Atrium: Using digitized biocollections to generate customizable field guides

Background/Question/Methods

The Digital Herbarium, the core module of the Atrium biodiversity information system (www.atrium-biodiversity.org), was designed to manage plant collection data and associated images for single institutions and multiple-institution regional biodiversity portals. Atrium provides many tools for entry, sorting, filtering, and analysis of botanical collection data. Users can browse collections by taxonomy, collector, project, geographic region, and many other options via advanced search capabilities. Users can view detailed collection data, high-resolution zoomable images, automatically generated distribution maps, and taxon descriptions at multiple taxonomic levels. Duplicate specimens at multiple institutions are managed under one collection record. All data and images are downloadable.

The Atrium Digital Herbarium provides administrative interfaces that allow collection managers and botanists with appropriate permission levels to enter and edit data online. One of the key features is an online annotation system that allows taxonomists to annotate specimens remotely. All collection data is versioned and additions and corrections of data are tracked for each object.  The full annotation history of each collection is provided. Collections managers can search and view recent annotations and automatically print annotation labels. Primary specimen labels can also be automatically generated using this label engine. A checklist generator creates and allows users to download family, genus, and species checklists by project, research site, geographic region, or any other user-generated dataset.

Atrium’s Workspace tool allows users to add collections, data, and images to a personal workspace for more in-depth studies, analysis, and download. The workspace, which can be shared between users, features a virtual herbarium table where two zoomable specimen images can be compared side by side for proper identification and annotation.  Users can select desired images representing any number of taxa of interest and save these to a workspace, and then use the Field Guide generator to select one of three field guide formats representing 1) image guide with taxon names, 2) taxon guide with morphological descriptions and images, or 3) collection guide with individual collection records and images. A printable PDF is automatically generated.

Results/Conclusions

Atrium’s user-generated field guides are infinitely customizable, sharable, and updateable.  This user-friendly tool enables a broad range of people to use online scientific collections of data and appreciate the value of these collections.  Professionals, students, and citizen scientists can all benefit from this simple and useful output from a biodiversity database.  Science and conservation initiatives benefit by facilitating broader use of biodiversity data.