Add miRBase groundings to GroundingMapper

indra/preassembler/grounding_mapper/mapper.py

@@ -8,7 +8,7 @@
 from copy import deepcopy
 from indra.statements import Agent
 from indra.databases import uniprot_client, hgnc_client, chebi_client, \
-    mesh_client, go_client
+    mesh_client, go_client, mirbase_client
 from indra.util import read_unicode_csv
 
 logger = logging.getLogger(__name__)
@@ -281,6 +281,7 @@ def standardize_db_refs(db_refs):
         """
         up_id = db_refs.get('UP')
         hgnc_id = db_refs.get('HGNC')
+        mirbase_id = db_refs.get('MIRBASE')
         # If we have a UP ID and no HGNC ID, we try to get a gene name,
         # and if possible, a HGNC ID from that
         if up_id and not hgnc_id:
@@ -289,8 +290,12 @@ def standardize_db_refs(db_refs):
                 hgnc_id = hgnc_client.get_hgnc_id(gene_name)
                 if hgnc_id:
                     db_refs['HGNC'] = hgnc_id
-        # Otherwise, if we don't have a UP ID but have an HGNC ID, we try to
-        # get the UP ID
+        elif mirbase_id and not hgnc_id:
+            hgnc_id = mirbase_client.get_hgnc_id_from_mirbase_id(mirbase_id)
+            if hgnc_id:
+                db_refs['HGNC'] = hgnc_id
+        # Otherwise, if we don't have a UP ID or miRBase ID but have an HGNC
+        # ID, we try to get the UP ID or miRBase ID
         elif hgnc_id:
             # Now get the Uniprot ID for the gene
             mapped_up_id = hgnc_client.get_uniprot_id(hgnc_id)
@@ -314,6 +319,17 @@ def standardize_db_refs(db_refs):
                 else:
                     db_refs['UP'] = mapped_up_id
 
+            mapped_mirbase_id = \
+                mirbase_client.get_mirbase_id_from_hgnc_id(hgnc_id)
+            if mapped_mirbase_id:
+                if mirbase_id and mapped_mirbase_id != mirbase_id:
+                    msg = 'Inconsistent groundings MIRBASE:%s not equal to ' \
+                          'MIRBASE:%s mapped from HGNC:%s, standardizing ' \
+                          'to MIRBASE:%s'
+                    logger.debug(msg, mirbase_id, mapped_mirbase_id,
+                                 hgnc_id, mapped_mirbase_id)
+                db_refs['MIRBASE'] = mapped_mirbase_id
+
         # Now try to improve chemical groundings
         pc_id = db_refs.get('PUBCHEM')
         chebi_id = db_refs.get('CHEBI')
@@ -364,8 +380,8 @@ def standardize_db_refs(db_refs):
         # further conflict to resolve.
         return db_refs
 
-    @staticmethod
-    def standardize_agent_name(agent, standardize_refs=True):
+    @classmethod
+    def standardize_agent_name(cls, agent, standardize_refs=True):
         """Standardize the name of an Agent based on grounding information.
 
         If an agent contains a FamPlex grounding, the FamPlex ID is used as a
@@ -391,7 +407,7 @@ def standardize_agent_name(agent, standardize_refs=True):
             return
 
         if standardize_refs:
-            agent.db_refs = GroundingMapper.standardize_db_refs(agent.db_refs)
+            agent.db_refs = cls.standardize_db_refs(agent.db_refs)
 
         # We next look for prioritized grounding, if missing, we return
         db_ns, db_id = agent.get_grounding()
@@ -405,6 +421,12 @@ def standardize_agent_name(agent, standardize_refs=True):
         # get_grounding returns
         elif db_ns == 'HGNC':
             agent.name = hgnc_client.get_hgnc_name(db_id)
+        elif db_ns == 'MIRBASE':
+            mirbase_id = agent.db_refs['MIRBASE']
+            mirbase_name = \
+                mirbase_client.get_mirbase_name_from_mirbase_id(mirbase_id)
+            if mirbase_name:
+                agent.name = mirbase_name
         elif db_ns == 'UP':
             # Try for the gene name
             gene_name = uniprot_client.get_gene_name(agent.db_refs['UP'],
@@ -426,8 +448,8 @@ def standardize_agent_name(agent, standardize_refs=True):
                 agent.name = go_name
         return
 
-    @staticmethod
-    def rename_agents(stmts):
+    @classmethod
+    def rename_agents(cls, stmts):
         """Return a list of mapped statements with updated agent names.
 
         Creates a new list of statements without modifying the original list.
@@ -448,7 +470,7 @@ def rename_agents(stmts):
         for _, stmt in enumerate(mapped_stmts):
             # Iterate over the agents
             for agent in stmt.agent_list():
-                GroundingMapper.standardize_agent_name(agent, True)
+                cls.standardize_agent_name(agent, True)
         return mapped_stmts
 
 

indra/statements/agent.py

@@ -131,6 +131,9 @@ def get_grounding(self):
             if isinstance(hgnc, list):
                 hgnc = hgnc[0]
             return 'HGNC', str(hgnc)
+        mirbase = self.db_refs.get('MIRBASE')
+        if mirbase:
+            return 'MIRBASE', mirbase
         up = self.db_refs.get('UP')
         if up:
             if isinstance(up, list):

indra/tests/test_groundingmapper.py

@@ -30,6 +30,19 @@ def test_map_standardize_up_hgnc():
     assert st.enz.db_refs['UP'] == st.sub.db_refs['UP']
 
 
+def test_map_standardize_mirbase_hgnc():
+    a1 = Agent('MIRLET7A1', db_refs={'HGNC': '31476'})
+    a2 = Agent('hsa-let-7a-1', db_refs={'MIRBASE': 'MI0000060'})
+    stmt = Phosphorylation(a1, a2) # not real statement
+    mapped_stmts = gm.map_stmts([stmt])
+    assert len(mapped_stmts) == 1
+    st = mapped_stmts[0]
+    assert 'MIRLET7A1' == st.enz.name == st.sub.name
+    assert '31476' == st.enz.db_refs['HGNC'] == st.sub.db_refs['HGNC']
+    assert 'MI0000060' == st.enz.db_refs['MIRBASE'] \
+                       == st.sub.db_refs['MIRBASE']
+
+
 def test_map_standardize_chebi_pc():
     a1 = Agent('X', db_refs={'PUBCHEM': '42611257'})
     a2 = Agent('Y', db_refs={'CHEBI': 'CHEBI:63637'})