Jekyll2026-08-31T19:33:33+00:00https://chem-bla-ics.linkedchemistry.info/feed/by_tag/chempedia.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenKasabi archive at the Internet Archive2024-08-15T00:00:00+00:002024-08-15T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2024/08/15/kasabi-archivesKasabi was an innovative RDF publishing platform from around 2011. Shortlived, and maybe just too early. I published two open datasets there. One was ChEMBL-RDF (see these posts). The second was a small data sets called ChemPedia, a open science effort to crowdsource chemical names. This is still very much needed, and possibly Wikidata could fill that gap, but it would first need to be able to handle all labels as statements itself.

Anyway, just before they shutdown because of, I understood, lack of commercial interest, they archived all data, including the ChemPedia datasets. I was happy to be reminded about that, because I am not sure I had archived that data.

]]>Egon WillighagenACS Liveblogging 1st Disclosures of Drug Candidates2010-04-22T00:00:00+00:002010-04-22T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2010/04/22/acs-liveblogging-1st-disclosures-ofCarmen liveblogged via her twitter account the disclosures of drug candidates at the past ACS meeting, and later aggregated the tweets in her blog. While many of her tweets made it into the FriendFeed room, the structure she drew up and shared did not make it. And until just know, I was not aware the had tweeted those too. The first twitpic she pushed was:

and I hope they will all end up in ChemPedia. I’ve done the above (6-2018-7215-8416):

Each structure I have transcribed, I will tweet with the tags #acs_sf and #chempedia, like in:

@carmendrahl http://twitpic.com/1a3b3v -> http://ur1.ca/wfar #chempedia #acs_sf

Oh, and if you happen to know the drug candidates name (or company code), please do deposit it in ChemPedia!

]]>Egon WillighagenChemPedia RDF #1: the SPARQL end point2009-11-19T00:00:00+00:002009-11-19T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2009/11/19/chempedia-rdf-1-sparql-end-pointWell, 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:

import net.sf.json.groovy.JsonSlurper;

input = new File("substances.json")
json = new JsonSlurper().parse(input);

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

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

prefix dc: <http://purl.org/dc/elements/1.1/>
prefix cp: <http://rdf.openmolecules.net/chempedia/onto#>

select distinct ?name ?score where {
  ?s a cp:Naming ;
     cp:hasName ?name ;
     cp:hasScore ?score .
} ORDER BY DESC(?score) LIMIT 10
]]>Egon WillighagenOpen Access / Open Data leads to added value2008-04-21T00:00:00+00:002008-04-21T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2008/04/21/open-access-open-data-leads-to-addedTwo companies recently showed two things:

  • open access and open data allow adding value
  • adding value is easier by forking

Rich’ MetaMolecular set up Chempedia which combines a substructure-searchable chemical Wikipedia. There is also a page to make links to new Wikipedia monographs. Not sure why Rich chose CAS instead of the InChI, given the recent controversy on validity of CAS numbers in Wikipedia … realize that this page is for new monograph, of which the CAS number is likely not verified yet, or? On the other hand, the InChI or InChIKey is not so abundant in Wikipedia yet (I really must make an updated list).

ChemSpider has been using a similar approach to add value to existing resources. The interesting thing in this case, is that these substructure searchable versions, have an interesting spin off: it allows ChemSpider to build a valuable DOI-InChI table. So far, I spotted:

If you wonder how to integrate all data again when things are so distributed, just consider userscripts .

]]>Egon Willighagen