The PhyloAlps Project

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Technologies

Operating System

• NixOS

Data Management System

• Small distributed relational databases: PostgreSQL + PostGIS
• Mapping of relational data to RDF:
  • 2 W3C recommandations from the RDB2RDF Working Group:
    1. Direct Mapping: RDB to RDF Mapping
    2. R2RML: RDB to RDF Mapping Language
  • RDB2RDF implementations:

Name	Language	Mapping language	Licence	Last update	Comment
D2RQ	Java	D2RQ mapping language	Free	22.06.2012
OpenLink Virtuoso RDF Views	C	Virtuoso Meta Schema Language / R2RML	Free	15.08.2018	Mapping to external database only available in commercial version
SPARQL Map	Java	R2RML	Free	31.08.2017
R2RML Parser	Java	R2RML	Free	11.02.2016
Ontop	Java	R2RML	Free	06.03.2018	Exists as a Protégé plugin
RDF4J aka Sesame + R2RML API	Java	R2RML	Free	11.08.2018
Triplify	PHP	Direct mapping	Free	05.03.2010
rdb2rdf	Python	Direct mapping	Free	24.11.2014
METAmorphoses	Java	Direct mapping	Free	07.02.2007
R2D2	PHP	D2RQ mapping language	Free	01.10.2006

• RDF triplestore and SPARQL endpoint:
  • OpenLink Virtuoso triplestore (C)

See also:

• What are the pros and cons of RDB2RDF tools? on Stack Overflow
• RDF and SQL on Wikipedia
• converter2rdf on the W3C wiki
• Graph DataBase on Wikipedia
• Knowledge Extraction on Wikipedia

Web Server

• Apache httpd Server
• NGINX

SSL Certificates

• Certbot

Back end

• Python framework (Django) + WSGI server (Gunicorn)
• Server-side JavaScript framework (NodeJS + MongoDB)
• PHP framework (Symfony or CakePHP)
• Java framework (Java Server Faces)

Front end

• HTML5
• CSS3 framework (Bulma) + CSS preprocessor (SASS/LESS)
• JavaScript + jQuery
• Slippy map (OpenLayers3)
• Dynamic tables (Datatables)
• Datepicker (jQuery UI)
• Iconset (FontAwesome)

Dataviz

• D3 for sets, graphs and tree structures
• ElasticSearch + Kibana
• Jupyter

Continuous Integration

• Build automation tools
  • Docker
  • Apache Maven
  • Apache Ant
  • Gradle
  • Bower
• CI Server
  • Jenkins
  • Travis
  • Buildbot
  • Strider
  • Gitlab CI
  • TeamCity