Grounding for biomedical entities with contextual disambiguation
Project description
Gilda: Grounding Integrating Learned Disambiguation
Gilda is a Python package and REST service that grounds (i.e., finds appropriate identifiers in namespaces for) named entities in biomedical text.
Installation
Gilda is deployed as a web service at http://grounding.indra.bio/ (see Usage instructions below), however, it can also be used locally as a Python package.
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 ~/.data/gilda/<version>
folder during
runtime (see pystow for options to
configure the location of this folder).
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 web service or used programmatically via its Python API. An introduction Jupyter notebook for using Gilda is available at https://github.com/indralab/gilda/blob/master/notebooks/gilda_introduction.ipynb
Use as a Python package
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
which, by default, launches the server at localhost:8001
(for local usage
replace the URL in the examples below with this address).
Below is an example request using curl
:
curl -X POST -H "Content-Type: application/json" -d '{"text": "kras"}' http://grounding.indra.bio/ground
The same request using Python's request package would be as follows:
import requests
requests.post('http://grounding.indra.bio/ground', json={'text': 'kras'})
Run web service with Docker
After cloning the repository locally, you can build and run a Docker image of Gilda using the following commands:
$ docker build -t gilda:latest .
$ docker run -d -p 8001:8001 gilda:latest
Alternatively, you can use docker-compose
to do both the initial build and
run the container based on the docker-compose.yml
configuration:
$ docker-compose up
Funding
The development of Gilda was funded under the DARPA Communicating with Computers program (ARO grant W911NF-15-1-0544).
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