taxopedia 1.0.0

Build cladograms from Wikipedia-scraped data.

Taxopedia

Build taxonomic trees (cladograms) from Wikipedia-scraped data.

Installation

Use the package manager pip to install taxopedia.

pip install taxopedia

Otherwise, download taxopedia.py, it's a single file!

Getting Started

import taxopedia

# create a tree... and get a bag of parsed biota boxes!
tree, bag = taxopedia.arboretum("Bears")

# pretty print the tree
print(tree.pretty())

# export multiple formats
tree.to_txt("Ursidae.txt")    # plain-text dendrogram
tree.to_html("Ursidae.html")  # diagram with images
tree.to_csv("Ursidae.csv")    # filled-out tabular data

Saving and Loading Progress

# save the biota bag (so you don't have to scrape it again!)
taxopedia.dump_bag("bag.json", bag)

# loading the biota bag
bag = taxopedia.load_bag("bag.json")

# how to get a tree from a bag
tree = taxopedia.make_tree(bag)

Example Output

The plain-text dedrogram is as follows. See docs folder for an example CSV and HTML file as well.

Kingdom: Animalia
└── Phylum: Chordata
    └── Class: Mammalia
        └── Order: Carnivora
            └── Suborder: Caniformia (Caniforms)
                └── Infraorder: Arctoidea (Arctoidea)
                    └── Family: Ursidae (Bears)
                        ├── Subfamily: Ailuropodinae (Ailuropodinae)
                        │   ├── Genus: Ailuropoda (Panda)
                        │   │   ├── Species: A. melanoleuca (Giant panda)
                        │   │   │   └── Subspecies: A. m. qinlingensis (Qinling panda/Brown panda)
                        │   │   ├── Species: A. baconi (Ailuropoda baconi)
                        │   │   └── Species: A. microta (Ailuropoda microta)
                        │   ├── Tribe: † Indarctini
                        │   │   └── Genus: † Indarctos (Indarctos)
                        │   └── Genus: † Miomaci (Miomaci)
                        ├── Subfamily: Tremarctinae (Tremarctinae)
                        │   ├── Genus: Tremarctos (Tremarctos)
                        │   │   ├── Species: T. ornatus (Spectacled bear)
                        │   │   └── Species: † T. floridanus (Tremarctos floridanus)
                        │   ├── Genus: Plionarctos (Plionarctos)
                        │   ├── Genus: † Arctodus (Short-faced bear)
                        │   └── Genus: † Arctotherium (Arctotherium)
                        ├── Subfamily: † Hemicyoninae (Hemicyoninae)
                        │   ├── Genus: † Cephalogale (Cephalogale)
                        │   ├── Genus: † Dinocyon (Dinocyon)
                        │   ├── Genus: † Hemicyon (Hemicyon)
                        │   ├── Genus: † Phoberocyon (Phoberocyon)
                        │   ├── Genus: † Phoberogale (Phoberogale)
                        │   └── Genus: † Plithocyon (Plithocyon)
                        ├── Genus: Ursus
                        │   ├── Species: U. arctos (Brown bear)
                        │   │   ├── Subspecies: U. a. arctos (Eurasian brown bear)
                        │   │   └── Subspecies: U. a. middendorffi / horribilis (Kodiak bear)
                        │   ├── Species: U. americanus (American black bear)
                        │   ├── Species: U. maritimus (Polar bear)
                        │   └── Species: U. thibetanus (Asian black bear)
                        ├── Subfamily: Ursinae (Ursinae)
                        │   ├── Genus: Helarctos
                        │   │   └── Species: H. malayanus (Sun bear)
                        │   └── Genus: Melursus
                        │       └── Species: M. ursinus (Sloth bear)
                        ├── Subfamily: † Ursavinae
                        │   └── Tribe: † Ursavini (Ursavini)
                        │       └── Genus: † Ursavus (Ursavus)
                        ├── Subfamily: † Agriotheriinae
                        │   └── Genus: † Agriotherium (Agriotherium)
                        ├── Tribe: Ailuropodini
                        │   └── Genus: † Ailurarctos (Ailurarctos)
                        ├── Genus: † Kretzoiarctos
                        │   └── Species: † K. beatrix (Kretzoiarctos beatrix)
                        └── Genus: † Zaragocyon
                            └── Species: † Z. daamsi (Zaragocyon)

License

MIT