phenotype

Disease, Phenotype, and Condition Lexicon

This directory contains a coherent, merged lexical index for the following resources:

1. Human Disease Ontology (DOID)
2. MONDO Disease Ontology (MONDO)
3. Human Phenotype Ontology (HPO)
4. Symptom Ontology (SYMP)
5. Medical Subject Headings (MeSH)
6. Experimental Factor Ontology (EFO)

Generating the Lexical Index

The index can be regenerated with:

python generate.py

Using in Python

Use in Python like in the following:

import biolexica
import gilda

INDEX = "phenotype"
URL = f"https://github.com/biopragmatics/biolexica/raw/main/lexica/{INDEX}/terms.tsv.gz"

grounder: gilda.Grounder = biolexica.load_grounder(URL)
scored_matches = grounder.ground("Alzheimer's disease")

Running an API

If you've cloned the repository, you can run:

python web.py

If you have biolexica[web] installed, you can do:

from biolexica.web import run_app

INDEX = "phenotype"
URL = f"https://github.com/biopragmatics/biolexica/raw/main/lexica/{INDEX}/terms.tsv.gz"

run_app(URL)