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5. Input files

The author prefers to maintain the source files for taxonomic arrangements as simple text files with a modest structure. This simplifies the preparation of original data files, as well as making them easier to maintain when new AOU checklists are made available. At this writing, files are available for all arrangements starting with the published AOU Check-List, Seventh Edition, proceeding through all the subsequent biennial supplements. All these data files are available online: see Section 2, “Files for downloading”.

This system supports multiple taxonomic arrangements. Each taxonomic arrangement is represented as a set of three text files:

The following sections describe the format of these raw files. Later sections will discuss the process of building the product files to be used by applications.

5.1. The ranks file

The AOU Check-List defines a lot more taxonomic ranks than most applications will care about, so the ranks file allows the application to specify which ranks are of interest. To prepare this file, use a text editor to enumerate the ranks in descending order, starting with the rank of the root taxon of the arrangement.

Each line defines one rank. Enter these items in order:

  1. A two-character code for the taxonomic rank, such as “-f” for Subfamily. If the code is only one character long (e.g., “f” for family), it should be placed in the first column, with a space in the second column.

  2. In the third column, put a space if the rank is mandatory, that is, if every lower taxon must be placed in such a rank.

    For ranks that are not always used (such as Subfamily in the AOU Check-List), enter a question mark (“?”) in this column to indicate that the rank is optional. Because they are the bedrock of the binomial system, genus and species ranks may not be optional.

  3. In the fourth column, specify the number of digits to be allocated in the taxonomic key for this rank. This value should be “1” if there are never more than 9 of this taxon in the next higher one; “2” if there are no more than 99; and so on. The first (root) taxon must have a value of “0 ”, or your taxonomic keys will have a useless, always-one prefix.

  4. On the remainder of the line, enter the name of the taxonomic rank, such as “Genus”.

Here is a sample ranks file.

c  0Class
o  2Order
f  2Family
g  2Genus
s  2Species
x  2Form

The numbers in this example allow for up to 99 orders per class, 99 families per order, 9 subfamilies per family, and so on.

The last three lines of this file use codes that do not actually appear in the standard forms file:

  • Code g is used for genus.

  • Code s is used for species.

  • Code x is used for identifiable forms that are subsets of species, such as races or morphs.

Applications that don't need to track subspecific forms should use a version of the ranks file that omits the x line. The g and s lines may not be omitted.

The order is important---always order the ranks from largest to smallest, as in the example above. The program doesn't know anything about taxonomic traditions. If you would like to create your own new ranks, like Infrasupertribes, go right ahead.