University of Glasgow

Roderic Page

Nice paper by Robert Huber and Jens Klump has appeared in *Computers &
Geosciences* entitled \"Charting taxonomic knowledge through ontologies
and ranking algorithms\"
([doi:10.1016/j.cageo.2008.02.016](http://dx.doi.org/10.1016/j.cageo.2008.02.016)).
The paper is not open access, but you can get some background from the
post [How TaxonRank
works](http://stratigraphynet.blogspot.com/2008/01/how-taxonrank-works.html).
Here\'s the abstract.  
  

> Since the inception of geology as a modern science, paleontologists
> have described a large number of fossil species. This makes fossilized
> organisms an important tool in the study of stratigraphy and past
> environments. Since taxonomic classifications of organisms, and
> thereby their names, change frequently, the correct application of
> this tool requires taxonomic expertise in finding correct synonyms for
> a given species name. Much of this taxonomic information has already
> been published in journals and books where it is compiled in carefully
> prepared synonymy lists. Because this information is scattered
> throughout the paleontological literature, it is difficult to find and
> sometimes not accessible. Also, taxonomic information in the
> literature is often difficult to interpret for non-taxonomists looking
> for taxonomic synonymies as part of their research.  
>   
> The highly formalized structure makes Open Nomenclature synonymy lists
> ideally suited for computer aided identification of taxonomic
> synonyms. Because a synonymy list is a list of citations related to a
> taxon name, its bibliographic nature allows the application of
> bibliometric techniques to calculate the impact of synonymies and
> taxonomic concepts. TaxonRank is a ranking algorithm based on
> bibliometric analysis and Internet page ranking algorithms. TaxonRank
> uses published synonymy list data stored in TaxonConcept, a taxonomic
> information system. The basic ranking algorithm has been modified to
> include a measure of confidence on species identification based on the
> Open Nomenclature notation used in synonymy list, as well as other
> synonymy specific criteria.  
>   
> The results of our experiments show that the output of the proposed
> ranking algorithm gives a good estimate of the impact a published
> taxonomic concept has on the taxonomic opinions in the geological
> community. Also, our results show that treating taxonomic synonymies
> as part of on an ontology is a way to record and manage taxonomic
> knowledge, and thus contribute to the preservation our scientific
> heritage.


Nice paper by Robert Huber and Jens Klump has appeared in
<em>
 Computers &amp; Geosciences
</em>
entitled "Charting taxonomic knowledge through ontologies and ranking algorithms" (doi:10.1016/j.cageo.2008.02.016). The paper is not open access, but you can get some background from the post How TaxonRank works. Here's the abstract.

Charting taxonomic knowledge

Stumbled across [Project
Xanadu](http://en.wikipedia.org/wiki/Project_Xanadu), Ted Nelson\'s
vision of the way the web should be (e.g., [BACK TO THE FUTURE:
Hypertext the Way It Used To
Be](http://xanadu.com/XanaduSpace/btf.htm)). Nelson coined the term
\"[transclusion](http://en.wikipedia.org/wiki/Transclusion)\", including
one document in side another by reference. The screen shot of [Xanadu
Space](http://xanarama.net/) may help illustrate the idea:  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGSyO-tIiEiaO-GAYhh5OvGKrF883tuh_WN93jQGfOLJiWVzHxfNEP6am8wtqJjnBW0sh8SynqTjPmSXl5yuyfYxarObLmL08JRdJbd6uuZyhil-LMt62dDYS19YtoHyRagtXv/s320/fwDemoOrigins-panorama2.png){#BLOGGER_PHOTO_ID_5174556763887519858
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGSyO-tIiEiaO-GAYhh5OvGKrF883tuh_WN93jQGfOLJiWVzHxfNEP6am8wtqJjnBW0sh8SynqTjPmSXl5yuyfYxarObLmL08JRdJbd6uuZyhil-LMt62dDYS19YtoHyRagtXv/s1600-h/fwDemoOrigins-panorama2.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Nelson envisages a web where instead of just one-way links, documents
include parts of other documents, and one can view a document
side-by-side with the source documents. Modern web browsers transclude
images (the image file is not \"physically\" in the document, rather it
exists elsewhere), but mostly they link to other documents via
hyperlinks.  
Ted Nelson\'s writings are a fascinating read, partly because they
remind you just how much of the web we take for granted, and how thinks
could be different (better?). One thing he objects to is that much of
the the web simulates paper  

> Much of the field has imitated paper: in word processing (Microsoft
> Word and Adobe Acrobat) and the World Wide Web, whose rectangular page
> layouts become a focal issue. It should be noted that these systems
> imitate paper under glass, since you can\'t annotate it.

Nelson also advocates every element of a document having its own unique
address, not just at book or article level. This resonates with what is
happing with digital libraries. Gregory Crane in his article \"What Do
You Do with a Million Books?\"
([doi:10.1045/march2006-crane](http://dx.doi.org/10.1045/march2006-crane))
notes that:  

> Most digital libraries still mimic their print predecessors, treating
> individual objects -- commonly chunks of PDF, RTF/Word, or HTML with
> no standard internal structure -- as its constituent units. As digital
> libraries mature and become better able to extract information (e.g.,
> personal and place names), each word and automatically identifiable
> chunk of words becomes a discrete object. In a sample 300 volume, 55
> million word collection of nineteenth-century American English,
> automatic named entity identification has added 12,000,000 tags. While
> this collection focuses on name rich historical materials and includes
> several reference works, this system already discovers thousands of
> references to named entities in most book length documents. We thus
> move from single catalogue entries with a few hundred words to
> thousands of tagged objects -- an increase of at least one order of
> magnitude with named entities and of at least two orders of magnitude
> when we consider each individual word as an object.

I discovered Crane\'s paper via Chris Freeland\'s post [On Name Finding
in the
BHL](http://biodiversitylibrary.blogspot.com/2008/03/on-name-finding-in-bhl.html).
Chris summarises BHL\'s work on scanning biodiversity literature and
extracting taxonomic names. BHL\'s output is at the level of pages,
rather than articles. Existing GUIDs for literature (such as DOIs and
SICIs) typically identify articles rather than pages (or page elements),
so there\'s a need to extending these to pages.  
  
Chris also raises the issue of ranking and relevance \-- \"What do you
do with 19,000 pages containing Hymenoptera?\". One possibility is to
explore Robert Huber\'s
[TaxonRank](http://stratigraphynet.blogspot.com/2008/01/how-taxonrank-works.html)
idea (inspired by Google\'s PageRank). This would require text mining to
build synonomy lists from scanned papers, challenging but not
impossible. But I suspect that the network of citations is what will
help build a sensible way to rank the 19,000 pages.  
  
A while ago people were speculating what Google could do to help
biodiversity informatics. I found much of this discussion to be vague,
with no clear notion of what Google could actually do. What I think
Google is exceptionally good at are two things we need to tackle \--
text mining, and extracting information from links. I think this is
where BHL and, by extension, EOL, should be devoting much of their
resources.


Stumbled across Project Xanadu, Ted Nelson's vision of the way the web should be (e.g., BACK TO THE FUTURE: Hypertext the Way It Used To Be). Nelson coined the term "transclusion", including one document in side another by reference.

Messaggi di Rogue Scholar

Charting taxonomic knowledge

Word for the day - "transclusion"