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    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.0​000228.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.
    16 years ago by @pitman
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    Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.
    16 years ago by @pitman
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    ACL Bibliographies Doug Arnold University of Essex January 14, 2008 This page gives access to the bibliographies I am constructing as part of the ACL Anthology. Here you will find bibtex, html, and pdf versions of the bibliographies. This is very much `work in progress', and I do not guarantee them as to accuracy, or anything else. I especially welcome corrections. The bibliographies are searchable by following this link (select the ACL bibliography from the pull down menu). * Computational Linguistics (Journal) * ACL Proceedings * EACL Proceedings * NAACL Proceedings * ANLP Proceedings * TINLAP * COLING * HLT Proceedings * Message Understanding Conferences (MUC) * Workshops * Coling Workshops * SIGs: Independent ACL SIG Meetings
    17 years ago by @pitman
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    I am investigating computational models for linguistic structures and processes, with application to language technologies and to the documentation of endangered languages. My current focus is on efficient query for databases of hierarchically annotated data. After completing a PhD on computational phonology at the University of Edinburgh in 1990, I worked on a series of European research projects and conducted linguistic fieldwork in Cameroon with SIL. In 1998 I moved to the University of Pennsylvania, becoming Associate Director of the LDC, and working on models and tools for linguistic annotation. In 2002 I returned home to Australia and established the Melbourne University Language Technology Group. In 2007 I was awarded the Kelvin Medal for excellence in teaching. Key Activities: Coordinating first year Informatics; developing the Natural Language Toolkit; writing a textbook on NLP; leading the Language Technology Group; working on an NSF project on Querying Linguistic Databases; and editing Cambridge Studies in Natural Language Processing and the ACL Anthology. Key Publications: Natural Language Processing in Python; Computational phonology: A constraint-based approach (Cambridge); A formal framework for linguistic annotation (Speech Communication); Seven dimensions of portability for language documentation and description (Language); Designing and evaluating an XPath dialect for linguistic queries (ICDE).
    17 years ago by @pitman
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