Chronological Thread 

< Chronological >      < Thread >

---

Hi Andrew,

I can see how the current CellML metadata specification works in terms
of defining biological entities, but I can't see any way to simply say
"look here for why I use this parameter value" or "plot this
experimental data with this trace to show that the simulation results
are reasonable". This is where something like a isDescribedBy
relationship would seem appropriate.

I think that given SBML uses the BioModels qualifiers (with no
extensions yet) that it would be advantageous for both the CellML and
SBML community to use a common standard for these annotations. As such,
if we find examples that can't be described with the current set of
BioModels qualifiers then we should be working with the BioModels
community to extend them. Do you have any examples in mind that don't fit?


David.

Andrew Miller wrote:
> David Nickerson wrote:
>> Hi all,
>>
>> Just wanted to see what people think about using the BioModels
>> qualifiers (http://biomodels.net/index.php?s=Qualifiers) in CellML
>> models? i.e., following the SBML annotation specification (see section 6
>> of the SBML level 2 version 2 specification).
>>
>> The reason I ask is that I am starting to look at how to reference
>> external data, for example to justify a parameter value or provide
>> experimental data for use in making a graph. At least for these examples
>> the http://biomodels.net/model-qualifiers/isDescribedBy qualifier seems
>> quite appropriate - where the referenced resource could be a journal
>> publication to justify a parameter value or a reference to some
>> experimental data.
>>
>> Before progressing too far with this, I thought I'd better check. One
>> problem I can see immediately is that the
>> http://biomodels.net/model-qualifiers/is and/or
>> http://biomodels.net/biology-qualifiers/is qualifiers are pretty much
>> the same as the cmeta:bio_entity already defined in the CellML Metadata
>> Specification. So is there already something in the CellML metadata
>> specification that will let me reference arbitrary (possibly external)
>> resources? Is it ok to just use the BioModels qualifiers that we want
>> without supporting them all? Or is there some other way to achieve the
>> same result?
>>
> The cmeta specification does allow you to give an identifier as a URI:
>
> <rdf:Description rdf:about="#myVariable">
> <cmeta:bio_entity>
> <rdf:Bag>
> <rdf:li rdf:parseType="Resource">
> <cmeta:identifier rdf:parseType="Resource">
> <cmeta:identifier_scheme>URI</cmeta:identifier_scheme>
>
> <rdf:value>http://www.example.org/papers/MyModel.html#myVariable</rdf:value>
> </cmeta:identifier>
> </rdf:li>
> </rdf:Bag>
> </cmeta:bio_entity>
> </rdf:Description>
> |
> |
>> I know Carey did some initial work looking at using the XML Resource
>> Directory Description Language (RDDL, www.rddl.org) to reference
>> external data. To make full use of this (especially in regard to model
>> curation), I think we would need to define our own natures (roles) and
>> purposes (arcroles) - which would essentially result in the same
>> metadata as using the BioModels qualifiers but with different namespaces.
>>
> If we are using the exact same semantics as they are, we could the
> BioModels namespaces. Of course, it is not clear that the semantics used
> are sufficient for useful machine interpretation, and so it would be
> worth reviewing the existing set, coming up with a range of examples,
> and possibly using these to create a richer set of semantics with their
> own URIs.
>
> Best regards,
> Andrew
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: david.nickerson at nus.edu.sg

---

• [cellml-discussion] BioModels qualifiers in CellML and references to external data, David Nickerson, 12/28/2006
  • [cellml-discussion] BioModels qualifiers in CellML and references to external data, Andrew Miller, 12/29/2006
    • [cellml-discussion] BioModels qualifiers in CellML andreferences to external data, David Nickerson, 12/29/2006

---

Archive powered by MHonArc 2.6.18.