TODO.md

TODO

Loading/Formatting

• loaders for stand-off format (BioNLP/brat)
• loader for PubAnnotation
• loader for EuropePMC
• accept CoNLL without offsets
• extend pubmed/pmc fetchers to include BioC API
• fetcher for PubTator Central

Representation

• support discontinuous spans
• support relations (BioC and PubTator)

Usability

• flattening strategies for overlapping entities (eg. for CoNLL output)
• convenience wrappers for directory-wise loading and serialising of standoff+text
• support the same range of sources for all input formats (path, url, file)
• loaders and formatters indicate if the format represents text and/or annotations
• iterator-compatible dump mechanism

Development

• add type hints
• add a test file with non-ASCII characters to verify proper offsets
• test format-specific parameters