Merge pull request #222 from Steinbeck-Lab/bioschemas

Bioschemas
Steinbeck-Lab · Aug 30, 2024 · 483e452 · 483e452
2 parents 383314d + 116d952
commit 483e452
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Showing 4 changed files with 105 additions and 16 deletions.
diff --git a/...s/Bioschema/MolecularEntityController.php → .../Bioschemas/MolecularEntityController.php b/...s/Bioschema/MolecularEntityController.php → .../Bioschemas/MolecularEntityController.php
@@ -1,6 +1,6 @@
 <?php
 
-namespace App\Http\Controllers\API\Schemas\Bioschema;
+namespace App\Http\Controllers\API\Schemas\Bioschemas;
 
 use App\Http\Controllers\Controller;
 use App\Models\Molecule;

diff --git a/app/Models/Molecule.php b/app/Models/Molecule.php
@@ -150,22 +150,23 @@ public function related()
     /**
      * Get schema json
      */
-    public function getSchema($type = 'bioschema')
+    public function getSchema($type = 'bioschemas')
     {
-        if ($type == 'bioschema') {
+        if ($type == 'bioschemas') {
             $moleculeSchema = Schema::MolecularEntity();
             $moleculeSchema['@id'] = $this->inchi_key;
             $moleculeSchema['dct:conformsTo'] = $this->prepareConformsTo();
 
             $moleculeSchema->identifier($this->identifier)
                 ->name($this->name)
                 ->url(env('APP_URL').'/compound/'.$this->identifier)
-                ->inChI($this->inchi)
-                ->inChIKey($this->inchi_key)
+                ->inChI($this->standard_inchi)
+                ->inChIKey($this->standard_inchi_key)
                 ->iupacName($this->iupac_name)
-                ->molecularFormula($this->molecular_formula)
-                ->molecularWeight($this->molecular_weight)
-                ->smiles($this->cannonical_smiles);
+                ->molecularFormula($this->properties->molecular_formula)
+                ->molecularWeight($this->properties->molecular_weight)
+                ->monoisotopicMolecularWeight($this->properties->exact_molecular_weight)
+                ->smiles($this->canonical_smiles);
 
             if ($this->synonyms || $this->cas) {
                 $alternateNames = $this->synonyms ?? [];
@@ -175,7 +176,95 @@ public function getSchema($type = 'bioschema')
                 $moleculeSchema->alternateName($alternateNames);
             }
 
