Initial implementation of adding an ontology subtree

mira/dkg/api.py

@@ -13,7 +13,7 @@
 
 from mira.dkg.client import AskemEntity, Entity, Relation
 from mira.dkg.utils import DKG_REFINER_RELS
-from mira.dkg.construct import add_resource_to_dkg
+from mira.dkg.construct import add_resource_to_dkg, extract_ontology_term
 
 __all__ = [
  "api_blueprint",
@@ -360,6 +360,27 @@ def add_relations(
  for relation in relation_list:
  request.app.state.client.add_relation(relation)
 
+ @api_blueprint.post(
+ "/add_ontology_subtree",
+ response_model=None,
+ tags=["relations"],
+ )
+ def add_ontology_subtree(
+ request: Request,
+ curie_to_add: str = Query(..., example="ncbitaxon:9871"),
+ add_subtree: bool = False
+ ):
+ """Given a curie, add the entry it corresponds to from its respective
+ ontology as a node to the DKG.
+ Can enable the `add_subtree` flag to add all subtree entries."""
+ nodes, edges = extract_ontology_term(curie_to_add, add_subtree)
+ entities = [Entity(**node_info) for node_info in nodes]
+ relations = [Relation(**edge_info) for edge_info in edges]
+ for entity in entities:
+ request.app.state.client.add_node(entity)
+ for relation in relations:
+ request.app.state.client.add_relation(relation)
+
 
  @api_blueprint.post(
  "/add_resources",

mira/dkg/construct.py

@@ -35,11 +35,11 @@
 import click
 import pyobo
 import pystow
+import networkx
 from bioontologies import obograph
-from bioontologies.obograph import Xref
 from bioregistry import manager
 from pydantic import BaseModel, Field
-from pyobo.struct import part_of
+from pyobo.struct import part_of, is_a
 from pyobo.sources import ontology_resolver
 from tabulate import tabulate
 from tqdm.auto import tqdm
@@ -54,7 +54,7 @@
 from mira.dkg.physical_constants import get_physical_constant_terms
 from mira.dkg.constants import EDGE_HEADER, NODE_HEADER
 from mira.dkg.utils import PREFIXES
-from mira.dkg.client import Synonym, Xref
+from mira.dkg.models import Synonym, Xref
 from mira.dkg.resources.cso import get_cso_obo
 from mira.dkg.resources.geonames import get_geonames_terms
 from mira.dkg.resources.extract_eiffel_ontology import get_eiffel_ontology_terms
@@ -421,6 +421,109 @@ def add_resource_to_dkg(resource_prefix: str):
  # handle resource names that we don't process
  return [], []
 
+def extract_ontology_term(curie: str, add_subtree: bool = False):
+ """Takes in a curie and extracts the information from the
+ entry in its respective resource ontology to add as a node into the
+ Epidemiology DKG.
+
+ There is an option to extract all the information from the entries
+ under the corresponding entry's subtree in its respective ontology.
+ Relation information is also extracted with this option.
+
+ Parameters
+ ----------
+ curie :
+ The curie for the entry that will be added as a node to the
+ Epidemiology DKG.
+ add_subtree :
+ Whether to add all the nodes and relations under the entry's subtree
+
+ Returns
+ -------
+ nodes : List[dict]
+ A list of node information added to the DKG, where each node is
+ represented as a dictionary.
+ edges : List[dict]
+ A list of edge information added to the DKG, where each edge is
+ represented as a dictionary.
+ """
+
+ nodes, edges = [], []
+ resource_prefix = curie.split(":")[0].lower()
+ if resource_prefix == "ncbitaxon":
+ # place-holder
+ # load ncbitaxon.obo using pyobo
+ # check to see if the obo is cached
+ # load the obo file as a networkx graph using obonet
+ # relabel the node indexes using lowercases
+ # pickle the new graph with relabeled indexes
+ # load the graph
+ # check to see if the graph is pickled and stored
+ graph = networkx.DiGraph()
+
+ node = graph.nodes.get(curie)
+ if not node:
+ return nodes, edges
+ if not add_subtree:
+ nodes.append(
+ {
+ "id": curie.lower(),
+ "name": node["name"],
+ "type": "class",
+ "description": "",
+ "obsolete": False,
+ "synonyms": [
+ Synonym(value=syn.split("\"")[1],
+ type="") for syn in
+ node.get("synonym", [])
+ ],
+ "alts": [],
+ "xrefs": [Xref(id=xref_curie.lower(), type="")
+ for xref_curie in node["xref"]],
+ "properties": {k: v for text in node[
+ "property_value"] for k, v in [text.split(" ")]}
+ }
+ )
+ return nodes, edges
+ else:
+ for node_curie in networkx.ancestors(graph, curie) | {curie}:
+ node_curie = node_curie.lower()
+ node_to_add = graph.nodes[node_curie]
+ nodes.append(
+ {
+ "id": node_curie.lower(),
+ "name": node_to_add["name"],
+ "type": "class",
+ "description": "",
+ "obsolete": False,
+ "synonyms": [
+ Synonym(value=syn.split("\"")[1],
+ type="") for syn in
+ node_to_add.get("synonym", [])
+ ],
+ "alts": [],
+ "xrefs": [Xref(id=xref_curie.lower(), type="")
+ for xref_curie in node_to_add.get("xref", [])],
+ "properties": {k: v for text in node_to_add.get(
+ "property_value", []) for k, v in [text.split(" ")]}
+ }
+ )
+ # Don't add relations where the original curie to add is the source
+ # of an is_a relation. Root nodes won't have an is_a relation.
+ if node_curie == curie or node_to_add["name"] == "root":
+ continue
+ edges.append(
+ {
+ "source_curie": node_curie.lower(),
+ "target_curie": node_to_add["is_a"][0].lower(),
+ "type": is_a.name,
+ "pred": is_a.curie,
+ "source": resource_prefix,
+ "graph": resource_prefix,
+ "version": ""
+ }
+ )
+ return nodes, edges
 
 @click.command()
 @click.option(

mira/dkg/resources/__init__.py

@@ -5,6 +5,7 @@
  "HERE",
  "get_resource_path",
  "SLIMS",
+ "get_ncbitaxon"
 ]
 
 HERE = os.path.dirname(os.path.abspath(__file__))