{ "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/2009/11/19/chempedia-rdf-1-sparql-end-point.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/qfhff-gen31", "url": "https://chem-bla-ics.linkedchemistry.info/2009/11/19/chempedia-rdf-1-sparql-end-point.html", "title": "ChemPedia RDF #1: the SPARQL end point", "content_html": "

Well, you might spot a pattern here; yes, another chemical SPARQL end point\n(actually, it shares the end point with the Solubility data ).\nThis time around Rich’s ChemPedia. Taking advantage of the\nCC0-licensed downloads ,\nI have created a small Groovy script (using this JSON library)\nto convert the ChemPedia JSON into\nNotation3:

\n\n
import net.sf.json.groovy.JsonSlurper;\n\ninput = new File(\"substances.json\")\njson = new JsonSlurper().parse(input);\n\nprintln \"@prefix dc: <http://purl.org/dc/elements/1.1/>\";\nprintln \"@prefix cp: <http://rdf.openmolecules.net/chempedia/onto#>\";\njson.each { it ->\n  println \"<\" + it.uri + \"> dc:identifier \\\"\" + it.gsid + \"\\\";\";\n  println \" <http://www.w3.org/2002/07/owl#sameAs> <http://rdf.openmolecules.net/?\" + it.inchi + \">;\";\n  println \"  <http://www.iupac.org/inchi> \\\"\" + it.inchi + \"\\\".\";\n  if (it.namings.size() > 0) {\n    for (int i = 0; i<it.namings.size(); i++) {\n      naming = it.namings.get(i);\n      namingURI = it.uri + \"/naming\" + i;\n      println \"<\" + it.uri + \"> cp:hasNaming \" +\n        \"<\" + namingURI + \">.\";\n      println \"<\" + namingURI + \"> a cp:Naming;\";\n      println \"  cp:hasName \\\"\" + naming.name + \"\\\";\";\n      println \"  cp:hasStatus \\\"\" + naming.status + \"\\\";\";\n      println \"  cp:hasScore \\\"\" + naming.score + \"\\\".\";\n    }\n  }\n}\n
\n\n

After uploading it into Virtuoso (now using DB.DBA.TTLP instead of\nDB.DBA.RDF_LOAD_RDFXML_MT ), we can now have our\nregular SPARQL fun with the data from ChemPedia. For example, list the 10 names with the most votes:

\n\n
prefix dc: <http://purl.org/dc/elements/1.1/>\nprefix cp: <http://rdf.openmolecules.net/chempedia/onto#>\n\nselect distinct ?name ?score where {\n  ?s a cp:Naming ;\n     cp:hasName ?name ;\n     cp:hasScore ?score .\n} ORDER BY DESC(?score) LIMIT 10\n
\n\n

References

\n
\n
Apodaca, R. (2009). Chempedia Data Downloads: Free as in Free. In Front Matter. Front Matter. https://doi.org/10.59350/kprj3-gyg97 CrossRef Scholia
\n
", "summary": "Well, you might spot a pattern here; yes, another chemical SPARQL end point (actually, it shares the end point with the Solubility data ). This time around Rich’s ChemPedia. Taking advantage of the CC0-licensed downloads , I have created a small Groovy script (using this JSON library) to convert the ChemPedia JSON into Notation3:", "date_published": "2009-11-19T00:00:00+00:00", "date_modified": "2026-05-05T00:00:00+00:00", "tags": ["rdf","sparql","chempedia","nmrshiftdb"], "_references": [ { "url": "https://doi.org/10.59350/kprj3-gyg97", "doi": "10.59350/kprj3-gyg97" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }