A Logical Model for Taxonomic Concepts for Expanding
Knowledge using Linked Open Data
Rathachai Chawuthai1, Hideaki Takeda2, Vilas Wuwongse3, and Utsugi Jinbo4
1

Asian Institute of Technology, Prathumtani, Thailandrathachai.chawuthai@ait.ac.th
2
National Institute of Informatics, Tokyo, Japan
takeda@nii.ac.jp
3
Thammasat University, Prathumtani, Thailand
wvilas@engr.tu.ac.th
4
National Museum of Nature and Science, Tokyo, Japanujinbo@kahaku.go.jp

Abstract. The variety of classification systems and the new discovery oftaxonomists lead to the diversity of biological information, especially taxon
concepts. The association among taxon concepts across research institutes isvery difficult to establish, because there is no single interpretation of the nameof a taxon concept. Owing to this difficulty, further expansion of morebiological knowledge is very complicated for taxonomists when they deal withmany sources of data or ambiguous concepts. In order to link some relevant
taxon concepts across research repositories, it is necessary to consider theprecise context of bioloical data also. As a result, we propose a logical modelfor taxon concepts in Resource Description Framework (RDF). Moreover, we
implement a prototype to demonstrate the feasibility of our approach. It has
been found that our model can publish taxon information as linked data and,hence, with additional benefits from Linked Open Data (LOD) cloud.
Keywords. Logical model, Linked data, Ontology, Taxon Concept

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Background

More than 1.4 million species throughout the world have been truly described andclassified with appropriate naming depended upon their characteristics; such as, morphological characters, living behaviors, DNA sequences, etc. [1-2]. Many taxonomists
have studied living things, research, and publish their knowledge for over hundredyears. However, before the information age, their researches were not completely
shared across all researchers around the world. Some researchers might have different
perspectives to classify and name their specimens. It is possible that the same species
may be classified and named differently [2]. For example, Papilio xuthus, Chinese
yellow swallowtail butterfly, has been given at least four names by four taxonomists.
As a result, scholars and researchers are inconvenient to study all information about
one living thing completely from a single taxonomic name.

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The Proposed Logical Model

Our paper presents a logical model and ontology for linking taxon concepts which
comprises a series of changes, the diversity of taxonomic classifications, and the variety of naming. For the purpose of linking data, we have developed our model by employing ontology of contextual knowledge evolution together with some widely accepted ontology such as LODAC [3] and SKOS [4]. This research proposed some
useful operations that specify the changes of taxon concepts; for instance, change
taxonomic hierarchy, rename, merge, replace, split, etc. We also introduced somekinds of links between taxon concepts, for example, common name, correct spelling,homonym, junior synonym, senior synonym, etc. The model is expressed in an ontology named Linked Taxonomic Knowledge (LTK). Moreover, we enhance the Contextual Knowledge for Archives (CKA) ontology in order to deal with both dynamic
and static information represented in RDF and hence the history of the taxon concept
can be traced back [5]. For example, two genera of owls named Nyctea and Bubo
have been merged into the latter genus Bubo. Following the change of genera, thescientific name of a snowy owl Nyctea scandiaca has been replaced by Bubo scandiacus in order to satisfy the convention of scientific name [6-7]. These facts will bepresented in RDF that satisfies the logical model from the CKA approach as follows:
ex:even1999
ex:mg1
ex:rp1

cka:interval
cka:assure
rdf:type
cka:conceptBefore
cka:conceptAfter
rdf:type
cka:conceptBefore
cka:conceptAfter[tl:beginAtDateTime “1999”] ;ex:mg1, ex:rp1 .
ltk:MergingTaxonConcept ;genus:Bubo, genus:Nyctea ;genus:Bubo_1999 .
ltk:ReplacingTaxonConcept ;species:Nyctea_scandiaca ;species:Bubo_scandiacus .

In practice, we implement prototype by having inference rule, so it can trace back to
the changes of these species’ names that are caused from the merging of the two genera. In addition, the application provides links to the relevant data with the data inLODAC. As a result, we found that our LTK model is feasible and suitable for collecting the change of taxon concepts and establishing links to relevant concepts acrossresearch institutes in order to expand more knowledge about taxon concepts.

References
1. Darwin, C., Peckham, M.: On the Origin of Species by Means of Natural Selection, or thePreservation of Favoured Races in the Struggle for Life. Penn Press, Philadelphia (1959)
2. Winston, J. E.: Describing Species: Practical Taxonomic Procedure for Biologists. Columbia University Press, New York (1999)
3. Linked Open Data for Academia, http://lod.ac/
4. http://www.w3.org/2009/08/skos-reference/skos.html
5. Chawuthai, R., Wuwongse, V., Takeda, H.: A Formal Approach to the Modeling of Digital
Archives. In: ICADL’12, Taipei (2012)
6. Wink, M., Heidrich, P.: A Guide to Owls of the World. Yale University Press (1999)
7. International Code of Zoological Nomenclature, http://www.iczn.org

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