{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2010/12/29/converting-json-to-rdfxml-with-groovy.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/2repm-7m232", "url": "https://chem-bla-ics.linkedchemistry.info/2010/12/29/converting-json-to-rdfxml-with-groovy.html", "title": "Converting JSON to RDF/XML with Groovy", "content_html": "

Mark’s new CCO/RDF hosting functionality\n(see also my post two days ago)\nrequires RDF/XML format, so I updated my code to convert the\nChempedia Substances data into RDF/XML instead of N3 (I have asked\nRich to put a new download link online). This is the\nGroovy code I used:

\n\n
import groovy.xml.MarkupBuilder\nimport groovy.util.IndentPrinter\n\ninput = new File(\"substances.json\")\njson = new JsonSlurper().parse(input);\n\ndef writer = new StringWriter()\ndef xml = new MarkupBuilder(\n  new IndentPrinter(new PrintWriter(writer))\n)\nxml.'rdf:RDF'(\n  'xmlns:rdf':\n    'http://www.w3.org/1999/02/22-rdf-syntax-ns#',\n  'xmlns:dc' :\n    'http://purl.org/dc/elements/1.1/',\n  'xmlns:iupac' :\n    'http://www.iupac.org/',\n  'xmlns:cp' :\n    'http://rdf.openmolecules.net/chempedia/onto#',\n  'xmlns:owl' :\n    'http://www.w3.org/2002/07/owl#'\n) {\n  json.each { substance ->\n    xml.'rdf:Description'(\n      'rdf:about': substance.uri\n    ) {\n      xml.'dc:identifier'(substance.gsid)\n      xml.'owl:sameAs'(\n        'rdf:resource' :\n        'http://rdf.openmolecules.net/?' +\n        substance.inchi\n      )\n      xml.'iupac:inchi'(\n        'http://rdf.openmolecules.net/?' +\n        substance.inchi\n      )\n      for (int i = 0; i<substance.namings.size(); i++)\n      {\n        naming = substance.namings.get(i);\n        namingURI = substance.uri + \"/naming\" + i;\n        xml.'cp:hasNaming' {\n          xml.'rdf:Description' {\n            xml.'cp:hasName'(naming.name)\n            xml.'cp:hasStatus'(naming.status)\n            xml.'cp:hasScore'(naming.score)\n          }\n        }\n      }\n    }\n  }\n}\nprintln writer.toString();\n
", "summary": "Mark’s new CCO/RDF hosting functionality (see also my post two days ago) requires RDF/XML format, so I updated my code to convert the Chempedia Substances data into RDF/XML instead of N3 (I have asked Rich to put a new download link online). This is the Groovy code I used:", "date_published": "2010-12-29T00:00:00+00:00", "date_modified": "2025-02-15T00:00:00+00:00", "tags": ["groovy","chemistry","rdf","json"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }