Introduction -to- Ecology

A course covering population, community, and ecosystem ecology for undergraduates

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Getting Data From The Web

Data on the web is increasingly available in ways that go beyond downloading csv files.

APIs

Often data is provided through an Application programming interface. An API is just an agreed up language for two different software components to talk to one another. On the web, using an API typically involves calling a specially structured URL, and handling the data that is returned.

eBird Examples

eBird is a real-time, online, checklist program that allows users to report their bird observations. It is currently adding several million records per month. This data can be queried using eBird’s API.

Let’s start by looking at the results of an API call in the browser.

Recent observations near Logan, UT

To find recent observations near Logan, we use this specially formatted url the includes the latitude and longitude.

XML

http://ebird.org/ws1.1/data/obs/geo/recent?lng=-111.83&lat=41.74

JSON

http://ebird.org/ws1.1/data/obs/geo/recent?lng=-111.83&lat=41.74&fmt=json

We can also access this data from Python

We could do this using urllib, but there are better ways to do this.

XML

One of the best modules for dealing with XML (and HTML) is BeautifulSoup. It makes it easy to work with tagged data.

from bs4 import BeautifulSoup
import urllib

url = "http://ebird.org/ws1.1/data/obs/geo/recent?lng=-111.83&lat=41.74"
webpage = urllib.urlopen(url)
webdata = BeautifulSoup(webpage)
print webdata.prettify()

for sighting in webdata.find_all('sighting'):
    print sighting.lat.text, sighting.lng.text, sighting.find('sci-name').text

This sort of approach will also work well for scraped HTML data.

JSON

The requests module makes dealing with web APIs incredibly easy.

import requests

url = "http://ebird.org/ws1.1/data/obs/geo/recent?lng=-111.83&lat=41.74&fmt=json"
recent_observations = requests.get(url)
recent_observations.json

Which then lets us do things like:

for observation in recent_observations.json:
    print observation['sciName'], observation['howMany']

Wrapping APIs

We can make it easier to use APIs in a particular language by writing a series of functions that build the proper URLs. Often someone has already done this for us, so it’s definitely worth looking around. For example, here’s a Python eBird wrapper. Then getting the data is as easy as importing a module.

from EBird import EBird

ebird = EBird()
ebird.recent_notable_observations_geo(41.7, -111)