Package de.isas.mztab2.model

Class Metadata

  • @Generated(value="io.swagger.codegen.languages.JavaClientCodegen",
           date="2019-08-07T11:10:11.690+02:00")
public class Metadata
extends Object
    The metadata section provides additional information about the dataset(s) reported in the mzTab file. All fields in the metadata section are optional apart from those noted as mandatory. The fields in the metadata section MUST be reported in order of the various fields listed here. The field’s name and value MUST be separated by a tab character.

    mzTab-M specification example(s):

    MTD     mzTab-version   2.0.0-M
MTD     mzTab-ID        MTBL1234
MTD     title   Effects of Rapamycin on metabolite profile
...

    • Constructor Detail

      • Metadata

        public Metadata()

    • Method Detail

      • getPrefix

        @NotNull
public @NotNull Metadata.PrefixEnum getPrefix()
        The metadata section prefix. MUST always be MTD.
        Returns:
        prefix

      • getMzTabVersion

        @NotNull
@Pattern(regexp="^\\d{1}\\.\\d{1}\\.\\d{1}-[A-Z]{1}$")
public @NotNull @Pattern(regexp="^\\d{1}\\.\\d{1}\\.\\d{1}-[A-Z]{1}$") String getMzTabVersion()
        The version of the mzTab file. The suffix MUST be "-M" for mzTab for metabolomics (mzTab-M).
        Returns:
        mzTabVersion

      • setMzTabVersion

        public void setMzTabVersion​(String mzTabVersion)
        Set mzTabVersion.

        mzTab-M specification example(s):

        MTD     mzTab-version   2.0.0-M
MTD     mzTab-version   2.0.1-M
        Parameters:
        mzTabVersion - a String parameter.
        See Also:
        Metadata#getMzTabVersion for validation constraints

      • getMzTabID

        @NotNull
public @NotNull String getMzTabID()
        The ID of the mzTab file, this could be supplied by the repository from which it is downloaded or a local identifier from the lab producing the file. It is not intended to be a globally unique ID but carry some locally useful meaning.
        Returns:
        mzTabID

      • getTitle

        public String getTitle()
        The file’s human readable title.
        Returns:
        title

      • getDescription

        public String getDescription()
        The file’s human readable description.
        Returns:
        description

      • getSampleProcessing

        @Valid
public @Valid List<SampleProcessing> getSampleProcessing()
        A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report. The order of the sample_processing items should reflect the order these processing steps were performed in. If multiple parameters are given for a step these MUST be separated by a “|”. If derivatization was performed, it MUST be reported here as a general step, e.g. 'silylation' and the actual derivatization agens MUST be specified in the Section 6.2.54 part.
        Returns:
        sampleProcessing

      • setSampleProcessing

        public void setSampleProcessing​(List<SampleProcessing> sampleProcessing)
        Set sampleProcessing.

        mzTab-M specification example(s):

        MTD     sample_processing[1]    [MSIO, MSIO:0000107, metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer,]
MTD     sample_processing[2]    [MSIO, MSIO:0000146, centrifugation,]
MTD     sample_processing[3]    [MSIO, MSIO:0000141, metabolite extraction,]
MTD     sample_processing[4]    [MSIO, MSIO:0000141, silylation,]
        Parameters:
        sampleProcessing - a List<SampleProcessing> parameter.
        See Also:
        Metadata#getSampleProcessing for validation constraints

      • getInstrument

        @Valid
public @Valid List<Instrument> getInstrument()
        The name, source, analyzer and detector of the instruments used in the experiment. Multiple instruments are numbered [1-n].
        Returns:
        instrument

      • setInstrument

        public void setInstrument​(List<Instrument> instrument)
        Set instrument.

        mzTab-M specification example(s):

        MTD     instrument[1]-name      [MS, MS:1000449, LTQ Orbitrap,]
MTD     instrument[1]-source    [MS, MS:1000073, ESI,]
…
MTD     instrument[2]-source    [MS, MS:1000598, ETD,]
MTD     instrument[1]-analyzer[1]       [MS, MS:1000291, linear ion trap,]
…
MTD     instrument[2]-analyzer[1]       [MS, MS:1000484, orbitrap,]
MTD     instrument[1]-detector  [MS, MS:1000253, electron multiplier,]
…
MTD     instrument[2]-detector  [MS, MS:1000348, focal plane collector,]
        Parameters:
        instrument - a List<Instrument> parameter.
        See Also:
        Metadata#getInstrument for validation constraints

      • getSoftware

        @NotNull
@Valid
public @NotNull @Valid List<Software> getSoftware()
        Software used to analyze the data and obtain the reported results. The parameter’s value SHOULD contain the software’s version. The order (numbering) should reflect the order in which the tools were used. A software setting used. This field MAY occur multiple times for a single software. The value of this field is deliberately set as a String, since there currently do not exist CV terms for every possible setting.
        Returns:
        software

      • setSoftware

        public void setSoftware​(List<Software> software)
        Set software.

        mzTab-M specification example(s):

        MTD     software[1]     [MS, MS:1002879, Progenesis QI, 3.0]
MTD     software[1]-setting     Fragment tolerance = 0.1 Da
…
MTD     software[2]-setting     Parent tolerance = 0.5 Da
        Parameters:
        software - a List<Software> parameter.
        See Also:
        Metadata#getSoftware for validation constraints

      • getPublication

        @Valid
public @Valid List<Publication> getPublication()
        A publication associated with this file. Several publications can be given by indicating the number in the square brackets after “publication”. PubMed ids must be prefixed by “pubmed:”, DOIs by “doi:”. Multiple identifiers MUST be separated by “|”.
        Returns:
        publication

      • setPublication

        public void setPublication​(List<Publication> publication)
        Set publication.

        mzTab-M specification example(s):

        MTD     publication[1]  pubmed:21063943|doi:10.1007/978-1-60761-987-1_6
MTD     publication[2]  pubmed:20615486|doi:10.1016/j.jprot.2010.06.008
        Parameters:
        publication - a List<Publication> parameter.
        See Also:
        Metadata#getPublication for validation constraints

      • getContact

        @Valid
public @Valid List<Contact> getContact()
        The contact’s name, affiliation and e-mail. Several contacts can be given by indicating the number in the square brackets after "contact". A contact has to be supplied in the format [first name] [initials] [last name].
        Returns:
        contact

      • setContact

        public void setContact​(List<Contact> contact)
        Set contact.

        mzTab-M specification example(s):

        MTD     contact[1]-name James D. Watson
MTD     contact[1]-affiliation  Cambridge University, UK
MTD     contact[1]-email        watson@cam.ac.uk
MTD     contact[2]-name Francis Crick
MTD     contact[2]-affiliation  Cambridge University, UK
MTD     contact[2]-email        crick@cam.ac.uk
        Parameters:
        contact - a List<Contact> parameter.
        See Also:
        Metadata#getContact for validation constraints

      • getUri

        @Valid
public @Valid List<Uri> getUri()
        A URI pointing to the file’s source data (e.g., a MetaboLights records).
        Returns:
        uri

      • getExternalStudyUri

        @Valid
public @Valid List<Uri> getExternalStudyUri()
        A URI pointing to an external file with more details about the study design (e.g., an ISA-TAB file).
        Returns:
        externalStudyUri

      • setExternalStudyUri

        public void setExternalStudyUri​(List<Uri> externalStudyUri)
        Set externalStudyUri.

        mzTab-M specification example(s):

        MTD     external_study_uri[1]   https://www.ebi.ac.uk/metabolights/MTBLS517/files/i_Investigation.txt
        Parameters:
        externalStudyUri - a List<Uri> parameter.
        See Also:
        Metadata#getExternalStudyUri for validation constraints

      • getQuantificationMethod

        @NotNull
@Valid
public @NotNull @Valid Parameter getQuantificationMethod()
        The quantification method used in the experiment reported in the file.
        Returns:
        quantificationMethod

