PubMed IDs for edge interactions

[bio-bean]

Hi, thanks so much for making this package, its really great and helpful!

I was wondering if there was a way to extract the PubMed IDs for edge interactions as in the PyPath module for python? I can't seem to find it in the interactions databases that I can download, so I wasn't sure if it was a download parameter or if that option wasn't available in the R package.

I've been downloading (all) interaction data like so:

interactions <- import_AllInteractions(from_cache_file = NULL,
                                        filter_databases = get_interaction_databases(),
                                        select_organism = 9606)

Thanks very much!

[deeenes]

Hi @bio-bean,

I am doing some refactoring and development on OmnipathR in these days, I gonna have a look also on this. Looking at the current source code: https://github.com/saezlab/OmnipathR/blob/master/R/import_Omnipath.R#L376 I see fields=references is there, which means you should have a column references with the PubMed IDs for each interaction, isn't it?

Best,

Denes

[bio-bean]

Hi Denes,

When I download the data as above, I get a references column but they have references to specific databases and (possibly an internal/within OmniPath ID?), like so:

source	target	source_genesymbol	target_genesymbol	is_directed	is_stimulation	is_inhibition	consensus_direction	consensus_stimulation	consensus_inhibition	dip_url	sources	references	nsources	nrefs
P0DP23	P48995	CALM1	TRPC1	1	0	1	1	0	1	TRIP	TRIP:11290752;TRIP:11983166;TRIP:12601176	1	3

Which is great that I know what database they came from, but I haven't been able to trace back to the pubmed IDs or literature references themselves, especially in sources like BioGRID or PhosphoSite.

Thanks so much for getting back to me!

[deeenes]

These are PubMed IDs, the first one in your example points to a paper about TRP channels: https://pubmed.ncbi.nlm.nih.gov/11290752/ We added the resource names recently because someone asked for it. I will add an option to OmnipathR to remove the resource labels.

[bio-bean]

Oh gosh! Thank you so much for pointing that out to me, sorry for missing this!

[bio-bean]

Hi, sorry I just have a follow up question related to this. When I look in the interactions databases (as above), there is a source in the source column called "Wang", but nothing more in the reference column - I was wondering what source this was, I can't seem to find anything on it.

[deeenes]

Hi, The Wang label refers to this resource: http://omnipathdb.org/info#HSN It doesn't provide PubMed IDs hence the references column is empty unless there are references from another resource. Wang (HSN) is supposed to be literature curated although they don't disclose much information about their methods and provide the interactions with very minimal attributes (only direction and sign).