Two weeks ago, a paper by Peter Ertl was published about Molecular structure input on the web\n(doi:10.1186/1758-2946-2-1). In this paper, he discusses the state of things and describes his\ncontribution to this field, the JME Molecule Editor. The article also cites the CDK, but only\nthe website and not one of the two papers (doi:10.1021/ci025584y, or\ndoi:10.2174/138161206777585274). This is not an isolated case, but a common pattern. In principle, the\nproper work is cited, and nothing is wrong. Practically it means, that a citation to the CDK website\ndoes not show up in the citation network. This is not a problem caused by these papers, but merely by the nature current citation\ndatabases work: they only count citations between journal articles, and only sometimes extend to books or conference abstracts.
\n\nNow, addressing the limitations of the current citation databases is technically simple, and purely blocked by social and commercial\naspects. The Citation Typing Ontology by David Shotton defines the framework\nto define citation types, independent from any existing database. The semantic web technologies will take it from there, and allow\naggregation etc.
\n\nThere are some things to think about on how to use such citation networks, though. If we calculate the impact of the CDK project,\nwe should combine citation counts to the website(s), papers, etc, after removal of duplicates, etc. The\ncito:cites does\nlink to resources, and the CDK paper resources is not the same as the CDK website resource. But, we could define a Project Class,\nwhere both are foo:partOf. Then, we could define that the triple chain the:citingWork cito:cites the:CDKArticle foo:partOf the:CDKProject\nwould imply the triple the:citingWork cito:cites the:CDKProject.
\n\nNow, while writing up this blog, I realize that my fork of this morning, A BIBO Citation Typing Ontology,\nmight actually be counter-productive in the long run, as I was only working out a solution to a simpler, but different problem, which the\nCiTO also addresses: a citation is not typed. When a paper does cite the CDK paper, we still do not know if it uses the CDK, or\nmerely mentioned it as related-but-unused, or even refuted work.
\n\nNow, as I am leaning towards the Biobliography Ontology as RDF-based system for my references, and been using this already in the\nRDF store hosting the ChEMBL data,\nI forked the CiTO to define rdfs:domain and rdfs:range on bibo:Document.\nThe CiTO 1.5 actually defines a large set of document types too, and I rather see BIBO reused.
\n\nThis indeed has the downside that the bibocto:cites cannot be used for the above chaining, and this might bite me seriously later.\nWell, nothing wrong with a failing experiment, right? For now, it will serve my purpose: setting up a citation database for the CDK\nproject papers.
\n\nSo, here goes (it’s RDFa-enabled; check this\nRDF pulled out):
\n\n@prefix bibo: <http://purl.org/ontology/bibo/>.\n@prefix bibocto: <http://github.com/egonw/bibo-cto/>.\n\n<urn:doi:10.1186/1758-2946-2-1> a bibo:Article ;\n bibocto:cites <urn:doi:10.1021/ci025584y> .\n\n\nI am not entirely happy about the error-prone XHTML+RDFa of the above example, and\nfiled a question of better solution on\nSemanticOverflow.
\n\nWhile the above example merely defines the citation of Peter Ertl’s article to the CDK (whether that is valid or not… would\nhe have cited the other paper perhaps?), the citation typing allows me to state how the CDK paper is cited. Now, Peter states:
\n\n\n\n\nIt is also gratifying to see the advent of open source movement in cheminformatics on the Internet, as advocated for example\nby the Blue Obelisk Group (40) and witnessed by collaborative projects\nlike Chemistry Development Kit CDK (41),\nJmol (42), Bioclipse (43) and several others.
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So, I think it is fair to state that:
\n\n<urn:doi:10.1186/1758-2946-2-1> bibocto:credits <urn:doi:10.1021/ci025584y> .\n\n\nwhich is very much appreciated!
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