      • getStudyVariable

        @NotNull
@Valid
public @NotNull @Valid List<StudyVariable> getStudyVariable()
        Specification of study_variable. (empty) name: A name for each study variable (experimental condition or factor), to serve as a list of the study variables that MUST be reported in the following tables. For software that does not capture study variables, a single study variable MUST be reported, linking to all assays. This single study variable MUST have the identifier “undefined“. assay_refs: Bar-separated references to the IDs of assays grouped in the study variable. average_function: The function used to calculate the study variable quantification value and the operation used is not arithmetic mean (default) e.g. “geometric mean”, “median”. The 1-n refers to different study variables. variation_function: The function used to calculate the study variable quantification variation value if it is reported and the operation used is not coefficient of variation (default) e.g. “standard error”. description: A textual description of the study variable. factors: Additional parameters or factors, separated by bars, that are known about study variables allowing the capture of more complex, such as nested designs.
        Returns:
        studyVariable

      • setStudyVariable

        public void setStudyVariable​(List<StudyVariable> studyVariable)
        Set studyVariable.

        mzTab-M specification example(s):

        MTD     study_variable[1]       control
MTD     study_variable[1]-assay_refs    assay[1]| assay[2]| assay[3]
MTD     study_variable-average_function [MS, MS:1002883, median, ]
MTD     study_variable-variation_function       [MS, MS:1002885, standard error, ]
MTD     study_variable[1]-description   Group B (spike-in 0.74 fmol/uL)
MTD     study_variable[1]-factors       [,,rapamycin dose,0.5mg]
MTD     study_variable[2]       1 minute
        Parameters:
        studyVariable - a List<StudyVariable> parameter.
        See Also:
        Metadata#getStudyVariable for validation constraints

      • getMsRun

        @NotNull
@Valid
public @NotNull @Valid List<MsRun> getMsRun()
        Specification of ms_run. location: Location of the external data file e.g. raw files on which analysis has been performed. If the actual location of the MS run is unknown, a “null” MUST be used as a place holder value, since the [1-n] cardinality is referenced elsewhere. If pre-fractionation has been performed, then [1-n] ms_runs SHOULD be created per assay. instrument_ref: If different instruments are used in different runs, instrument_ref can be used to link a specific instrument to a specific run. format: Parameter specifying the data format of the external MS data file. If ms_run[1-n]-format is present, ms_run[1-n]-id_format SHOULD also be present, following the parameters specified in Table 1. id_format: Parameter specifying the id format used in the external data file. If ms_run[1-n]-id_format is present, ms_run[1-n]-format SHOULD also be present. fragmentation_method: The type(s) of fragmentation used in a given ms run. scan_polarity: The polarity mode of a given run. Usually only one value SHOULD be given here except for the case of mixed polarity runs. hash: Hash value of the corresponding external MS data file defined in ms_run[1-n]-location. If ms_run[1-n]-hash is present, ms_run[1-n]-hash_method SHOULD also be present. hash_method: A parameter specifying the hash methods used to generate the String in ms_run[1-n]-hash. Specifics of the hash method used MAY follow the definitions of the mzML format. If ms_run[1-n]-hash is present, ms_run[1-n]-hash_method SHOULD also be present.
        Returns:
        msRun

      • setMsRun

        public void setMsRun​(List<MsRun> msRun)
        Set msRun.

        mzTab-M specification example(s):

        COM     location can be a local or remote URI
MTD     ms_run[1]-location      file:///C:/path/to/my/file.mzML
MTD     ms_run[1]-instrument_ref        instrument[1]
MTD     ms_run[1]-format        [MS, MS:1000584, mzML file, ]
MTD     ms_run[1]-id_format     [MS, MS:1000530, mzML unique identifier, ]
MTD     ms_run[1]-fragmentation_method[1]       [MS, MS:1000133, CID, ]
COM     for mixed polarity scan scenarios
MTD     ms_run[1]-scan_polarity[1]      [MS, MS:1000130, positive scan, ]
MTD     ms_run[1]-scan_polarity[2]      [MS, MS:1000129, negative scan, ]
MTD     ms_run[1]-hash_method   [MS, MS:1000569, SHA-1, ]
MTD     ms_run[1]-hash  de9f2c7fd25e1b3afad3e85a0bd17d9b100db4b3
        Parameters:
        msRun - a List<MsRun> parameter.
        See Also:
        Metadata#getMsRun for validation constraints

