pheno-ranker-ui

The web ui (R-Shiny application) for Pheno-Ranker, a tool designed for performing semantic similarity analysis on phenotypic data structured in JSON format, such as Beacon v2 Models or Phenopackets v2

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

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 1 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary

Keywords

beacon-v2 clinical-data data-exploration json phenopackets-v2 r semantic-similarity semantic-similarity-measures shiny

Last synced: 4 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: CNAG-Biomedical-Informatics
License: gpl-3.0
Language: R
Default Branch: main
Homepage:
Size: 19.6 MB

Statistics

Stars: 2
Watchers: 1
Forks: 0
Open Issues: 35
Releases: 0

Topics

beacon-v2 clinical-data data-exploration json phenopackets-v2 r semantic-similarity semantic-similarity-measures shiny

Created about 2 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation Support

README.md

Pheno-Ranker: a toolkit for comparison 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

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 devdocs/howtoselfhostwkeycloakloginenabled.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:

Leist, I.C. et al., (2024). Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond. BMC Bioinformatics. DOI: 10.1186/s12859-024-05993-2

AUTHOR

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

COPYRIGHT AND LICENSE

GPLv3 - GNU General Public License v3.0

Owner

Name: CNAG Biomedical Informatics
Login: CNAG-Biomedical-Informatics
Kind: organization
Location: Spain

Repositories: 1
Profile: https://github.com/CNAG-Biomedical-Informatics

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Pheno-Ranker-UI
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Ivo Christopher
    family-names: Leist
    email: Ivo.leist@cnag.eu
    affiliation: >-
      Centro Nacional de Análisis Genómico (CNAG),
      Universitat de Barcelona (UB)
    orcid: "https://orcid.org/0000-0002-9772-443X"
repository-code: >-
  https://github.com/CNAG-Biomedical-Informatics/pheno-ranker-ui
url: "https://pheno-ranker.cnag.eu"
abstract: >-
  The web ui (R-Shiny application) for Pheno-Ranker, a tool
  designed for performing semantic similarity analysis on
  phenotypic data structured in JSON format, such as Beacon
  v2 Models or Phenopackets v2 and beyond
keywords:
  - json
  - R
  - shiny
  - semantic-similarity
  - data-exploration
  - clinical-data
  - beacon-v2
  - phenopackets-v2
license: GPL-3.0
commit: bbfdd9310cead55516eac7d8163bd1509c5c9c25
version: 0.0.0.9022
date-released: "2024-09-04"
preferred-citation:
  type: unpublished
  authors:
    - given-names: Ivo Christopher
      family-names: Leist
    - given-names: María
      family-names: Rivas-Torrubia
    - given-names: Marta Eugenia
      family-names: Alarcón Riquelme
    - given-names: Guillermo
      family-names: Barturen
    - name: PRECISESADS Clinical Consortium
    - given-names: Ivo Glynne
      family-names: Gut
    - given-names: Manuel
      family-names: Rueda
  title: "Pheno-Ranker: A Toolkit for Comparison of Phenotypic Data Stored in GA4GH Standards and Beyond."
  year: 2024

GitHub Events

Total

Push event: 7
Pull request event: 4
Create event: 6

Last Year

Push event: 7
Pull request event: 4
Create event: 6

Committers

Last synced: over 1 year ago

All Time

Total Commits: 349
Total Committers: 2
Avg Commits per committer: 174.5
Development Distribution Score (DDS): 0.06

Past Year

Commits: 349
Committers: 2
Avg Commits per committer: 174.5
Development Distribution Score (DDS): 0.06

Top Committers

Name	Email	Commits
Ivo Leist	i**t@g**m	328
Ivo	I**t@g**m	21

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 0
Total pull requests: 40
Average time to close issues: N/A
Average time to close pull requests: about 3 hours
Total issue authors: 0
Total pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 40
Average time to close issues: N/A
Average time to close pull requests: about 3 hours
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 0

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Issue Authors

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IvoLeist (72)

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Dependencies

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