# The PhyloAlps Project

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[TNRS](tnrs) |
[Model](model) |
[Architecture](archi) |
[Technologies](techno) |
[User Profiles](profiles) |
[Meetings](meetings) |
[Biblio](biblio)

## 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]

[NixOS]:https://nixos.org/
[postgresql]:https://www.postgresql.org/
[postgis]:http://postgis.net/
[R2RML]:https://www.w3.org/TR/r2rml/
[R2RML Parser]:https://github.com/nkons/r2rml-parser
[SPARQL Map]:https://github.com/tomatophantastico/sparqlmap/
[Direct Mapping]:https://www.w3.org/TR/rdb-direct-mapping/
[rdf]:http://rdfs.org/
[RDB2RDF implementations]:https://www.w3.org/2001/sw/rdb2rdf/wiki/Implementations
[rdb2rdf working group]:https://www.w3.org/2001/sw/rdb2rdf/
[D2RQ]:http://d2rq.org/
[r2d2]:http://aksw.org/Projects/R2D2.html
[METAmorphoses]:http://metamorphoses.sourceforge.net/METAmorphoses_processor/
[openlink virtuoso triplestore]:https://virtuoso.openlinksw.com/
[openlink virtuoso rdf views]:https://virtuoso.openlinksw.com/whitepapers/relational%20rdf%20views%20mapping.html
[ontop]:https://github.com/ontop/ontop/wiki
[rdb2rdf]:https://pypi.org/project/rdb2rdf/
[triplify]:https://sourceforge.net/projects/triplify/
[rdf4j]:http://rdf4j.org/
[r2rml api]:https://github.com/R2RML-api/R2RML-api
[allegrograph]:http://franz.com/agraph/allegrograph/
[marklogic]:http://www.marklogic.com/
[What are the pros and cons of RDB2RDF tools?]:https://stackoverflow.com/questions/45476632/what-are-the-pros-and-cons-of-rdb2rdf-tools
[RDF and SQL]:https://www.w3.org/wiki/RdfAndSql
[converter2rdf]:https://www.w3.org/wiki/ConverterToRdf#SQL
[graph database]:https://en.wikipedia.org/wiki/Graph_database
[knowledge extraction]:https://en.wikipedia.org/wiki/Knowledge_extraction
[nodejs]:https://nodejs.org/en/
[mongodb]:https://www.mongodb.com/
[django]:https://www.djangoproject.com/
[gunicorn]:https://gunicorn.org/
[symfony]:https://symfony.com/
[cakephp]:https://cakephp.org/
[java server faces]:http://www.oracle.com/technetwork/java/javaee/javaserverfaces-139869.html
[html5]:https://www.w3.org/TR/html5/
[css3 framework]:https://www.keycdn.com/blog/front-end-frameworks/
[bulma]:http://bulma.io/
[sass]:http://sass-lang.com/
[less]:http://lesscss.org/
[javascript]:https://www.javascript.com/
[jquery]:https://jquery.com/
[jquery ui]:https://jqueryui.com/
[fontawesome]:https://fontawesome.com/
[openlayers3]:https://openlayers.org/
[datatables]:https://datatables.net/
[elasticsearch]:https://www.elastic.co/
[kibana]:https://www.elastic.co/products/kibana
[d3]:https://d3js.org/
[jupyter]:https://jupyter.org/
[Apache httpd Server]:https://httpd.apache.org/
[NGINX]:https://www.nginx.com/
[certbot]:https://certbot.eff.org/
[Jenkins]:https://jenkins.io/
[Travis]:https://travis-ci.org/
[Buildbot]:https://buildbot.net/
[Strider]:https://strider-cd.github.io/
[Gitlab CI]:https://about.gitlab.com/gitlab-ci/
[TeamCity]:https://www.jetbrains.com/teamcity/
[Docker]:https://www.docker.com/
[Apache Maven]:https://maven.apache.org/
[Apache Ant]:https://ant.apache.org/
[Gradle]:https://gradle.org/
[bower]:https://bower.io/