Skip to content

Commit

Permalink
Merge pull request #1005 from NFDI4Chem/bioschemas
Browse files Browse the repository at this point in the history 
fix: add NMRium info checks
  • Loading branch information
@CS76
CS76 authored Jan 10, 2024
2 parents c96c728 + 53b0f03 commit c2bf8c6
Showing 1 changed file with 90 additions and 45 deletions.
135 changes: 90 additions & 45 deletions app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php
View file
Original file line number Diff line number Diff line change
Expand Up @@ -263,38 +263,40 @@ public function prepareExperiment($dataset)
$info = BioschemasHelper::getNMRiumInfo($dataset);
$experimentSchema = null;
if ($info) {
$chmo = BioschemasHelper::prepareDefinedTermSet('Chemical Methods Ontology', 'http://purl.obolibrary.org/obo/chmo.owl');

$nucleus = $info->nucleus;
$experiment = $info->experiment;
$experimentSchema = $experiment;

if ($experiment == '1d') {
if ($nucleus == '1H') {
$experiment = 'proton';
} elseif ($nucleus == '13C') {
$experiment = 'c13';
if (property_exists($info, 'nucleus') && property_exists($info, 'experiment')) {
$chmo = BioschemasHelper::prepareDefinedTermSet('Chemical Methods Ontology', 'http://purl.obolibrary.org/obo/chmo.owl');

$nucleus = $info->nucleus;
$experiment = $info->experiment;
$experimentSchema = $experiment;

if ($experiment == '1d') {
if ($nucleus == '1H') {
$experiment = 'proton';
} elseif ($nucleus == '13C') {
$experiment = 'c13';
}
}
}

