Python

Installation

fenominal can be installed from PyPI using pip.

pip install fenominal

Using fenominal

Fenominal can be run like this:

import json
from fenominal import Fenominal

# Point this to a valid HPO JSON file path on your system
fenominal = Fenominal("path/to/hp.json")
result = fenominal.map_text("Patient presents with severe microcephaly.")
print(json.loads(result))

The output of the command is a list of dictionaries with this structure:

[
  {
    "term_id": "string (ontology term ID — HP:xxxxxxx or MAXO:xxxxxxx, depending on which ontology was loaded)",
    "label": "string (Ontology term name)",
    "span": {
      "start": "integer (Character start index)",
      "end": "integer (Character end index)"
    },
    "is_observed": "boolean (Presence of concept referred to by Ontology term)"
  }
]

This corresponds to the FenominalHit struct of the Rust fenominal library.

MAxO

fenominal defaults to HPO, but can be used for Medical Action Ontology (MAxO) by adding a second argument of simply "maxo".

from fenominal import Fenominal

hpo_miner = Fenominal("/some/path/hp.json")    
maxo_miner = Fenominal("/some/path/maxo.json", "maxo")

hpo_hits = json.loads(hpo_miner.map_text("Intellectual disability, macrocephaly"))
maxo_hits = json.loads(maxo_miner.map_text("cardiac catheterization, lymphadenectomy"))

print(hpo_hits)
print(maxo_hits)