Hello Swapna,
The BEL Framework 2/3 only supports BEL version 1.0 (see wiki). BEL version 2.0 exists as a specification with examples at the moment.
We are working on support for BEL version 2.0 inside the bel.rb library for use with the next generation of the OpenBEL platform (includes network compilation). More information will be available on this shortly.
-Tony
Hi Swapna,
In BEL v1.0, there is unfortunately no good way to express protein fragments. truncation()/trunc() is really meant to express protein variants with a mutation that results in a premature stop codon – see http://wiki.openbel.org/display/BLD/Modifications#Modifications-_Toc166642432truncation%28%29,trunc%28%29 . In converting BEL v1.0 statements to v2.0, trunc() should get upgraded to var() since it is essentially a special kind of substitution or a frameshift mutation.
What I have been recommending for representation of fragments in BEL v1.0 is to create a new term outside of the existing namespaces, and link it to the root/parent protein via a reaction term. This does not have the advantages of using a value from a controlled vocabulary, but can be named pretty clearly and will have obvious linkage to the parent protein in the compiled network. For example (where “NS” is some namespace prefix, and “YFG” is your favorite gene):
rxn(reactants(p(NS:YFG)), products(p(“YFG 10 kDa fragment”)))
For your second question, the current way to handle it would be to use a vocabulary with cell type-specific biological process terms. GO has many of these like “fibroblast apoptotic process”, but is not comprehensive so you may need to create an appropriate vocabulary. In the specific example you give it is probably not necessary to note that the secreted factor comes from fibroblasts, though you may want to add separate statement(s) about the upstream controller(s) of that secreted factor, annotated with the correct cell context. Note that BEL doesn’t currently provide any relationship to link these cell type-specific biological processes to the relevant cell types. Depending on your needs, you may want to add this to the BEL language working group “wish list” on the wiki (http://wiki.openbel.org/display/BLWG/BEL+Language+wish+list) and document with some specific use cases.
Best,
Natalie