Re: SBML L2v2 specification vote #4: References to controlled vocabularies
23 Dec '05 01:02
Howard Salis wrote:
> 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
This is perfectly OK with everybody I think. Nobody I know of can claim
that they fully implemented the SBML specification and I guess it will
be quite some time until someone does. On the other hand, the SBML spec
has to clearly state how SBML files are to be interpreted and int his
case I would like to see it stated in the specs that if there is a
MathML term and an sboTerm that it is the MathML term that tells you
what the kinetic is going to be. If this is not specified, mailboxes of
software developers are going to be full of mails from users complaining
about software xy that has different simulation results than software yz.
So if your programs warns the user that the MathML term has been ignored
and that this might pose a problem, then this is fine and everyone is happy.
> 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?)
It might have been a joke, but if so, it was a rather bad one and people
have been offended as you knew damn well even before you posted. I think
you should either grow up fast and stop those kindergarden postings or
stop posting because this does not help discussion. What we surely don't
need here are trolls.
>> 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.
> -Howard Salis