Data Loading Instructions

The general layers of data within Symbiota are: user, taxonomic, occurrence (specimen), images, floristic, identification key, and taxon profile (common names, text descriptions, etc). Web-based management interfaces exist for several of these data layers, though data will need to be loaded and managed by hand for those layers that are still in development. Below are detailed instructions on loading the different layers of data needed. Note that the easiest way to find a data editing page is to visit the sitemap.php page located in base Symbiota folder. Data editing modules available for your given permissions will be listed in the editing panel at the bottom of the page.

  1. User and permissions – Default administrative user are installed with the following login: admin; password: admin. Make sure to change password or better yet, create a new user (/profile/newprofile.php), assign admin rights (/profile/usermanagement.php), and then delete default admin user.
  2. Taxonomic Thesaurus – The establishment of a central taxonomic thesaurus is required for all Symbiota modules (Occurrence, Floristic, and Key Modules). Taxonomic names are stored within a recursive data structure that defines the taxonomic hierarchy. See Taxonomic Schema page for more details covering the data structure.
    • Names can be added one by one to the default thesaurus through: /taxa/admin/taxonomyloader.php. Once entered, taxon names and ranking can be edited via: /taxa/admin/taxonomydisplay.php
    • Batch Loading – Multiple names can be loaded from a flat, CVS text file or an ITIS download file. See Taxonomy Batch Loading instructions for more details on this process.
    • Look in /config/schema/data/ folder to find taxonomic thesaurus data that may serve as a base for your taxonomic thesaurus.
  3. Occurrence (specimen) Records – Several methods are successfully being employed for uploading and refreshing specimen data.
  4. Images – Within the Symbiota configuration file (/config/symbini.php), set $imageRootPath equal to the path where you plan on storing images. The web server will need write access to this folder. Then set the $imageRootUrl variable to the URL prefix needed to reach this folder via a browser. This variable will be used to create the image URLs that will be stored in the “images” table. For Linux OS, the web server can get write access to a file system on another server via a mount and an alias can be created in the Apache configuration file to redirect to the images stored on the external server.
  5. Biotic Survey Data (floras / faunas) – Setting the $floraModIsActive variable equal to “1” within the symbini.php file will active the ability to create species checklist. Species within the checklist can then be linked to specimen vouchers within collections. Checklists can be created within ones user profile and then made public by adding them to a flora/fauna projects. Projects can be created using the editing features available within sitemap.php.
  6. Identification Key Data – Setting the $keyModIsActive variable within symbini.php file equal to “1” will activate the interactive identification key features. The first step to creating keys is to add the morphological characters into the kmcharacters table and then the character states into the kmcs table. User interfaces for character and character state management are not yet available, thus the data will need to be loaded directly into the table by hand. As characters are loaded, they will need to be linked to the taxonomic hierarchy at the ranking level that they are most relevant. For example, habit (tree, shrub, herb, vine, etc) might be linked to the kingdom “Plantae” and ligule length linked to Poaceae. Once the characters and states are defined, traits can be coded for species, genera, and families using the editing tools located in sitemap.php. Note that morphology is inherited between species and family. For example, character states coded at the family level will be inherited by the genera and species within that group. Inheritance will not take place if a different character state was explicitly coded for a species.
  7. Taxon Profile Support Data (common names, text descriptions, etc) – to be completed