OmniPath webservice disease filter

[Schaarschmidt, Marco]

Dear Team of Omnipath,

I am Marco Schaarschmidt working as a student assistant at the Hasso Plattner Institute, University of Potsdam, Germany. I would like to use your data via web service access for a gene expression simulator.

However, I have a question concerning the filters of the web service. Is it possible to filter the interactions by disease, e.g. Breast cancer? If it is possible, how exactly can I do that? 

 

Thank you very much for your answer!

 

Best regards,

 

Marco Schaarschmidt

[Dénes Türei]

Dear Marco,

Thanks for your interest.
Disease, tissue or cell type specificity or expression or functional
annotation data is not available at all in the web service at the
moment.
OmniPath is a generic network of prior knowledge and it's up to the
users to combine it with data regarding their topic of interest.
We don't plan to add expression data in the near future because for
that purpose already huge and well designed repositories are
available.
We will add soon some annotations for proteins which will probably
cover their relation with diseases (data from DisGeNet) and their
immunohistochemistry based tissue expression from Human Protein Atlas.
Overall if you use our Python module, pypath instead of the web
service, it is able to include Human Protein Atlas data. But for your
purpose it's much easier to fetch your expression data from elsewhere
and combine with OmniPath yourself.

Best wishes,

Denes

El mié., 20 feb. 2019 a las 9:14, Schaarschmidt, Marco
(<Marco.Sch...@student.hpi.uni-potsdam.de>) escribió:

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--
Denes Turei, Ph.D.

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