if ($experiment == 'proton') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('1H nuclear magnetic resonance spectroscopy', ['1H-NMR spectrometry', 'proton nuclear magnetic resonance spectroscopy', '1H-NMR spectroscopy', '1H-NMR', '1H NMR', '1H NMR spectroscopy', '1H nuclear magnetic resonance spectrometry', 'proton NMR'], 'CHMO:0000593', 'http://purl.obolibrary.org/obo/CHMO_0000593', $chmo);
} elseif ($experiment == 'c13') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('13C nuclear magnetic resonance spectroscopy', ['13C-NMR spectrometry', '13C nuclear magnetic resonance spectrometry', '13C-NMR spectroscopy', 'carbon NMR', '13C NMR spectroscopy', '13C NMR', 'C-NMR'], 'CHMO:0000595', 'http://purl.obolibrary.org/obo/CHMO_0000595', $chmo);
} elseif ($experiment == 'cosy') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('correlation spectroscopy', ['correlation spectrometry', 'correlated spectroscopy', 'correlated spectrometry', 'COSY'], 'CHMO:0000599', 'http://purl.obolibrary.org/obo/CHMO_0000599', $chmo);
} elseif ($experiment == 'hmbc') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('heteronuclear multiple bond coherence', ['HMBC', 'HMBC NMR'], 'CHMO:0000601', 'http://purl.obolibrary.org/obo/CHMO_0000601', $chmo);
} elseif ($experiment == 'hmqc') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('heteronuclear multiple quantum coherence', ['HMQC', 'HMQC NMR'], 'CHMO:0000603', 'http://purl.obolibrary.org/obo/CHMO_0000603', $chmo);
} elseif ($experiment == 'hsqc') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('heteronuclear single quantum coherence', ['HSQC'], 'CHMO:0000604', 'http://purl.obolibrary.org/obo/CHMO_0000604', $chmo);
} elseif ($experiment == 'tocsy') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('total correlation spectroscopy', ['homonuclear Hartmann-Hahn spectroscopy', 'homonuclear Hartmann Hahn spectroscopy', 'total correlation spectrometry', 'HOHAHA spectroscopy', 'TOCSY', 'total correlated spectroscopy', 'homonuclear Hartmann,Hahn spectroscopy', 'HOHAHA spectrometry'], 'CHMO:0000605', 'http://purl.obolibrary.org/obo/CHMO_0000605', $chmo);
} elseif ($experiment == 'roesy') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('rotating frame Overhauser effect spectroscopy', ['rotating frame Overhauser enhancement spectroscopy', 'rotating frame Overhauser enhancement spectrometry', 'rOesy', 'cross-relaxation appropriate for minimolecules eμlated by locked spins', 'ROESY', 'CAMELPSIN', 'rotational Overhauser effect spectroscopy', 'rotating frame Overhauser effect spectrometry', 'ROESY NMR'], 'CHMO:0000610', 'http://purl.obolibrary.org/obo/CHMO_0000610', $chmo);
} elseif ($experiment == 'dept') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('distortionless enhancement with polarization transfer', ['distortionless enhancement with polarisation transfer', 'distortionless enhancement by polarisation transfer', 'distortionless enhancement by polarization transfer', 'DEPT NMR', 'DEPT', 'distortionless enhancement with polarization transfer'], 'CHMO:0000596', 'http://purl.obolibrary.org/obo/CHMO_0000596', $chmo);
if ($experiment == 'proton') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('1H nuclear magnetic resonance spectroscopy', ['1H-NMR spectrometry', 'proton nuclear magnetic resonance spectroscopy', '1H-NMR spectroscopy', '1H-NMR', '1H NMR', '1H NMR spectroscopy', '1H nuclear magnetic resonance spectrometry', 'proton NMR'], 'CHMO:0000593', 'http://purl.obolibrary.org/obo/CHMO_0000593', $chmo);
} elseif ($experiment == 'c13') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('13C nuclear magnetic resonance spectroscopy', ['13C-NMR spectrometry', '13C nuclear magnetic resonance spectrometry', '13C-NMR spectroscopy', 'carbon NMR', '13C NMR spectroscopy', '13C NMR', 'C-NMR'], 'CHMO:0000595', 'http://purl.obolibrary.org/obo/CHMO_0000595', $chmo);
} elseif ($experiment == 'cosy') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('correlation spectroscopy', ['correlation spectrometry', 'correlated spectroscopy', 'correlated spectrometry', 'COSY'], 'CHMO:0000599', 'http://purl.obolibrary.org/obo/CHMO_0000599', $chmo);
} elseif ($experiment == 'hmbc') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('heteronuclear multiple bond coherence', ['HMBC', 'HMBC NMR'], 'CHMO:0000601', 'http://purl.obolibrary.org/obo/CHMO_0000601', $chmo);
} elseif ($experiment == 'hmqc') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('heteronuclear multiple quantum coherence', ['HMQC', 'HMQC NMR'], 'CHMO:0000603', 'http://purl.obolibrary.org/obo/CHMO_0000603', $chmo);
} elseif ($experiment == 'hsqc') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('heteronuclear single quantum coherence', ['HSQC'], 'CHMO:0000604', 'http://purl.obolibrary.org/obo/CHMO_0000604', $chmo);
} elseif ($experiment == 'tocsy') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('total correlation spectroscopy', ['homonuclear Hartmann-Hahn spectroscopy', 'homonuclear Hartmann Hahn spectroscopy', 'total correlation spectrometry', 'HOHAHA spectroscopy', 'TOCSY', 'total correlated spectroscopy', 'homonuclear Hartmann,Hahn spectroscopy', 'HOHAHA spectrometry'], 'CHMO:0000605', 'http://purl.obolibrary.org/obo/CHMO_0000605', $chmo);
} elseif ($experiment == 'roesy') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('rotating frame Overhauser effect spectroscopy', ['rotating frame Overhauser enhancement spectroscopy', 'rotating frame Overhauser enhancement spectrometry', 'rOesy', 'cross-relaxation appropriate for minimolecules eμlated by locked spins', 'ROESY', 'CAMELPSIN', 'rotational Overhauser effect spectroscopy', 'rotating frame Overhauser effect spectrometry', 'ROESY NMR'], 'CHMO:0000610', 'http://purl.obolibrary.org/obo/CHMO_0000610', $chmo);
} elseif ($experiment == 'dept') {
$experimentSchema = BioschemasHelper::prepareDefinedTerm('distortionless enhancement with polarization transfer', ['distortionless enhancement with polarisation transfer', 'distortionless enhancement by polarisation transfer', 'distortionless enhancement by polarization transfer', 'DEPT NMR', 'DEPT', 'distortionless enhancement with polarization transfer'], 'CHMO:0000596', 'http://purl.obolibrary.org/obo/CHMO_0000596', $chmo);
}
}
}

