[Taxacom] Tracking usages of biological collections, environmental terms and species traits in prospective publishing

Lyubomir Penev lyubo.penev at gmail.com
Fri Aug 21 17:38:09 CDT 2015


Definitely, markup could be restricted to sections of taxon treatments, for
example morphological terms can be tagged within the Description and
Diagnosis sections  only, ecological and environmental terms within Ecology
and Biology sections and so on, which will of course increase the semantic
value of the markup. The XML schema we use, TaxPub
<http://www.ncbi.nlm.nih.gov/books/NBK47081/>, allows to model all this in
the XML version of the article.

Ideally, the tagger should use different ontologies for the different taxa,
for example the Hymenoptera Anatomy Ontology
<http://portal.hymao.org/projects/32/public/ontology/>  should be used for
all papers/treatments dealing with hymenopterans, etc.

Linking to machine-readable ontologies would allow harvesting mechanisms to
disambiguate the meaning of identical/similar terms used in different
domains or taxa.

In the current pilot we marked up all text against three exemplar
ontologies, so what is there that is what is marked up. Sure, there is
still a long way to go to increase the usability of this kind of markup.
Most of it will probably be used for content mining and less by humans
during reading the article.

Thank you for the comment!

Lyubomir

On Fri, Aug 21, 2015 at 10:41 PM, Lawrence Kirkendall <
lawrence.kirkendall at bio.uib.no> wrote:

> The idea of a Terms button sounds like it could be a really useful
> development, and could really help readers not expert in the taxa being
> discussed. Implementation seems to be problematic, however. Clearly, this
> feature will be difficult to use if all or nearly all words in a text are
> included; surely the aim is to help readers with highly specialized
> terminology. Yet, perfectly ‘normal' English terms like “adult”, “finger”,
> “forest”, “highway”, and “tooth” are in this list, as is the questionable
> “leafmound”. Not in the list are dozens of specialized morpological terms
> such as “paranota”, “prozonite”, “ozopore”, and “ozopores”.
>
>
>
>
> Prof. Lawrence Kirkendall
> Department of Biology
> Univ. Bergen
>
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