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Annotation package workshop 2010: Notes

19–21 May 2010


Scope and organisation: what are the goals of the workshop? Who are the end users?
- Draft proposal


What we will do is go through the topics and figure out what the new RDF looks like, and then determine if the package should be a replacement/extension/in parallel (or combination of the above).

- Which annotation (all or some of it) belong in the annotation package? Does this package replace/extend/exist in parallel with current controlled annotation?

The element <Annotation> must remain in the core, as will the proprietary annotation.

The scope of this package is only the SBML-controlled annotation. Eventually, with SBML Level 4, all annotation could move out. However, with Level 3, the annotation package will be restricted to SBML-controlled annotation.

If we do a replacement: Remember, if you want to convert from L2 to L3 then you would require the converted model to import the annotation package.

- How will this proposal be written in practice? Do we take out Section 6 and others from the Core specification?


  1. ordering of RDF elements; rewording of 6.3 to show which bits are part of the RDF spec already; 6.6 and ordering of history elements, multiple people associated with which modifications? For 6.6, it is anachronistic and could be changed.
  2. There are a number of requirements in the MIRIAM checklist that can be described using Dublin Core but aren't currently. These additional dc: terms could go either in the core or in the package.
  3. Stick with RDF? (versus, e.g. RDFa). Probably less work to keep RDF, and try to change as little as possible.
  4. sboTerm attribute. It is important that we say definitively whether/when it is appropriate to use SBO terms within the MIRIAM RDF annotation. Never.

Discussion points

Annotation format

- SBO term attribute? Is it removable?
- Some annotation can remain in the core
- Frank wants his sboTerm!!
- Are we happy with the annotation element structure as it is?

- Should the annotation package cover "non-standard" annotation, such as CellDesigner layout tags?

We should also say something in the spec about the (semantic) difference between having 3 bqbiol with 1 bag each and having 1 bqbiol with 3 bags inside!

Topic list on Google Docs

- In scope or not? Prioritised, then assigned to groups to sort out as "homework"

Relationship of annot package to Groups package

- How would annotation package deal with *other* packages?
- How can Groups be consistently annotated?
- Allyson: specific example of Groups package *is* in scope.

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