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feat: Simplify mass cytometry template #41

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merged 4 commits into from
Jul 2, 2024
Merged

feat: Simplify mass cytometry template #41

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5f849da
remove Data normalization process
sellth Oct 17, 2023
3c58f94
add ontology info for processes
sellth Oct 17, 2023
059e36b
simplify template
sellth Jun 11, 2024
0313d1a
remove Normalization Passport
sellth Jun 26, 2024
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42 changes: 6 additions & 36 deletions cubi_isa_templates/isatab-mass_cytometry/cookiecutter.json
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@@ -1,53 +1,23 @@
{
"investigation_identifier": "Investigation_ID",
"investigation_title": "Investigation Title",
"investigation_title": "",
"investigation_description": "",
"source_names": "source1,source2",
"organism": [
"Homo sapiens",
"Mus musculus",
"Other"
],
"_organism_taxon": {
"Homo sapiens": "9606",
"Mus musculus": "10090"
},
"material": [
"Cell line",
"Organoid",
"PBMC sample",
"Other"
],
"_material_ncit": {
"Cell line": "#C16403",
"Organoid": "#C172259",
"PBMC sample": "#C178965"
},
"tissue": [
"No",
"Intestinal epithelium",
"Other"
],
"_tissue_ncit": {
"Intestinal epithelium": "#C49240"
},
"source_characteristics": "Origin,Passage",
"sample_suffixes": "sample1,sample2",
"sample_characteristics": "Frozen",
"_source_names": "Source1,Source2",
"source_characteristics": "Material Type,Origin,Passage",
"_sample_suffixes": "Sample1,Sample2",
"sample_factors": "Treatment target,Treatment substance,Treatment time",
"sample_factor_types": "intracellular structure,chemical compound,time span",
"sample_characteristics": "Frozen",
"dissociation_type": ["No", "pre-fix Trypsin", "post-fix Trypsin", "post-fix Octo"],
"sample_multiplexing": ["No", "SBT Pd 20-plex", "TOBis 35-plex", "Other"],
"__s_file_name": "{{cookiecutter.investigation_identifier|replace(' ', '_')|replace('/', '_')}}",
"__assay_prefix": "{{cookiecutter.__s_file_name}}",
"__output_dir": "Required variable. Do not remove.",
"__prompts__": {
"investigation_identifier": "Short project title or acronym",
"investigation_title": "Longer project title",
"investigation_title": "Longer project title (optional)",
"investigation_description": "Description of project (optional)",
"source_names": "Patient IDs, cell lines, model systems, etc.",
"source_characteristics": "Additional source characteristics as comma-separated list",
"sample_suffixes": "List of suffixes to create unique sample IDs from source names",
"sample_factors": "Sample factors as comma-separated list",
"sample_factor_types": "Sample factor types as comma-separated list (same length as factors)",
"sample_characteristics": "Sample characteristics as comma-separated list",
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8 changes: 4 additions & 4 deletions ...ometry/{{cookiecutter.__output_dir}}/a_{{cookiecutter.__assay_prefix}}_mass_cytometry.txt
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@@ -1,8 +1,8 @@
{% set source_names = cookiecutter.source_names.split(",") -%}
{% set sample_suffixes = cookiecutter.sample_suffixes.split(",") -%}
Sample Name{% if cookiecutter.dissociation_type != "No" %} Protocol REF Parameter Value[Dissociation method] Performer Date{% endif %}{% if cookiecutter.sample_multiplexing != "No" %} Protocol REF Parameter Value[Multiplexing method] Parameter Value[Barcode ID] Parameter Value[Barcode key] Comment[Report file] Performer Date{% endif %} Protocol REF Parameter Value[Antibody panel] Comment[Report file] Performer Date Protocol REF Assay Name Parameter Value[Cell count pre acquisition] Parameter Value[Cells acquired] Comment[Report file] Performer Date Raw Data File Protocol REF Parameter Value[Method] Performer Date Derived Data File Protocol REF Comment[Report file] Performer Date Derived Data File
{% set source_names = cookiecutter._source_names.split(",") -%}
{% set sample_suffixes = cookiecutter._sample_suffixes.split(",") -%}
