microbex 0.0.3

a rule-based clinical concept extraction tool to capture microorganisms and estimate infection status on semi-structured microbiology culture reports.

MicrobEx (Microbiology Concept Extractor):

This code was developed to provide an open-source python package to extract clinical concepts from free-text semi-structured microbiology reports. The two primary outputs for this package are (1) an binary estimation of patient bacterial infection status and (2) a list of all clinically relevant microorganisms found in the report. These outputs were validated on two independent datasets and achieved f-1 scores over 0.95 on both outputs when compared to expert review. Full details on background, algorithm, and validation results can be seen at our paper here: (currently being written, will update once submitted to archive).

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✨ package

Requirements

* python >=3.6.8
* pandas >=0.25.0

Install

pip install microbex

Usage

instantiation:

def init(self, data: pd.core.frame.DataFrame, ###check if this requirement works. can work on this late. text_col: str, #previously text_col_main culture_id_col: str, #previously culture_id_main visit_id_col: str, #previously visit_id_main ):

the microbex class instantiation takes in a pandas dataframe with 3 expected columns (colnames are provided as kwargs):

• parsed_note (kwarg: text_col):
  • microbiology report txt in either a raw or (**perferable) chopped up into components (eg gram stain/growth report/ab susceptability)
• culture_id (kwarg: culture_id_col):
  • a primary key tied to a given sample/specimen + microbiological exam order.
  • Often a microbiology order can be tied to numerous components (eg gram stain/growth report/ ab susceptability). additionally these can be appended to same report or added as a new report tied to same sample + order. all of these tied to a sample+order should share same culture_id
• visit_id (kwarg: visit_id_col):
  • primary key for patient's visit/encounter
  • can be 1-many:1 to culture_id or 1:1 (in which case can specify as culture_id)
  • in some datasets a patient may have multiple cultures performed in a visit/encounter.

Inline:

import microbex as me
d={'parsed_note': 'No Salmonella, Shigella, Campylobacter, Aeromonas or Plesiomonas isolated.', 'culture_id': 1, 'visit_id': 1}
df=pd.DataFrame(data=d, index=[1])

obj1= me.Microbex(df,
              text_col='parsed_note',
              culture_id_col='culture_id',
              visit_id_col='visit_id')

## see microbex.annotate() docstring for description of kwargs
obj1.annotate(staph_neg_correction=False, 
              specimen_col=None,
              review_suggestions=False,
              likelyneg_block_skip=False
             )

print(obj1.annotated_data.head())

obj1.annotated_data.to_pickle("<designated_save_path>'.pkl")
#note: while annotated_data can be saved as a csv, there are some columns which are made of lists in each cell. the formatting of these can sometimes not interpreted correctly.
## pkl files preserve dtype and resolve this issue. 

Run tests

commandline

• this test compares a freshly annotated sample_dataset with an imported pre-annotated expected version.

cd microbex
pytest -v

Author

👤 Garrett Eickelberg

🤝 Contributing

Contributions, issues and feature requests are welcome!
Feel free to check issues page. You can also take a look at the contributing guide

Show your support

Give a ⭐️ if this project helped you!

Credits

Markdown Readme Generator

📝 License

This project is MIT licensed.

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