Sorry to step-in as well :-)
We've been playing with annotations for a while. As you know, SBML
Level 2 Version 1 annotation scheme was CellML metadata, and we
derived the current RDF scheme from it. The initial reason to get away
from CellML metadata was precisely the PubMed issue. Many models ar
On Thu, 29 Mar 2007, Matt wrote:
> We have been working on
> trying to integrate explicitly with biopax (http://www.biopax.org/
> states and generics proposal - level 2 was too limiting) in the hope
> that other databases (like GO, reactome, KEGG, DIP, signalling
> gateway, etc) get dragged along
By all means, step in as much as possible.
Can you explain in more detail or point to explanations of
bqmodel:isDescribedBy?
Specifically:
- what is its intended meaning?
- when more than one of these is defined on a resource, how is this
interpreted? For example: is there some precedence implied
On 3/29/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
> On Thu, 29 Mar 2007, Matt wrote:
>
> > We have been working on
> > trying to integrate explicitly with biopax (http://www.biopax.org/
> > states and generics proposal - level 2 was too limiting) in the hope
> > that other databases (like G
On Thu, 29 Mar 2007, Matt wrote:
>> BioPAX annotatation scheme is very fragile and in practise almost
>> unusable.
>
> How is that?
Because the annotation is free-form. I can use UniProt, uniprot, Uni-Prot etc.
> That was always going to wash out in practice. I'm not sure a rule for
> generatin
On Thu, 29 Mar 2007, Matt wrote:
> Can you explain in more detail or point to explanations of
> bqmodel:isDescribedBy?
You can find some explanations at:
http://www.ebi.ac.uk/compneur-srv/miriam-main/mdb?section=qualifiers
Note tha qualifiers are optional to be MIRIAM-compliant. I personaly
th
On 3/29/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
> On Thu, 29 Mar 2007, Matt wrote:
>
> > Can you explain in more detail or point to explanations of
> > bqmodel:isDescribedBy?
>
> You can find some explanations at:
>
> http://www.ebi.ac.uk/compneur-srv/miriam-main/mdb?section=qualifiers
> So there is no simple way to determine if this is a reference to a
> journal article except through interpreting the URI?
Exactly. But this interpretation is unambiguous, so this is not a problem.
This does not require more work than parsing an XML element
, with the exception that you do not
On 3/30/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
>
> > So there is no simple way to determine if this is a reference to a
> > journal article except through interpreting the URI?
>
> Exactly. But this interpretation is unambiguous, so this is not a problem.
> This does not require more wor
