No JSON object could be decoded Python

Question

I'm trying to get some data from this website . I can enter 'text' and 'longest_only' parameters but when I pass 'ontologies' param, it says No JSON object could be decoded. Here's the complete URL

http://data.bioontology.org/annotator?text=lung cancer,bone marrow&ontologies=NCIT&longest_only=true

I'm using Python 2.7

Answer 1

The argument is ontologies[] , since you can specify more than one. Your request should be similar to the one that the online search uses:

text=lung+cancer%2Cbone+marrow&ontologies%5B%5D=NCIT&longest_only=true&raw=true

Simply execute the same search there, and use the developer tools option of your favorite browser to check what is the actual payload being sent.

Answer 2

This is not an answer, but the only place I can show the error that I see when executing the sample code. I placed the code in a new module in main and run it in Python 3.4.

import requests

if __name__ == '__main__':
    url = 'http://bioportal.bioontology.org/annotator'
    params = {
        'text': 'lung cancer,bone marrow',
        'ontologies': 'NCIT',
        'longest_only': 'true'
    }

    session = requests.Session()
    session.get(url)

    response = session.post(url, data=params)
    data = response.json()

    # get the annotations
    for annotation in data['annotations']:
        print (annotation['annotatedClass']['prefLabel'])

I receive the following error.

Traceback (most recent call last):
  File "/Users/.../Sandbox/Ontology.py", line 21, in <module>
    data = response.json()
  File "/Users/erwin/anaconda/lib/python3.4/site-packages/requests/models.py", line 799, in json
    return json.loads(self.text, **kwargs)
  File "/Users/erwin/anaconda/lib/python3.4/json/__init__.py", line 318, in loads
    return _default_decoder.decode(s)
  File "/Users/erwin/anaconda/lib/python3.4/json/decoder.py", line 343, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/Users/erwin/anaconda/lib/python3.4/json/decoder.py", line 361, in raw_decode
    raise ValueError(errmsg("Expecting value", s, err.value)) from None
ValueError: Expecting value: line 1 column 1 (char 0)