Re: [Miase-discuss] Schema annotations

[Richard A. <ra...@st...>]

But the concept - of needing a human readable and machine readable  
exegesis of an element - is still needed. Possible 'note' could be  
replaced with 'comment'?
Harder to think of a replacement for 'annotation'.

Richard


> Richard Adams wrote:
>>
>> Yes, that's another option, although using the same terms people   
>> are familiar with from sbml is probably desirable, and its up to   
>> the implementation to deal with it.
>
> True as well - although I thought actually that a disadvantage of
> using "annotation" and "notes" was that it is too close to SBML - and
> we definitely want other people to join as well, not only SBMLer ;-)
>
> The problem that I rather see is that it is hard to find appropriate
> other terms...
>
> Oh, and can you try to answer to the list - I think only I got your
> mail this time. I remember Nicolas had the same problem when using the
> "reply" button, but can't remember how he solved it!?
> Dagmar
>
>>
>>
>>> Did you consider the option of renaming the annotation and notes element
>>> to something else in SED-ML if we run into namespace conflicts?
>>>
>>> Dagmar
>>>
>>>
>>> Frank Bergmann wrote:
>>>> Personally I don't mind, as I would not consume the schema as such. Though
>>>> your concerns are valid at which point would we stop adding non-critical
>>>> elements. For the problem at hand it might make more sense to take 'notes'
>>>> and 'annotation' out from the sbml-math schema. I would prefer to have the
>>>> sed-ml file annotated, rather than the math-ml ...
>>>>
>>>> If that won't work, perhaps you could keep the JAXB annotations separate
>>>> from the miase schema in jlibsedml, perhaps having your ant   
>>>> script merge the
>>>> two.
>>>>
>>>> What do you think?
>>>>
>>>> Best
>>>> Frank
>>>>
>>>>
>>>>> -----Original Message-----
>>>>> From: Richard Adams [mailto:ra...@st...]
>>>>> Sent: Monday, February 16, 2009 8:08 AM
>>>>> To: mia...@li...
>>>>> Subject: [Miase-discuss] Schema annotations
>>>>>
>>>>>
>>>>> Sorry, probably didn't explain very well - the .xsd schema definition
>>>>> allows application specific annotations. The changes to the schema I'm
>>>>> proposing would
>>>>> not be included in .miase files, but in the schema itself, inside the
>>>>> notes and annotation element  definitions.
>>>>>
>>>>>  The problem arises, as JAXB comes across 'notes' and 'annotation'
>>>>> defined in both sbml-mathml and sedml schemas. When generating classes
>>>>> from the schema, it gets confused as it attempts to create classes of
>>>>> the same name twice. To prevent this happening, you  can add a
>>>>> processing instruction in the notes element declaration in the sedml
>>>>> schema, saying 'don't create another notes class for this notes
>>>>> element, create a class called 'SedmlNotes instead'.
>>>>>
>>>>> Just looking through the JAXB docs, there doesn't seem to be an
>>>>> obvious solution readily available, e.g., to make the classes in two
>>>>> different packages,
>>>>> which would prevent the need for these annotations.
>>>>>
>>>>> Basically, there are a quite a lot of processing instructions which
>>>>> could be included, for example, specifying java collection classes,
>>>>> method names, class names, javadoc. Some of these, but not all, can be
>>>>> put in an external file, called a binding file, so I'm just thinking
>>>>> that these schema annotations  could pollute the schema definition
>>>>> somewhat.
>>>>>
>>>>> Cheers
>>>>>  Richard
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> I'm sorry, i don't quite see the issue ... the schema right now says
>>>>>> that you are free to put under the annotation element pretty much
>>>>>> anything, and as far as MIASE goes, it will be ignored. The same goes
>>>>>> for the notes section.
>>>>>>
>>>>>> i've never used jaxb so I'm not sure what the issues are. Could you
>>>>>> explain further?
>>>>>>
>>>>> best
>>>>> Frank
>>>>>
>>>>> On Feb 14, 2009, at 2:28 PM, Richard Adams wrote:
>>>>>
>>>>>
>>>>>> Hi all,
>>>>>> Just wondering, it is possible to add <xsd:annotation><xsd:appinfo>
>>>>>> elements
>>>>>> into a schema for tool-specific customization of schema processing.
>>>>>> Is this tolerable in the sed-ml schema, or would it clutter up the
>>>>>> schema too much?
>>>>>>
>>>>>> Just wondered as Dagmar's last change ( to add the notes/annotation
>>>>>> elements) causes a namespace conflict to the JAXB schema parser with
>>>>>> the elements of the same name defined in sbml-mathml. One way round
>>>>>> this is to add this jaxb specific annotations in the .xsd file to
>>>>>> produce classes with different names. An alternative is to specify
>>>>>> instructions in a separate 'binding' file, this would be ideal but
>>>>>> I've not got it to work yet.
>>>>>>
>>>>>> Basically it would add:
>>>>>>
>>>>>> <xs:annotation>
>>>>>> <xs:appinfo>
>>>>>> <jxb:class name="SedMLNotes">
>>>>>> </jxb:class>
>>>>>> </xs:appinfo>
>>>>>>
>>>>> -- 
>>>>> Dr Richard Adams
>>>>> Senior Software Developer,
>>>>> Computational Systems Biology Group,
>>>>> University of Edinburgh
>>>>> Tel: 0131 650 8281/8285
>>>>> email : ric...@ed...
>>>>>
>>>>> -- 
>>>>> The University of Edinburgh is a charitable body, registered in
>>>>> Scotland, with registration number SC005336.
>>>>>
>>>>>
>>>>>
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>>>>
>>>>
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>>
>>
>>



-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8281/8285
email : ric...@ed...

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.