drug-named-entity-recognition 0.1

Finds drug names in a string

Drug named entity recognition

Developed by Fast Data Science, https://fastdatascience.com

Source code at https://github.com/fastdatascience/drug_named_entity_recognition

This is a lightweight Python library for finding drug names in a string.

Please note this library finds only high confidence drugs.

It also only finds the English names of these drugs. Names in other languages are not supported.

It also doesn’t find short code names of drugs, such as abbreviations commonly used in medicine, such as “Ceph” for “Cephradin” - as these are highly ambiguous.

Requirements

Python 3.9 and above

Installation

pip install drug-named-entity-recognition

Usage examples

You must first tokenise your input text using a tokeniser of your choice (NLTK, spaCy, etc).

You pass a list of strings to the find_drugs function.

Example 1

from drug_named_entity_recognition import find_drugs

find_drugs("i bought some Phenoxymethylpenicillin".split(" "))

outputs a list of tuples.

[({'name': 'Phenoxymethylpenicillin',
   'synonyms': {'Penicillin', 'Phenoxymethylpenicillin'},
   'nhs_url': 'https://www.nhs.uk/medicines/phenoxymethylpenicillin',
   'drugbank_id': 'DB00417'},
  3,
  3)]

You can ignore case with:

find_drugs("i bought some phenoxymethylpenicillin".split(" "), is_ignore_case=True)

Data sources

The main data source is from Drugbank, augmented by datasets from the NHS, MeSH, Medline Plus and Wikipedia.

Update the Drugbank dictionary

If you want to update the dictionary, you can use the data dump from Drugbank and replace the file drugbank vocabulary.csv:

• Download the open data dump from https://go.drugbank.com/releases/latest#open-data

Update the Wikipedia dictionary

If you want to update the Wikipedia dictionary, download the dump from:

• https://meta.wikimedia.org/wiki/Data_dump_torrents#English_Wikipedia

and run extract_drug_names_and_synonyms_from_wikipedia_dump.py

Update the MeSH dictionary

If you want to update the dictionary, download the open data dump from https://www.nlm.nih.gov/

and run extract_drug_names_and_synonyms_from_mesh_dump.py