{"id":15014116,"url":"https://github.com/nlpatvcu/medacy","last_synced_at":"2025-04-05T05:09:15.083Z","repository":{"id":33362158,"uuid":"150755179","full_name":"NLPatVCU/medaCy","owner":"NLPatVCU","description":":hospital: Medical Text Mining and Information Extraction with spaCy","archived":false,"fork":false,"pushed_at":"2022-11-01T20:05:09.000Z","size":9222,"stargazers_count":434,"open_issues_count":23,"forks_count":91,"subscribers_count":26,"default_branch":"master","last_synced_at":"2025-04-05T05:09:09.716Z","etag":null,"topics":["clinical-text-processing","information-extraction","machine-learning","medical-natural-language-processing","medical-text-mining","metamap","natural-language-processing","spacy"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NLPatVCU.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-09-28T14:48:36.000Z","updated_at":"2025-03-30T20:32:46.000Z","dependencies_parsed_at":"2023-01-15T00:35:26.559Z","dependency_job_id":null,"html_url":"https://github.com/NLPatVCU/medaCy","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NLPatVCU%2FmedaCy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NLPatVCU%2FmedaCy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NLPatVCU%2FmedaCy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NLPatVCU%2FmedaCy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NLPatVCU","download_url":"https://codeload.github.com/NLPatVCU/medaCy/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247289429,"owners_count":20914464,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["clinical-text-processing","information-extraction","machine-learning","medical-natural-language-processing","medical-text-mining","metamap","natural-language-processing","spacy"],"created_at":"2024-09-24T19:45:12.862Z","updated_at":"2025-04-05T05:09:15.058Z","avatar_url":"https://github.com/NLPatVCU.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![spaCy](https://img.shields.io/badge/built%20with-spaCy-09a3d5.svg)](https://spacy.io)\n\n# medaCy\n:hospital: Medical Text Mining and Information Extraction with spaCy :hospital:\n\nMedaCy is a text processing and learning framework built over [spaCy](https://spacy.io/) to support the lightning fast \nprototyping, training, and application of highly predictive medical NLP models. It is designed to streamline researcher \nworkflow by providing utilities for model training, prediction and organization while insuring the replicability of systems.\n\n![alt text](https://nlp.cs.vcu.edu/images/Edit_NanomedicineDatabase.png \"Nanoinformatics\")\n\n# :star2: Features\n- Highly predictive, shared-task dominating out-of-the-box trained models for medical named entity recognition.\n- Customizable pipelines with detailed development instructions and documentation.\n- Allows the designing of replicable NLP systems for reproducing results and encouraging the distribution of models whilst still allowing for privacy.\n- Active community development spearheaded and maintained by [NLP@VCU](https://nlp.cs.vcu.edu/).\n- Detailed [API](https://medacy.readthedocs.io/en/latest/).\n\n## :thought_balloon: Where to ask questions\n\nMedaCy is actively maintained by a team of researchers at Virginia Commonwealth University. The best way to\nreceive immediate responses to any questions is to raise an issue. Make sure to first consult the \n[API](https://medacy.readthedocs.io/en/latest/).  See how to formulate a good issue or feature request in the [Contribution Guide](CONTRIBUTING.md).\n\n## :computer: Installation Instructions\nMedaCy can be installed for general use or for pipeline development / research purposes.\n\n| Application | Run           |\n| ----------- |:-------------:|\n| Prediction and Model Training (stable) | `pip install git+https://github.com/NLPatVCU/medaCy.git` |\n| Prediction and Model Training (latest) | `pip install git+https://github.com/NLPatVCU/medaCy.git@development` |\n| Pipeline Development and Contribution  | [See Contribution Instructions](/CONTRIBUTING.md) |\n\n\n# :books: Power of medaCy\nAfter installing medaCy and [medaCy's clinical model](guide/models/clinical_notes_model.md), simply run:\n\n```python\nfrom medacy.model.model import Model\n\nmodel = Model.load_external('medacy_model_clinical_notes')\nannotation = model.predict(\"The patient was prescribed 1 capsule of Advil for 5 days.\")\nprint(annotation)\n```\nand receive instant predictions:\n```python\n[\n    ('Drug', 40, 45, 'Advil'),\n    ('Dosage', 27, 28, '1'), \n    ('Form', 29, 36, 'capsule'),\n    ('Duration', 46, 56, 'for 5 days')\n]\n```\n\nMedaCy can also be used through its command line interface, documented [here](./guide/command_line_interface.md)\n\nTo explore medaCy's other models or train your own, visit the [examples section](guide).\n\nReference\n=========\n```bibtex\n@ARTICLE {\n    author  = \"Andriy Mulyar, Natassja Lewinski and Bridget McInnes\",\n    title   = \"TAC SRIE 2018: Extracting Systematic Review Information with MedaCy\",\n    journal = \"National Institute of Standards and Technology (NIST) 2018 Systematic Review Information Extraction (SRIE) \u003e Text Analysis Conference\",\n    year    = \"2018\",\n    month   = \"nov\"\n}\n```\n\nLicense\n=======\nThis package is licensed under the GNU General Public License.\n\nAuthors\n=======\nCurrent contributors: Steele Farnsworth, Anna Conte, Gabby Gurdin, Aidan Kierans, Aidan Myers, and Bridget T. McInnes\n\nFormer contributors: Andriy Mulyar, Jorge Vargas, Corey Sutphin, and Bobby Best\n\nAcknowledgments\n===============\n- [VCU Natural Language Processing Lab](https://nlp.cs.vcu.edu/) ![alt text](https://nlp.cs.vcu.edu/images/vcu_head_logo \"VCU\")\n- [Nanoinformatics Vertically Integrated Projects](https://rampages.us/nanoinformatics/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnlpatvcu%2Fmedacy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnlpatvcu%2Fmedacy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnlpatvcu%2Fmedacy/lists"}