Metadata-Version: 2.1
Name: gilda
Version: 0.2.1
Summary: Grounding for biomedical entities with contextual disambiguation
Home-page: https://github.com/indralab/gilda
Author: Benjamin M. Gyori, Harvard Medical School
Author-email: benjamin_gyori@hms.harvard.edu
License: UNKNOWN
Description: # Gilda: Grounding Integrating Learned Disambiguation
        [![License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
        [![Build](https://travis-ci.org/indralab/gilda.svg)](https://travis-ci.org/indralab/gilda)
        [![Documentation](https://readthedocs.org/projects/gilda/badge/?version=latest)](https://gilda.readthedocs.io/en/latest/?badge=latest)
        
        ## Installation
        Gilda is deployed as a web service at http://grounding.indra.bio/ground (see Usage
        instructions below), it only needs to be installed if used locally.
        
        The recommended method to install Gilda is via Github as:
        ```bash
        pip install git+https://github.com/indralab/gilda.git
        ```
        Note that Gilda uses a single large resource file for grounding, which is automatically downloaded
        into the `~/.gilda/<version>` folder during runtime. Given some additional dependencies, the grounding
        resource file can also be regenerated locally by running `python -m gilda.generate_terms`.
        
        ## Usage
        Gilda can either be used as a REST service (recommended) or programmatically via its Python API.
        An introduction Jupyter notebook for using Gilda as a service is available at
        https://github.com/indralab/gilda/blob/master/notebooks/gilda_introduction.ipynb
        
        The REST service accepts POST requests with a JSON header on the /ground endpoint.
        There is a public REST service running on AWS but the service can also be run locally as
        
        ```bash
        python -m gilda.app
        ```
        
        Below is an example request using `curl`:
        
        ```bash
        curl -X POST -H "Content-Type: application/json" -d '{"text": "kras"}' http://localhost:8001/ground
        ```
        
        The same request using Python's request package would be as follows:
        
        ```python
        requests.post('http://localhost:8001/ground', json={'text': 'kras'})
        ```
        
        The above requests can also be used to interact with the public service, by using the
        appropriate URL instead of `localhost:8001`.
        
        As for using Gilda as a Python package, the documentation at
        http://gilda.readthedocs.org provides detailed descriptions of each module
        of Gilda and their usage.
        
        ## Funding
        The development of Gilda is funded under the DARPA Communicating with Computers program (ARO grant W911NF-15-1-0544).
        
Keywords: nlp,biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: terms
Provides-Extra: benchmarks
