Proceedings of TDWG : Conference Abstract
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Corresponding author: Régine Vignes-Lebbe (regine.vignes_lebbe@upmc.fr)
Received: 16 Aug 2017 | Published: 17 Aug 2017
© 2017 Amélie Pinel, Sylvain Bouquin, Estelle Bourdon, Adeline Kerner, Régine Vignes-Lebbe
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Pinel A, Bouquin S, Bourdon E, Kerner A, Vignes-Lebbe R (2017) Three years of Xper3 assessment: towards sharing semantic taxonomic content of identification keys. Proceedings of TDWG 1: e20382. https://doi.org/10.3897/tdwgproceedings.1.20382
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Xper3 is a collaborative system that manages structured descriptive data on taxa or specimens. It is available online and linked to web services including two services for identification: a free (multiple) access key (
KB owners are free to publicize their keys in publications (
This has two consequences:
In order to solve the first problem, we analyse Xper3 metadata (e.g., name of KB, owner, number of contributors, date of creation, date of last modification) and we provide an overview of the existing content. Firstly, 48% of KB are empty or inactive with extremely limited content (fewer than 3 taxa or characters), which has not been accessed for a long time. We discard these KB in our analysis and only consider the 1300 active KB. We also discard “test” KB and duplicate KB. Surprisingly, we discovered 15 medical KB for diagnosis of various diseases and 34 non-taxonomic KB (e.g., wine, fashion, computing equipment). For taxonomic KB, we present the taxonomic and geographic distribution of the KB (angiosperms and arthropods are prevailing taxa) and we compare with the number of known species.
The second point concerns semantic data sharing. We compute the rate of terms (character, character state) duplicated in several KB in the same taxonomic groups, in order to evaluate the interest in sharing resources between Xper3 KB. Then we look for existing ontologies in the bioportal (https://bioportal.bioontology.org/ontologies). Although Xper3 may manage structured data, its data model does not use an ontology language like RDF*
We will be contacting KB owners to obtain more detailed metadata and to facilitate the automatic publishing of authorized KB on the Xper3 website. We plan also to implement an easy link between Xper3 and external ontologies to help editing new KB and to export KB data models to existing ontologies.
Xper3, knowledge base, identification keys, ontology
Régine Vignes Lebbe
RDF: Resource Description Framework. This language of the semantic web uses triples “subject - predicate - value”
OWL: Web Ontology Language