_0000086 Sample collection {{sample_name|replace("-", "_")}}-N1
{% endfor %}

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