fix: parse through NCBITaxon ancestors (#259)

## Reason for Change

previously, we skipped over parsing through `NCBITaxon` ancestors since
we had no prior use for this. now that we do have a use, we should
actually parse through this so that we understand the ancestor /
descendant terms.

this retains the filter to only go through a subgraph of the `NCBITaxon`
graph that's `NCBITaxon:33208` (Animal) or below.

note that previously, the `ontology-processing` job took 24 mins. with
this change, it will take 2 hrs 5 mins. the generated
`NCBITaxon-ontology.json` also increased in size from 140 MB to 990 MB.

## Testing

download ontology asset and inspect "NCBITaxon:10090" (mus musculus).
previously, this is what we had:
```
  "NCBITaxon:10090": {
    "ancestors": {},
    "label": "Mus musculus",
    "synonyms": [
      "house mouse",
      "mouse"
    ],
    "deprecated": false
  },
```

now, we have:

```
"NCBITaxon:100900": {
    "ancestors": {
      "NCBITaxon:2162899": 1,
      "NCBITaxon:39087": 2,
      "NCBITaxon:337677": 3,
      "NCBITaxon:337687": 4,
      "NCBITaxon:1963758": 5,
      "NCBITaxon:9989": 6,
      "NCBITaxon:314147": 7,
      "NCBITaxon:314146": 8,
      "NCBITaxon:1437010": 9,
      "NCBITaxon:9347": 10,
      "NCBITaxon:32525": 11,
      "NCBITaxon:40674": 12,
      "NCBITaxon:32524": 13,
      "NCBITaxon:32523": 14,
      "NCBITaxon:1338369": 15,
      "NCBITaxon:8287": 16,
      "NCBITaxon:117571": 17,
      "NCBITaxon:117570": 18,
      "NCBITaxon:7776": 19,
      "NCBITaxon:7742": 20,
      "NCBITaxon:89593": 21,
      "NCBITaxon:7711": 22,
      "NCBITaxon:33511": 23,
      "NCBITaxon:33213": 24,
      "NCBITaxon:6072": 25,
      "NCBITaxon:33208": 26,
      "NCBITaxon:33154": 27,
      "NCBITaxon:2759": 28,
      "NCBITaxon:131567": 29,
      "NCBITaxon:1": 30
    },
    "label": "Alexandromys middendorffii",
    "synonyms": [
      "Middendorf's vole"
    ],
    "deprecated": false
  },
```

---------

Co-authored-by: github-actions <[email protected]>

Author: joyceyan

api/python/ontology-assets-version.txt

@@ -1 +1 @@
-016968365dd92ee02154dc95656535c0e26c8eff
+4656b5d9baf5e10c5838ed9813ed94c563560515

ontology-assets/NCBITaxon-ontology-v2023-06-20.json.gz

@@ -245,15 +245,12 @@ def _extract_ontology_term_metadata(
         # Gets ancestors
         ancestors = _get_ancestors(onto_term, allowed_ontologies)
 
-        # Special Case: skip the current term if it is an NCBI Term, but not a descendant of 'NCBITaxon:33208'.
+        # Special Case: skip the current term if it is an NCBI Term, but not a descendant of 'NCBITaxon:33208' (Animal)
         if onto.name == "NCBITaxon" and "NCBITaxon:33208" not in ancestors:
             continue
 
         term_dict[term_id] = dict()
-
-        # only write the ancestors if it's not NCBITaxon, as this saves a lot of disk space and there is
-        # no current use-case for NCBITaxon
-        term_dict[term_id]["ancestors"] = {} if onto.name == "NCBITaxon" else ancestors
+        term_dict[term_id]["ancestors"] = ancestors
 
         if cross_ontology_terms := _extract_cross_ontology_terms(term_id, map_to_cross_ontologies, cross_ontology_map):
             term_dict[term_id]["cross_ontology_terms"] = cross_ontology_terms