Merge pull request #29 from TheJacksonLaboratory/add_ancestor_descend…

…ant_tests_on_graph Add methods for testing ancestor/descendant relationships to `OntologyGraph`
ielis · May 26, 2023 · 9bd5080 · 9bd5080
2 parents 01ba82c + 7a961f8
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diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb
@@ -418,6 +418,50 @@
     "    print(f\"{term.identifier.value} - {term.name}\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "c219878d-ae6e-4279-b7b7-993b4e2110dc",
+   "metadata": {},
+   "source": [
+    "## Term relationship tests\n",
+    "\n",
+    "We can check if a term is a *parent* or an *ancestor* of another term using the ontology graph:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "9f02ea88-694b-4d4a-a2cd-8e604d40cf18",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "arachnodactyly = TermId.from_curie('HP:0001166')\n",
+    "abnormality_of_the_hand = TermId.from_curie('HP:0001155')\n",
+    "long_fingers = TermId.from_curie('HP:0100807')\n",
+    "\n",
+    "assert o.graph.is_parent_of(long_fingers, arachnodactyly)\n",
+    "assert o.graph.is_ancestor_of(abnormality_of_the_hand, arachnodactyly)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5efc4a21-b115-4511-80fd-cf02d3afdc46",
+   "metadata": {},
+   "source": [
+    "Similarly, we can check if a term is a *child* or a *descendant* of another term:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "df6344dd-9b72-4d94-88aa-201a9578fc7b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert o.graph.is_child_of(arachnodactyly, long_fingers)\n",
+    "assert o.graph.is_descendant_of(arachnodactyly, long_fingers)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "a94bcf99-fb72-4b83-bc3d-805fd7a30cb6",
@@ -439,7 +483,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 14,
    "id": "3b2f58cc-e008-4153-96b5-1abbd4db9e47",
    "metadata": {},
    "outputs": [],
@@ -487,7 +531,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 15,
    "id": "0e668a54-c146-47be-921e-72ab29ee7d28",
    "metadata": {},
    "outputs": [],
@@ -531,7 +575,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 16,
    "id": "b575229e-1c08-4d02-aaa3-012c9a8c80bd",
    "metadata": {},
    "outputs": [],
@@ -571,7 +615,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 17,
    "id": "654026c8-0e98-45ee-b245-0fa72f8498c3",
    "metadata": {},
    "outputs": [
@@ -616,7 +660,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 18,
    "id": "215903d1-5c3f-4b0f-8fa0-486ef272f5a8",
    "metadata": {},
    "outputs": [
@@ -645,7 +689,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 19,
    "id": "0b1e1b30-e70e-4ec9-89c9-5c702d24ea25",
    "metadata": {},
    "outputs": [
@@ -672,7 +716,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 20,
    "id": "5c4bf517-3e4c-4444-9ada-8bdd9cdcbbbe",
    "metadata": {
     "tags": []
@@ -684,7 +728,7 @@
        "HpoFrequency(identifier=HP:0040283, lower_bound=0.05, upper_bound=0.29)"
       ]
      },
-     "execution_count": 18,
+     "execution_count": 20,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -705,7 +749,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 21,
    "id": "03e7bc93-a58e-422e-a9e1-b04f40956dfb",
    "metadata": {
     "tags": []
@@ -728,7 +772,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 22,
    "id": "7daaab3e-6ead-4230-88d5-b8c080b3730b",
    "metadata": {
     "tags": []
@@ -759,7 +803,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 23,
    "id": "d7bf2281-d8ed-4373-b094-ef7df0c60aa8",
    "metadata": {
     "tags": []
@@ -790,7 +834,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 24,
    "id": "2ddccd09-43d8-448d-8df1-f55ae8eeb658",
    "metadata": {
     "tags": []
@@ -821,7 +865,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 25,
    "id": "0c183a9c-802b-43a1-8bf9-b0e81e5a26f1",
    "metadata": {
     "tags": []
@@ -867,7 +911,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 26,
    "id": "9b5e5216-abde-4b8e-888b-fd12b43ce92e",
    "metadata": {
     "tags": []
@@ -879,7 +923,7 @@
        "'Parsed 12429 diseases'"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 26,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -905,7 +949,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 27,
    "id": "b4303dc6-a653-4720-8a50-0600d655b679",
    "metadata": {
     "tags": []
@@ -933,7 +977,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 28,
    "id": "45035d68-baad-4e69-ab51-5e9c9e0aad86",
    "metadata": {
     "tags": []
@@ -962,7 +1006,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 29,
    "id": "e061b854-2218-4355-8a9f-d6ef9988f588",
    "metadata": {
     "tags": []
@@ -995,7 +1039,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 30,
    "id": "2faad640-4765-49c5-9eba-535018782e5b",
    "metadata": {
     "tags": []
@@ -1046,7 +1090,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 31,
    "id": "fe09955e-9a7d-49dc-9cd7-e7db4b876af5",
    "metadata": {
     "tags": []
@@ -1068,7 +1112,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 32,
    "id": "7ad52558-e398-413f-8d65-0e67d6099d42",
    "metadata": {
     "tags": []
@@ -1083,8 +1127,8 @@
     }
    ],
    "source": [
-    "ic_arachnodactyly = term_id2ic[arachnodactyly.identifier]\n",
-    "print(f'IC of {arachnodactyly.name}: {ic_arachnodactyly} nats')"
+    "ic_arachnodactyly = term_id2ic[arachnodactyly]\n",
+    "print(f'IC of Arachnodactyly: {ic_arachnodactyly} nats')"
    ]
   },
   {
@@ -1137,7 +1181,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 33,
    "id": "deb939b7-847f-4b9f-a823-61ea8e9cbb1a",
    "metadata": {
     "tags": []
@@ -1149,7 +1193,7 @@
        "{'annotated_items_version': '2023-04-05', 'ontology_version': '2023-04-06'}"
       ]
      },
-     "execution_count": 31,
+     "execution_count": 33,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1172,16 +1216,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
-   "id": "4e4afd86-1c26-454e-a627-07b29eb00f01",
-   "metadata": {
-    "tags": []
-   },
+   "execution_count": 34,
+   "id": "6f4dec17-d7df-442a-b803-2aabe86ca1b4",
+   "metadata": {},
    "outputs": [],
    "source": [
     "from hpotk.algorithm.similarity import precalculate_ic_mica_for_hpo_concept_pairs, SimilarityContainer\n",
     "\n",
-    "#sc: SimilarityContainer = precalculate_ic_mica_for_hpo_concept_pairs(term_id2ic, o)"
+    "# sc: SimilarityContainer = precalculate_ic_mica_for_hpo_concept_pairs(term_id2ic, o)"
    ]
   },
   {
@@ -1196,7 +1238,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 35,
    "id": "bea2ed63-59bc-4081-a9e8-d81ec6d06d80",
    "metadata": {
     "tags": []
@@ -1216,7 +1258,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 36,
    "id": "0ade7bf4-7d4c-4f5d-b612-dd3f8d9e2c57",
    "metadata": {
     "tags": []

