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edam-browser

Stand-alone, lightweight, and fast JavaScript browser for EDAM and other ontologies

https://github.com/edamontology/edam-browser

Science Score: 67.0%

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 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary

Keywords

edam edam-annotations edam-ontology ontologies ontology-engineering ontology-search ontology-services visualization visualization-javascript-widget
Last synced: 6 months ago · JSON representation ·

Repository

Stand-alone, lightweight, and fast JavaScript browser for EDAM and other ontologies

Basic Info
Statistics
  • Stars: 14
  • Watchers: 10
  • Forks: 24
  • Open Issues: 32
  • Releases: 3
Topics
edam edam-annotations edam-ontology ontologies ontology-engineering ontology-search ontology-services visualization visualization-javascript-widget
Created over 8 years ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License Code of conduct Citation Codemeta

README.md

EDAM stand-alone browser using D3.js

Build Status DOI

The EDAM Browser is a client-side web-based visualization javascript widget. Its goals are to help annotating bioscientific resources and services with EDAM, and to facilitate and foster community contributions to EDAM.

screenshot

Use it ...

... online

Go to https://edamontology.github.io/edam-browser/

... locally

  1. Download/clone the repository

  2. Change to working directory : cd edam-browser

Option 1: using npm
  • npm install
  • npm run dev
Option 2: using yarn
  • yarn install
  • yarn dev

... with a custom ontology

EDAM Browser can render ontology described in JSON following the schema; see here for more information on how to load a custom ontology.

Third-party integration

Demo

A demo showing you how to add the tree visualization and how you can interact with the it programmatically is available at https://edamontology.github.io/edam-browser/demo.html

Dependencies

The EDAM Browser relies on D3.js 4.13.0, JQuery 3.2.1, JQuery UI 1.12.1, Boostrap 3.3.7, and Font Awesome 5.6.0

Owner

  • Name: EDAMontology
  • Login: edamontology
  • Kind: organization
  • Email: edam@elixir-dk.org

EDAMontology is an umbrella organisation for the development and maintenance of the EDAM ontology and related tools and works.

Citation (CITATION.cff) 

cff-version: 1.0.3
message: If you use this software, please cite it as below.
authors:
  - family-names: Brancotte
    given-names: Bryan
    orcid: https://orcid.org/0000-0001-8669-5525
  - family-names: Blanchet
    given-names: Christophe
  - family-names: Ménager
    given-names: Hervé
    orcid: https://orcid.org/0000-0002-7552-1009
title: edam-browser
version: v1.0.1
doi: 10.5281/zenodo.1314288
date-released: 2018-07-18
references:
  - type: article
    authors:
    - family-names: Brancotte
      given-names: Bryan
      orcid: https://orcid.org/0000-0001-8669-5525
    - family-names: Blanchet
      given-names: Christophe
    - family-names: Ménager
      given-names: Hervé
      orcid: https://orcid.org/0000-0002-7552-1009
    title: "A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it"
    year: 2018
    journal: Journal of Open Source Software
    volume: 3
    issue: e86
    doi: 10.21105/joss.00698
    url: https://doi.org/10.21105/joss.00698

CodeMeta (codemeta.json) 

{
  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
  "@type": "Code",
  "author": [
    {
      "@id": "0000-0001-8669-5525",
      "@type": "Person",
      "email": "bryan.brancotte@pasteur.fr",
      "name": "Bryan Brancotte",
      "affiliation": "Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, Paris, France"
    },
    {
      "@id": "",
      "@type": "Person",
      "email": "christophe.blanchet@france-bioinformatique.fr",
      "name": "Christophe Blanchet",
      "affiliation": "French Institute of Bioinformatics, CNRS IFB-Core, Gif-sur-Yvette, France"
    },
    {
      "@id": "0000-0002-7552-1009",
      "@type": "Person",
      "email": "herve.menager@pasteur.fr",
      "name": "Hervé Ménager",
      "affiliation": "Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, Paris, France"
    }
  ],
  "identifier": "",
  "codeRepository": "https://github.com/IFB-ElixirFr/edam-browser",
  "datePublished": "2018-02-06",
  "dateModified": "2018-02-06",
  "dateCreated": "2018-02-06",
  "description": "The EDAM Browser is a client-side web-based visualization javascript widget. Its goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.",
  "keywords": "javascript, bioinformatics, d3js, d3.js, ontology, visualization, edamontology, ontology",
  "license": "MIT",
  "title": "EDAM Browser",
  "version": "v1.0.0"
}

GitHub Events

Total
  • Issues event: 3
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 3
  • Member event: 5
  • Push event: 8
  • Pull request event: 3
  • Fork event: 2
  • Create event: 1
Last Year
  • Issues event: 3
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 3
  • Member event: 5
  • Push event: 8
  • Pull request event: 3
  • Fork event: 2
  • Create event: 1

Dependencies

package.json npm
  • @babel/core ^7.14.8 development
  • @babel/preset-env ^7.14.9 development
  • @fortawesome/fontawesome-free ^5.15.3 development
  • cssnano ^5.0.6 development
  • jshint ^2.9.5 development
  • live-server ^1.2.1 development
  • bootstrap ^3.4.1
  • d3 ^4.13.0
  • edam2json-js ^0.2.3
  • ga-gtag ^1.1.0
  • gh-pages ^3.2.3
  • jquery ^3.2.1
  • jquery-ui-bundle ^1.12.1-migrate
  • jquery-ui-dist ^1.12.1
  • jquery-ui-themeroller ^0.0.5
  • jquery-ui-themes ^1.12.0
  • parcel-bundler ^1.12.5
  • popper.js ^1.16.1
  • regenerator-runtime ^0.13.7
.github/workflows/publish.yaml actions
  • actions/checkout v1 composite
  • peaceiris/actions-gh-pages v3 composite