To facilitate manual annotation of the taxonomic dataset, we make use of the Brat Rapid Annotation Tool (BRAT), a web-based tool for text annotation. We adapted it specific for the semantic annotation of taxonomic elements in biodiversity literature. As shown in Figure 1, all mentions of taxonomic names in the text were manually tagged and linked to the identifiers of the external taxonomic databases (e.g., uBio Name Bank, Catalogue of Life, and Encyclopaedia of Life) if possible.
Figure 1. Adapted BRAT Annotation Tool
Annotated mentions were also assigned to several categories that indicate specific linguistic or semantic features of mentions, e.g. taxonomic rank, genus abbreviation or omission, which can be used in evaluation analysis as shown in Figure 2.
Figure 2. Taxonomic Name Tagging
This adapted annotation tool can be easily extended for semantic annotation of other taxonomic elements (e.g., bibliography, habitats, geographic distribution of organisms, and the collection of specimen), which are also considered as playing import roles in the integration and re-purpose of biodiversity information across diverse sources.
Currently, this adapted BRAT annotation tool is installed on our department web server, and is only accessed by the internal staff.