Add miRTarBase processor

doc/modules/sources/index.rst

@@ -41,6 +41,7 @@ Standard Molecular Pathway Databases
    biogrid/index
    hprd/index
    trrust
+   mirtarbase/index
 
 Custom Knowledge Bases
 ----------------------

doc/modules/sources/mirtarbase/index.rst

@@ -0,0 +1,4 @@
+miRTarBase (:py:mod:`indra.sources.mirtarbase`)
+===============================================
+.. automodule:: indra.sources.mirtarbase
+    :members:

indra/sources/mirtarbase.py

@@ -0,0 +1,135 @@
+# -*- coding: utf-8 -*-
+
+"""An INDRA processor for miRTarBase."""
+
+import logging
+
+import pandas as pd
+
+from indra.databases import hgnc_client, mirbase_client
+from indra.statements import Agent, DecreaseAmount, Evidence
+
+__all__ = [
+    'MirtarbaseProcessor',
+]
+
+logger = logging.getLogger(__name__)
+
+VERSION = '7.0'
+DATA_URL = 'http://mirtarbase.mbc.nctu.edu.tw/' \
+           'cache/download/{}/miRTarBase_MTI.xlsx'.format(VERSION)
+
+
+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
+            write = logger.info
+        else:
+            it = tqdm(df.values, total=len(df.index))
+            write = it.write
+
+        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:
+                write('Issue with row: {row}'.format(row=row))
+                continue
+
+            try:
+                entrez_id = str(int(entrez_id))
+            except ValueError:
+                write('Issue on {mirtarbase_id} with Entrez ID'
+                      '{entrez_id}'.format(mirtarbase_id=mirtarbase_id,
+                                           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()