CiteULike CiTO Use Case #1: Wordles

2010-10-31T00:00:00+00:00

Last month I reported a few things I missed in CiteULike. One of them was support for CiTO (see doi:10.1186/2041-1480-1-S1-S6), a great Citation Typing Ontology.

I promised the CiTO author, David, my use cases, but have been horribly busy in the past few weeks with my new position, wrapping up my past position, and thinking on my position after Cambridge. But finally, here it is. Based on source code I wrote and released earlier, the first use case I represent is the Wordle one, which I showed with manual work in February.

Now that all the data is semantically marked up in CiteULike, I can easily extract all paper titles (or whatever is available in CiteULike) for all papers that cite the first CDK paper (doi:10.1021/ci025584y). Using the JSON interface, I have this Groovy script to extract all titles:

import groovyx.net.http.HTTPBuilder
import groovyx.net.http.Method
import static groovyx.net.http.ContentType.JSON

culUrl = "http://www.citeulike.org/";

citotags = [
  "cito--cites",
  "cito--usesMethodIn",
  "cito--discusses",
  "cito--extends"
// there are more, but these are all
// I use right now
]

papers = [
  "1073448",
  "423382"
]

http = new HTTPBuilder(culUrl)

papers.each { paper ->
  println "# Processing $paper..."
  citotags.each { tag ->
    citation = "$tag--$paper".toLowerCase()
    http.request(Method.valueOf("GET"), JSON) {
      uri.path = "/json/user/egonw/tag/$citation"

      response.success = { resp,json ->
        json.each { article ->
          tripleCount = 0;
          article.tags.each { artTag ->
            if (artTag.startsWith(tag)) tripleCount++
          }
          if (tripleCount > 0) {
            title = article.title
            title = title.replaceAll("\\{","")
            title = title.replaceAll("\\}","")
            println "$title"
          }
        }
      }
    }
  }
}

The output is two blocks which I can easily copy/paste into Wordle. Now, I think I heard one can actually download the java code, so I am tempted to integrate it later, but for now copy/paste will do fine, after the data handling is mostly automated: with a few lines extra I can make such visualizations for any paper I annotated in CiteULike with CiTO.

The CDK I paper

The CDK II paper

Interesting differences… more statistics will soon follow. See Further statistics on the papers citing the CDK for the kind of analyses I have in mind.

chem-bla-ics

CiteULike CiTO Use Case #1: Wordles