xnomo3: A system for representing bird taxonomy |  |
xnomo3: A system for representing bird taxonomy | |
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 ranks file describes the set
of taxonomic ranks (or levels or aggregates) of
interest to the applications programs. The AOU Check-List
describes a number of taxa such as subclasses and
superorders that are not usually of interest, so those
aggregates can be omitted from the ranks file. If
different applications have different needs, they can
provide different versions of the ranks file. For
example, some applications might wish to use subfamily
rank, while other applications might not.
See Section 5.1, “The ranks file”.
The standard forms file
describes all the standard taxa,
that is, all those in the approved arrangement. A
typical source for this file is the AOU Check-List.
Section 5.2, “
Preparing the standard forms (.std)
file
”.
The alternate forms file
enumerates all names and identifiable forms other than
the standard taxa. Some are obsolete names (e.g.,
rather than “Cardinal,” the preferred
name is now “Northern Cardinal”). Some
are names for proper subsets of species (e.g., races or
color morphs like Eurasian Green-winged Teal or Blue
Goose). Some are names for larger aggregates (e.g.,
“hawk spp.”). See Section 5.3, “
Preparing the alternate forms (.alt) file
”.
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.
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:
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.
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.
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.
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 -f?1Subfamily 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.