Merge pull request #1457 from bgyori/pubmed_mesh

Extend MeSH-PubMed and NCBI Taxonomy connection

indra/databases/mesh_client.py

@@ -22,6 +22,8 @@
 mesh_name_to_id_name = {}
 mesh_id_to_tree_numbers = {}
 mesh_supp_to_primary = {}
+mesh_to_ncbitaxon = {}
+ncbitaxon_to_mesh = {}
 
 
 def _load_mesh_file(path, supplementary):
@@ -31,7 +33,15 @@ def _load_mesh_file(path, supplementary):
             mesh_id, mesh_label, mesh_terms_str, mapped_to_str = terms
             mesh_supp_to_primary[mesh_id] = mapped_to_str.split(',')
         else:
-            mesh_id, mesh_label, mesh_terms_str, tree_number_str = terms
+            mesh_id, mesh_label, mesh_terms_str, \
+                tree_number_str, taxon_ids = terms
+            if taxon_ids:
+                taxon_ids = taxon_ids.split('|')
+                for taxon_id in taxon_ids:
+                    # Note that these seem to be one-to-one so
+                    # we don't need to worry about overwriting
+                    ncbitaxon_to_mesh[taxon_id] = mesh_id
+                mesh_to_ncbitaxon[mesh_id] = taxon_ids
             # This is a rare corner case where an entry is outside the
             # tree structure, e.g., D005260, D008297
             if not tree_number_str:

indra/literature/pubmed_client.py

@@ -199,6 +199,31 @@ def get_ids_for_gene(hgnc_name, **kwargs):
     return ids
 
 
+def get_mesh_term_search_str(mesh_id, major_topic=False):
+    """Return a search string for a given MeSH ID.
+
+    Parameters
+    ----------
+    mesh_id : str
+        The MeSH ID of a term to search for, e.g., D009101.
+    major_topic : bool
+        If True, the given MeSH ID is considered as a major topic.
+        Default: False
+    """
+    from indra.databases import mesh_client
+    mesh_name = mesh_client.get_mesh_name(mesh_id)
+    if not mesh_name:
+        logger.error('Could not get MeSH name for ID %s' % mesh_id)
+        return None
+    if mesh_id.startswith('C') and not major_topic:
+        # Get pmids for supplementary concepts as well
+        search_term = f'{mesh_name} [nm]'
+        return search_term
+    suffix = 'majr' if major_topic else 'mh'
+    search_term = '%s [%s]' % (mesh_name, suffix)
+    return search_term
+
+
 def get_ids_for_mesh(mesh_id, major_topic=False, **kwargs):
     """Return PMIDs that are annotated with a given MeSH ID.
 
@@ -214,19 +239,35 @@ def get_ids_for_mesh(mesh_id, major_topic=False, **kwargs):
         Any further PudMed search arguments that are passed to
         get_ids.
     """
-    from indra.databases import mesh_client
-    mesh_name = mesh_client.get_mesh_name(mesh_id)
-    if not mesh_name:
-        logger.error('Could not get MeSH name for ID %s' % mesh_id)
+    search_str = get_mesh_term_search_str(mesh_id, major_topic)
+    ids = get_ids(search_str, use_text_word=False, **kwargs)
+    return ids
+
+
+def get_ids_for_mesh_terms(mesh_terms, major_topics=None, **kwargs):
+    """Return PMIDs that are annotated with a given list of MeSH terms.
+
+    Parameters
+    ----------
+    mesh_terms : list of str
+        A list of MeSH IDs of terms to search for, e.g., ['D009101', 'D009102'].
+    major_topics : Optional[list of bool]
+        A list of booleans indicating whether the corresponding MeSH term
+        should be considered as a major topic. If None, all terms are considered
+        as major topics.
+    **kwargs
+        Any further PudMed search arguments that are passed to
+        get_ids.
+    """
+    if major_topics is None:
+        major_topics = [False] * len(mesh_terms)
+    search_strs = [get_mesh_term_search_str(mesh_id, major_topic)
+                   for mesh_id, major_topic in zip(mesh_terms, major_topics)]
+    search_strs = [s for s in search_strs if s is not None]
+    if not search_strs:
         return []
-    suffix = 'majr' if major_topic else 'mh'
-    search_term = '%s [%s]' % (mesh_name, suffix)
-    ids = get_ids(search_term, use_text_word=False, **kwargs)
-    if mesh_id.startswith('C') and not major_topic:
-        # Get pmids for supplementary concepts as well
-        search_term = '%s [nm]' % mesh_name
-        ids2 = get_ids(search_term, use_text_word=False, **kwargs)
-        ids = list(set(ids) | set(ids2))
+    search_str = ' AND '.join([f'({s})' for s in search_strs])
+    ids = get_ids(search_str, use_text_word=False, **kwargs)
     return ids