[sbml-discuss] SBML L2v2 specification vote #2: Permitting nested units

Andrew Finney afinney at physiomics-plc.com
Wed Dec 7 12:15:19 PST 2005


The topic of this vote is: 
  SBML Level 2 Version 2 Specification - PERMITTING NESTED UNITS

The URL for the voting page is:
  http://www.surveymonkey.com/s.asp?u=959081579083

Additional background is available in the minutes from the October SBML
Forum meeting at
  http://www.sbml.org/forums/index.php?t=msg&th=713&rid=2

Description: Currently, SBML Level 2 Version 1 does not allow
user-defined units to be defined in terms of other user-defined units.
This means that, for example, "hour" cannot be defined in terms of a
user-defined "minute" unit.

Among the arguments *for* allowing nested units in SBML Level 2 Version
2 are the following.  First, it allows units to be defined in a more
direct manner.  Second, nested unit definitions are permitted in CellML,
and allowing them in SBML would allow closer interoperability with that
standard.

Among the arguments *against* allowing nested units are the following.
First, the experiences of at least one prominent group dealing with
databases of models is that most models have errors in their unit
definitions.  Increasing the complexity of the SBML unit scheme would
seem to increase the opportunities for errors, which would not help
bring about more correct models.  Second, efforts at creating a
translator from CellML to SBML have shown that unravelling nested units
is actually surprisingly difficult, due to the way that multipliers and
exponents interact.  Do the arguments for nested units outweigh the
implementation complexity and corresponding risks of errors?  Third, if
one wanted to provide a user with the ability to define quantities in
terms of non-base units (such as "hours"), it seems a software user
interface could easily provide this while hiding the internal
representation used in the translation to SBML (although in this case
the actual nested units supplied by the user would not be encoded in the
SBML and passed to other software applications, only the derived units
would be encoded in the SBML).

Should nested units be permitted in SBML Level 2 Version 2?

Please cast your vote by using the voting page at
  http://www.surveymonkey.com/s.asp?u=959081579083  

--
Andrew and Mike


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