Semantic Vernacular System: an Observation-based, Community-powered, and Semantics-enabled Naming System for Organisms

The Semantic Vernacular System is a novel naming system for creating named, machine-interpretable descriptions for groups of organisms. Unlike the traditional scientific naming system, which is based on evolutionary relationships, it emphasizes the observable features of organisms. By independently naming the descriptions composed of sets of ob- servational features, as well as maintaining connections to scientific names, it preserves the observational data used to identify organisms. The system is designed to support a peer- review mechanism for creating new names, and uses a controlled vocabulary encoded in the Web Ontology Language to represent the observational features. A prototype of the system is currently under development in collaboration with the Mushroom Observer website. It allows users to propose new names and descriptions, provide feedback on those proposals, and ulti- mately have them formally approved. This effort aims at offering the mycology community a knowledge base of fungal observational features and a tool for identifying fungal observations.

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Fungi are typically referred to by either scientific or common names. Neither of these terminologies meets the need for well-defined, persistent definitions of groups of fungi who exhibit similar macroscopic qualities, but may be dissimilar genetically. We propose a community-developed vocabulary that can be used to identify mushrooms based on properties that can be observed in the field (without microscopic or genomic examination). We show how an ontology can be used to develop and organize the terms and definitions and to enable applications based on the vocabulary.