Omnipath: database schema

[Marcio Luis Acencio]

Dear all,

Here's Marcio, postdoc at Astrid Lægreid and Martin Kuiper's group at the Norwegian University of Science and Technology. Among other things, we have worked on Biogateway (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755819/),  a semantic systems biology tool that provides a single point to query a variety of resources.

We are planning to include Omnipath in our list of resources as it contains a comprehensive collection of manually curated causal interactions. However, for this end, it would be nice to know the Omnipath database schema, i.e. all the fields associated to each interaction.

Could you please let us know how to obtain this schema? Is it possible to do it using pypath?

Best regards,

Marcio

_________________________

Marcio Luis Acencio, PhD

Postdoctoral Fellow

Department of Cancer Research and Molecular Medicine

Norwegian University of Science and Technology (NTNU)

Telephone: +47 72 82 6925

e-mail: marcio.l...@ntnu.no

[Dénes Türei]

Hi Marcio,

Thank you for your mail. I am very glad you connect OmniPath into your service.
I haven't compiled yet a description of data structures in pypath but
indeed it would be useful to have one.

In pypath all the annotations of molecules and interactions are stored
in vertex and edge attributes of the igraph object.
Most of these attributes are built-in Python objects but some of them
are special e.g. the Direction objects.
In OmniPath every interaction must have sources (databases),
references (PubMed IDs), directions and effect signs (these can be
undirected or unknown).
The presence of further annotations depends on which data do you load.

For example:

import pypath
pa = pypath.PyPath()
pa.init_network(pypath.data_formats.pathway)

# the sources of the first edge; it is a `set` object:
pa.graph.es[0]['sources']

# the directions for the same edge, this is a `Direction` object:
pa.graph.es[0]['dirs']

For the `Direction` object I advise to use the `sources`,
`positive_sources`, `negative_sources` attributes and the
`which_dirs()` method.

If you load enzyme-substrate interactions, you will have `Ptm`
objects. This and other potentially useful stuff are documented here:
http://pypath.omnipathdb.org/
and here: http://pypath.omnipathdb.org/notebooks/intro.html

Please tell me if you have any question. Unfortunately I don't have a
nice schema, but if you ask for specific details should be easy to
answer.

Best wishes,

Denes

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--
Denes Turei, Ph.D.

postdoc @ Uniklinik RWTH Aachen & EMBL Heidelberg
+4915166299976 Germany
+447442970610 UK
de...@ebi.ac.uk
http://www.ebi.ac.uk/~denes
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