lvg-norm 1.3.0

Python implementation of LVG Norm (https://lhncbc.nlm.nih.gov/LSG/Projects/lvg/current/docs/userDoc/tools/norm.html)

lvg_norm

Python implementation of LVG Norm (https://lhncbc.nlm.nih.gov/LSG/Projects/lvg/current/docs/userDoc/tools/norm.html).

This package focuses on the norm flow from the NLM Lexical Tools. It bundles the LVG-derived resources needed by the normalizer and exposes both a Python API and a small CLI.

What It Does

Given an input string, lvg_norm produces one or more normalized forms by applying an LVG-inspired pipeline. Two presets are available:

pipeline="medical" (default)

The full LVG-inspired flow, best for free-text English (MeSH/UMLS-style content):

q0 -> g -> rs -> o -> t -> l -> B -> Ct -> q7 -> q8 -> w

In practice, that means it handles things like:

• Unicode folding
• Possessive stripping
• Parenthetic plural cleanup
• Stopword removal
• Lexicon/rule-based uninflection
• Citation-form mapping
• Final token sorting

The implementation is aimed at the norm tool behavior, not the full LVG suite.

pipeline="chemical"

For IUPAC names and small-molecule nomenclature, where punctuation is structural and word order is meaningful. The flow is reduced to:

q0 -> q7 -> q8 -> casefold + whitespace collapse

Genitives, parenthetic-plural removal, punctuation-to-space, stopword stripping, English uninflection/citation lookup, and the final token sort are all skipped. This preserves locants, hyphens, parens, brackets, primes, stereo descriptors, and substitution-position prefixes (N-, 1H-, D-, …). Greek letters are still expanded via the LVG nonStripMap (α → alpha), but they remain glued to their parent name because the punctuation step is skipped. ± is mapped to +/- for the same reason.

Use pipeline="medical" for prose, pipeline="chemical" for chemistry names — the two are not designed to be mixed within a single call. If you can run names through OPSIN first, do that; reach for pipeline="chemical" when you need fuzzy matching on messy strings that OPSIN can't parse.

Install

From PyPI:

pip install lvg-norm

From the repository:

pip install .

For local development with uv:

uv sync --group dev

Python API

The distribution name is lvg-norm, while the Python import package is lvg_norm.

from lvg_norm import NormNormalizer, lvg_normalize

lvg_normalize("β-lactam antibiotics")
# ['antibiotic beta lactam']

normer = NormNormalizer(max_combinations=5)
normer.normalize("HNF1A p.Q125*")
# ['hnf1a p q125', 'hnf1on p q125', 'hnf1um p q125']

# Chemistry preset for IUPAC / small-molecule names
lvg_normalize("(2S,3R)-2,3-dihydro-1H-indole", pipeline="chemical")
# ['(2s,3r)-2,3-dihydro-1h-indole']
lvg_normalize("β-lactam antibiotics", pipeline="chemical")
# ['beta-lactam antibiotics']
lvg_normalize("(±)-tartaric acid", pipeline="chemical")
# ['(+/-)-tartaric acid']

CLI

The package installs a lvg-norm command:

lvg-norm "β-lactam antibiotics"
lvg-norm --file inputs.txt
echo "HNF1A p.Q125*" | lvg-norm

Useful flags:

• --pipeline {medical,chemical} to pick the preset (default: medical)
• --stopwords PATH to provide an extra stopword list
• --no-lvg-stopwords to disable the bundled LVG stopword list
• --max-combinations N to cap variant expansion

Development

uv sync --group dev
pytest
ruff check .
ruff format --check .