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Please output the metadata mapping between mzTab-m and ISA-Tab used by this software in a tabular format.
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deepwiki-mztabm2mtbls.md

https://deepwiki.com/search/please-output-the-metadata-map_f86c7f48-1235-41c3-9b98-6534f35b839a

Metadata Mapping Between mzTab-M and ISA-Tab

Based on the software implementation, here is the comprehensive metadata mapping between mzTab-M and ISA-Tab formats used by this conversion tool:

Core Study Metadata

mzTab-M Source Field ISA-Tab Target Description Mapper
metadata.title study.title Study title MetadataBaseMapper
metadata.description study.description Study description MetadataBaseMapper
metadata.mzTab_version Comment[mztab:metadata:mzTab_version] mzTab version tracking MetadataBaseMapper
metadata.mzTab_ID Comment[mztab:metadata:mzTab_ID] mzTab identifier MetadataBaseMapper
metadata.uri Comment[mztab:metadata:uri] Study URI references MetadataBaseMapper
metadata.external_study_uri Comment[mztab:metadata:external_study_uri] External study references MetadataBaseMapper
metadata.quantification_method study.study_design_descriptors.design_types Quantification method as design type MetadataBaseMapper
metadata.custom[] study.study_design_descriptors.design_types Custom ontology annotations MetadataBaseMapper

Sample Metadata

mzTab-M Source Field ISA-Tab Target Description Mapper
sample.id Comment[mztab:metadata:sample:id] Sample identifier preservation MetadataSampleMapper
sample.description Comment[mztab:metadata:sample:description] Sample description MetadataSampleMapper
sample.name Sample Name / Source Name Primary sample identifier MetadataSampleMapper
sample.species Characteristics[Organism] Biological organism MetadataSampleMapper
sample.tissue Characteristics[Organism part] Tissue/organ information MetadataSampleMapper
sample.disease Characteristics[Disease] Disease state MetadataSampleMapper
sample.cell_type Characteristics[Cell type] Cell type classification MetadataSampleMapper
sample.custom Characteristics[*] Custom characteristics MetadataSampleMapper
study_variable.factors[] Factor Value[*] Study factors from variables MetadataSampleMapper

Contact Metadata

mzTab-M Source Field ISA-Tab Target Description Mapper
contact.name Person.first_name, Person.mid_initials, Person.last_name Parsed contact name MetadataContactMapper
contact.email Person.email Contact email address MetadataContactMapper
contact.affiliation Person.affiliation Contact affiliation MetadataContactMapper
contact.id Comment[mztab:metadata:contact:id] Contact identifier MetadataContactMapper
contact.orcid Comment[mztab:metadata:contact:orcid] ORCID identifier MetadataContactMapper

Assay Metadata

mzTab-M Source Field ISA-Tab Target Description Mapper
assay.id Comment[mztab:metadata:assay:id] Assay identifier tracking MetadataAssayMapper
assay.name Extract Name Assay name MetadataAssayMapper
ms_run.id Comment[mztab:metadata:ms_run:id] MS run identifier MetadataAssayMapper
ms_run.name Comment[mztab:metadata:ms_run:name] MS run name MetadataAssayMapper
ms_run.location Derived Spectral Data File Data file location MetadataAssayMapper
ms_run.scan_polarity Parameter Value[Scan polarity] Scan polarity information MetadataAssayMapper
ms_run.instrument_ref Comment[mztab:metadata:ms_run:instrument:id] Instrument reference MetadataAssayMapper
instrument.name Parameter Value[Instrument] Instrument name MetadataAssayMapper
instrument.source Parameter Value[Ion source] Ion source type MetadataAssayMapper
instrument.analyzer Parameter Value[Mass analyzer] Mass analyzer type MetadataAssayMapper

Publication Metadata

mzTab-M Source Field ISA-Tab Target Description Mapper
publication.items[Type.doi] Publication.doi DOI identifier MetadataPublicationMapper
publication.items[Type.pubmed] Publication.pubmed_id PubMed identifier MetadataPublicationMapper
publication.items[Type.uri] Publication.title Publication URI MetadataPublicationMapper
Publication status Publication.publication_status "published" (EFO:0001796) or "in preparation" (EFO:0001795) MetadataPublicationMapper

Database References

mzTab-M Source Field ISA-Tab Target Description Mapper
database.param.name Protocol components (Metabolite identification) Database name MetadataDatabaseMapper
database.param.cv_label Protocol components (ontology source) Ontology source reference MetadataDatabaseMapper
database.param.cv_accession Protocol components (ontology term) Ontology term identifier MetadataDatabaseMapper
database.version Comment[mztab:metadata:database:version] Database version MetadataDatabaseMapper
database.uri Comment[mztab:metadata:database:uri] Database URI MetadataDatabaseMapper
database.prefix Comment[mztab:metadata:database:prefix] Database prefix MetadataDatabaseMapper

Sample Processing

mzTab-M Source Field ISA-Tab Target Description Mapper
sample_processing[] Extraction protocol description Sample processing steps with ontological annotation MetadataSampleProcessingMapper

Derivatization Agents

mzTab-M Source Field ISA-Tab Target Description Mapper
derivatization_agent[] Extraction protocol description Derivatization agent details with ontological annotation MetadataDerivationAgentMapper

Software Information

mzTab-M Source Field ISA-Tab Target Description Mapper
software[] Data transformation protocol components Software used in data processing MetadataSoftwareMapper

Controlled Vocabulary

mzTab-M Source Field ISA-Tab Target Description Mapper
cv[] investigation.ontology_source_references Ontology source references MetadataCvMapper

Provenance Information

mzTab-M Source Field ISA-Tab Target Description Mapper
Source file location Comment[mztab:source_file:location] Original mzTab file location MetadataBaseMapper
Source file hash Comment[mztab:source_file:hash:sha256] SHA256 hash of source file MetadataBaseMapper

Notes

The mapping system uses a polymorphic design pattern where each mapper class handles specific aspects of the metadata conversion. 10 The system preserves metadata that doesn't have direct ISA-Tab equivalents as structured comments with the mztab: namespace prefix. 9 This ensures comprehensive data preservation while maintaining ISA-Tab compliance for MetaboLights submission.

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