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Data harvest #25

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Data harvest #25

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3317320
Fix and simplify data harvesting logic
rfdougherty Jan 3, 2026
1341527
Add shell scripts to manifest
rfdougherty Jan 3, 2026
bd25c58
Update Drugbank and MeSH
rfdougherty Jan 3, 2026
d88c8b9
commit version change
rfdougherty Jan 3, 2026
4f64685
Forgot to add nltk dep
rfdougherty Jan 3, 2026
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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -12,7 +12,7 @@ authors:
repository-code: 'https://github.com/fastdatascience/drug_named_entity_recognition'
url: 'https://fastdatascience.com/drug-named-entity-recognition-python-library/'
license: MIT
version: 2.0.9
version: 2.0.10
date-released: '2024-10-04'
url: 'https://zenodo.org/doi/10.5281/zenodo.10970631'
doi: 10.5281/zenodo.10970631
doi: 10.5281/zenodo.10970631
1 change: 1 addition & 0 deletions MANIFEST.in
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Expand Up @@ -9,6 +9,7 @@ include cross_check_against_common_english_vocab.py
include find_short_drug_names.py
include smiles_example_python.py
include structure_mol_example_python.py
include *.sh
recursive-include harvesting_data_from_source *.py
recursive-include harvesting_data_from_source *.csv
recursive-include src *.bz2
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -405,12 +405,12 @@ MIT License. Copyright (c) 2023 [Fast Data Science](https://fastdatascience.com)

## ✍️ Citing the Drug Named Entity Recognition library

Wood, T.A., Drug Named Entity Recognition [Computer software], Version 2.0.9, accessed at [https://fastdatascience.com/drug-named-entity-recognition-python-library](https://fastdatascience.com/drug-named-entity-recognition-python-library), Fast Data Science Ltd (2024)
Wood, T.A., Drug Named Entity Recognition [Computer software], Version 2.0.10, accessed at [https://fastdatascience.com/drug-named-entity-recognition-python-library](https://fastdatascience.com/drug-named-entity-recognition-python-library), Fast Data Science Ltd (2024)

```
@unpublished{drugnamedentityrecognition,
AUTHOR = {Wood, T.A.},
TITLE = {Drug Named Entity Recognition (Computer software), Version 2.0.9},
TITLE = {Drug Named Entity Recognition (Computer software), Version 2.0.10},
YEAR = {2024},
Note = {To appear},
url = {https://zenodo.org/doi/10.5281/zenodo.10970631},
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62 changes: 0 additions & 62 deletions harvesting_data_from_source/01_drugbank_download_vocabulary.py
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@rfdougherty rfdougherty Jan 3, 2026

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logic subsumed in the shell script.

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62 changes: 0 additions & 62 deletions harvesting_data_from_source/03_nhs_get_drug_data_from_api.py
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logic subsumed in the shell script.

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