Metadata-Version: 2.1
Name: medcat
Version: 0.2.9.9
Summary: Concept annotation tool for Electronic Health Records
Home-page: https://github.com/CogStack/MedCAT
Author: w-is-h
Author-email: w.kraljevic@gmail.com
License: UNKNOWN
Description: # Medical  <img src="https://github.com/CogStack/MedCAT/blob/master/media/cat-logo.png" width=45> oncept Annotation Tool
        
        A simple tool for concept annotation from UMLS/SNOMED or any other source. Paper on [arXiv](https://arxiv.org/abs/1912.10166). 
        
        ## Demo
        A demo application is available at [MedCAT](https://medcat.rosalind.kcl.ac.uk). Please note that this was trained on MedMentions
        and contains a very small portion of UMLS (<1%). 
        
        
        ### Install using PIP
        1. Install MedCAT 
        
        `pip install --upgrade medcat`
        
        2. Install the scispacy models
        
        `pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.2.3/en_core_sci_md-0.2.3.tar.gz`
        
        3. Downlad the Vocabulary and CDB from the Models section bellow
        
        4. How to use:
        ```python
        from medcat.cat import CAT
        from medcat.utils.vocab import Vocab
        from medcat.cdb import CDB 
        
        vocab = Vocab()
        # Load the vocab model you downloaded
        vocab.load_dict('<path to the vocab file>')
        
        # Load the cdb model you downloaded
        cdb = CDB()
        cdb.load_dict('<path to the cdb file>') 
        
        # create cat
        cat = CAT(cdb=cdb, vocab=vocab)
        cat.train = False
        
        # Test it
        doc = "My simple document with kidney failure"
        doc_spacy = cat(doc)
        # Entities are in
        doc_spacy._.ents
        # Or to get a json
        doc_json = cat.get_json(doc)
        
        # To have a look at the results:
        from spacy import displacy
        # Note that this will not show all entites, but only the longest ones
        displacy.serve(doc_spacy, style='ent')
        
        # To train - unsupervised, set the train flag to True and run
        #documents through MedCAT
        cat.train = True
        
        # To run cat on a large number of documents, this will
        #also run trainnig as the flag is set to True.
        data = [(<doc_id>, <text>), (<doc_id>, <text>), ...]
        docs = cat.multi_processing(data)
        
        # To explicitly run trainnig you can do
        f = open("<some file with a lot of medical text>", 'r')
        # If you want fine tune set it to True, old training will be preserved
        cat.run_training(f, fine_tune=True)
        ```
        
        
        ### Building a new Concept Database
        
        ```python
        from medcat.cat import CAT
        from medcat.utils.vocab import Vocab
        from medcat.cdb import CDB 
        
        vocab = Vocab()
        # Load the vocab model you downloaded
        vocab.load_dict('<path to the vocab file>')
        
        # If you have an existing CDB
        cdb = CDB()
        cdb.load_dict('<path to the cdb file>') 
        
        # You can now add concepts from a CSV file, examples of the files can be found in ./examples
        preparator = PrepareCDB(vocab=vocab)
        csv_paths = ['<path to your csv_file>', '<another one>', ...] 
        # e.g.
        csv_paths = ['./examples/simple_cdb.csv']
        cdb = preparator.prepare_csvs(csv_paths)
        
        # Save the new CDB for later
        cdb.save_dict("<path to a file where it will be saved>")
        # Done
        ```
        
        ## If building from source, the requirements are
        `python >= 3.5`
        
        All the rest can be instaled using `pip` from the requirements.txt file, by running:
        
        `pip install -r requirements.txt`
        
        
        ## Results
        
        | Dataset | SoftF1 | Description |
        | --- | :---: | --- |
        | MedMentions | 0.84 | The whole MedMentions dataset without any modifications or supervised training |
        | MedMentions | 0.828 | MedMentions only for concepts that require disambiguation, or names that map to more CUIs |
        | MedMentions | 0.97 | Medmentions filterd by TUI to only concepts that are a disease |
        
        
        ## Models
        A basic trained model is made public for the vocabulary and CDB. It is trained for the ~ 35K concepts available in `MedMentions`. It is quite limited
        so the performance might not be the best.
        
        Vocabulary [Download](https://s3-eu-west-1.amazonaws.com/zkcl/vocab.dat) - Built from MedMentions
        
        CDB [Download](https://s3-eu-west-1.amazonaws.com/zkcl/cdb-medmen.dat) - Built from MedMentions
        
        
        (Note: This is was compiled from MedMentions and does not have any data from [NLM](https://www.nlm.nih.gov/research/umls/) as
        that data is not publicaly available.)
        
        
        ## Acknowledgement
        Entity extraction was trained on [MedMentions](https://github.com/chanzuckerberg/MedMentions) In total it has ~ 35K entites from UMLS
        
        The dictionary was compiled from [Wiktionary](https://en.wiktionary.org/wiki/Wiktionary:Main_Page) In total ~ 800K unique words `For now NOT made publicaly available`
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
