[sbml-discuss] SBML L2v2 vote #4 references

zucker at research.dfci.harvard.edu zucker at research.dfci.harvard.edu
Mon Dec 19 18:41:47 PST 2005


Hi folks,

  I just read through the December 5 version of the LeNoverre & Finney
AnnotationURI proposal.

First of all, thank you for providing such a well-documented
specification, and for providing so many examples to clarify the usage of
the AnnotationURI proposal.


To make sure I understand, do you agree with the following summary?

1. In all cases, we want to represent a relationship between an SBML
metaid and one or more URI's.  The syntax recommended forms a subject,
predicate, object triple:

<metaid> relationship <uri> .
or
<metaid> relationship { <uri1> <uri2>...<urin> } .


where the subject is the metaid, the predicate is an arbitrary
relationship, and the object is a URI or a bag of URI's.  The rest of the
paper recommends specific Dublin Core vocabulary terms to use as the
relationship predicate.


2. When you don't want to specify the relationship at all, use the
dc:relationship vocabulary term.

3. When you want to specify that resource identified by the metaid is a
version of a resource identified by the URI, use
<metaid> <dc:isVersionOf> <uri> .

4. When you want to specify that the resource referenced by the metaid has
several versions, each of which are identified by a separate URI, use
<metaid> <dc:hasVersion> {<uri1>, <uri2>..<urin>} .

5. When you want to specify that the resource referenced by the metaid is
a part of the resource identified by the URI, use
<metaid> <dc:isPartOf> <uri> .

6. When you want to specify that the resource referenced by the metaid has
several parts, each of which are identified by a separate URI, use
dc:hasPart
<metaid> <dc:hasPart> {<uri1> <uri2>...<urin>} .

7. When you want to specify that the resource referenced by the metaid is
also referenced by a publication identified by a URI, use
<metaid> <dc:isReferenceBy> <uri> .

8. By making this syntax part of the SBML standard, you ensure a minimal
level of metadata comprehension by SBML software, even if it is not fully
RDF compliant.

Sincerely,

Jeremy






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