Nomencurator: a nomenclatural history model to handle multiple taxonomic views

Abstract

Evolutionary studies are generating increasing numbers of phylogenies which, in turn, sometimes result in changes to hierarchical organization and therefore changes in taxonomic nomenclature. A three-layered data model for a nomenclature database has been developed in order to elucidate the information structure in nomenclature and as a means to organize and manage a large, dynamic knowledge-base. In contrast to most other taxonomic databases, the model is publication-oriented rather than taxon-oriented and dynamic rather than static, in order to mimic the processes that taxonomists use naturally. The three-layered structure requires data integrity localized to each publication, instead of global data integrity, which relaxes constraints common to taxonomic databases and permits multiple taxonomic opinions: taxon names are made available as metadata within the model. Its prototype implementation, written in C + + , has an autonomous self-identification mechanism to avoid spurious data-inflation in a publication-oriented data model. Self-identification is also desirable for distributed implementations of the nomenclature database. Publication-oriented design also will make maintenance easier than for taxon-oriented databases, much of the maintenance workload being amenable t o automation. The three-layered data model was designed for use by taxonomists, but is also able to provide concise, reduced expression for non-experts required in biodiversity research, for example.

Presenting and preserving the change in taxonomic knowledge for linked data

“…Due to such a change in taxonomic names, when one who studies species data accesses only information containing only the present scientific name, she or he sometimes misses important information that was recorded with its former scientific names. This means that the scientific names and taxonomy lack a single interpretation in biology [29,49]. Thus, to understand taxonomy thoroughly, we therefore need to know all synonyms across multiple datasets and then link their associated information together via the Internet [18].…”

“…A poor data model leads to the lack of linkability among different datasets [37]. A scientific name alone is not enough for introducing a precise link [3,22,23,25,32,33,37,38,49]. The International Organization for Plant Information (IOPI) model [3] used taxonomic names together with circumscription references as potential taxa for linking data among multiple taxonomic views.…”

The potential of using sets of specimens to handle species concepts

“…The expression of taxonomic and nomenclatural acts as functions on sets may aid the design of systems that record and track species concepts, which will by necessity need to be stored in databases. This approach is the reverse of [9] who developed an object-orientated model, and later showed it could be made into a relational database. Such a system could also be used to automatically describe relationships between subjects between taxonomic concepts as described by [8].…”

Scientific Names Are Ambiguous as Identifiers for Biological Taxa: Their Context and Definition Are Required for Accurate Data Integration

“…A strength of the TCS schema is that it supports many recent innovative models and implementations of taxonomic information as well as dealing with legacy data. Several of these models have been developed specifically to allow the representation of multiple, alternative taxonomic views (HICLAS [25,26]; PROMETHEUS [27]; BERLIN/IOPI [7][8][9]; TAXONOMER [22]; NOMENCURATOR [28]; uBIO www.ubio.org), rather than the standardized single view represented by many global taxonomic checklists (e.g. ITIS www.itis.usda.org; Species2000 www.sp2000.org).…”