diff --git a/src/hpotk/graph/_api.py b/src/hpotk/graph/_api.py
@@ -62,6 +62,52 @@ def is_leaf(self, node: NODE) -> bool:
             return False
         return True
 
+    def is_parent_of(self, sub: NODE, obj: NODE) -> bool:
+        """
+        Return `True` if the subject `sub` is a parent of the object `obj`.
+
+        :param sub: a graph node.
+        :param obj: other graph node.
+        :return: `True` if the `sub` is a parent of the `obj`.
+        """
+        return self._run_query(self.get_parents, sub, obj)
+
+    def is_ancestor_of(self, sub: NODE, obj: NODE) -> bool:
+        """
+        Return `True` if the subject `sub` is an ancestor of the object `obj`.
+
+        :param sub: a graph node.
+        :param obj: other graph node.
+        :return: `True` if the `sub` is an ancestor of the `obj`.
+        """
+        return self._run_query(self.get_ancestors, sub, obj)
+
+    def is_child_of(self, sub: NODE, obj: NODE) -> bool:
+        """
+        Return `True` if the `sub` is a child of the `obj`.
+
+        :param sub: a graph node.
+        :param obj: other graph node.
+        :return: `True` if the `sub` is a child of the `obj`.
+        """
+        return self._run_query(self.get_children, sub, obj)
+
+    def is_descendant_of(self, sub: NODE, obj: NODE) -> bool:
+        """
+        Return `True` if the `sub` is a descendant of the `obj`.
+
+        :param sub: a graph node.
+        :param obj: other graph node.
+        :return: `True` if the `sub` is a descendant of the `obj`.
+        """
+        return self._run_query(self.get_descendants, sub, obj)
+
+    @staticmethod
+    def _run_query(func: typing.Callable[[NODE], typing.Iterable[NODE]],
+                   sub: NODE,
+                   obj: NODE) -> bool:
+        return any(sub == term_id for term_id in func(obj))
+
     @abc.abstractmethod
     def __contains__(self, item: NODE) -> bool:
         pass