      • getAssay

        @NotNull
@Valid
public @NotNull @Valid List<Assay> getAssay()
        Specification of assay. (empty) name: A name for each assay, to serve as a list of the assays that MUST be reported in the following tables. custom: Additional custom parameters or values for a given assay. external_uri: An external reference uri to further information about the assay, for example via a reference to an object within an ISA-TAB file. sample_ref: An association from a given assay to the sample analysed. ms_run_ref: An association from a given assay to the source MS run. All assays MUST reference exactly one ms_run unless a workflow with pre-fractionation is being encoded, in which case each assay MUST reference n ms_runs where n fractions have been collected. Multiple assays SHOULD reference the same ms_run to capture multiplexed experimental designs.
        Returns:
        assay

      • setAssay

        public void setAssay​(List<Assay> assay)
        Set assay.

        mzTab-M specification example(s):

        MTD     assay[1]        first assay
MTD     assay[1]-custom[1]      [MS, , Assay operator, Fred Blogs]
MTD     assay[1]-sample_ref     sample[1]
MTD     assay[1]-ms_run_ref     ms_run[1]
MTD     assay[1]-external_uri   https://www.ebi.ac.uk/metabolights/MTBLS517/files/i_Investigation.txt?STUDYASSAY=a_e04_c18pos.txt
MTD     assay[2]        second assay
MTD     assay[2]-sample_ref     sample[2]
        Parameters:
        assay - a List<Assay> parameter.
        See Also:
        Metadata#getAssay for validation constraints

      • getSample

        @Valid
public @Valid List<Sample> getSample()
        Specification of sample. (empty) name: A name for each sample to serve as a list of the samples that MUST be reported in the following tables. Samples MUST be reported if a statistical design is being captured (i.e. bio or tech replicates). If the type of replicates are not known, samples SHOULD NOT be reported. species: The respective species of the samples analysed. For more complex cases, such as metagenomics, optional columns and userParams should be used. tissue: The respective tissue(s) of the sample. cell_type: The respective cell type(s) of the sample. disease: The respective disease(s) of the sample. description: A human readable description of the sample. custom: Custom parameters describing the sample’s additional properties. Dates MUST be provided in ISO-8601 format.
        Returns:
        sample

      • setSample

        public void setSample​(List<Sample> sample)
        Set sample.

        mzTab-M specification example(s):

        COM     Experiment where all samples consisted of the same two species
MTD     sample[1]       individual number 1
MTD     sample[1]-species[1]    [NCBITaxon, NCBITaxon:9606, Homo sapiens, ]
MTD     sample[1]-tissue[1]     [BTO, BTO:0000759, liver, ]
MTD     sample[1]-cell_type[1]  [CL, CL:0000182, hepatocyte, ]
MTD     sample[1]-disease[1]    [DOID, DOID:684, hepatocellular carcinoma, ]
MTD     sample[1]-disease[2]    [DOID, DOID:9451, alcoholic fatty liver, ]
MTD     sample[1]-description   Hepatocellular carcinoma samples.
MTD     sample[1]-custom[1]     [,,Extraction date, 2011-12-21]
MTD     sample[1]-custom[2]     [,,Extraction reason, liver biopsy]
MTD     sample[2]       individual number 2
MTD     sample[2]-species[1]    [NCBITaxon, NCBITaxon:9606, Homo sapiens, ]
MTD     sample[2]-tissue[1]     [BTO, BTO:0000759, liver, ]
MTD     sample[2]-cell_type[1]  [CL, CL:0000182, hepatocyte, ]
MTD     sample[2]-description   Healthy control samples.
        Parameters:
        sample - a List<Sample> parameter.
        See Also:
        Metadata#getSample for validation constraints

      • getCustom

        @Valid
public @Valid List<Parameter> getCustom()
        Any additional parameters describing the analysis reported.
        Returns:
        custom

