Biomedical Engineering Reference
In-Depth Information
1. Although originating in a commercial environment, PDF is now -
and has been for some considerable time - an open format. The
specifi cations of the PDF have been publically available for many
years, and have been formally 'public domain' since 2008, when
Adobe released the format as ISO 32000-1 and offi cially waived any
patents relating to creating or consuming PDF content [9]. It is,
however, undoubtedly a more verbose, and arguably less-elegant
format than more recent offerings.
2. The PDF has the potential to be as 'semantically rich' as any of the
other alternatives (e.g. eBook, XHTML), and, since version 1.4 in
2001, has had the facility to include arbitrarily sophisticated
meta-data. The fact that virtually no publishers use this feature is not
a fault of the PDF, and such semantic richness is just as conspicuously
absent from the other formats used to publish scientifi c material.
Speculation as to which link in the chain between author,
publisher, and consumer causes this omission, we leave entirely to
the reader.
Regardless of whether the PDF is a suitable vehicle for disseminating
scientifi c knowledge, there are two irrefutable facts: fi rst, it is by far the
most popular medium by which scientifi c articles are consumed
(accounting for over 80% of downloaded articles); and second, even if
publishers move to a more 'web friendly' format at some point in the
future, vast numbers of legacy articles will remain only as PDFs (many of
which are digital scans of back-catalogues that pre-date even this ancient
format, some of which have had text extracted via optical character
recognition, while many exist only as images) - at the very least, these
would require converting into something more 'semantic'. In spite of
signifi cant effort by publishers to enhance their online/HTML content
with additional links, meta-data, data and multimedia extensions, the
PDF stubbornly remains the format of choice for most readers. The
recent growth in modern tools for managing collections of PDFs (e.g.
Mendeley [10] and Papers [11]) gives additional backing to the view that
the PDF is not in any danger of disappearing yet.
In an attempt to bridge the divide between what scientists actually
read, and what computers need to support the process of taming the
scientifi c literature, we embarked on a project to build a new tool for
linking the content of articles with research data. The resulting software
- Utopia Documents [12, 13] - combines all the advantages of the PDF
with the interactivity and interconnectedness of a blog or web page.
Acting as an alternative desktop application to Adobe Acrobat and other
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