Sample Name{% if cookiecutter.dissociation_type != "No" %} Protocol REF Parameter Value[Dissociation method] Performer Date{% endif %}{% if cookiecutter.sample_multiplexing != "No" %} Protocol REF Parameter Value[Multiplexing method] Parameter Value[Barcode ID] Parameter Value[Barcode key] Comment[Report file] Performer Date{% endif %} Protocol REF Parameter Value[Antibody panel] Comment[Report file] Performer Date Protocol REF Assay Name Parameter Value[Cell count pre acquisition] Parameter Value[Cells acquired] Comment[Report file] Performer Date Derived Data File Protocol REF Comment[Report file] Performer Date Derived Data File
{%+ for source_name in source_names -%}
{%+ for sample_suffix in sample_suffixes -%}
{{source_name|replace("-", "_")}}_{{sample_suffix|replace("-", "_")}}{% if cookiecutter.dissociation_type != "No"%} Dissociation {{cookiecutter.dissociation_type}} {% endif %}{% if cookiecutter.sample_multiplexing != "No" %} Multiplexing {{cookiecutter.sample_multiplexing}} {% endif %} Antibody staining Mass cytometry Data normalization EQ four element calibration beads Data processing
{{source_name|replace("-", "_")}}_{{sample_suffix|replace("-", "_")}}{% if cookiecutter.dissociation_type != "No"%} Dissociation {{cookiecutter.dissociation_type}} {% endif %}{% if cookiecutter.sample_multiplexing != "No" %} Multiplexing {{cookiecutter.sample_multiplexing}} {% endif %} Antibody staining Mass cytometry Data processing
{% endfor -%}
{% endfor -%}
35 changes: 20 additions & 15 deletions cubi_isa_templates/isatab-mass_cytometry/{{cookiecutter.__output_dir}}/i_Investigation.txt
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@@ -1,13 +1,18 @@
{% set sample_factors = cookiecutter.sample_factors.split(",") -%}
{% set sample_factor_types = cookiecutter.sample_factor_types.split(",") -%}
{% if cookiecutter.investigation_title -%}
{% set investigation_title = cookiecutter.investigation_title -%}
{% else -%}
{% set investigation_title = cookiecutter.investigation_identifier -%}
{% endif %}
ONTOLOGY SOURCE REFERENCE
Term Source Name UO OBI NCBITAXON OMIM HP ORPHA NCIT
Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO http://data.bioontology.org/ontologies/NCIT
Term Source Version 217 49 21 23 599 26 128
Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology National Cancer Institute Thesaurus
INVESTIGATION
Investigation Identifier {{cookiecutter.investigation_identifier}}
Investigation Title {{cookiecutter.investigation_title}}
Investigation Title {{investigation_title}}
Investigation Description {{cookiecutter.investigation_description}}
Investigation Submission Date ""
Investigation Public Release Date ""
Expand Down Expand Up @@ -65,20 +70,20 @@ Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo
Study Assay Technology Type Term Source REF OBI
Study Assay Technology Platform Standard BioTools
STUDY PROTOCOLS
Study Protocol Name Sample collection Dissociation Multiplexing Antibody staining Mass cytometry Data normalization Data processing
Study Protocol Type sample collection Dissociation Multiplexing Antibody staining Mass cytometry Data normalization Data processing
Study Protocol Type Term Accession Number "" "" "" "" "" "" ""
Study Protocol Type Term Source REF "" "" "" "" "" "" ""
Study Protocol Description "" "" "" "" "Data acquisition" "Bead standard normalization" "De-multiplexing & quality gating"
Study Protocol URI "" "" "" "" "" "" ""
Study Protocol Version "" "" "" "" "" "" ""
Study Protocol Parameters Name Method Dissociation method Multiplexing method;Barcode ID;Barcode key Antibody panel Cell count pre acquisition;Cells acquired Method
Study Protocol Parameters Name Term Accession Number "" "" ";;" "" ";" "" ""
Study Protocol Parameters Name Term Source REF "" "" ";;" "" ";" "" ""
Study Protocol Components Name "" "" "" "" "" "" ""
Study Protocol Components Type "" "" "" "" "" "" ""
Study Protocol Components Type Term Accession Number "" "" "" "" "" "" ""
Study Protocol Components Type Term Source REF "" "" "" "" "" "" ""
Study Protocol Name Sample collection Dissociation Multiplexing Antibody staining Mass cytometry Data processing
Study Protocol Type material sampling process Dissociation Multiplexing Antibody staining mass cytometry assay data transformation