      • getCv

        @NotNull
@Valid
public @NotNull @Valid List<CV> getCv()
        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. "MS" for PSI-MS. full_name: A string describing the full names of the controlled vocabularies/ontologies used in the mzTab file. version: A string describing the version of the controlled vocabularies/ontologies used in the mzTab file. uri: A string containing the URIs of the controlled vocabularies/ontologies used in the mzTab file.
        Returns:
        cv

      • setCv

        public void setCv​(List<CV> cv)
        Set cv.

        mzTab-M specification example(s):

        MTD     cv[1]-label     MS
MTD     cv[1]-full_name PSI-MS controlled vocabulary
MTD     cv[1]-version   4.1.11
MTD     cv[1]-uri       https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
        Parameters:
        cv - a List<CV> parameter.
        See Also:
        Metadata#getCv for validation constraints

      • getDatabase

        @NotNull
@Valid
public @NotNull @Valid List<Database> getDatabase()
        Specification of databases. (empty): The description of databases used. For cases, where a known database has not been used for identification, a userParam SHOULD be inserted to describe any identification performed e.g. de novo. If no identification has been performed at all then "no database" should be inserted followed by null. prefix: The prefix used in the “identifier” column of data tables. For the “no database” case "null" must be used. version: The database version is mandatory where identification has been performed. This may be a formal version number e.g. “1.4.1”, a date of access “2016-10-27” (ISO-8601 format) or “Unknown” if there is no suitable version that can be annotated. uri: The URI to the database. For the “no database” case, "null" must be reported.
        Returns:
        database

      • setDatabase

        public void setDatabase​(List<Database> database)
        Set database.

        mzTab-M specification example(s):

        MTD     database[1]     [MIRIAM, MIR:00100079, HMDB, ]
MTD     database[1]-prefix      hmdb
MTD     database[1]-version     3.6
MTD     database[1]-uri http://www.hmdb.ca/
MTD     database[2]     [,, "de novo", ]
MTD     database[2]-prefix      dn
MTD     database[2]-version     Unknown
MTD     database[2]-uri null
MTD     database[3]     [,, "no database", null ]
MTD     database[3]-prefix      null
MTD     database[3]-version     Unknown
MTD     database[3]-uri null
        Parameters:
        database - a List<Database> parameter.
        See Also:
        Metadata#getDatabase for validation constraints

      • getDerivatizationAgent

        @Valid
public @Valid List<Parameter> getDerivatizationAgent()
        A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.
        Returns:
        derivatizationAgent

      • setDerivatizationAgent

        public void setDerivatizationAgent​(List<Parameter> derivatizationAgent)
        Set derivatizationAgent.

        mzTab-M specification example(s):

        MTD     derivatization_agent[1] [XLMOD, XLMOD:07014, N-methyl-N-t-butyldimethylsilyltrifluoroacetamide, ]
        Parameters:
        derivatizationAgent - a List<Parameter> parameter.
        See Also:
        Metadata#getDerivatizationAgent for validation constraints

      • getSmallMoleculeQuantificationUnit

        @NotNull
@Valid
public @NotNull @Valid Parameter getSmallMoleculeQuantificationUnit()
        Defines what type of units are reported in the small molecule summary quantification / abundance fields.
        Returns:
        smallMoleculeQuantificationUnit

      • getSmallMoleculeFeatureQuantificationUnit

        @NotNull
@Valid
public @NotNull @Valid Parameter getSmallMoleculeFeatureQuantificationUnit()
        Defines what type of units are reported in the small molecule feature quantification / abundance fields.
        Returns:
        smallMoleculeFeatureQuantificationUnit

      • getSmallMoleculeIdentificationReliability

        @Valid
public @Valid Parameter getSmallMoleculeIdentificationReliability()
        The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.
        Returns:
        smallMoleculeIdentificationReliability

