- mzTab_m_swagger.yml Swagger / OpenAPI REST specification.
- How to use the jmzTab-m object model.
- The jmzTab-m reference implementation.
- The mzTab-M specification homepage.
Package Overview
- API - The data model for the mzTab-M 2.0 data standard format for metabolomics.
- IO - Reading, writing and basic validation of mzTab-M data files in JSON, CSV or object format.
- VALIDATION - semantic validation with rule mapping and controlled vocabular terms.
- VALIDATION RULES - xml mapping file rules object model.
- CLI - the command line interface for reading, validation and conversion of mzTab-M 2.0 JSON and CSV files.
- TEST UTILS - utilities for extracting and testing of mzTab-M test files.
mzTab-M structure and object model mapping
mzTab-M is a hierarchical, table-based data format. It consists of four levels that capture different aspects of the result data.
The Metadata Level
This level defines metadata that describes the origin of the data, e.g. assays and ms runs, the contact persons, study variables, methods and preprocessing and which databases, quantification and identification methods were used.
The Summary Level
This level reports identified small molecules, their chemical name, SMILES etc., together with their quantities across assays and within study variables.
The MS Feature and Quantitation Level
This level reports the feature level data for each assay, which are used to calculate the quantities reported in the summary level. A feature is characterized by m/z, adduct, charge, retention time and other properties.
The Identification Evidence Level
This level reports evidence for (groups of) features reported on the feature level across assays. Evidence may be a database hit, score, etc. Evidence entries also cross-link the grouped features to the actual ms-runs and scan number.
Simplified mzTab-M example with MS1 and MS2 level evidence
mzTab-M object model
Package | Description |
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de.isas.lipidomics.mztab2.validation |
This package contains classes that provide the basic validator infrastructure used in the jmztabm-validation module.
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de.isas.lipidomics.mztab2.validation.constraints |
This package contains custom validation annotations for the javax.validation framework.
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de.isas.lipidomics.mztab2.validation.validators |
This package contains custom validators that implement the
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de.isas.mztab2.cli |
This package contains the command line interface for jmzTab-M validation and conversion.
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de.isas.mztab2.cvmapping |
This package contains classes for controlled vocabulary term access, comparison, results and external cv parameter resolution.
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de.isas.mztab2.io |
This package contains implementations for reading and writing of mzTab-M files.
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de.isas.mztab2.io.formats |
This package defines formats for Jackson that define, which serializer should be used for a particular object type.
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de.isas.mztab2.io.serialization |
This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
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de.isas.mztab2.io.validators |
This package contains implementations for validation of mzTab-M parts during parsing.
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de.isas.mztab2.model |
Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
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de.isas.mztab2.test.utils |
This package contains custom JUnit Rules for extraction of class path resource files and additional logging for testing.
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de.isas.mztab2.validation |
This package contains interfaces and implementations for the semantic validation via CvTerms.
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de.isas.mztab2.validation.handlers |
This package contains implementations for the semantic validation controlled vocabulary term rules.
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info.psidev.cvmapping |
This package contains the generated Java objects created via XML binding from the PSI-MS mapping file schema.
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uk.ac.ebi.pride.jmztab2 |
This package contains jmzTab-M model and utility classes that were adapted from the original jmzTab implementation.
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uk.ac.ebi.pride.jmztab2.model |
This package contains model classes for mzTab-M structural features like mandatory and optional columns.
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uk.ac.ebi.pride.jmztab2.utils |
This package contains the property file mapping for mzTab-M's validation messages.
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uk.ac.ebi.pride.jmztab2.utils.errors |
This package contains error type definitions and related classes used during mzTab validation.
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uk.ac.ebi.pride.jmztab2.utils.parser |
This package contains text file line parser implementations for the mzTab-M document sections.
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