Interface to WormBase (www.wormbase.org) curation data, including literature management and NLP functions
Project description
WBtools
Interface to WormBase curation database and Text Mining functions
Access WormBase paper corpus information by loading pdf files (converted to txt) and curation info from the WormBase database. The package also exposes text mining functions on papers' fulltext.
Installation
pip install wbtools
Usage example
Get sentences from a WormBase paper
from wbtools.literature.corpus import CorpusManager
paper_id = "000050564"
cm = CorpusManager()
cm.load_from_wb_database(db_name="wb_dbname", db_user="wb_dbuser", db_password="wb_dbpasswd", db_host="wb_dbhost",
paper_ids=[paper_id])
sentences = cm.get_paper(paper_id).get_text_docs(split_sentences=True)
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