      • getIdConfidenceMeasure

        @NotNull
@Valid
public @NotNull @Valid List<Parameter> getIdConfidenceMeasure()
        The type of small molecule confidence measures or scores MUST be reported as a CV parameter [1-n]. The CV parameter definition should formally state whether the ordering is high to low or vice versa. The order of the scores SHOULD reflect their importance for the identification and be used to determine the identification’s rank.
        Returns:
        idConfidenceMeasure

      • setIdConfidenceMeasure

        public void setIdConfidenceMeasure​(List<Parameter> idConfidenceMeasure)
        Set idConfidenceMeasure.

        mzTab-M specification example(s):

        MTD     id_confidence_measure[1]        [MS,MS:1002889,Progenesis MetaScope Score,]
MTD     id_confidence_measure[2]        [MS,MS:1002890,fragmentation score,]
MTD     id_confidence_measure[3]        [MS,MS:1002891,isotopic fit score,]
        Parameters:
        idConfidenceMeasure - a List<Parameter> parameter.
        See Also:
        Metadata#getIdConfidenceMeasure for validation constraints

      • getColunitSmallMolecule

        @Valid
public @Valid List<ColumnParameterMapping> getColunitSmallMolecule()
        Defines the used unit for a column in the small molecule section. The format of the value has to be \{column name}=\{Parameter defining the unit}. This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule-quantification_unit.
        Returns:
        colunitSmallMolecule

      • setColunitSmallMolecule

        public void setColunitSmallMolecule​(List<ColumnParameterMapping> colunitSmallMolecule)
        Set colunitSmallMolecule.

        mzTab-M specification example(s):

        COM     colunit for optional small molecule summary column with the name 'opt_global_cv_MS:MS:1002954_collisional_cross_sectional_area'
MTD     colunit-small_molecule  opt_global_cv_MS:MS:1002954_collisional_cross_sectional_area=[UO,UO:00003241, square angstrom,]
        Parameters:
        colunitSmallMolecule - a List<ColumnParameterMapping> parameter.
        See Also:
        Metadata#getColunitSmallMolecule for validation constraints

      • getColunitSmallMoleculeFeature

        @Valid
public @Valid List<ColumnParameterMapping> getColunitSmallMoleculeFeature()
        Defines the used unit for a column in the small molecule feature section. The format of the value has to be \{column name}=\{Parameter defining the unit}. This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule_feature-quantification_unit.
        Returns:
        colunitSmallMoleculeFeature

      • setColunitSmallMoleculeFeature

        public void setColunitSmallMoleculeFeature​(List<ColumnParameterMapping> colunitSmallMoleculeFeature)
        Set colunitSmallMoleculeFeature.

        mzTab-M specification example(s):

        COM     colunit for optional small molecule feature column with the name 'opt_ms_run[1]_cv_MS:MS:1002476_ion_mobility_drift_time' referencing ms_run[1]
MTD     colunit-small_molecule_feature  opt_ms_run[1]_cv_MS:MS:1002476_ion_mobility_drift_time=[UO,UO:0000031, minute,]
        Parameters:
        colunitSmallMoleculeFeature - a List<ColumnParameterMapping> parameter.
        See Also:
        Metadata#getColunitSmallMoleculeFeature for validation constraints

      • getColunitSmallMoleculeEvidence

        @Valid
public @Valid List<ColumnParameterMapping> getColunitSmallMoleculeEvidence()
        Defines the used unit for a column in the small molecule evidence section. The format of the value has to be \{column name}=\{Parameter defining the unit}.
        Returns:
        colunitSmallMoleculeEvidence

      • setColunitSmallMoleculeEvidence

        public void setColunitSmallMoleculeEvidence​(List<ColumnParameterMapping> colunitSmallMoleculeEvidence)
        Set colunitSmallMoleculeEvidence.

        mzTab-M specification example(s):

        COM     colunit for optional small molecule evidence column with the name 'opt_global_mass_error'
MTD     colunit-small_molecule_evidence opt_global_mass_error=[UO, UO:0000169, parts per million, ]
        Parameters:
        colunitSmallMoleculeEvidence - a List<ColumnParameterMapping> parameter.
        See Also:
        Metadata#getColunitSmallMoleculeEvidence for validation constraints

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object