JavaDoc API documentation for the jmztab-m data model, io and validation packages.

• 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

Logical structure of the mzTab-M format. An mzTab-M file is organized into four levels that capture different aspects of the result data.

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

Simplified mzTab-M example from lipidomics, reporting evidence in the form of diagnostic fragments from MS2 for an MS1 signal.

mzTab-M object model

mzTab-M model generated from the OpenAPI swagger model specification. Please see the mzTab-M specification or the API model package summary and JavaDoc for more details.

Packages

Package	Description
de.isas.lipidomics.mztab2.validation	This package contains classes that provide the basic validator infrastructure used in the jmztabm-validation module.
de.isas.lipidomics.mztab2.validation.constraints	This package contains custom validation annotations for the javax.validation framework.
de.isas.lipidomics.mztab2.validation.validators	This package contains custom validators that implement the
de.isas.mztab2.cli	This package contains the command line interface for jmzTab-M validation and conversion.
de.isas.mztab2.cvmapping	This package contains classes for controlled vocabulary term access, comparison, results and external cv parameter resolution.
de.isas.mztab2.io	This package contains implementations for reading and writing of mzTab-M files.
de.isas.mztab2.io.formats	This package defines formats for Jackson that define, which serializer should be used for a particular object type.
de.isas.mztab2.io.serialization	This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
de.isas.mztab2.io.validators	This package contains implementations for validation of mzTab-M parts during parsing.
de.isas.mztab2.model	Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
de.isas.mztab2.test.utils	This package contains custom JUnit Rules for extraction of class path resource files and additional logging for testing.
de.isas.mztab2.validation	This package contains interfaces and implementations for the semantic validation via CvTerms.
de.isas.mztab2.validation.handlers	This package contains implementations for the semantic validation controlled vocabulary term rules.
info.psidev.cvmapping	This package contains the generated Java objects created via XML binding from the PSI-MS mapping file schema.
uk.ac.ebi.pride.jmztab2	This package contains jmzTab-M model and utility classes that were adapted from the original jmzTab implementation.
uk.ac.ebi.pride.jmztab2.model	This package contains model classes for mzTab-M structural features like mandatory and optional columns.
uk.ac.ebi.pride.jmztab2.utils	This package contains the property file mapping for mzTab-M's validation messages.
uk.ac.ebi.pride.jmztab2.utils.errors	This package contains error type definitions and related classes used during mzTab validation.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.