A system for representing bird taxonomy

Abstract

Describes a system for representing taxonomic arrangements of bird checklists, and an interface for retrieving such data using the Python programming language.

This publication is available in Web form and also as a PDF document. Please forward any comments to john@nmt.edu.

Table of Contents

1. Introduction

2. Requirements

3. The six-letter bird code system

3.1. Design goals for bird code systems
3.2. Origins of the six-letter code system
3.3. Rules for the six-letter code system
3.4. Handling collisions

4. Input files

4.1. The ranks file
4.2. Preparing the standard forms (.std) file
4.3. Preparing the alternate forms (.alt) file

5. Building the standard product files

6. Flat output files

6.1. The tree (.tre) file
6.2. The abbreviations (.ab6) file
6.3. The collisions (.col) file

7. Schema for the XML product file

7.1. taxonomySystem: the XML root element
7.2. rankSet: Taxonomic ranks in use
7.3. taxonomy: The classification tree
7.4. abbrSet: Bird code definitions
7.5. collisionSet: List of collision codes

8. The Python taxonomy package, txny.py: the interface

8.1. Class Txny: the complete system
8.2. Class Hier: The set of taxonomic ranks
8.3. Class Rank: One taxonomic rank
8.4. The Taxon class: One node in the classification tree

9. The abbr.py module

9.1. class BirdId

1. Introduction

This document describes a system for representing bird phylogenies, that is, taxonomic arrangements of bird types, as computer files.

Data files for the AOU Check-List, 7th ed., and also for the 42nd-47th Supplements are available online as .zip archives: aou7.zip, aou742.zip, aou743.zip, aou744.zip, aou745.zip, aou746.zip, and aou747.zip.

Source files described herein: