Symbiota - A virtual platform for creating voucher-based biodiversity information communities

Abstract

We review the Symbiota software platform for creating voucher-based biodiversity information portals and communities. Symbiota was originally conceived to promote small- to medium-sized, regionally and/or taxonomically themed collaborations of natural history collections. Over the past eight years the taxonomically diverse portals have grown into an important resource in North America and beyond for mobilizing, integrating, and using specimen- and observation-based occurrence records and derivative biodiversity information products. Designed to mirror the conceptual structure of traditional floras and faunas, Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization. The themed portals enable meaningful access to biodiversity data for anyone from specialist to high school student. Symbiota emulates functionality of modern Content Management Systems, providing highly sophisticated yet intuitive user interfaces for data entry, batch processes, and editing. Each kind of content provision may be selectively accessed by authenticated information providers. Occupying a fairly specific niche in the biodiversity informatics arena, Symbiota provides extensive data exchange facilities and collaborates with other development projects to incorporate and not duplicate functionality as appropriate.

Keywords: Biodiversity informatics; Open Source; digitization; economy of scale; natural history collection; virtual collection portals.

Figure 1.

Partial screenshot of the Search Collections panel for SEINet, showing Symbiota's ability to integrate the identities of individual member collections (with their respective logos and links to portal-configured homepages), regional portals (only four out of nine portals shown here), and multi-portal 'hubs'. All screenshots used in this paper were taken in February 2014.

Figure 2.

Screenshot of the Collection Management Panel for administrators of the University of Wisconsin Lichen Collection. The Data Editor Control Panel facilitates most day-to-day tasks related to specimen digitization as well as loan activity, whereas the Administration Control Panel focuses on managing the collection's appearance in the portal.

Figure 3.

SCAN portal homepage for the Arizona State University Hasbrouck Insect Collection, which is being managed "Live" in SCAN, with an account of the collection's holdings, contact information, and Collection Statistics as of December, 2013.

Figure 4.

Screenshot of the occurrence data form corresponding to the SEINet specimen ASU0023423 – Echinomastus johnsonii (Parry ex. Engelm.) E.M. Baxter (common name: Johnson's fishhook cactus – pertaining to the ASU Vascular Plant Herbarium collection. This is the primary Symbiota contributor interface through which individual specimen records are entered and edited. At the highest level, contributors can switch from the Occurrence Data tab to the Determination History, Images (see also right half), Genetic Links (e.g. to GenBank; Benson et al. 2012), and Administrative tabs. Entry personnel can zoom in on the label. Many data fields have inherent auto-completion or uniqueness/compliance checking functions, or can be expanded via the +-pencil icon for more fine-scale data entry. The Latest Identification data field section is linked to the taxonomic thesaurus, thereby ensuring correct integration of the Scientific Name with the portal-level taxonomy. Georeferencing support tools including Google Earth mapping and an embedded GEOLocate module. Under Curation, the Processing Status may be set to (e.g.) "Pending Review" to support filtering and data quality control practices among collection members.

Figure 5.

Screenshot of results displayed based on the search criteria ‘Grand Canyon’ which returns 378 records in 142 taxa. The Specimens panel (center tab) shown on the left presents an abbreviated summary view for each record that is expandable (not shown here). A Species List (left tab), shown on the right and Maps view (right tab, unselected), shown on bottom, are also available. A data icon in the top right corner facilitates downloading of the entire search results in Darwin Core or Symbiota CSV text file format (no permissions required). High-density occurrences of records are 'integrated' at coarser geographic scales and become resolved into separate latitude/longitude points at finer levels.

Figure 6.

Screenshots of several stages in an exemplary sequence of using the Dynamic Key function in Symbiota. (A) Using the Dynamic Map interface, a rectangle is selected; the coordinates correspond to the bounding box are selected. Users can restrict the subsequent checklist creation process ("Build Checklist") through specification of a Taxon Filter (i.e., higher taxa down to family, listed alphabetically). (B) Using these search criteria, the module will search vouchers in Symbiota that may satisfy these conditions, and integrate the pertinent voucher list into a taxon (family/species) list with 2178 species-level matches. The Dynamic Key interface (left menu) is initially simple, including choices regarding e.g. habit. (C) In this example, selecting only two criteria from the list will (1) reduce the count of taxon matches to 6 and (2) display a remaining taxa-specific list of traits suitable for further determination, drawn from the character inheritance hierarchy of the corresponding key in Symbiota. These can either be further scrutinized with the dynamic key or determined through viewing of individual species profile pages.

Figure 7.

Screenshot of the homepage of the SEINet-derived San Pedro Riparian National Conservation Area checklist, a 'member' checklist of the Arizona Flora biotic inventory 'family' (Makings 2006, 2014). Checklist administrator functions are available in the top right corner ("A" – Administration, "V" – Manage Linked Vouchers, "Spp" – Edit Species List). The selected screenshot shows the entire list in alphabetical order, Taxon Authors, Common Names, and Notes & Vouchers. Clicking on vouchers listed for each taxon will display specimen details including images, when available. A Google Map thumbnail can be clicked for a more expansive map view.

Figure 8.

Screenshot of the Species Profile page of Lecanora cenisia. Ach. (Lecanoraceae) in CNALH (http://lichenportal.org/portal/taxa/index.php?taxauthid=1&taxon=53780&cl=2), with an outlink to the corresponding Encyclopedia of Life page (http://eol.org/pages/196725), common names, an assortment of accredited and clickable thumbnail images including in situ photographs and herbarium voucher scans (additional images and links are displayed when clicking links below), an Interactive Map for documented species occurrences, and taxonomic diagnosis (based on Nash et al. 2001 – also linked).