SmartGraph API

Cite Us

Zahoránszky-Kőhalmi G, Walker B, Miller N, Yang B, Penna DVL, Binder J, et al. SmartGraph API: Programmatic Knowledge Mining in Network- Pharmacology Setting. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-0psx3 This content is a preprint and has not been peer-reviewed.

Local Deployment

The following deployment steps deploy 3 services used by SmartGraph. The services are:

• SmartGraph API
• SmartGraph Neo4j database
• SmartGraph Web Socket server
  • Used by the SmartGraph UI to connect to Neo4J, for more about the WebSocket server see the README within the 'websocket-server' directory.

Prerequisites

• Environment template files

This repository contains environment template files that are necessary for the configure.py script to generate the single .env file for the Docker images. The template environment files can be found in the template_config directory of this repository. Of note, the files in that directory are of demonstrative purposes, and reflect the structure as key-value pairs. Accordingly, they need to be modified in order to use real values, such as URLS, credentials, etc. tailerd to the environment at hand.

• System support for Docker technology.

• Make sure you have the Smartgraph Neo4j knowldgebase located at the location defined in the docker-compose.yml file. By default, this location is: $HOME/docker/smartgraph_volume/neo4j_data .

Note, the SmartGraph Neo4j database for reproducibility purpose is available from the corresponding author of the SmartGraph API paper per request.

Compiling Docker Containers

• Run configuration script:

python3 configure.py path_to_config_template_files

In the command above, replace the "path_to_config_template_files" with the actual path (without trailing slash), e.g.: python3 configure.py template_config . (If using this example,. make sure you modify the content of the files in the template_config directory as necessary.)

• From the root of the repository:

docker-compose -f docker-compose.yml build --parallel

docker-compose -f docker-compose.yml up -d

Documentation via SWAGGER

Visit http://127.0.0.1:5070/docs or use the URL respective to the deployment type (CI/QA/Prod).

License Related Remarks

This repository contains a data subdirectory, all of its content (recursively) falls under the CC BY 4.0 International license as indicated by the data/LICENSE file. All other files and directories fall under the MIT source code license as indicated by the LICENSE file in the root of this repository.

Please observe the data/NOTES and NOTES file (latter in the root of this repository) for additional information in relevant to license issues.