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[bioontology-support] Problems with annotator API calls

Colin Morris colin at
Thu Apr 4 18:40:04 PDT 2013


Calls to the annotator that were previously working seem to be giving empty
results. I'll paste an example call posted through python with the requests
library below. I tried putting the same text through the web interface with
the same ontologies, and was able to get results.

>>> import requests
>>> url = ''
>>> data = {'withDefaultStopWords': 'true', 'apikey': <apikey>,
'textToAnnotate': 'Whether mesial temporal lobe epilepsy with hippocampal
sclerosis (MTLE-HS) is a condition with a unique biological background that
can be delineated from other TLE, is unresolved. Here we performed a
comparative analysis of two TLE patient cohorts - one cohort with HS and
one without HS - in order to identify phenotypic characteristics
specifically associated with MTLE-HS.Epidemiological data and clinical and
diagnostic features were compared between patients with MTLE-HS and TLE
patients without HS. When appropriate, data were compared with healthy
controls.Fifty-six (26%) patients were diagnosed with MTLE-HS and 162 (74%)
with other TLE. Age at epilepsy onset was lower in patients with MTLE-HS (P
= 0.003) than in TLE patients without HS. Incidence of simple partial
seizures was higher in the MTLE-HS group (P = 0.006), as were complex
partial seizures (P = 0.001), ictal psychiatric symptoms (P = 0.015), and
autonomic symptoms (P < 0.001). Interictal psychiatric symptoms, including
depression, were less frequent in MTLE-HS (P = 0.043). MTLE-HS patients had
a higher incidence of childhood febrile seizures (FS; P = 0.043) than TLE
patients without HS. In contrast, the former group had the lower frequency
of first-grade family members with childhood FS (P = 0.019).We identified
phenotypic characteristics that distinguish MTLE-HS from other types of
TLE. These characteristics will be important in diagnostics, treatment, and
determination of prognosis, and provide a basis for future
phenotype-genotype studies.\n', 'ontologiesToKeepInResult':
'1070,1352,1101,1351,1348', 'format': 'tabDelimited'}
>>> resp =, data)
>>> resp.text
>>> resp.status_code
>>> resp.headers
{'date': 'Fri, 05 Apr 2013 01:37:44 GMT', 'content-length': '0',
'content-type': 'text/plain;charset=UTF-8', 'connection': 'close',
'server': 'Apache/2.2.13 (Red Hat)'}
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