{ "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/2010/10/31/citeulike-cito-use-case-1-wordles.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/npbqm-gfa49", "url": "https://chem-bla-ics.linkedchemistry.info/2010/10/31/citeulike-cito-use-case-1-wordles.html", "title": "CiteULike CiTO Use Case #1: Wordles", "content_html": "

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

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I promised the CiTO author, David, my use cases, but have been horribly\nbusy 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\nwrote and released earlier, the first use case I represent is the\nWordle one, which I showed with manual work in February .

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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\nCDK paper (doi:10.1021/ci025584y). Using the JSON interface, I have\nthis Groovy script to extract all titles:

\n\n
import groovyx.net.http.HTTPBuilder\nimport groovyx.net.http.Method\nimport static groovyx.net.http.ContentType.JSON\n\nculUrl = \"http://www.citeulike.org/\";\n\ncitotags = [\n  \"cito--cites\",\n  \"cito--usesMethodIn\",\n  \"cito--discusses\",\n  \"cito--extends\"\n// there are more, but these are all\n// I use right now\n]\n\npapers = [\n  \"1073448\",\n  \"423382\"\n]\n\nhttp = new HTTPBuilder(culUrl)\n\npapers.each { paper ->\n  println \"# Processing $paper...\"\n  citotags.each { tag ->\n    citation = \"$tag--$paper\".toLowerCase()\n    http.request(Method.valueOf(\"GET\"), JSON) {\n      uri.path = \"/json/user/egonw/tag/$citation\"\n\n      response.success = { resp,json ->\n        json.each { article ->\n          tripleCount = 0;\n          article.tags.each { artTag ->\n            if (artTag.startsWith(tag)) tripleCount++\n          }\n          if (tripleCount > 0) {\n            title = article.title\n            title = title.replaceAll(\"\\\\{\",\"\")\n            title = title.replaceAll(\"\\\\}\",\"\")\n            println \"$title\"\n          }\n        }\n      }\n    }\n  }\n}\n
\n\n

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,\nbut 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\nI annotated in CiteULike with CiTO.

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The CDK I paper

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\"\"

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The CDK II paper

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\"\"

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

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References

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Shotton, D. (2010). CiTO, the Citation Typing Ontology. Journal of Biomedical Semantics, 1(S1). https://doi.org/10.1186/2041-1480-1-s1-s6 CrossRef Scholia
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Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., & Willighagen, E. (2003). The Chemistry Development Kit (CDK):  An Open-Source Java Library for Chemo- and Bioinformatics. Journal of Chemical Information and Computer Sciences, 43(2), 493–500. https://doi.org/10.1021/ci025584y CrossRef Scholia
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", "summary": "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.", "date_published": "2010-10-31T00:00:00+00:00", "date_modified": "2026-09-27T00:00:00+00:00", "tags": ["cito","citeulike","cdk","wordle"], "_references": [ { "url": "https://doi.org/10.1186/2041-1480-1-S1-S6", "doi": "10.1186/2041-1480-1-S1-S6" } , { "url": "https://doi.org/10.1021/CI025584Y", "doi": "10.1021/CI025584Y" } ], "_citations": [ { "url": "https://doi.org/10.1016/j.websem.2012.08.001", "doi": "10.1016/j.websem.2012.08.001" , "cito": [ "credits" ] } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }