Establishing a Regional Flora or Fauna

The central premise of the Symbiota Software Project is to design tools that foster bio-collaboration. While this software could be installed to only feature a local flora or the data from a single herbarium, it is better suited for the creation of a regional flora/fauna through the integration of numerous collections and biodiversity datasets. The greater the number of specimen and observation recorded integrated into the system, the higher the quality of distribution maps, dynamic checklists, and other features built directly from specimen data. Once a regional data node is established, researches can feature a local flora by creating a species list within the network, or linking a group of species lists within a Symbiota Project. See the Local Floras page for more details. Stable financial and technical support is an essential component for maintaining a healthy virtual flora. While the initial installation of the software is not too difficult, there still remains a certain amount of technical web and data management skills needed to establish and maintain a quality dataset. Ideally, the data node would be established by an organization capable of supplying technical support to a network of data providers and managers participating in the project.

If you are interested in becoming a data contributor for an already established data portal, contact the portal administrator for more information on gaining access to their data editing modules. Individual collections interested in supplying specimen data to a portal should first read the Specimen Integration page.

System Requirements

• Apache HTTP Server (2.x or better)
  • See Apache HTTP Server Project for more information
• PHP (5.x or better)
  • PHP Project
  • Enable extensions: GD image library, mbstring, zip, exif, php-xml
  • Optional: Pear package Image_Barcode - enable barcode generation on specimen labels
• MySQL (5.x or better, yet 5.1 or better recommended)
  • MySQL Database Server Project
• SVN Client - Needed for installation via source code
  • e.g. Tortoise SVN - implemented as a Microsoft Windows shell extension

Source Code

• Symbiota Project on Source Forge
  • SVN checkout instructions
• Installation Instructions from source code

Configuration Files and Custom Look & Feel

• Header - The header graphics defined within the header.php include determines the header design for all pages
• Footer - Footer layout is defined in the footer.php file
• Menu - What central features are include or excluded are controlled by modifying the menu.php file
• Cascading Style Sheet - A set of css can be used to customize layout, fonts, and so much more
• Symbiota ini - Several configuration variables are defined within the symbini.php include

Data Requirements

• Specimen Records – Since occurrence records serve as the core information for generating distribution maps, dynamic checklists, dynamic keys, and vouchered species lists, this data is critical for establishing a digital portal. Observations based on physical specimens have greater value in that they can be reverified years after the observation took place. An annotations to the identification of a physical specimen will automatically adjust distribution maps, species lists, and other components within the network. At times where it is not possible, practical, or politically acceptable to make a physical collection (i.e. birds), a simple observation will suffice, especially if it is backed up with a quality photo.
• Taxonomic Data – Needed for establishing taxonomic thesaurus. The central purpose of the thesaurus is to resolve taxonomic discrepancies that are typically exist when integrating multiple specimen datasets. Loading multiple taxonomies into the system gives the user the ability to toggle species checklists between different taxonomic options. For more information on the Taxonomic Thesaurus.
• Species Lists – While species lists can be generated dynamically from occurrence records, well managed static lists have greater potential for accuracy. Static species lists give researchers full control over species composition, taxonomy placements, area specific comments, and voucher assignments. An annotation of a specimen voucher linked to a species list will flag the associated species as needing review. Another method for establishing a species list is through the Group Survey module. Survey species lists are defined by project members linking occurrence records to a survey project. An annotation of a voucher specimen linked to a survey will automatically adjust the associated species list to match the new identification.
• Morphological Character Information – Interactive identification keys are generated directly from descriptive data stored in a relational data representation of the DELTA data standard. The management interface is coordinated with the hierarchy defined within the taxonomic thesaurus, thus facilitating the implementation of character inheritance. Since genera inherit family characters and species inherit genera characters, only the characteristic that distinguish a species from its close relatives need to be entered.
• Images - The system is designed to handle both specimen and field images. Field images are linked only to the taxonomic name. Specimen images and photo vouchers are linked to the specimen records.
• See Data Loading Instructions for more in depth details on the data infrastructure.

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