Recent Releases of drug-named-entity-recognition
drug-named-entity-recognition - v2.0.9
Added molecular weight calculation by @abdullahwaqar
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Published by woodthom2 7 months ago
drug-named-entity-recognition - v2.0.8
Add support for SMILES, molecular weight and molecular formulae
Some code copied over from @jaydugad https://github.com/jaydugad/drugnamedentity_recognition/
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Published by woodthom2 11 months ago
drug-named-entity-recognition - 2.0.7
Switch from command line unzip to Python native zip function
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Published by woodthom2 11 months ago
drug-named-entity-recognition - 2.0.6
Add OMOP support, fix character indices issue
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Published by woodthom2 11 months ago
drug-named-entity-recognition - v2.0.5
v2.0.5
Bugfixes for https://github.com/fastdatascience/drugnamedentity_recognition/issues/11 key error
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Published by woodthom2 about 1 year ago
drug-named-entity-recognition - v2.0.3
Fix download script
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Published by woodthom2 over 1 year ago
drug-named-entity-recognition - v2.0.1
Bug fix for drugs with multiple redirects/synonyms
Error extracting this drug Restasis:
match_data = dict(drug_canonical_to_data[m]) | drug_variant_to_variant_data.get(cand_norm, {})
KeyError: 'ciclosporin'
The reason for the error was that "restasis" was in the database as a synonym of "ciclosporin" "ciclosporin" was a synonym of "ciclosporine"
It does a look up for a name to its canonical form and then looks for the data under that canonical form. But in this case there was no data under "ciclosporin", it was all under "ciclosporine" and we were doing a dictionary lookup under a key that did not exist.
I have changed the code that compiles the library database, so that if there is something that redirects as a synonym to another synonym, they are now normalised to be a single redirect. A bit like if you visit a website example.com/page1.html and it redirects you to example.com/page2.html which then sends you to example.com/page3.html - a web designer would need to fix all redirects so that page1 goes straight to page3.
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Published by woodthom2 over 1 year ago
drug-named-entity-recognition - v2.0
A number of bugs have been fixed and the way that data is pulled from source APIs has been streamlined and cleaned up.
Molecular structures
drugs = find_drugs("i bought some Mounjaro".split(" "), is_include_structure=True)
this will return the atomic structure of the drug if that data is available.
Fuzzy matching/spelling tolerance
You can get drugs even with spelling mistakes:
drugs = find_drugs("i bought some Monjaro".split(" "), is_include_structure=True, is_fuzzy_match=True)
Add and remove drugs (customise the drugs list)
Now you can modify the drug recogniser's behaviour if there is a particular drug which it isn't finding:
To reset the drugs dictionary
from drug_named_entity_recognition.drugs_finder import find_drugs, add_custom_drug_synonym, reset_drugs_data, \
add_custom_new_drug, remove_drug_synonym
reset_drugs_data()
To add a synonym
add_custom_drug_synonym("potato", "sertraline")
To add a new drug
add_custom_new_drug("potato", {"name": "solanum tuberosum"})
To remove an existing drug
remove_drug_synonym("sertraline")
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Published by woodthom2 over 1 year ago
drug-named-entity-recognition - v1.0.5
iFull Changelog: https://github.com/fastdatascience/drugnamedentity_recognition/compare/v1.0.3...v1.0.5
Updated NHS and MeSH and Drugbank dictionaries
Fixed Insulin
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Published by woodthom2 over 1 year ago
drug-named-entity-recognition - v1.0.3
Update drug dictionaries Remove duplicates Add feature where generic drug names are returned
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Published by woodthom2 almost 2 years ago
drug-named-entity-recognition - v1.0.2
Update MeSH and Drugbank vocabulary
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Published by woodthom2 over 2 years ago
drug-named-entity-recognition - v1.0.1
Update MeSH and Drugbank dictionaries to 2023 Fix error in splitting named entities Move to Github actions deployment to Pypi with Tox
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Published by woodthom2 over 2 years ago