Package de.isas.mztab2.model
Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
- How to use the jmzTab-m object model.
- The jmzTab-m reference implementation.
- The mzTab-M specification homepage.
- Metadata - The metadata section provides additional information about the dataset(s) reported in the mzTab file
- SmallMoleculeSummary - Each row of the small molecule summary section is intended to report one final result to be communicated in terms of a molecule that has been quantified.
- SmallMoleculeFeature - Each row of the small molecule feature section represents individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified. Different adducts or derivatives and different charge states of individual molecules should be reported as separate SMF rows.
- SmallMoleculeEvidence - Each row of the small molecule evidence section represents evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules. In a typical case, each row represents one result from a single search or intepretation of a piece of evidence e.g. a database search with a fragmentation spectrum. Multiple results from a given input data item (e.g. one fragment spectrum) SHOULD share the same value under evidence_input_id.
- Since:
- 1.0.0
- Version:
- 1.0.2
- Author:
- nilshoffmann
-
Interface Summary Interface Description IndexedElement Indexed elements (IDs) define a unique ID for a collection of multiple metadata elements of the same type within the mzTab-M document, e.g. for sample, assay, study variable etc. -
Class Summary Class Description Assay Specification of assay.ColumnParameterMapping Defines the used unit for a column in the mzTab-M file.Comment Comment lines can be placed anywhere in an mzTab file.Contact The contact’s name, affiliation and e-mail.CV Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.Database Specification of databases.Error ErrorIndexedElementImpl Implementation of IndexedElement where more information is required than just the id.Instrument The name, source, analyzer and detector of the instruments used in the experiment.Metadata The metadata section provides additional information about the dataset(s) reported in the mzTab file.MsRun Specification of ms_run.MzTab mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.MzTabAccess Utility class for easier access to linked information within an mztab-M data object.OptColumnMapping Additional columns can be added to the end of the small molecule table.Parameter mzTab makes use of CV parameters.Publication A publication associated with this file.PublicationItem A publication item, defined by a qualifier and a native accession, e.g. pubmed id.Sample Specification of sample.SampleProcessing A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.SmallMoleculeEvidence The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.SmallMoleculeFeature The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.SmallMoleculeSummary The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.Software Software used to analyze the data and obtain the reported results.SpectraRef Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.StringList A typed list of strings.StudyVariable Specification of study_variable.Uri A URI pointing to the file’s source data (e.g., a MetaboLights records) or an external file with more details about the study design.ValidationMessage ValidationMessage -
Enum Summary Enum Description Assay.Properties Property enumeration for Assay.ColumnParameterMapping.Properties Property enumeration for ColumnParameterMapping.Comment.PrefixEnum Gets or Sets prefixComment.Properties Property enumeration for Comment.Contact.Properties Property enumeration for Contact.CV.Properties Property enumeration for CV.Database.Properties Property enumeration for Database.Error.Properties Property enumeration for Error.Instrument.Properties Property enumeration for Instrument.Metadata.PrefixEnum The metadata section prefix.Metadata.Properties Property enumeration for Metadata.MsRun.Properties Property enumeration for MsRun.MzTab.Properties Property enumeration for MzTab.OptColumnMapping.Properties Property enumeration for OptColumnMapping.Parameter.Properties Property enumeration for Parameter.Publication.Properties Property enumeration for Publication.PublicationItem.Properties Property enumeration for PublicationItem.PublicationItem.TypeEnum The type qualifier of this publication item.Sample.Properties Property enumeration for Sample.SampleProcessing.Properties Property enumeration for SampleProcessing.SmallMoleculeEvidence.HeaderPrefixEnum The small molecule evidence table header prefix.SmallMoleculeEvidence.PrefixEnum The small molecule evidence table row prefix.SmallMoleculeEvidence.Properties Property enumeration for SmallMoleculeEvidence.SmallMoleculeFeature.HeaderPrefixEnum The small molecule feature table header prefix.SmallMoleculeFeature.PrefixEnum The small molecule feature table row prefix.SmallMoleculeFeature.Properties Property enumeration for SmallMoleculeFeature.SmallMoleculeSummary.HeaderPrefixEnum The small molecule table header prefix.SmallMoleculeSummary.PrefixEnum The small molecule table row prefix.SmallMoleculeSummary.Properties Property enumeration for SmallMoleculeSummary.Software.Properties Property enumeration for Software.SpectraRef.Properties Property enumeration for SpectraRef.StudyVariable.Properties Property enumeration for StudyVariable.Uri.Properties Property enumeration for Uri.ValidationMessage.CategoryEnum Gets or Sets categoryValidationMessage.MessageTypeEnum Gets or Sets messageTypeValidationMessage.Properties Property enumeration for ValidationMessage.