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saezlab
CellphoneDB v4
Hi,
CellphoneDB recently released version v4 of its database and I was wondering if it will be included into the consensus resource of LIANA anytime soon. I'm very interested in the "non-peptidic molecules (i.e., not encoded by a gene) acting as ligands. Examples of these include steroid hormones (e.g., estrogen)." As far as I could tell there are no steroid hormones included in the consensus resource at the moment. It would be very convenient if they would become part of the LIANA consensus so one could use it without manual additions.
In the documentation it is mentioned that you "plan to continuously update this resource". Do you have a general plan how to include updates of the different databases once they become available? (If you plan to update the consensus occasionally some kind of version number to keep track of that, would be nice.)
Thank you very much
Hi @JanLeipzig,
I'm very interested in the "non-peptidic molecules
Indeed that's a good point. I have actually written a version of LIANA specifically for metabolite-receptor interactions, inspired by MEBOCOST. However, before I push it into the main branch, I wanted to wait a bit for the authors to possibly refine the method and to also get a better feeling of it myself. We also plan to make a consensus resource for those, but this would be a separate thing from the peptide ligand-receptor resource.
In the documentation it is mentioned that you "plan to continuously update this resource". (If you plan to update the consensus occasionally some kind of version number to keep track of that, would be nice.)
I only update the Consensus resource, together with LIANA, so taking note of LIANA's version would also reflect the version of the consensus resource.
Do you have a general plan how to include updates of the different databases once they become available?
We do indeed, we plan to keep adding resources to OmniPath, and hence to LIANA. Though, notably we would only include manually-curated resources in the Consensus resource.
@deeenes I assume updating to CellPhoneDBv4 should be just a matter of changing the source url to https://github.com/ventolab/CellphoneDB-data in pypath
Also, if I remember correctly from Luz, they have now dealt with the ambiguity of partner_a and partner_b.
Another difference now is that they also add small molecules that are thought to have specific interactions with a given receptor.
Cool, @dbdimitrov you can transfer this issue to pypath, I will take a look soon :)
Hi, I don't know why I haven't answered this one (edit: bc I answered in email), I'm very sorry about that! CellPhoneDB is up to date in OmniPath. The tables that OmniPath uses have been last updated 8 March 2023 (4.1.0), while 5 April 2023 there was a full contents update.
I know it's not too straightforward to find this information. We're preparing a better solution with clear versioning and database build reports, stay tuned for that :)
Hi, Thanks for the amazing resource and tool! CellPhoneDB just have a new update (v5). I guess it is not yet updated in if I fetch now using OmniPathR? And maybe you want to consider allowing different version by appending ..v4, ..v5 etc.
Kind regards, Saeed
