CAS2IOB is a converter of UIMA CAS XMI files exported from the INCEpTION annotation platform into IOB TSV files. In contrast to the internal convertor in INCEpTION, it handles the nested NER tags, NEL tags and components, and saves them into multiple columns of a TSV-file:
TOKEN NE-COARSE NE-FINE NE-FINE-COMP NE-NESTED NEL-WikidataQID
It reads the UIMA CAS XMI files using dkpro-cassis library.
pip install cas2iobImport cas2iob:
import cas2iobConvert ./input.xmi with ./TypeSystem.xml into ./output.tsv:
cas2iob.file('./input.xmi', 'output.tsv')Convert all files in ./input folder with ./TypeSystem.xml into ./output folder:
cas2iob.folder('./input', './output')If ./TypeSystem.xml is located in a different folder, add it to the commands above as the third argument.
If you don't want to include column names in a TSV-file, add the forth argument metadata=False.
% cas2iob --help
Usage: cas2iob [OPTIONS] INPUT_PATH OUTPUT_PATH [TYPESYSTEM_XML] [METADATA]
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * input_path PATH [default: None] [required] │
│ * output_path PATH [default: None] [required] │
│ typesystem_xml [TYPESYSTEM_XML] [default: ./TypeSystem.xml] │
│ metadata [METADATA] [default: True] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy │
│ it or customize the installation. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯Shigapov, Renat. (2023). CAS2IOB: A converter of UIMA CAS XMI files with nested NER tags, NEL tags and components into IOB TSV files. Zenodo. https://doi.org/10.5281/zenodo.8420111