Re: [sbml-annot] Annot package

[Kieran S. <Kie...@ma...>]

As Nicolas pointed out, there are existing Miriam/identifiers.org methodologies for supporting controlled annotation of most of the keys in these notes fields already (BIOCYC, KEGG, REFERENCES). Some of the other keys are just notes and should remain that way (NOTES, WHAT_I_HAD_FOR_BREAKFAST) and there's a final set of keys dealt with specifically by the FBC package (GENE_ASSOCIATION, CHARGE). What are the other keys that we would like to annotate, but are unable to do with the current setup?

k

On 24 Jul 2013, at 17:32, Ben Heavner wrote:

> Sorry, I didn't mean to suggest that the Neurospora model is how it should be done, or that any of the custom notes I've compiled on the google doc spreadsheet I built are good, should be directly supported by SBML standardization of custom notes fields, or are the right way to do things. Rather, as Brett pointed out, it's an example of how things are meandering in the absence of a good way to do it, and demonstration that people are putting custom key:value pairs in notes fields at the moment.
> 
> I wholeheartedly agree that these annotations are better machine parsed than intended to be human readable, and so should be moved out of the notes field. My efforts to modify the COBRA Toolbox to deal with these fields better is part of instigated this round of discussion.
> 
> And I do rather like the "what I had for breakfast: 2.5 eggs" example. :)
> 
> -b
> 
> 
> On Wed, Jul 24, 2013 at 7:44 AM, Nicolas Le Novere <n.l...@gm...> wrote:
> Hello,
> 
> Why not using the usual SBML controlled annotation for BIOCYC, KEGG and REFERENCES? They would then be available to all tools supporting MIRIAM annotations. If using the Identifiers.org versions, they would even become resolvable and provide direct access.
> 
> If you want, in addition, to add notes so they are visible for instance in a webrowser, this is understandable. But there as well, you should use Identifiers.org forms instead of proprietary forms. That way, your notes will be resolvable.