Merge pull request MOZI-AI#14 from noskill/pharmagkb

use ChEBI instead of human readable names
DaddyWesker · May 6, 2020 · c753be1 · c753be1
2 parents f8d2978 + 38026ae
commit c753be1
Showing 1 changed file with 21 additions and 8 deletions.
diff --git a/pharmagkb.py b/pharmagkb.py
@@ -232,19 +232,25 @@ def process_small_molecules(pathway, ns, pathway_id, chem_data, id_map, pharma2c
     tmp = list()
     for smallmolecule in pathway.findall('./bp:SmallMolecule', ns):
         molecule_drug, name = parse_molecule(smallmolecule, ns, chem_data, pharma2chebi)
-        molecule = CMoleculeNode(name)
-        member = CMemberLink(molecule,
-                    CConceptNode(pathway_id))
+        molecule = None
         for db_name in ('ChEBI', 'PubChem', 'DrugBank'):
             if db_name in molecule_drug:
-                name_node = CConceptNode("{0}:{1}".format(db_name, molecule_drug[db_name]))
+                name_node = CMoleculeNode("{0}:{1}".format(db_name, molecule_drug[db_name]))
                 ctx = CContextLink(
                         CConceptNode(pathway_id),
                         CEvaluationLink(
                             CPredicateNode("has_{0}_id".format(db_name.lower())),
-                            CListLink(molecule,
+                            CListLink(CConceptNode(name),
                                     name_node)))
+                if molecule is None:
+                    molecule = name_node
                 tmp.append(ctx)
+
+        if molecule is None:
+            molecule = CConceptNode(name)
+        member = CMemberLink(molecule,
+                    CConceptNode(pathway_id))
+
         tmp.append(member)
         id_map[about(smallmolecule, ns)] = [molecule]
         tmp += generate_locations(smallmolecule, ns, [molecule], pathway_id)
@@ -428,14 +434,18 @@ def parse_control(control, pathway, ns, pathway_id, id_map):
             control_type = control_type_elem.text
         else:
             print("no control type in {0}".format(about(control, ns)))
+    tmp = []
     if controlled and controller and control_type:
-        res = CEvaluationLink(
+        ev = CEvaluationLink(
                     CPredicateNode(control_name_map[control_type]),
                     CListLink(
                         wrap_list(controller),
                         wrap_list(controlled)))
-        result.append(res)
-    id_map[about(control, ns)] = result
+        tmp.append(ev)
+        ctx = CContextLink(CConceptNode(pathway_id),
+                   ev)
+        result.append(ctx)
+    id_map[about(control, ns)] = tmp
     return result
 
 
@@ -578,6 +588,9 @@ def convert_pathway(pathway, chem_data, genes_data, pharma2uniprot, pathway_id,
                  CListLink(CConceptNode(pathway_id),
                            CConceptNode(pathway_name)))
     tmp = [ev_name]
+    tmp.append(CInheritanceLink(
+                  CConceptNode(pathway_id),
+                  CConceptNode('pathway')))
     id_map = dict()
     tmp += process_proteins(pathway, ns, pathway_id, genes_data, pharma2uniprot, id_map)
     tmp += process_small_molecules(pathway, ns, pathway_id, chem_data, id_map, pharma2chebi)