Grounding for biomedical entities with contextual disambiguation
Project description
Gilda: Grounding Integrating Learned Disambiguation
Installation
Gilda is deployed as a web service at http://grounding.indra.bio/ (see Usage instructions below), it only needs to be installed if used locally.
The recommended method to install Gilda is through PyPI as
pip install gilda
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 or programmatically via its Python API. An introduction Jupyter notebook for using Gilda as a is available at https://github.com/indralab/gilda/blob/master/notebooks/gilda_introduction.ipynb
Use via Python API
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. A basic usage example is as follows
import gilda
scored_matches = gilda.ground('ER', context='Calcium is released from the ER.')
Use as a web service
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
python -m gilda.app
Below is an example request using curl
:
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:
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
.
Funding
The development of Gilda is funded under the DARPA Communicating with Computers program (ARO grant W911NF-15-1-0544).
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