Comments (6)
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).
from omnipathr.
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
from omnipathr.
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!
from omnipathr.
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.
from omnipathr.
Oh gosh! Thank you so much for pointing that out to me, sorry for missing this!
from omnipathr.
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.
from omnipathr.
Related Issues (20)
- Orthology translation does not work: `oma_pairwise` fails with HTTP 503 HOT 8
- Error Installing OmnipathR when trying to install liana HOT 1
- PDPK1 and PDK1 are mixed up
- omnipathdb has expired certificate HOT 1
- CDK6 -> RUNX1 interaction should be consensus inhibition
- get_collectri() and OmnipathR download not working HOT 4
- CellPhoneDB Version HOT 2
- error when run import_omnipath_annotations HOT 1
- Clarification about commercial licenses HOT 3
- TIME OUT for import_intercell_network HOT 6
- Error when Testing the pipeline HOT 3
- loading package failed HOT 1
- import_all_interactions only shows transcriptional HOT 2
- connection problem HOT 2
- cannot open the connection to 'https://omnipathdb.org/resources' HOT 2
- Error: Error installing package 'OmnipathR': when trying to install LianaR HOT 4
- Omnipath failing to install in GitHub actions. HOT 1
- Installation error HOT 3
- wrong TGFB1-SMAD7 interaction
- Error in get_collectri()
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from omnipathr.