added identifiers for swiss lipids

saezlab · Nov 20, 2024 · 9184864 · 9184864
1 parent 9666016
commit 9184864
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Showing 2 changed files with 21 additions and 2 deletions.
diff --git a/omnipath_metabo/data/resource-labels.yaml b/omnipath_metabo/data/resource-labels.yaml
@@ -35,3 +35,9 @@ lipidmaps:
   LIPIDBANK_ID: LipidBank
   PLANTFA_ID: PlantFAdb
   NAME: Name
+swisslipids:
+  CHEBI: ChEBI
+  LIPID MAPS: LIPID MAPS
+  HMDB: HMDB
+  MetaNetX: MetaNetX
+  Synonyms*: Synonym 
diff --git a/omnipath_metabo/schema/_structure.py b/omnipath_metabo/schema/_structure.py
@@ -140,9 +140,17 @@ def __iter__(self):
             }
 
 
-class SwissLipids():
+class SwissLipids(ResourceBase):
     scheme = Structure
     name = 'SwissLipids'
+    id_fields = [
+        'CHEBI',
+        'LIPID MAPS',
+        'HMDB',
+        'MetaNetX',
+        'Synonyms*'
+        ]
+
     def __iter__(self):
         for met in swisslipids.swisslipids_lipids():
             if met['Mass (pH7.3)'] == '':
@@ -160,7 +168,12 @@ def __iter__(self):
                     met['SMILES (pH7.3)'],
                     met['InChI (pH7.3)'],
                 ),
-                'properties':(mass, 0, charge, met['Formula (pH7.3)'])
+                'properties':(mass, 0, charge, met['Formula (pH7.3)']),
+                'identifiers':[
+                    (name, key)
+                    for key in self.id_fields
+                    if (name := met[key])
+                ]
                 }