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Development #1006

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merged 2 commits into from
Jan 10, 2024
Merged

Development #1006

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53b0f03
fix: add NMRium info checks
NRayya Jan 10, 2024
c2bf8c6
Merge pull request #1005 from NFDI4Chem/bioschemas
CS76 Jan 10, 2024
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135 changes: 90 additions & 45 deletions app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php
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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);
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Switch case can be used instead of adding multiple else if statements, which makes the code easier to handle. An example of simple php switch case can be found here https://www.w3schools.com/php/php_switch.asp

}
}
}

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, ];

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