Expand All @@ -311,22 +313,62 @@ public function prepareNMRiumInfo($dataset)
{
$info = BioschemasHelper::getNMRiumInfo($dataset);
if ($info) {
$solvent = $info->solvent;
$nucleus = $info->nucleus;
$solvent = null;
$nucleus = null;
$dimension = null;
$probeName = null;
$experiment = null;
$temperature = null;
$baseFrequency = null;
$fieldStrength = null;
$numberOfScans = null;
$pulseSequence = null;
$spectralWidth = null;
$numberOfPoints = null;
$relaxationTime = null;

if (property_exists($info, 'solvent')) {
$solvent = $info->solvent;
}
if (property_exists($info, 'nucleus')) {
$nucleus = $info->nucleus;
}
if (is_string($nucleus)) {
$nucleus = [$nucleus];
}
$dimension = $info->dimension;
$probeName = $info->probeName;
$experiment = $info->experiment;
$temperature = $info->temperature;
$baseFrequency = $info->baseFrequency;
$fieldStrength = $info->fieldStrength;
$numberOfScans = $info->numberOfScans;
$pulseSequence = $info->pulseSequence;
$spectralWidth = $info->spectralWidth;
$numberOfPoints = $info->numberOfPoints;
$relaxationTime = $info->relaxationTime;
if (property_exists($info, 'dimension')) {
$dimension = $info->dimension;
}
if (property_exists($info, 'probeName')) {
$probeName = $info->probeName;
}
if (property_exists($info, 'experiment')) {
$experiment = $info->experiment;
}
if (property_exists($info, 'temperature')) {
$temperature = $info->temperature;
}
if (property_exists($info, 'baseFrequency')) {
$baseFrequency = $info->baseFrequency;
}
if (property_exists($info, 'fieldStrength')) {
$fieldStrength = $info->fieldStrength;
}
if (property_exists($info, 'numberOfScans')) {
$numberOfScans = $info->numberOfScans;
}
if (property_exists($info, 'pulseSequence')) {
$pulseSequence = $info->pulseSequence;
}
if (property_exists($info, 'spectralWidth')) {
$spectralWidth = $info->spectralWidth;
}
if (property_exists($info, 'numberOfPoints')) {
$numberOfPoints = $info->numberOfPoints;
}
if (property_exists($info, 'relaxationTime')) {
$relaxationTime = $info->relaxationTime;
}

$solventProperty = BioschemasHelper::preparePropertyValue('NMR solvent', 'NMR:1000330', $solvent, null);
$nucleusProperty = BioschemasHelper::preparePropertyValue('acquisition nucleus', 'NMR:1400083', $nucleus, null);
Expand All @@ -343,9 +385,12 @@ public function prepareNMRiumInfo($dataset)
$relaxationTimeProperty = BioschemasHelper::preparePropertyValue('relaxation time measurement', 'FIX:0000202', $relaxationTime, 'http://purl.obolibrary.org/obo/UO_0000010');

$keywords = [$solvent, $dimension.'D'];
foreach ($nucleus as $keyword) {
array_push($keywords, $keyword);
if ($nucleus !== null) {
foreach ($nucleus as $keyword) {
array_push($keywords, $keyword);
}
}

$variables = [$solventProperty, $nucleusProperty, $dimensionProperty, $probeNameProperty,
$temperatureProperty, $baseFrequencyProperty, $fieldStrengthProperty, $numberOfScansProperty, $pulseSequenceProperty, $spectralWidthProperty, $numberOfPointsProperty, $relaxationTimeProperty, ];

Expand Down

0 comments on commit c2bf8c6

Please sign in to comment.