Hi,
As discussed at the last CellML meeting, there are some models which
reference both the paper about the model, and a reference about the
biology. Since there is no way to determine between them, this creates
problems for CellML metadata processing tools which want to identify the
paper abo
I don't think this is a good idea.
- I think bioentity should be depreciated, it has not intrinsic semantic value.
- If it is used currently, it should be left as its current minimum
specification which is to label and point to other bioinformatics
database IDs.
- The problem is not 'biologically
Matt wrote:
> I don't think this is a good idea.
>
> - I think bioentity should be depreciated, it has not intrinsic semantic
> value.
>
It does, unfortunately, seem to usually target a literal node at the
moment. It would be nice for this to at least be a resource, which could
provide furthe
Wow, I haven't posted to this list in a long time...
But I feel compelled to give a little advice as
someone who's spent a lot of time integrating
biological information and therefore has made a lot of
mistakes!
By all means, have a best practice encouraging people
to use the GO cellular_component
Melanie!
Thanks for your thoughts. You are right about the mess mapping to
different ontologies and vocabs produces. 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
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
On Fri, 30 Mar 2007, Matt wrote:
> In those cases, for example bqs, where the object of the reference is
> indeterminate or not of interest, it would be helpful to be able to
> filter metadata without having to have knowledge of the values (in
> this case reference URI schemes or identifiers) to
On 3/30/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
> On Fri, 30 Mar 2007, Matt wrote:
>
> > In those cases, for example bqs, where the object of the reference is
> > indeterminate or not of interest, it would be helpful to be able to
> > filter metadata without having to have knowledge of th
On Fri, 30 Mar 2007, Matt wrote:
>>> In those cases, for example bqs, where the object of the reference is
>>> indeterminate or not of interest, it would be helpful to be able to
>>> filter metadata without having to have knowledge of the values (in
>>> this case reference URI schemes or identifi
Hi Nicolas,
On 3/30/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
On Fri, 30 Mar 2007, Matt wrote:
>>> In those cases, for example bqs, where the object of the reference is
>>> indeterminate or not of interest, it would be helpful to be able to
>>> filter metadata without having to have kno
> I misunderstand the scope of the property isDescribedBy. I also don't
> think reverse engineering URIs to obtain meaning is a good practice.
But ... you do not reverse engineer anything. The URI IS the meaning. In
the English dictionary, there is a word "publication", with a definition.
Well, i
Hi Nicolas. Thanks for the in-depth reply.
On 3/31/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
>
> > I misunderstand the scope of the property isDescribedBy. I also don't
> > think reverse engineering URIs to obtain meaning is a good practice.
>
> But ... you do not reverse engineer anything.
>> > I misunderstand the scope of the property isDescribedBy. I also don't
>> > think reverse engineering URIs to obtain meaning is a good practice.
>>
>> But ... you do not reverse engineer anything.
>
> Though you have to pull apart the URI correctly to discover the key.
You mean to split urn:M
On 4/1/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
>
> >> > I misunderstand the scope of the property isDescribedBy. I also don't
> >> > think reverse engineering URIs to obtain meaning is a good practice.
> >>
> >> But ... you do not reverse engineer anything.
> >
> > Though you have to pull
> You will always need to pull apart the 'URI' (table2 MIRIAM document)
> to retrieve the datatype and identifier.
Well, yes you have to recognise what belongs to the data-type and what
belong to the identifier. But you do that all the time in RDF anyway. And
beside, we do it for you and can retur
On 4/3/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
> > You will always need to pull apart the 'URI' (table2 MIRIAM document)
> > to retrieve the datatype and identifier.
>
> Well, yes you have to recognise what belongs to the data-type and what
> belong to the identifier. But you do that all t
24 matches
Mail list logo
