Comments (6)
@cmungall Would you have anything for this?
from helpdesk.
Hi there
Following on from #15 can I just clarify:
GO is not a protein-protein interaction database. GO is for describing the function of gene products. Sometimes that involves describing interaction partners of a gene to give more context for a function.
Are you interested in
- querying human protein-protein interaction data in general from a variety of sources (biogrid, intact, etc)?
- taking the subset of GO annotations that have protein-interaction data and extracting your fields from that. Note that for some species (including human) this may turn out to be similar to the results for 1, since some groups essentially include all IntAct PPIs in their GO annotations.
I can provide sample python code for either, although its only 2 that is within the scope of GO. If it truly is 2 that you're after, it may help to have more context about what you're trying to do, to make sure our advice doesn't lead you astray
from helpdesk.
Im interested in 1.
Furthermore, I'm not a biologist so I thought maybe I can extract from go someway direct interactions between proteins.
I would love a biological explaination why I was confused :)
from helpdesk.
Yes, GO does include PPI annotations but it's not the primary purpose of GO. You may be better going to another database, or aggregating. I can provide some code that helps. But it may help to know more about your broader goals. You may also want to do a broader review of the landscape of PPI databases and evaluate which fit your needs best
from helpdesk.
Here is an example of code to extract the binding partner information from a GO association file: https://github.com/geneontology/go-notebooks/blob/master/PPI_from_GAF.ipynb
from helpdesk.
Thank you for the great suggestions. It helped me a lot to understand what I need to do.
from helpdesk.
Related Issues (20)
- Question: How to esablish to which entities the Source and Target in a GO-CAMS relation point to? (Newbie question) HOT 5
- New User Onboarding
- fission yeast annotaions use 2 different species labels HOT 14
- I would like to work with all GO-CAM statements available. For this purpose, would you recommend me to use the available... HOT 2
- BUG?: PomBase annotation has disappeared from AmiGO HOT 4
- Duplicate annotation in AmiGO HOT 3
- New User Onboarding HOT 4
- Include PMID in error log report HOT 1
- Issue when using API (Gene Ontology Ribbon Sandbox) with plant genes and GO terms HOT 4
- Gene Ontology Ribbon JSON formating HOT 1
- New User Onboarding HOT 1
- GO term is a URL HOT 1
- rdf.geneontology.org not available (timeout occured) HOT 8
- Feature request: Easy to find OWL data for a single GO term HOT 6
- New User Onboarding
- How to use GO to compare 2 sets of data HOT 10
- Cycle in the go-basic.obo graph HOT 10
- GO snapshot is not updating HOT 5
- Git hub action ot report direct annotations is not working HOT 1
- Different annotation date for the same annotation HOT 2
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 helpdesk.