In [1]:

    

from __future__ import print_function

from collections import defaultdict

import requests

import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline


    

In [2]:

    

def do_request(service, a1=None, a2=None, a3=None, **kwargs):
    server = 'http://api.gbif.org/v1'
    params = ''
    for a in [a1, a2, a3]:
        if a is not None:
            params += '/' + a
    req = requests.get('%s/%s%s' % (server, service, params),
                       params=kwargs,
                       headers={'Content-Type': 'application/json'})
    if not req.ok:
        req.raise_for_status()
    return req.json()


    

In [3]:

    

req = do_request('species', 'search', q='bear')
print(req['count'])
req['results'][0]


    

    




19206






    
Out[3]:





{u'authorship': u'',
 u'canonicalName': u'Ursus white bear',
 u'class': u'Mammalia',
 u'classKey': 106223020,
 u'datasetKey': u'fab88965-e69d-4491-a04d-e3198b626e52',
 u'descriptions': [],
 u'family': u'Ursidae',
 u'familyKey': 106657396,
 u'genus': u'Ursus',
 u'genusKey': 106658119,
 u'habitats': [],
 u'higherClassificationMap': {u'106148414': u'Metazoa',
  u'106151875': u'Carnivora',
  u'106223020': u'Mammalia',
  u'106522535': u'Chordata',
  u'106657396': u'Ursidae',
  u'106658119': u'Ursus'},
 u'key': 106189791,
 u'kingdom': u'Metazoa',
 u'kingdomKey': 106148414,
 u'nameType': u'SCINAME',
 u'nomenclaturalStatus': [],
 u'numDescendants': 0,
 u'numOccurrences': 0,
 u'order': u'Carnivora',
 u'orderKey': 106151875,
 u'parent': u'Ursus',
 u'parentKey': 106658119,
 u'phylum': u'Chordata',
 u'phylumKey': 106522535,
 u'rank': u'SPECIES',
 u'scientificName': u'Ursus sp. Shennongjia white bear',
 u'species': u'Ursus white bear',
 u'speciesKey': 106189791,
 u'synonym': False,
 u'taxonID': u'373678',
 u'threatStatuses': [],
 u'vernacularNames': []}

In [4]:

    

req_short = do_request('species', 'search', q='bear', rank='family')
print(req_short['count'])
bear = req_short['results'][0]
bear


    

    




645






    
Out[4]:





{u'authorship': u'G. Fischer de Waldheim, 1817',
 u'canonicalName': u'Ursidae',
 u'class': u'Mammalia',
 u'classKey': 143045262,
 u'datasetKey': u'cbb6498e-8927-405a-916b-576d00a6289b',
 u'descriptions': [{u'description': u'Below follows a list of the different species of bears. Bears indented are a subspecies or type of the species listed above it that is non-indented.'},
  {u'description': u'American Black Bear Cinnamon Bear Kermode Bear Asiatic Black Bear Baluchistan Bear or Pakistan Black Bear Formosan black bear Brown bear Atlas bear Bergman\'s bear Blue bear Eurasian brown bear European brown bear Gobi bear Grizzly bear Himalayan brown bear Nandi bear Ussuri brown bear Kamchatka brown bear Kodiak bear Marsican brown bear (critically endangered) Mexican grizzly bear East Siberian brown bear Syrian brown bear Giant Panda Qinling Panda Sloth bear Sri Lankan sloth bear Sun bear Polar bear Ursid hybrid Grizzly\u2013polar bear hybrid Spectacled Bear Extinct bear species Agriotherium Tremarctos floridanus Florida spectacled bear Ailuropoda microta Dwarf Giant Panda Ursus Arctos Californicus "California Grizzly Bear"'}],
 u'extinct': False,
 u'family': u'Ursidae',
 u'familyKey': 110503853,
 u'habitats': [],
 u'higherClassificationMap': {u'116630539': u'Animalia',
  u'143035196': u'Chordata',
  u'143045262': u'Mammalia',
  u'143045479': u'Carnivora'},
 u'key': 110503853,
 u'kingdom': u'Animalia',
 u'kingdomKey': 116630539,
 u'nameType': u'WELLFORMED',
 u'nomenclaturalStatus': [],
 u'nubKey': 9681,
 u'numDescendants': 35,
 u'numOccurrences': 0,
 u'order': u'Carnivora',
 u'orderKey': 143045479,
 u'parent': u'Carnivora',
 u'parentKey': 143045479,
 u'phylum': u'Chordata',
 u'phylumKey': 143035196,
 u'rank': u'FAMILY',
 u'scientificName': u'Ursidae G. Fischer de Waldheim, 1817',
 u'synonym': False,
 u'taxonID': u'1599257',
 u'threatStatuses': [],
 u'vernacularNames': [{u'language': u'eng', u'vernacularName': u'Bear'}]}

In [5]:

