Example 6: 2D nmrML Example
nmrML file for a heteronuclear 2D experiment. The data represents the bmse00400-exp06 ([1H,13C]-HSQC) data set from PDBj-BMRB. The substance under investigation is ethanesulfonate (http://bmrbdep.pdbj.org/bms/bmse000400)
sample nmrML
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<nmrML xmlns="http://nmrml.org/schema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" accession="bmse000400" accession_url="http://bmrbdep.pdbj.org/bms/bmse000400" id="bmse000400-exp06" version="v1.0.rc1" xsi:schemaLocation="http://nmrml.org/schema http://nmrml.org/schema/v1.0.rc1/nmrML.xsd">
<cvList>
<cv URI="http://nmrml.org/cv/v1.1.0/nmrCV.owl" fullName="nmrML Controlled Vocabulary" id="NMRCV" version="1.1.0"/>
<cv URI="http://unit-ontology.googlecode.com/svn/trunk/uo.owl/" fullName="Unit Ontology" id="UO" version="3.2.0"/>
<cv URI="http://purl.obolibrary.org/obo/chebi.owl" fullName="Chemical entities of biological interest" id="ChEBI" version="ChEBI Release version 108"/>
</cvList>
<fileDescription>
<fileContent>
<cvTerm accession="NMR:1400160" cvRef="NMRCV" name="2D FID"/>
<cvTerm accession="NMR:1000223" cvRef="NMRCV" name="chemical shift"/>
</fileContent>
</fileDescription>
<contactList>
<contact email="cui@nmrfam.wisc.edu" fullname="Qiu Cui" id="entry_author_1" organization="Madison Metabolomics Consortium"/>
<contact email="ian.lewis2@ucalgary.ca" fullname="Ian Lewis" id="entry_author_2" organization="Madison Metabolomics Consortium"/>
<contact email="mfjofre@chem.wisc.edu" fullname="Francisca Jofre" id="entry_author_3" organization="Madison Metabolomics Consortium"/>
<contact email="wombats@nmrfam.wisc.edu" fullname="Mark E. Anderson" id="entry_author_4" organization="Madison Metabolomics Consortium"/>
<contact email="markley@nmrfam.wisc.edu" fullname="John L. Markley" id="entry_author_5" organization="Madison Metabolomics Consortium"/>
</contactList>
<sourceFileList>
<sourceFile id="NMR-STAR_3.1_FILE" location="http://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/NMR_STAR_experimental_entries/bmse000400.str" name="bmse000400.str">
<cvTerm accession="NMR:1000113" cvRef="NMRCV" name="NMR Star 3.1 file format"/>
</sourceFile>
<sourceFile id="BMRB-XML_FILE" location="http://bmrbpub.protein.osaka-u.ac.jp/archive/xml/bmse000400.xml.gz" name="bmse000400.xml.gz">
<cvTerm accession="NMR:1000439" cvRef="NMRCV" name="BMRB/XML file format"/>
</sourceFile>
<sourceFile id="FID_FILE" location="http://www.bmrb.wisc.edu/metabolomics/standards/Ethanesulfonic_acid/nmr/bmse000400/1H_13C_HSQC/ser" name="ser" sha1="a979ed42e5a28066a476557d713c76ce081541da">
<cvParam accession="NMR:1000264" cvRef="NMRCV" name="Bruker FID file"/>
</sourceFile>
<sourceFile id="PULSEPROGRAM_FILE" location="http://www.bmrb.wisc.edu/metabolomics/standards/Ethanesulfonic_acid/nmr/bmse000400/1H_13C_HSQC/pulseprogram" name="pulseprogram">
<cvParam accession="NMR:1400320" cvRef="NMRCV" name="Bruker UXNMR/XWIN-NMR format"/>
<cvParam accession="NMR:1400122" cvRef="NMRCV" name="pulse sequence file"/>
</sourceFile>
