Taxonomic Entity Augmentation (TEA)
TEA provides taxonomic entity augmentation for biological texts. It supports species-name substitution, strain-name scrambling, sentence windowing, token-budget handling, and token-level label materialisation from curated data.
Installation
python -m pip install taxonomic-entity-augmentation
Augmentation example
from bio_tea import TEA
class WhitespaceTokenizer:
def tokenize(self, text, **kwargs):
return text.split()
tea = TEA(WhitespaceTokenizer(), rseed=42)
print(tea.switch("Escherichia coli was measured in culture."))
print(tea.scramble("The strain ATCC 25922 was included.", ["ATCC 25922"], force_diff=True))
Dataset utility commands
The package includes command-line utilities for generated TEA example sets:
bio-tea-inspect --help
bio-tea-sample --help
bio-tea-validate --help
bio-tea-stats --help
bio-tea-qa --help
bio-tea-manifest-compare --help
Utilities that operate on curated TEA source data require TEA_curated_data. Download v1.1 and point TEA to the extracted directory:
wget https://github.com/tznurmin/TEA_curated_data/archive/refs/tags/v1.1.tar.gz -qO - | tar -xz
mv TEA_curated_data-1.1 TEA_curated_data
export TEA_CURATED_ROOT="$PWD/TEA_curated_data"
TEA_CURATED_DATA is also accepted. TEA_curated_data is external to TEA and
separately licensed.
Licence
- Code: Apache License 2.0
- Vendored UniProt organism list: Creative Commons Attribution 4.0, with data attribution
- TEA_curated_data is external and separately licensed
1 maintainer
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