Metadata-Version: 2.1
Name: medspacy
Version: 0.1.0.2
Summary: Library for clinical NLP with spaCy.
Home-page: UNKNOWN
Author: medSpaCy
Author-email: medspacy.dev@gmail.com
License: UNKNOWN
Description: [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
        ![Build Status](https://github.com/medspacy/medspacy/workflows/medspacy/badge.svg)
        
        # medspacy
        Library for clinical NLP with spaCy. 
        
        ![alt text](./images/medspacy_logo.png "medSpaCy logo")
        
        **MedSpaCy is currently in beta.**
        
        
        # Overview
        MedSpaCy is a library of tools for performing clinical NLP and text processing tasks with the popular [spaCy](spacy.io) 
        framework. The `medspacy` package brings together a number of other packages, each of which implements specific 
        functionality for common clinical text processing specific to the clinical domain, such as sentence segmentation, 
        contextual analysis and attribute assertion, and section detection.
        
        `medspacy` is modularized so that each component can be used independently. All of `medspacy` is designed to be used 
        as part of a `spacy` processing pipeline. Each of the following modules is available as part of `medspacy`:
        - `medspacy.preprocess`: Destructive preprocessing for modifying clinical text before processing
        - `medspacy.sentence_splitter`: Clinical sentence segmentation
        - `medspacy.ner`: Utilities for extracting concepts from clinical text
        - `medspacy.context`: Implementation of the [ConText](https://www.sciencedirect.com/science/article/pii/S1532046409000744)
        for detecting semantic modifiers and attributes of entities, including negation and uncertainty
        - `medspacy.section_detection`: Clinical section detection and segmentation
        - `medspacy.postprocess`: Flexible framework for modifying and removing extracted entities
        - `medspacy.io`: Utilities for converting processed texts to structured data and interacting with databases
        - `medspacy.visualization`: Utilities for visualizing concepts and relationships extracted from text
        - `SpacyQuickUMLS`: UMLS concept extraction compatible with spacy and medspacy implemented by [QuickUMLS](https://github.com/Georgetown-IR-Lab/QuickUMLS).  More detail on this component, how to use it, how to generate UMLS resources beyond the small UMLS sample can be found in [this notebook](notebooks/11-QuickUMLS_Extraction.ipynb).
        	- NOTE: This component is installed by default on MacOS and Linux but not Windows.  For more defails and Windows installation: [QuickUMLS on Windows](windows_and_quickumls.md)
        
        Future work could include I/O, relations extraction, and pre-trained clinical models.
        
        # Usage
        ## Installation
        You can install `medspacy` using `setup.py`:
        ```bash
        python setup.py install
        ```
        
        Or with pip:
        ```bash
        pip install medspacy
        ```
        
        If you download other models, you can use them by providing the model itself or model name to `medspacy.load(model_name)`:
        ```python
        import spacy; import medspacy
        # Option 1: Load default
        nlp = medspacy.load()
        
        # Option 2: Load from existing model
        nlp = spacy.load("en_core_web_sm", disable={"ner"})
        nlp = medspacy.load(nlp)
        
        # Option 3: Load from model name
        nlp = medspacy.load("en_core_web_sm", disable={"ner"})
        ```
        
        ### Requirements
        The following packages are required and installed when `medspacy` is installed:
        - spaCy 2.3 (spaCy 3 is not currently supported)
        - [pyrush](https://github.com/medspacy/PyRuSH)
            
        ## Basic Usage
        Here is a simple example showing how to implement and visualize a simple rule-based pipeline using `medspacy`:
        ```python
        import medspacy
        from medspacy.ner import TargetRule
        from medspacy.visualization import visualize_ent
        
        # Load medspacy model
        nlp = medspacy.load()
        
        text = """
        Past Medical History:
        1. Atrial fibrillation
        2. Type II Diabetes Mellitus
        
        Assessment and Plan:
        There is no evidence of pneumonia. Continue warfarin for Afib. Follow up for management of type 2 DM.
        """
        
        # Add rules for target concept extraction
        target_matcher = nlp.get_pipe("target_matcher")
        target_rules = [
            TargetRule("atrial fibrillation", "PROBLEM"),
            TargetRule("atrial fibrillation", "PROBLEM", pattern=[{"LOWER": "afib"}]),
            TargetRule("pneumonia", "PROBLEM"),
            TargetRule("Type II Diabetes Mellitus", "PROBLEM", 
                      pattern=[
                          {"LOWER": "type"},
                          {"LOWER": {"IN": ["2", "ii", "two"]}},
                          {"LOWER": {"IN": ["dm", "diabetes"]}},
                          {"LOWER": "mellitus", "OP": "?"}
                      ]),
            TargetRule("warfarin", "MEDICATION")
        ]
        target_matcher.add(target_rules)
        
        doc = nlp(text)
        visualize_ent(doc)
        ```
        
        `Output:`
        ![alt text](./images/simple_text_visualization.png "Example of clinical text processed by medSpaCy")
        
        For more detailed examples and explanations of each component, see the [notebooks](./notebooks) folder.
        
        # Made with medSpaCy
        Here are some links to projects or tutorials which use medSpacy. If you have a project which uses medSpaCy which you'd like to use, let us know!
        - [VA_COVID-19_NLP_BSV](https://github.com/abchapman93/VA_COVID-19_NLP_BSV): An NLP pipeline for identifying positive cases of COVID-19 from clinical text. Deployed as part of the Department of Veterans Affairs response to COVID-19
        - [clinspacy](https://ml4lhs.github.io/clinspacy/index.html): An R wrapper for spaCy, sciSpaCy, and medSpaCy for performing clinical NLP and UMLS linking in R
        - [mimic34md2020_materials](https://github.com/Melbourne-BMDS/mimic34md2020_materials): A crash course in clinical data science from the University of Melbourne. For medSpaCy materials, see `notebooks/nlp-*.ipynb`
        
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