-            return $moleculeSchema;
+            if ($this->organisms) {
+                $organisms = $this->organisms ?? [];
+                $names = []; 
+                foreach($organisms as $organism) {
+                    $name = $organism->name;
+                    array_push($names, $name);
+                }
+                $moleculeSchema->taxonomicRange($names);
+            }
+
+            $additionalPropertysSchemas = [];
+            $moleculeAdditionalPropertys = array(
+                "annotation_level" => "Annotation level"
+            );
+
+            foreach($moleculeAdditionalPropertys as $key => $value) {
+                $propertySchema = Schema::PropertyValue();
+                $propertySchema->name($value)
+                ->value($this->$key);
+                array_push($additionalPropertysSchemas, $propertySchema);
+            }
+
+            $propertyAdditionalPropertys = array(
+                "total_atom_count" => "Total atom count",
+                "aromatic_rings_count" => "Aromatic rings count",
+                "qed_drug_likeliness" => "QED drug likeliness",
+                "formal_charge" => "Formal charge",
+                "contains_sugar" => "Contains sugar",
+                "np_likeness" => "NP likeness",
+                "chemical_class" => "Chemical class",
+                "chemical_sub_class" => "Chemical sub class",
+                "chemical_super_class" => "Chemical super class",
+            );
+
+            foreach($propertyAdditionalPropertys as $key => $value) {
+                $propertySchema = Schema::PropertyValue();
+                $propertySchema->name($value)
+                ->value($this->properties->$key);
+                array_push($additionalPropertysSchemas, $propertySchema);
+            }
+
+            if ($this->geo_locations) {
+                $geo_locations = $this->geo_locations ?? [];
+                $names = []; 
+                foreach($geo_locations as $geo_location) {
+                    $name = $geo_location->name;
+                    array_push($names, $name);
+                }
+                $propertySchema = Schema::PropertyValue();
+                $propertySchema->name("Geographic location")
+                ->value($names);
+                array_push($additionalPropertysSchemas, $propertySchema);
+            }
+
+            $moleculeSchema->additionalProperty($additionalPropertysSchemas);
+
+            $datasetSchema = Schema::Dataset();
+            $catalogs = [];
+            if ($this->collections) {
+                $collections = $this->collections ?? [];
+                foreach($collections as $collection) {
+                    $dataCatalogSchema = Schema::DataCatalog();
+                    $dataCatalogSchema->name("Geographic location")
+                    // ->license($collection->licenses->url)
+                    ->additionalType("collection")
+                    ->description($collection->description)
+                    ->identifier($collection->identifier)
+                    ->url($collection->url)
+                    ->name($collection->title);
+                }
+                array_push($catalogs, $dataCatalogSchema);
+            }
+
+            $datasetSchema->includedInDataCatalog($catalogs)
+            ->about($moleculeSchema);
+
+            $citationsSchemas = [];
+            if ($this->citations) {
+                $citations = $this->citations ?? [];
+                foreach($citations as $citation) {
+                    $citationSchema = Schema::CreativeWork();
+                    $citationSchema->identifier($citation->doi)
+                    ->headline($citation->title)
+                    ->author($citation->authors);
+                    array_push($citationsSchemas, $citationSchema);
+                }
+            }
+            $datasetSchema->citation($citationsSchemas);
+            return $datasetSchema;
         }
     }
 

diff --git a/routes/api.php b/routes/api.php
@@ -4,7 +4,7 @@
 use App\Http\Controllers\API\Auth\RegisterController;
 use App\Http\Controllers\API\Auth\VerificationController;
 use App\Http\Controllers\API\CompoundController;
-use App\Http\Controllers\API\Schemas\Bioschema\MolecularEntityController;
+use App\Http\Controllers\API\Schemas\Bioschemas\MolecularEntityController;
 use App\Http\Controllers\API\SearchController;
 use Illuminate\Support\Facades\Route;
 use Laravel\Fortify\Features;
@@ -54,7 +54,7 @@
 });
 
 Route::prefix('schemas')->group(function () {
-    Route::prefix('bioschema')->group(function () {
+    Route::prefix('bioschemas')->group(function () {
         Route::get('/{id}', [MolecularEntityController::class, 'moleculeSchema']);
     });
 });
@@ -72,7 +72,7 @@
 //     // Schemas
 //     Route::get('/compounds', [CompoundController::class, 'list']);
 //     Route::prefix('schemas')->group(function () {
-//         Route::prefix('bioschema')->group(function () {
+//         Route::prefix('bioschemas')->group(function () {
 //             Route::get('/{id}', [MolecularEntityController::class, 'moleculeSchema']);
 //         });
 //     });

diff --git a/storage/api-docs/api-docs.json b/storage/api-docs/api-docs.json
@@ -252,19 +252,19 @@
                 }
             }
         },
-        "/api/v1/schemas/bioschema/{id}": {
+        "/api/v1/schemas/bioschemas/{id}": {
             "get": {
                 "tags": [
                     "schemas"
                 ],
-                "summary": "Get bioschema schema details by COCONUT id.",
-                "description": "Get bioschema schema details by COCONUT id.",
+                "summary": "Get bioschemas schema details by COCONUT id.",
+                "description": "Get bioschemas schema details by COCONUT id.",
                 "operationId": "moleculeSchema",
                 "parameters": [
                     {
                         "name": "id",
                         "in": "path",
-                        "description": "COCONUT id - bioschema",
+                        "description": "COCONUT id - bioschemas",
                         "required": true,
                         "schema": {
                             "type": "string"