pylitsense

The pylitsense package is an unofficial Python wrapper for the NCBI LitSense API. It allows you to query the LitSense API and get back a list of LitSenseResult objects, which contain the text of relevant sentences and a score of their similarity to your query.

NCBI describes LitSense as follows:

LitSense is a unique search system for making sense of the biomedical literature at the sentence level, providing a unified access to over half a billion statements extracted from PubMed and PubMed Central.

Given a query, LitSense finds the best-matching sentences based on overlapping terms as well as semantic similarity via a cutting-edge neural embedding approach.

For example, given this query:

"Breast cancers with HER2 amplification"

You will receive an array of results, each with a score of how relevant it is to your query, like this:

[
    LitSenseResult(
        text='HER2 amplification/overexpression accounts for aggressive clinical features of HER2 positive breast cancer.', 
        score=0.9443494081497192, 
        annotations=[
            '79|4|gene|2064', 
            '93|13|disease|MESH:D001943', 
            '0|4|gene|2064'
        ],
        pmid=28800870,
        pmcid=None,
        section='abstract'
    ), 
    ...
]

Installation

pip install pylitsense

Usage

from pylitsense.pylitsense import PyLitSense

# Initialize
pls = PyLitSense()

# Query
results = pls.query("your query here")

# Print results
for result in results:
    print(result.text, result.score)

Parameters

• query_str (str): The query string for the API.
• rerank (bool, optional): Whether to rerank the results. Defaults to True. It seems that this refers to reranking using "semantic vectors" (embeddings).
• limit (int, optional): Limit the number of results. Defaults to None (no limit).
• min_score (float, optional): Minimum score threshold for results. Defaults to None (no minimum score).

Limitations

The LitSense API itself has the following limitations:

• Maximum of 100 results per query
• Rate limit of one request per user per second

In addition, this package is:

• Only tested on Python 3.9, 3.10, and 3.11