Fundamentally, this is all just about trying to reduce the confusion that commonly occurs when we're talking about build plans. If somebody shares a sequence, is it for the bit they want synthesized, what a vector will look like after the synthesized bit gets stuck in, what gets digested out of the vector, or what it looks like as part of the final construct after it gets ligated together with other constructs?
When we were collaborating on building the new iGEM distribution, we ran into a lot of confusion amongst the many different participants along these lines, so we worked out a standard vocabulary for describing what we were talking about, with intuitive names for different stages in typical digestion/ligation assembly processes.
And once we humans were clear on what we wanted to say to one another, it was easy enough to take the next step and use SBOL3 to make a simple description to describe it to the machines as well, including the exact reactions one would want to run to actually execute the plan. This is one of the nice things about SBOL, which you can't do with formats like GenBank, FASTA, or GFF: describe not just a construct, but its relationship with other constructs and your whole plan for how to use it.
We're still using this vocabulary quite extensively in the iGEM Engineering Committee, as well as using the representations in our software, and we hope that others will find it useful for clarifying their discussions as well.
