Detection Method Tracking

[Mitch Wagner]

Hi there!

The group I am a part of is looking to incorporate Omnipath's curated information into our own database, whose goal is to centralize all of the protein interaction, functional annotation, and orthology datasets used by our lab.

Part of the information we want to keep track of is the detection method for an interaction (PSICQUIC's detmethod field is a good example):

http://www.ebi.ac.uk/Tools/webservices/psicquic/view/help.xhtml

While going through the documentation for Omipath, I was having trouble determining if this information is available for consumption. I was wondering if you incorporate that information into Omnipath, and if so, if you would be willing to provide a few examples of how to properly access it.

Thank you for your time!

Mitch Wagner

--

Mitch Wagner
VT Computer Science, 2016
mit...@vt.edu | (757) 292-8121

[Dénes Türei]

Hi Mitch,

Thank you for your interest.

The software behind OmniPath is `pypath` and what you see in the
webservice is a limited view of the data structure built by `pypath`.

In `pypath` we have input definitions in the `data_formats` submodule.
Let's see for example DIP:

https://github.com/saezlab/pypath/blob/33046f80ac65863b567bfeee1d1c810e98596bb9/src/pypath/data_formats.py#L557

Here `inFile='get_dip'` means to use the `pypath.dataio.get_dip()`
method to obtain the data.
You see `extraEdgeAttrs` contains `dip_methods`, and it says the
methods are in column `4` and separated by `;`.
Then if you load DIP in `pypath`, the `igraph` object in the
`pypath.main.PyPath()` instance going to have an edge attribute
`dip_methods` having for each edge a list with the methods. This works
the same way for the data sources which provide methods, e.g.
`dd_methods`, `netpath_methods`, `trip_methods`, `hprd_methods`,
`matrixdb_methods`, etc. Hence you can access these, for example for
edge `0`, like this:

>>> pa = pypath.PyPath()
>>> pa.init_network({'dip': pypath.data_formats.interaction['dip']})
>>> pa.graph.es[0]['dip_methods']
['two hybrid']

You might be wondering why we have separate edge attribute for each
resource. This is because their nomenclature is not always the same
and we did not standardize them. To merge these annotations one would
need to translate them to a controlled vocabulary from a standard
ontology.

I hope it helps, please tell me if you have more questions.

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
public key: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x5706A4B609DD65A6