Study Protocol Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000744" "" "" "" "http://purl.obolibrary.org/obo/OBI_0002115" "http://purl.obolibrary.org/obo/OBI_0200000"
Study Protocol Type Term Source REF "OBI" "" "" "" "OBI" "OBI"
Study Protocol Description "" "" "" "" "Data acquisition" "De-multiplexing & quality gating"
Study Protocol URI "" "" "" "" "" ""
Study Protocol Version "" "" "" "" "" ""
Study Protocol Parameters Name Method Dissociation method Multiplexing method;Barcode ID;Barcode key Antibody panel Cell count pre acquisition;Cells acquired
Study Protocol Parameters Name Term Accession Number "" "" ";;" "" ";" ""
Study Protocol Parameters Name Term Source REF "" "" ";;" "" ";" ""
Study Protocol Components Name "" "" "" "" "" ""
Study Protocol Components Type "" "" "" "" "" ""
Study Protocol Components Type Term Accession Number "" "" "" "" "" ""
Study Protocol Components Type Term Source REF "" "" "" "" "" ""
STUDY CONTACTS
Study Person Last Name
Study Person First Name
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8 changes: 4 additions & 4 deletions .../isatab-mass_cytometry/{{cookiecutter.__output_dir}}/s_{{cookiecutter.__s_file_name}}.txt
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@@ -1,11 +1,11 @@
{% set source_characteristics = cookiecutter.source_characteristics.split(",") -%}
{% set source_names = cookiecutter.source_names.split(",") -%}
{% set sample_suffixes = cookiecutter.sample_suffixes.split(",") -%}
{% set source_names = cookiecutter._source_names.split(",") -%}
{% set sample_suffixes = cookiecutter._sample_suffixes.split(",") -%}
{% set sample_characteristics = cookiecutter.sample_characteristics.split(",") -%}
{% set sample_factors = cookiecutter.sample_factors.split(",") -%}
Source Name Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Material] Term Source REF Term Accession Number{% if cookiecutter.tissue != "No" %} Characteristics[Tissue] Term Source REF Term Accession Number{% endif %}{%+ for characteristic in source_characteristics %} Characteristics[{{characteristic}}]{% endfor %} Protocol REF Parameter Value[Method] Performer Date Sample Name{%+ for characteristic in sample_characteristics %} Characteristics[{{characteristic}}]{% endfor %}{%+ for factor in sample_factors %} Factor Value[{{factor}}]{% endfor %}
Source Name Characteristics[Organism] Term Source REF Term Accession Number{%+ for characteristic in source_characteristics %} Characteristics[{{characteristic}}]{% endfor %} Protocol REF Parameter Value[Method] Performer Date Sample Name{%+ for characteristic in sample_characteristics %} Characteristics[{{characteristic}}]{% endfor %}{%+ for factor in sample_factors %} Factor Value[{{factor}}]{% endfor %}
{%+ for source_name in source_names -%}
{%+ for sample_suffix in sample_suffixes -%}
{{source_name|replace("-", "_")}} {{cookiecutter.organism}}{% if cookiecutter.organism != "Other" %} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter._organism_taxon[cookiecutter.organism]}}{% else %} {% endif %} {{cookiecutter.material}}{% if cookiecutter.material != "Other" %} NCIT http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl{{cookiecutter._material_ncit[cookiecutter.material]}}{% else %} {% endif %}{% if cookiecutter.tissue != "No" %} {{cookiecutter.tissue}}{% if cookiecutter.tissue != "Other" %} NCIT http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl{{cookiecutter._tissue_ncit[cookiecutter.tissue]}}{% else %} {% endif %}{% endif %}{%+ for characteristic in source_characteristics %} {% endfor %} Sample collection {{source_name|replace("-", "_")}}_{{sample_suffix|replace("-", "_")}}{%+ for characteristic in sample_characteristics %} {% endfor %}{%+ for factor in sample_factors %} {% endfor %}
{{source_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606{%+ for characteristic in source_characteristics %} {% endfor %} Sample collection {{source_name|replace("-", "_")}}_{{sample_suffix|replace("-", "_")}}{%+ for characteristic in sample_characteristics %} {% endfor %}{%+ for factor in sample_factors %} {% endfor %}
{% endfor -%}
{% endfor -%}
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