pritishaw / gilda

Grounding of biomedical named entities with contextual disambiguation

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), 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 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 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).