pylitsense 0.1.0

Unofficial Python wrapper for the NCBI LitSense API

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