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Help topics



  1. User interface
  2. XML output
  3. HTTP Requests
  4. Web service access
  5. Contact


MeSH UP can be accessed both through the online user interface, and as a web service.

User interface

Simply copy and paste the text to be annotated using the text area on the front page. You can also upload a text file using the controls provided at the top of the form. MeSH UP handles plain text input. Up to 70,000 characters can be annotated in a single request.

XML output

An XML version of the results can be obtained using the Download as XML button in the results page. The structure of the resulting XML is rather self-explanatory. For a given piece of text, a ranked list of MeSH terms is returned along with their relevance scores and original MeSH identifiers, e.g.: 

<document xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:z="http://wwwdev.ebi.ac.uk/z" source="Whatizit">
  <text>
    <list>
      <term rank="7.2613845" heading="Influenza, Human">D007251</term>
      <term rank="7.2613845" heading="Humans">D006801</term>
      <term rank="6.599168" heading="Disease Outbreaks">D004196</term>
      <term rank="2.718323" heading="Influenza Vaccines">D007252</term>
      <term rank="2.3816266" heading="Public Health Administration">D011635</term>
      <term rank="2.100799" heading="Health Policy">D006291</term>
      <term rank="2.0512083" heading="World Health">D014943</term>
      <term rank="2.002719" heading="Antiviral Agents">D000998</term>
      <term rank="1.679832" heading="World Health Organization">D014944</term>
      <term rank="1.6622167" heading="Influenza A virus">D009980</term>
      <term rank="1.6606703" heading="Health Planning Guidelines">D006287</term>
      <term rank="1.658648" heading="Korea">D007723</term>
      <term rank="1.516959" heading="Public Health">D011634</term>
      <term rank="1.4992186" heading="Influenza A Virus, H5N1 Subtype">D053124</term>
    </list>
  </text>
</document>


HTTP Requests

MeSH UP supports automatic HTTP requests. The following Python script illustrates the use of MeSH UP through HTTP POST requests:

import sys, urllib2, urllib

# Text to be annotated:

text = """"
Influenza vaccination acceptance among health-care workers: a nationwide survey.

We conducted a nationwide survey to investigate reasons for influenza vaccine uptake or refusal among health-care workers (HCWs) in Greece. Vaccination rates increased with increasing age, and among HCWs working in Northern Greece, in direct contact with patients, and with influenza vaccination in the past. Self-protection was the main reason for vaccination (89.1%), whereas 55.2% of HCWs reported vaccination to protect patients. Main reasons for refusing vaccination were perception of not being at risk for influenza (43.2%) and fear of vaccine adverse effects (33.4%).

"""

# MeSH UP's url:
url = 'http://www.ebi.ac.uk:80/Rebholz-srv/MeshUP/GetMeSHAnnotation'
urldata = {'method':'POST'}

# POST the text in the 'text' parameter:

data = urllib.urlencode([('text', text)])
req = urllib2.Request(url,urldata)

fd = urllib2.urlopen(req, data)

data = fd.read()

#Print the results in XML

print data
Web service access

Web service access to MeSH UP is also provided as part of the Whatizit infrastructure.



Contact

You can contact us at: tm-support ( at ) ebi.ac.uk spacer
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