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DosageExtractor

Parses and extracts drug dosage

Attributes:

Name Type Description
model str

The name of the model to be used for dosage extraction.
dosage_extractor Language

The Spacy pipeline for dosage extraction.
Source code in miade/dosageextractor.py 
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class DosageExtractor:
    """
    Parses and extracts drug dosage

    Attributes:
        model (str): The name of the model to be used for dosage extraction.
        dosage_extractor (Language): The Spacy pipeline for dosage extraction.
    """

    def __init__(self, model: str = "en_core_med7_lg"):
        self.model = model
        self.dosage_extractor = self._create_drugdoseade_pipeline()

    def _create_drugdoseade_pipeline(self) -> Language:
        """
        Creates a spacy pipeline with given model (default med7)
        and customised pipeline components for dosage extraction

        Returns:
            nlp (spacy.Language): The Spacy pipeline for dosage extraction.
        """
        nlp = spacy.load(self.model)
        nlp.add_pipe("preprocessor", first=True)
        nlp.add_pipe("pattern_matcher", before="ner")
        nlp.add_pipe("entities_refiner", after="ner")

        log.info(f"Loaded drug dosage extractor with model {self.model}")

        return nlp

    def extract(self, text: str, calculate: bool = True) -> Optional[Dosage]:
        """
        Processes a string that contains dosage instructions (excluding drug concept as this is handled by core)

        Args:
            text (str): The string containing dosage instructions.
            calculate (bool): Whether to calculate duration from total and daily dose, if given.

        Returns:
            The dosage object with parsed dosages in CDA format.
        """
        doc = self.dosage_extractor(text)

        log.debug(f"NER results: {[(e.text, e.label_, e._.total_dose) for e in doc.ents]}")
        log.debug(f"Lookup results: {doc._.results}")

        dosage = Dosage.from_doc(doc=doc, calculate=calculate)

        if all(v is None for v in [dosage.dose, dosage.frequency, dosage.route, dosage.duration]):
            return None

        return dosage

    def __call__(self, text: str, calculate: bool = True):
        return self.extract(text, calculate)

extract(text, calculate=True)

Processes a string that contains dosage instructions (excluding drug concept as this is handled by core)

Parameters:

Name Type Description Default
text str

The string containing dosage instructions.

 required
calculate bool

Whether to calculate duration from total and daily dose, if given.

 True

Returns:

Type Description
Optional[Dosage]

The dosage object with parsed dosages in CDA format.
Source code in miade/dosageextractor.py 
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def extract(self, text: str, calculate: bool = True) -> Optional[Dosage]:
    """
    Processes a string that contains dosage instructions (excluding drug concept as this is handled by core)

    Args:
        text (str): The string containing dosage instructions.
        calculate (bool): Whether to calculate duration from total and daily dose, if given.

    Returns:
        The dosage object with parsed dosages in CDA format.
    """
    doc = self.dosage_extractor(text)

    log.debug(f"NER results: {[(e.text, e.label_, e._.total_dose) for e in doc.ents]}")
    log.debug(f"Lookup results: {doc._.results}")

    dosage = Dosage.from_doc(doc=doc, calculate=calculate)

    if all(v is None for v in [dosage.dose, dosage.frequency, dosage.route, dosage.duration]):
        return None

    return dosage