These pages contain suggestions and guidelines for representing scientific findings in BEL.
Representation of Experimental Data
In a causal BEL Statement, the subject term frequently represents an experimentally manipulated entity while the object term represents a measured entity. Our best practices apply different levels of inference for mapping subject and object terms, particularly for representing 'omic data.
Subject Terms (Perturbations)
- How should I represent gene knock out or RNAi experiments?
- How should I represent chemical inhibitor experiments?
- How should I represent overexpression experiments?
- When should I use the protein abundance vs. the activity of a protein?
- How do I represent observations resulting from manipulation of two or more entities?
- How do I represent experiments that use site-directed mutants?
Object terms (measurements)
Here are some common questions and answers on representation of protein modifications in BEL:
- How do I represent removal of a protein modification (e.g., dephosphorylation, deubiquitination)?
- How do I represent a protein modification within a complex
- How do I represent a situation where one protein modification initiates additional modifications?
- How do I represent a situation where multiple phosphorylations are required for a protein's activity?
- How do I represent a protein modification when specific information is not available?