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gpml2rdf

GPML2RDF converter

https://github.com/wikipathways/gpml2rdf

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.0%) to scientific vocabulary

Keywords

java semantic-web wikipathways wikipathways-gpml-files
Last synced: 6 months ago · JSON representation

Repository

GPML2RDF converter

Basic Info
  • Host: GitHub
  • Owner: wikipathways
  • License: apache-2.0
  • Language: Java
  • Default Branch: main
  • Size: 23.6 MB
Statistics
  • Stars: 4
  • Watchers: 10
  • Forks: 2
  • Open Issues: 40
  • Releases: 2
Topics
java semantic-web wikipathways wikipathways-gpml-files
Created almost 11 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

GPML2RDF

GPML2RDF creates RDF for WikiPathways [1,2]. Use cases, examples SPARQL queries, downloads, etc, are available from the WikiPathways RDF Portal: http://rdf.wikipathways.org/

Installation

Setup

Clone or download this repository, and then import as an "Existing Java Project" in Eclipse.

There are two dependencies. You can make them available to Maven using the instructions below.

Start from the GPML2RDF folder for both the WikiPathways API client, and PathVisio Core

PathVisio Core

shell git clone https://github.com/PathVisio/pathvisio.git cd pathvisio git switch 3.4.0-alpha origin/3.4.0-alpha ant clean core.jar mvn install:install-file -Dfile=modules/org.pathvisio.core.jar -DgroupId=org.pathvisio \ -DartifactId=pathvisio-core -Dversion=3.4.0 -Dpackaging=jar

WikiPathways API client

shell git clone https://github.com/wikipathways/wikipathways-api-client-java.git cd wikipathways-api-client-java cd org.wikipathways.client mvn -Dmaven.test.failure.ignore=true clean install

Compiling

There is a pom.xml and you can compile the code with:

shell cd WP2RDF mvn clean install

A single archive with all dependencies can be created with:

shell mvn package

Try different pathways

Add GPML file in resources directory --> Open WP2RDF class --> Change pathwayFile location

1.Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico AR. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLOS Computational Biology. 2016 Jun;12(6):e1004989+. Available from: https://doi.org/10.1371/journal.pcbi.1004989
2.Miller RA, Kutmon M, Bohler A, Waagmeester A, Evelo CT, Willighagen EL. Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions. Yoon BJ, editor. PLoS ONE. 2022 Apr 18;17(4):e0263057. Available from: https://doi.org/10.1371/journal.pone.0263057

Owner

  • Name: WikiPathways
  • Login: wikipathways
  • Kind: organization

Open source software development related to the WikiPathways project

GitHub Events

Total
  • Issues event: 4
  • Issue comment event: 1
  • Push event: 2
Last Year
  • Issues event: 4
  • Issue comment event: 1
  • Push event: 2

Dependencies

WP2RDF/pom.xml maven
  • org.apache.jena:jena-arq 4.5.0
  • org.apache.jena:jena-core 4.5.0
  • org.bridgedb:org.bridgedb 3.0.17-SNAPSHOT
  • org.bridgedb:org.bridgedb.bio 3.0.17-SNAPSHOT
  • org.bridgedb:org.bridgedb.rdb 3.0.17-SNAPSHOT
  • org.eclipse:osgi 3.10.0-v20140606-1445
  • org.jdom:jdom2 2.0.6.1
  • org.pathvisio:pathvisio-core 3.4.0-bridgedb-3.0.1-1
  • org.wikipathways:webservice.api.lib 3.3.0-GPMLRDF-1
  • junit:junit 4.13.2 test
.github/workflows/maven.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v1 composite