{"id":37029503,"url":"https://github.com/sbgn/libsbgn","last_synced_at":"2026-01-14T03:32:54.432Z","repository":{"id":70716411,"uuid":"60818433","full_name":"sbgn/libsbgn","owner":"sbgn","description":"Libraries for the Systems Biology Graphical Notation (SBGN); Java and 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security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"Binary-Artifacts","score":0,"reason":"binaries present in source code","details":["Warn: binary detected: org.sbgn/buildlib/hamcrest-core-1.3.jar:1","Warn: binary detected: org.sbgn/buildlib/junit-4.13.1.jar:1","Warn: binary detected: org.sbgn/lib/ant-1.7.0.jar:1","Warn: binary detected: org.sbgn/lib/ant-launcher-1.7.0.jar:1","Warn: binary detected: 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tools/xsddoc-1.0/lib/xerces.jar:1","Warn: binary detected: tools/xsddoc-1.0/lib/xercesImpl.jar:1","Warn: binary detected: tools/xsddoc-1.0/lib/xml-apis.jar:1","Warn: binary detected: tools/xsddoc-1.0/lib/xsddoc.jar:1","Warn: binary detected: validation/lib/ant-schematron.jar:1","Warn: binary detected: validation/lib/saxon9he.jar:1"],"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"License","score":9,"reason":"license file detected","details":["Info: project has a license file: LICENSE.txt:0","Warn: project license file does not contain an FSF or OSI license."],"documentation":{"short":"Determines if the project has defined a 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.github/workflows/jdk16-maven.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk17-ant-build.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk17-ant-docs.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk17-ant-tests.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk17-ant.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk17-maven.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk21-ant-build.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk21-ant-docs.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk21-ant-tests.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk21-ant.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk21-maven.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk8-ant-build.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk8-ant-docs.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk8-ant-tests.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk8-ant.yml:1","Warn: no topLevel permission defined: .github/workflows/jdk8-maven.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Signed-Releases","score":0,"reason":"Project has not signed or included provenance with any releases.","details":["Warn: release artifact milestone3.3 not signed: https://api.github.com/repos/sbgn/libsbgn/releases/26503294","Warn: release artifact milestone2jardep not signed: https://api.github.com/repos/sbgn/libsbgn/releases/25141121","Warn: release artifact milestone2jar not signed: https://api.github.com/repos/sbgn/libsbgn/releases/25141059","Warn: release artifact milestone3.2 not signed: https://api.github.com/repos/sbgn/libsbgn/releases/18500712","Warn: release artifact milestone3.1 not signed: https://api.github.com/repos/sbgn/libsbgn/releases/17417998","Warn: release artifact milestone3.3 does not have provenance: https://api.github.com/repos/sbgn/libsbgn/releases/26503294","Warn: release artifact milestone2jardep does not have provenance: https://api.github.com/repos/sbgn/libsbgn/releases/25141121","Warn: release artifact milestone2jar does not have provenance: https://api.github.com/repos/sbgn/libsbgn/releases/25141059","Warn: release artifact milestone3.2 does not have provenance: https://api.github.com/repos/sbgn/libsbgn/releases/18500712","Warn: release artifact milestone3.1 does not have provenance: https://api.github.com/repos/sbgn/libsbgn/releases/17417998"],"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'","Warn: branch protection not enabled for branch 'attic'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all 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https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk11-ant-docs.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk11-ant-tests.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk11-ant-tests.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk11-ant.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk11-ant.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk11-maven.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk11-maven.yml:25: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk11-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant-build.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant-build.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant-docs.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant-docs.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant-tests.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant-tests.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-ant.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-maven.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk16-maven.yml:25: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk16-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant-build.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant-build.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant-docs.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant-docs.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant-tests.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant-tests.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-ant.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-maven.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk17-maven.yml:25: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk17-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant-build.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant-build.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant-docs.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant-docs.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant-tests.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant-tests.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant-tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-ant.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-ant.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-maven.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk21-maven.yml:25: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk21-maven.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk8-ant-build.