cell

Cell and Cell Line Lexicon

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

1. Medical Subject Headings (MeSH) (children of mesh:D002477)
2. Experimental Factor Ontology (EFO) (children of efo:0000324)
3. Cellosaurus
4. Cancer Cell Line Encyclopedia (CCLE)
5. DepMap
6. BRENDA Tissue Ontology (BTO)
7. Cell Ontology (CL)
8. Cell Line Ontology (CLO)

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 = "cell"
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("HeLA")

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

run_app(URL)