validation system to confirm names of IDs

validation_identifiers/api_access.py

@@ -0,0 +1,143 @@
+#Import libraries
+import requests
+
+def write_output_file (file, graph_id, node_id, original_name, preferred_name):
+    """
+    write outputfile
+    """
+    file.writerow({'graph_id': graph_id, #graph id
+                     'node_id': node_id, # node identifier
+                     'original_node_name': original_name, #original node name
+                     "preferred_node_name":preferred_name}) #prederred node name
+
+
+def access_MESH_API(node_id): 
+    """
+    Return preferred name of MESH identifiers
+    """
+
+    session = requests.Session()
+    node_id = node_id.strip("MESH:")
+
+    api_access = f"https://id.nlm.nih.gov/mesh/lookup/details?descriptor={node_id}"
+    #print(api_access)
+
+    with session.get(api_access) as res:
+
+        res = res.json()
+        preferred_name =  [term["label"] for term in res["terms"]if term["preferred"] == True] 
+
+
+        return (preferred_name[0])
+
+def access_GO_API(node_id): 
+    """
+    Return preferred name of GO identifiers
+    """
+    session = requests.Session()
+    api_access = f"http://api.geneontology.org/api/ontology/term/{node_id}"
+    #print(api_access)
+
+    with session.get(api_access) as res:
+        res = res.json()
+        preferred_name = res["label"]
+
+        return preferred_name
+
+def access_UniProt_API(node_id): 
+    """
+    Return preferred name of UniProt identifiers
+    """
+    session = requests.Session()
+    node_id = node_id.strip("UniProt:")
+
+    try: 
+        api_access = f"https://www.ebi.ac.uk/proteins/api/proteins/P{node_id}"
+        #print(api_access)
+
+        with session.get(api_access) as res:
+            res = res.json()
+
+            try: 
+                preferred_name = res["protein"]["recommendedName"]["fullName"]["value"]
+            except: 
+                preferred_name = res["protein"]["recommendedName"]["shortName"]["value"]
+
+            return preferred_name
+    except:
+        api_access = f"https://www.ebi.ac.uk/proteins/api/proteins/{node_id}"
+        #print(api_access)
+        with session.get(api_access) as res:
+            res = res.json()
+
+            try: 
+                preferred_name = res["protein"]["recommendedName"]["fullName"]["value"]
+            except: 
+                preferred_name = res["protein"]["recommendedName"]["shortName"]["value"]
+
+            return preferred_name
+
+def access_nodenormalizer_API(node_id): 
+    """
+   Return preferred name of HP,NCBITaxon, UBERON,REACT, PR identifiers
+    """
+    session = requests.Session()
+    prefix = node_id.split(":")[0]
+    _id = node_id.split(":")[1]
+    api_access = f"https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie={prefix}%3A{_id}&conflate=true"
+    #print(api_access)
+
+    with requests.get(api_access) as res:
+        res = res.json()
+        preferred_name = res[node_id]["id"]["label"]
+
+        return preferred_name
+
+def access_mychem_API(node_id):
+    """
+    Return preferred name of CHEBI
+    """
+    session = requests.Session()
+    api_access = f"http://mychem.info/v1/chem/{node_id}"
+    #print(api_access)
+
+    with requests.get(api_access) as res:
+        res = res.json()
+        try:
+            preferred_name = (res["chebi"]["name"])
+            return preferred_name
+
+        except:
+            preferred_name = (res["aeolus"]["drug_name"])
+            return preferred_name
+
+
+def access_interpro_API(node_id):
+    """
+    Return preferred name of InterPro
+    """
+
+    node_id = node_id.strip("InterPro:IPR")
+    session = requests.Session()
+    api_access = f"https://www.ebi.ac.uk/interpro/api/protein/reviewed/entry/interpro/ipr{node_id}"
+
+    with requests.get(api_access) as res:
+        res = res.json()
+        preferred_name = res["results"][0]["metadata"]["name"]
+
+        return preferred_name
+
+def access_pfam_API(node_id):
+    """
+    Return preferred name of Pfam
+    """
+
+    node_id = node_id.strip("Pfam:")
+    session = requests.Session()
+    api_access = f"https://www.ebi.ac.uk/interpro/api/entry/pfam/pf{node_id}"
+
+    with requests.get(api_access) as res:
+        res = res.json()
+        preferred_name = res["metadata"]["name"]["name"]
+
+        return preferred_name