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[bioontology-support] [BioPortal] Feedback from Pranita Mahajan

Michael Dorf mdorf at stanford.edu
Tue Jun 18 11:06:15 PDT 2019


Hi Pranita,

Thank you for contacting us. I don’t know what your planned algorithm is for finding a connection between a symptom and disease, but here are a few BioPortal REST services that may be of help:

All classes of SYMP ontology
—————————————
The default page size is 50. You can iterate over all the pages, processing each symptom individually:
http://data.bioontology.org/ontologies/SYMP/classes

All mappings of SYMP ontology
——————————————
This service may give you possible connections between various symptoms and terms from other ontologies.
http://data.bioontology.org/ontologies/SYMP/mappings

Mappings between two ontologies
———————————————
This particular one is all the mappings between the Symptom and Disease ontologies. It may provide some idea on how these two related
http://data.bioontology.org/mappings?ontologies=SYMP,DOID

You may find some other services that may be of use as well. Here is the link to our REST services documentation:
http://data.bioontology.org/documentation

Unfortunately, we don’t have any resident Python experts on our team, so I can’t provide you with the exact sample code that you require. We do have some examples of Python code that may be of help:
https://github.com/ncbo/ncbo_rest_sample_code/tree/master/python

While they don’t offer the exact scenario you are looking for, they give you an idea on how to connect to our services and use them to extract data you are interested in.

Hope this helps!

Michael



On Jun 18, 2019, at 6:42 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Pranita Mahajan

Email: pranita.mahajan at gmail.com<mailto:pranita.mahajan at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FSYMP%3Fp%3Dsummary

Feedback:

I want to read symptom ontology in python and query it to find relation between symptom and disease, for example something like, cold and fever may lead to flu. Will it be possible to do so using available symptom ontology and Python? It will be great help if you can provide resources or related links.

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