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https://github.com/albertmeronyo/stardog-r
Wrapping R calls as SPARQL custom functions in Stardog. For great justice.
https://github.com/albertmeronyo/stardog-r
Last synced: 10 days ago
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Wrapping R calls as SPARQL custom functions in Stardog. For great justice.
- Host: GitHub
- URL: https://github.com/albertmeronyo/stardog-r
- Owner: albertmeronyo
- License: gpl-3.0
- Created: 2014-12-10T12:33:07.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2015-06-11T16:21:33.000Z (over 9 years ago)
- Last Synced: 2024-10-05T23:21:46.665Z (3 months ago)
- Language: Java
- Size: 414 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 4
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Stardog/R
=========
Stardog extension wrapping R function calls as SPARQL custom functions.
## About
This extension expands the standard functionality of SPARQL in [Stardog](http://www.stardog.com/)'s query engine, by allowing R functions (such as test statistics) to be called directly from SPARQL queries.
## Build and Setup
You'll need a Stardog installation with a valid license. Stardog distributions and community and developer licenses can be obtained for free at http://www.stardog.com
You'll need to install the Java/R Interface (JRI). Please follow the instructions to install JRI at http://rforge.net/JRI/ (quick howto: execute `install.packages("rJava")` in your R environment).
1. Set your local Stardog install and home paths in `project.properties`
2. `cd function; ant dist`
3. A file `stardog-function-examples-1.0.jar` will be generated in `function/dist`. Copy that jar into `$STARDOG_HOME/server/pack/`
4. Add the following lines to the script `$STARDOG_HOME/bin/stardog-admin`:
1. Make Stardog aware of where your R install lives: `export R_HOME="/usr/lib/R"` (Linux), or `export R_HOME="/Library/Frameworks/R.framework/Resources"` (MacOS X)
2. Make Stardog aware of where your JRI shared libraries live. This can be achieved in [many ways](http://www.chilkatsoft.com/java-loadLibrary-MacOSX.asp). Recommended: in Linux, modify the LD_LIBRARY_PATH environment variable (add `export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/R/site-library/rJava/jri` using your valid JRI path to `$STARDOG_HOME/bin/stardog-admin`; in MacOS X, it's easier to symlink the library `libjri.so` in your Java library path (you can get your Java library path by `System.out.println(System.getProperty("java.library.path"));`).
5. Run the Stardog server
6. R calls are available under the `stardog: ` namespace. For instance, this SPARQL query executes the Wilcoxon signed-rank test over two given RDF Data Cube slices:
`./stardog query mydb "prefix stardog: prefix eg: select ?foo where { bind(stardog:R(\"wilcox.test\", eg:slice1, eg:slice2, eg:height) as ?foo)}"`
## Motivation
Basically we pretend to cover transformation and analysis of Linked Data in the Web dataspace, with full statistical support and in one single SPARQL query. An example would be transforming the following set of observations so they become dimensionally comparable:
```
:o1 a qb:Observation ;
maritalstatus:maritalStatus maritalstatus:single ;
sdmx-dimension:age sdmx-code:12-to-18 ;
sdmx-dimension:sex sdmx-code:sex-F ;
sdmx-dimension:refArea dbpedia:Barcelona ;
sdmx-dimension:refTime "1991-01-01"^^xsd:date ;
:population "12"^^xml:decimal .
:o2 a qb:Observation ;
maritalstatus:maritalStatus maritalstatus:single ;
sdmx-dimension:age sdmx-code:12-to-14 ;
sdmx-dimension:sex sdmx-code:sex-F ;
sdmx-dimension:refArea dbpedia:Barcelona ;
sdmx-dimension:refTime "2001-01-01"^^xsd:date ;
:population "142"^^xml:decimal .
:o3 a qb:Observation ;
maritalstatus:maritalStatus maritalstatus:single ;
sdmx-dimension:age sdmx-code:14-to-18 ;
sdmx-dimension:refArea dbpedia:Catalonia ;
sdmx-dimension:refTime "2011-01-01"^^xsd:date ;
:population "84"^^xml:decimal .
```
But we also aim at executing variable coding, dataset cleansing and regression analysis natively in SPARQL.
## Requirements
- JDK/JRE 1.7
- Ant 1.9.4
- R >= 3.0.2
- JRI >= 0.5-5