Word add-in for ontology recognition: semantic enrichment of scientific literature

Abstract

BackgroundIn the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely necessary and new media are allowing information and knowledge to be more interactive and immediate. One approach to making knowledge more accessible is the addition of machine-readable semantic data to scholarly articles.ResultsThe Word add-in presented here will assist authors in this effort by automatically recognizing and highlighting words or phrases that are likely information-rich, allowing authors to associate semantic data with those words or phrases, and to embed that data in the document as XML. The add-in and source code are publicly available at http://www.codeplex.com/UCSDBioLit.ConclusionsThe Word add-in for ontology term recognition makes it possible for an author to add semantic data to a document as it is being written and it encodes these data using XML tags that are effectively a standard in life sciences literature. Allowing authors to mark-up their own work will help increase the amount and quality of machine-readable literature metadata.

Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over

“…The use of ontologies and their significance is well studied by Hur et al ( 2011 , 2015 ) in their work on gene-gene interactions and vaccines. Many more recommendations to improve the scientific literature's human and computer accessibility are available (Stevens et al, 2002 ; Leitner and Valencia, 2008 ; Sainani, 2008 ; Attwood et al, 2009 ; Fink et al, 2010 ) talking of liquid publications 7 etc. are discussed in greater depths.…”

Authoring and Publishing Units and Quantities in Semantic Documents

“…the semantic L A T E X extensions sT E X [25], SALT [19], the Ontology Add-in for Microsoft Office Word [14], or the semantic content management system PAUX [33]) have so far neglected the specific use case of units. This can be partially explained by the lack of a widely agreed standard representation, as well as different primary development foci -mathematics for sT E X, rhetorical structures for SALT, life sciences terminology for the Word ontology add-in, and educational texts from areas unrelated to physics, such as law, for PAUX.…”

The Five Stars of Online Journal Articles – an article evaluation framework

“…). An open-source plugin to Word 2007 has been published that permits semantic markup of named entities according to chosen ontologies [7], and it is hoped that other such authoring tools will soon become available. Editors and publishers can also provide semantic enhancements, as exemplified by the Royal Society of Chemistry's Project Prospect journals 6 , and by Elsevier's Article of the Future 7 .…”

“…http://www.rsc.org/Publishing/Journals/ProjectProspect/ 7. http://www.elsevier.com/wps/find/authored_newsitem.cws _home/companynews05_01979 8.…”