Merge pull request #232 from RobokopU24/binding-predicate-update

Modified predicates affected by biolink:binds
RobokopU24 · Jul 19, 2024 · 1f01b43 · 1f01b43
2 parents ec6b7d8 + 734cc6e
commit 1f01b43
Show file tree

Hide file tree

Showing 4 changed files with 26 additions and 26 deletions.
diff --git a/Common/predicates.py b/Common/predicates.py
@@ -8,43 +8,43 @@
     "allosteric_antagonist": f"{DGIDB}:antagonist",
     "allosteric_modulator": f"{DGIDB}:modulator",
     "antagonist": f"{DGIDB}:antagonist",
-    "antibody": f"{DGIDB}:binder",
-    "antibody_binding": f"{DGIDB}:binder",
+    "antibody": f"RO:0002436",
+    "antibody_binding": f"RO:0002436",
     "antisense_inhibitor": f"{DGIDB}:inhibitor",
-    "app_ki": f"RO:0002434",
-    "app_km": f"RO:0002434",
-    "binding_agent": f"{DGIDB}:binder",
+    "app_ki": f"RO:0002434",  # apparent Ki?  if so change to RO:0002436
+    "app_km": f"RO:0002434",  # apperent Km?  if so change to RO:0002436
+    "binding_agent": f"RO:0002436",
     "blocker": f"{DGIDB}:blocker",
     "channel_blocker": f"{DGIDB}:channel_blocker",
     "ec50": f"{DGIDB}:agonist",
-    "ed50": f"RO:0002434",
+    "ed50": f"RO:0002434",  # Effective Dose. Where does this predicate come from? CB (2024_07): "it makes no sense to have an ed50 between a chemical and a gene/protein"
     "gating_inhibitor": f"{DGIDB}:gating_inhibitor",
-    "gi50": f"RO:0002434",
+    "gi50": f"{DGIDB}:Inhibitor",  # Growth Inhibitor
     "ic50": f"{DGIDB}:inhibitor",
     "inhibitor": f"{DGIDB}:inhibitor",
-    "interacts_with": f"RO:0002434",
+    "interacts_with": f"RO:0002434",  # Where does this predicate come from? Possiblely needs to be modified to RO:0002436
     "inverse_agonist": f"{DGIDB}:inverse_agonist",
-    "ka": f"RO:0002434",
-    "kact": f"RO:0002434",
-    "kb": f"{DGIDB}:binder",
-    "kd": f"{DGIDB}:binder",
-    "kd1": f"RO:0002434",
+    "ka": f"RO:0002436",
+    "kact": f"RO:0002436",  # is this a miss type of kcat?
+    "kb": f"RO:0002436",  # {DGIDB}:binder maps to biolink:binds which is depreciated
+    "kd": f"RO:0002436",
+    "kd1": f"RO:0002436",  # RO:0002434 maps to biolink:related_to
     "ki": f"{DGIDB}:inhibitor",
-    "km": f"RO:0002434",
-    "ks": f"RO:0002434",
+    "km": f"RO:0002436",
+    "ks": f"RO:0002436",
     "modulator": f"{DGIDB}:modulator",
-    "mic": f"RO:0002434",
-    "mpc": f"RO:0002434",
+    "mic": f"RO:0002434",  # What is this referring to?
+    "mpc": f"RO:0002434",  # What is this referring to?
     "negative_modulator": f"{CHEMBL_MECHANISM}:negative_modulator",
     "negative_allosteric_modulator": f"{CHEMBL_MECHANISM}:negative_modulator",
     "opener": f"{CHEMBL_MECHANISM}:opener",
     "other": f"{DGIDB}:other",
     "partial_agonist": f"{DGIDB}:partial_agonist",
-    "pa2": f"RO:0002434",
+    "pa2": f"RO:0002434",  # What is this referring to?
     "pharmacological_chaperone": f"{DGIDB}:chaperone",
     "positive_allosteric_modulator": f"{CHEMBL_MECHANISM}:positive_modulator",
     "positive_modulator": f"{CHEMBL_MECHANISM}:positive_modulator",
     "releasing_agent": f"{CHEMBL_MECHANISM}:releasing_agent",
     "substrate": f"{CHEMBL_MECHANISM}:substrate",
-    "xc50": f"RO:0002434"
+    "xc50": f"RO:0002436"  # This is related to ec50 and ic50 both of which describe binding events
 }
diff --git a/parsers/BINDING/src/loadBINDINGDB.py b/parsers/BINDING/src/loadBINDINGDB.py
@@ -52,7 +52,7 @@ class BINDINGDBLoader(SourceDataLoader):
     source_data_url = "https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes"
     license = "All data and download files in bindingDB are freely available under a 'Creative Commons BY 3.0' license.'"
     attribution = 'https://www.bindingdb.org/rwd/bind/info.jsp'
-    parsing_version = '1.5'
+    parsing_version = '1.6'
 
     def __init__(self, test_mode: bool = False, source_data_dir: str = None):
         """
@@ -66,12 +66,12 @@ def __init__(self, test_mode: bool = False, source_data_dir: str = None):
         self.affinity_threshold = LOG_SCALE_AFFINITY_THRESHOLD
 
         self.measure_to_predicate = {
-            "pKi": "biolink:binds",
+            "pKi": "{DGIDB}:inhibitor", #inhibition constant
             "pIC50": "CTD:decreases_activity_of",
-            "pKd": "biolink:binds",
+            "pKd": "RO:0002436",
             "pEC50": "CTD:increases_activity_of",
-            "k_on": "biolink:binds",
-            "k_off": "biolink:binds"
+            "k_on": "RO:0002436",
+            "k_off": "RO:0002436"
         }
 
         self.bindingdb_version = None

diff --git a/parsers/drugcentral/src/loaddrugcentral.py b/parsers/drugcentral/src/loaddrugcentral.py
@@ -22,7 +22,7 @@ class DrugCentralLoader(SourceDataLoader):
     source_data_url = "https://drugcentral.org/download"
     license = "https://drugcentral.org/privacy"
     attribution = "https://drugcentral.org/about"
-    parsing_version: str = '1.4'
+    parsing_version: str = '1.5'
 
     omop_relationmap = {'off-label use': 'RO:0002606',  # is substance that treats
                         'reduce risk': 'RO:0002606',  # is substance that treats

diff --git a/parsers/gtopdb/src/loadGtoPdb.py b/parsers/gtopdb/src/loadGtoPdb.py
@@ -57,7 +57,7 @@ class GtoPdbLoader(SourceDataLoader):
     source_data_url = "http://www.guidetopharmacology.org/"
     license = "https://www.guidetopharmacology.org/about.jsp#license"
     attribution = "https://www.guidetopharmacology.org/citing.jsp"
-    parsing_version: str = '1.3'
+    parsing_version: str = '1.4'
 
     def __init__(self, test_mode: bool = False, source_data_dir: str = None):
         """