Symbiota Overview

Symbiota is a software package specifically designed for the establishment of specimen-based virtual flora/fauna web portals that foster a bio-collaborative environment within a given region. The effort and time needed to build and manage a truly robust, information-rich biodiversity portal can be overwhelming for any one institution. Symbiota provides tools that allow biological communities to join forces and build collaborative resources that better serve the whole community, from the novice to the expert. Building upon a foundation of authoritatively identified specimens ensures a high level of data integrity. Furthermore, these expert-reviewed specimens serve as the data backbone that allows users to dynamically generate maps, species lists, and identification keys for any well-collected area.

The Symbiota framework includes a growing number of  modules.. The Occurrence Module gives users the ability to query specimen or other observation records by taxonomic, geographic, or collector criteria. Results can be rendered as a simple list of specimen records, distribution map, or as a unique species list. The Floristic/Faunistic Module features searchable species lists that have been compiled through floristic or faunistic research. The Key Module uses species lists and/or occurrence records to dynamically generate interactive identification keys from a hierarchically arranged morphological dataset. Any one of these modules can be installed to function on its own, but the system’s full potential is best achieved when the three modules are configured to work together. For example, linking species lists to voucher records allows users to view the specimen records that verify the observation, often with an image of the actual specimen. Furthermore, specimen occurrence records integrated with morphological data enables an identification process that allows users to first limit possible identifications geographically based on expert-reviewed observations, and then on morphology criteria. The virtual environment allows us to continue the tradition of integrating these types of data sets with the added ability to establish extremely extensive floras that are complete and accurate, yet flexible enough to be of value to both the novice and the expert biologist.

Below is a timeline of module development, including modules that are being planned.

Specimen Module

  • Query by scientific name, synonym, taxonomic group, geography, and/or collector criteria
  • Dynamically generate species list from specimen records
  • Resolve taxonomic discrepancies within specimen-generated species list
  • Render species lists according to different taxonomic options
  • Generate distribution maps featuring one or multiple species on a single map
  • Protect distribution details for rare or threatened species

Spatial Module

  • Map over 100k occurrences on several GIS backgrounds
  • Timeline provides visualization in occurrences over time (e.g., invasive species, geographic focus of a collection)
  • Heat maps
  • Color occurrences by taxa collection
  • Download csv of species or records
  • Filter by occurrences with images or genetic data
  • Filter by observation versus specimen

Floristic/Faunistic Checklist Module

  • Direct links to voucher specimen records
  • Links to images of voucher specimens
  • Method of performing group surveys (floras) with specimen review by experts
  • Ability to render list as image thumbnails
  • The ability to toggle species list according to different taxonomic options
  • Synonym or common name searches
  • Ability for author(s) to edit/manage species list online
  • User ability to build personal checklists (e.g. backyard or schoolyard species lists)

Identification Key Module

  • Ability to dynamically generate identification key for any taxonomic and morphologically complex species list (e.g. grasses, cacti, trees all in same key)
  • Ability to edit morphology directly from key, thus allowing authors to integrate development with key use
  • Efficient algorithms that can handle extremely large species lists

Fieldguide Batch Module

  • Screen images through neural net process to obtain computer-aided identification
  • Compare computer and human identifications
  • Download results as csv that show up to three identification suggestions

Geolocate Module

  • Batch georeference records by linking to Geolocate workflow embedded in Symbiota portal
  • provides uncertainty estimation, suggested