Comments (3)
Hi,
This is a good point, I'll try to implement it.
The license parameter currently only makes sure that each record is supported by at least one evidence that fits the chosen licensing requirements. All other columns (sources
, references
) remain unchanged. Recently we introduced a feature that is able to reconstruct the data frames based on any subset of resources. Currently it doesn't care about the license, but it would be easy to fix that.
from omnipathr.
Thank you!
from omnipathr.
Hello @deeenes and @InesdeSantiago do you have any update related to this ticket?
I am using the following queries:
options(omnipath.license = 'commercial')
omnipath_show_db()
as.data.frame(get_annotation_resources())
as.data.frame(get_resources(query_type, datasets = NULL, generic_categories = NULL))
but the result is the same as if I run this:
options(omnipath.license = 'academic')
omnipath_show_db()
as.data.frame(get_annotation_resources())
as.data.frame(get_resources(query_type, datasets = NULL, generic_categories = NULL))
Ideally what I would expect is that the sources that cannot be used, wont appear right?
Later looking in your nicely and very well commented code I found this function resource_info()
that list in kind of a json :
library(tidyverse)
resource_info_json <- resource_info()
#if you want the json:
jsonlite::toJSON(resource_info_json, auto_unbox = TRUE) %>% jsonlite::prettify()
My suggestions:
- would it be possible maybe to include the link to the original URL?(this may help to ping the page and keep an eye in changes in the licensing)
- and also include in the documentation that when we see something like this:
(I mean a resource associated with another resource with underscore) this means that the first_resource_name is used by the second_resource_name, and that's the only one to be used for the "Queries" described by the resource_info() object?
I understand it is a huge project and not sure if I am big enough to push some changes into it. But I could try, at least with the documentation atm if that helps.
Many thanks for this great effort!
from omnipathr.
Related Issues (20)
- Orthology translation does not work: `oma_pairwise` fails with HTTP 503 HOT 8
- OmniPath failling to install in GH action HOT 2
- kegg_pathways_download returns fewer pathways HOT 1
- 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
- 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 17
- Omnipath failing to install in GitHub actions. HOT 3
- 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.