<sourceFile id="ACQUISITION_FILE" location="http://www.bmrb.wisc.edu/metabolomics/standards/Ethanesulfonic_acid/nmr/bmse000400/1H_13C_HSQC/acqus" name="acqus">
<cvParam accession="NMR:1400320" cvRef="NMRCV" name="Bruker UXNMR/XWIN-NMR format"/>
<cvParam accession="NMR:1400165" cvRef="NMRCV" name="1D NMR acquisition parameter set"/>
</sourceFile>
<sourceFile id="ACQUISITION2_FILE" location="http://www.bmrb.wisc.edu/metabolomics/standards/Ethanesulfonic_acid/nmr/bmse000400/1H_13C_HSQC/acqu2s" name="acqu2s">
<cvParam accession="NMR:1400320" cvRef="NMRCV" name="Bruker UXNMR/XWIN-NMR format"/>
<cvParam accession="NMR:1400166" cvRef="NMRCV" name="2D NMR acquisition parameter set"/>
</sourceFile>
<sourceFile id="PROCESSING_FILE" location="http://www.bmrb.wisc.edu/metabolomics/standards/Ethanesulfonic_acid/nmr/bmse000400/1H_13C_HSQC/pdata/1/procs" name="procs">
<cvParam accession="NMR:1400320" cvRef="NMRCV" name="Bruker UXNMR/XWIN-NMR format"/>
<cvParam accession="NMR:1000250" cvRef="NMRCV" name="Bruker processing parameter file"/>
</sourceFile>
<sourceFile id="PROCESSING2_FILE" location="http://www.bmrb.wisc.edu/metabolomics/standards/Ethanesulfonic_acid/nmr/bmse000400/1H_13C_HSQC/pdata/1/proc2s" name="proc2s">
<cvParam accession="NMR:1400320" cvRef="NMRCV" name="Bruker UXNMR/XWIN-NMR format"/>
<cvParam accession="NMR:1000250" cvRef="NMRCV" name="Bruker processing parameter file"/>
</sourceFile>
<sourceFile id="REAL_DATA_FILE" location="http://www.bmrb.wisc.edu/metabolomics/standards/Ethanesulfonic_acid/nmr/bmse000400/1H_13C_HSQC/pdata/1/2rr" name="2rr" sha1="d73ca4075f02f7fbc1314d31918d68d763ed30d1">
<cvParam accession="NMR:1400320" cvRef="NMRCV" name="Bruker UXNMR/XWIN-NMR format"/>
<cvParam accession="NMR:1400162" cvRef="NMRCV" name="2D spectrum"/>
<userParam name="2RR file"/>
</sourceFile>
</sourceFileList>
<softwareList>
<software accession="NMR:1000093" cvRef="NMRCV" id="NMRPipe" name="NMRPipe software"/>
<software accession="NMR:1400214" cvRef="NMRCV" id="XWIN-NMR" name="Bruker NMR software" version="3.5"/>
<software accession="NMR:1000322" cvRef="NMRCV" id="NMRDraw" name="NMR spectrum vizualisation software" version="2.3"/>
<software accession="NMR:1400270" cvRef="NMRCV" id="NUTS" name="Acorn NMR Inc" version="1D Version - 20060331"/>
</softwareList>
<instrumentConfigurationList>
<instrumentConfiguration id="Bruker_DMX_500">
<cvParam accession="NMR:1400255" cvRef="NMRCV" name="NMR instrument vendor" value="Bruker"/>
<cvParam accession="NMR:1000122" cvRef="NMRCV" name="Bruker instrument model" value="DMX"/>
<cvParamWithUnit accession="NMR:1400253" cvRef="NMRCV" name="magnetic field strength" unitAccession="UO_0000325" unitCvRef="UO" unitName="megaHertz" value="500"/>
<cvTerm accession="NMR:1400198" cvRef="NMRCV" name="Bruker NMR instrument"/>
<softwareRef ref="XWIN-NMR"/>
</instrumentConfiguration>
</instrumentConfigurationList>
<sampleList>
<sample originalBiologicalSampleReference="https://pubchem.ncbi.nlm.nih.gov/compound/3717105">
<postBufferpH>7.4</postBufferpH>
<buffer accession="CHEBI_37586" cvRef="ChEBI" name="sodium phosphate"/>
<fieldFrequencyLock fieldFrequencyLockName="D2O"/>
