Advancing Semantic Similarity Analysis of Phenotypic Data Stored in GA4GH Standards and Beyond

Documentation: https://cnag-biomedical-informatics.github.io/pheno-ranker-ui

Web APP Playground: https://pheno-ranker.cnag.eu

• User: pheno
• Password: ranker

CLI Source Code: https://github.com/cnag-biomedical-informatics/pheno-ranker

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pheno-ranker-ui is a web-interface for the CPAN's module Pheno::Ranker which is a tool designed for performing semantic similarity analysis on phenotypic data structured in JSON format, such as Beacon v2 Models or Phenopackets v2.

Getting Started

General pre-requisite:

• Ideally a unix (GNU/Linux, MacOS) based distribution. Windows with WSL (Windows Subsystem for Linux) enabled or Docker Deskop should work as well - not tested

• Docker and Docker compose installed

Quick Start

no SSL and user authentication 0. git clone this repo and then navigate into the folder pheno-ranker-ui

1. rename the file example.env to .env and fill in the variables
2. Run docker compose up -d
3. Open your browser and go to http://localhost:3838

For self-hosters:

SSL and keycloak-based user authentication

pheno-ranker is designed to be run as a collection of microservices. Please consult dev_docs/how_to_self_host_w_keycloak_login_enabled.md how to prepare your environment and run the services.

CITATION

The author requests that any published work that utilizes pheno-ranker-UI includes a cite to the the following reference:

Ivo C. et al., (2024). Advancing Semantic Similarity Analysis of Phenotypic Data Stored in GA4GH Standards and Beyond. Submitted. [Software]. Available from https://github.com/cnag-biomedical-informatics/pheno-ranker

AUTHOR

Written by Ivo Christopher Leist, PhD student at CNAG https://www.cnag.eu.

COPYRIGHT AND LICENSE

Copyright (C) 2023-2024, Ivo Christopher Leist - CNAG.

GPLv3 - GNU General Public License v3.0