Creating a new species file

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The Species File Software is designed to facilitate the creation of new taxonomic databases and associated websites. Before describing the steps in the creation process, it is important to understand the four elements of an SFS application:


Template database

This contains an initialized set of tables, including constraints and relationships, necessary to support the SFS application. In most cases, the tables are empty; however, some of the tables have a few rows of data in order to satisfy inter-table relationships. The template database also contains stored procedures (programs that interact with the table data), user-defined functions (simple subroutines that also interact with the table data), and views (representations of the most commonly-used relationships between the tables to improve efficient access to the table data).

File specific software template

This is a set of software that will be unique to the target application. For example, the home page would contain information about the specific order or infraclass, etc. A list of hyperlinks would connect to websites relevant to the subject matter. This template is basically a blank slate, waiting for the custodian to fill in the information. In addition to presentation content, there are some housekeeping chores that must be performed before the website can be connected to the database and brought on line.

SFS common software

This set of software provides the functionality of the website and its connection to the database. It contains the user interface which allows visitors to view the taxonomic hierarchy including citations, specimen data, type data, images and more. It provides access to searches for many different types of data (e.g., references, publications, specimen depositories) and to keys if available. For the editor, the SFS interface allows the user to add or modify existing data. There is also an administrative component, requiring special login access, that allows the user to review edit log entries, run integrity tests, assign experts, edit high-level information about the database, etc.


A website must be created on a web server in order to run the SFS application. Duties of the website administrator include handling shares, permissions, security, application pool, and file system. The administrator will also perform DNS and IP assignment and mapping.

The creation process consists of the following steps, some of which are done by the Species File Group (SFG), and others by the custodian who will be the owner of the species file.

  1. Create the starting species file. This is done by the SFG using more detailed instructions in an internal design document.
    1. Create a new Visual Studio solution based on the file specific template and the common software code.
    2. Initialize critical constants.
    3. Create the new database as a copy of the template database.
    4. Grant full access privileges to the custodian.
  2. Customize the home page and other components of the file specific section.
    1. The database custodian must define the content of these web pages including the logo design.
    2. The content must be added as HTML in the file specific section. This can be done by either the SFG or the custodian.
  3. Enter the taxonomic framework, usually done by the custodian.
    1. Add the context taxa. These are taxa outside the scope of the apex taxon used to show the apex taxon in its hierarchical context. More specific instructions are found by clicking on "Admin" in the menu bar, clicking on "Make a restricted taxon change," and clicking on "Edit taxonomic context."
    2. Add valid taxa subordinate to the apex taxon and at a rank of family or higher. More specific instructions are found by clicking on "Admin" in the menu bar, clicking on "Make a restricted taxon change," and clicking on "Add or change a valid taxon at family rank or higher."
  4. Add content to the database. Although this can be by entering the data item by item, there is usually a pre-existing database. The Species File Group has several specialized programs to facilitate the import process. The procedure must be adapted to the data structure of the pre-existing database.

Unless the custodian has good knowledge of the software involved, it is best to complete these initial steps on a server managed by the Species File Group. However, the objective is to transfer the species file to a server under control of the custodian. The Species File Group will continue to provide periodic updates to the software. Arrangements can be made for the custodian to participate in new development for any portion of the Species File Software.

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