--- a +++ b/README.md @@ -0,0 +1,84 @@ +[](https://spacy.io) + +# medaCy +:hospital: Medical Text Mining and Information Extraction with spaCy :hospital: + +MedaCy is a text processing and learning framework built over [spaCy](https://spacy.io/) to support the lightning fast +prototyping, training, and application of highly predictive medical NLP models. It is designed to streamline researcher +workflow by providing utilities for model training, prediction and organization while insuring the replicability of systems. + + + +# :star2: Features +- Highly predictive, shared-task dominating out-of-the-box trained models for medical named entity recognition. +- Customizable pipelines with detailed development instructions and documentation. +- Allows the designing of replicable NLP systems for reproducing results and encouraging the distribution of models whilst still allowing for privacy. +- Active community development spearheaded and maintained by [NLP@VCU](https://nlp.cs.vcu.edu/). +- Detailed [API](https://medacy.readthedocs.io/en/latest/). + +## :thought_balloon: Where to ask questions + +MedaCy is actively maintained by a team of researchers at Virginia Commonwealth University. The best way to +receive immediate responses to any questions is to raise an issue. Make sure to first consult the +[API](https://medacy.readthedocs.io/en/latest/). See how to formulate a good issue or feature request in the [Contribution Guide](CONTRIBUTING.md). + +## :computer: Installation Instructions +MedaCy can be installed for general use or for pipeline development / research purposes. + +| Application | Run | +| ----------- |:-------------:| +| Prediction and Model Training (stable) | `pip install git+https://github.com/NLPatVCU/medaCy.git` | +| Prediction and Model Training (latest) | `pip install git+https://github.com/NLPatVCU/medaCy.git@development` | +| Pipeline Development and Contribution | [See Contribution Instructions](/CONTRIBUTING.md) | + + +# :books: Power of medaCy +After installing medaCy and [medaCy's clinical model](guide/models/clinical_notes_model.md), simply run: + +```python +from medacy.model.model import Model + +model = Model.load_external('medacy_model_clinical_notes') +annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.") +print(annotation) +``` +and receive instant predictions: +```python +[ + ('Drug', 40, 45, 'Advil'), + ('Dosage', 27, 28, '1'), + ('Form', 29, 36, 'capsule'), + ('Duration', 46, 56, 'for 5 days') +] +``` + +MedaCy can also be used through its command line interface, documented [here](./guide/command_line_interface.md) + +To explore medaCy's other models or train your own, visit the [examples section](guide). + +Reference +========= +```bibtex +@ARTICLE { + author = "Andriy Mulyar, Natassja Lewinski and Bridget McInnes", + title = "TAC SRIE 2018: Extracting Systematic Review Information with MedaCy", + journal = "National Institute of Standards and Technology (NIST) 2018 Systematic Review Information Extraction (SRIE) > Text Analysis Conference", + year = "2018", + month = "nov" +} +``` + +License +======= +This package is licensed under the GNU General Public License. + +Authors +======= +Current contributors: Steele Farnsworth, Anna Conte, Gabby Gurdin, Aidan Kierans, Aidan Myers, and Bridget T. McInnes + +Former contributors: Andriy Mulyar, Jorge Vargas, Corey Sutphin, and Bobby Best + +Acknowledgments +=============== +- [VCU Natural Language Processing Lab](https://nlp.cs.vcu.edu/)  +- [Nanoinformatics Vertically Integrated Projects](https://rampages.us/nanoinformatics/)