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7e925bb Nov 29, 2016
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Webservice

One instance of the pypath webservice running at the domain http://omnipathdb.org/, serving the OmniPath data with additional enzyme-substrate interactions. It implements a very simple REST style API, you can make requests by HTTP protocol (browser, wget, curl or whatever). The webservice currently recognizes 6 types of queries: interactions, ptms, resources, network, about and info.

A request without any parameter, gives some basic numbers about the actual loaded dataset:

http://omnipathdb.org

The about tells the version number:

http://omnipathdb.org/about

The network prints basic statistics about the whole network:

http://omnipathdb.org/network

The resources returns the list of all resources with their size:

http://omnipathdb.org/resources

The info returns a HTML page with comprehensive information about the resources:

http://omnipathdb.org/info

The interactions accepts some parameters and returns interactions in tabular format. This example returns all interactions of EGFR (P00533), with sources and references listed:

http://omnipathdb.org/interactions/P00533/?fields=sources&fields=references

The parameters can be omitted. More UniProts can be given separated by comma, and JSON format is available too (better for import to Python!):

http://omnipathdb.org/interactions/P00533,O15117,Q96FE5?format=json

Another interface is ptms, to list enzymes, substrates and PTMs.

http://omnipathdb.org/ptms/P00533?ptm_type=phosphorylation&fields=sources&fields=references

To list all interactions simply request:

http://omnipathdb.org/interactions

To list all PTMs similarly:

http://omnipathdb.org/ptms