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org.pathvisio.io.rdf

Library for saving GPMLRDF and WPRDF for a GPML data model

https://github.com/egonw/org.pathvisio.io.rdf

Science Score: 44.0%

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    CITATION.cff file
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    Low similarity (8.3%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

Library for saving GPMLRDF and WPRDF for a GPML data model

Basic Info
  • Host: GitHub
  • Owner: egonw
  • License: apache-2.0
  • Language: Java
  • Default Branch: main
  • Size: 173 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 4
Created about 4 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation Authors

README.md

build

org.pathvisio.io.rdf

Library for saving GPMLRDF and WPRDF for a GPML data model. It consists of two parts, a libGPML extension to convert GPML into RDF, and a command line tool that allows one to do just that from the command line.

Installing

In this directory, follow the following instructions:

cd org.pathvisio.io.rdf mvn clean install

And

cd org.wikipathways.rdf mvn clean install

Creating WPRDF and GPMLRDF

cd org.wikipathways.rdf java -cp target/gpml2rdf-4.0.0-SNAPSHOT.jar org.wikipathways.wp2rdf.CreateGPMLRDF path/to/WP4297.gpml WP4297.ttl java -cp target/gpml2rdf-4.0.0-SNAPSHOT.jar org.wikipathways.wp2rdf.CreateWPRDF path/to/WP4297.gpml WP4297.ttl

Or generate them in one go with:

java -cp org.wikipathways.rdf/target/gpml2rdf-4.0.3.jar org.wikipathways.wp2rdf.CreateRDF WP1028.gpml WP1028.gpml.ttl WP1028.wp.ttl

Using ROBOT to find differences

./robot diff --left WP1028.wp.real.ttl --right WP1028.wp.ttl

Release alpha versions

This code is nowhere close to be replacing the current GPMLRDF, but a 4.0.0 series will be released as alpha to start putting together the full toolchain, which requires testing the whole workflow in action.

Version are updated with:

mvn versions:set -DnewVersion=4.0.0 git commit -m "New release" -a

Owner

  • Name: Egon Willighagen
  • Login: egonw
  • Kind: user
  • Location: Maastricht, The Netherlands
  • Company: @BiGCAT-UM

Open scientist teaching and doing research at Maastricht University.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite the WikiPathways RDF paper."
title: libGPML export library for GPMLRDF and WPRDF
url: "https://github.com/egonw/org.pathvisio.io.rdf"
preferred-citation:
  type: article
  title: "Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources"
  authors:
  - family-names: Waagmeester
    given-names: Andra
  - family-names: Summer-Kutmon
    given-names: Martina
  - family-names: Riutta
    given-names: Anders
  - family-names: Miller
    given-names: Ryan
  - family-names: Willighagen
    given-names: Egon
  - family-names: Evelo
    given-names: Chris T
  - family-names: Pico
    given-names: Alexander R.
  doi: 10.1371/JOURNAL.PCBI.1004989
  year: 2016
  month: 6
  day: 23
  journal: PLOS Computational Biology
  volume: 12
  issue: 6
  url: https://doi.org/10.1371/JOURNAL.PCBI.1004989

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Dependencies

.github/workflows/maven.yml actions
  • actions/checkout v3 composite
  • actions/setup-java v3 composite
org.pathvisio.io.rdf/pom.xml maven
  • org.apache.jena:jena-arq 4.9.0
  • org.pathvisio:org.pathvisio.libgpml 4.0.3
  • org.junit.jupiter:junit-jupiter 5.10.0 test
  • org.junit.jupiter:junit-jupiter-engine 5.10.0 test
org.wikipathways.rdf/pom.xml maven
  • commons-cli:commons-cli 1.5.0
  • org.pathvisio:org.pathvisio.io.rdf 4.0.2
  • org.slf4j:slf4j-api 2.0.9
  • org.slf4j:slf4j-simple 2.0.9