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Adventures in semantic publishing: exemplar semantic enhancements of a research article.

Shotton D, Portwin K, Klyne G, Miles A - PLoS Comput. Biol. (2009)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Image Bioinformatics Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom. david.shotton@zoo.ox.ac.uk

ABSTRACT
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 (http://purl.org/net/cito/). The enhanced article, which is available at http://dx.doi.org/10.1371/journal.pntd.0000228.x001, 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.

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Related in: MedlinePlus

The Tag Tree for instances of the semantic concept Habitat.
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pcbi-1000361-g007: The Tag Tree for instances of the semantic concept Habitat.

Mentions: Tag trees. Below the tag cloud, these same terms are segregated into the nine semantic classes used for highlighting the text (date, disease, habitat, institution, organism, person, place, protein, and taxon). The persons list includes both people mentioned in the text and the authors of the article, whose names are shown in bold font, but excludes the authors of cited references. In these lists, we maintained the colors and relative sizes of the terms from the tag cloud, and ordered them, where appropriate, into informal hierarchies—particularly noticeable for places and organisms. We call these displays tag trees (Figure 7). Tag trees provide a novel way of combining the benefits of a tag cloud with the semantic order of a hierarchy. To make the tag cloud and tag trees work effectively, we combined similar terms manually. For example, the terms “refuse”, “accumulated refuse”, “open accumulated refuse”, “refuse deposit”, “refuse deposits”, “open refuse deposit”, and “open refuse deposits” appearing in the article were amalgamated into a single term, “refuse deposit”, with an appropriate weighting.


Adventures in semantic publishing: exemplar semantic enhancements of a research article.

Shotton D, Portwin K, Klyne G, Miles A - PLoS Comput. Biol. (2009)

The Tag Tree for instances of the semantic concept Habitat.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2663789&req=5

pcbi-1000361-g007: The Tag Tree for instances of the semantic concept Habitat.
Mentions: Tag trees. Below the tag cloud, these same terms are segregated into the nine semantic classes used for highlighting the text (date, disease, habitat, institution, organism, person, place, protein, and taxon). The persons list includes both people mentioned in the text and the authors of the article, whose names are shown in bold font, but excludes the authors of cited references. In these lists, we maintained the colors and relative sizes of the terms from the tag cloud, and ordered them, where appropriate, into informal hierarchies—particularly noticeable for places and organisms. We call these displays tag trees (Figure 7). Tag trees provide a novel way of combining the benefits of a tag cloud with the semantic order of a hierarchy. To make the tag cloud and tag trees work effectively, we combined similar terms manually. For example, the terms “refuse”, “accumulated refuse”, “open accumulated refuse”, “refuse deposit”, “refuse deposits”, “open refuse deposit”, and “open refuse deposits” appearing in the article were amalgamated into a single term, “refuse deposit”, with an appropriate weighting.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Image Bioinformatics Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom. david.shotton@zoo.ox.ac.uk

ABSTRACT
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 (http://purl.org/net/cito/). The enhanced article, which is available at http://dx.doi.org/10.1371/journal.pntd.0000228.x001, 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.

Show MeSH
Related in: MedlinePlus