<chemicalShiftStandard accession="NMR:1000027" cvRef="NMRCV" name="2,2-Dimethyl-2-silapentane-5-sulfonate"/>
<solventType accession="CHEBI_42465" cvRef="ChEBI" name="ethanesulfonic acid" unitAccession="UO_0000063" unitCvRef="UO" unitName="millimolar" value="100"/>
<solventType accession="CHEBI_41981" cvRef="ChEBI" name="dideuterium oxide" unitAccession="UO_0000187" unitCvRef="UO" unitName="percent" value="100"/>
<additionalSoluteList>
<solute name="sodium azide">
<concentrationInSample unitAccession="UO_0000064" unitCvRef="UO" unitName="micromolar" value="500"/>
</solute>
</additionalSoluteList>
</sample>
</sampleList>
<acquisition>
<acquisitionMultiD>
<acquisitionParameterSet numberOfScans="4" numberOfSteadyStateScans="4">
<contactRefList>
<contactRef ref="entry_author_1"/>
<contactRef ref="entry_author_2"/>
<contactRef ref="entry_author_3"/>
<contactRef ref="entry_author_4"/>
<contactRef ref="entry_author_5"/>
</contactRefList>
<softwareRef ref="XWIN-NMR"/>
<sampleContainer accession="NMR:1400132" cvRef="NMRCV" name="NMR sample tube"/>
<sampleAcquisitionTemperature unitAccession="UO_0000012" unitCvRef="UO" unitName="kelvin" value="298"/>
<spinningRate unitAccession="UO_0000106" unitCvRef="UO" unitName="hertz" value="0"/>
<relaxationDelay unitAccession="UO_0000010" unitCvRef="UO" unitName="second" value="1"/>
<pulseSequence>
<userParam name="Pulse Program" value="c13hsqcse.cui"/>
</pulseSequence>
<acquisitionParameterRefList>
<acquisitionParameterFileRef ref="ACQUISITION2_FILE"/>
</acquisitionParameterRefList>
<directDimensionParameterSet decoupled="false" numberOfDataPoints="4096">
<acquisitionNucleus accession="NMR:1400151" cvRef="NMRCV" name="1H"/>
<effectiveExcitationField unitAccession="UO_0000325" unitCvRef="UO" unitName="megaHertz" value="499.84"/>
<sweepWidth unitAccession="UO_0000106" unitCvRef="UO" unitName="hertz" value="7002.80112044818"/>
<pulseWidth unitAccession="UO_0000029" unitCvRef="UO" unitName="microsecond" value="1"/>
<irradiationFrequency unitAccession="UO_0000325" unitCvRef="UO" unitName="megaHertz" value="499.842349248"/>
<samplingStrategy accession="NMR:1000349" cvRef="NMRCV" name="uniform sampling"/>
</directDimensionParameterSet>
<encodingScheme accession="NMR:1400057" cvRef="NMRCV" name="echo anti-echo coherence selection"/>
<indirectDimensionParameterSet decoupled="false" numberOfDataPoints="256">
<acquisitionNucleus accession="NMR:1400154" cvRef="NMRCV" name="13C"/>
<effectiveExcitationField unitAccession="UO_0000325" unitCvRef="UO" unitName="megaHertz" value="125.684533"/>
<sweepWidth unitAccession="UO_0000106" unitCvRef="UO" unitName="hertz" value="7541.47812971342"/>
<pulseWidth unitAccession="UO_0000029" unitCvRef="UO" unitName="microsecond" value="1"/>
<irradiationFrequency unitAccession="UO_0000325" unitCvRef="UO" unitName="megaHertz" value="125.68830353599"/>
<samplingStrategy accession="NMR:1000349" cvRef="NMRCV" name="uniform sampling"/>
</indirectDimensionParameterSet>
</acquisitionParameterSet>
<fidData byteFormat="complex128" compressed="true" encodedLength="11184816">