    

import time
def get_all_records(rec_field, service, a1=None, a2=None, a3=None, **kwargs):
    records = []
    all_done = False
    offset = 0
    num_iter = 0
    while not all_done and num_iter < 100:  # arbitrary
        req = do_request(service, a1=a1, a2=a2, a3=a3, offset=offset, **kwargs)
        all_done = req['endOfRecords']
        if not all_done:
            time.sleep(1)
        offset += req['limit']
        records.extend(req[rec_field])
        num_iter += 1
    return records


    

In [6]:

    

def get_leaves(nub):
    leaves = []
    recs = get_all_records('results', 'species', str(nub), 'children')
    if len(recs) == 0:
        return None
    for rec in recs:
        rec_leaves = get_leaves(rec['nubKey'])
        if rec_leaves is None:
            leaves.append(rec)
        else:
            leaves.extend(rec_leaves)
    return leaves


    

In [7]:

    

records = get_all_records('results', 'species', str(bear['nubKey']), 'children')
leaves = get_leaves(bear['nubKey'])


    

In [8]:

    

#[leaf['nameType'] for leaf in leaves]
for rec in leaves:
    print(rec['scientificName'], rec['rank'], end=' ')
    vernaculars = do_request('species', str(rec['nubKey']), 'vernacularNames', language='en')['results']
    for vernacular in vernaculars:
        if vernacular['language'] == 'eng':
            print(vernacular['vernacularName'], end='')
            break
    print()


    

    




Agriarctos Kretzoi, 1942 GENUS 
Ailurarctos Qiu Zhanxiang & Qi Guoquin, 1989 GENUS 
Ailuropoda baconi SPECIES 
Ailuropoda fovealis SPECIES 
Ailuropoda melanoleuca (David, 1869) SPECIES Bamboo Bear
Ailuropoda microta SPECIES 
Ailuropoda wulingshanensis SPECIES 
Cynodon helveticus SPECIES 
Arctodus pristinus SPECIES 
Arctodus simus SPECIES 
Harpaleocyon Hürzeler, 1944 GENUS 
Helarctos malayanus euryspilus Horsfield, 1825 SUBSPECIES 
Helarctos malayanus subsp. malayanus SUBSPECIES 
Hyaenarctos Owen, 1845 GENUS 
Indarctos anthracitis SPECIES 
Indarctos arctoides SPECIES 
Indarctos atticus SPECIES 
Indarctos nevadensis SPECIES 
Indarctos oregonensis SPECIES 
Indarctos salmontanus SPECIES 
Indarctos vireti SPECIES 
Indarctos zdanskyi SPECIES 
Melursus ursinus inornatus Pucheran, 1855 SUBSPECIES Sri Lankan Sloth Bear
Melursus ursinus ursinus (Shaw, 1791) SUBSPECIES 
Metarctos Gaudry, 1860 GENUS 
Myadus GENUS 
Pararctotherium Ameghino, 1904 GENUS 
Phoberocyon aurelianensis SPECIES 
Phoberocyon huerzeleri SPECIES 
Phoberocyon johnhenryi SPECIES 
Plionarctos edensis SPECIES 
Plionarctos harroldorum SPECIES 
Thalarctos Gray, 1825 GENUS 
Thaumastocyon GENUS 
Tremarctos floridanus SPECIES 
Tremarctos ornatus (F. G. Cuvier, 1825) SPECIES Spectacled Bear
Ursavus brevirhinus SPECIES 
Ursavus elmensis SPECIES 
Ursavus pawniensis SPECIES 
Ursavus primaevus SPECIES 
Ursus abstrusus SPECIES 
Ursus americanus altifrontalis Elliot, 1903 SUBSPECIES 
Ursus americanus amblyceps Baird, 1859 SUBSPECIES 
Ursus americanus californiensis Miller, 1900 SUBSPECIES 
Ursus americanus carlottae Osgood, 1901 SUBSPECIES Haida Gwaii Black Bear
Ursus americanus cinnamomum Audubon & Bachman, 1854 SUBSPECIES Cinnamon bear
Ursus americanus emmonsii Dall, 1895 SUBSPECIES Glacier bear
Ursus americanus eremicus Merriam, 1904 SUBSPECIES 
Ursus americanus floridanus Merriam, 1896 SUBSPECIES Florida black bear
Ursus americanus hamiltoni Cameron, 1957 SUBSPECIES Newfoundland Black Bear
Ursus americanus kermodei Hornaday, 1905 SUBSPECIES Kermode bear
Ursus americanus luteolus Griffith, 1821 SUBSPECIES 
Ursus americanus machetes Elliot, 1903 SUBSPECIES 
Ursus americanus perniger J. A. Allen, 1910 SUBSPECIES 
Ursus americanus pugnax Swarth, 1911 SUBSPECIES 
Ursus americanus subsp. americanus SUBSPECIES 
Ursus americanus vancouveri Hall, 1928 SUBSPECIES 
Ursus arctos alascensis Merriam, 1896 SUBSPECIES 
Ursus arctos beringianus Middendorff, 1851 SUBSPECIES Kamchatka brown bear
Ursus arctos californicus Merriam, 1896 SUBSPECIES California grizzly bear
Ursus arctos collaris F. G. Cuvier, 1824 SUBSPECIES East Siberian Brown Bear
Ursus arctos crowtheri Schinz, 1844 SUBSPECIES Atlas bear
Ursus arctos dalli Merriam, 1896 SUBSPECIES 
Ursus arctos gyas Merriam, 1902 SUBSPECIES 
Ursus arctos horribilis Ord, 1815 SUBSPECIES Alaska Peninsula Brown Bear
Ursus arctos isabellinus Horsfield, 1826 SUBSPECIES Himalayan Brown Bear
Ursus arctos lasiotus Gray, 1867 SUBSPECIES Ussuri Brown Bear
Ursus arctos middendorffi Merriam, 1896 SUBSPECIES Kodiak bear
Ursus arctos pruinosus Blyth, 1854 SUBSPECIES 
Ursus arctos sitkensis Merriam, 1896 SUBSPECIES ABC Brown Bears
Ursus arctos stikeenensis Merriam, 1914 SUBSPECIES 
Ursus arctos subsp. arctos SUBSPECIES Eurasian brown bear
Ursus arctos syriacus Hemprich & Ehrenberg, 1828 SUBSPECIES Syrian brown bear
Ursus inopinatus SPECIES MacFarlane s bear
Ursus malayanus SPECIES 
Ursus maritimus Phipps, 1774 SPECIES Polar Bear
Ursus spelaeus Rosenmüller & Heinroth SPECIES Cave bear
Ursus thibetanus formosanus Swinhoe, 1864 SUBSPECIES Formosan black bear
Ursus thibetanus gedrosianus Blanford, 1877 SUBSPECIES Baluchistan Bear
Ursus thibetanus japonicus Schlegel, 1857 SUBSPECIES 
Ursus thibetanus laniger (Pocock, 1932) SUBSPECIES 
Ursus thibetanus mupinensis (Heude, 1901) SUBSPECIES 
Ursus thibetanus subsp. thibetanus SUBSPECIES 
Ursus thibetanus ussuricus (Heude, 1901) SUBSPECIES 

