fix: parse through NCBITaxon ancestors

[joyceyan]

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
  },

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.41%. Comparing base (d27fe21) to head (4656b5d).

Additional details and impacted files

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  Coverage   89.41%   89.41%           
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  Files          19       19           
  Lines        1361     1361           
  Branches      125      125           
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  Hits         1217     1217           
  Misses        124      124           
  Partials       20       20           

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