Add miRTarBase processor

References sorgerlab#255 

This doesn't update the BioPAX processor, but at least it gives a sure-fire set of miRNA-target interactions. Right now it's lacking in the species specificity or the propagation of the experimental conditions. The database even has confidence information associated with each, so this could be used to calculate BELIEF scores.

indra/sources/mirtarbase.py

@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+
+"""An INDRA processor for miRTarBase."""
+
+import pandas as pd
+
+from indra.databases import hgnc_client, mirbase_client
+from indra.statements import Agent, DecreaseAmount, Evidence
+
+__all__ = [
+    'MirtarbaseProcessor',
+]
+
+VERSION = '7.0'
+DATA_URL = f'http://mirtarbase.mbc.nctu.edu.tw/' \
+    f'cache/download/{VERSION}/miRTarBase_MTI.xlsx'
+
+
+class MirtarbaseProcessor:
+    """Extracts INDRA statements from miRTarBase curated interactions.
+
+    Parameters
+    ----------
+    mirtarbase_file : Optional[str]
+        The file path or URL to the miRTarBase file as a Excel document.
+        If not provided, the miRTarBase data is downloaded from the
+        miRTarBase website.
+
+    Attributes
+    ----------
+    statements: list[indra.statements.DecreaseAmount]
+        Extracted INDRA DecreaseAmount statements.
+    """
+
+    def __init__(self, mirtarbase_file=None):
+        df = pd.read_excel(mirtarbase_file or DATA_URL)
+
+        try:
+            from tqdm import tqdm
+        except ImportError:
+            it = df.values
+        else:
+            it = tqdm(df.values, total=len(df.index))
+
+        self.statements = []
+        for row in it:
+            try:
+                (mirtarbase_id, mirna_name, mirna_species, gene_name,
+                 entrez_id, target_species, exp, sup_type, pmid) = row
+            except ValueError:
+                it.write(f'Issue with row: {row}')
+                continue
+
+            try:
+                entrez_id = str(int(entrez_id))
+            except ValueError:
+                it.write(f'Issue on {mirtarbase_id} with'
+                         f' Entrez ID {entrez_id}')
+                continue
+
+            target_db_refs = self._make_target_db_refs(entrez_id)
+            target_agent = Agent(gene_name, db_refs=target_db_refs)
+
+            mirna_db_refs = self._make_mirna_db_refs(mirna_name)
+            mirna_agent = Agent(mirna_name, db_refs=mirna_db_refs)
+
+            # TODO use experimental context information
+            # TODO use species information (corresponding to gene)
+
+            evidence = Evidence(
+                source_api='mirtarbase',
+                source_id=mirtarbase_id,
+                pmid=pmid,
+            )
+
+            statement = DecreaseAmount(
+                mirna_agent,
+                target_agent,
+                evidence=evidence
+            )
+            self.statements.append(statement)
+
+    @staticmethod
+    def _make_target_db_refs(entrez_id):
+        db_refs = {
+            'TEXT': entrez_id,
+        }
+
+        hgnc_id = hgnc_client.get_hgnc_from_entrez(entrez_id)
+        if hgnc_id is not None:
+            db_refs['HGNC'] = hgnc_id
+            up_id = hgnc_client.get_uniprot_id(hgnc_id)
+            if up_id is not None:
+                db_refs['UP'] = up_id
+
+        return db_refs
+
+    @staticmethod
+    def _make_mirna_db_refs(mirna_name):
+        db_refs = {
+            'TEXT': mirna_name,
+        }
+
+        mirbase_id = \
+            mirbase_client.get_mirbase_id_from_mirbase_name(mirna_name)
+        if mirbase_id is not None:
+            db_refs['MIRBASE'] = mirbase_id
+            hgnc_id = mirbase_client.get_hgnc_id_from_mirbase_id(mirbase_id)
+            if hgnc_id is not None:
+                db_refs['HGNC'] = hgnc_id
+
+        return db_refs
+
+
+def main():
+    mp = MirtarbaseProcessor()
+    stmts = mp.statements
+    print(stmts[0])
+
+    import pickle
+    import os
+    path = os.path.join(os.path.expanduser('~'), 'Desktop', 'mirbase_indra.pkl')
+    with open(path, 'wb') as f:
+        pickle.dump(stmts, f)
+
+
+if __name__ == '__main__':
+    main()