Re: SBML L2v2 specification vote #4: References to controlled vocabularies
22 Dec '05 12:13
So here's a practical question to get the discussion on something
useful: What happens when a program receives an SBML file that it can't
fully read? Well, what happens now (there are plenty of programs out
there that either do not support SBML or only support certain parts of
it)? I think a good answer is that a warning should be issued to the
user (as suggested by Ralph and others). The user can then decide
whether he can manually fix the problem or switch to some other software.
But, imo, a bad solution is to start ostracizing developers who only
support certain aspects of SBML and not others. What purpose does this
If you have the sboTerms, you can write down the correct MathML
expression for other programs to use. But if you don't have the
sboTerms, then only programs that can read the MathML expressions can
read the SBML file. So including the sboTerms actually gives you readily
accessible information about the reaction rate law/etc. Of course, by
using the sboTerms you are limiting the number of possible reaction rate
laws to the ones in the database. But there really aren't that many
useful rate laws. No more than 1000. This is a small number for a database.
>>(Can I be the first to coin the phrase 'SBML Nazi'? Akin to
>>Fashion/Grammar. Or is that too politically incorrect?)
>I, for one, find that term deeply offensive.
It's a joke. No need to be offended. (As a Jewish guy myself, I am
not offended when someone uses the word 'Nazi' to simply denote fascist
behavior. For example, I found the Seinfeld episode on the Soup Nazi to
be extremely funny. ) But, I digress.