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?
- 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.
- 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.
- Stick with RDF? (versus, e.g. RDFa). Probably less work to keep RDF, and try to change as little as possible.
- sboTerm attribute. It is important that we say definitively whether/when it is appropriate to use SBO terms within the MIRIAM RDF annotation. Never.
- 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.