CellPhoneDB v5 (update and is_ppi flag)

[dbdimitrov]

Hey Denes,

Recently, CellPhoneDB got bumped to v5, and the data is stored here:
https://github.com/ventolab/cellphonedb-data/tree/master

Seems to have changed format from:

pypath/pypath/resources/urls.py

Line 1103 in bf81f34

'cellphonedb': {

Let me know if I can help with this.
Daniel

[dbdimitrov]

@deeenes also please use the is_ppi flag, I found a lot of erroneous interactions between enzymes and receptors. (no metabolite)

[dbdimitrov]

Maybe how I process it here would help:

saezlab/liana-py#60

[npalacioescat]

Hi Daniel,

As far as I could find, pypath i already using the CellPhoneDB git as a source for the data (see here and then here), so I think it is already using the v5 version of the data.

What I found out now when checking this, is that although the retrieval of interactions works fine:

> from pypath.inputs import cellphonedb
> list(cellphonedb.cellphonedb_interactions())[-1]
CellphonedbInteraction(id_a='P16070', id_b='O43914', sources='CellPhoneDB', references='', interaction_type='unknown-unknown', type_a='unknown', type_b='unknown')

When you try to retrieve the ligand-receptor interactions it returns a tuple of empty sets:

> cellphonedb.cellphonedb_ligands_receptors()
(set(), set())

This seems to be an issue in how the complex annotations were being imported, and therefore the ligand/receptor attributes were being all labeled as False, I think I fixed it in #279

Regarding the use of is_ppi flag, seems a bit more complex to implement (and I wouldn't want to break anything), so maybe we can discuss in person and I could try to take a look into it, or we can wait for @deeenes to come back 😅

Since this should resolve your initial question, I'll close the issue and we can discuss the is_ppi thing later :)

Best

[dbdimitrov]

@Nic-Nic thanks Nico. Though I would say the is_ppi is crucial since there are now a lot of enzyme-enzyme interactions imported ad ligand-receptors 😅

[dbdimitrov]

I renamed the issue and reopened since the two comments are tied. The flag was introduced along with the update of the database. 🙂

[dbdimitrov]

PS. Also, there is no need to implement the flag, it's simply about setting it to False, when whe resource is obtained. We don't want to include those, and I can think of limited use of having them even if we do.