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List of functions in the tool collection
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Overview
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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
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.. autofunction:: ner_for_protein_structures.annotation_conversion.bioc_annotations_to_csv.main


Convert annotations in BioC formatted XML to JSON
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.. autofunction:: ner_for_protein_structures.annotation_conversion.bioc_annotations_to_json.main


Fetch fulltext, open access publications in BioC formatted XML using PubMedCentral IDs
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.. autofunction:: ner_for_protein_structures.bioc_xml_tools.get_bioc_xml_from_pmc.main


Run NER predictions on BioC formatted XML files with a trained model - locally
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.. autofunction:: ner_for_protein_structures.ner_inference.run_local_inference_for_ner.main


Run NER predictions on BioC formatted XML files with a trained model - remotely
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.. autofunction:: ner_for_protein_structures.ner_inference.run_hf_inference_for_ner.main


Processing BioC formatted XML files to turn annotations into IOB format for SemEval calculations
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.. autofunction:: ner_for_protein_structures.annotation_conversion.process_bioc_xml_for_performance_stats.main


Processing BioC formatted XML files to turn annotations into IOB format for model training
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.. autofunction:: ner_for_protein_structures.annotation_conversion.process_bioc_xml_for_training.main


Running SemEval to calculate performance statistics
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.. autofunction:: ner_for_protein_structures.sem_eval.run_semeval_analysis.main


Converting EuropePMC/JATS style XML to BioC XML
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.. autofunction:: ner_for_protein_structures.bioc_xml_tools.pmcxml_to_biocxml.main