In [9]:

    

basis_of_record = defaultdict(int)
country = defaultdict(int)
zero_occurrences = 0
count_extinct = 0
for rec in leaves:
    #print(rec['scientificName'], rec['rank'], rec['taxonID'])
    occurrences = get_all_records('results', 'occurrence', 'search', taxonKey=rec['nubKey'])
    for occurrence in occurrences:
        basis_of_record[occurrence['basisOfRecord']] += 1
        country[occurrence.get('country', 'NA')] += 1
        #there is also publisingCountry
    if len(occurrences) > 0:
        zero_occurrences += 1
    profiles = do_request('species', str(rec['nubKey']), 'speciesProfiles')['results']
    for profile in profiles:
        if profile.get('extinct', False):
            count_extinct += 1
            break


    

In [10]:

    

countries, obs_countries = zip(*sorted(country.items(), key=lambda x: x[1]))
basis_name, basis_cnt = zip(*sorted(basis_of_record.items(), key=lambda x: x[1]))
fig = plt.figure(figsize=(16, 9))
ax = fig.add_subplot(1, 2, 1)
ax.barh(np.arange(10) - 0.5, obs_countries[-10:])
ax.set_title('Top 10 countries per occurences')
ax.set_yticks(range(10))
ax.set_ylim(0.5, 9.5)
ax.set_yticklabels(countries[-10:])
#refer metadata problems

ax = fig.add_subplot(2, 2, 2)
ax.set_title('Basis of record')
ax.bar(np.arange(len(basis_name)), basis_cnt, color='g')
basis_name = [x.replace('OBSERVATION', 'OBS').replace('_SPECIMEN', '') for x in basis_name]
ax.set_xticks(0.5 + np.arange(len(basis_name)))
ax.set_xticklabels(basis_name, size='x-small')

ax = fig.add_subplot(2, 2, 4)
other = len(leaves) - zero_occurrences - count_extinct
pie_values = [zero_occurrences, count_extinct, other]
labels = ['No occurence (%d)' % zero_occurrences,
          'Extinct (%d)' % count_extinct, 'Other (%d)' % other]
ax.pie(pie_values, labels=labels,
       colors=['cyan', 'magenta', 'yellow'])
ax.set_title('Status for each species')


    

    
Out[10]:





<matplotlib.text.Text at 0x7f91c3a463d0>






    

In [11]:

    

#distribution of observations of horribilis per year
#probably not put...


    

In [12]:

    

horribilis = get_all_records('results', 'occurrence', 'search', taxonKey=6163845)


    

In [13]:

    

years = defaultdict(int)
for x in horribilis:
    years[x.get('year', None)] += 1
xs, ys = zip(*[(y, cnt) for y, cnt in years.items() if y is not None])
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(xs, ys, '.')


    

    
Out[13]:





[<matplotlib.lines.Line2D at 0x7f91c4d58910>]






    

In [ ]: