Sunday, April 19, 2009

Adventures In Semantic Publishing: Exemplar Semantic Enhancements Of A Research Article

Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article

David Shotton, Katie Portwin, Graham Klyne, Alistair Miles

Image Bioinformatics Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom

Scientific innovation depends on finding, integrating, and re-using the products of previous research. Here we explore how recent developments in Web technology, particularly those related to the publication of data and metadata, might assist that process by providing semantic enhancements to journal articles within the mainstream process of scholarly journal publishing.

We exemplify this by describing semantic enhancements we have made to a recent biomedical research article taken from PLoS Neglected Tropical Diseases, providing enrichment to its content and increased access to datasets within it. These semantic enhancements include provision of live DOIs and hyperlinks; semantic markup of textual terms, with links to relevant third-party information resources; interactive figures; a re-orderable reference list; a document summary containing a study summary, a tag cloud, and a citation analysis; and two novel types of semantic enrichment: the first, a Supporting Claims Tooltip to permit “Citations in Context”, and the second, Tag Trees that bring together semantically related terms.

In addition, we have published downloadable spreadsheets containing data from within tables and figures, have enriched these with provenance information, and have demonstrated various types of data fusion (mashups) with results from other research articles and with Google Maps. We have also published machine-readable RDF metadata both about the article and about the references it cites, for which we developed a Citation Typing Ontology, CiTO


The enhanced article, which is available at

presents a compelling existence proof of the possibilities of semantic publication.

We hope the showcase of examples and ideas it contains, described in this paper, will excite the imaginations of researchers and publishers, stimulating them to explore the possibilities of semantic publishing for their own research articles, and thereby break down present barriers to the discovery and re-use of information within traditional modes of scholarly communication.

Citation: Shotton D, Portwin K, Klyne G, Miles A (2009) Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Comput Biol 5(4): e1000361. doi:10.1371/journal.pcbi.1000361


See Also

Creative ways to semantically enrich an Open Access PLoS research article

1 comment:

Geoff Barker said...

At the Powerhouse Museum in Sydney we are looking at ways to deliver curatorial content through our the narrative module in KEMu and OPAC server but the footnoting limitations etc have led us towards using pdf documents and your example is inspirational. Thanks.