A Logical Model for Taxonomic Concepts for Expanding Knowledge using Linked Open Data

OverviewMillions of species throughout the world

have been classified and named by different

perspectives among taxonomists. For example,

the Chinese peacock butterfly named Papilio

bianor okinawensis and Papilio bianor

ryukyuensis have been reclassified many

times. The up-to-date information may not be

enough for researchers to learn from a single

taxonomic name, whereas, the history of

change and linked data of it can expand more

knowledge about taxon concepts.A logical model for taxon concepts in

RDF has been proposed in order to record the

change of taxon concepts and publish in

LOD.

1. To develop ontology to present the change of taxon concepts and open link to public.2. To Implement a prototype to ensure the feasibility of the model.

Linked Taxonomic Knowledge (LTK) Ontology

Prototype

https://sites.google.com/site/linkedtaxon

Download LTK Ontology: please visit

Web Interface Service Data

JenaRDF

Framework

SESAMERDF

Store

Papilio bianor okinawensis(P. b. okinawaensis)has been named by Fruhstorfer since 1898

Papilio bianor ryukyuensis (P. b. ryukyuensis)has been named by

Fujioka since 1975

One taxonomist has reclassified by merging into the older name P. b. okinawensis

P. b. okinawensis P. b. ryukyuensis

Afterwards, a taxonomist has considered to split that name into P. b. okinawensis and P. b. ryukyuensis again.

Discover moreinformation

Example Problem

In this case, if present-day researchers study a species named P. b. ryukyuensis, they may consume only information about .

However, some information of , that were recorded by with name P. b. okinawaensis, might be missing. Because, at that time, P. b. ryukyuensis were interpreted as P. b. okinawaensis.

Let’s start with the scenario of the changes of two species of Chinese peacock butterflies . . . . . . .

Objectives

Rathachai CHAWUTHAIAsian Institute of Technologyrathachai.c@gmail.com

Hideaki TAKEDANational Institute of Informatics

Vilas WUWONGSEThammasat University

Utsugi JINBONational Museum of Nature and Science

Please visit

The prototype is a web-based system that comprises three service layers: web interface, business service, and RDF data store. (1) the Web Interface allows a user to create the knowledge of taxon concepts in RDF. It also demonstrates the temporal context and link of taxon concepts. Furthermore, it presents the reasons and details about changes of them. (2), the Java Servlet Service is made for managing and computing RDF data by using the power of Jena reasoning engine. Other applications can access data via this layer. (3) The Data layer, we used SESAME, a RDF store, to record data. Moreover, the prototype can publish data to LOD cloud, and provide SPARQL endpoint for other services.

Chan

ges o

f Tax

on C

once

pt

Name

RenameNew name

Spelling sequence

Synonym

Junior Synonym

Senior Synonym

Common Name

HomonymJunior Homonym

Senior Homonym

Classification

RemodelMerging

Splitting

Hierarchy Change

Promoting

Demoting

Changing higher taxon

The logical model is expressed in an ontology named Linked Taxonomic Knowledge (LTK). This model extends ontology of Contextual Knowledge for Archives (CKA) by focusing on the operations of changes of taxon concepts.

The classification of changes of taxon concepts is

Moreover, the LTK also reuses some properties from SKOS and LODAC. For example the property representing higher rank of taxon concepts called ltk:higherTaxon is derived from skos:broaderTransitive and species:hasSuperTaxon.

Example of properties are

Property rdfs:subPropertyOfltk:higherTaxon cka:higherClass, skos:broaderTransitive, and

species:hasSuperTaxon

ltk:mergedInto cka:serialLinkTo, and skos:relatedMatchltk:synonym skos:exactMatch

The LTK ontology describes the change of taxon concepts by identifying the operation of changes firstly. The operation is represented by a Class that can be ltk:MergeingTaxonConcept, ltk:SplitingTaxonConcept, ltk:ReplacingTaxonConcept, ltk:ChangingHigherTaxon, ltk:CorrectSpellingLink, ltk:CommonNameLink, ltk:JuniorSynonymLink, ltk:SeniorSynonymLink, etc. After that, it needs to assign some parameters of the operation by properties cka:conceptBefore (a concept before change) and cka:conceptAfter (a concept after change). Finally, an aspect of time has to be added by a property tl:beginAtDateTime.

The example RDF model illustrates that the species:Pb_okinawensis and species:Pb_ryukyuensis have been merged into species:Pb_okinawensis_yyyy. The suffix _yyyy (represent the year of change) shows that the concept species:Pb_okinawensis_yyyy differs from the concept species:Pb_okinawensis because the former is broader than the latter. Thus, every change of taxon concepts results to a new identity and some old relationships have to be transferred to the new one.

cka:conceptAfter

cka:conceptBefore

ltk:MergingTaxonConcept

species:Pb_okinawensis

species:Pb_ryukyuensis

species:Pb_okinawensis_yyyy

cka:conceptBeforerdf:type

“YYYY-MM-dd”

tl:beginAtDateTime