Abstract
BackgroundThe scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, because more than one name may point to the same taxon and multiple taxa may share the same name. In addition, scientific names change over time, which makes them open to various interpretations. Applying machine-understandable semantics to these names enables efficient processing of biological content in information systems. The first step is to use unique persistent identifiers instead of name strings when referring to taxa. The most commonly used identifiers are Life Science Identifiers (LSID), which are traditionally used in relational databases, and more recently HTTP URIs, which are applied on the Semantic Web by Linked Data applications.ResultsWe introduce two models for expressing taxonomic information in the form of species checklists. First, we show how species checklists are presented in a relational database system using LSIDs. Then, in order to gain a more detailed representation of taxonomic information, we introduce meta-ontology TaxMeOn to model the same content as Semantic Web ontologies where taxa are identified using HTTP URIs. We also explore how changes in scientific names can be managed over time.ConclusionsThe use of HTTP URIs is preferable for presenting the taxonomic information of species checklists. An HTTP URI identifies a taxon and operates as a web address from which additional information about the taxon can be located, unlike LSID. This enables the integration of biological data from different sources on the web using Linked Data principles and prevents the formation of information silos. The Linked Data approach allows a user to assemble information and evaluate the complexity of taxonomical data based on conflicting views of taxonomic classifications. Using HTTP URIs and Semantic Web technologies also facilitate the representation of the semantics of biological data, and in this way, the creation of more “intelligent” biological applications and services.Electronic supplementary materialThe online version of this article (doi:10.1186/2041-1480-5-40) contains supplementary material, which is available to authorized users.
Highlights
The scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names
Three other attributes are assigned to the scientific name: 1) a reference to the original publication in which the taxon description was first published, 2) a status of a name indicating its validity in the checklist, and 3) a taxonomic rank expressing level in a hierarchical classification
In order to recognise the orthographic variants of scientific names, Life Science Identifiers (LSID) are accommodated to the names as well
Summary
The scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, because more than one name may point to the same taxon and multiple taxa may share the same name. The most commonly used identifiers are Life Science Identifiers (LSID), which are traditionally used in relational databases, and more recently HTTP URIs, which are applied on the Semantic Web by Linked Data applications. Data is often presented using a variety of terms, vocabularies, and languages, which presents a barrier to interoperability and Scientific names are important for interlinking information about taxa in all fields of the Life Sciences. Difficulties arise when a particular taxon can be referred to using multiple names, since scientists’ opinions differ on how evolutionary units should be organised into classifications. Researchers may use the same name with a different meaning when referring to taxa. Efforts are made to provide usable taxonomies for non-taxonomists
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