List of functions in the tool collection

Overview

Below is a collection of the various functions included in this package. Detailed descriptions can be found in their respective sections.

Convert annotations in BioC formatted XML to CSV

Convert annotations in BioC formatted XML to JSON

Fetch fulltext, open access publications in BioC formatted XML using PubMedCentral IDs

Run NER predictions on BioC formatted XML files with a trained model - locally

Run NER predictions on BioC formatted XML files with a trained model - remotely

Processing BioC formatted XML files to turn annotations into IOB format for SemEval calculations

Processing BioC formatted XML files to turn annotations into IOB format for model training

Running SemEval to calculate performance statistics

Converting EuropePMC/JATS style XML to BioC XML