Presenting and Preserving the Change in Taxonomic Knowledge for Linked Data

Tracking #: 1123-2335

Authors: 
Rathachai Chawuthai
Hideaki Takeda
Vilas Wuwongse
Utsugi Jinbo

Responsible editor: 
Pascal Hitzler

Submission type: 
Full Paper
Abstract: 
Taxonomic knowledge provides a scientific name to each organismal group and is thus indispensable information for understanding biodiversity. However, the various perspectives of classifying organisms and changes in taxonomic knowledge have led to inconsistent classification information among different databases and repositories. To have a precise understanding of taxonomy, one needs to integrate relevant data across taxonomic databases. This is difficult to establish due to the ambiguity in taxon interpretation. Most researchers in earlier stages employed the Linked Open Data (LOD) technique to establish links in taxonomy transition. However, they overlooked the temporal representation of taxa and underlying knowledge of the change in taxonomy, so it is difficult for learners to gain perspective on how some identifiers of taxa are linked. To this end, this research is aimed at developing a model for presenting and preserving the change in taxonomic knowledge in the Resource Description Framework (RDF). Specifically, the proposed model takes advantage of linking Internet resources representing taxa, presenting historical information of taxa, and preserving the background knowledge of the change in taxonomic knowledge in order to enable a better understanding of organisms. We implement a prototype to demonstrate the feasibility and the performance of our approach. The results show that the proposed model is able to handle various practical cases of changes in taxonomic works and provides open and accurate access to linked data for biodiversity.
Full PDF Version: 
Tags: 
Reviewed

Decision/Status: 
Accept

Solicited Reviews:
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Review #1
By Anne Thessen submitted on 17/Aug/2015
Suggestion:
Minor Revision
Review Comment:

I liked this paper very much. This version is much better. Overall, the English is good, but could use some proof-reading attention.
Possible typo - Is the first instance of Buidae_2 on page 9 supposed to be Buidae_1?
The paper is very good, but I have some questions.
1. How would this system handle disagreement between taxonomists? For example, according to one person a taxon is merged with another, but according to another person the taxa remain distinct.
2. Can the cause and effect statements accommodate pointers to actual studies? For example on p12-13 it says that rp1 was caused by mg1, but what data justified the merge?
Just as a comment - I can see a good use case for this system to be automatic annotation of historical data with current, accepted names.


Comments

First of all, we were impressed by the reviewer comments and suggestions, which were constructive and helpful in improving our manuscript. Our responses are in the following statements.

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Possible typo - Is the first instance of Buidae_2 on page 9 supposed to be Buidae_1?

[Response]: We accepted this mistake and edited it.

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1. How would this system handle disagreement between taxonomists? For example, according to one person a taxon is merged with another, but according to another person the taxa remain distinct.

[Response]: We also understand this issue; however, our work does not aim to assemble every change into a single dataset. We developed this approach based on the ground of Semantic Web, because we realized that this technology is designed for supporting the exchangeability of multiple data repositories (or data spaces).

In this case, the different perspectives among communities of taxonomists can be represented by data in different spaces. In practice, one space can be one RDF graph model that is responded by one LTK system. Every community should have own installation of the LTK system. When data spaces are separated, a community of taxonomists can work with data from some agreed systems.

In addition, we recommended data providers to reuse an existing URI (if applicable) or to give a link to an existing URI from a well-known repository in order to link some data across some spaces.

In future, a mashup tool can access various data spaces in order to present both the whole history of the change in taxonomies and the association among different taxonomies based on the different agreements among communities of taxonomists. Thus, learners are able learn and understand any taxonomies from different time and/or different space.

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2. Can the cause and effect statements accommodate pointers to actual studies? For example on p12-13 it says that rp1 was caused by mg1, but what data justified the merge?

[Response]: We provided the metadata about the change by assigning references to the event entity. The previous version of our manuscript contained these metadata in the RDF statements on the 12th page. In the final version (camera-ready), we added some descriptions about those metadata at the last sentence of that page.

  • bibo:performer : Names of researchers who discovered the changes.
  • bibo:issuer : Names of researchers who gathered and reported the changes.
  • dct:source : URIs of publications that mentioned the changes.

In the example RDF statement, we used Richard C. Bank as an issuer, because he mentioned the change of some species names that are caused by the merging between the genera Bubo and Nyctea in the checklist of the North American birds.

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Sincerely yours,
Authors