Forums

The topic of this vote is:
REFERENCES TO CONTROLLED VOCABULARIES

The URL for the voting page is:
http://www.surveymonkey.com/s.asp?u=207211607892

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

The SBML Level 2 Version Specification is at:
http://sbml.org/wiki/sbml-level-2-version-2.pdf

This survey involves multiple questions.

One of the proposed additions in SBML Level 2 Version 2 is
an attribute that would permit directly annotating certain
SBML elements with links to resources such as controlled
vocabulary terms. The need for such a capability in SBML is
widely acknowledged.

The proposal for SBML Level 2 Version 2 is to add an
attribute to the elements Model, Rule, KineticLaw,
Parameter, SpeciesReference, and Constraint. This is
proposed to be called 'sboTerm' and its data type would be a
URI. The set of values that can be assigned to this
attribute would be limited to a specific ontology, the
Systems Biology Ontology (SBO), developed and maintained
independently from SBML.

Under the proposal as currently formulated, the URI value of
an 'sboTerm' attribute on any given element in a model must
refer to a single SBO term that best defines the entity
represented by the SBML element in question. An example of
the type of relationship intended is:

KineticLaw in reaction R1 is a
first-order irreversible mass action rate law

Note the careful use of the words "defines" and "entity
represented by the SBML element" in the paragraph above.
The relationship between the SBML element and the URI is:

the "thing" represented by this SBML element *is an*
instance of the "thing" represented by the referenced
SBO term

One of the requirements to be imposed on SBO will be that it
is constructed in such a way that not more than one term is
appropriate as a value of an 'sboTerm' attribute. SBO will
not encode biological and biochemical concepts already
encoded by other ontologies.

'sboTerm' supersedes the previously proposed definitionURL
as first proposed in the discussion referenced here:
http://www.sbml.org/forums/index.php?t=tree&goto=2323&rid=0
http://www.sbml.org/forums/index.php?t=tree&goto=2237&rid=0
http://www.sbml.org/forums/index.php?t=tree&goto=2343&rid=0

Here are the questions:

1) Do you think the introduction of the 'sboTerm' attribute
as described above is a good idea for SBML Level 2
Version 2?

2) In which XML namespace should the attribute 'sboTerm'
reside?

a) The new level 2 version 2 namespace,
"http://www.sbml.org/sbml/level2/version2". In this
case, the attribute would appear in an SBML document
simply as 'sboTerm', in the same way as other SBML
elements appear.

b) The SBO namespace. In this case, the attribute would
have to appear with a namespace prefix in an SBML
document.

(Note that this question is not about whether having to
use a namespace prefix is pleasant or unpleasant; the
question is about whether the 'sboTerm' attribute should
be considered part of the SBML namespace.)

3) The 'sboTerm' attribute is not a general purpose
mechanism for linking SBML elements to particular
resource like controlled vocabulary terms. It is now
widely believed in the SBML community that SBML needs
such a mechanism. Andrew Finney and Nicolas Le Novere
proposed a scheme here:
http://www.sbml.org/forums/index.php?t=tree&goto=1435&rid=0
http://www.sbml.org/forums/index.php?t=tree&goto=1436&rid=0

The specification for this scheme is available here:
http://www.ebi.ac.uk/compneur-srv/sbml/proposals/AnnotationURI.pdf

The Finney-Le Novere scheme would supersede the use of
the CellML metadata scheme defined in SBML Level 2
Version 1, and the use of the CellML metadata scheme
would be deprecated in SBML Level 2 Version 2.

Do you think the Finney-Le Novere scheme should be part
of Level 2 Version 2?


Please cast your vote by using the voting page at
http://www.surveymonkey.com/s.asp?u=207211607892

Andrew and Mike