WIP: First pass at dataframes #338

ontobio/ontol_dataframe.py

@@ -0,0 +1,65 @@
+from ontobio import Ontology
+import pandas as pd
+import numpy as np
+
+def make_ontology_dataframe(onts=None,
+                            ont_map=None,
+                            xref_prefixes=[],
+                            relations=[]):
+    items = []
+
+    # create a map
+    if ont_map is None:
+        ont_map = {}
+        for ont in onts:
+            ont_map[ont.id] = ont
+
+    for ont_id, ont in ont_map.items():
+        for nid in ont.nodes():
+            n = ont.node(nid)
+            tdobj = ont.text_definition(nid)
+            if tdobj is None:
+                td = ''
+            else:
+                td = tdobj.val
+            xrefs = ont.xrefs(nid)
+            isa_parents = ont.parents(nid, relations=['subClassOf'])
+            isa_children = ont.children(nid, relations=['subClassOf'])
+            parents = ont.parents(nid)
+            children = ont.children(nid)
+            syns = [s.val for s in ont.synonyms(nid)]
+            item = {
+                'id': nid,
+                'label': ont.label(nid),
+                'type' : n.get('type'),
+                'prefix': ont.prefix(nid),
+                'ontology': ont_id,
+                'children': children,
+                'children_count': len(children),
+                'parents': parents,
+                'parent_count': len(parents),
+                'isa_parents': isa_parents,
+                'isa_parent_count': len(isa_parents),
+                'isa_children': isa_children,
+                'isa_children_count': len(isa_children),
+                'synonyms': syns,
+                'synonym_count': len(syns),
+                'parent_count': len(parents),
+                'xrefs': xrefs,
+                'xref_count': len(xrefs),
+                'text_definition': td
+
+            }
+            for p in xref_prefixes:
+                p_xrefs = [x for x in xrefs if ont.prefix(x) == p]
+                item['xrefs_'+p] = p_xrefs
+                item['count_xrefs_'+p] = len(p_xrefs)
+            for r in relations:
+                r_parents = ont.parents(relations=[r])
+                rn = ont.label(r, id_if_null=True)
+                item['parents_'+rn] = r_parents
+                item['count_parents_'+rn] = len(r_parents)
+
+            # TODO: xrefs by src
+            items.append(item)
+    return pd.DataFrame(items)

tests/test_ontol_dataframe.py

@@ -0,0 +1,15 @@
+from ontobio.ontol_factory import OntologyFactory
+import ontobio.ontol_dataframe as ofr
+import logging
+
+
+def test_ldef():
+    """
+    Load ontology from JSON
+    """
+    factory = OntologyFactory()
+    print("Creating ont")
+    ont = factory.create('tests/resources/pato.json')
+
+    df = ofr.make_ontology_dataframe([ont])
+    print(df)