pubtatortool 0.6.1

A package for loading and manipulating PubTator files as Python objects.

The PubTator Parsing Tool

A Python package for loading and manipulating PubTator files as Python objects.

Installation

This package is on the Python Package Index. You can install it using pip install pubtatortool.

Usage

For basic word tokenization and simple operations

from pubtatortool import PubTatorCorpus
train_corpus = PubTatorCorpus(['train_corpus_part_1.txt',
                               'train_corpus_part_2.txt'])
dev_corpus = PubTatorCorpus(['dev_corpus.txt'])
test_corpus = PubTatorCorpus(['test_corpus.txt'])

For wordpiece tokenization and full ability to encode and decode text for use with machine learning models

from pubtatortool import PubTatorCorpus
from pubtatortool.tokenization import get_tokenizer
tokenizer = get_tokenizer(tokenization='wordpiece', vocab='bert-base-cased')
train_corpus = PubTatorCorpus(['train_corpus_part_1.txt',
                               'train_corpus_part_2.txt'], tokenizer)
dev_corpus = PubTatorCorpus(['dev_corpus.txt'], tokenizer)
test_corpus = PubTatorCorpus(['test_corpus.txt'], tokenizer)

You can then serialize a corpus using Pickle, iterate over documents using corpus.document_list, and perform various operations on documents regardless of tokenization policy, even if it is lossy, without worrying about mention and text decoupling.

For example, you can create a TSV-formatted file from a PubTator file in 10 lines of code:

from pubtatortool import PubTatorCorpus
from pubtatortool.tokenization import get_tokenizer
tokenizer = get_tokenizer(tokenization='wordpiece', vocab='bert-base-cased')
corpus = PubTatorCorpus(['mycorpus.txt'], tokenizer)
with open('outfile.txt', 'w') as outfile:
    for doc in corpus.document_list:
        for sentence, targets in zip(doc.sentences, doc.sentence_targets()):
            for token, label in zip(sentence, targets):
                print("{tok}\t{lab}".format(tok=token, lab=label),
                      file=outfile)
            print('', file=outfile)