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk8-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk8-ant-build.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk8-ant-build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/jdk8-ant-docs.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/sbgn/libsbgn/jdk8-ant-docs.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: 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LibSBGN\n[![](https://jitpack.io/v/sbgn/libsbgn.svg)](https://jitpack.io/#sbgn/libsbgn)\n\n[![](https://github.com/sbgn/libsbgn/actions/workflows/jdk8-maven.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk8-maven.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk11-maven.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk11-maven.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk16-maven.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk16-maven.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk17-maven.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk17-maven.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk21-maven.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk21-maven.yml)\n\n[![](https://github.com/sbgn/libsbgn/actions/workflows/jdk8-ant.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk8-ant.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk11-ant.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk11-ant.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk16-ant.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk16-ant.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk17-ant.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk17-ant.yml) [![](https://github.com/sbgn/libsbgn/actions/workflows/jdk21-ant.yml/badge.svg)](https://github.com/sbgn/libsbgn/actions/workflows/jdk21-ant.yml)\n\n\nSoftware support library for the [Systems Biology Graphical Notation (SBGN)](http://www.sbgn.org).\n\nDocumentation about LibSBGN and the development process is available from the Wiki  \nhttps://github.com/sbgn/sbgn/wiki/LibSBGN  \nDocumentation about SBGN is available from the SBGN homepage    \nhttp://sbgn.org\n\n## How to cite\n**Software support for SBGN maps: SBGN-ML and LibSBGN**  \n*van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F.*  \nBioinformatics, 28(15):2016-2021, 2012 [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/22581176)\n\n## Using libsbgn\n\nAs of milestone 3, thanks to [jitpack.io](https://jitpack.io/#sbgn/libsbgn), it is easy to use libsbgn right away withL \n\n### gradle: \n\nStep 1. Add the JitPack repository to your build file\n\nAdd it in your root build.gradle at the end of repositories:\n\n\tallprojects {\n\t\trepositories {\n\t\t\t...\n\t\t\tmaven { url 'https://jitpack.io' }\n\t\t}\n\t}\nStep 2. Add the dependency\n\n\tdependencies {\n\t        implementation 'com.github.sbgn:libsbgn:Tag'\n\t}\n\n\n### Maven\nStep 1. Add the JitPack repository to your build file\n\n\t\u003crepositories\u003e\n\t\t\u003crepository\u003e\n\t\t    \u003cid\u003ejitpack.io\u003c/id\u003e\n\t\t    \u003curl\u003ehttps://jitpack.io\u003c/url\u003e\n\t\t\u003c/repository\u003e\n\t\u003c/repositories\u003e\nStep 2. Add the dependency\n\n\t\u003cdependency\u003e\n\t    \u003cgroupId\u003ecom.github.sbgn\u003c/groupId\u003e\n\t    \u003cartifactId\u003elibsbgn\u003c/artifactId\u003e\n\t    \u003cversion\u003eTag\u003c/version\u003e\n\t\u003c/dependency\u003e \n\n### sbt\n\nAdd it in your build.sbt at the end of resolvers:\n\n \n    resolvers += \"jitpack\" at \"https://jitpack.io\"\n        \n    \nStep 2. Add the dependency\n\n\t\n\tlibraryDependencies += \"com.github.sbgn\" % \"libsbgn\" % \"Tag\"\n\n### leiningen\n\nAdd it in your project.clj at the end of repositories:\n\n \n    :repositories [[\"jitpack\" \"https://jitpack.io\"]]\n        \n    \nStep 2. Add the dependency\n\n\t\n\t:dependencies [[com.github.sbgn/libsbgn \"Tag\"]]\t\nShare this release: \n\n## Example code\nIf you would like to see how to use libsbgn, have a look at some of the examples: \n\n* [reading SBGN](org.sbgn/examples/org/sbgn/ReadExample.java)\n* [writing SBGN](org.sbgn/examples/org/sbgn/WriteExample.java)\n* [writing SBGN with annotation glyph](org.sbgn/examples/org/sbgn/WriteExampleAnnotation.java)\n* [reading SBGN render information](org.sbgn/examples/org/sbgn/ReadExampleWithRender.java)\n* [writing SBGN render information](org.sbgn/examples/org/sbgn/WriteRenderExtensionExample.java)\n\n\n## How to build\n\nTo build the java version of LibSBGN, you need to have installed:\n\n* Git [download](https://git-scm.com/downloads)\n* Java JDK [download](http://www.oracle.com/technetwork/java/javase/downloads/index-jsp-138363.html)\n* Ant [download](https://ant.apache.org/bindownload.cgi)\n\n### Building with Maven\n\nFirst clone the repository via\n```\ngit clone https://github.com/sbgn/libsbgn.git\ncd libsbgn\n```\n\nthen compile using `mvn install`.\n\n\n### Building with Ant\n\nAdd Git, Java JDK, and Ant to your path\n\nFirst clone the repository via\n```\ngit clone https://github.com/sbgn/libsbgn.git\ncd libsbgn\n```\n\nGet the latest stable release otherwise you will work with the unstable development version\n```\ngit fetch\ngit checkout milestone-2\n```\n\nThan build the library with ant from the source directory\n```\nant -f ant-build-script.xml\n```\nThis will result in the creation of `/dist/org.sbgn.jar` which you can include in your project.\n\nTo build the documentation in `/docs/` use\n```\nant -f ant-build-script.xml doc\n```\n\nTo run the tests use \n```\nant -f ant-build-script.xml test\n``` \n\n## Files\n\nHere is an explanation of the directories in this project:\n\n\n    cpp_binding    - C++ version of LibSBGN  \n    example-files  - some example SBGN-ML files, larger and more complete than the test-cases  \n    licenses       - license information  \n    org.sbgn       - LibSBGN source code (Java version)  \n    resources      - general resources, including XML Schema (SBGN.xsd)  \n    specifications - Auto-generated documentation for the XML Schema  \n\ttest-files     - SBGN-ML test cases and reference images  \n    tools\t\t   - \n    validation     - schematron validation rules, test-cases and resources  \n    \n\n## Authors\n\nAlice Villeger  \nAugustin Luna  \nFrank Bergmann  \nMartijn van Iersel  \nSarah Boyd  \nTobias Czauderna  \nStuart Moodie  \nMatthias König  \n\n### Contact\n\nContact our mailinglist:  \nsbgn-libsbgn@lists.sourceforge.net\n\nOur official website:  \nhttps://github.com/sbgn/libsbgn\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbgn%2Flibsbgn","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsbgn%2Flibsbgn","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbgn%2Flibsbgn/lists"}